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Taylor SKB, Hartman JH, Gupta BP. Neurotrophic factor MANF regulates autophagy and lysosome function to promote proteostasis in C. elegans. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.07.31.551399. [PMID: 38260421 PMCID: PMC10802257 DOI: 10.1101/2023.07.31.551399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
The conserved mesencephalic astrocyte-derived neurotrophic factor (MANF) protects dopaminergic neurons but also functions in several other tissues. Previously, we showed that Caenorhabditis elegans manf-1 null mutants have increased ER stress, dopaminergic neurodegeneration, protein aggregation, slower growth, and a reduced lifespan. The multiple requirements of MANF in different systems suggest its essential role in regulating cellular processes. However, how intracellular and extracellular MANF regulates broader cellular function remains unknown. Here, we report a novel mechanism of action for manf-1 that involves the autophagy transcription factor HLH-30/TFEB-mediated signaling to regulate lysosomal function and aging. We generated multiple transgenic strains overexpressing MANF-1 and found that animals had extended lifespan, reduced protein aggregation, and improved neuronal health. Using a fluorescently tagged MANF-1, we observed different tissue localization of MANF-1 depending on the ER retention signal. Further subcellular analysis showed that MANF-1 localizes within cells to the lysosomes. These findings were consistent with our transcriptomic studies and, together with analysis of autophagy regulators, demonstrate that MANF-1 regulates protein homeostasis through increased autophagy and lysosomal activity. Collectively, our findings establish MANF as a critical regulator of the stress response, proteostasis, and aging.
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Affiliation(s)
- Shane K. B. Taylor
- Department of Biology, McMaster University, Hamilton, ON L8S 4K1, Canada
| | - Jessica H. Hartman
- Department of Biochemistry & Molecular Biology and Department of Regenerative Medicine & Cell Biology, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Bhagwati P. Gupta
- Department of Biology, McMaster University, Hamilton, ON L8S 4K1, Canada
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Basiri M, Ghaffari ME, Ruan J, Murugesan V, Kleytman N, Belinsky G, Akhavan A, Lischuk A, Guo L, Klinger K, Mistry PK. Osteonecrosis in Gaucher disease in the era of multiple therapies: Biomarker set for risk stratification from a tertiary referral center. eLife 2023; 12:e87537. [PMID: 37249220 PMCID: PMC10317498 DOI: 10.7554/elife.87537] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 05/22/2023] [Indexed: 05/31/2023] Open
Abstract
Background A salutary effect of treatments for Gaucher disease (GD) has been a reduction in the incidence of avascular osteonecrosis (AVN). However, there are reports of AVN in patients receiving enzyme replacement therapy (ERT) , and it is not known whether it is related to individual treatments, GBA genotypes, phenotypes, biomarkers of residual disease activity, or anti-drug antibodies. Prompted by development of AVN in several patients receiving ERT, we aimed to delineate the determinants of AVN in patients receiving ERT or eliglustat substrate reduction therapy (SRT) during 20 years in a tertiary referral center. Methods Longitudinal follow-ups of 155 GD patients between 2001 and 2021 were analyzed for episodes of AVN on therapy, type of therapy, GBA1 genotype, spleen status, biomarkers, and other disease indicators. We applied mixed-effects logistic model to delineate the independent correlates of AVN while receiving treatment. Results The patients received cumulative 1382 years of treatment. There were 16 episodes of AVN in 14 patients, with two episodes, each occurring in two patients. Heteroallelic p.Asn409Ser GD1 patients were 10 times (95% CI, 1.5-67.2) more likely than p.Asn409Ser homozygous patients to develop osteonecrosis during treatment. History of AVN prior to treatment initiation was associated with 4.8-fold increased risk of AVN on treatment (95% CI, 1.5-15.2). The risk of AVN among patients receiving velaglucerase ERT was 4.68 times higher compared to patients receiving imiglucerase ERT (95% CI, 1.67-13). No patient receiving eliglustat SRT suffered AVN. There was a significant correlation between GlcSph levels and AVN. Together, these biomarkers reliably predicted risk of AVN during therapy (ROC AUC 0.894, p<0.001). Conclusions There is a low, but significant risk of AVN in GD in the era of ERT/SRT. We found that increased risk of AVN was related to GBA genotype, history of AVN prior to treatment initiation, residual serum GlcSph level, and the type of ERT. No patient receiving SRT developed AVN. These findings exemplify a new approach to biomarker applications in a rare inborn error of metabolism to evaluate clinical outcomes in comprehensively followed patients and will aid identification of GD patients at higher risk of AVN who will benefit from closer monitoring and treatment optimization. Funding LSD Training Fellowship from Sanofi to MB.
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Affiliation(s)
- Mohsen Basiri
- Department of Internal Medicine, Yale UniversityNew HavenUnited States
| | - Mohammad E Ghaffari
- Department of ENT, Head and Neck Surgery, Guilan University of Medical SciencesRashtIslamic Republic of Iran
| | - Jiapeng Ruan
- Department of Internal Medicine, Yale UniversityNew HavenUnited States
| | | | | | - Glenn Belinsky
- Department of Internal Medicine, Yale UniversityNew HavenUnited States
| | - Amir Akhavan
- Department of Computer and Information Science, University of Massachusetts DartmouthDartmoutUnited States
| | - Andrew Lischuk
- Department of Radiology and Biomedical Imaging, Yale UniversityNew HavenUnited States
| | - Lilu Guo
- Translational Sciences, SanofiFraminghamUnited States
| | | | - Pramod K Mistry
- Department of Internal Medicine, Yale UniversityNew HavenUnited States
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Pandey MK. Exploring Pro-Inflammatory Immunological Mediators: Unraveling the Mechanisms of Neuroinflammation in Lysosomal Storage Diseases. Biomedicines 2023; 11:biomedicines11041067. [PMID: 37189685 DOI: 10.3390/biomedicines11041067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 03/17/2023] [Accepted: 03/22/2023] [Indexed: 04/05/2023] Open
Abstract
Lysosomal storage diseases are a group of rare and ultra-rare genetic disorders caused by defects in specific genes that result in the accumulation of toxic substances in the lysosome. This excess accumulation of such cellular materials stimulates the activation of immune and neurological cells, leading to neuroinflammation and neurodegeneration in the central and peripheral nervous systems. Examples of lysosomal storage diseases include Gaucher, Fabry, Tay–Sachs, Sandhoff, and Wolman diseases. These diseases are characterized by the accumulation of various substrates, such as glucosylceramide, globotriaosylceramide, ganglioside GM2, sphingomyelin, ceramide, and triglycerides, in the affected cells. The resulting pro-inflammatory environment leads to the generation of pro-inflammatory cytokines, chemokines, growth factors, and several components of complement cascades, which contribute to the progressive neurodegeneration seen in these diseases. In this study, we provide an overview of the genetic defects associated with lysosomal storage diseases and their impact on the induction of neuro-immune inflammation. By understanding the underlying mechanisms behind these diseases, we aim to provide new insights into potential biomarkers and therapeutic targets for monitoring and managing the severity of these diseases. In conclusion, lysosomal storage diseases present a complex challenge for patients and clinicians, but this study offers a comprehensive overview of the impact of these diseases on the central and peripheral nervous systems and provides a foundation for further research into potential treatments.
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Affiliation(s)
- Manoj Kumar Pandey
- Cincinnati Children’s Hospital Medical Center, Division of Human Genetics, Cincinnati, OH 45229-3026, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45267-0515, USA
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Trivedi VS, Magnusen AF, Rani R, Marsili L, Slavotinek AM, Prows DR, Hopkin RJ, McKay MA, Pandey MK. Targeting the Complement-Sphingolipid System in COVID-19 and Gaucher Diseases: Evidence for a New Treatment Strategy. Int J Mol Sci 2022; 23:ijms232214340. [PMID: 36430817 PMCID: PMC9695449 DOI: 10.3390/ijms232214340] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 11/08/2022] [Accepted: 11/10/2022] [Indexed: 11/22/2022] Open
Abstract
Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2)-induced disease (COVID-19) and Gaucher disease (GD) exhibit upregulation of complement 5a (C5a) and its C5aR1 receptor, and excess synthesis of glycosphingolipids that lead to increased infiltration and activation of innate and adaptive immune cells, resulting in massive generation of pro-inflammatory cytokines, chemokines and growth factors. This C5a-C5aR1-glycosphingolipid pathway- induced pro-inflammatory environment causes the tissue damage in COVID-19 and GD. Strikingly, pharmaceutically targeting the C5a-C5aR1 axis or the glycosphingolipid synthesis pathway led to a reduction in glycosphingolipid synthesis and innate and adaptive immune inflammation, and protection from the tissue destruction in both COVID-19 and GD. These results reveal a common involvement of the complement and glycosphingolipid systems driving immune inflammation and tissue damage in COVID-19 and GD, respectively. It is therefore expected that combined targeting of the complement and sphingolipid pathways could ameliorate the tissue destruction, organ failure, and death in patients at high-risk of developing severe cases of COVID-19.
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Affiliation(s)
- Vyoma Snehal Trivedi
- Cincinnati Children’s Hospital Medical Center, Division of Human Genetics, 3333 Burnet Avenue, Building R1, MLC 7016, Cincinnati, OH 45229, USA
| | - Albert Frank Magnusen
- Cincinnati Children’s Hospital Medical Center, Division of Human Genetics, 3333 Burnet Avenue, Building R1, MLC 7016, Cincinnati, OH 45229, USA
| | - Reena Rani
- Cincinnati Children’s Hospital Medical Center, Division of Human Genetics, 3333 Burnet Avenue, Building R1, MLC 7016, Cincinnati, OH 45229, USA
| | - Luca Marsili
- Department of Neurology, James J. and Joan A. Gardner Center for Parkinson’s Disease and Movement Disorders, University of Cincinnati, 3113 Bellevue Ave, Cincinnati, OH 45219, USA
| | - Anne Michele Slavotinek
- Cincinnati Children’s Hospital Medical Center, Division of Human Genetics, 3333 Burnet Avenue, Building R1, MLC 7016, Cincinnati, OH 45229, USA
- Department of Pediatrics, College of Medicine, University of Cincinnati, 3230 Eden Ave, Cincinnati, OH 45267, USA
| | - Daniel Ray Prows
- Cincinnati Children’s Hospital Medical Center, Division of Human Genetics, 3333 Burnet Avenue, Building R1, MLC 7016, Cincinnati, OH 45229, USA
- Department of Pediatrics, College of Medicine, University of Cincinnati, 3230 Eden Ave, Cincinnati, OH 45267, USA
| | - Robert James Hopkin
- Cincinnati Children’s Hospital Medical Center, Division of Human Genetics, 3333 Burnet Avenue, Building R1, MLC 7016, Cincinnati, OH 45229, USA
- Department of Pediatrics, College of Medicine, University of Cincinnati, 3230 Eden Ave, Cincinnati, OH 45267, USA
| | - Mary Ashley McKay
- Cincinnati Children’s Hospital Medical Center, Division of Human Genetics, 3333 Burnet Avenue, Building R1, MLC 7016, Cincinnati, OH 45229, USA
| | - Manoj Kumar Pandey
- Cincinnati Children’s Hospital Medical Center, Division of Human Genetics, 3333 Burnet Avenue, Building R1, MLC 7016, Cincinnati, OH 45229, USA
- Department of Pediatrics, College of Medicine, University of Cincinnati, 3230 Eden Ave, Cincinnati, OH 45267, USA
- Correspondence:
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Magnusen AF, Rani R, McKay MA, Hatton SL, Nyamajenjere TC, Magnusen DNA, Köhl J, Grabowski GA, Pandey MK. C-X-C Motif Chemokine Ligand 9 and Its CXCR3 Receptor Are the Salt and Pepper for T Cells Trafficking in a Mouse Model of Gaucher Disease. Int J Mol Sci 2021; 22:ijms222312712. [PMID: 34884512 PMCID: PMC8657559 DOI: 10.3390/ijms222312712] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2021] [Revised: 11/08/2021] [Accepted: 11/18/2021] [Indexed: 02/07/2023] Open
Abstract
Gaucher disease is a lysosomal storage disease, which happens due to mutations in GBA1/Gba1 that encodes the enzyme termed as lysosomal acid β-glucosidase. The major function of this enzyme is to catalyze glucosylceramide (GC) into glucose and ceramide. The deficiency of this enzyme and resultant abnormal accumulation of GC cause altered function of several of the innate and adaptive immune cells. For example, augmented infiltration of T cells contributes to the increased production of pro-inflammatory cytokines, (e.g., IFNγ, TNFα, IL6, IL12p40, IL12p70, IL23, and IL17A/F). This leads to tissue damage in a genetic mouse model (Gba19V/-) of Gaucher disease. The cellular mechanism(s) by which increased tissue infiltration of T cells occurs in this disease is not fully understood. Here, we delineate role of the CXCR3 receptor and its exogenous C-X-C motif chemokine ligand 9 (CXCL9) in induction of increased tissue recruitment of CD4+ T and CD8+ T cells in Gaucher disease. Intracellular FACS staining of macrophages (Mϕs) and dendritic cells (DCs) from Gba19V/- mice showed elevated production of CXCL9. Purified CD4+ T cells and the CD8+ T cells from Gba19V/- mice showed increased expression of CXCR3. Ex vivo and in vivo chemotaxis experiments showed CXCL9 involvement in the recruitment of Gba19V/- T cells. Furthermore, antibody blockade of the CXCL9 receptor (CXCR3) on T cells caused marked reduction in CXCL9- mediated chemotaxis of T cells in Gba19V/- mice. These data implicate abnormalities of the CXCL9-CXCR3 axis leading to enhanced tissue recruitment of T cells in Gaucher disease. Such results provide a rationale for blockade of the CXCL9/CXCR3 axis as potential new therapeutic targets for the treatment of inflammation in Gaucher disease.
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Affiliation(s)
- Albert Frank Magnusen
- Division of Human Genetics, Cincinnati Children’s Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH 45229, USA; (A.F.M.); (M.A.M.); (S.L.H.); (T.C.N.); (D.N.A.M.)
| | - Reena Rani
- Division of Immunobiology, Cincinnati Children’s Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH 45229, USA;
| | - Mary Ashley McKay
- Division of Human Genetics, Cincinnati Children’s Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH 45229, USA; (A.F.M.); (M.A.M.); (S.L.H.); (T.C.N.); (D.N.A.M.)
| | - Shelby Loraine Hatton
- Division of Human Genetics, Cincinnati Children’s Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH 45229, USA; (A.F.M.); (M.A.M.); (S.L.H.); (T.C.N.); (D.N.A.M.)
| | - Tsitsi Carol Nyamajenjere
- Division of Human Genetics, Cincinnati Children’s Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH 45229, USA; (A.F.M.); (M.A.M.); (S.L.H.); (T.C.N.); (D.N.A.M.)
| | - Daniel Nii Aryee Magnusen
- Division of Human Genetics, Cincinnati Children’s Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH 45229, USA; (A.F.M.); (M.A.M.); (S.L.H.); (T.C.N.); (D.N.A.M.)
| | - Jörg Köhl
- Institute for Systemic Inflammation Research, University of Lübeck, 23562 Lübeck, Germany;
- Department of Pediatrics and Division of Immunobiology, Cincinnati Children’s Hospital Medical Center, College of Medicine, University of Cincinnati, 3333 Burnet Avenue, Cincinnati, OH 45229, USA
| | - Gregory Alex Grabowski
- Department of Molecular Genetics, Biochemistry and Microbiology, Division of Human Genetics, Cincinnati Children’s Hospital Medical Center, College of Medicine, University of Cincinnati, 3333 Burnet Avenue, Cincinnati, OH 45229, USA;
- Department of Pediatrics, Division of Human Genetics, Cincinnati Children’s Hospital Medical Center, College of Medicine, University of Cincinnati, 3333 Burnet Avenue, Cincinnati, OH 45229, USA
| | - Manoj Kumar Pandey
- Department of Pediatrics, Division of Human Genetics, Cincinnati Children’s Hospital Medical Center, College of Medicine, University of Cincinnati, 3333 Burnet Avenue, Cincinnati, OH 45229, USA
- Correspondence:
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Grabowski GA, Antommaria AHM, Kolodny EH, Mistry PK. Gaucher disease: Basic and translational science needs for more complete therapy and management. Mol Genet Metab 2021; 132:59-75. [PMID: 33419694 PMCID: PMC8809485 DOI: 10.1016/j.ymgme.2020.12.291] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 11/15/2020] [Accepted: 12/18/2020] [Indexed: 12/12/2022]
Affiliation(s)
- Gregory A Grabowski
- Department of Pediatrics, University of Cincinnati College of Medicine, United States of America; Department of Molecular Genetics, Biochemistry and Microbiology, University of Cincinnati College of Medicine, United States of America; Division of Human Genetics, Cincinnati Children's Research Foundation, Cincinnati, OH, United States of America.
| | - Armand H M Antommaria
- Department of Pediatrics, University of Cincinnati College of Medicine, United States of America; Lee Ault Carter Chair of Pediatric Ethics, Cincinnati Children's Research Foundation, Cincinnati, OH, United States of America.
| | - Edwin H Kolodny
- Department of Neurology, New York University Grossman School of Medicine, New York, NY, United States of America.
| | - Pramod K Mistry
- Departments of Medicine and Pediatrics, Yale School of Medicine, New Haven, CT, United States of America.
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Parenti G, Medina DL, Ballabio A. The rapidly evolving view of lysosomal storage diseases. EMBO Mol Med 2021; 13:e12836. [PMID: 33459519 PMCID: PMC7863408 DOI: 10.15252/emmm.202012836] [Citation(s) in RCA: 88] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 11/09/2020] [Accepted: 11/10/2020] [Indexed: 12/17/2022] Open
Abstract
Lysosomal storage diseases are a group of metabolic disorders caused by deficiencies of several components of lysosomal function. Most commonly affected are lysosomal hydrolases, which are involved in the breakdown and recycling of a variety of complex molecules and cellular structures. The understanding of lysosomal biology has progressively improved over time. Lysosomes are no longer viewed as organelles exclusively involved in catabolic pathways, but rather as highly dynamic elements of the autophagic-lysosomal pathway, involved in multiple cellular functions, including signaling, and able to adapt to environmental stimuli. This refined vision of lysosomes has substantially impacted on our understanding of the pathophysiology of lysosomal disorders. It is now clear that substrate accumulation triggers complex pathogenetic cascades that are responsible for disease pathology, such as aberrant vesicle trafficking, impairment of autophagy, dysregulation of signaling pathways, abnormalities of calcium homeostasis, and mitochondrial dysfunction. Novel technologies, in most cases based on high-throughput approaches, have significantly contributed to the characterization of lysosomal biology or lysosomal dysfunction and have the potential to facilitate diagnostic processes, and to enable the identification of new therapeutic targets.
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Affiliation(s)
- Giancarlo Parenti
- Telethon Institute of Genetics and Medicine, Pozzuoli, Italy.,Department of Translational Medical Sciences, Section of Pediatrics, Federico II University, Naples, Italy
| | - Diego L Medina
- Telethon Institute of Genetics and Medicine, Pozzuoli, Italy.,Department of Translational Medical Sciences, Section of Pediatrics, Federico II University, Naples, Italy
| | - Andrea Ballabio
- Telethon Institute of Genetics and Medicine, Pozzuoli, Italy.,Department of Translational Medical Sciences, Section of Pediatrics, Federico II University, Naples, Italy.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Jan and Dan Duncan Neurological Research Institute, Texas Children Hospital, Houston, TX, USA.,SSM School for Advanced Studies, Federico II University, Naples, Italy
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8
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Yu FPS, Molino S, Sikora J, Rasmussen S, Rybova J, Tate E, Geurts AM, Turner PV, Mckillop WM, Medin JA. Hepatic pathology and altered gene transcription in a murine model of acid ceramidase deficiency. J Transl Med 2019; 99:1572-1592. [PMID: 31186526 DOI: 10.1038/s41374-019-0271-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Revised: 04/04/2019] [Accepted: 05/06/2019] [Indexed: 12/30/2022] Open
Abstract
Farber disease (FD) is a rare lysosomal storage disorder (LSD) characterized by systemic ceramide accumulation caused by a deficiency in acid ceramidase (ACDase). In its classic form, FD manifests with painful lipogranulomatous nodules in extremities and joints, respiratory complications, and neurological involvement. Hepatosplenomegaly is commonly reported, and severe cases of FD cite liver failure as a cause of early death. Mice homozygous for an orthologous patient mutation in the ACDase gene (Asah1P361R/P361R) recapitulate the classical form of human FD. In this study, we demonstrate impaired liver function and elevation of various liver injury markers in Asah1P361R/P361R mice as early as 5 weeks of age. Histopathology analyses demonstrated significant formation and recruitment of foamy macrophages, invasion of neutrophils, progressive tissue fibrosis, increased cell proliferation and death, and significant storage pathology within various liver cell types. Lipidomic analyses revealed alterations to various lipid concentrations in both serum and liver tissue. A significant accumulation of ceramide and other sphingolipids in both liver and hepatocytes was noted. Sphingolipid acyl chains were also altered, with an increase in long acyl chain sphingolipids coinciding with a decrease in ultra-long acyl chains. Hepatocyte transcriptome analyses revealed significantly altered gene transcription. Molecular pathways related to inflammation were found activated, and molecular pathways involved in lipid metabolism were found deactivated. Altered gene transcription within the sphingolipid pathway itself was also observed. The data presented herein demonstrates that deficiency in ACDase results in liver pathology as well as sphingolipid and gene transcription profile changes that lead to impaired liver function.
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Affiliation(s)
- Fabian P S Yu
- Department of Pediatrics, Medical College of Wisconsin, Milwaukee, WI, USA.,Institute of Medical Science, University of Toronto, Toronto, ON, Canada
| | - Salvatore Molino
- Department of Pediatrics, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Jakub Sikora
- Rare Diseases Research Unit, Department of Pediatrics and Adolescent Medicine, Charles University, 1st Faculty of Medicine and General University Hospital, Prague, Czech Republic.,Institute of Pathology, Charles University, 1st Faculty of Medicine and General University Hospital, Prague, Czech Republic
| | - Shauna Rasmussen
- Department of Physiology, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Jitka Rybova
- Department of Pediatrics, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Everett Tate
- Department of Pediatrics, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Aron M Geurts
- Department of Physiology, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Patricia V Turner
- Department of Pathobiology, University of Guelph, Guelph, ON, Canada
| | - William M Mckillop
- Department of Pediatrics, Medical College of Wisconsin, Milwaukee, WI, USA.
| | - Jeffrey A Medin
- Department of Pediatrics, Medical College of Wisconsin, Milwaukee, WI, USA.,Institute of Medical Science, University of Toronto, Toronto, ON, Canada.,Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI, USA.,University Health Network, Toronto, ON, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
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9
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Ługowska A, Hetmańczyk-Sawicka K, Iwanicka-Nowicka R, Fogtman A, Cieśla J, Purzycka-Olewiecka JK, Sitarska D, Płoski R, Filocamo M, Lualdi S, Bednarska-Makaruk M, Koblowska M. Gene expression profile in patients with Gaucher disease indicates activation of inflammatory processes. Sci Rep 2019; 9:6060. [PMID: 30988500 PMCID: PMC6465595 DOI: 10.1038/s41598-019-42584-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Accepted: 04/01/2019] [Indexed: 01/26/2023] Open
Abstract
Gaucher disease (GD) is a rare inherited metabolic disease caused by pathogenic variants in the GBA1 gene. So far, the pathomechanism of GD was investigated mainly in animal models. In order to delineate the molecular changes in GD cells we analysed gene expression profile in cultured skin fibroblasts from GD patients, control individuals and, additionally, patients with Niemann-Pick type C disease (NPC). We used expression microarrays with subsequent validation by qRT-PCR method. In the comparison GD patients vs. controls, the most pronounced relative fold change (rFC) in expression was observed for genes IL13RA2 and IFI6 (up-regulated) and ATOH8 and CRISPLD2 (down-regulated). Products of up-regulated and down-regulated genes were both enriched in genes associated with immune response. In addition, products of down-regulated genes were associated with cell-to-cell and cell-to-matrix interactions, matrix remodelling, PI3K-Akt signalling pathway and a neuronal survival pathway. Up-regulation of PLAU, IFIT1, TMEM158 and down-regulation of ATOH8 and ISLR distinguished GD patients from both NPC patients and healthy controls. Our results emphasize the inflammatory character of changes occurring in human GD cells indicating that further studies on novel therapeutics for GD should consider anti-inflammatory agents.
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Affiliation(s)
- Agnieszka Ługowska
- Department of Genetics, Institute of Psychiatry and Neurology, Warsaw, Poland.
| | | | - Roksana Iwanicka-Nowicka
- Laboratory of Microarray Analysis, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
- Laboratory of Systems Biology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Anna Fogtman
- Laboratory of Microarray Analysis, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Jarosław Cieśla
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | | | - Dominika Sitarska
- Department of Genetics, Institute of Psychiatry and Neurology, Warsaw, Poland
| | - Rafał Płoski
- Department of Medical Genetics, Warsaw Medical University, Warsaw, Poland
| | - Mirella Filocamo
- Laboratorio di Genetica Molecolare e Biobanche, Istituto G. Gaslini, L.go G. Gaslini -16147, Genova, Italy
| | - Susanna Lualdi
- Laboratorio di Genetica Molecolare e Biobanche, Istituto G. Gaslini, L.go G. Gaslini -16147, Genova, Italy
| | | | - Marta Koblowska
- Laboratory of Microarray Analysis, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
- Laboratory of Systems Biology, Faculty of Biology, University of Warsaw, Warsaw, Poland
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Grabowski GA, Whitley C. Ten plus one challenges in diseases of the lysosomal system. Mol Genet Metab 2017; 120:38-46. [PMID: 27923545 DOI: 10.1016/j.ymgme.2016.11.388] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Revised: 11/28/2016] [Accepted: 11/28/2016] [Indexed: 01/01/2023]
Abstract
The advent of the first effective specific therapy for a lysosomal storage disease (LSDs), Gaucher disease type 1, by Roscoe O. Brady was foundational for development of additional treatments for this group of rare diseases. The past 26years, since the approval of enzyme therapy for Gaucher disease type 1, have witnessed a burgeoning understanding of LSDs at genetic, molecular, biochemical, cell biologic, and clinical levels. Simultaneously, this expansion of knowledge has exposed our incomplete understanding of the individual pathophysiologies of LSDs as well as difficult challenges for improvement in therapy and therapeutic outcomes for afflicted individuals. Here, 10 such challenges/problems representing major impediments, which need to be overcome, to move forward toward the goals of more effective and complete therapies for these devastating diseases.
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Affiliation(s)
- Gregory A Grabowski
- Children's Hospital Medical Center, Cincinnati, OH, United States; Kiniksa Pharmaceuticals, Ltd., Wellesley, MA, United States.
| | - Chester Whitley
- Department of Pediatrics, University of Minnesota, School of Medicine, Minneapolis, MN, United States; Department of Experimental and Clinical Pharmacology, University of Minnesota, School of Medicine, Minneapolis, MN, United States
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11
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Dasgupta N, Xu YH, Li R, Peng Y, Pandey MK, Tinch SL, Liou B, Inskeep V, Zhang W, Setchell KDR, Keddache M, Grabowski GA, Sun Y. Neuronopathic Gaucher disease: dysregulated mRNAs and miRNAs in brain pathogenesis and effects of pharmacologic chaperone treatment in a mouse model. Hum Mol Genet 2015; 24:7031-48. [PMID: 26420838 DOI: 10.1093/hmg/ddv404] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2015] [Accepted: 09/21/2015] [Indexed: 01/10/2023] Open
Abstract
Defective lysosomal acid β-glucosidase (GCase) in Gaucher disease causes accumulation of glucosylceramide (GC) and glucosylsphingosine (GS) that distress cellular functions. To study novel pathological mechanisms in neuronopathic Gaucher disease (nGD), a mouse model (4L;C*), an analogue to subacute human nGD, was investigated for global profiles of differentially expressed brain mRNAs (DEGs) and miRNAs (DEmiRs). 4L;C* mice displayed accumulation of GC and GS, activated microglial cells, reduced number of neurons and aberrant mitochondrial function in the brain followed by deterioration in motor function. DEGs and DEmiRs were characterized from sequencing of mRNA and miRNA from cerebral cortex, brain stem, midbrain and cerebellum of 4L;C* mice. Gene ontology enrichment and pathway analysis showed preferential mitochondrial dysfunction in midbrain and uniform inflammatory response and identified novel pathways, axonal guidance signaling, synaptic transmission, eIF2 and mammalian target of rapamycin (mTOR) signaling potentially involved in nGD. Similar analyses were performed with mice treated with isofagomine (IFG), a pharmacologic chaperone for GCase. IFG treatment did not alter the GS and GC accumulation significantly but attenuated the progression of the disease and altered numerous DEmiRs and target DEGs to their respective normal levels in inflammation, mitochondrial function and axonal guidance pathways, suggesting its regulation on miRNA and the associated mRNA that underlie the neurodegeneration in nGD. These analyses demonstrate that the neurodegenerative phenotype in 4L;C* mice was associated with dysregulation of brain mRNAs and miRNAs in axonal guidance, synaptic plasticity, mitochondria function, eIF2 and mTOR signaling and inflammation and provides new insights for the nGD pathological mechanism.
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Affiliation(s)
- Nupur Dasgupta
- Division of Human Genetics, Cincinnati Children's Hospital Research Foundation, Cincinnati, OH 45229, USA
| | - You-Hai Xu
- Division of Human Genetics, Cincinnati Children's Hospital Research Foundation, Cincinnati, OH 45229, USA
| | - Ronghua Li
- Division of Human Genetics, Cincinnati Children's Hospital Research Foundation, Cincinnati, OH 45229, USA, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | - Yanyan Peng
- Division of Human Genetics, Cincinnati Children's Hospital Research Foundation, Cincinnati, OH 45229, USA
| | - Manoj K Pandey
- Division of Human Genetics, Cincinnati Children's Hospital Research Foundation, Cincinnati, OH 45229, USA, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | - Stuart L Tinch
- Division of Human Genetics, Cincinnati Children's Hospital Research Foundation, Cincinnati, OH 45229, USA
| | - Benjamin Liou
- Division of Human Genetics, Cincinnati Children's Hospital Research Foundation, Cincinnati, OH 45229, USA
| | - Venette Inskeep
- Division of Human Genetics, Cincinnati Children's Hospital Research Foundation, Cincinnati, OH 45229, USA
| | - Wujuan Zhang
- Division of Pathology, Cincinnati Children's Hospital Research Foundation, Cincinnati, OH 45229, USA and
| | - Kenneth D R Setchell
- Division of Pathology, Cincinnati Children's Hospital Research Foundation, Cincinnati, OH 45229, USA and Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | - Mehdi Keddache
- Division of Human Genetics, Cincinnati Children's Hospital Research Foundation, Cincinnati, OH 45229, USA
| | - Gregory A Grabowski
- Division of Human Genetics, Cincinnati Children's Hospital Research Foundation, Cincinnati, OH 45229, USA
| | - Ying Sun
- Division of Human Genetics, Cincinnati Children's Hospital Research Foundation, Cincinnati, OH 45229, USA, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
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12
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Kolitz SE, Towfic F, Grossman I, Hayden MR, Zeskind B. Use of genetic technologies to compare medicines. Clin Genet 2014; 86:441-6. [PMID: 25046029 DOI: 10.1111/cge.12462] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2014] [Revised: 07/14/2014] [Accepted: 07/16/2014] [Indexed: 11/27/2022]
Abstract
In order to ensure that patients receive the safest and most effective medicines possible, it is often necessary to compare medicines and assess the extent to which they are similar in their clinical impact. Full clinical trials with appropriate endpoints remain the only method to compare the clinical impact of two medicines with absolute certainty. Other available methods (including physicochemical analysis, genomics, and transcriptomics) can provide partial information about certain aspects of a medicine's biological impact, with possible clinical implications. Especially for biologics and non-biological complex drugs, which are more difficult to characterize by physicochemical means than small molecules, genomics and transciptomic studies can yield valuable insights for physicians, regulators, and drug developers. In this review, we cite and summarize a variety of studies that exemplify the emerging science of applying genomics and transcriptomics technologies to compare medicines. We discuss key aspects of experimental design, conduct of genetic assays, and advanced data analysis, all of which are critical for the successful execution of such studies. Finally, we propose new areas for which such studies can be applied to maximize patient benefit and reduce safety issues.
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Affiliation(s)
- S E Kolitz
- Immuneering Corporation, Cambridge, MA, USA
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13
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Zhang ZH, Jhaveri DJ, Marshall VM, Bauer DC, Edson J, Narayanan RK, Robinson GJ, Lundberg AE, Bartlett PF, Wray NR, Zhao QY. A comparative study of techniques for differential expression analysis on RNA-Seq data. PLoS One 2014; 9:e103207. [PMID: 25119138 PMCID: PMC4132098 DOI: 10.1371/journal.pone.0103207] [Citation(s) in RCA: 151] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2014] [Accepted: 06/30/2014] [Indexed: 01/23/2023] Open
Abstract
Recent advances in next-generation sequencing technology allow high-throughput cDNA sequencing (RNA-Seq) to be widely applied in transcriptomic studies, in particular for detecting differentially expressed genes between groups. Many software packages have been developed for the identification of differentially expressed genes (DEGs) between treatment groups based on RNA-Seq data. However, there is a lack of consensus on how to approach an optimal study design and choice of suitable software for the analysis. In this comparative study we evaluate the performance of three of the most frequently used software tools: Cufflinks-Cuffdiff2, DESeq and edgeR. A number of important parameters of RNA-Seq technology were taken into consideration, including the number of replicates, sequencing depth, and balanced vs. unbalanced sequencing depth within and between groups. We benchmarked results relative to sets of DEGs identified through either quantitative RT-PCR or microarray. We observed that edgeR performs slightly better than DESeq and Cuffdiff2 in terms of the ability to uncover true positives. Overall, DESeq or taking the intersection of DEGs from two or more tools is recommended if the number of false positives is a major concern in the study. In other circumstances, edgeR is slightly preferable for differential expression analysis at the expense of potentially introducing more false positives.
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Affiliation(s)
- Zong Hong Zhang
- The University of Queensland, Queensland Brain Institute, Brisbane, Queensland, Australia
| | - Dhanisha J. Jhaveri
- The University of Queensland, Queensland Brain Institute, Brisbane, Queensland, Australia
| | - Vikki M. Marshall
- The University of Queensland, Queensland Brain Institute, Brisbane, Queensland, Australia
| | - Denis C. Bauer
- The University of Queensland, Queensland Brain Institute, Brisbane, Queensland, Australia
- CSIRO Preventative Health Flagship and CSIRO Computational Informatics, Sydney, New South Wales, Australia
| | - Janette Edson
- The University of Queensland, Queensland Brain Institute, Brisbane, Queensland, Australia
- The University of Queensland, Diamantina Institute, Brisbane, Queensland, Australia
| | - Ramesh K. Narayanan
- The University of Queensland, Queensland Brain Institute, Brisbane, Queensland, Australia
| | - Gregory J. Robinson
- The University of Queensland, Queensland Brain Institute, Brisbane, Queensland, Australia
| | - Andreas E. Lundberg
- Swedish University of Agricultural Sciences, Department of Clinical Sciences, Uppsala, Sweden
| | - Perry F. Bartlett
- The University of Queensland, Queensland Brain Institute, Brisbane, Queensland, Australia
| | - Naomi R. Wray
- The University of Queensland, Queensland Brain Institute, Brisbane, Queensland, Australia
| | - Qiong-Yi Zhao
- The University of Queensland, Queensland Brain Institute, Brisbane, Queensland, Australia
- * E-mail:
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14
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Barranger JA, Brady RO, Grabowski GA, Mankin H, Mistry PK, Weinreb NJ. Position statement: National Gaucher Foundation Medical Advisory Board, January 7, 2014. Am J Hematol 2014; 89:457-8. [PMID: 24488939 DOI: 10.1002/ajh.23687] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2014] [Accepted: 01/29/2014] [Indexed: 11/07/2022]
Affiliation(s)
| | | | | | - Henry Mankin
- Department of Orthopedic Surgery; Massachusetts General Hospital; Boston MA
| | | | - Neal J. Weinreb
- University Research Foundation for Lysosomal Storage Diseases; Coral Springs FL
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15
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Huang HJ, Lee CC, Chen CYC. Pharmacological chaperone design for reducing risk factor of Parkinson's disease from traditional chinese medicine. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE : ECAM 2014; 2014:830490. [PMID: 24527054 PMCID: PMC3914314 DOI: 10.1155/2014/830490] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/11/2013] [Revised: 12/13/2013] [Accepted: 12/15/2013] [Indexed: 01/11/2023]
Abstract
Dysfunction of β -glucocerebrosidase (GCase) has no hydrolytic activity in patients of Gaucher's disease and increasing the risk factor for Parkinson's disease occurrence. Pharmacological chaperone design has been used to treat with misfolded protein in related disease, which utilized a small compound to cause protein folding correctly. This study employed the world largest traditional Chinese medicine (TCM) database for searching for potential lead compound as pharmacological chaperone, and we also performed molecular dynamics (MD) simulations to observe the stability of binding conformation between ligands and active site of GCase structure. The docking results from database screening show that N-methylmescaline and shihunine have high binding ability to GCase than tetrahydroxyazepanes. From MD simulation analysis, tetrahydroxyazepanes displayed high opportunity of ligand migration instead of our TCM candidates, and H-bonds number was decreased in the end of MD snapshot. Our result indicated that binding conformation of N-methylmescaline and shihunine remains stable during MD simulation, demonstrating that the two candidates are suitable for GCase binding and might be potential as pharmacological chaperone for GCase folding correctly.
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Affiliation(s)
- Hung-Jin Huang
- Department of Chinese Pharmaceutical Sciences and Chinese Medicine Resources, College of Pharmacy, China Medical University, Taichung 40402, Taiwan
| | - Cheng-Chun Lee
- School of Medicine, College of Medicine, China Medical University, Taichung 40402, Taiwan
| | - Calvin Yu-Chian Chen
- School of Medicine, College of Medicine, China Medical University, Taichung 40402, Taiwan
- Department of Biotechnology, Asia University, Taichung 41354, Taiwan
- China Medical University Beigang Hospital, Yunlin 65152, Taiwan
- Computational and Systems Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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