1
|
Chen S, Lo CH, Liu Z, Wang Q, Ning K, Li T, Sun Y. Base editing correction of OCRL in Lowe syndrome: ABE-mediated functional rescue in patient-derived fibroblasts. Hum Mol Genet 2024; 33:1142-1151. [PMID: 38557732 DOI: 10.1093/hmg/ddae045] [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: 12/18/2023] [Revised: 02/27/2024] [Accepted: 03/04/2024] [Indexed: 04/04/2024] Open
Abstract
Lowe syndrome, a rare X-linked multisystem disorder presenting with major abnormalities in the eyes, kidneys, and central nervous system, is caused by mutations in OCRL gene (NG_008638.1). Encoding an inositol polyphosphate 5-phosphatase, OCRL catalyzes the hydrolysis of PI(4,5)P2 into PI4P. There are no effective targeted treatments for Lowe syndrome. Here, we demonstrate a novel gene therapy for Lowe syndrome in patient fibroblasts using an adenine base editor (ABE) that can efficiently correct pathogenic point mutations. We show that ABE8e-NG-based correction of a disease-causing mutation in a Lowe patient-derived fibroblast line containing R844X mutation in OCRL gene, restores OCRL expression at mRNA and protein levels. It also restores cellular abnormalities that are hallmarks of OCRL dysfunction, including defects in ciliogenesis, microtubule anchoring, α-actinin distribution, and F-actin network. The study indicates that ABE-mediated gene therapy is a feasible treatment for Lowe syndrome, laying the foundation for therapeutic application of ABE in the currently incurable disease.
Collapse
Affiliation(s)
- Siyu Chen
- Department of Ophthalmology, Stanford University School of Medicine, 1651 Page Mill Road, Rm 2220, Palo Alto, CA 94304, United States
| | - Chien-Hui Lo
- Department of Ophthalmology, Stanford University School of Medicine, 1651 Page Mill Road, Rm 2220, Palo Alto, CA 94304, United States
| | - Zhiquan Liu
- Department of Ophthalmology, Stanford University School of Medicine, 1651 Page Mill Road, Rm 2220, Palo Alto, CA 94304, United States
| | - Qing Wang
- Department of Ophthalmology, Stanford University School of Medicine, 1651 Page Mill Road, Rm 2220, Palo Alto, CA 94304, United States
| | - Ke Ning
- Department of Ophthalmology, Stanford University School of Medicine, 1651 Page Mill Road, Rm 2220, Palo Alto, CA 94304, United States
| | - Tingting Li
- Department of Ophthalmology, Stanford University School of Medicine, 1651 Page Mill Road, Rm 2220, Palo Alto, CA 94304, United States
- Department of Ophthalmology, Shanghai East Hospital, Tongji University School of Medicine, 150 Jimo Road, Pudong district, Shanghai 200120, China
| | - Yang Sun
- Department of Ophthalmology, Stanford University School of Medicine, 1651 Page Mill Road, Rm 2220, Palo Alto, CA 94304, United States
- Palo Alto Veterans Administration, 3801 Miranda Avenue, Palo Alto, CA 94304, United States
| |
Collapse
|
2
|
Yi H, Yun Y, Choi WH, Hwang HY, Cha JH, Seok H, Song JJ, Lee JH, Lee SY, Kim D. CRISPR-based editing strategies to rectify EYA1 complex genomic rearrangement linked to haploinsufficiency. MOLECULAR THERAPY. NUCLEIC ACIDS 2024; 35:102199. [PMID: 38766525 PMCID: PMC11101721 DOI: 10.1016/j.omtn.2024.102199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Accepted: 04/21/2024] [Indexed: 05/22/2024]
Abstract
Pathogenic structure variations (SVs) are associated with various types of cancer and rare genetic diseases. Recent studies have used Cas9 nuclease with paired guide RNAs (gRNAs) to generate targeted chromosomal rearrangements, focusing on producing fusion proteins that cause cancer, whereas research on precision genome editing for rectifying SVs is limited. In this study, we identified a novel complex genomic rearrangement (CGR), specifically an EYA1 inversion with a deletion, implicated in branchio-oto-renal/branchio-oto syndrome. To address this, two CRISPR-based approaches were tested. First, we used Cas9 nuclease and paired gRNAs tailored to the patient's genome. The dual CRISPR-Cas9 system induced efficient correction of paracentric inversion in patient-derived fibroblast, and effectively restored the expression of EYA1 mRNA and protein, along with its transcriptional activity required to regulate the target gene expression. Additionally, we used CRISPR activation (CRISPRa), which leads to the upregulation of EYA1 mRNA expression in patient-derived fibroblasts. Moreover, CRISPRa significantly improved EYA1 protein expression and transcriptional activity essential for target gene expression. This suggests that CRISPRa-based gene therapies could offer substantial translational potential for approximately 70% of disease-causing EYA1 variants responsible for haploinsufficiency. Our findings demonstrate the potential of CRISPR-guided genome editing for correcting SVs, including those with EYA1 CGR linked to haploinsufficiency.
Collapse
Affiliation(s)
- Hwalin Yi
- Department of Precision Medicine, Sungkyunkwan University School of Medicine, Suwon 16419, Republic of Korea
| | - Yejin Yun
- Department of Otorhinolaryngology, Seoul National University College of Medicine, Seoul National University Hospital, Seoul 03080, South Korea
| | - Won Hoon Choi
- Department of Otorhinolaryngology, Seoul National University College of Medicine, Seoul National University Hospital, Seoul 03080, South Korea
| | - Hye-Yeon Hwang
- Department of Precision Medicine, Sungkyunkwan University School of Medicine, Suwon 16419, Republic of Korea
| | - Ju Hyuen Cha
- Department of Otorhinolaryngology, Seoul National University College of Medicine, Seoul National University Hospital, Seoul 03080, South Korea
| | - Heeyoung Seok
- Department of Transdisciplinary Research and Collaboration, Genomics Core Facility, Biomedical Research Institute, Seoul National University Hospital, Seoul 03080, South Korea
| | - Jae-Jin Song
- Department of Otorhinolaryngology, Seoul National University College of Medicine, Seoul National University Bundang Hospital, Seongnam, South Korea
| | - Jun Ho Lee
- Department of Otorhinolaryngology, Seoul National University College of Medicine, Seoul National University Hospital, Seoul 03080, South Korea
| | - Sang-Yeon Lee
- Department of Otorhinolaryngology, Seoul National University College of Medicine, Seoul National University Hospital, Seoul 03080, South Korea
- Department of Genomic Medicine, Seoul National University Hospital, Seoul 03080, Republic of Korea
- Sensory Organ Research Institute, Seoul National University Medical Research Center, Seoul 03080, Republic of Korea
| | - Daesik Kim
- Department of Precision Medicine, Sungkyunkwan University School of Medicine, Suwon 16419, Republic of Korea
| |
Collapse
|
3
|
Yun Y, Lee SY. Updates on Genetic Hearing Loss: From Diagnosis to Targeted Therapies. J Audiol Otol 2024; 28:88-92. [PMID: 38695053 PMCID: PMC11065549 DOI: 10.7874/jao.2024.00157] [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: 02/22/2024] [Revised: 03/21/2024] [Accepted: 04/04/2024] [Indexed: 05/05/2024] Open
Abstract
Sensorineural hearing loss (SNHL) is the most common sensory disorder, with a high Mendelian genetic contribution. Considering the genotypic and phenotypic heterogeneity of SNHL, the advent of next-generation sequencing technologies has revolutionized knowledge on its genomic architecture. Nonetheless, the conventional application of panel and exome sequencing in real-world practice is being challenged by the emerging need to explore the diagnostic capability of whole-genome sequencing, which enables the detection of both noncoding and structural variations. Small molecules and gene therapies represent good examples of how breakthroughs in genetic understanding can be translated into targeted therapies for SNHL. For example, targeted small molecules have been used to ameliorate autoinflammatory hearing loss caused by gain-of-function variants of NLRP3 and inner ear proteinopathy with OSBPL2 variants underlying dysfunctional autophagy. Strikingly, the successful outcomes of the first-in-human trial of OTOF gene therapy highlighted its potential in the treatment of various forms of genetic hearing loss. clustered regularly interspaced short palindromic repeats (CRISPR)-based technologies are currently being developed for site-specific genome editing to treat human genetic disorders. These advancements have led to an era of genotype- and mechanism-based precision medicine in SNHL practice.
Collapse
Affiliation(s)
- Yejin Yun
- Department of Otorhinolaryngology, Seoul National University College of Medicine, Seoul National University Hospital, Seoul, Korea
| | - Sang-Yeon Lee
- Department of Otorhinolaryngology, Seoul National University College of Medicine, Seoul National University Hospital, Seoul, Korea
- Department of Genomic Medicine, Seoul National University Hospital, Seoul, Korea
- Sensory Organ Research Institute, Seoul National University Medical Research Center, Seoul, Korea
| |
Collapse
|
4
|
Pan X, Li Y, Huang P, Staecker H, He M. Extracellular vesicles for developing targeted hearing loss therapy. J Control Release 2024; 366:460-478. [PMID: 38182057 DOI: 10.1016/j.jconrel.2023.12.050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Revised: 12/19/2023] [Accepted: 12/28/2023] [Indexed: 01/07/2024]
Abstract
Substantial efforts have been made for local administration of small molecules or biologics in treating hearing loss diseases caused by either trauma, genetic mutations, or drug ototoxicity. Recently, extracellular vesicles (EVs) naturally secreted from cells have drawn increasing attention on attenuating hearing impairment from both preclinical studies and clinical studies. Highly emerging field utilizing diverse bioengineering technologies for developing EVs as the bioderived therapeutic materials, along with artificial intelligence (AI)-based targeting toolkits, shed the light on the unique properties of EVs specific to inner ear delivery. This review will illuminate such exciting research field from fundamentals of hearing protective functions of EVs to biotechnology advancement and potential clinical translation of functionalized EVs. Specifically, the advancements in assessing targeting ligands using AI algorithms are systematically discussed. The overall translational potential of EVs is reviewed in the context of auditory sensing system for developing next generation gene therapy.
Collapse
Affiliation(s)
- Xiaoshu Pan
- Department of Pharmaceutics, College of Pharmacy, University of Florida, Gainesville, Florida 32610, United States
| | - Yanjun Li
- Department of Medicinal Chemistry, Center for Natural Products, Drug Discovery and Development, University of Florida, Gainesville, Florida 32610, United States
| | - Peixin Huang
- Department of Otolaryngology, Head and Neck Surgery, University of Kansas School of Medicine, Kansas City, Kansas 66160, United States
| | - Hinrich Staecker
- Department of Otolaryngology, Head and Neck Surgery, University of Kansas School of Medicine, Kansas City, Kansas 66160, United States.
| | - Mei He
- Department of Pharmaceutics, College of Pharmacy, University of Florida, Gainesville, Florida 32610, United States.
| |
Collapse
|
5
|
Lye J, Delaney DS, Leith FK, Sardesai VS, McLenachan S, Chen FK, Atlas MD, Wong EYM. Recent Therapeutic Progress and Future Perspectives for the Treatment of Hearing Loss. Biomedicines 2023; 11:3347. [PMID: 38137568 PMCID: PMC10741758 DOI: 10.3390/biomedicines11123347] [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: 11/16/2023] [Revised: 12/06/2023] [Accepted: 12/11/2023] [Indexed: 12/24/2023] Open
Abstract
Up to 1.5 billion people worldwide suffer from various forms of hearing loss, with an additional 1.1 billion people at risk from various insults such as increased consumption of recreational noise-emitting devices and ageing. The most common type of hearing impairment is sensorineural hearing loss caused by the degeneration or malfunction of cochlear hair cells or spiral ganglion nerves in the inner ear. There is currently no cure for hearing loss. However, emerging frontier technologies such as gene, drug or cell-based therapies offer hope for an effective cure. In this review, we discuss the current therapeutic progress for the treatment of hearing loss. We describe and evaluate the major therapeutic approaches being applied to hearing loss and summarize the key trials and studies.
Collapse
Affiliation(s)
- Joey Lye
- Hearing Therapeutics, Ear Science Institute Australia, Nedlands, WA 6009, Australia; (J.L.); (D.S.D.); (F.K.L.); (V.S.S.); (M.D.A.)
- Centre for Ear Sciences, Medical School, The University of Western Australia, Nedlands, WA 6009, Australia
| | - Derek S. Delaney
- Hearing Therapeutics, Ear Science Institute Australia, Nedlands, WA 6009, Australia; (J.L.); (D.S.D.); (F.K.L.); (V.S.S.); (M.D.A.)
- Faculty of Health Sciences, Curtin Health Innovation Research Institute, Curtin University, Bentley, WA 6102, Australia
| | - Fiona K. Leith
- Hearing Therapeutics, Ear Science Institute Australia, Nedlands, WA 6009, Australia; (J.L.); (D.S.D.); (F.K.L.); (V.S.S.); (M.D.A.)
- Centre for Ear Sciences, Medical School, The University of Western Australia, Nedlands, WA 6009, Australia
| | - Varda S. Sardesai
- Hearing Therapeutics, Ear Science Institute Australia, Nedlands, WA 6009, Australia; (J.L.); (D.S.D.); (F.K.L.); (V.S.S.); (M.D.A.)
| | - Samuel McLenachan
- Ocular Tissue Engineering Laboratory, Lions Eye Institute, Nedlands, WA 6009, Australia; (S.M.); (F.K.C.)
- Centre for Ophthalmology and Visual Sciences, The University of Western Australia, Nedlands, WA 6009, Australia
| | - Fred K. Chen
- Ocular Tissue Engineering Laboratory, Lions Eye Institute, Nedlands, WA 6009, Australia; (S.M.); (F.K.C.)
- Centre for Ophthalmology and Visual Sciences, The University of Western Australia, Nedlands, WA 6009, Australia
- Vitroretinal Surgery, Royal Perth Hospital, Perth, WA 6000, Australia
- Ophthalmology, Department of Surgery, University of Melbourne, East Melbourne, VIC 3002, Australia
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, East Melbourne, VIC 3002, Australia
| | - Marcus D. Atlas
- Hearing Therapeutics, Ear Science Institute Australia, Nedlands, WA 6009, Australia; (J.L.); (D.S.D.); (F.K.L.); (V.S.S.); (M.D.A.)
- Centre for Ear Sciences, Medical School, The University of Western Australia, Nedlands, WA 6009, Australia
| | - Elaine Y. M. Wong
- Hearing Therapeutics, Ear Science Institute Australia, Nedlands, WA 6009, Australia; (J.L.); (D.S.D.); (F.K.L.); (V.S.S.); (M.D.A.)
- Centre for Ear Sciences, Medical School, The University of Western Australia, Nedlands, WA 6009, Australia
- Curtin Medical School, Faculty of Health Sciences, Curtin University, Bentley, WA 6102, Australia
| |
Collapse
|
6
|
Ivanchenko MV, Hathaway DM, Mulhall EM, Booth KT, Wang M, Peters CW, Klein AJ, Chen X, Li Y, György B, Corey DP. PCDH15 Dual-AAV Gene Therapy for Deafness and Blindness in Usher Syndrome Type 1F. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.09.566447. [PMID: 38014037 PMCID: PMC10680673 DOI: 10.1101/2023.11.09.566447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
Usher syndrome type 1F (USH1F), resulting from mutations in the protocadherin-15 (PCDH15) gene, is characterized by congenital lack of hearing and balance, and progressive blindness in the form of retinitis pigmentosa. In this study, we explore a novel approach for USH1F gene therapy, exceeding the single AAV packaging limit by employing a dual adeno-associated virus (AAV) strategy to deliver the full-length PCDH15 coding sequence. We demonstrate the efficacy of this strategy in mouse USH1F models, effectively restoring hearing and balance in these mice. Importantly, our approach also proves successful in expressing PCDH15 in clinically relevant retinal models, including human retinal organoids and non-human primate retina, showing efficient targeting of photoreceptors and proper protein expression in the calyceal processes. This research represents a major step toward advancing gene therapy for USH1F and the multiple challenges of hearing, balance, and vision impairment.
Collapse
|
7
|
Totten DJ, Booth KTA, Mosier KM, Cumpston EC, Whitted C, Okechuku V, Koontz NA, Nelson RF. Human cochlear diffusion from the cerebrospinal fluid space with gadolinium contrast. Mol Ther 2023; 31:2566-2569. [PMID: 37582360 PMCID: PMC10492018 DOI: 10.1016/j.ymthe.2023.08.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 07/01/2023] [Accepted: 08/01/2023] [Indexed: 08/17/2023] Open
Affiliation(s)
- Douglas J Totten
- Department of Otolaryngology, Head & Neck Surgery, Indiana University, Indianapolis. IN 46202, USA
| | - Kevin T A Booth
- Department of Otolaryngology, Head & Neck Surgery, Indiana University, Indianapolis. IN 46202, USA; Department of Medical & Molecular Genetics, Indiana University, Indianapolis, IN 46202, USA
| | - Kristine M Mosier
- Department of Otolaryngology, Head & Neck Surgery, Indiana University, Indianapolis. IN 46202, USA; Department of Radiology & Imaging Sciences, Indiana University, Indianapolis, IN 46202, USA
| | - Evan C Cumpston
- Department of Otolaryngology, Head & Neck Surgery, Indiana University, Indianapolis. IN 46202, USA
| | - Cody Whitted
- School of Medicine, Indiana University, IN 46202, USA
| | - Vanessa Okechuku
- School of Medicine, Meharry Medical College, Nashville, TN 37208, USA
| | - Nicholas A Koontz
- Department of Otolaryngology, Head & Neck Surgery, Indiana University, Indianapolis. IN 46202, USA; Department of Radiology & Imaging Sciences, Indiana University, Indianapolis, IN 46202, USA
| | - Rick F Nelson
- Department of Otolaryngology, Head & Neck Surgery, Indiana University, Indianapolis. IN 46202, USA; Department of Neurological Surgery, Indiana University, Indianapolis, IN 46202, USA.
| |
Collapse
|