1
|
Korotkova D, Borisyuk A, Guihur A, Bardyn M, Kuttler F, Reymond L, Schuhmacher M, Amen T. Fluorescent fatty acid conjugates for live cell imaging of peroxisomes. Nat Commun 2024; 15:4314. [PMID: 38773129 PMCID: PMC11109271 DOI: 10.1038/s41467-024-48679-2] [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: 04/25/2023] [Accepted: 05/09/2024] [Indexed: 05/23/2024] Open
Abstract
Peroxisomes are eukaryotic organelles that are essential for multiple metabolic pathways, including fatty acid oxidation, degradation of amino acids, and biosynthesis of ether lipids. Consequently, peroxisome dysfunction leads to pediatric-onset neurodegenerative conditions, including Peroxisome Biogenesis Disorders (PBD). Due to the dynamic, tissue-specific, and context-dependent nature of their biogenesis and function, live cell imaging of peroxisomes is essential for studying peroxisome regulation, as well as for the diagnosis of PBD-linked abnormalities. However, the peroxisomal imaging toolkit is lacking in many respects, with no reporters for substrate import, nor cell-permeable probes that could stain dysfunctional peroxisomes. Here we report that the BODIPY-C12 fluorescent fatty acid probe stains functional and dysfunctional peroxisomes in live mammalian cells. We then go on to improve BODIPY-C12, generating peroxisome-specific reagents, PeroxiSPY650 and PeroxiSPY555. These probes combine high peroxisome specificity, bright fluorescence in the red and far-red spectrum, and fast non-cytotoxic staining, making them ideal tools for live cell, whole organism, or tissue imaging of peroxisomes. Finally, we demonstrate that PeroxiSPY enables diagnosis of peroxisome abnormalities in the PBD CRISPR/Cas9 cell models and patient-derived cell lines.
Collapse
Affiliation(s)
- Daria Korotkova
- Global Health Institute, Faculty of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Anya Borisyuk
- Global Health Institute, Faculty of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Anthony Guihur
- Department of Plant Molecular Biology, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Manon Bardyn
- Biomolecular Screening Facility, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Fabien Kuttler
- Biomolecular Screening Facility, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Luc Reymond
- Biomolecular Screening Facility, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Milena Schuhmacher
- Institute of Bioengineering, Faculty of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Triana Amen
- Global Health Institute, Faculty of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.
- School of Biological Sciences, University of Southampton, Southampton, UK.
| |
Collapse
|
2
|
Chen L, Yan J, Shi H, Zhang Z, Zhao Y, Zhao Y, Wang Y, Ou J. Intervention mechanism of marine-based chito-oligosaccharide on acute liver injury induced by AFB 1 in rats. BIORESOUR BIOPROCESS 2024; 11:13. [PMID: 38647922 PMCID: PMC10992386 DOI: 10.1186/s40643-023-00708-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Accepted: 11/22/2023] [Indexed: 04/25/2024] Open
Abstract
Aflatoxin B1 (AFB1) is extremely hepatotoxic, a causative agent of liver cancer, and can cause symptoms of acute or chronic liver damage. Chito-oligosaccharides (COS), obtained from the degradation of chitosan derived from shrimp and crab shells, is a natural antioxidant substance and its antitumor properties have been widely studied, but less research has been done on the prevention of AFB1-induced acute liver injury. In this study, rats were acutely exposed to 1 mg/kg BW AFB1 and simultaneously gavaged with different doses of COS for 8 days. The results showed that COS attenuated the hepatic histopathological changes and reduced serum biochemical indices (ALT, AST, ALP, and TBIL) in rats. It significantly inhibited MDA content and promoted SOD and GSH-Px activity production. Moreover, it also improved hepatocyte apoptosis. Furthermore, AFB1-vs-HCOS differential genes were enriched with 622 GO entries, and 380 were Biological Processes, 170 were Molecular Functions, 72 were Cellular Components. Differentially expressed genes (DEGs) analyzed by KEGG enrichment were more enriched in pathways, such as metabolism, PPAR signaling pathway, and peroxisome. Q-PCR technique verified that Lama5, Egr1, Cyp2b1, and Gadd45g in DEGs were associated with oxidative stress damage and apoptosis. In conclusion, COS intervention reduces the effect of AFB1 on hepatic genes and thus reduces the changes in hepatic gene function.
Collapse
Affiliation(s)
- Lin Chen
- College of Food Sciences and Technology, Shanghai Ocean University, Shanghai, 201306, China
| | - Jiahui Yan
- College of Food Sciences and Technology, Shanghai Ocean University, Shanghai, 201306, China
| | - Huijun Shi
- College of Food Sciences and Technology, Shanghai Ocean University, Shanghai, 201306, China
| | - Zhaohuan Zhang
- College of Food Sciences and Technology, Shanghai Ocean University, Shanghai, 201306, China
- Shanghai Engineering Research Center of Aquatic Product Processing and Preservation, Shanghai, 201306, China
- Laboratory of Quality and Safety Risk Assessment for Aquatic Product on Storage and Preservation, Ministry of Agriculture and Rural Affairs, Shanghai, 201306, China
| | - YueLiang Zhao
- College of Food Sciences and Technology, Shanghai Ocean University, Shanghai, 201306, China
| | - Yong Zhao
- College of Food Sciences and Technology, Shanghai Ocean University, Shanghai, 201306, China
- Shanghai Engineering Research Center of Aquatic Product Processing and Preservation, Shanghai, 201306, China
- Laboratory of Quality and Safety Risk Assessment for Aquatic Product on Storage and Preservation, Ministry of Agriculture and Rural Affairs, Shanghai, 201306, China
| | - Yuan Wang
- Engineering Research Center of Modern Preparation Technology of TCM, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China.
| | - Jie Ou
- College of Food Sciences and Technology, Shanghai Ocean University, Shanghai, 201306, China.
- Shanghai Engineering Research Center of Aquatic Product Processing and Preservation, Shanghai, 201306, China.
- Laboratory of Quality and Safety Risk Assessment for Aquatic Product on Storage and Preservation, Ministry of Agriculture and Rural Affairs, Shanghai, 201306, China.
| |
Collapse
|
3
|
Germain K, So RWL, DiGiovanni LF, Watts JC, Bandsma RHJ, Kim PK. Upregulated pexophagy limits the capacity of selective autophagy. Nat Commun 2024; 15:375. [PMID: 38195640 PMCID: PMC10776696 DOI: 10.1038/s41467-023-44005-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Accepted: 11/27/2023] [Indexed: 01/11/2024] Open
Abstract
Selective autophagy is an essential process to maintain cellular homeostasis through the constant recycling of damaged or superfluous components. Over a dozen selective autophagy pathways mediate the degradation of diverse cellular substrates, but whether these pathways can influence one another remains unknown. We address this question using pexophagy, the autophagic degradation of peroxisomes, as a model. We show in cells that upregulated pexophagy impairs the selective autophagy of both mitochondria and protein aggregates by exhausting the autophagy initiation factor, ULK1. We confirm this finding in cell models of the pexophagy-mediated form of Zellweger Spectrum Disorder, a disease characterized by peroxisome dysfunction. Further, we extend the generalizability of limited selective autophagy by determining that increased protein aggregate degradation reciprocally reduces pexophagy using cell models of Parkinson's Disease and Huntington's Disease. Our findings suggest that the degradative capacity of selective autophagy can become limited by an increase in one substrate.
Collapse
Affiliation(s)
- Kyla Germain
- Cell Biology Program, The Hospital for Sick Children, Toronto, ON, M5G 1X8, Canada
- Department of Biochemistry, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - Raphaella W L So
- Department of Biochemistry, University of Toronto, Toronto, ON, M5S 1A8, Canada
- Tanz Centre for Research in Neurodegenerative Diseases, Toronto, ON, M5T 0S8, Canada
| | - Laura F DiGiovanni
- Cell Biology Program, The Hospital for Sick Children, Toronto, ON, M5G 1X8, Canada
- Department of Biochemistry, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - Joel C Watts
- Department of Biochemistry, University of Toronto, Toronto, ON, M5S 1A8, Canada
- Tanz Centre for Research in Neurodegenerative Diseases, Toronto, ON, M5T 0S8, Canada
| | - Robert H J Bandsma
- Translational Medicine Program, The Hospital for Sick Children, Toronto, ON, M5G 1X8, Canada.
- Department of Nutritional Sciences, Faculty of Medicine, University of Toronto, Toronto, ON, M5S1A8, Canada.
| | - Peter K Kim
- Cell Biology Program, The Hospital for Sick Children, Toronto, ON, M5G 1X8, Canada.
- Department of Biochemistry, University of Toronto, Toronto, ON, M5S 1A8, Canada.
| |
Collapse
|
4
|
Yan B, Cao L, Gao L, Wei S, Wang M, Tian Y, Yang J, Chen E. PEX26 Functions as a Metastasis Suppressor in Colorectal Cancer. Dig Dis Sci 2024; 69:112-122. [PMID: 37957408 DOI: 10.1007/s10620-023-08168-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 10/23/2023] [Indexed: 11/15/2023]
Abstract
BACKGROUND/AIMS Aberrant Peroxisomal Biogenesis Factor 26 (PEX26) occurs in multiple cell process. However, the role of PEX26 in colorectal cancer (CRC) development remains unknown. We aimed to study PEX26 expression, regulation, and function in CRC cells. METHODS Using the bioinformatic analysis, real-time quantitative PCR, and immunohistochemistry staining, we detected the expression of PEX26 in CRC and normal tissues. We performed functional experiments in vitro to elucidate the effect of PEX26 on CRC cells. We analyzed the RNA-seq data to reveal the downstream regulating network of PEX26. RESULTS PEX26 is significantly down-regulated in CRC and its low expression correlates with the poor overall survival of CRC patients. We further demonstrated that PEX26 over-expression inhibits the ability of CRC cell migration, invasion, and epithelial-mesenchymal transition (EMT), while PEX26 knockdown promotes the malignant phenotypes of migration, invasion, and EMT via activating the Wnt pathway. CONCLUSION Overall, our results showed that the loss of PEX26 contributes to the malignant phenotype of CRC. PEX26 may serve as a novel metastasis repressor for CRC.
Collapse
Affiliation(s)
- Bianbian Yan
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, School of Life Sciences, Northwest University, Xi'an, China
- Institute of Preventive Genomic Medicine, School of Life Sciences, Northwest University, Xi'an, China
| | - Lichao Cao
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, School of Life Sciences, Northwest University, Xi'an, China
- Institute of Preventive Genomic Medicine, School of Life Sciences, Northwest University, Xi'an, China
| | - Liyang Gao
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, School of Life Sciences, Northwest University, Xi'an, China
- Institute of Preventive Genomic Medicine, School of Life Sciences, Northwest University, Xi'an, China
| | - Shangqing Wei
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, School of Life Sciences, Northwest University, Xi'an, China
- Institute of Preventive Genomic Medicine, School of Life Sciences, Northwest University, Xi'an, China
| | - Mengwei Wang
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, School of Life Sciences, Northwest University, Xi'an, China
- Institute of Preventive Genomic Medicine, School of Life Sciences, Northwest University, Xi'an, China
| | - Ye Tian
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, School of Life Sciences, Northwest University, Xi'an, China
- Institute of Preventive Genomic Medicine, School of Life Sciences, Northwest University, Xi'an, China
| | - Jin Yang
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, School of Life Sciences, Northwest University, Xi'an, China
- Institute of Preventive Genomic Medicine, School of Life Sciences, Northwest University, Xi'an, China
| | - Erfei Chen
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, School of Life Sciences, Northwest University, Xi'an, China.
- Institute of Preventive Genomic Medicine, School of Life Sciences, Northwest University, Xi'an, China.
| |
Collapse
|
5
|
Gragnaniello V, Gueraldi D, Puma A, Commone A, Cazzorla C, Loro C, Porcù E, Stornaiuolo M, Miglioranza P, Salviati L, Wanders RJA, Burlina A. Abnormal activation of MAPKs pathways and inhibition of autophagy in a group of patients with Zellweger spectrum disorders and X-linked adrenoleukodystrophy. Orphanet J Rare Dis 2023; 18:358. [PMID: 37974207 PMCID: PMC10652488 DOI: 10.1186/s13023-023-02940-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Accepted: 10/01/2023] [Indexed: 11/19/2023] Open
Abstract
BACKGROUND Zellweger spectrum disorders (ZSD) and X-linked adrenoleukodystrophy (X-ALD) are inherited metabolic diseases characterized by dysfunction of peroxisomes, that are essential for lipid metabolism and redox balance. Oxidative stress has been reported to have a significant role in the pathogenesis of neurodegenerative diseases such as peroxisomal disorders, but little is known on the intracellular activation of Mitogen-activated protein kinases (MAPKs). Strictly related to oxidative stress, a correct autophagic machinery is essential to eliminated oxidized proteins and damaged organelles. The aims of the current study are to investigate a possible implication of MAPK pathways and autophagy impairment as markers and putative therapeutic targets in X-ALD and ZSDs. METHODS Three patients with ZSD (2 M, 1 F; age range 8-17 years) and five patients with X-ALD (5 M; age range 5- 22 years) were enrolled. A control group included 6 healthy volunteers. To evaluate MAPKs pathway, p-p38 and p-JNK were assessed by western blot analysis on peripheral blood mononuclear cells. LC3II/LC3I ratio was evaluated ad marker of autophagy. RESULTS X-ALD and ZSD patients showed elevated p-p38 values on average 2- fold (range 1.21- 2.84) and 3.30-fold (range 1.56- 4.26) higher when compared with controls, respectively. p-JNK expression was on average 12-fold (range 2.20-19.92) and 2.90-fold (range 1.43-4.24) higher in ZSD and X-ALD patients than in controls. All patients had altered autophagic flux as concluded from the reduced LC3II/I ratio. CONCLUSIONS In our study X-ALD and ZSD patients present an overactivation of MAPK pathways and an inhibition of autophagy. Considering the absence of successful therapies and the growing interest towards new therapies with antioxidants and autophagy inducers, the identification and validation of biomarkers to monitor optimal dosing and biological efficacy of the treatments is of prime interest.
Collapse
Affiliation(s)
- Vincenza Gragnaniello
- Division of Inherited Metabolic Diseases, Department of Women's and Children's Health, University - Hospital of Padova, Padua, Italy
- Division of Inherited Metabolic Diseases, Department of Women's and Children's Health, University of Padua, Padua, Italy
| | - Daniela Gueraldi
- Division of Inherited Metabolic Diseases, Department of Women's and Children's Health, University - Hospital of Padova, Padua, Italy
| | - Andrea Puma
- Division of Inherited Metabolic Diseases, Department of Women's and Children's Health, University - Hospital of Padova, Padua, Italy
| | - Anna Commone
- Division of Inherited Metabolic Diseases, Department of Women's and Children's Health, University - Hospital of Padova, Padua, Italy
| | - Chiara Cazzorla
- Division of Inherited Metabolic Diseases, Department of Women's and Children's Health, University - Hospital of Padova, Padua, Italy
| | - Christian Loro
- Division of Inherited Metabolic Diseases, Department of Women's and Children's Health, University - Hospital of Padova, Padua, Italy
| | - Elena Porcù
- Division of Inherited Metabolic Diseases, Department of Women's and Children's Health, University - Hospital of Padova, Padua, Italy
| | - Maria Stornaiuolo
- Division of Inherited Metabolic Diseases, Department of Women's and Children's Health, University - Hospital of Padova, Padua, Italy
| | - Paolo Miglioranza
- Division of Inherited Metabolic Diseases, Department of Women's and Children's Health, University - Hospital of Padova, Padua, Italy
| | - Leonardo Salviati
- Clinical Genetics Unit, Department of Women's and Children's Health, and Myology Center, University of Padova, Padua, Italy
| | - Ronald J A Wanders
- Laboratory Genetic Metabolic Diseases, Department of Clinical Chemistry, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, The Netherlands
- Department of Pediatrics, Emma Children's Hospital, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Alberto Burlina
- Division of Inherited Metabolic Diseases, Department of Women's and Children's Health, University - Hospital of Padova, Padua, Italy.
- Division of Inherited Metabolic Diseases, Department of Women's and Children's Health, University of Padua, Padua, Italy.
| |
Collapse
|
6
|
Pandey S, Dodt G. Purification of a Recombinant Human PEX1/PEX6 AAA+ ATPase Complex from HEK293TT Cells. Methods Mol Biol 2023; 2643:359-372. [PMID: 36952198 DOI: 10.1007/978-1-0716-3048-8_25] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/24/2023]
Abstract
The heteromeric complex of the two AAA+ ATPases PEX1 and PEX6 is involved in the export of the monoubiquitinated import receptor PEX5 from the peroxisomal membrane. Mutations in this complex make up for over 60% of the patients with Peroxisomal Biogenesis Disorders. To have better options for the treatment of the milder mutations we purified the human PEX1/PEX6 complex after overexpression of plasmids encoding tagged proteins from HEK293TT cells. We used a combination of a HisTrap Column (Ni-NTA chromatography) and a Strep-Tactin®XT cartridge for small-scale purification of the complex using the His-tag of PEX1 and the Strep-tagII of PEX6.
Collapse
Affiliation(s)
- Saroj Pandey
- Interfaculty Institute of Biochemistry (IFIB), Cell Biochemistry, University of Tuebingen, Tuebingen, Germany
| | - Gabriele Dodt
- Interfaculty Institute of Biochemistry (IFIB), Cell Biochemistry, University of Tuebingen, Tuebingen, Germany.
| |
Collapse
|
7
|
Kim YH, Jo DS, Park NY, Bae JE, Kim JB, Lee HJ, Kim SH, Kim SH, Lee S, Son M, Park K, Jeong K, Yeom E, Cho DH. Inhibition of BRD4 Promotes Pexophagy by Increasing ROS and ATM Activation. Cells 2022; 11:cells11182839. [PMID: 36139416 PMCID: PMC9497081 DOI: 10.3390/cells11182839] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 09/09/2022] [Accepted: 09/10/2022] [Indexed: 01/18/2023] Open
Abstract
Although autophagy regulates the quality and quantity of cellular compartments, the regulatory mechanisms underlying peroxisomal autophagy (pexophagy) remain largely unknown. In this study, we identified several BRD4 inhibitors, including molibresib, a novel pexophagy inducer, via chemical library screening. Treatment with molibresib promotes loss of peroxisomes selectively, but not mitochondria, ER, or Golgi apparatus in HeLa cells. Consistently, depletion of BRD4 expression also induced pexophagy in RPE cells. In addition, the inhibition of BRD4 by molibresib increased autophagic degradation of peroxisome ATG7-dependency. We further found that molibresib produced reactive oxygen species (ROS), which potentiates ATM activation. Inhibition of ROS or ATM suppressed the loss of peroxisomes in molibresib-treated cells. Taken together, our data suggest that inhibition of BRD4 promotes pexophagy by increasing ROS and ATM activation.
Collapse
Affiliation(s)
- Yong Hwan Kim
- BK21 FOUR KNU Creative BioResearch Group, School of Life Sciences, Kyungpook National University, Daegu 41566, Korea
| | - Doo Sin Jo
- BK21 FOUR KNU Creative BioResearch Group, School of Life Sciences, Kyungpook National University, Daegu 41566, Korea
| | - Na Yeon Park
- BK21 FOUR KNU Creative BioResearch Group, School of Life Sciences, Kyungpook National University, Daegu 41566, Korea
| | - Ji-Eun Bae
- Brain Science and Engineering Institute, Kyungpook National University, Daegu 41566, Korea
| | - Joon Bum Kim
- BK21 FOUR KNU Creative BioResearch Group, School of Life Sciences, Kyungpook National University, Daegu 41566, Korea
| | - Ha Jung Lee
- BK21 FOUR KNU Creative BioResearch Group, School of Life Sciences, Kyungpook National University, Daegu 41566, Korea
| | - So Hyun Kim
- BK21 FOUR KNU Creative BioResearch Group, School of Life Sciences, Kyungpook National University, Daegu 41566, Korea
| | - Seong Hyun Kim
- BK21 FOUR KNU Creative BioResearch Group, School of Life Sciences, Kyungpook National University, Daegu 41566, Korea
| | - Sunwoo Lee
- BK21 FOUR KNU Creative BioResearch Group, School of Life Sciences, Kyungpook National University, Daegu 41566, Korea
| | - Mikyung Son
- Orgasis Corp., Suwon 16229, Gyeonggi-do, Korea
| | - Kyuhee Park
- Bio-Center, Gyeonggido Business & Science Accelerator, Suwon 16229, Gyeonggi-do, Korea
| | - Kwiwan Jeong
- Bio-Center, Gyeonggido Business & Science Accelerator, Suwon 16229, Gyeonggi-do, Korea
| | - Eunbyul Yeom
- BK21 FOUR KNU Creative BioResearch Group, School of Life Sciences, Kyungpook National University, Daegu 41566, Korea
| | - Dong-Hyung Cho
- BK21 FOUR KNU Creative BioResearch Group, School of Life Sciences, Kyungpook National University, Daegu 41566, Korea
- Orgasis Corp., Suwon 16229, Gyeonggi-do, Korea
- Correspondence: ; Tel.: +82-53-950-5382
| |
Collapse
|
8
|
Cheung A, Argyriou C, Yergeau C, D’Souza Y, Riou É, Lévesque S, Raymond G, Daba M, Rtskhiladze I, Tkemaladze T, Adang L, La Piana R, Bernard G, Braverman N. Clinical, neuroradiological, and molecular characterization of patients with atypical Zellweger spectrum disorder caused by PEX16 mutations: a case series. Neurogenetics 2022; 23:115-127. [DOI: 10.1007/s10048-022-00684-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 01/12/2022] [Indexed: 10/19/2022]
|
9
|
Fazi C, Lodi L, Magi L, Canessa C, Giovannini M, Pelosi C, Pochiero F, Procopio E, Donati MA, Azzari C, Ricci S. Case Report: Zellweger Syndrome and Humoral Immunodeficiency: The Relevance of Newborn Screening for Primary Immunodeficiency. Front Pediatr 2022; 10:852943. [PMID: 35402347 PMCID: PMC8990230 DOI: 10.3389/fped.2022.852943] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 02/03/2022] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Zellweger syndrome (ZS) is a congenital autosomal recessive disease within the spectrum of peroxisome biogenesis disorders, characterized by the impairment of peroxisome assembly. The presence of peroxisome enzyme deficiencies leads to complex developmental sequelae, progressive disabilities, and multiorgan damage, due to intracellular accumulation of very-long-chain fatty acids (VLCFAs). CASE PRESENTATION We report the case of an infant affected by ZS in which agammaglobulinemia, detected through neonatal screening of congenital immunodeficiencies, appeared as a peculiar trait standing out among all the other classical characteristics of the syndrome. The exome analysis through next-generation sequencing (NGS), which had previously confirmed the diagnostic suspicion of ZS, was repeated, but no mutations causative of inborn error of immunity (humoral defect) were detected. CONCLUSION In this case, no genetic variants accountable for the abovementioned agammaglobulinemia were detected. Given that the scientific literature reports the involvement of peroxisomes in the activation of Nuclear Factor κ-light-chain-enhancer of activated B cells (NF-κB) pathway, which is crucial for B-cell survival, with this work, we hypothesize the existence of a link between ZS and humoral immunodeficiencies. Further studies are required to confirm this hypothesis.
Collapse
Affiliation(s)
- C Fazi
- Pediatric Immunology Division, Meyer Children's Hospital, Florence, Italy
| | - L Lodi
- Pediatric Immunology Division, Meyer Children's Hospital, Florence, Italy.,Department of Health Sciences, University of Florence, Florence, Italy
| | - L Magi
- Neonatology Division, San Donato Hospital, Arezzo, Italy
| | - C Canessa
- Pediatric Immunology Division, Meyer Children's Hospital, Florence, Italy
| | - M Giovannini
- Pediatric Allergy Division, Meyer Children's Hospital, Florence, Italy
| | - C Pelosi
- Department of Health Sciences, University of Florence, Florence, Italy
| | - F Pochiero
- Department of Metabolic Diseases, Meyer Children's Hospital, Florence, Italy
| | - E Procopio
- Department of Metabolic Diseases, Meyer Children's Hospital, Florence, Italy
| | - M A Donati
- Department of Metabolic Diseases, Meyer Children's Hospital, Florence, Italy
| | - C Azzari
- Pediatric Immunology Division, Meyer Children's Hospital, Florence, Italy.,Department of Health Sciences, University of Florence, Florence, Italy
| | - S Ricci
- Pediatric Immunology Division, Meyer Children's Hospital, Florence, Italy.,Department of Health Sciences, University of Florence, Florence, Italy
| |
Collapse
|
10
|
Argyriou C, Polosa A, Song JY, Omri S, Steele B, Cécyre B, McDougald DS, Di Pietro E, Bouchard JF, Bennett J, Hacia JG, Lachapelle P, Braverman NE. AAV-mediated PEX1 gene augmentation improves visual function in the PEX1-Gly844Asp mouse model for mild Zellweger spectrum disorder. MOLECULAR THERAPY-METHODS & CLINICAL DEVELOPMENT 2021; 23:225-240. [PMID: 34703844 PMCID: PMC8516995 DOI: 10.1016/j.omtm.2021.09.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Accepted: 09/01/2021] [Indexed: 12/01/2022]
Abstract
Patients with Zellweger spectrum disorder (ZSD) commonly present with vision loss due to mutations in PEX genes required for peroxisome assembly and function. Here, we evaluate PEX1 retinal gene augmentation therapy in a mouse model of mild ZSD bearing the murine equivalent (PEX1-p[Gly844Asp]) of the most common human mutation. Experimental adeno-associated virus 8.cytomegalovirus.human PEX1.hemagglutinin (AAV8.CMV.HsPEX1.HA) and control AAV8.CMV.EGFP vectors were administered by subretinal injection in contralateral eyes of early (5-week-old)- or later (9-week-old)-stage retinopathy cohorts. HsPEX1.HA protein was expressed in the retina with no gross histologic side effects. Peroxisomal metabolic functions, assessed by retinal C26:0 lysophosphatidylcholine (lyso-PC) levels, were partially normalized after therapeutic vector treatment. Full-field flash electroretinogram (ffERG) analyses at 8 weeks post-injection showed a 2-fold improved retinal response in the therapeutic relative to control vector-injected eyes. ffERG improved by 1.6- to 2.5-fold in the therapeutic vector-injected eyes when each cohort reached 25 weeks of age. At 32 weeks of age, the average ffERG response was double in the therapeutic relative to control vector-injected eyes in both cohorts. Optomotor reflex analyses trended toward improvement. These proof-of-concept studies represent the first application of gene augmentation therapy to treat peroxisome biogenesis disorders and support the potential for retinal gene delivery to improve vision in these patients.
Collapse
Affiliation(s)
- Catherine Argyriou
- Department of Human Genetics, McGill University, Montreal, QC, Canada.,Research Institute of the McGill University Health Centre, Montreal, QC, Canada
| | - Anna Polosa
- Department of Ophthalmology & Visual Sciences, McGill University, Montreal, QC, Canada.,Research Institute of the McGill University Health Centre, Montreal, QC, Canada
| | - Ji Yun Song
- Center for Advanced Retinal and Ocular Therapeutics, F.M. Kirby Center for Molecular Ophthalmology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Samy Omri
- Research Institute of the McGill University Health Centre, Montreal, QC, Canada
| | - Bradford Steele
- Department of Biochemistry and Molecular Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Bruno Cécyre
- School of Optometry, Université de Montréal, Montreal, QC, Canada
| | - Devin S McDougald
- Center for Advanced Retinal and Ocular Therapeutics, F.M. Kirby Center for Molecular Ophthalmology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Erminia Di Pietro
- Research Institute of the McGill University Health Centre, Montreal, QC, Canada
| | | | - Jean Bennett
- Center for Advanced Retinal and Ocular Therapeutics, F.M. Kirby Center for Molecular Ophthalmology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Joseph G Hacia
- Department of Biochemistry and Molecular Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Pierre Lachapelle
- Department of Ophthalmology & Visual Sciences, McGill University, Montreal, QC, Canada.,Research Institute of the McGill University Health Centre, Montreal, QC, Canada
| | - Nancy E Braverman
- Department of Human Genetics, McGill University, Montreal, QC, Canada.,Research Institute of the McGill University Health Centre, Montreal, QC, Canada
| |
Collapse
|
11
|
Perea-Romero I, Blanco-Kelly F, Sanchez-Navarro I, Lorda-Sanchez I, Tahsin-Swafiri S, Avila-Fernandez A, Martin-Merida I, Trujillo-Tiebas MJ, Lopez-Rodriguez R, Rodriguez de Alba M, Iancu IF, Romero R, Quinodoz M, Hakonarson H, Garcia-Sandova B, Minguez P, Corton M, Rivolta C, Ayuso C. NGS and phenotypic ontology-based approaches increase the diagnostic yield in syndromic retinal diseases. Hum Genet 2021; 140:1665-1678. [PMID: 34448047 PMCID: PMC8553673 DOI: 10.1007/s00439-021-02343-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 08/10/2021] [Indexed: 02/08/2023]
Abstract
Syndromic retinal diseases (SRDs) are a group of complex inherited systemic disorders, with challenging molecular underpinnings and clinical management. Our main goal is to improve clinical and molecular SRDs diagnosis, by applying a structured phenotypic ontology and next-generation sequencing (NGS)-based pipelines. A prospective and retrospective cohort study was performed on 100 probands with an a priori diagnosis of non-Usher SRDs, using available clinical data, including Human Phenotype Ontology annotation, and further classification into seven clinical categories (ciliopathies, specific syndromes and five others). Retrospective molecular diagnosis was assessed using different molecular and bioinformatic methods depending on availability. Subsequently, uncharacterized probands were prospectively screened using other NGS approaches to extend the number of analyzed genes. After phenotypic classification, ciliopathies were the most common SRD (35%). A global characterization rate of 52% was obtained, with six cases incompletely characterized for a gene that partially explained the phenotype. An improved characterization rate was achieved addressing prospective cases (83%) and well-recognizable syndrome (62%) subgroups. The 27% of the fully characterized cases were reclassified into a different clinical category after identification of the disease-causing gene. Clinical-exome sequencing is the most appropriate first-tier approach for prospective cases, whereas whole-exome sequencing and bioinformatic reanalysis increases the diagnosis of uncharacterized retrospective cases to 45%, mostly those with unspecific symptoms. Our study describes a comprehensive approach to SRDs in daily clinical practice and the importance of thorough clinical assessment and selection of the most appropriate molecular test to be used to solve these complex cases and elucidate novel associations.
Collapse
Affiliation(s)
- I Perea-Romero
- Department of Genetics, Health Research Institute-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain.,Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - F Blanco-Kelly
- Department of Genetics, Health Research Institute-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain.,Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - I Sanchez-Navarro
- Department of Genetics, Health Research Institute-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
| | - I Lorda-Sanchez
- Department of Genetics, Health Research Institute-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain.,Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - S Tahsin-Swafiri
- Department of Genetics, Health Research Institute-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain.,Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - A Avila-Fernandez
- Department of Genetics, Health Research Institute-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain.,Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - I Martin-Merida
- Department of Genetics, Health Research Institute-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain.,Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - M J Trujillo-Tiebas
- Department of Genetics, Health Research Institute-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain.,Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - R Lopez-Rodriguez
- Department of Genetics, Health Research Institute-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain.,Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - M Rodriguez de Alba
- Department of Genetics, Health Research Institute-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
| | - I F Iancu
- Department of Genetics, Health Research Institute-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain.,Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - R Romero
- Department of Genetics, Health Research Institute-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain.,Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - M Quinodoz
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland.,Department of Ophthalmology, University of Basel, Basel, Switzerland.,Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | - H Hakonarson
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, USA.,Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA, USA.,Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Blanca Garcia-Sandova
- Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain.,Department of Ophthalmology, Health Research Institute-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
| | - P Minguez
- Department of Genetics, Health Research Institute-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain.,Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - M Corton
- Department of Genetics, Health Research Institute-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain.,Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - C Rivolta
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland.,Department of Ophthalmology, University of Basel, Basel, Switzerland.,Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | - C Ayuso
- Department of Genetics, Health Research Institute-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain. .,Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain.
| |
Collapse
|
12
|
Bernardo A, De Nuccio C, Visentin S, Martire A, Minghetti L, Popoli P, Ferrante A. Myelin Defects in Niemann-Pick Type C Disease: Mechanisms and Possible Therapeutic Perspectives. Int J Mol Sci 2021; 22:ijms22168858. [PMID: 34445564 PMCID: PMC8396228 DOI: 10.3390/ijms22168858] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 08/11/2021] [Accepted: 08/16/2021] [Indexed: 12/25/2022] Open
Abstract
Niemann–Pick type C (NPC) disease is a wide-spectrum clinical condition classified as a neurovisceral disorder affecting mainly the liver and the brain. It is caused by mutations in one of two genes, NPC1 and NPC2, coding for proteins located in the lysosomes. NPC proteins are deputed to transport cholesterol within lysosomes or between late endosome/lysosome systems and other cellular compartments, such as the endoplasmic reticulum and plasma membrane. The first trait of NPC is the accumulation of unesterified cholesterol and other lipids, like sphingosine and glycosphingolipids, in the late endosomal and lysosomal compartments, which causes the blockade of autophagic flux and the impairment of mitochondrial functions. In the brain, the main consequences of NPC are cerebellar neurodegeneration, neuroinflammation, and myelin defects. This review will focus on myelin defects and the pivotal importance of cholesterol for myelination and will offer an overview of the molecular targets and the pharmacological strategies so far proposed, or an object of clinical trials for NPC. Finally, it will summarize recent data on a new and promising pharmacological perspective involving A2A adenosine receptor stimulation in genetic and pharmacological NPC dysmyelination models.
Collapse
Affiliation(s)
- Antonietta Bernardo
- National Center for Drug Research and Evaluation, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy; (A.B.); (S.V.); (A.M.); (P.P.)
| | - Chiara De Nuccio
- Research Coordination and Support Service, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy; (C.D.N.); (L.M.)
| | - Sergio Visentin
- National Center for Drug Research and Evaluation, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy; (A.B.); (S.V.); (A.M.); (P.P.)
| | - Alberto Martire
- National Center for Drug Research and Evaluation, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy; (A.B.); (S.V.); (A.M.); (P.P.)
| | - Luisa Minghetti
- Research Coordination and Support Service, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy; (C.D.N.); (L.M.)
| | - Patrizia Popoli
- National Center for Drug Research and Evaluation, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy; (A.B.); (S.V.); (A.M.); (P.P.)
| | - Antonella Ferrante
- National Center for Drug Research and Evaluation, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy; (A.B.); (S.V.); (A.M.); (P.P.)
- Correspondence: ; Tel.: +39-06-49902050
| |
Collapse
|
13
|
Sorrentino VG, Thota S, Gonzalez EA, Rameshwar P, Chang VT, Etchegaray JP. Hypomethylating Chemotherapeutic Agents as Therapy for Myelodysplastic Syndromes and Prevention of Acute Myeloid Leukemia. Pharmaceuticals (Basel) 2021; 14:641. [PMID: 34358067 PMCID: PMC8308509 DOI: 10.3390/ph14070641] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 06/29/2021] [Accepted: 06/30/2021] [Indexed: 12/11/2022] Open
Abstract
Myelodysplastic Syndromes (MDSs) affect the elderly and can progress to Acute Myeloid Leukemia (AML). Epigenetic alterations including DNA methylation and chromatin modification may contribute to the initiation and progression of these malignancies. DNA hypomethylating agents such as decitabine and azacitidine are used as therapeutic treatments and have shown to promote expression of genes involved in tumor suppression, apoptosis, and immune response. Another anti-cancer drug, the proteasome inhibitor bortezomib, is used as a chemotherapeutic treatment for multiple myeloma (MM). Phase III clinical trials of decitabine and azacitidine used alone and in combination with other chemotherapeutics demonstrated their capacity to treat hematological malignancies and prolong the survival of MDS and AML patients. Although phase III clinical trials examining bortezomib's role in MDS and AML patients are limited, its underlying mechanisms in MM highlight its potential as a chemotherapeutic for such malignancies. Further research is needed to better understand how the epigenetic mechanisms mediated by these chemotherapeutic agents and their targeted gene networks are associated with the development and progression of MDS into AML. This review discusses the mechanisms by which decitabine, azacitidine, and bortezomib alter epigenetic programs and their results from phase III clinical trials.
Collapse
Affiliation(s)
- Vincent G. Sorrentino
- Department of Biological Sciences, Rutgers University—Newark, Newark, NJ 07102, USA; (V.G.S.); (S.T.); (E.A.G.)
| | - Srijan Thota
- Department of Biological Sciences, Rutgers University—Newark, Newark, NJ 07102, USA; (V.G.S.); (S.T.); (E.A.G.)
| | - Edward A. Gonzalez
- Department of Biological Sciences, Rutgers University—Newark, Newark, NJ 07102, USA; (V.G.S.); (S.T.); (E.A.G.)
| | - Pranela Rameshwar
- Department of Medicine, Division of Hematology/Oncology, Rutgers New Jersey Medical School, Newark, NJ 07103, USA;
| | - Victor T. Chang
- Department of Medicine, Division of Hematology/Oncology, Rutgers New Jersey Medical School, Newark, NJ 07103, USA;
- Veteran Affairs New Jersey Health Care System, East Orange, NJ 07018, USA;
| | - Jean-Pierre Etchegaray
- Department of Biological Sciences, Rutgers University—Newark, Newark, NJ 07102, USA; (V.G.S.); (S.T.); (E.A.G.)
| |
Collapse
|
14
|
Dahabieh MS, Huang F, Goncalves C, Flores González RE, Prabhu S, Bolt A, Di Pietro E, Khoury E, Heath J, Xu ZY, Rémy-Sarrazin J, Mann KK, Orthwein A, Boisvert FM, Braverman N, Miller WH, Del Rincón SV. Silencing PEX26 as an unconventional mode to kill drug-resistant cancer cells and forestall drug resistance. Autophagy 2021; 18:540-558. [PMID: 34074205 DOI: 10.1080/15548627.2021.1936932] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Promoting the macroautophagy/autophagy-mediated degradation of specific proteins and organelles can potentially be utilized to induce apoptosis in cancer cells or sensitize tumor cells to therapy. To examine this concept, we enriched for autophagosomes from histone deacetylase inhibitor (HDACi)-sensitive U937 lymphoma cells and isogenic HDACi-resistant cells. Mass spectrometry on autophagosome-enriched fractions revealed that HDACi-resistant cells undergo elevated pexophagy, or autophagy of the peroxisome, an organelle that supports tumor growth. To disturb peroxisome homeostasis, we enhanced pexophagy in HDACi-resistant cells via genetic silencing of peroxisome exportomer complex components (PEX1, PEX6, or PEX26). This consequently sensitized resistant cells to HDACi-mediated apoptosis, which was rescued by inhibiting ATM/ataxia-telangiectasia mutated (ATM serine/threonine kinase), a mediator of pexophagy. We subsequently engineered melanoma cells to stably repress PEX26 using CRISPR interference (CRISPRi). Melanoma cells with repressed PEX26 expression showed evidence of both increased pexophagy and peroxisomal matrix protein import defects versus single guide scrambled (sgSCR) controls. In vivo studies showed that sgPEX26 melanoma xenografts recurred less compared to sgSCR xenografts, following the development of resistance to mitogen-activated protein kinase (MAPK)-targeted therapy. Finally, prognostic analysis of publicly available datasets showed that low expression levels of PEX26, PEX6 and MTOR, were significantly associated with prolonged patient survival in lymphoma, lung cancer and melanoma cohorts. Our work highlighted that drugs designed to disrupt peroxisome homeostasis may serve as unconventional therapies to combat therapy resistance in cancer.Abbreviations: ABCD3/PMP70: ATP binding cassette subfamily D member 3; ACOX1: acyl-CoA oxidase 1; AP: autophagosome; COX: cytochrome c oxidase; CQ: chloroquine; CRISPRi: clustered regularly interspaced short palindromic repeats interference; DLBCL: diffuse large B-cell lymphoma; GO: gene ontology; dCas9: Cas9 endonuclease dead, or dead Cas9; HDACi: histone deacetylase inhibitors; IHC: Immunohistochemistry; LAMP2: lysosomal associated membrane protein 2; LCFAs: long-chain fatty acids; LFQ-MS: label-free quantitation mass spectrometry; LPC: lysophoshatidylcholine; MAP1LC3B/LC3B: microtubule associated protein 1 light chain 3 beta; MTOR: mechanistic target of rapamycin kinase; PBD: peroxisome biogenesis disorders; PTS1: peroxisomal targeting signal 1; ROS: reactive oxygen species; sgRNA: single guide RNA; VLCFAs: very-long chain fatty acids; Vor: vorinostat; WO: wash-off.
Collapse
Affiliation(s)
- Michael S Dahabieh
- Lady Davis Institute, McGill University, Montréal, Canada.,Department of Experimental Medicine, McGill University, Montréal, Canada
| | - Fan Huang
- Lady Davis Institute, McGill University, Montréal, Canada.,Department of Experimental Medicine, McGill University, Montréal, Canada
| | | | - Raúl Ernesto Flores González
- Lady Davis Institute, McGill University, Montréal, Canada.,Department of Experimental Medicine, McGill University, Montréal, Canada
| | - Sathyen Prabhu
- Lady Davis Institute, McGill University, Montréal, Canada.,Department of Experimental Medicine, McGill University, Montréal, Canada
| | - Alicia Bolt
- Lady Davis Institute, McGill University, Montréal, Canada
| | - Erminia Di Pietro
- Department of Human Genetics and Pediatrics, Research Institute of McGill University Children's Hospital, Montréal, Canada
| | - Elie Khoury
- Lady Davis Institute, McGill University, Montréal, Canada.,Department of Experimental Medicine, McGill University, Montréal, Canada
| | - John Heath
- Lady Davis Institute, McGill University, Montréal, Canada.,Department of Experimental Medicine, McGill University, Montréal, Canada
| | - Zi Yi Xu
- Lady Davis Institute, McGill University, Montréal, Canada
| | | | - Koren K Mann
- Lady Davis Institute, McGill University, Montréal, Canada.,Department of Experimental Medicine, McGill University, Montréal, Canada.,Department of Oncology, McGill University, Montréal, Canada
| | - Alexandre Orthwein
- Lady Davis Institute, McGill University, Montréal, Canada.,Department of Experimental Medicine, McGill University, Montréal, Canada.,Department of Oncology, McGill University, Montréal, Canada
| | | | - Nancy Braverman
- Department of Human Genetics and Pediatrics, Research Institute of McGill University Children's Hospital, Montréal, Canada
| | - Wilson H Miller
- Lady Davis Institute, McGill University, Montréal, Canada.,Department of Experimental Medicine, McGill University, Montréal, Canada.,Department of Oncology, McGill University, Montréal, Canada
| | - Sonia V Del Rincón
- Lady Davis Institute, McGill University, Montréal, Canada.,Department of Experimental Medicine, McGill University, Montréal, Canada.,Department of Oncology, McGill University, Montréal, Canada
| |
Collapse
|
15
|
Barczykowski AL, Langan TJ, Vanderver A, Jalal K, Carter RL. Death rates in the U.S. due to Leukodystrophies with pediatric forms. Am J Med Genet A 2021; 185:2361-2373. [PMID: 33960638 DOI: 10.1002/ajmg.a.62248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Revised: 03/26/2021] [Accepted: 04/16/2021] [Indexed: 11/08/2022]
Abstract
To use national mortality and state death certificate records to estimate disease specific mortality rates among pediatric and adult populations for 23 leukodystrophies (LDs) with pediatric forms. Additionally, to calculate yearly prevalence and caseload of the most severe LD cases that will eventually result in pediatric death (i.e., pediatric fatality cases). Death certificate records describing cause of death were collected from states based on 10 ICD-10 codes associated with the 23 LDs. Deaths in the U.S. with these codes were distributed into categories based on proportions identified in state death certificate data. Mortality rates, prevalence, and caseload were calculated from resulting expected numbers, population sizes, and average lifetimes. An estimated 1.513 per 1,000,000 0-17 year old's died of these LDs at average age 5.2 years and 0.194 for those ≥18 at an average age of 42.3 years. Prevalence of pediatric fatality cases of these LDs declined from 1999 through 2007 and then remained constant at 6.2 per million children per year through 2012. Epidemiological information, currently lacking for rare diseases, is useful to newborn screening programs, research funding agencies, and care centers for LD patients. Methods used here are generally useful for studying rare diseases.
Collapse
Affiliation(s)
- Amy L Barczykowski
- Population Health Observatory, School of Public Health and Health Professions, University at Buffalo, Buffalo, New York, USA.,Department of Biostatistics, School of Public Health and Health Professions, University at Buffalo, Buffalo, New York, USA
| | - Thomas J Langan
- Hunter James Kelly Research Institute, School of Medicine and Biomedical Sciences School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, New York, USA.,Department of Neurology, School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, New York, USA
| | - Adeline Vanderver
- The Division of Neurology, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA.,The Department of Neurology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Kabir Jalal
- Population Health Observatory, School of Public Health and Health Professions, University at Buffalo, Buffalo, New York, USA.,Department of Biostatistics, School of Public Health and Health Professions, University at Buffalo, Buffalo, New York, USA
| | - Randy L Carter
- Population Health Observatory, School of Public Health and Health Professions, University at Buffalo, Buffalo, New York, USA.,Department of Biostatistics, School of Public Health and Health Professions, University at Buffalo, Buffalo, New York, USA
| |
Collapse
|
16
|
Das Y, Swinkels D, Baes M. Peroxisomal Disorders and Their Mouse Models Point to Essential Roles of Peroxisomes for Retinal Integrity. Int J Mol Sci 2021; 22:ijms22084101. [PMID: 33921065 PMCID: PMC8071455 DOI: 10.3390/ijms22084101] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 04/12/2021] [Accepted: 04/13/2021] [Indexed: 12/31/2022] Open
Abstract
Peroxisomes are multifunctional organelles, well known for their role in cellular lipid homeostasis. Their importance is highlighted by the life-threatening diseases caused by peroxisomal dysfunction. Importantly, most patients suffering from peroxisomal biogenesis disorders, even those with a milder disease course, present with a number of ocular symptoms, including retinopathy. Patients with a selective defect in either peroxisomal α- or β-oxidation or ether lipid synthesis also suffer from vision problems. In this review, we thoroughly discuss the ophthalmological pathology in peroxisomal disorder patients and, where possible, the corresponding animal models, with a special emphasis on the retina. In addition, we attempt to link the observed retinal phenotype to the underlying biochemical alterations. It appears that the retinal pathology is highly variable and the lack of histopathological descriptions in patients hampers the translation of the findings in the mouse models. Furthermore, it becomes clear that there are still large gaps in the current knowledge on the contribution of the different metabolic disturbances to the retinopathy, but branched chain fatty acid accumulation and impaired retinal PUFA homeostasis are likely important factors.
Collapse
|
17
|
Bürgi J, Ekal L, Wilmanns M. Versatile allosteric properties in Pex5-like tetratricopeptide repeat proteins to induce diverse downstream function. Traffic 2021; 22:140-152. [PMID: 33580581 DOI: 10.1111/tra.12785] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Revised: 01/30/2021] [Accepted: 02/10/2021] [Indexed: 01/11/2023]
Abstract
Proteins composed of tetratricopeptide repeat (TPR) arrays belong to the α-solenoid tandem-repeat family that have unique properties in terms of their overall conformational flexibility and ability to bind to multiple protein ligands. The peroxisomal matrix protein import receptor Pex5 comprises two TPR triplets that recognize protein cargos with a specific C-terminal Peroxisomal Targeting Signal (PTS) 1 motif. Import of PTS1-containing protein cargos into peroxisomes through a transient pore is mainly driven by allosteric binding, coupling and release mechanisms, without a need for external energy. A very similar TPR architecture is found in the functionally unrelated TRIP8b, a regulator of the hyperpolarization-activated cyclic nucleotide-gated (HCN) ion channel. TRIP8b binds to the HCN ion channel via a C-terminal sequence motif that is nearly identical to the PTS1 motif of Pex5 receptor cargos. Pex5, Pex5-related Pex9, and TRIP8b also share a less conserved N-terminal domain. This domain provides a second protein cargo-binding site and plays a distinct role in allosteric coupling of initial cargo loading by PTS1 motif-mediated interactions and different downstream functional readouts. The data reviewed here highlight the overarching role of molecular allostery in driving the diverse functions of TPR array proteins, which could form a model for other α-solenoid tandem-repeat proteins involved in translocation processes across membranes.
Collapse
Affiliation(s)
- Jérôme Bürgi
- European Molecular Biology Laboratory, Hamburg Unit, Hamburg, Germany
| | - Lakhan Ekal
- European Molecular Biology Laboratory, Hamburg Unit, Hamburg, Germany
| | - Matthias Wilmanns
- European Molecular Biology Laboratory, Hamburg Unit, Hamburg, Germany.,University Hamburg Clinical Center Hamburg-Eppendorf, Hamburg, Germany
| |
Collapse
|
18
|
Das Y, Swinkels D, Kocherlakota S, Vinckier S, Vaz FM, Wever E, van Kampen AHC, Jun B, Do KV, Moons L, Bazan NG, Van Veldhoven PP, Baes M. Peroxisomal Multifunctional Protein 2 Deficiency Perturbs Lipid Homeostasis in the Retina and Causes Visual Dysfunction in Mice. Front Cell Dev Biol 2021; 9:632930. [PMID: 33604342 PMCID: PMC7884615 DOI: 10.3389/fcell.2021.632930] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 01/11/2021] [Indexed: 01/09/2023] Open
Abstract
Patients lacking multifunctional protein 2 (MFP2), the central enzyme of the peroxisomal β-oxidation pathway, develop retinopathy. This pathway is involved in the metabolism of very long chain (VLCFAs) and polyunsaturated (PUFAs) fatty acids, which are enriched in the photoreceptor outer segments (POS). The molecular mechanisms underlying the retinopathy remain, however, elusive. Here, we report that mice with MFP2 inactivation display decreased retinal function already at the age of 3 weeks, which is accompanied by a profound shortening of the photoreceptor outer and inner segments, but with preserved photoreceptor ultrastructure. Furthermore, MFP2 deficient retinas exhibit severe changes in gene expression with downregulation of genes involved in the phototransduction pathway and upregulation of inflammation related genes. Lipid profiling of the mutant retinas revealed a profound reduction of DHA-containing phospholipids. This was likely due to a hampered systemic supply and retinal traffic of this PUFA, although we cannot exclude that the local defect of peroxisomal β-oxidation contributes to this DHA decrease. Moreover, very long chain PUFAs were also reduced, with the exception of those containing ≥ 34 carbons that accumulated. The latter suggests that there is an uncontrollable elongation of retinal PUFAs. In conclusion, our data reveal that intact peroxisomal β-oxidation is indispensable for retinal integrity, most likely by maintaining PUFA homeostasis.
Collapse
Affiliation(s)
- Yannick Das
- Laboratory of Cell Metabolism, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Leuven, Belgium
| | - Daniëlle Swinkels
- Laboratory of Cell Metabolism, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Leuven, Belgium
| | - Sai Kocherlakota
- Laboratory of Cell Metabolism, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Leuven, Belgium
| | - Stefan Vinckier
- Laboratory of Angiogenesis and Vascular Metabolism, Department of Oncology, KU Leuven-VIB, Leuven, Belgium
| | - Frédéric M Vaz
- Laboratory of Genetic Metabolic Diseases, Department of Clinical Chemistry and Pediatrics, Amsterdam University Medical Center (UMC), University of Amsterdam, Amsterdam, Netherlands.,Core Facility Metabolomics, Amsterdam University Medical Center (UMC), Amsterdam, Netherlands
| | - Eric Wever
- Laboratory of Genetic Metabolic Diseases, Department of Clinical Chemistry and Pediatrics, Amsterdam University Medical Center (UMC), University of Amsterdam, Amsterdam, Netherlands.,Core Facility Metabolomics, Amsterdam University Medical Center (UMC), Amsterdam, Netherlands.,Bioinformatics Laboratory, Department of Epidemiology and Data Science, Amsterdam Public Health Research Institute, Amsterdam University Medical Center (UMC), University of Amsterdam, Amsterdam, Netherlands
| | - Antoine H C van Kampen
- Bioinformatics Laboratory, Department of Epidemiology and Data Science, Amsterdam Public Health Research Institute, Amsterdam University Medical Center (UMC), University of Amsterdam, Amsterdam, Netherlands.,Biosystems Data Analysis, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, Netherlands
| | - Bokkyoo Jun
- Neuroscience Center of Excellence, School of Medicine, Louisiana State University Health New Orleans, New Orleans, LA, United States
| | - Khanh V Do
- Neuroscience Center of Excellence, School of Medicine, Louisiana State University Health New Orleans, New Orleans, LA, United States
| | - Lieve Moons
- Animal Physiology and Neurobiology, Department of Biology, KU Leuven, Leuven, Belgium
| | - Nicolas G Bazan
- Neuroscience Center of Excellence, School of Medicine, Louisiana State University Health New Orleans, New Orleans, LA, United States
| | - Paul P Van Veldhoven
- Lipid Biochemistry and Protein Interactions (LIPIT), Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | - Myriam Baes
- Laboratory of Cell Metabolism, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Leuven, Belgium
| |
Collapse
|
19
|
Taatjes DJ, Roth J. In focus in HCB. Histochem Cell Biol 2020; 153:289-293. [PMID: 32382788 PMCID: PMC7205545 DOI: 10.1007/s00418-020-01879-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Affiliation(s)
- Douglas J Taatjes
- Department of Pathology and Laboratory Medicine, Larner College of Medicine, University of Vermont, Burlington, VT, 05405, USA.
| | - Jürgen Roth
- University of Zurich, 8091, Zurich, Switzerland
| |
Collapse
|
20
|
Turton N, Rutherford T, Thijssen D, Hargreaves IP. Putative adjunct therapies to target mitochondrial dysfunction and oxidative stress in phenylketonuria, lysosomal storage disorders and peroxisomal disorders. Expert Opin Orphan Drugs 2020. [DOI: 10.1080/21678707.2020.1850254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/06/2022]
Affiliation(s)
- Nadia Turton
- School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, Liverpool, UK
| | - Tricia Rutherford
- Department of research and development, Vitaflo International Ltd, Liverpool, UK
| | - Dick Thijssen
- School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, Liverpool, UK
| | - Iain P Hargreaves
- School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, Liverpool, UK
| |
Collapse
|
21
|
Mahalingam SS, Shukla N, Farré JC, Zientara-Rytter K, Subramani S. Balancing the Opposing Principles That Govern Peroxisome Homeostasis. Trends Biochem Sci 2020; 46:200-212. [PMID: 33046344 DOI: 10.1016/j.tibs.2020.09.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 09/14/2020] [Accepted: 09/22/2020] [Indexed: 12/12/2022]
Abstract
Despite major advances in our understanding of players and mechanisms involved in peroxisome biogenesis and peroxisome degradation, very few studies have focused on unraveling the multi-layered connections between, and the coordination of, these two opposing processes that regulate peroxisome homeostasis. The intersection between these processes also provides exciting avenues for future research. This review highlights the links between peroxisome biogenesis and degradation, incorporating an integrative approach that is critical not only for a mechanistic understanding, but also for manipulating the balance between these processes in relevant disease models.
Collapse
Affiliation(s)
- Shanmuga S Mahalingam
- Section of Molecular Biology, Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093-0322, USA
| | - Nandini Shukla
- Section of Molecular Biology, Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093-0322, USA
| | - Jean-Claude Farré
- Section of Molecular Biology, Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093-0322, USA
| | - Katarzyna Zientara-Rytter
- Section of Molecular Biology, Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093-0322, USA
| | - Suresh Subramani
- Section of Molecular Biology, Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093-0322, USA.
| |
Collapse
|
22
|
Stinson JL, Brault JA, Delk PR, Graham BH, Karmazyn B, Hall B, Weaver DD. An apparent new syndrome of extreme short stature, microcephaly, dysmorphic faces, intellectual disability, and a bone dysplasia of unknown etiology. Am J Med Genet A 2020; 182:1562-1571. [PMID: 32426895 DOI: 10.1002/ajmg.a.61619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Revised: 04/06/2020] [Accepted: 04/14/2020] [Indexed: 11/12/2022]
Abstract
We report on a 26-year-old male with extreme short stature, microcephaly, macroglossia, other dysmorphic features, severe intellectual disability, and a bone dysplasia. The patient had an extensive genetic and biochemical evaluation that was all normal or noninformative. Recently, the proband died following a period of not eating. He likely had a previously undescribed syndrome of unknown etiology.
Collapse
Affiliation(s)
- Jennifer L Stinson
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Jennifer A Brault
- Department of Pediatrics, Divisions of Pediatric Neurology, and Genetic and Genomic Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Paula R Delk
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Brett H Graham
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Boaz Karmazyn
- Department of Radiology and Imaging Sciences, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Bryan Hall
- Greenwood Genetics Center, Greenwood, South Carolina, USA
| | - David D Weaver
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana, USA
| |
Collapse
|
23
|
Miyamoto T, Hosoba K, Itabashi T, Iwane AH, Akutsu SN, Ochiai H, Saito Y, Yamamoto T, Matsuura S. Insufficiency of ciliary cholesterol in hereditary Zellweger syndrome. EMBO J 2020; 39:e103499. [PMID: 32368833 PMCID: PMC7298307 DOI: 10.15252/embj.2019103499] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2019] [Revised: 03/13/2020] [Accepted: 03/20/2020] [Indexed: 11/22/2022] Open
Abstract
Primary cilia are antenna‐like organelles on the surface of most mammalian cells that receive sonic hedgehog (Shh) signaling in embryogenesis and carcinogenesis. Cellular cholesterol functions as a direct activator of a seven‐transmembrane oncoprotein called Smoothened (Smo) and thereby induces Smo accumulation on the ciliary membrane where it transduces the Shh signal. However, how cholesterol is supplied to the ciliary membrane remains unclear. Here, we report that peroxisomes are essential for the transport of cholesterol into the ciliary membrane. Zellweger syndrome (ZS) is a peroxisome‐deficient hereditary disorder with several ciliopathy‐related features and cells from these patients showed a reduced cholesterol level in the ciliary membrane. Reverse genetics approaches revealed that the GTP exchange factor Rabin8, the Rab GTPase Rab10, and the microtubule minus‐end‐directed kinesin KIFC3 form a peroxisome‐associated complex to control the movement of peroxisomes along microtubules, enabling communication between peroxisomes and ciliary pocket membranes. Our findings suggest that insufficient ciliary cholesterol levels may underlie ciliopathies.
Collapse
Affiliation(s)
- Tatsuo Miyamoto
- Department of Genetics and Cell Biology, Research Institute for Radiation Biology and Medicine, Hiroshima University, Hiroshima, Japan
| | - Kosuke Hosoba
- Department of Genetics and Cell Biology, Research Institute for Radiation Biology and Medicine, Hiroshima University, Hiroshima, Japan.,Program of Biomedical Science, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Japan
| | - Takeshi Itabashi
- Laboratory for Cell Field Structure, RIKEN Center for Biosystems Dynamics Research, Higashi-Hiroshima, Japan
| | - Atsuko H Iwane
- Laboratory for Cell Field Structure, RIKEN Center for Biosystems Dynamics Research, Higashi-Hiroshima, Japan
| | - Silvia Natsuko Akutsu
- Department of Genetics and Cell Biology, Research Institute for Radiation Biology and Medicine, Hiroshima University, Hiroshima, Japan
| | - Hiroshi Ochiai
- Program of Biomedical Science, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Japan
| | - Yumiko Saito
- Program of Biomedical Science, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Japan.,Program of Life and Environmental Sciences, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Japan
| | - Takashi Yamamoto
- Program of Biomedical Science, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Japan.,Program of Mathematical and Life Sciences, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Japan
| | - Shinya Matsuura
- Department of Genetics and Cell Biology, Research Institute for Radiation Biology and Medicine, Hiroshima University, Hiroshima, Japan
| |
Collapse
|
24
|
García-García G, Sanchez-Navarro I, Aller E, Jaijo T, Fuster-Garcia C, Rodríguez-Munoz A, Vallejo E, Tellería JJ, Vázquez S, Beltrán S, Derdak S, Zurita O, Villaverde-Montero C, Avila-Fernández A, Corton M, Blanco-Kelly F, Hakonarson H, Millán JM, Ayuso C. Exome sequencing identifies PEX6 mutations in three cases diagnosed with Retinitis Pigmentosa and hearing impairment. Mol Vis 2020; 26:216-225. [PMID: 32214787 PMCID: PMC7090270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Accepted: 03/16/2020] [Indexed: 11/07/2022] Open
Abstract
Purpose The aim of the present work is the molecular diagnosis of three patients with deafness and retinal degeneration. Methods Three patients from two unrelated families were initially analyzed with custom gene panels for Usher genes, non-syndromic hearing loss, or inherited syndromic retinopathies and further investigated by means of clinical or whole exome sequencing. Results The study allowed us to detect likely pathogenic variants in PEX6, a gene typically involved in peroxisomal biogenesis disorders (PBDs). Beside deaf-blindness, both families showed additional features: Siblings from Family 1 showed enamel alteration and abnormal peroxisome. In addition, the brother had mild neurodevelopmental delay and nephrolithiasis. The case II:1 from Family 2 showed intellectual disability, enamel alteration, and dysmorphism. Conclusions We have reported three new cases with pathogenic variants in PEX6 presenting with milder forms of the Zellweger spectrum disorders (ZSD). The three cases showed distinct clinical features. Thus, expanding the phenotypic spectrum of PBDs and ascertaining exome sequencing is an effective strategy for an accurate diagnosis of clinically overlapping and genetically heterogeneous disorders such as deafness-blindness association.
Collapse
Affiliation(s)
- Gema García-García
- Research group on Molecular, Cellular and Genomic Biomedicine, Health Research, Institute La Fe (IIS La Fe) and Mixed Unit for Rare diseases IIS La Fe - CIPF, Valencia, Spain,Centre for Biomedical Research on Rare Diseases (CIBERER), Madrid, Spain
| | - Iker Sanchez-Navarro
- Centre for Biomedical Research on Rare Diseases (CIBERER), Madrid, Spain,Department of Genetics, IIS-Fundación Jiménez Díaz University Hospital (IIS-FJD, UAM), Madrid, Spain
| | - Elena Aller
- Research group on Molecular, Cellular and Genomic Biomedicine, Health Research, Institute La Fe (IIS La Fe) and Mixed Unit for Rare diseases IIS La Fe - CIPF, Valencia, Spain,Centre for Biomedical Research on Rare Diseases (CIBERER), Madrid, Spain,Genetics Unit, La Fe University Hospital, Valencia, Spain
| | - Teresa Jaijo
- Research group on Molecular, Cellular and Genomic Biomedicine, Health Research, Institute La Fe (IIS La Fe) and Mixed Unit for Rare diseases IIS La Fe - CIPF, Valencia, Spain,Centre for Biomedical Research on Rare Diseases (CIBERER), Madrid, Spain,Genetics Unit, La Fe University Hospital, Valencia, Spain
| | - Carla Fuster-Garcia
- Research group on Molecular, Cellular and Genomic Biomedicine, Health Research, Institute La Fe (IIS La Fe) and Mixed Unit for Rare diseases IIS La Fe - CIPF, Valencia, Spain
| | - Ana Rodríguez-Munoz
- Research group on Molecular, Cellular and Genomic Biomedicine, Health Research, Institute La Fe (IIS La Fe) and Mixed Unit for Rare diseases IIS La Fe - CIPF, Valencia, Spain
| | - Elena Vallejo
- Department of Ophthalmology, Medina del Campo Hospital, Valladolid, Spain
| | | | - Selma Vázquez
- University Hospital of Valladolid, Valladolid, Spain
| | - Sergi Beltrán
- National Center of Genomic Analysis (CNAG-CRG) Centre for Genomic Regulation, Barcelona, Spain
| | - Sophia Derdak
- National Center of Genomic Analysis (CNAG-CRG) Centre for Genomic Regulation, Barcelona, Spain
| | - Olga Zurita
- Centre for Biomedical Research on Rare Diseases (CIBERER), Madrid, Spain,Department of Genetics, IIS-Fundación Jiménez Díaz University Hospital (IIS-FJD, UAM), Madrid, Spain
| | - Cristina Villaverde-Montero
- Centre for Biomedical Research on Rare Diseases (CIBERER), Madrid, Spain,Department of Genetics, IIS-Fundación Jiménez Díaz University Hospital (IIS-FJD, UAM), Madrid, Spain
| | - Almudena Avila-Fernández
- Centre for Biomedical Research on Rare Diseases (CIBERER), Madrid, Spain,Department of Genetics, IIS-Fundación Jiménez Díaz University Hospital (IIS-FJD, UAM), Madrid, Spain
| | - Marta Corton
- Centre for Biomedical Research on Rare Diseases (CIBERER), Madrid, Spain,Department of Genetics, IIS-Fundación Jiménez Díaz University Hospital (IIS-FJD, UAM), Madrid, Spain
| | - Fiona Blanco-Kelly
- Centre for Biomedical Research on Rare Diseases (CIBERER), Madrid, Spain,Department of Genetics, IIS-Fundación Jiménez Díaz University Hospital (IIS-FJD, UAM), Madrid, Spain
| | - Hakon Hakonarson
- The Center for Applied Genomics, The Children’s Hospital of Philadelphia, Philadelphia, PA,Department of Pediatrics, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - José M. Millán
- Research group on Molecular, Cellular and Genomic Biomedicine, Health Research, Institute La Fe (IIS La Fe) and Mixed Unit for Rare diseases IIS La Fe - CIPF, Valencia, Spain,Centre for Biomedical Research on Rare Diseases (CIBERER), Madrid, Spain
| | - Carmen Ayuso
- Centre for Biomedical Research on Rare Diseases (CIBERER), Madrid, Spain,Department of Genetics, IIS-Fundación Jiménez Díaz University Hospital (IIS-FJD, UAM), Madrid, Spain
| |
Collapse
|
25
|
Demaret T, Courtoy GE, Ravau J, Van Der Smissen P, Najimi M, Sokal EM. Accurate and live peroxisome biogenesis evaluation achieved by lentiviral expression of a green fluorescent protein fused to a peroxisome targeting signal 1. Histochem Cell Biol 2020; 153:295-306. [PMID: 32124009 DOI: 10.1007/s00418-020-01855-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/17/2020] [Indexed: 12/30/2022]
Abstract
Peroxisomes are ubiquitous organelles formed by peroxisome biogenesis (PB). During PB, peroxisomal matrix proteins harboring a peroxisome targeting signal (PTS) are imported inside peroxisomes by peroxins, encoded by PEX genes. Genetic alterations in PEX genes lead to a spectrum of incurable diseases called Zellweger spectrum disorders (ZSD). In vitro drug screening is part of the quest for a cure in ZSD by restoring PB in ZSD cell models. In vitro PB evaluation is commonly achieved by immunofluorescent staining or transient peroxisome fluorescent reporter expression. Both techniques have several drawbacks (cost, time-consuming technique, etc.) which we overcame by developing a third-generation lentiviral transfer plasmid expressing an enhanced green fluorescent protein fused to PTS1 (eGFP-PTS1). By eGFP-PTS1 lentiviral transduction, we quantified PB and peroxisome motility in ZSD and control mouse and human fibroblasts. We confirmed the stable eGFP-PTS1 expression along cell passages. eGFP signal analysis distinguished ZSD from control eGFP-PTS1-transduced cells. Live eGFP-PTS1 transduced cells imaging quantified peroxisomes motility. In conclusion, we developed a lentiviral transfer plasmid allowing stable eGFP-PTS1 expression to study PB (deposited on Addgene: #133282). This tool meets the needs for in vitro PB evaluation and ZSD drug discovery.
Collapse
Affiliation(s)
- Tanguy Demaret
- Laboratoire d'Hépatologie Pédiatrique et Thérapie Cellulaire, Unité PEDI, Institut de Recherche Expérimentale et Clinique (IREC), Université Catholique de Louvain (UCLouvain), 1200, Brussels, Belgium
| | - Guillaume E Courtoy
- IREC Imaging Platform (2IP), Institut de Recherche Expérimentale et Clinique (IREC), Université Catholique de Louvain (UCLouvain), 1200, Brussels, Belgium
| | - Joachim Ravau
- Laboratoire d'Hépatologie Pédiatrique et Thérapie Cellulaire, Unité PEDI, Institut de Recherche Expérimentale et Clinique (IREC), Université Catholique de Louvain (UCLouvain), 1200, Brussels, Belgium
| | - Patrick Van Der Smissen
- Platform for Imaging Cells and Tissues (PICT), de Duve Institute, Université Catholique de Louvain (UCLouvain), 1200, Brussels, Belgium
| | - Mustapha Najimi
- Laboratoire d'Hépatologie Pédiatrique et Thérapie Cellulaire, Unité PEDI, Institut de Recherche Expérimentale et Clinique (IREC), Université Catholique de Louvain (UCLouvain), 1200, Brussels, Belgium
| | - Etienne M Sokal
- Laboratoire d'Hépatologie Pédiatrique et Thérapie Cellulaire, Unité PEDI, Institut de Recherche Expérimentale et Clinique (IREC), Université Catholique de Louvain (UCLouvain), 1200, Brussels, Belgium.
| |
Collapse
|
26
|
A Mechanistic Perspective on PEX1 and PEX6, Two AAA+ Proteins of the Peroxisomal Protein Import Machinery. Int J Mol Sci 2019; 20:ijms20215246. [PMID: 31652724 PMCID: PMC6862443 DOI: 10.3390/ijms20215246] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Revised: 10/18/2019] [Accepted: 10/21/2019] [Indexed: 12/11/2022] Open
Abstract
In contrast to many protein translocases that use ATP or GTP hydrolysis as the driving force to transport proteins across biological membranes, the peroxisomal matrix protein import machinery relies on a regulated self-assembly mechanism for this purpose and uses ATP hydrolysis only to reset its components. The ATP-dependent protein complex in charge of resetting this machinery—the Receptor Export Module (REM)—comprises two members of the “ATPases Associated with diverse cellular Activities” (AAA+) family, PEX1 and PEX6, and a membrane protein that anchors the ATPases to the organelle membrane. In recent years, a large amount of data on the structure/function of the REM complex has become available. Here, we discuss the main findings and their mechanistic implications.
Collapse
|
27
|
Cook KC, Moreno JA, Jean Beltran PM, Cristea IM. Peroxisome Plasticity at the Virus-Host Interface. Trends Microbiol 2019; 27:906-914. [PMID: 31331665 DOI: 10.1016/j.tim.2019.06.006] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Revised: 06/12/2019] [Accepted: 06/19/2019] [Indexed: 02/07/2023]
Abstract
Peroxisomes are multifunctional organelles with roles in cellular metabolism, cytotoxicity, and signaling. The plastic nature of these organelles allows them to respond to diverse biological processes, such as virus infections, by remodeling their biogenesis, morphology, and composition to enhance specific functions. During virus infections in humans, peroxisomes act as important immune signaling organelles, aiding the host by orchestrating antiviral signaling. However, more recently it was discovered that peroxisomes can also benefit the virus, facilitating virus-host interactions that rewire peroxisomes to support cellular processes for virus replication and spread. Here, we describe recent studies that uncovered this double-edged character of peroxisomes during infection, highlighting mechanisms that viruses have coevolved to take advantage of peroxisome plasticity. We also provide a perspective for future studies by comparing the established roles of peroxisomes in plant infections and discussing the promise of virology studies as a venue to reveal the uncharted biology of peroxisomes.
Collapse
Affiliation(s)
- Katelyn C Cook
- Department of Molecular Biology, Princeton University, Lewis Thomas Laboratory, Washington Road, Princeton, NJ 08544, USA
| | - Jorge A Moreno
- Department of Molecular Biology, Princeton University, Lewis Thomas Laboratory, Washington Road, Princeton, NJ 08544, USA
| | - Pierre M Jean Beltran
- Department of Molecular Biology, Princeton University, Lewis Thomas Laboratory, Washington Road, Princeton, NJ 08544, USA
| | - Ileana M Cristea
- Department of Molecular Biology, Princeton University, Lewis Thomas Laboratory, Washington Road, Princeton, NJ 08544, USA.
| |
Collapse
|
28
|
Genome Wide Analysis of WD40 Proteins in Saccharomyces cerevisiae and Their Orthologs in Candida albicans. Protein J 2019; 38:58-75. [PMID: 30511317 DOI: 10.1007/s10930-018-9804-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The WD40 domain containing proteins are present in the lower organisms (Monera) to higher complex metazoans with involvement in diverse cellular processes. The WD40 repeats fold into β propeller structure due to which the proteins harbouring WD40 domains function as scaffold by offering platform for interactions, bring together diverse cellular proteins to form a single complex for mediating downstream effects. Multiple functions of WD40 domain containing proteins in lower eukaryote as in Fungi have been reported with involvement in vegetative and reproductive growth, virulence etc. In this article insilico analysis of the WDR proteins in the budding yeast Saccharomyces cerevisiae was performed. By WDSP software 83 proteins in S. cerevisiae were identified with at least one WD40 motif. WD40 proteins with 6 or more WD40 motifs were considered for further studies. The WD40 proteins in yeast which are involved in various biological processes show distribution on all chromosomes (16 chromosomes in yeast) except chromosome 1. Besides the WD40 domain some of these proteins also contain other protein domains which might be responsible for the diversity in the functions of WD40 proteins in the budding yeast. These proteins in budding yeast were analysed by DAVID and Blast2Go software for functional and domains categorization. Candida albicans, an opportunistic fungal pathogen also have orthologs of these WD40 proteins with possible similar functions. This is the first time genome wide analysis of WD40 proteins in lower eukaryote i.e. budding yeast. This data may be useful in further study of the functional diversity of yeast proteomes.
Collapse
|
29
|
Wanders RJA, Vaz FM, Ferdinandusse S, Kemp S, Ebberink MS, Waterham HR. Laboratory Diagnosis of Peroxisomal Disorders in the -Omics Era and the Continued Importance of Biomarkers and Biochemical Studies. JOURNAL OF INBORN ERRORS OF METABOLISM AND SCREENING 2018. [DOI: 10.1177/2326409818810285] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Affiliation(s)
- Ronald J. A. Wanders
- Laboratory Genetic Metabolic Diseases, Departments of Clinical Chemistry and Pediatrics, EmmaChildren’s Hospital, Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands
| | - Frédéric M. Vaz
- Laboratory Genetic Metabolic Diseases, Departments of Clinical Chemistry and Pediatrics, EmmaChildren’s Hospital, Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands
| | - Sacha Ferdinandusse
- Laboratory Genetic Metabolic Diseases, Departments of Clinical Chemistry and Pediatrics, EmmaChildren’s Hospital, Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands
| | - Stephan Kemp
- Laboratory Genetic Metabolic Diseases, Departments of Clinical Chemistry and Pediatrics, EmmaChildren’s Hospital, Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands
| | - Merel S. Ebberink
- Laboratory Genetic Metabolic Diseases, Departments of Clinical Chemistry and Pediatrics, EmmaChildren’s Hospital, Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands
| | - Hans R. Waterham
- Laboratory Genetic Metabolic Diseases, Departments of Clinical Chemistry and Pediatrics, EmmaChildren’s Hospital, Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands
| |
Collapse
|
30
|
MacLean GE, Argyriou C, Di Pietro E, Sun X, Birjandian S, Saberian P, Hacia JG, Braverman NE. Zellweger spectrum disorder patient-derived fibroblasts with the PEX1-Gly843Asp allele recover peroxisome functions in response to flavonoids. J Cell Biochem 2018; 120:3243-3258. [PMID: 30362618 DOI: 10.1002/jcb.27591] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2018] [Accepted: 08/08/2018] [Indexed: 01/03/2023]
Abstract
Zellweger spectrum disorder (ZSD) results from biallelic mutations in PEX genes required for peroxisome biogenesis. PEX1-G843D is a common hypomorphic allele in the patient population that is associated with milder disease. In prior work using a PEX1-G843D/null patient fibroblast line expressing a green fluorescent protein (GFP) reporter with a peroxisome-targeting signal (GFP-PTS1), we demonstrated that treatments with the chemical chaperone betaine and flavonoid acacetin diacetate recovered peroxisome functions. To identify more effective compounds for preclinical investigation, we evaluated 54 flavonoids using this cell-based phenotype assay. Diosmetin showed the most promising combination of potency and efficacy (EC50 2.5 µM). All active 5',7'-dihydroxyflavones showed greater average efficacy than their corresponding flavonols, whereas the corresponding flavanones, isoflavones, and chalcones tested were inactive. Additional treatment with the proteostasis regulator bortezomib increased the percentage of import-rescued cells over treatment with flavonoids alone. Cotreatments of diosmetin and betaine showed the most robust additive effects, as confirmed by three independent functional assays in primary PEX1-G843D patient cells, but neither agent was active alone or in combination in patient cells homozygous for the PEX1 c.2097_2098insT null allele. Moreover, diosmetin treatment increased PEX1, PEX6, and PEX5 protein levels in PEX1-G843D patient cells, but none of these proteins increased in PEX1 null cells. We propose that diosmetin acts as a pharmacological chaperone that improves the stability, conformation, and functions of PEX1/PEX6 exportomer complexes required for peroxisome assembly. We suggest that diosmetin, in clinical use for chronic venous disease, and related flavonoids warrant further preclinical investigation for the treatment of PEX1-G843D-associated ZSD.
Collapse
Affiliation(s)
- Gillian E MacLean
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada
| | - Catherine Argyriou
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada
| | - Erminia Di Pietro
- Department of Pediatrics, Research Institute of the McGill University Health Center, Montreal, Quebec, Canada
| | - Xuting Sun
- Department of Biotechnology, McGill University, Montreal, Quebec, Canada
| | - Sara Birjandian
- Department of Biotechnology, McGill University, Montreal, Quebec, Canada
| | - Panteha Saberian
- Department of Biotechnology, McGill University, Montreal, Quebec, Canada
| | - Joseph G Hacia
- Department of Biochemistry and Molecular Medicine, Keck School of Medicine, Los Angeles, California
| | - Nancy E Braverman
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada.,Department of Pediatrics, Research Institute of the McGill University Health Center, Montreal, Quebec, Canada
| |
Collapse
|
31
|
Castro IG, Schuldiner M, Zalckvar E. Mind the Organelle Gap - Peroxisome Contact Sites in Disease. Trends Biochem Sci 2018; 43:199-210. [PMID: 29395653 PMCID: PMC6252078 DOI: 10.1016/j.tibs.2018.01.001] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Revised: 12/23/2017] [Accepted: 01/02/2018] [Indexed: 12/20/2022]
Abstract
The eukaryotic cell is organized as a complex grid system where membrane-bound cellular compartments, organelles, must be localized to the right place at the right time. One way to facilitate correct organelle localization and organelle cooperation is through membrane contact sites, areas of close proximity between two organelles that are bridged by protein/lipid complexes. It is now clear that all organelles physically contact each other. The main focus of this review is contact sites of peroxisomes, central metabolic hubs whose defects lead to a variety of diseases. New peroxisome contacts, their tethering complexes and functions have been recently discovered. However, if and how peroxisome contacts contribute to the development of peroxisome-related diseases is still a mystery.
Collapse
Affiliation(s)
- Inês Gomes Castro
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Maya Schuldiner
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel.
| | - Einat Zalckvar
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel.
| |
Collapse
|