1
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Medoh UN, Abu-Remaileh M. The Bis(monoacylglycero)-phosphate Hypothesis: From Lysosomal Function to Therapeutic Avenues. Annu Rev Biochem 2024. [PMID: 38603559 DOI: 10.1146/annurev-biochem-092823-113814] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/13/2024]
Abstract
Lysosomes catabolize and recycle lipids and other biological molecules to maintain cellular homeostasis in diverse nutrient environments. Lysosomal lipid catabolism relies on the stimulatory activity of bis(monoacylglycero)phosphate (BMP), an enigmatic lipid whose levels are altered across myriad lysosome-associated diseases. Here, we review the discovery of BMP over half a century ago and its structural properties that facilitate the activation of lipid hydrolases and recruitment of their coactivators. We further discuss the current, yet incomplete, understanding of BMP catabolism and anabolism. To conclude, we discuss its role in lysosome-associated diseases and the potential for modulating its levels by pharmacologically activating and inhibiting the BMP synthase to therapeutically target lysosomal storage disorders, drug-induced phospholipidosis, Alzheimer's disease, Parkinson's disease, frontotemporal dementia, cancer, and viral infection.
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Affiliation(s)
- Uche N Medoh
- 1Department of Chemical Engineering, Stanford University, Stanford, California, USA;
- 2Department of Genetics, Stanford University, Stanford, California, USA
- 3The Institute for Chemistry, Engineering & Medicine for Human Health (Sarafan ChEM-H), Stanford University, Stanford, California, USA
- 4Department of Biochemistry, Stanford University School of Medicine, Stanford, California, USA
- 5Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, Maryland, USA
| | - Monther Abu-Remaileh
- 1Department of Chemical Engineering, Stanford University, Stanford, California, USA;
- 2Department of Genetics, Stanford University, Stanford, California, USA
- 3The Institute for Chemistry, Engineering & Medicine for Human Health (Sarafan ChEM-H), Stanford University, Stanford, California, USA
- 5Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, Maryland, USA
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2
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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3
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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4
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Crossley MP, Song C, Bocek MJ, Choi JH, Kousouros JN, Sathirachinda A, Lin C, Brickner JR, Bai G, Lans H, Vermeulen W, Abu-Remaileh M, Cimprich KA. Author Correction: R-loop-derived cytoplasmic RNA-DNA hybrids activate an immune response. Nature 2024; 626:E6. [PMID: 38263519 DOI: 10.1038/s41586-024-07064-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2024]
Affiliation(s)
- Magdalena P Crossley
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA, USA
| | - Chenlin Song
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA, USA
| | - Michael J Bocek
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA, USA
| | - Jun-Hyuk Choi
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA, USA
- Biometrology Group, Division of Chemical and Biological Metrology, Korea Research Institute of Standards and Science, Daejeon, South Korea
- Department of Bio-Analytical Science, University of Science & Technology, Daejeon, South Korea
| | - Joseph N Kousouros
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA, USA
| | - Ataya Sathirachinda
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA, USA
| | - Cindy Lin
- Department of Chemical Engineering, Stanford University, Stanford, CA, USA
- Department of Genetics, Stanford University, Stanford, CA, USA
- The Institute for Chemistry, Engineering & Medicine for Human Health (ChEM-H), Stanford University, Stanford, CA, USA
| | - Joshua R Brickner
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA, USA
| | - Gongshi Bai
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA, USA
| | - Hannes Lans
- Department of Molecular Genetics, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Wim Vermeulen
- Department of Molecular Genetics, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Monther Abu-Remaileh
- Department of Chemical Engineering, Stanford University, Stanford, CA, USA
- Department of Genetics, Stanford University, Stanford, CA, USA
- The Institute for Chemistry, Engineering & Medicine for Human Health (ChEM-H), Stanford University, Stanford, CA, USA
| | - Karlene A Cimprich
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA, USA.
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5
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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6
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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7
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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. Res Sq 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] [What about the content of this article? (0)] [Affiliation(s)] [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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8
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Haney MS, Pálovics R, Munson CN, Long C, Johansson P, 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 microglia. bioRxiv 2023:2023.07.21.549930. [PMID: 37546938 PMCID: PMC10401952 DOI: 10.1101/2023.07.21.549930] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
Abstract
Several genetic risk factors for Alzheimer's Disease (AD) implicate genes involved in lipid metabolism and many of these lipid genes are highly expressed in glial cells. However, the relationship between lipid metabolism in glia and AD pathology remains poorly understood. Through single-nucleus RNA-sequencing of AD brain tissue, we have identified a microglial state defined by the expression of the lipid droplet (LD) associated enzyme ACSL1 with ACSL1-positive microglia most abundant in AD patients with the APOE4/4 genotype. In human iPSC-derived microglia (iMG) fibrillar Aβ (fAβ) induces ACSL1 expression, triglyceride synthesis, and LD accumulation in an APOE-dependent manner. Additionally, conditioned media from LD-containing microglia leads to Tau phosphorylation and neurotoxicity in an APOE-dependent manner. Our findings suggest a link between genetic risk factors for AD with microglial LD accumulation and neurotoxic microglial-derived factors, potentially providing novel therapeutic strategies for AD.
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Affiliation(s)
- Michael S. Haney
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA 94305, USA
- Wu Tsai Neurosciences Institute, Stanford University, Stanford, CA, USA
- Equal contribution
| | - Róbert Pálovics
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA 94305, USA
- Wu Tsai Neurosciences Institute, Stanford University, Stanford, CA, USA
- Equal contribution
| | - Christy Nicole Munson
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA 94305, USA
- Wu Tsai Neurosciences Institute, Stanford University, Stanford, CA, USA
| | - Chris Long
- Department of Materials Science & Engineering Department, Stanford University, Stanford, CA 94305, USA
| | - Patrik Johansson
- Department of Materials Science & Engineering Department, Stanford University, Stanford, CA 94305, USA
| | - Oscar Yip
- Gladstone Institute of Neurological Disease, Gladstone Institutes, San Francisco, CA, US
| | - 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 92093, USA
| | - Johannes CM Schlachetzki
- Department of Cellular and Molecular Medicine, University of California, San Diego, San Diego, CA 92093, USA
| | - Andy Tsai
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA 94305, 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 94305, 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 94305, 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 94305, 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 94305, 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 94305, 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 94305, USA
- Wu Tsai Neurosciences Institute, Stanford University, Stanford, CA, USA
| | - Yung-Hua Wang
- Gladstone Institute of Neurological Disease, Gladstone Institutes, San Francisco, CA, US
| | - Chengzhong Wang
- Gladstone Institute of Neurological Disease, Gladstone Institutes, San Francisco, CA, US
| | - Nicole Koutsodendris
- Gladstone Institute of Neurological Disease, Gladstone Institutes, San Francisco, CA, US
- Development and Stem Cell Biology Graduate Program, University of California, San Francisco, US
| | - 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, US
| | - 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, Stanford, CA 94305, USA
| | - Yadong Huang
- Gladstone Institute of Neurological Disease, Gladstone Institutes, San Francisco, CA, US
- Biomedical Sciences Graduate Program, University of California, San Francisco, US
- Development and Stem Cell Biology Graduate Program, University of California, San Francisco, US
- 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 94305, 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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9
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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10
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Tanzo JT, Li VL, Wiggenhorn AL, Moya-Garzon MD, Wei W, Lyu X, Dong W, Tahir UA, Chen ZZ, Cruz DE, Deng S, Shi X, Zheng S, Guo Y, Sims M, Abu-Remaileh M, Wilson JG, Gerszten RE, Long JZ, Benson MD. CYP4F2 is a human-specific determinant of circulating N-acyl amino acid levels. J Biol Chem 2023:104764. [PMID: 37121548 DOI: 10.1016/j.jbc.2023.104764] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 04/21/2023] [Accepted: 04/23/2023] [Indexed: 05/02/2023] Open
Abstract
N-acyl amino acids are a large family of circulating lipid metabolites that modulate energy expenditure and fat mass in rodents. However, little is known about the regulation and potential cardiometabolic functions of N-acyl amino acids in humans. Here, we analyze the cardiometabolic phenotype associations and genomic associations of four plasma N-acyl amino acids (N-oleoyl-leucine, N-oleoyl-phenylalanine, N-oleoyl-serine, and N-oleoyl-glycine) in 2,351 individuals from the Jackson Heart Study. We find that plasma levels of specific N-acyl amino acids are associated with cardiometabolic disease endpoints independent of free amino acid plasma levels and in patterns according to the amino acid head group. By integrating whole genome sequencing data with N-acyl amino acid levels, we identify that the genetic determinants of N-acyl amino acid levels also cluster according to amino acid head group. Furthermore, we identify the CYP4F2 locus as a genetic determinant of plasma N-oleoyl-leucine and N-oleoyl-phenylalanine levels in human plasma. In experimental studies, we demonstrate that CYP4F2-mediated hydroxylation of N-oleoyl-leucine and N-oleoyl-phenylalanine results in metabolic diversification and production of many previously unknown lipid metabolites with varying characteristics of the fatty acid tail group, including several that structurally resemble fatty acid hydroxy fatty acids (FAHFAs). These studies provide a structural framework for understanding the regulation and disease-associations of N-acyl amino acids in humans and identify that the diversity of this lipid signaling family can be significantly expanded through CYP4F-mediated ω-hydroxylation.
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Affiliation(s)
- Julia T Tanzo
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA; Stanford ChEM-H, Stanford University, Stanford, CA, USA; Stanford Diabetes Research Center, Stanford University, Stanford, CA, USA
| | - Veronica L Li
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA; Stanford ChEM-H, Stanford University, Stanford, CA, USA; Department of Chemistry, Stanford University, Stanford, CA, USA; Wu Tsai Human Performance Alliance, Stanford University, CA, USA
| | - Amanda L Wiggenhorn
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA; Stanford ChEM-H, Stanford University, Stanford, CA, USA; Department of Chemistry, Stanford University, Stanford, CA, USA
| | - Maria Dolores Moya-Garzon
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA; Stanford ChEM-H, Stanford University, Stanford, CA, USA
| | - Wei Wei
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA; Stanford ChEM-H, Stanford University, Stanford, CA, USA; Department of Biology, Stanford University, Stanford, CA, USA
| | - Xuchao Lyu
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA; Stanford ChEM-H, Stanford University, Stanford, CA, USA; Wu Tsai Human Performance Alliance, Stanford University, CA, USA
| | - Wentao Dong
- Stanford ChEM-H, Stanford University, Stanford, CA, USA; Department of Chemical Engineering, Stanford University, Stanford, CA, USA
| | - Usman A Tahir
- Division of Cardiovascular Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA
| | - Zsu-Zsu Chen
- Division of Cardiovascular Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA
| | - Daniel E Cruz
- Division of Cardiovascular Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA
| | - Shuliang Deng
- Division of Cardiovascular Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA
| | - Xu Shi
- Division of Cardiovascular Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA
| | - Shuning Zheng
- Division of Cardiovascular Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA
| | - Yan Guo
- Univ of Mississippi Medical Center, Jackson, MS
| | - Mario Sims
- Univ of Mississippi Medical Center, Jackson, MS
| | - Monther Abu-Remaileh
- Stanford ChEM-H, Stanford University, Stanford, CA, USA; Department of Chemical Engineering, Stanford University, Stanford, CA, USA
| | - James G Wilson
- Division of Cardiovascular Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA
| | - Robert E Gerszten
- Division of Cardiovascular Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA; Broad Institute of Harvard and MIT, Cambridge, MA
| | - Jonathan Z Long
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA; Stanford ChEM-H, Stanford University, Stanford, CA, USA; Stanford Diabetes Research Center, Stanford University, Stanford, CA, USA; Wu Tsai Human Performance Alliance, Stanford University, CA, USA.
| | - Mark D Benson
- Division of Cardiovascular Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA.
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11
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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. Sci Adv 2023; 9:eadf8966. [PMID: 37075117 PMCID: PMC10115416 DOI: 10.1126/sciadv.adf8966] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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12
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Tanzo JT, Li VL, Wiggenhorn AL, Moya-Garzon MD, Wei W, Lyu X, Dong W, Tahir UA, Chen ZZ, Cruz DE, Deng S, Shi X, Zheng S, Guo Y, Sims M, Abu-Remaileh M, Wilson JG, Gerszten RE, Long JZ, Benson MD. CYP4F2 is a human-specific determinant of circulating N-acyl amino acid levels. bioRxiv 2023:2023.03.09.531581. [PMID: 36945562 PMCID: PMC10028954 DOI: 10.1101/2023.03.09.531581] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2023]
Abstract
N-acyl amino acids are a large family of circulating lipid metabolites that modulate energy expenditure and fat mass in rodents. However, little is known about the regulation and potential cardiometabolic functions of N-acyl amino acids in humans. Here, we analyze the cardiometabolic phenotype associations and genetic regulation of four plasma N-fatty acyl amino acids (N-oleoyl-leucine, N-oleoyl-phenylalanine, N-oleoyl-serine, and N-oleoyl-glycine) in 2,351 individuals from the Jackson Heart Study. N-oleoyl-leucine and N-oleoyl-phenylalanine were positively associated with traits related to energy balance, including body mass index, waist circumference, and subcutaneous adipose tissue. In addition, we identify the CYP4F2 locus as a human-specific genetic determinant of plasma N-oleoyl-leucine and N-oleoyl-phenylalanine levels. In vitro, CYP4F2-mediated hydroxylation of N-oleoyl-leucine and N-oleoyl-phenylalanine results in metabolic diversification and production of many previously unknown lipid metabolites with varying characteristics of the fatty acid tail group, including several that structurally resemble fatty acid hydroxy fatty acids (FAHFAs). By contrast, FAAH-regulated N-oleoyl-glycine and N-oleoyl-serine were inversely associated with traits related to glucose and lipid homeostasis. These data uncover a human-specific enzymatic node for the metabolism of a subset of N-fatty acyl amino acids and establish a framework for understanding the cardiometabolic roles of individual N-fatty acyl amino acids in humans.
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13
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Hsu J, Fatuzzo N, Weng N, Michno W, Dong W, Kienle M, Dai Y, Pasca A, Abu-Remaileh M, Rasgon N, Bigio B, Nasca C, Khosla C. Carnitine octanoyltransferase is important for the assimilation of exogenous acetyl-L-carnitine into acetyl-CoA in mammalian cells. J Biol Chem 2023; 299:102848. [PMID: 36587768 PMCID: PMC9898754 DOI: 10.1016/j.jbc.2022.102848] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Revised: 12/20/2022] [Accepted: 12/23/2022] [Indexed: 12/31/2022] Open
Abstract
In eukaryotes, carnitine is best known for its ability to shuttle esterified fatty acids across mitochondrial membranes for β-oxidation. It also returns to the cytoplasm, in the form of acetyl-L-carnitine (LAC), some of the resulting acetyl groups for posttranslational protein modification and lipid biosynthesis. While dietary LAC supplementation has been clinically investigated, its effects on cellular metabolism are not well understood. To explain how exogenous LAC influences mammalian cell metabolism, we synthesized isotope-labeled forms of LAC and its analogs. In cultures of glucose-limited U87MG glioma cells, exogenous LAC contributed more robustly to intracellular acetyl-CoA pools than did β-hydroxybutyrate, the predominant circulating ketone body in mammals. The fact that most LAC-derived acetyl-CoA is cytosolic is evident from strong labeling of fatty acids in U87MG cells by exogenous 13C2-acetyl-L-carnitine. We found that the addition of d3-acetyl-L-carnitine increases the supply of acetyl-CoA for cytosolic posttranslational modifications due to its strong kinetic isotope effect on acetyl-CoA carboxylase, the first committed step in fatty acid biosynthesis. Surprisingly, whereas cytosolic carnitine acetyltransferase is believed to catalyze acetyl group transfer from LAC to coenzyme A, CRAT-/- U87MG cells were unimpaired in their ability to assimilate exogenous LAC into acetyl-CoA. We identified carnitine octanoyltransferase as the key enzyme in this process, implicating a role for peroxisomes in efficient LAC utilization. Our work has opened the door to further biochemical investigations of a new pathway for supplying acetyl-CoA to certain glucose-starved cells.
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Affiliation(s)
- Jake Hsu
- Department of Chemical Engineering, Stanford University, Stanford, California, USA
| | - Nina Fatuzzo
- Department of Chemistry, Stanford University, Stanford, California, USA
| | - Nielson Weng
- Department of Chemistry, Stanford University, Stanford, California, USA
| | - Wojciech Michno
- Division of Neonatology, Department of Pediatrics, Stanford University, Stanford, California, USA
| | - Wentao Dong
- Department of Chemical Engineering, Stanford University, Stanford, California, USA; Department of Genetics, Stanford University, Stanford, California, USA
| | - Maryline Kienle
- Department of Chemistry, Stanford University, Stanford, California, USA
| | - Yuqin Dai
- Sarafan ChEM-H, Stanford, California, USA
| | - Anca Pasca
- Division of Neonatology, Department of Pediatrics, Stanford University, Stanford, California, USA
| | - Monther Abu-Remaileh
- Department of Chemical Engineering, Stanford University, Stanford, California, USA; Department of Genetics, Stanford University, Stanford, California, USA; Sarafan ChEM-H, Stanford, California, USA
| | - Natalie Rasgon
- Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, California, USA
| | - Benedetta Bigio
- Department of Psychiatry, Grossman School of Medicine, New York University, New York, New York, USA
| | - Carla Nasca
- Department of Psychiatry, Grossman School of Medicine, New York University, New York, New York, USA; Department of Neuroscience and Physiology, New York University Neuroscience Institute, Grossman School of Medicine, New York University, New York, New York, USA; Harold and Margaret Milliken Hatch Laboratory of Neuroendocrinology, The Rockefeller University, New York, New York, USA
| | - Chaitan Khosla
- Department of Chemical Engineering, Stanford University, Stanford, California, USA; Department of Chemistry, Stanford University, Stanford, California, USA; Sarafan ChEM-H, Stanford, California, USA.
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14
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Crossley MP, Song C, Bocek MJ, Choi JH, Kousouros JN, Sathirachinda A, Lin C, Brickner JR, Bai G, Lans H, Vermeulen W, Abu-Remaileh M, Cimprich KA. R-loop-derived cytoplasmic RNA-DNA hybrids activate an immune response. Nature 2023; 613:187-194. [PMID: 36544021 PMCID: PMC9949885 DOI: 10.1038/s41586-022-05545-9] [Citation(s) in RCA: 75] [Impact Index Per Article: 75.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 11/08/2022] [Indexed: 12/24/2022]
Abstract
R-loops are RNA-DNA-hybrid-containing nucleic acids with important cellular roles. Deregulation of R-loop dynamics can lead to DNA damage and genome instability1, which has been linked to the action of endonucleases such as XPG2-4. However, the mechanisms and cellular consequences of such processing have remained unclear. Here we identify a new population of RNA-DNA hybrids in the cytoplasm that are R-loop-processing products. When nuclear R-loops were perturbed by depleting the RNA-DNA helicase senataxin (SETX) or the breast cancer gene BRCA1 (refs. 5-7), we observed XPG- and XPF-dependent cytoplasmic hybrid formation. We identify their source as a subset of stable, overlapping nuclear hybrids with a specific nucleotide signature. Cytoplasmic hybrids bind to the pattern recognition receptors cGAS and TLR3 (ref. 8), activating IRF3 and inducing apoptosis. Excised hybrids and an R-loop-induced innate immune response were also observed in SETX-mutated cells from patients with ataxia oculomotor apraxia type 2 (ref. 9) and in BRCA1-mutated cancer cells10. These findings establish RNA-DNA hybrids as immunogenic species that aberrantly accumulate in the cytoplasm after R-loop processing, linking R-loop accumulation to cell death through the innate immune response. Aberrant R-loop processing and subsequent innate immune activation may contribute to many diseases, such as neurodegeneration and cancer.
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Affiliation(s)
- Magdalena P Crossley
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA, USA
| | - Chenlin Song
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA, USA
| | - Michael J Bocek
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA, USA
| | - Jun-Hyuk Choi
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA, USA
- Biometrology Group, Division of Chemical and Biological Metrology, Korea Research Institute of Standards and Science, Daejeon, South Korea
- Department of Bio-Analytical Science, University of Science & Technology, Daejeon, South Korea
| | - Joseph N Kousouros
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA, USA
| | - Ataya Sathirachinda
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA, USA
| | - Cindy Lin
- Department of Chemical Engineering, Stanford University, Stanford, CA, USA
- Department of Genetics, Stanford University, Stanford, CA, USA
- The Institute for Chemistry, Engineering & Medicine for Human Health (ChEM-H), Stanford University, Stanford, CA, USA
| | - Joshua R Brickner
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA, USA
| | - Gongshi Bai
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA, USA
| | - Hannes Lans
- Department of Molecular Genetics, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Wim Vermeulen
- Department of Molecular Genetics, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Monther Abu-Remaileh
- Department of Chemical Engineering, Stanford University, Stanford, CA, USA
- Department of Genetics, Stanford University, Stanford, CA, USA
- The Institute for Chemistry, Engineering & Medicine for Human Health (ChEM-H), Stanford University, Stanford, CA, USA
| | - Karlene A Cimprich
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA, USA.
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15
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Laqtom NN, Dong W, Medoh UN, Cangelosi AL, Dharamdasani V, Chan SH, Kunchok T, Lewis CA, Heinze I, Tang R, Grimm C, Dang Do AN, Porter FD, Ori A, Sabatini DM, Abu-Remaileh M. CLN3 is required for the clearance of glycerophosphodiesters from lysosomes. Nature 2022; 609:1005-1011. [PMID: 36131016 PMCID: PMC10510443 DOI: 10.1038/s41586-022-05221-y] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2020] [Accepted: 08/10/2022] [Indexed: 11/09/2022]
Abstract
Lysosomes have many roles, including degrading macromolecules and signalling to the nucleus1. Lysosomal dysfunction occurs in various human conditions, such as common neurodegenerative diseases and monogenic lysosomal storage disorders (LSDs)2-4. For most LSDs, the causal genes have been identified but, in some, the function of the implicated gene is unknown, in part because lysosomes occupy a small fraction of the cellular volume so that changes in lysosomal contents are difficult to detect. Here we develop the LysoTag mouse for the tissue-specific isolation of intact lysosomes that are compatible with the multimodal profiling of their contents. We used the LysoTag mouse to study CLN3, a lysosomal transmembrane protein with an unknown function. In children, the loss of CLN3 causes juvenile neuronal ceroid lipofuscinosis (Batten disease), a lethal neurodegenerative LSD. Untargeted metabolite profiling of lysosomes from the brains of mice lacking CLN3 revealed a massive accumulation of glycerophosphodiesters (GPDs)-the end products of glycerophospholipid catabolism. GPDs also accumulate in the lysosomes of CLN3-deficient cultured cells and we show that CLN3 is required for their lysosomal egress. Loss of CLN3 also disrupts glycerophospholipid catabolism in the lysosome. Finally, we found elevated levels of glycerophosphoinositol in the cerebrospinal fluid of patients with Batten disease, suggesting the potential use of glycerophosphoinositol as a disease biomarker. Our results show that CLN3 is required for the lysosomal clearance of GPDs and reveal Batten disease as a neurodegenerative LSD with a defect in glycerophospholipid metabolism.
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Affiliation(s)
- Nouf N Laqtom
- Department of Chemical Engineering, Stanford University, Stanford, CA, USA
- Department of Genetics, Stanford University, Stanford, CA, USA
- The Institute for Chemistry, Engineering & Medicine for Human Health (ChEM-H), Stanford University, Stanford, CA, USA
| | - Wentao Dong
- Department of Chemical Engineering, Stanford University, Stanford, CA, USA
- Department of Genetics, Stanford University, Stanford, CA, USA
- The Institute for Chemistry, Engineering & Medicine for Human Health (ChEM-H), Stanford University, Stanford, CA, USA
| | - Uche N Medoh
- Department of Chemical Engineering, Stanford University, Stanford, CA, USA
- Department of Genetics, Stanford University, Stanford, CA, USA
- The Institute for Chemistry, Engineering & Medicine for Human Health (ChEM-H), Stanford University, Stanford, CA, USA
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
| | - Andrew L Cangelosi
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
- Koch Institute for Integrative Cancer Research, Cambridge, MA, USA
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
| | | | - Sze Ham Chan
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
- Department of Pharmacology, University of Virginia School of Medicine, Charlottesville, VA, USA
| | - Tenzin Kunchok
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
| | | | - Ivonne Heinze
- Leibniz Institute on Aging-Fritz Lipmann Institute, Jena, Germany
| | - Rachel Tang
- Walther Straub Institute of Pharmacology and Toxicology, Faculty of Medicine, Ludwig-Maximilians-Universität, Munich, Germany
| | - Christian Grimm
- Walther Straub Institute of Pharmacology and Toxicology, Faculty of Medicine, Ludwig-Maximilians-Universität, Munich, Germany
| | - An N Dang Do
- Division of Translational Medicine, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD, USA
| | - Forbes D Porter
- Division of Translational Medicine, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD, USA
| | - Alessandro Ori
- Leibniz Institute on Aging-Fritz Lipmann Institute, Jena, Germany
| | | | - Monther Abu-Remaileh
- Department of Chemical Engineering, Stanford University, Stanford, CA, USA.
- Department of Genetics, Stanford University, Stanford, CA, USA.
- The Institute for Chemistry, Engineering & Medicine for Human Health (ChEM-H), Stanford University, Stanford, CA, USA.
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16
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Dong W, Rawat ES, Stephanopoulos G, Abu-Remaileh M. Isotope tracing in health and disease. Curr Opin Biotechnol 2022; 76:102739. [PMID: 35738210 PMCID: PMC9555185 DOI: 10.1016/j.copbio.2022.102739] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 04/16/2022] [Accepted: 04/27/2022] [Indexed: 11/16/2022]
Abstract
Biochemical characterization of metabolism provides molecular insights for understanding biology in health and disease. Over the past decades, metabolic perturbations have been implicated in cancer, neurodegeneration, and diabetes, among others. Isotope tracing is a technique that allows tracking of labeled atoms within metabolites through biochemical reactions. This technique has become an integral component of the contemporary metabolic research. Isotope tracing measures substrate contribution to downstream metabolites and indicates its utilization in cellular metabolic networks. In addition, isotopic labeling data are necessary for quantitative metabolic flux analysis. Here, we review recent work utilizing metabolic tracing to study health and disease, and highlight its application to interrogate subcellular, intercellular, and in vivo metabolism. We further discuss the current challenges and opportunities to expand the utility of isotope tracing to new research areas.
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Affiliation(s)
- 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 (ChEM-H), Stanford University, Stanford, CA 94305, USA; Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, 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 & Medicine for Human Health (ChEM-H), Stanford University, Stanford, CA 94305, USA; Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
| | - Gregory Stephanopoulos
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, 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 (ChEM-H), Stanford University, Stanford, CA 94305, USA; Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA.
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17
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Forcina GC, Pope L, Murray M, Dong W, Abu-Remaileh M, Bertozzi CR, Dixon SJ. Ferroptosis regulation by the NGLY1/NFE2L1 pathway. Proc Natl Acad Sci U S A 2022; 119:e2118646119. [PMID: 35271393 PMCID: PMC8931371 DOI: 10.1073/pnas.2118646119] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Accepted: 01/20/2022] [Indexed: 01/07/2023] Open
Abstract
SignificanceFerroptosis is an oxidative form of cell death whose biochemical regulation remains incompletely understood. Cap'n'collar (CNC) transcription factors including nuclear factor erythroid-2-related factor 1 (NFE2L1/NRF1) and NFE2L2/NRF2 can both regulate oxidative stress pathways but are each regulated in a distinct manner, and whether these two transcription factors can regulate ferroptosis independent of one another is unclear. We find that NFE2L1 can promote ferroptosis resistance, independent of NFE2L2, by maintaining the expression of glutathione peroxidase 4 (GPX4), a key protein that prevents lethal lipid peroxidation. NFE2L2 can also promote ferroptosis resistance but does so through a distinct mechanism that appears independent of GPX4 protein expression. These results suggest that NFE2L1 and NFE2L2 independently regulate ferroptosis.
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Affiliation(s)
| | - Lauren Pope
- Department of Biology, Stanford University, Stanford, CA 94305
| | | | - Wentao Dong
- Department of Chemical Engineering, Stanford University, Stanford, CA 94305
- Stanford ChEM-H, Stanford University, Stanford, CA 94305
| | - Monther Abu-Remaileh
- Department of Chemical Engineering, Stanford University, Stanford, CA 94305
- Stanford ChEM-H, Stanford University, Stanford, CA 94305
| | - Carolyn R. Bertozzi
- Stanford ChEM-H, Stanford University, Stanford, CA 94305
- Department of Chemistry, Stanford University, Stanford, CA 94305
- HHMI, Stanford University, Stanford, CA 94305
| | - Scott J. Dixon
- Department of Biology, Stanford University, Stanford, CA 94305
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18
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Fassl A, Brain C, Abu-Remaileh M, Stukan I, Butter D, Stepien P, Feit AS, Bergholz J, Michowski W, Otto T, Sheng Q, Loo A, Michael W, Tiedt R, DeAngelis C, Schiff R, Jiang B, Jovanovic B, Nowak K, Ericsson M, Cameron M, Gray N, Dillon D, Zhao JJ, Sabatini DM, Jeselsohn R, Brown M, Polyak K, Sicinski P. Increased lysosomal biomass is responsible for the resistance of triple-negative breast cancers to CDK4/6 inhibition. Sci Adv 2020; 6:eabb2210. [PMID: 32704543 PMCID: PMC7360435 DOI: 10.1126/sciadv.abb2210] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2020] [Accepted: 05/04/2020] [Indexed: 05/28/2023]
Abstract
Inhibitors of cyclin-dependent kinases CDK4 and CDK6 have been approved for treatment of hormone receptor-positive breast cancers. In contrast, triple-negative breast cancers (TNBCs) are resistant to CDK4/6 inhibition. Here, we demonstrate that a subset of TNBC critically requires CDK4/6 for proliferation, and yet, these TNBC are resistant to CDK4/6 inhibition due to sequestration of CDK4/6 inhibitors into tumor cell lysosomes. This sequestration is caused by enhanced lysosomal biogenesis and increased lysosomal numbers in TNBC cells. We developed new CDK4/6 inhibitor compounds that evade the lysosomal sequestration and are efficacious against resistant TNBC. We also show that coadministration of lysosomotropic or lysosome-destabilizing compounds (an antibiotic azithromycin, an antidepressant siramesine, an antimalaria compound chloroquine) renders resistant tumor cells sensitive to currently used CDK4/6 inhibitors. Lastly, coinhibition of CDK2 arrested proliferation of CDK4/6 inhibitor-resistant cells. These observations may extend the use of CDK4/6 inhibitors to TNBCs that are refractory to current anti-CDK4/6 therapies.
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Affiliation(s)
- Anne Fassl
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Christopher Brain
- Novartis Institute for Biomedical Research, Cambridge, MA 02139, USA
| | - Monther Abu-Remaileh
- Whitehead Institutes for Biomedical Research and Massachusetts Institute of Technology, Cambridge, MA 02142, USA
- Departments of Chemical Engineering and Genetics, Stanford University, Stanford, CA 94305, USA
- Institute for Chemistry, Engineering and Medicine for Human Health (ChEM-H), Stanford University, 290 Jane Stanford Way, Stanford, CA 94305, USA
| | - Iga Stukan
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Deborah Butter
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Piotr Stepien
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Avery S. Feit
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
- Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Johann Bergholz
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Wojciech Michowski
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Tobias Otto
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Qing Sheng
- Novartis Institute for Biomedical Research, Cambridge, MA 02139, USA
| | - Alice Loo
- Novartis Institute for Biomedical Research, Cambridge, MA 02139, USA
| | - Walter Michael
- Novartis Institute for Biomedical Research, Cambridge, MA 02139, USA
| | - Ralph Tiedt
- Novartis Institutes for Biomedical Research, Oncology Disease Area, 4057 Basel, Switzerland
| | - Carmine DeAngelis
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Medicine and Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Clinical Medicine and Surgery, University of Naples Federico II, Naples, Italy
| | - Rachel Schiff
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Medicine and Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Baishan Jiang
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Bojana Jovanovic
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
- Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Karolina Nowak
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Maria Ericsson
- Electron Microscopy Facility, Harvard Medical School, Boston, MA 02115, USA
| | - Michael Cameron
- Department of Molecular Therapeutics, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Nathanael Gray
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Deborah Dillon
- Department of Pathology, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Jean J. Zhao
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - David M. Sabatini
- Whitehead Institutes for Biomedical Research and Massachusetts Institute of Technology, Cambridge, MA 02142, USA
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
- Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Rinath Jeselsohn
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
- Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Myles Brown
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
- Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Kornelia Polyak
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
- Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Piotr Sicinski
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
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19
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Weber RA, Yen FS, Nicholson SPV, Alwaseem H, Bayraktar EC, Alam M, Timson RC, La K, Abu-Remaileh M, Molina H, Birsoy K. Maintaining Iron Homeostasis Is the Key Role of Lysosomal Acidity for Cell Proliferation. Mol Cell 2020; 77:645-655.e7. [PMID: 31983508 DOI: 10.1016/j.molcel.2020.01.003] [Citation(s) in RCA: 119] [Impact Index Per Article: 29.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Revised: 11/20/2019] [Accepted: 12/26/2019] [Indexed: 02/07/2023]
Abstract
The lysosome is an acidic multi-functional organelle with roles in macromolecular digestion, nutrient sensing, and signaling. However, why cells require acidic lysosomes to proliferate and which nutrients become limiting under lysosomal dysfunction are unclear. To address this, we performed CRISPR-Cas9-based genetic screens and identified cholesterol biosynthesis and iron uptake as essential metabolic pathways when lysosomal pH is altered. While cholesterol synthesis is only necessary, iron is both necessary and sufficient for cell proliferation under lysosomal dysfunction. Remarkably, iron supplementation restores cell proliferation under both pharmacologic and genetic-mediated lysosomal dysfunction. The rescue was independent of metabolic or signaling changes classically associated with increased lysosomal pH, uncoupling lysosomal function from cell proliferation. Finally, our experiments revealed that lysosomal dysfunction dramatically alters mitochondrial metabolism and hypoxia inducible factor (HIF) signaling due to iron depletion. Altogether, these findings identify iron homeostasis as the key function of lysosomal acidity for cell proliferation.
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Affiliation(s)
- Ross A Weber
- Laboratory of Metabolic Regulation and Genetics, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA; Tri-Institutional MD-PhD Program, Weill Cornell Medicine, Rockefeller University, Memorial Sloan Kettering Cancer Center, 1300 York Avenue, New York, NY 10065, USA
| | - Frederick S Yen
- Laboratory of Metabolic Regulation and Genetics, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Shirony P V Nicholson
- Laboratory of Metabolic Regulation and Genetics, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA; Institute of Pathology, Medical University of Graz, Auenbruggerplatz 25, Graz 8036, Austria
| | - Hanan Alwaseem
- Proteomics Resource Center, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Erol C Bayraktar
- Laboratory of Metabolic Regulation and Genetics, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Mohammad Alam
- Laboratory of Metabolic Regulation and Genetics, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Rebecca C Timson
- Laboratory of Metabolic Regulation and Genetics, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Konnor La
- Laboratory of Metabolic Regulation and Genetics, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Monther Abu-Remaileh
- Departments of Chemical Engineering and Genetics and the Institute for Chemistry, Engineering & Medicine for Human Health (ChEM-H), Stanford University, 443 Via Ortega, Stanford, CA 94205, USA
| | - Henrik Molina
- Proteomics Resource Center, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Kıvanç Birsoy
- Laboratory of Metabolic Regulation and Genetics, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA.
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20
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Rogala KB, Gu X, Kedir JF, Abu-Remaileh M, Bianchi LF, Bottino AMS, Dueholm R, Niehaus A, Overwijn D, Fils ACP, Zhou SX, Leary D, Laqtom NN, Brignole EJ, Sabatini DM. Structural basis for the docking of mTORC1 on the lysosomal surface. Science 2019; 366:468-475. [PMID: 31601708 PMCID: PMC7176403 DOI: 10.1126/science.aay0166] [Citation(s) in RCA: 110] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Accepted: 10/01/2019] [Indexed: 12/14/2022]
Abstract
The mTORC1 (mechanistic target of rapamycin complex 1) protein kinase regulates growth in response to nutrients and growth factors. Nutrients promote its translocation to the lysosomal surface, where its Raptor subunit interacts with the Rag guanosine triphosphatase (GTPase)-Ragulator complex. Nutrients switch the heterodimeric Rag GTPases among four different nucleotide-binding states, only one of which (RagA/B•GTP-RagC/D•GDP) permits mTORC1 association. We used cryo-electron microscopy to determine the structure of the supercomplex of Raptor with Rag-Ragulator at a resolution of 3.2 angstroms. Our findings indicate that the Raptor α-solenoid directly detects the nucleotide state of RagA while the Raptor "claw" threads between the GTPase domains to detect that of RagC. Mutations that disrupted Rag-Raptor binding inhibited mTORC1 lysosomal localization and signaling. By comparison with a structure of mTORC1 bound to its activator Rheb, we developed a model of active mTORC1 docked on the lysosome.
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Affiliation(s)
- Kacper B Rogala
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
- Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Koch Institute for Integrative Cancer Research, Cambridge, MA 02139, USA
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Xin Gu
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
- Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Koch Institute for Integrative Cancer Research, Cambridge, MA 02139, USA
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Jibril F Kedir
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
- Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Koch Institute for Integrative Cancer Research, Cambridge, MA 02139, USA
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Monther Abu-Remaileh
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
- Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Koch Institute for Integrative Cancer Research, Cambridge, MA 02139, USA
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Laura F Bianchi
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | | | - Rikke Dueholm
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Anna Niehaus
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Daan Overwijn
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | | | - Sherry X Zhou
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Daniel Leary
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Nouf N Laqtom
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Edward J Brignole
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- MIT.nano, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - David M Sabatini
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA.
- Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Koch Institute for Integrative Cancer Research, Cambridge, MA 02139, USA
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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21
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Abu-Remaileh M, Abu-Remaileh M, Akkawi R, Knani I, Udi S, Pacold ME, Tam J, Aqeilan RI. WWOX somatic ablation in skeletal muscles alters glucose metabolism. Mol Metab 2019; 22:132-140. [PMID: 30755385 PMCID: PMC6437662 DOI: 10.1016/j.molmet.2019.01.010] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/09/2018] [Revised: 01/18/2019] [Accepted: 01/25/2019] [Indexed: 12/21/2022] Open
Abstract
OBJECTIVE WWOX, a well-established tumor suppressor, is frequently lost in cancer and plays important roles in DNA damage response and cellular metabolism. METHODS We re-analyzed several genome-wide association studies (GWAS) using the Type 2 Diabetes Knowledge Portal website to uncover WWOX's association with metabolic syndrome (MetS). Using several engineered mouse models, we studied the effect of somatic WWOX loss on glucose homeostasis. RESULTS Several WWOX variants were found to be strongly associated with MetS disorders. In mouse models, somatic ablation of Wwox in skeletal muscle (WwoxΔSKM) results in weight gain, glucose intolerance, and insulin resistance. Furthermore, WwoxΔSKM mice display reduced amounts of slow-twitch fibers, decreased mitochondrial quantity and activity, and lower glucose oxidation levels. Mechanistically, we found that WWOX physically interacts with the cellular energy sensor AMP-activated protein kinase (AMPK) and that its loss is associated with impaired activation of AMPK, and with significant accumulation of the hypoxia inducible factor 1 alpha (HIF1α) in SKM. CONCLUSIONS Our studies uncover an unforeseen role of the tumor suppressor WWOX in whole-body glucose homeostasis and highlight the intimate relationship between cancer progression and metabolic disorders, particularly obesity and type-2 diabetes. SUBJECT AREAS Genetics, Metabolic Syndrome, Diabetes.
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Affiliation(s)
- Muhannad Abu-Remaileh
- The Lautenberg Center for General and Tumor Immunology, Department of Immunology and Cancer Research-IMRIC, Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Monther Abu-Remaileh
- Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02142, USA
| | - Rania Akkawi
- The Lautenberg Center for General and Tumor Immunology, Department of Immunology and Cancer Research-IMRIC, Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Ibrahim Knani
- Obesity and Metabolism Laboratory, The Institute for Drug Research, School of Pharmacy, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9112001, Israel
| | - Shiran Udi
- Obesity and Metabolism Laboratory, The Institute for Drug Research, School of Pharmacy, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9112001, Israel
| | - Micheal E Pacold
- Department of Radiation Oncology, New York University Langone Medical Center, 522 First Avenue, Smilow 907, New York, NY, USA
| | - Joseph Tam
- Obesity and Metabolism Laboratory, The Institute for Drug Research, School of Pharmacy, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9112001, Israel
| | - Rami I Aqeilan
- The Lautenberg Center for General and Tumor Immunology, Department of Immunology and Cancer Research-IMRIC, Hebrew University-Hadassah Medical School, Jerusalem, Israel; Department of Cancer Biology and Genetics, Wexner Medical Center, The Ohio State University, Columbus, OH, USA.
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22
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Beyaz S, Mana MD, Roper J, Kedrin D, Saadatpour A, Hong SJ, Bauer-Rowe KE, Xifaras ME, Akkad A, Arias E, Pinello L, Katz Y, Shinagare S, Abu-Remaileh M, Mihaylova MM, Lamming DW, Dogum R, Guo G, Bell GW, Selig M, Nielsen GP, Gupta N, Ferrone CR, Deshpande V, Yuan GC, Orkin SH, Sabatini DM, Yilmaz ÖH. Author Correction: High-fat diet enhances stemness and tumorigenicity of intestinal progenitors. Nature 2018; 560:E26. [DOI: 10.1038/s41586-018-0187-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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23
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Yu Z, Surface LE, Park CY, Horlbeck MA, Wyant GA, Abu-Remaileh M, Peterson TR, Sabatini DM, Weissman JS, O'Shea EK. Identification of a transporter complex responsible for the cytosolic entry of nitrogen-containing bisphosphonates. eLife 2018; 7:36620. [PMID: 29745899 PMCID: PMC6021172 DOI: 10.7554/elife.36620] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Accepted: 05/09/2018] [Indexed: 11/13/2022] Open
Abstract
Nitrogen-containing-bisphosphonates (N-BPs) are a class of drugs widely prescribed to treat osteoporosis and other bone-related diseases. Although previous studies have established that N-BPs function by inhibiting the mevalonate pathway in osteoclasts, the mechanism by which N-BPs enter the cytosol from the extracellular space to reach their molecular target is not understood. Here, we implemented a CRISPRi-mediated genome-wide screen and identified SLC37A3 (solute carrier family 37 member A3) as a gene required for the action of N-BPs in mammalian cells. We observed that SLC37A3 forms a complex with ATRAID (all-trans retinoic acid-induced differentiation factor), a previously identified genetic target of N-BPs. SLC37A3 and ATRAID localize to lysosomes and are required for releasing N-BP molecules that have trafficked to lysosomes through fluid-phase endocytosis into the cytosol. Our results elucidate the route by which N-BPs are delivered to their molecular target, addressing a key aspect of the mechanism of action of N-BPs that may have significant clinical relevance. As some people age, their bones may become weak, brittle, and break easily. This condition is called osteoporosis. To treat osteoporosis, doctors often prescribe drugs called nitrogen-containing bisphosphonates (NBPs). These drugs destroy cells called osteoclasts, which break down bone. This helps restore bone mass. To kill osteoclasts, the drugs must enter these cells. First, they must pass through an oily protective layer called a membrane. It is not completely clear how NBPs, which prefer to stay in water-like environments, can cross this oily membrane and enter osteoclasts. Understanding how NBPs cross the membrane is important to ensure the drugs work effectively. If NBPs do not efficiently cross the membrane, they will not work properly and may cause harmful side effects. Many patients who take NBPs suffer from side effects such as abnormal fractures. Now, Yu et al. show that two proteins help NBPs cross the membrane. In the experiments, proteins were removed from human cancer cells one at a time using a technique called CRISPRi. CRISPRi enabled the researchers to systematically turn off the genes for each protein and track what affect this had on the NBPs’ ability to cross the membrane. When one of the two genes called SLC37A3 and ATRAID was turned off, NBPs could not get into cells. The protein produced by the SLC37A3 gene opens a gate in the cell membrane allowing NBPs to enter osteoclasts. The protein made by the ATRAID gene helps this gate protein, and without it, the SLC37A3 proteins are unstable and NBPs cannot enter. Some people have variations of the SLC37A3 and ATRAID genes. Testing whether these genetic variations may alter NBPs’ ability to cross the membrane of osteoclasts in mice, might one day help physicians predict which patients with have side effects.
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Affiliation(s)
- Zhou Yu
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, United States.,Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States
| | - Lauren E Surface
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, United States.,Faculty of Arts and Sciences Center for Systems Biology, Harvard University, Cambridge, United States.,Department of Chemistry and Chemical Biology, Harvard University, Cambridge, United States.,Howard Hughes Medical Institute, Bethesda, United States
| | - Chong Yon Park
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, United States
| | - Max A Horlbeck
- Howard Hughes Medical Institute, Bethesda, United States.,Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, United States.,Center for RNA Systems Biology, University of California, San Francisco, San Francisco, United States
| | - Gregory A Wyant
- Howard Hughes Medical Institute, Bethesda, United States.,Whitehead Institute for Biomedical Research, Cambridge, United States.,Department of Biology, Massachusetts Institute of Technology, Cambridge, United States.,Koch Institute for Integrative Cancer Research, Cambridge, United States.,Broad Institute of MIT and Harvard, Cambridge, United States
| | - Monther Abu-Remaileh
- Howard Hughes Medical Institute, Bethesda, United States.,Whitehead Institute for Biomedical Research, Cambridge, United States.,Department of Biology, Massachusetts Institute of Technology, Cambridge, United States.,Koch Institute for Integrative Cancer Research, Cambridge, United States.,Broad Institute of MIT and Harvard, Cambridge, United States
| | - Timothy R Peterson
- Division of Bone & Mineral Diseases, Department of Genetics, Institute for Public Health, Washington University School of Medicine, St. Louis, United States
| | - David M Sabatini
- Howard Hughes Medical Institute, Bethesda, United States.,Whitehead Institute for Biomedical Research, Cambridge, United States.,Department of Biology, Massachusetts Institute of Technology, Cambridge, United States.,Koch Institute for Integrative Cancer Research, Cambridge, United States.,Broad Institute of MIT and Harvard, Cambridge, United States
| | - Jonathan S Weissman
- Howard Hughes Medical Institute, Bethesda, United States.,Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, United States.,Center for RNA Systems Biology, University of California, San Francisco, San Francisco, United States
| | - Erin K O'Shea
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, United States.,Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States.,Faculty of Arts and Sciences Center for Systems Biology, Harvard University, Cambridge, United States.,Department of Chemistry and Chemical Biology, Harvard University, Cambridge, United States.,Howard Hughes Medical Institute, Bethesda, United States
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24
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Wyant GA, Abu-Remaileh M, Frenkel EM, Laqtom NN, Dharamdasani V, Lewis CA, Chan SH, Heinze I, Ori A, Sabatini DM. NUFIP1 is a ribosome receptor for starvation-induced ribophagy. Science 2018; 360:751-758. [PMID: 29700228 DOI: 10.1126/science.aar2663] [Citation(s) in RCA: 223] [Impact Index Per Article: 37.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Accepted: 03/19/2018] [Indexed: 12/11/2022]
Abstract
The lysosome degrades and recycles macromolecules, signals to the master growth regulator mTORC1 [mechanistic target of rapamycin (mTOR) complex 1], and is associated with human disease. We performed quantitative proteomic analyses of rapidly isolated lysosomes and found that nutrient levels and mTOR dynamically modulate the lysosomal proteome. Upon mTORC1 inhibition, NUFIP1 (nuclear fragile X mental retardation-interacting protein 1) redistributes from the nucleus to autophagosomes and lysosomes. Upon these conditions, NUFIP1 interacts with ribosomes and delivers them to autophagosomes by directly binding to microtubule-associated proteins 1A/1B light chain 3B (LC3B). The starvation-induced degradation of ribosomes via autophagy (ribophagy) depends on the capacity of NUFIP1 to bind LC3B and promotes cell survival. We propose that NUFIP1 is a receptor for the selective autophagy of ribosomes.
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Affiliation(s)
- Gregory A Wyant
- Whitehead Institute for Biomedical Research and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA.,Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02142, USA.,Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Monther Abu-Remaileh
- Whitehead Institute for Biomedical Research and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA.,Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02142, USA.,Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Evgeni M Frenkel
- Whitehead Institute for Biomedical Research and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA.,Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02142, USA.,Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Nouf N Laqtom
- Whitehead Institute for Biomedical Research and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA.,Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02142, USA.,Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Vimisha Dharamdasani
- Whitehead Institute for Biomedical Research and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA.,Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02142, USA.,Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Caroline A Lewis
- Whitehead Institute for Biomedical Research and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Sze Ham Chan
- Whitehead Institute for Biomedical Research and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Ivonne Heinze
- Leibniz Institute on Aging-Fritz Lipmann Institute, 07745 Jena, Germany
| | - Alessandro Ori
- Leibniz Institute on Aging-Fritz Lipmann Institute, 07745 Jena, Germany.
| | - David M Sabatini
- Whitehead Institute for Biomedical Research and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA. .,Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02142, USA.,Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
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25
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Wyant GA, Abu-Remaileh M, Wolfson RL, Chen WW, Freinkman E, Danai LV, Vander Heiden MG, Sabatini DM. mTORC1 Activator SLC38A9 Is Required to Efflux Essential Amino Acids from Lysosomes and Use Protein as a Nutrient. Cell 2017; 171:642-654.e12. [PMID: 29053970 DOI: 10.1016/j.cell.2017.09.046] [Citation(s) in RCA: 293] [Impact Index Per Article: 41.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Revised: 07/18/2017] [Accepted: 09/25/2017] [Indexed: 12/17/2022]
Abstract
The mTORC1 kinase is a master growth regulator that senses many environmental cues, including amino acids. Activation of mTORC1 by arginine requires SLC38A9, a poorly understood lysosomal membrane protein with homology to amino acid transporters. Here, we validate that SLC38A9 is an arginine sensor for the mTORC1 pathway, and we uncover an unexpectedly central role for SLC38A9 in amino acid homeostasis. SLC38A9 mediates the transport, in an arginine-regulated fashion, of many essential amino acids out of lysosomes, including leucine, which mTORC1 senses through the cytosolic Sestrin proteins. SLC38A9 is necessary for leucine generated via lysosomal proteolysis to exit lysosomes and activate mTORC1. Pancreatic cancer cells, which use macropinocytosed protein as a nutrient source, require SLC38A9 to form tumors. Thus, through SLC38A9, arginine serves as a lysosomal messenger that couples mTORC1 activation to the release from lysosomes of the essential amino acids needed to drive cell growth.
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Affiliation(s)
- Gregory A Wyant
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, 9 Cambridge Center, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Cambridge, MA 02139, USA; Koch Institute for Integrative Cancer Research, 77 Massachusetts Avenue, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02142, USA
| | - Monther Abu-Remaileh
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, 9 Cambridge Center, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Cambridge, MA 02139, USA; Koch Institute for Integrative Cancer Research, 77 Massachusetts Avenue, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02142, USA
| | - Rachel L Wolfson
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, 9 Cambridge Center, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Cambridge, MA 02139, USA; Koch Institute for Integrative Cancer Research, 77 Massachusetts Avenue, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02142, USA; Harvard Medical School M.D.-Ph.D. Program, Daniel C. Tosteson Medical Education Center, 260 Longwood Avenue, Boston, MA 02115, USA
| | - Walter W Chen
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, 9 Cambridge Center, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Cambridge, MA 02139, USA; Koch Institute for Integrative Cancer Research, 77 Massachusetts Avenue, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02142, USA; Harvard Medical School M.D.-Ph.D. Program, Daniel C. Tosteson Medical Education Center, 260 Longwood Avenue, Boston, MA 02115, USA
| | - Elizaveta Freinkman
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, 9 Cambridge Center, Cambridge, MA 02142, USA
| | - Laura V Danai
- Koch Institute for Integrative Cancer Research, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Matthew G Vander Heiden
- Koch Institute for Integrative Cancer Research, 77 Massachusetts Avenue, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02142, USA; Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - David M Sabatini
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, 9 Cambridge Center, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Cambridge, MA 02139, USA; Koch Institute for Integrative Cancer Research, 77 Massachusetts Avenue, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02142, USA.
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26
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Abu-Remaileh M, Wyant GA, Kim C, Laqtom NN, Abbasi M, Chan SH, Freinkman E, Sabatini DM. Lysosomal metabolomics reveals V-ATPase- and mTOR-dependent regulation of amino acid efflux from lysosomes. Science 2017; 358:807-813. [PMID: 29074583 DOI: 10.1126/science.aan6298] [Citation(s) in RCA: 363] [Impact Index Per Article: 51.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Accepted: 10/03/2017] [Indexed: 01/09/2023]
Abstract
The lysosome degrades and recycles macromolecules, signals to the cytosol and nucleus, and is implicated in many diseases. Here, we describe a method for the rapid isolation of mammalian lysosomes and use it to quantitatively profile lysosomal metabolites under various cell states. Under nutrient-replete conditions, many lysosomal amino acids are in rapid exchange with those in the cytosol. Loss of lysosomal acidification through inhibition of the vacuolar H+-adenosine triphosphatase (V-ATPase) increased the luminal concentrations of most metabolites but had no effect on those of the majority of essential amino acids. Instead, nutrient starvation regulates the lysosomal concentrations of these amino acids, an effect we traced to regulation of the mechanistic target of rapamycin (mTOR) pathway. Inhibition of mTOR strongly reduced the lysosomal efflux of most essential amino acids, converting the lysosome into a cellular depot for them. These results reveal the dynamic nature of lysosomal metabolites and that V-ATPase- and mTOR-dependent mechanisms exist for controlling lysosomal amino acid efflux.
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Affiliation(s)
- Monther Abu-Remaileh
- Whitehead Institute for Biomedical Research and Massachusetts Institute of Technology, Department of Biology, 9 Cambridge Center, Cambridge, MA 02142, USA.,Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,Koch Institute for Integrative Cancer Research, 77 Massachusetts Avenue, Cambridge, MA 02139, USA.,Broad Institute of Harvard and Massachusetts Institute of Technology, 7 Cambridge Center, Cambridge, MA 02142, USA
| | - Gregory A Wyant
- Whitehead Institute for Biomedical Research and Massachusetts Institute of Technology, Department of Biology, 9 Cambridge Center, Cambridge, MA 02142, USA.,Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,Koch Institute for Integrative Cancer Research, 77 Massachusetts Avenue, Cambridge, MA 02139, USA.,Broad Institute of Harvard and Massachusetts Institute of Technology, 7 Cambridge Center, Cambridge, MA 02142, USA
| | - Choah Kim
- Whitehead Institute for Biomedical Research and Massachusetts Institute of Technology, Department of Biology, 9 Cambridge Center, Cambridge, MA 02142, USA.,Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,Koch Institute for Integrative Cancer Research, 77 Massachusetts Avenue, Cambridge, MA 02139, USA.,Broad Institute of Harvard and Massachusetts Institute of Technology, 7 Cambridge Center, Cambridge, MA 02142, USA
| | - Nouf N Laqtom
- Whitehead Institute for Biomedical Research and Massachusetts Institute of Technology, Department of Biology, 9 Cambridge Center, Cambridge, MA 02142, USA.,Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,Koch Institute for Integrative Cancer Research, 77 Massachusetts Avenue, Cambridge, MA 02139, USA.,Broad Institute of Harvard and Massachusetts Institute of Technology, 7 Cambridge Center, Cambridge, MA 02142, USA
| | - Maria Abbasi
- Whitehead Institute for Biomedical Research and Massachusetts Institute of Technology, Department of Biology, 9 Cambridge Center, Cambridge, MA 02142, USA.,Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,Koch Institute for Integrative Cancer Research, 77 Massachusetts Avenue, Cambridge, MA 02139, USA.,Broad Institute of Harvard and Massachusetts Institute of Technology, 7 Cambridge Center, Cambridge, MA 02142, USA
| | - Sze Ham Chan
- Whitehead Institute for Biomedical Research and Massachusetts Institute of Technology, Department of Biology, 9 Cambridge Center, Cambridge, MA 02142, USA
| | - Elizaveta Freinkman
- Whitehead Institute for Biomedical Research and Massachusetts Institute of Technology, Department of Biology, 9 Cambridge Center, Cambridge, MA 02142, USA
| | - David M Sabatini
- Whitehead Institute for Biomedical Research and Massachusetts Institute of Technology, Department of Biology, 9 Cambridge Center, Cambridge, MA 02142, USA. .,Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,Koch Institute for Integrative Cancer Research, 77 Massachusetts Avenue, Cambridge, MA 02139, USA.,Broad Institute of Harvard and Massachusetts Institute of Technology, 7 Cambridge Center, Cambridge, MA 02142, USA
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27
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Kanarek N, Freinkman E, Cantor J, Abu-Remaileh M, Wang T, Sabatini DM. Abstract 4988: Genome-wide CRISPR screen and metabolite profiling reveal a new mechanism of methotrexate sensitivity. Cancer Res 2017. [DOI: 10.1158/1538-7445.am2017-4988] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
The chemotherapeutic drug methotrexate (MTX) inhibits nucleotide biosynthesis and causes cell death by blocking DNA and RNA production. While MTX has had tremendous success as an anti-cancer treatment and is the subject of nearly a thousand ongoing clinical trials, we do not fully understand why certain cancers are more sensitive to it and why resistance emerges. To study these questions, we used a CRISPR-based genetic screen to identify genes that confer sensitivity to MTX. We identified an enzyme that plays a key role in a metabolic pathway that was not known to be associated with MTX sensitivity. Inhibition of the pathway, either by genetic loss of several genes in the pathway or through nutritional modulations, causes dramatic resistance to MTX in cultured cancer cells. Our results improved our understanding of the cellular response to MTX, and suggest that expression levels of enzymes in the pathway may serve as clinical predictor for MTX response in patients.
Citation Format: Naama Kanarek, Elizaveta Freinkman, Jason Cantor, Monther Abu-Remaileh, Tim Wang, David M. Sabatini. Genome-wide CRISPR screen and metabolite profiling reveal a new mechanism of methotrexate sensitivity [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 4988. doi:10.1158/1538-7445.AM2017-4988
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Affiliation(s)
- Naama Kanarek
- MIT Whitehead Inst. for Biomed. Research, Cambridge, MA
| | | | - Jason Cantor
- MIT Whitehead Inst. for Biomed. Research, Cambridge, MA
| | | | - Tim Wang
- MIT Whitehead Inst. for Biomed. Research, Cambridge, MA
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28
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Pacold ME, Brimacombe KR, Chan SH, Rohde JM, Lewis CA, Swier LJYM, Possemato R, Chen WW, Sullivan LB, Fiske BP, Cho S, Freinkman E, Birsoy K, Abu-Remaileh M, Shaul YD, Liu CM, Zhou M, Koh MJ, Chung H, Davidson SM, Luengo A, Wang AQ, Xu X, Yasgar A, Liu L, Rai G, Westover KD, Vander Heiden MG, Shen M, Gray NS, Boxer MB, Sabatini DM. A PHGDH inhibitor reveals coordination of serine synthesis and one-carbon unit fate. Nat Chem Biol 2016; 12:452-8. [PMID: 27110680 PMCID: PMC4871733 DOI: 10.1038/nchembio.2070] [Citation(s) in RCA: 337] [Impact Index Per Article: 42.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2015] [Accepted: 03/24/2016] [Indexed: 01/07/2023]
Abstract
Serine is a both a proteinogenic amino acid and the source of one-carbon units essential for de novo purine and deoxythymidine synthesis. In the canonical glucose-derived serine synthesis pathway, Homo sapiens phosphoglycerate dehydrogenase (PHGDH) catalyzes the first, rate-limiting step. Genetic loss of PHGDH is toxic towards PHGDH-overexpressing breast cancer cell lines even in the presence of exogenous serine. Here, we use a quantitative high-throughput screen to identify small molecule PHGDH inhibitors. These compounds reduce the production of glucose-derived serine in cells and suppress the growth of PHGDH-dependent cancer cells in culture and in orthotopic xenograft tumors. Surprisingly, PHGDH inhibition reduced the incorporation into nucleotides of one-carbon units from glucose-derived and exogenous serine. We conclude that glycolytic serine synthesis coordinates the use of one-carbon units from endogenous and exogenous serine in nucleotide synthesis, and suggest that one-carbon unit wasting may contribute to the efficacy of PHGDH inhibitors in vitro and in vivo.
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Affiliation(s)
- Michael E Pacold
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts, USA.,Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.,Koch Institute for Integrative Cancer Research, Cambridge, Massachusetts, USA.,Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.,Dana-Farber Cancer Institute, Longwood Center, Boston, Massachusetts, USA.,Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Kyle R Brimacombe
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, USA
| | - Sze Ham Chan
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts, USA.,Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.,Koch Institute for Integrative Cancer Research, Cambridge, Massachusetts, USA.,Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.,Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Jason M Rohde
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, USA
| | - Caroline A Lewis
- Koch Institute for Integrative Cancer Research, Cambridge, Massachusetts, USA
| | - Lotteke J Y M Swier
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts, USA.,Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.,Koch Institute for Integrative Cancer Research, Cambridge, Massachusetts, USA.,Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | | | - Walter W Chen
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts, USA.,Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.,Koch Institute for Integrative Cancer Research, Cambridge, Massachusetts, USA.,Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Lucas B Sullivan
- Koch Institute for Integrative Cancer Research, Cambridge, Massachusetts, USA
| | - Brian P Fiske
- Koch Institute for Integrative Cancer Research, Cambridge, Massachusetts, USA
| | - Steve Cho
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts, USA.,Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.,Koch Institute for Integrative Cancer Research, Cambridge, Massachusetts, USA.,Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | | | - Kıvanç Birsoy
- Laboratory of Metabolic Regulation and Genetics, The Rockefeller University, New York, New York, USA
| | - Monther Abu-Remaileh
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts, USA.,Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.,Koch Institute for Integrative Cancer Research, Cambridge, Massachusetts, USA.,Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Yoav D Shaul
- Department of Biochemistry and Molecular Biology, The Institute for Medical Research Israel-Canada, The Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Chieh Min Liu
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts, USA.,Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.,Koch Institute for Integrative Cancer Research, Cambridge, Massachusetts, USA.,Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Minerva Zhou
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts, USA.,Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.,Koch Institute for Integrative Cancer Research, Cambridge, Massachusetts, USA.,Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Min Jung Koh
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts, USA.,Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.,Koch Institute for Integrative Cancer Research, Cambridge, Massachusetts, USA.,Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Haeyoon Chung
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts, USA.,Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.,Koch Institute for Integrative Cancer Research, Cambridge, Massachusetts, USA.,Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Shawn M Davidson
- Koch Institute for Integrative Cancer Research, Cambridge, Massachusetts, USA
| | - Alba Luengo
- Koch Institute for Integrative Cancer Research, Cambridge, Massachusetts, USA
| | - Amy Q Wang
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, USA
| | - Xin Xu
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, USA
| | - Adam Yasgar
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, USA
| | - Li Liu
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, USA
| | - Ganesha Rai
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, USA
| | | | | | - Min Shen
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, USA
| | - Nathanael S Gray
- Dana-Farber Cancer Institute, Longwood Center, Boston, Massachusetts, USA
| | - Matthew B Boxer
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, USA
| | - David M Sabatini
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts, USA.,Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.,Koch Institute for Integrative Cancer Research, Cambridge, Massachusetts, USA.,Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
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29
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Aran D, Abu-Remaileh M, Levy R, Meron N, Toperoff G, Edrei Y, Bergman Y, Hellman A. Embryonic Stem Cell (ES)-Specific Enhancers Specify the Expression Potential of ES Genes in Cancer. PLoS Genet 2016; 12:e1005840. [PMID: 26886256 PMCID: PMC4757527 DOI: 10.1371/journal.pgen.1005840] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2015] [Accepted: 01/12/2016] [Indexed: 11/18/2022] Open
Abstract
Cancers often display gene expression profiles resembling those of undifferentiated cells. The mechanisms controlling these expression programs have yet to be identified. Exploring transcriptional enhancers throughout hematopoietic cell development and derived cancers, we uncovered a novel class of regulatory epigenetic mutations. These epimutations are particularly enriched in a group of enhancers, designated ES-specific enhancers (ESSEs) of the hematopoietic cell lineage. We found that hematopoietic ESSEs are prone to DNA methylation changes, indicative of their chromatin activity states. Strikingly, ESSE methylation is associated with gene transcriptional activity in cancer. Methylated ESSEs are hypermethylated in cancer relative to normal somatic cells and co-localized with silenced genes, whereas unmethylated ESSEs tend to be hypomethylated in cancer and associated with reactivated genes. Constitutive or hematopoietic stem cell-specific enhancers do not show these trends, suggesting selective reactivation of ESSEs in cancer. Further analyses of a hypomethylated ESSE downstream to the VEGFA gene revealed a novel regulatory circuit affecting VEGFA transcript levels across cancers and patients. We suggest that the discovered enhancer sites provide a framework for reactivation of ES genes in cancer.
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Affiliation(s)
- Dvir Aran
- Developmental Biology and Cancer Research, The Institute for Medical Research Israel-Canada (IMRIC), The Hebrew University-Hadassah Medical School, Jerusalem, Israel
- Institute for Computational Health Sciences, University of California, San Francisco, California, United States of America
| | - Monther Abu-Remaileh
- Developmental Biology and Cancer Research, The Institute for Medical Research Israel-Canada (IMRIC), The Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Revital Levy
- Developmental Biology and Cancer Research, The Institute for Medical Research Israel-Canada (IMRIC), The Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Nurit Meron
- Developmental Biology and Cancer Research, The Institute for Medical Research Israel-Canada (IMRIC), The Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Gidon Toperoff
- Developmental Biology and Cancer Research, The Institute for Medical Research Israel-Canada (IMRIC), The Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Yifat Edrei
- Developmental Biology and Cancer Research, The Institute for Medical Research Israel-Canada (IMRIC), The Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Yehudit Bergman
- Developmental Biology and Cancer Research, The Institute for Medical Research Israel-Canada (IMRIC), The Hebrew University-Hadassah Medical School, Jerusalem, Israel
- * E-mail: (YB); (AH)
| | - Asaf Hellman
- Developmental Biology and Cancer Research, The Institute for Medical Research Israel-Canada (IMRIC), The Hebrew University-Hadassah Medical School, Jerusalem, Israel
- * E-mail: (YB); (AH)
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Birsoy K, Wang T, Chen WW, Freinkman E, Abu-Remaileh M, Sabatini DM. An Essential Role of the Mitochondrial Electron Transport Chain in Cell Proliferation Is to Enable Aspartate Synthesis. Cell 2015; 162:540-51. [PMID: 26232224 DOI: 10.1016/j.cell.2015.07.016] [Citation(s) in RCA: 863] [Impact Index Per Article: 95.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2015] [Revised: 07/05/2015] [Accepted: 07/08/2015] [Indexed: 12/16/2022]
Abstract
The mitochondrial electron transport chain (ETC) enables many metabolic processes, but why its inhibition suppresses cell proliferation is unclear. It is also not well understood why pyruvate supplementation allows cells lacking ETC function to proliferate. We used a CRISPR-based genetic screen to identify genes whose loss sensitizes human cells to phenformin, a complex I inhibitor. The screen yielded GOT1, the cytosolic aspartate aminotransferase, loss of which kills cells upon ETC inhibition. GOT1 normally consumes aspartate to transfer electrons into mitochondria, but, upon ETC inhibition, it reverses to generate aspartate in the cytosol, which partially compensates for the loss of mitochondrial aspartate synthesis. Pyruvate stimulates aspartate synthesis in a GOT1-dependent fashion, which is required for pyruvate to rescue proliferation of cells with ETC dysfunction. Aspartate supplementation or overexpression of an aspartate transporter allows cells without ETC activity to proliferate. Thus, enabling aspartate synthesis is an essential role of the ETC in cell proliferation.
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Affiliation(s)
- Kıvanç Birsoy
- Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Koch Institute for Integrative Cancer Research, 77 Massachusetts Avenue, Cambridge, MA 02139, USA; Broad Institute of Harvard and Massachusetts Institute of Technology, 7 Cambridge Center, Cambridge, MA 02142, USA
| | - Tim Wang
- Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Koch Institute for Integrative Cancer Research, 77 Massachusetts Avenue, Cambridge, MA 02139, USA; Broad Institute of Harvard and Massachusetts Institute of Technology, 7 Cambridge Center, Cambridge, MA 02142, USA
| | - Walter W Chen
- Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Koch Institute for Integrative Cancer Research, 77 Massachusetts Avenue, Cambridge, MA 02139, USA; Broad Institute of Harvard and Massachusetts Institute of Technology, 7 Cambridge Center, Cambridge, MA 02142, USA
| | - Elizaveta Freinkman
- Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02142, USA
| | - Monther Abu-Remaileh
- Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Koch Institute for Integrative Cancer Research, 77 Massachusetts Avenue, Cambridge, MA 02139, USA; Broad Institute of Harvard and Massachusetts Institute of Technology, 7 Cambridge Center, Cambridge, MA 02142, USA
| | - David M Sabatini
- Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Koch Institute for Integrative Cancer Research, 77 Massachusetts Avenue, Cambridge, MA 02139, USA; Broad Institute of Harvard and Massachusetts Institute of Technology, 7 Cambridge Center, Cambridge, MA 02142, USA.
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31
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Abu-Remaileh M, Bender S, Raddatz G, Ansari I, Cohen D, Gutekunst J, Musch T, Linhart H, Breiling A, Pikarsky E, Bergman Y, Lyko F. Chronic inflammation induces a novel epigenetic program that is conserved in intestinal adenomas and in colorectal cancer. Cancer Res 2015; 75:2120-30. [PMID: 25808873 DOI: 10.1158/0008-5472.can-14-3295] [Citation(s) in RCA: 73] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2014] [Accepted: 02/12/2015] [Indexed: 12/13/2022]
Abstract
Chronic inflammation represents a major risk factor for tumor formation, but the underlying mechanisms have remained largely unknown. Epigenetic mechanisms can record the effects of environmental challenges on the genome level and could therefore play an important role in the pathogenesis of inflammation-associated tumors. Using single-base methylation maps and transcriptome analyses of a colitis-induced mouse colon cancer model, we identified a novel epigenetic program that is characterized by hypermethylation of DNA methylation valleys that are characterized by low CpG density and active chromatin marks. This program is conserved and functional in mouse intestinal adenomas and results in silencing of active intestinal genes that are involved in gastrointestinal homeostasis and injury response. Further analyses reveal that the program represents a prominent feature of human colorectal cancer and can be used to correctly classify colorectal cancer samples with high accuracy. Together, our results show that inflammatory signals establish a novel epigenetic program that silences a specific set of genes that contribute to inflammation-induced cellular transformation.
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Affiliation(s)
- Monther Abu-Remaileh
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Hebrew University Medical School, Jerusalem, Israel
| | - Sebastian Bender
- Division of Epigenetics, DKFZ-ZMBH Alliance, German Cancer Research Center, Heidelberg, Germany
| | - Günter Raddatz
- Division of Epigenetics, DKFZ-ZMBH Alliance, German Cancer Research Center, Heidelberg, Germany
| | - Ihab Ansari
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Hebrew University Medical School, Jerusalem, Israel
| | - Daphne Cohen
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Hebrew University Medical School, Jerusalem, Israel
| | - Julian Gutekunst
- Division of Epigenetics, DKFZ-ZMBH Alliance, German Cancer Research Center, Heidelberg, Germany
| | - Tanja Musch
- Division of Epigenetics, DKFZ-ZMBH Alliance, German Cancer Research Center, Heidelberg, Germany
| | - Heinz Linhart
- Division of Epigenetics, DKFZ-ZMBH Alliance, German Cancer Research Center, Heidelberg, Germany. Salem Medical Center, University of Heidelberg, Heidelberg, Germany. Department of Hematology/Oncology, University of Heidelberg Medical Center, Heidelberg, Germany
| | - Achim Breiling
- Division of Epigenetics, DKFZ-ZMBH Alliance, German Cancer Research Center, Heidelberg, Germany
| | - Eli Pikarsky
- The Lautenberg Center for Immunology, Institute for Medical Research Israel-Canada, Hebrew University Medical School, Jerusalem, Israel
| | - Yehudit Bergman
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Hebrew University Medical School, Jerusalem, Israel.
| | - Frank Lyko
- Division of Epigenetics, DKFZ-ZMBH Alliance, German Cancer Research Center, Heidelberg, Germany.
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Ludwig G, Nejman D, Hecht M, Orlanski S, Abu-Remaileh M, Yanuka O, Sandler O, Marx A, Roberts D, Benvenisty N, Bergman Y, Mendelsohn M, Cedar H. Aberrant DNA methylation in ES cells. PLoS One 2014; 9:e96090. [PMID: 24852222 PMCID: PMC4031077 DOI: 10.1371/journal.pone.0096090] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2013] [Accepted: 04/03/2014] [Indexed: 11/18/2022] Open
Abstract
Both mouse and human embryonic stem cells can be differentiated in vitro to produce a variety of somatic cell types. Using a new developmental tracing approach, we show that these cells are subject to massive aberrant CpG island de novo methylation that is exacerbated by differentiation in vitro. Bioinformatics analysis indicates that there are two distinct forms of abnormal de novo methylation, global as opposed to targeted, and in each case the resulting pattern is determined by molecular rules correlated with local pre-existing histone modification profiles. Since much of the abnormal methylation generated in vitro appears to be stably maintained, this modification may inhibit normal differentiation and could predispose to cancer if cells are used for replacement therapy. Excess CpG island methylation is also observed in normal placenta, suggesting that this process may be governed by an inherent program.
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Affiliation(s)
- Guy Ludwig
- Department of Developmental Biology and Cancer Research, The Hebrew University–Hadassah Medical School, Jerusalem, Israel
| | - Deborah Nejman
- Department of Developmental Biology and Cancer Research, The Hebrew University–Hadassah Medical School, Jerusalem, Israel
| | - Merav Hecht
- Department of Developmental Biology and Cancer Research, The Hebrew University–Hadassah Medical School, Jerusalem, Israel
| | - Shari Orlanski
- Department of Developmental Biology and Cancer Research, The Hebrew University–Hadassah Medical School, Jerusalem, Israel
| | - Monther Abu-Remaileh
- Department of Developmental Biology and Cancer Research, The Hebrew University–Hadassah Medical School, Jerusalem, Israel
| | - Ofra Yanuka
- Department of Genetics, Silberman Institute of Life Sciences, The Hebrew University, Jerusalem, Israel
| | - Oded Sandler
- Department of Biochemistry and Molecular Biology, The Hebrew University–Hadassah Medical School, Jerusalem, Israel
| | - Amichai Marx
- Department of Biochemistry and Molecular Biology, The Hebrew University–Hadassah Medical School, Jerusalem, Israel
| | - Douglas Roberts
- Agilent Technologies, Inc., Agilent Laboratories, Santa Clara, California, United States of America
| | - Nissim Benvenisty
- Department of Genetics, Silberman Institute of Life Sciences, The Hebrew University, Jerusalem, Israel
| | - Yehudit Bergman
- Department of Developmental Biology and Cancer Research, The Hebrew University–Hadassah Medical School, Jerusalem, Israel
| | - Monica Mendelsohn
- Department of Biochemistry and Molecular Biophysics, Columbia College of Physicians and Surgeons, New York, New York, United States of America
| | - Howard Cedar
- Department of Developmental Biology and Cancer Research, The Hebrew University–Hadassah Medical School, Jerusalem, Israel
- * E-mail:
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33
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Epsztejn-Litman S, Feldman N, Abu-Remaileh M, Shufaro Y, Gerson A, Ueda J, Deplus R, Fuks F, Shinkai Y, Cedar H, Bergman Y. De novo DNA methylation promoted by G9a prevents reprogramming of embryonically silenced genes. Nat Struct Mol Biol 2008; 15:1176-1183. [PMID: 18953337 PMCID: PMC2581722 DOI: 10.1038/nsmb.1476] [Citation(s) in RCA: 324] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2007] [Accepted: 07/15/2008] [Indexed: 12/17/2022]
Abstract
The pluripotency-determining gene Oct3/4 (also called Pou5f1) undergoes postimplantation silencing in a process mediated by the histone methyltransferase G9a. Microarray analysis now shows that this enzyme may operate as a master regulator that inactivates numerous early-embryonic genes by bringing about heterochromatinization of methylated histone H3K9 and de novo DNA methylation. Genetic studies in differentiating embryonic stem cells demonstrate that a point mutation in the G9a SET domain prevents heterochromatinization but still allows de novo methylation, whereas biochemical and functional studies indicate that G9a itself is capable of bringing about de novo methylation through its ankyrin domain, by recruiting Dnmt3a and Dnmt3b independently of its histone methyltransferase activity. These modifications seem to be programmed for carrying out two separate biological functions: histone methylation blocks target-gene reactivation in the absence of transcriptional repressors, whereas DNA methylation prevents reprogramming to the undifferentiated state.
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Affiliation(s)
- Silvina Epsztejn-Litman
- Departments of Experimental Medicine and Cellular Biochemistry Hebrew University Medical School Ein Kerem Jerusalem, 91120 ISRAEL
| | - Nirit Feldman
- Departments of Experimental Medicine and Cellular Biochemistry Hebrew University Medical School Ein Kerem Jerusalem, 91120 ISRAEL
| | - Monther Abu-Remaileh
- Departments of Experimental Medicine and Cellular Biochemistry Hebrew University Medical School Ein Kerem Jerusalem, 91120 ISRAEL
| | - Yoel Shufaro
- IVF Unit, The Department of OB/GYN The Hadassah Human Embryonic Stem Cell Research Center Hadassah Hebrew University Medical Center Jerusalem, 91120 ISRAEL
| | - Ariela Gerson
- Departments of Experimental Medicine and Cellular Biochemistry Hebrew University Medical School Ein Kerem Jerusalem, 91120 ISRAEL
| | - Jun Ueda
- Experimental Research Center for Infectious Disease Institute for Virus Research Kyoto University Sakyo-Ku, Kyoto 606-8507 JAPAN
| | - Rachel Deplus
- Laboratory of Cancer Epigenetics Faculty of Medicine Free University of Brussels Brussels 1070 BELGIUM
| | - François Fuks
- Laboratory of Cancer Epigenetics Faculty of Medicine Free University of Brussels Brussels 1070 BELGIUM
| | - Yoichi Shinkai
- Experimental Research Center for Infectious Disease Institute for Virus Research Kyoto University Sakyo-Ku, Kyoto 606-8507 JAPAN
| | - Howard Cedar
- Departments of Experimental Medicine and Cellular Biochemistry Hebrew University Medical School Ein Kerem Jerusalem, 91120 ISRAEL
| | - Yehudit Bergman
- Departments of Experimental Medicine and Cellular Biochemistry Hebrew University Medical School Ein Kerem Jerusalem, 91120 ISRAEL
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