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Qin W, Liang F, Lin SJ, Petree C, Huang K, Zhang Y, Li L, Varshney P, Mourrain P, Liu Y, Varshney GK. ABE-ultramax for high-efficiency biallelic adenine base editing in zebrafish. Nat Commun 2024; 15:5613. [PMID: 38965236 PMCID: PMC11224239 DOI: 10.1038/s41467-024-49943-1] [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: 10/27/2023] [Accepted: 06/20/2024] [Indexed: 07/06/2024] Open
Abstract
Advancements in CRISPR technology, particularly the development of base editors, revolutionize genetic variant research. When combined with model organisms like zebrafish, base editors significantly accelerate and refine in vivo analysis of genetic variations. However, base editors are restricted by protospacer adjacent motif (PAM) sequences and specific editing windows, hindering their applicability to a broad spectrum of genetic variants. Additionally, base editors can introduce unintended mutations and often exhibit reduced efficiency in living organisms compared to cultured cell lines. Here, we engineer a suite of adenine base editors (ABEs) called ABE-Ultramax (Umax), demonstrating high editing efficiency and low rates of insertions and deletions (indels) in zebrafish. The ABE-Umax suite of editors includes ABEs with shifted, narrowed, or broadened editing windows, reduced bystander mutation frequency, and highly flexible PAM sequence requirements. These advancements have the potential to address previous challenges in disease modeling and advance gene therapy applications.
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Affiliation(s)
- Wei Qin
- Genes & Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
| | - Fang Liang
- Institute of Modern Aquaculture Science and Engineering, School of Life Sciences, South China Normal University, Guangzhou, Guangdong, 510631, China
| | - Sheng-Jia Lin
- Genes & Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
| | - Cassidy Petree
- Genes & Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
| | - Kevin Huang
- Genes & Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
| | - Yu Zhang
- Genes & Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
| | - Lin Li
- Key Laboratory of Brain, Cognition and Education Sciences, Ministry of Education, South China Normal University, 510631, Guangzhou, China
- Institute for Brain Research and Rehabilitation, and Guangdong Key Laboratory of Mental Health and Cognitive Science, South China Normal University, 510631, Guangzhou, China
| | - Pratishtha Varshney
- Genes & Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
| | - Philippe Mourrain
- Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA, USA
| | - Yanmei Liu
- Key Laboratory of Brain, Cognition and Education Sciences, Ministry of Education, South China Normal University, 510631, Guangzhou, China.
- Institute for Brain Research and Rehabilitation, and Guangdong Key Laboratory of Mental Health and Cognitive Science, South China Normal University, 510631, Guangzhou, China.
| | - Gaurav K Varshney
- Genes & Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA.
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Cellular and Molecular Mechanisms of Pathogenesis Underlying Inherited Retinal Dystrophies. Biomolecules 2023; 13:biom13020271. [PMID: 36830640 PMCID: PMC9953031 DOI: 10.3390/biom13020271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 01/23/2023] [Accepted: 01/27/2023] [Indexed: 02/04/2023] Open
Abstract
Inherited retinal dystrophies (IRDs) are congenital retinal degenerative diseases that have various inheritance patterns, including dominant, recessive, X-linked, and mitochondrial. These diseases are most often the result of defects in rod and/or cone photoreceptor and retinal pigment epithelium function, development, or both. The genes associated with these diseases, when mutated, produce altered protein products that have downstream effects in pathways critical to vision, including phototransduction, the visual cycle, photoreceptor development, cellular respiration, and retinal homeostasis. The aim of this manuscript is to provide a comprehensive review of the underlying molecular mechanisms of pathogenesis of IRDs by delving into many of the genes associated with IRD development, their protein products, and the pathways interrupted by genetic mutation.
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Chen CT, Shao Z, Fu Z. Dysfunctional peroxisomal lipid metabolisms and their ocular manifestations. Front Cell Dev Biol 2022; 10:982564. [PMID: 36187472 PMCID: PMC9524157 DOI: 10.3389/fcell.2022.982564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 08/17/2022] [Indexed: 11/13/2022] Open
Abstract
Retina is rich in lipids and dyslipidemia causes retinal dysfunction and eye diseases. In retina, lipids are not only important membrane component in cells and organelles but also fuel substrates for energy production. However, our current knowledge of lipid processing in the retina are very limited. Peroxisomes play a critical role in lipid homeostasis and genetic disorders with peroxisomal dysfunction have different types of ocular complications. In this review, we focus on the role of peroxisomes in lipid metabolism, including degradation and detoxification of very-long-chain fatty acids, branched-chain fatty acids, dicarboxylic acids, reactive oxygen/nitrogen species, glyoxylate, and amino acids, as well as biosynthesis of docosahexaenoic acid, plasmalogen and bile acids. We also discuss the potential contributions of peroxisomal pathways to eye health and summarize the reported cases of ocular symptoms in patients with peroxisomal disorders, corresponding to each disrupted peroxisomal pathway. We also review the cross-talk between peroxisomes and other organelles such as lysosomes, endoplasmic reticulum and mitochondria.
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Affiliation(s)
- Chuck T. Chen
- Department of Nutritional Sciences, Temerty Faculty of Medicine, University of Toronto, Toronto, ON, Canada
| | - Zhuo Shao
- Post-Graduate Medical Education, University of Toronto, Toronto, ON, Canada
- Division of Clinical and Metabolic Genetics, the Hospital for Sick Children, University of Toronto, Toronto, ON, Canada
- The Genetics Program, North York General Hospital, University of Toronto, Toronto, ON, Canada
| | - Zhongjie Fu
- Department of Ophthalmology, Boston Children’s Hospital, Harvard Medical School, Boston, MA, United States
- *Correspondence: Zhongjie Fu,
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Daich Varela M, Jani P, Zein WM, D'Souza P, Wolfe L, Chisholm J, Zalewski C, Adams D, Warner BM, Huryn LA, Hufnagel RB. The peroxisomal disorder spectrum and Heimler syndrome: Deep phenotyping and review of the literature. AMERICAN JOURNAL OF MEDICAL GENETICS PART C-SEMINARS IN MEDICAL GENETICS 2020; 184:618-630. [PMID: 32866347 DOI: 10.1002/ajmg.c.31823] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 07/14/2020] [Accepted: 07/21/2020] [Indexed: 12/20/2022]
Abstract
The spectrum of peroxisomal disorders is wide and comprises individuals that die in the first year of life, as well as people with sensorineural hearing loss, retinal dystrophy and amelogenesis imperfecta. In this article, we describe three patients; two diagnosed with Heimler syndrome and a third one with a mild-intermediate phenotype. We arrived at these diagnoses by conducting complete ophthalmic (National Eye Institute), auditory (National Institute of Deafness and Other Communication Disorders), and dental (National Institute of Dental and Craniofacial Research) evaluations, as well as laboratory and genetic testing. Retinal degeneration with macular cystic changes, amelogenesis imperfecta, and sensorineural hearing loss were features shared by the three patients. Patients A and C had pathogenic variants in PEX1 and Patient B, in PEX6. Besides analyzing these cases, we review the literature regarding mild peroxisomal disorders, their pathophysiology, genetics, differential diagnosis, diagnostic methods, and management. We suggest that peroxisomal disorders are considered in every child with sensorineural hearing loss and retinal degeneration. These patients should have a dental evaluation to rule out amelogenesis imperfecta as well as audiologic examination and laboratory testing including peroxisomal biomarkers and genetic testing. Appropriate diagnosis can lead to better genetic counseling and management of the associated comorbidities.
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Affiliation(s)
- Malena Daich Varela
- Ophthalmic Genetics and Visual Function Branch, National Eye Institute, National Institutes of Health (NIH), Bethesda, Maryland, USA
| | - Priyam Jani
- National Institute of Dental and Craniofacial Research, NIH, Bethesda, Maryland, USA
| | - Wadih M Zein
- Ophthalmic Genetics and Visual Function Branch, National Eye Institute, National Institutes of Health (NIH), Bethesda, Maryland, USA
| | - Precilla D'Souza
- Office of the Clinical Director, National Human Genome Research Institute, NIH, Bethesda, Maryland, USA
| | - Lynne Wolfe
- Undiagnosed Diseases Program, Common Fund, NIH, Bethesda, Maryland, USA
| | - Jennifer Chisholm
- Audiology Unit, Otolaryngology Branch, National Institute on Deafness and Other Communication Disorders, NIH, Bethesda, Maryland, USA
| | - Christopher Zalewski
- Audiology Unit, Otolaryngology Branch, National Institute on Deafness and Other Communication Disorders, NIH, Bethesda, Maryland, USA
| | - David Adams
- Office of the Clinical Director, National Human Genome Research Institute, NIH, Bethesda, Maryland, USA.,Undiagnosed Diseases Program, Common Fund, NIH, Bethesda, Maryland, USA
| | - Blake M Warner
- National Institute of Dental and Craniofacial Research, NIH, Bethesda, Maryland, USA
| | - Laryssa A Huryn
- Ophthalmic Genetics and Visual Function Branch, National Eye Institute, National Institutes of Health (NIH), Bethesda, Maryland, USA
| | - Robert B Hufnagel
- Ophthalmic Genetics and Visual Function Branch, National Eye Institute, National Institutes of Health (NIH), Bethesda, Maryland, USA
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