1
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Hallows WC, Skvorak K, Agard N, Kruse N, Zhang X, Zhu Y, Botham RC, Chng C, Shukla C, Lao J, Miller M, Sero A, Viduya J, Ismaili MHA, McCluskie K, Schiffmann R, Silverman AP, Shen JS, Huisman GW. Optimizing human α-galactosidase for treatment of Fabry disease. Sci Rep 2023; 13:4748. [PMID: 36959353 PMCID: PMC10036536 DOI: 10.1038/s41598-023-31777-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 03/17/2023] [Indexed: 03/25/2023] Open
Abstract
Fabry disease is caused by a deficiency of α-galactosidase A (GLA) leading to the lysosomal accumulation of globotriaosylceramide (Gb3) and other glycosphingolipids. Fabry patients experience significant damage to the heart, kidney, and blood vessels that can be fatal. Here we apply directed evolution to generate more stable GLA variants as potential next generation treatments for Fabry disease. GLAv05 and GLAv09 were identified after screening more than 12,000 GLA variants through 8 rounds of directed evolution. Both GLAv05 and GLAv09 exhibit increased stability at both lysosomal and blood pH, stability to serum, and elevated enzyme activity in treated Fabry fibroblasts (19-fold) and GLA-/- podocytes (10-fold). GLAv05 and GLAv09 show improved pharmacokinetics in mouse and non-human primates. In a Fabry mouse model, the optimized variants showed prolonged half-lives in serum and relevant tissues, and a decrease of accumulated Gb3 in heart and kidney. To explore the possibility of diminishing the immunogenic potential of rhGLA, amino acid residues in sequences predicted to bind MHC II were targeted in late rounds of GLAv09 directed evolution. An MHC II-associated peptide proteomics assay confirmed a reduction in displayed peptides for GLAv09. Collectively, our findings highlight the promise of using directed evolution to generate enzyme variants for more effective treatment of lysosomal storage diseases.
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Affiliation(s)
| | - Kristen Skvorak
- Codexis Inc.,, 200 Penobscot Drive, Redwood City, CA, 94063, USA
| | - Nick Agard
- Codexis Inc.,, 200 Penobscot Drive, Redwood City, CA, 94063, USA
- Genentech, South San Francisco, CA, 94080, USA
| | - Nikki Kruse
- Codexis Inc.,, 200 Penobscot Drive, Redwood City, CA, 94063, USA
| | - Xiyun Zhang
- Codexis Inc.,, 200 Penobscot Drive, Redwood City, CA, 94063, USA
- Fornia BioSolutions Inc US, Hayward, CA, 94545, USA
| | - Yu Zhu
- Codexis Inc.,, 200 Penobscot Drive, Redwood City, CA, 94063, USA
| | - Rachel C Botham
- Codexis Inc.,, 200 Penobscot Drive, Redwood City, CA, 94063, USA
| | - Chinping Chng
- Codexis Inc.,, 200 Penobscot Drive, Redwood City, CA, 94063, USA
| | - Charu Shukla
- Codexis Inc.,, 200 Penobscot Drive, Redwood City, CA, 94063, USA
| | - Jessica Lao
- Codexis Inc.,, 200 Penobscot Drive, Redwood City, CA, 94063, USA
- Octant, Emeryville, CA, 94608, USA
| | - Mathew Miller
- Codexis Inc.,, 200 Penobscot Drive, Redwood City, CA, 94063, USA
| | - Antoinette Sero
- Codexis Inc.,, 200 Penobscot Drive, Redwood City, CA, 94063, USA
| | - Judy Viduya
- Codexis Inc.,, 200 Penobscot Drive, Redwood City, CA, 94063, USA
| | - Moulay Hicham Alaoui Ismaili
- Codexis Inc.,, 200 Penobscot Drive, Redwood City, CA, 94063, USA
- Glycomine, San Mateo, CA, 94070, USA
| | - Kerryn McCluskie
- Codexis Inc.,, 200 Penobscot Drive, Redwood City, CA, 94063, USA
- Glycomine, San Mateo, CA, 94070, USA
| | - Raphael Schiffmann
- Institute of Metabolic Disease, Baylor Research Institute, Dallas, TX, 75246, USA
- 4D Molecular Therapeutics, Emeryville, CA, 94608, USA
| | - Adam P Silverman
- Codexis Inc.,, 200 Penobscot Drive, Redwood City, CA, 94063, USA
| | - Jin-Song Shen
- Institute of Metabolic Disease, Baylor Research Institute, Dallas, TX, 75246, USA
- 4D Molecular Therapeutics, Emeryville, CA, 94608, USA
| | - Gjalt W Huisman
- Codexis Inc.,, 200 Penobscot Drive, Redwood City, CA, 94063, USA
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2
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Kytidou K, Beenakker TJM, Westerhof LB, Hokke CH, Moolenaar GF, Goosen N, Mirzaian M, Ferraz MJ, de Geus M, Kallemeijn WW, Overkleeft HS, Boot RG, Schots A, Bosch D, Aerts JMFG. Human Alpha Galactosidases Transiently Produced in Nicotiana benthamiana Leaves: New Insights in Substrate Specificities with Relevance for Fabry Disease. FRONTIERS IN PLANT SCIENCE 2017; 8:1026. [PMID: 28680430 PMCID: PMC5478728 DOI: 10.3389/fpls.2017.01026] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Accepted: 05/29/2017] [Indexed: 05/25/2023]
Abstract
Deficiency of α-galactosidase A (α-GAL) causes Fabry disease (FD), an X-linked storage disease of the glycosphingolipid globtriaosylcerammide (Gb3) in lysosomes of various cells and elevated plasma globotriaosylsphingosine (Lyso-Gb3) toxic for podocytes and nociceptive neurons. Enzyme replacement therapy is used to treat the disease, but clinical efficacy is limited in many male FD patients due to development of neutralizing antibodies (Ab). Therapeutic use of modified lysosomal α-N-acetyl-galactosaminidase (α-NAGAL) with increased α-galactosidase activity (α-NAGALEL) has therefore been suggested. We transiently produced in Nicotiana benthamiana leaves functional α-GAL, α-NAGAL, and α-NAGALEL enzymes for research purposes. All enzymes could be visualized with activity-based probes covalently binding in their catalytic pocket. Characterization of purified proteins indicated that α-NAGALEL is improved in activity toward artificial 4MU-α-galactopyranoside. Recombinant α-NAGALEL and α-NAGAL are not neutralized by Ab-positive FD serum tested and are more stable in human plasma than α-GAL. Both enzymes hydrolyze the lipid substrates Gb3 and Lyso-Gb3 accumulating in Fabry patients. The addition to FD sera of α-NAGALEL, and to a lesser extent that of α-NAGAL, results in a reduction of the toxic Lyso-Gb3. In conclusion, our study suggests that modified α-NAGALEL might reduce excessive Lyso-Gb3 in FD serum. This neo-enzyme can be produced in Nicotiana benthamiana and might be further developed for the treatment of FD aiming at reduction of circulating Lyso-Gb3.
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Affiliation(s)
- Kassiani Kytidou
- Department of Medical Biochemistry, Leiden Institute of ChemistryLeiden, Netherlands
| | | | - Lotte B. Westerhof
- Wageningen University and Research, Plant Sciences GroupWageningen, Netherlands
| | - Cornelis H. Hokke
- Department of Parasitology, Centre of Infectious Diseases, Leiden University Medical CenterLeiden, Netherlands
| | - Geri F. Moolenaar
- Cloning and Protein Purification Facility of Leiden Institute of ChemistryLeiden, Netherlands
| | - Nora Goosen
- Cloning and Protein Purification Facility of Leiden Institute of ChemistryLeiden, Netherlands
| | - Mina Mirzaian
- Department of Medical Biochemistry, Leiden Institute of ChemistryLeiden, Netherlands
| | - Maria J. Ferraz
- Department of Medical Biochemistry, Leiden Institute of ChemistryLeiden, Netherlands
| | - Mark de Geus
- Department of Medical Biochemistry, Leiden Institute of ChemistryLeiden, Netherlands
| | - Wouter W. Kallemeijn
- Department of Medical Biochemistry, Leiden Institute of ChemistryLeiden, Netherlands
| | - Herman S. Overkleeft
- Department of Bio-organic Synthesis, Leiden Institute of ChemistryLeiden, Netherlands
| | - Rolf G. Boot
- Department of Medical Biochemistry, Leiden Institute of ChemistryLeiden, Netherlands
| | - Arjen Schots
- Wageningen University and Research, Plant Sciences GroupWageningen, Netherlands
| | - Dirk Bosch
- Wageningen University and Research, Plant Sciences GroupWageningen, Netherlands
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3
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Meghdari M, Gao N, Abdullahi A, Stokes E, Calhoun DH. Carboxyl-terminal truncations alter the activity of the human α-galactosidase A. PLoS One 2015; 10:e0118341. [PMID: 25719393 PMCID: PMC4342250 DOI: 10.1371/journal.pone.0118341] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2014] [Accepted: 01/13/2015] [Indexed: 12/17/2022] Open
Abstract
Fabry disease is an X-linked inborn error of glycolipid metabolism caused by deficiency of the human lysosomal enzyme, α-galactosidase A (αGal), leading to strokes, myocardial infarctions, and terminal renal failure, often leading to death in the fourth or fifth decade of life. The enzyme is responsible for the hydrolysis of terminal α-galactoside linkages in various glycolipids. Enzyme replacement therapy (ERT) has been approved for the treatment of Fabry disease, but adverse reactions, including immune reactions, make it desirable to generate improved methods for ERT. One approach to circumvent these adverse reactions is the development of derivatives of the enzyme with more activity per mg. It was previously reported that carboxyl-terminal deletions of 2 to 10 amino acids led to increased activity of about 2 to 6-fold. However, this data was qualitative or semi-quantitative and relied on comparison of the amounts of mRNA present in Northern blots with αGal enzyme activity using a transient expression system in COS-1 cells. Here we follow up on this report by constructing and purifying mutant enzymes with deletions of 2, 4, 6, 8, and 10 C-terminal amino acids (Δ2, Δ4, Δ6, Δ8, Δ10) for unambiguous quantitative enzyme assays. The results reported here show that the kcat/Km approximately doubles with deletions of 2, 4, 6 and 10 amino acids (0.8 to 1.7-fold effect) while a deletion of 8 amino acids decreases the kcat/Km (7.2-fold effect). These results indicate that the mutated enzymes with increased activity constructed here would be expected to have a greater therapeutic effect on a per mg basis, and could therefore reduce the likelihood of adverse infusion related reactions in Fabry patients receiving ERT treatment. These results also illustrate the principle that in vitro mutagenesis can be used to generate αGal derivatives with improved enzyme activity.
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Affiliation(s)
- Mariam Meghdari
- Chemistry Dept., City College of New York, New York, NY, USA
| | - Nicholas Gao
- Chemistry Dept., City College of New York, New York, NY, USA
| | - Abass Abdullahi
- Biology & Medical Lab Technology, Bronx Community College, Bronx, NY, USA
| | - Erin Stokes
- Chemistry Dept., City College of New York, New York, NY, USA
| | - David H. Calhoun
- Chemistry Dept., City College of New York, New York, NY, USA
- * E-mail:
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4
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Unzueta U, Vázquez F, Accardi G, Mendoza R, Toledo-Rubio V, Giuliani M, Sannino F, Parrilli E, Abasolo I, Schwartz S, Tutino ML, Villaverde A, Corchero JL, Ferrer-Miralles N. Strategies for the production of difficult-to-express full-length eukaryotic proteins using microbial cell factories: production of human alpha-galactosidase A. Appl Microbiol Biotechnol 2015; 99:5863-74. [DOI: 10.1007/s00253-014-6328-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2014] [Revised: 12/12/2014] [Accepted: 12/14/2014] [Indexed: 12/28/2022]
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5
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Bayraktar H, Önal S. Concentration and purification of α-galactosidase from watermelon (Citrullus vulgaris) by three phase partitioning. Sep Purif Technol 2013. [DOI: 10.1016/j.seppur.2013.08.040] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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6
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Spadiut O, Rossetti L, Dietzsch C, Herwig C. Purification of a recombinant plant peroxidase produced in Pichia pastoris by a simple 2-step strategy. Protein Expr Purif 2012; 86:89-97. [DOI: 10.1016/j.pep.2012.09.008] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2012] [Revised: 09/19/2012] [Accepted: 09/20/2012] [Indexed: 10/27/2022]
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7
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Purification of α-galactosidase from pepino (Solanum muricatum) by three-phase partitioning. Sep Purif Technol 2011. [DOI: 10.1016/j.seppur.2011.09.026] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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8
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Wu X, Katz E, Della Valle MC, Mascioli K, Flanagan JJ, Castelli JP, Schiffmann R, Boudes P, Lockhart DJ, Valenzano KJ, Benjamin ER. A pharmacogenetic approach to identify mutant forms of α-galactosidase A that respond to a pharmacological chaperone for Fabry disease. Hum Mutat 2011; 32:965-77. [PMID: 21598360 PMCID: PMC3170878 DOI: 10.1002/humu.21530] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2011] [Accepted: 04/27/2011] [Indexed: 12/11/2022]
Abstract
Fabry disease is caused by mutations in the gene (GLA) that encodes α-galactosidase A (α-Gal A). The iminosugar AT1001 (GR181413A, migalastat hydrochloride, 1-deoxygalactonojirimycin) is a pharmacological chaperone that selectively binds and stabilizes α-Gal A, increasing total cellular levels and activity for some mutant forms (defined as “responsive”). In this study, we developed a cell-based assay in cultured HEK-293 cells to identify mutant forms of α-Gal A that are responsive to AT1001. Concentration-dependent increases in α-Gal A activity in response to AT1001 were shown for 49 (60%) of 81 mutant forms. The responses of α-Gal A mutant forms were generally consistent with the responses observed in male Fabry patient-derived lymphoblasts. Importantly, the HEK-293 cell responses of 19 α-Gal A mutant forms to a clinically achievable concentration of AT1001 (10 µM) were generally consistent with observed increases in α-Gal A activity in peripheral blood mononuclear cells from male Fabry patients orally administered AT1001 during Phase 2 clinical studies. This indicates that the cell-based responses can identify mutant forms of α-Gal A that are likely to respond to AT1001 in vivo. Thus, the HEK-293 cell-based assay may be a useful aid in the identification of Fabry patients with AT1001-responsive mutant forms. Hum Mutat 32:1–13, 2011. © 2011 Wiley-Liss, Inc.
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Affiliation(s)
- Xiaoyang Wu
- Amicus Therapeutics, Cranbury, New Jersey 08512, USA
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9
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Okutucu B, Çelem EB, Önal S. Immobilization of α-galactosidase on galactose-containing polymeric beads. Enzyme Microb Technol 2010. [DOI: 10.1016/j.enzmictec.2009.12.005] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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10
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Çalci E, Demir T, Biçak Çelem E, Önal S. Purification of tomato (Lycopersicon esculentum) α-galactosidase by three-phase partitioning and its characterization. Sep Purif Technol 2009. [DOI: 10.1016/j.seppur.2009.09.004] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Yavuz H, Özden K, Kin EP, Denizli A. Concanavalin A Binding on PHEMA Beads and Their Interactions with Myeloma Cells. JOURNAL OF MACROMOLECULAR SCIENCE PART A-PURE AND APPLIED CHEMISTRY 2009. [DOI: 10.1080/10601320802594774] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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12
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Liquid chromatography of recombinant proteins and protein drugs. J Chromatogr B Analyt Technol Biomed Life Sci 2008; 866:133-53. [DOI: 10.1016/j.jchromb.2008.01.041] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2007] [Revised: 12/17/2007] [Accepted: 01/18/2008] [Indexed: 01/12/2023]
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13
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Ishii S, Chang HH, Kawasaki K, Yasuda K, Wu HL, Garman S, Fan JQ. Mutant alpha-galactosidase A enzymes identified in Fabry disease patients with residual enzyme activity: biochemical characterization and restoration of normal intracellular processing by 1-deoxygalactonojirimycin. Biochem J 2007; 406:285-95. [PMID: 17555407 PMCID: PMC1948963 DOI: 10.1042/bj20070479] [Citation(s) in RCA: 103] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Fabry disease is a lysosomal storage disorder caused by the deficiency of alpha-Gal A (alpha-galactosidase A) activity. In order to understand the molecular mechanism underlying alpha-Gal A deficiency in Fabry disease patients with residual enzyme activity, enzymes with different missense mutations were purified from transfected COS-7 cells and the biochemical properties were characterized. The mutant enzymes detected in variant patients (A20P, E66Q, M72V, I91T, R112H, F113L, N215S, Q279E, M296I, M296V and R301Q), and those found mostly in mild classic patients (A97V, A156V, L166V and R356W) appeared to have normal K(m) and V(max) values. The degradation of all mutants (except E59K) was partially inhibited by treatment with kifunensine, a selective inhibitor of ER (endoplasmic reticulum) alpha-mannosidase I. Metabolic labelling and subcellular fractionation studies in COS-7 cells expressing the L166V and R301Q alpha-Gal A mutants indicated that the mutant protein was retained in the ER and degraded without processing. Addition of DGJ (1-deoxygalactonojirimycin) to the culture medium of COS-7 cells transfected with a large set of missense mutant alpha-Gal A cDNAs effectively increased both enzyme activity and protein yield. DGJ was capable of normalizing intracellular processing of mutant alpha-Gal A found in both classic (L166V) and variant (R301Q) Fabry disease patients. In addition, the residual enzyme activity in fibroblasts or lymphoblasts from both classic and variant hemizygous Fabry disease patients carrying a variety of missense mutations could be substantially increased by cultivation of the cells with DGJ. These results indicate that a large proportion of mutant enzymes in patients with residual enzyme activity are kinetically active. Excessive degradation in the ER could be responsible for the deficiency of enzyme activity in vivo, and the DGJ approach may be broadly applicable to Fabry disease patients with missense mutations.
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Affiliation(s)
- Satoshi Ishii
- *Department of Human Genetics, Mount Sinai School of Medicine, Fifth Avenue at 100th Street, New York, NY 10029, U.S.A
- †Department of Agricultural and Life Sciences, Obihiro University of Agriculture and Veterinary Medicine, Obihiro, 080-8555, Japan
| | - Hui-Hwa Chang
- *Department of Human Genetics, Mount Sinai School of Medicine, Fifth Avenue at 100th Street, New York, NY 10029, U.S.A
| | - Kunito Kawasaki
- †Department of Agricultural and Life Sciences, Obihiro University of Agriculture and Veterinary Medicine, Obihiro, 080-8555, Japan
| | - Kayo Yasuda
- *Department of Human Genetics, Mount Sinai School of Medicine, Fifth Avenue at 100th Street, New York, NY 10029, U.S.A
| | - Hui-Li Wu
- *Department of Human Genetics, Mount Sinai School of Medicine, Fifth Avenue at 100th Street, New York, NY 10029, U.S.A
| | - Scott C. Garman
- ‡Department of Biochemistry and Molecular Biology, University of Massachusetts, 710 North Pleasant Street, Amherst, MA 01003, U.S.A
| | - Jian-Qiang Fan
- *Department of Human Genetics, Mount Sinai School of Medicine, Fifth Avenue at 100th Street, New York, NY 10029, U.S.A
- To whom correspondence should be addressed (email )
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Akeboshi H, Chiba Y, Kasahara Y, Takashiba M, Takaoka Y, Ohsawa M, Tajima Y, Kawashima I, Tsuji D, Itoh K, Sakuraba H, Jigami Y. Production of recombinant beta-hexosaminidase A, a potential enzyme for replacement therapy for Tay-Sachs and Sandhoff diseases, in the methylotrophic yeast Ogataea minuta. Appl Environ Microbiol 2007; 73:4805-12. [PMID: 17557860 PMCID: PMC1951009 DOI: 10.1128/aem.00463-07] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2007] [Accepted: 05/24/2007] [Indexed: 01/28/2023] Open
Abstract
Human beta-hexosaminidase A (HexA) is a heterodimeric glycoprotein composed of alpha- and beta-subunits that degrades GM2 gangliosides in lysosomes. GM2 gangliosidosis is a lysosomal storage disease in which an inherited deficiency of HexA causes the accumulation of GM2 gangliosides. In order to prepare a large amount of HexA for a treatment based on enzyme replacement therapy (ERT), recombinant HexA was produced in the methylotrophic yeast Ogataea minuta instead of in mammalian cells, which are commonly used to produce recombinant enzymes for ERT. The problem of antigenicity due to differences in N-glycan structures between mammalian and yeast glycoproteins was potentially resolved by using alpha-1,6-mannosyltransferase-deficient (och1Delta) yeast as the host. Genes encoding the alpha- and beta-subunits of HexA were integrated into the yeast cell, and the heterodimer was expressed together with its isozymes HexS (alphaalpha) and HexB (betabeta). A total of 57 mg of beta-hexosaminidase isozymes, of which 13 mg was HexA (alphabeta), was produced per liter of medium. HexA was purified with immobilized metal affinity column for the His tag attached to the beta-subunit. The purified HexA was treated with alpha-mannosidase to expose mannose-6-phosphate (M6P) residues on the N-glycans. The specific activities of HexA and M6P-exposed HexA (M6PHexA) for the artificial substrate 4MU-GlcNAc were 1.2 +/- 0.1 and 1.7 +/- 0.3 mmol/h/mg, respectively. The sodium dodecyl sulfate-polyacrylamide gel electrophoresis pattern suggested a C-terminal truncation in the beta-subunit of the recombinant protein. M6PHexA was incorporated dose dependently into GM2 gangliosidosis patient-derived fibroblasts via M6P receptors on the cell surface, and degradation of accumulated GM2 ganglioside was observed.
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Affiliation(s)
- Hiromi Akeboshi
- Research Center for Glycoscience, AIST Tsukuba Central 6, 1-1-1 Higashi, Tsukuba, Ibaraki, Japan
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