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Burnight ER, Fenner BJ, Han IC, DeLuca AP, Whitmore SS, Bohrer LR, Andorf JL, Sohn EH, Mullins RF, Tucker BA, Stone EM. Demonstration of the pathogenicity of a common non-exomic mutation in ABCA4 using iPSC-derived retinal organoids and retrospective clinical data. Hum Mol Genet 2024; 33:1379-1390. [PMID: 37930186 PMCID: PMC11305681 DOI: 10.1093/hmg/ddad176] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 09/25/2023] [Accepted: 10/10/2023] [Indexed: 11/07/2023] Open
Abstract
Mutations in ABCA4 are the most common cause of Mendelian retinal disease. Clinical evaluation of this gene is challenging because of its extreme allelic diversity, the large fraction of non-exomic mutations, and the wide range of associated disease. We used patient-derived retinal organoids as well as DNA samples and clinical data from a large cohort of patients with ABCA4-associated retinal disease to investigate the pathogenicity of a variant in ABCA4 (IVS30 + 1321 A>G) that occurs heterozygously in 2% of Europeans. We found that this variant causes mis-splicing of the gene in photoreceptor cells such that the resulting protein contains 36 incorrect amino acids followed by a premature stop. We also investigated the phenotype of 10 patients with compound genotypes that included this mutation. Their median age of first vision loss was 39 years, which is in the mildest quintile of a large cohort of patients with ABCA4 disease. We conclude that the IVS30 + 1321 A>G variant can cause disease when paired with a sufficiently deleterious opposing allele in a sufficiently permissive genetic background.
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Affiliation(s)
- Erin R Burnight
- Institute for Vision Research, Carver College of Medicine, University of Iowa, 375 Newton Road, Iowa City, IA 52242, United States
- Department of Ophthalmology and Visual Sciences, Carver College of Medicine, University of Iowa, 200 Hawkins Drive, Iowa City, IA 52242, United States
| | - Beau J Fenner
- Institute for Vision Research, Carver College of Medicine, University of Iowa, 375 Newton Road, Iowa City, IA 52242, United States
- Department of Ophthalmology and Visual Sciences, Carver College of Medicine, University of Iowa, 200 Hawkins Drive, Iowa City, IA 52242, United States
| | - Ian C Han
- Institute for Vision Research, Carver College of Medicine, University of Iowa, 375 Newton Road, Iowa City, IA 52242, United States
- Department of Ophthalmology and Visual Sciences, Carver College of Medicine, University of Iowa, 200 Hawkins Drive, Iowa City, IA 52242, United States
| | - Adam P DeLuca
- Institute for Vision Research, Carver College of Medicine, University of Iowa, 375 Newton Road, Iowa City, IA 52242, United States
- Department of Ophthalmology and Visual Sciences, Carver College of Medicine, University of Iowa, 200 Hawkins Drive, Iowa City, IA 52242, United States
| | - S Scott Whitmore
- Institute for Vision Research, Carver College of Medicine, University of Iowa, 375 Newton Road, Iowa City, IA 52242, United States
- Department of Ophthalmology and Visual Sciences, Carver College of Medicine, University of Iowa, 200 Hawkins Drive, Iowa City, IA 52242, United States
| | - Laura R Bohrer
- Institute for Vision Research, Carver College of Medicine, University of Iowa, 375 Newton Road, Iowa City, IA 52242, United States
- Department of Ophthalmology and Visual Sciences, Carver College of Medicine, University of Iowa, 200 Hawkins Drive, Iowa City, IA 52242, United States
| | - Jeaneen L Andorf
- Institute for Vision Research, Carver College of Medicine, University of Iowa, 375 Newton Road, Iowa City, IA 52242, United States
- Department of Ophthalmology and Visual Sciences, Carver College of Medicine, University of Iowa, 200 Hawkins Drive, Iowa City, IA 52242, United States
| | - Elliott H Sohn
- Institute for Vision Research, Carver College of Medicine, University of Iowa, 375 Newton Road, Iowa City, IA 52242, United States
- Department of Ophthalmology and Visual Sciences, Carver College of Medicine, University of Iowa, 200 Hawkins Drive, Iowa City, IA 52242, United States
| | - Robert F Mullins
- Institute for Vision Research, Carver College of Medicine, University of Iowa, 375 Newton Road, Iowa City, IA 52242, United States
- Department of Ophthalmology and Visual Sciences, Carver College of Medicine, University of Iowa, 200 Hawkins Drive, Iowa City, IA 52242, United States
| | - Budd A Tucker
- Institute for Vision Research, Carver College of Medicine, University of Iowa, 375 Newton Road, Iowa City, IA 52242, United States
- Department of Ophthalmology and Visual Sciences, Carver College of Medicine, University of Iowa, 200 Hawkins Drive, Iowa City, IA 52242, United States
| | - Edwin M Stone
- Institute for Vision Research, Carver College of Medicine, University of Iowa, 375 Newton Road, Iowa City, IA 52242, United States
- Department of Ophthalmology and Visual Sciences, Carver College of Medicine, University of Iowa, 200 Hawkins Drive, Iowa City, IA 52242, United States
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Fenner BJ, Whitmore SS, DeLuca AP, Andorf JL, Daggett HT, Luse MA, Haefeli LM, Riley JB, Critser DB, Wilkinson ME, Dumitrescu AV, Drack AV, Boyce TM, Russell JF, Binkley EM, Sohn EH, Russell SR, Boldt HC, Mullins RF, Tucker BA, Scheetz TE, Han IC, Stone EM. A Retrospective Longitudinal Study of 460 Patients with ABCA4-Associated Retinal Disease. Ophthalmology 2024; 131:985-997. [PMID: 38309476 PMCID: PMC11398085 DOI: 10.1016/j.ophtha.2024.01.035] [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: 08/05/2023] [Revised: 01/17/2024] [Accepted: 01/26/2024] [Indexed: 02/05/2024] Open
Abstract
PURPOSE To investigate the distribution of genotypes and natural history of ABCA4-associated retinal disease in a large cohort of patients seen at a single institution. DESIGN Retrospective, single-institution cohort review. PARTICIPANTS Patients seen at the University of Iowa between November 1986 and August 2022 clinically suspected to have disease caused by sequence variations in ABCA4. METHODS DNA samples from participants were subjected to a tiered testing strategy progressing from allele-specific screening to whole genome sequencing. Charts were reviewed, and clinical data were tabulated. The pathogenic severity of the most common alleles was estimated by studying groups of patients who shared 1 allele. Groups of patients with shared genotypes were reviewed for evidence of modifying factor effects. MAIN OUTCOME MEASURES Age at first uncorrectable vision loss, best-corrected visual acuity, and the area of the I2e isopter of the Goldmann visual field. RESULTS A total of 460 patients from 390 families demonstrated convincing clinical features of ABCA4-associated retinal disease. Complete genotypes were identified in 399 patients, and partial genotypes were identified in 61. The median age at first vision loss was 16 years (range, 4-76 years). Two hundred sixty-five families (68%) harbored a unique genotype, and no more than 10 patients shared any single genotype. Review of the patients with shared genotypes revealed evidence of modifying factors that in several cases resulted in a > 15-year difference in age at first vision loss. Two hundred forty-one different alleles were identified among the members of this cohort, and 161 of these (67%) were found in only a single individual. CONCLUSIONS ABCA4-associated retinal disease ranges from a very severe photoreceptor disease with an onset before 5 years of age to a late-onset retinal pigment epithelium-based condition resembling pattern dystrophy. Modifying factors frequently impact the ABCA4 disease phenotype to a degree that is similar in magnitude to the detectable ABCA4 alleles themselves. It is likely that most patients in any cohort will harbor a unique genotype. The latter observations taken together suggest that patients' clinical findings in most cases will be more useful for predicting their clinical course than their genotype. FINANCIAL DISCLOSURE(S) Proprietary or commercial disclosure may be found in the Footnotes and Disclosures at the end of this article.
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Affiliation(s)
- Beau J Fenner
- The University of Iowa Institute for Vision Research and the Department of Ophthalmology and Visual Sciences, Carver College of Medicine, The University of Iowa, Iowa City, Iowa; Singapore National Eye Centre; Singapore Eye Research Institute; and Ophthalmology and Visual Sciences Academic Clinical Programme, SingHealth Duke-NUS Academic Medical Centre, Duke-NUS Graduate Medical School, Singapore, Republic of Singapore
| | - S Scott Whitmore
- The University of Iowa Institute for Vision Research and the Department of Ophthalmology and Visual Sciences, Carver College of Medicine, The University of Iowa, Iowa City, Iowa
| | - Adam P DeLuca
- The University of Iowa Institute for Vision Research and the Department of Ophthalmology and Visual Sciences, Carver College of Medicine, The University of Iowa, Iowa City, Iowa
| | - Jean L Andorf
- The University of Iowa Institute for Vision Research and the Department of Ophthalmology and Visual Sciences, Carver College of Medicine, The University of Iowa, Iowa City, Iowa
| | - Heather T Daggett
- The University of Iowa Institute for Vision Research and the Department of Ophthalmology and Visual Sciences, Carver College of Medicine, The University of Iowa, Iowa City, Iowa
| | - Meagan A Luse
- The University of Iowa Institute for Vision Research and the Department of Ophthalmology and Visual Sciences, Carver College of Medicine, The University of Iowa, Iowa City, Iowa
| | - Lorena M Haefeli
- The University of Iowa Institute for Vision Research and the Department of Ophthalmology and Visual Sciences, Carver College of Medicine, The University of Iowa, Iowa City, Iowa
| | - Janet B Riley
- The University of Iowa Institute for Vision Research and the Department of Ophthalmology and Visual Sciences, Carver College of Medicine, The University of Iowa, Iowa City, Iowa
| | - Douglas B Critser
- The University of Iowa Institute for Vision Research and the Department of Ophthalmology and Visual Sciences, Carver College of Medicine, The University of Iowa, Iowa City, Iowa
| | - Mark E Wilkinson
- The University of Iowa Institute for Vision Research and the Department of Ophthalmology and Visual Sciences, Carver College of Medicine, The University of Iowa, Iowa City, Iowa
| | - Alina V Dumitrescu
- The University of Iowa Institute for Vision Research and the Department of Ophthalmology and Visual Sciences, Carver College of Medicine, The University of Iowa, Iowa City, Iowa
| | - Arlene V Drack
- The University of Iowa Institute for Vision Research and the Department of Ophthalmology and Visual Sciences, Carver College of Medicine, The University of Iowa, Iowa City, Iowa
| | - Timothy M Boyce
- The University of Iowa Institute for Vision Research and the Department of Ophthalmology and Visual Sciences, Carver College of Medicine, The University of Iowa, Iowa City, Iowa
| | - Jonathan F Russell
- The University of Iowa Institute for Vision Research and the Department of Ophthalmology and Visual Sciences, Carver College of Medicine, The University of Iowa, Iowa City, Iowa
| | - Elaine M Binkley
- The University of Iowa Institute for Vision Research and the Department of Ophthalmology and Visual Sciences, Carver College of Medicine, The University of Iowa, Iowa City, Iowa
| | - Elliott H Sohn
- The University of Iowa Institute for Vision Research and the Department of Ophthalmology and Visual Sciences, Carver College of Medicine, The University of Iowa, Iowa City, Iowa
| | - Stephen R Russell
- The University of Iowa Institute for Vision Research and the Department of Ophthalmology and Visual Sciences, Carver College of Medicine, The University of Iowa, Iowa City, Iowa
| | - H Culver Boldt
- The University of Iowa Institute for Vision Research and the Department of Ophthalmology and Visual Sciences, Carver College of Medicine, The University of Iowa, Iowa City, Iowa
| | - Robert F Mullins
- The University of Iowa Institute for Vision Research and the Department of Ophthalmology and Visual Sciences, Carver College of Medicine, The University of Iowa, Iowa City, Iowa
| | - Budd A Tucker
- The University of Iowa Institute for Vision Research and the Department of Ophthalmology and Visual Sciences, Carver College of Medicine, The University of Iowa, Iowa City, Iowa
| | - Todd E Scheetz
- The University of Iowa Institute for Vision Research and the Department of Ophthalmology and Visual Sciences, Carver College of Medicine, The University of Iowa, Iowa City, Iowa
| | - Ian C Han
- The University of Iowa Institute for Vision Research and the Department of Ophthalmology and Visual Sciences, Carver College of Medicine, The University of Iowa, Iowa City, Iowa
| | - Edwin M Stone
- The University of Iowa Institute for Vision Research and the Department of Ophthalmology and Visual Sciences, Carver College of Medicine, The University of Iowa, Iowa City, Iowa.
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Mullin NK, Voigt AP, Flamme-Wiese MJ, Liu X, Riker MJ, Varzavand K, Stone EM, Tucker BA, Mullins RF. Multimodal single-cell analysis of nonrandom heteroplasmy distribution in human retinal mitochondrial disease. JCI Insight 2023; 8:e165937. [PMID: 37289546 PMCID: PMC10443808 DOI: 10.1172/jci.insight.165937] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Accepted: 06/02/2023] [Indexed: 06/10/2023] Open
Abstract
Variants within the high copy number mitochondrial genome (mtDNA) can disrupt organelle function and lead to severe multisystem disease. The wide range of manifestations observed in patients with mitochondrial disease results from varying fractions of abnormal mtDNA molecules in different cells and tissues, a phenomenon termed heteroplasmy. However, the landscape of heteroplasmy across cell types within tissues and its influence on phenotype expression in affected patients remains largely unexplored. Here, we identify nonrandom distribution of a pathogenic mtDNA variant across a complex tissue using single-cell RNA-Seq, mitochondrial single-cell ATAC sequencing, and multimodal single-cell sequencing. We profiled the transcriptome, chromatin accessibility state, and heteroplasmy in cells from the eyes of a patient with mitochondrial encephalopathy, lactic acidosis, and stroke-like episodes (MELAS) and from healthy control donors. Utilizing the retina as a model for complex multilineage tissues, we found that the proportion of the pathogenic m.3243A>G allele was neither evenly nor randomly distributed across diverse cell types. All neuroectoderm-derived neural cells exhibited a high percentage of the mutant variant. However, a subset of mesoderm-derived lineage, namely the vasculature of the choroid, was near homoplasmic for the WT allele. Gene expression and chromatin accessibility profiles of cell types with high and low proportions of m.3243A>G implicate mTOR signaling in the cellular response to heteroplasmy. We further found by multimodal single-cell sequencing of retinal pigment epithelial cells that a high proportion of the pathogenic mtDNA variant was associated with transcriptionally and morphologically abnormal cells. Together, these findings show the nonrandom nature of mitochondrial variant partitioning in human mitochondrial disease and underscore its implications for mitochondrial disease pathogenesis and treatment.
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Affiliation(s)
- Nathaniel K. Mullin
- University of Iowa Institute for Vision Research, Iowa City, Iowa, USA
- Department of Ophthalmology and Visual Sciences and
- Medical Scientist Training Program, University of Iowa, Iowa City, Iowa, USA
| | - Andrew P. Voigt
- University of Iowa Institute for Vision Research, Iowa City, Iowa, USA
- Department of Ophthalmology and Visual Sciences and
- Medical Scientist Training Program, University of Iowa, Iowa City, Iowa, USA
| | - Miles J. Flamme-Wiese
- University of Iowa Institute for Vision Research, Iowa City, Iowa, USA
- Department of Ophthalmology and Visual Sciences and
| | - Xiuying Liu
- University of Iowa Institute for Vision Research, Iowa City, Iowa, USA
- Department of Ophthalmology and Visual Sciences and
| | - Megan J. Riker
- University of Iowa Institute for Vision Research, Iowa City, Iowa, USA
- Department of Ophthalmology and Visual Sciences and
| | - Katayoun Varzavand
- University of Iowa Institute for Vision Research, Iowa City, Iowa, USA
- Department of Ophthalmology and Visual Sciences and
| | - Edwin M. Stone
- University of Iowa Institute for Vision Research, Iowa City, Iowa, USA
- Department of Ophthalmology and Visual Sciences and
| | - Budd A. Tucker
- University of Iowa Institute for Vision Research, Iowa City, Iowa, USA
- Department of Ophthalmology and Visual Sciences and
| | - Robert F. Mullins
- University of Iowa Institute for Vision Research, Iowa City, Iowa, USA
- Department of Ophthalmology and Visual Sciences and
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Abstract
PURPOSE OF REVIEW Stargardt disease is the most common inherited macular dystrophy but has a wide clinical spectrum, and several inherited macular dystrophies have phenotypic similarities that can make clinical diagnosis challenging. This review seeks to highlight key clinical and multimodal imaging features to aid clinicians in accurate diagnosis. RECENT FINDINGS Multimodal imaging has provided additional information to aid in the diagnosis of Stargardt disease and its masquerades. These data from multimodal imaging are important to correlate with findings from clinical examination to help support the clinical diagnosis or guide molecular investigations. SUMMARY This review highlights the key similarities and differences, in history, clinical examination and multimodal imaging, to help distinguish between Stargardt disease and other macular dystrophies. These findings can help direct a focused molecular analysis for accurate diagnosis, which is critical in the era of gene and stem cell therapies.
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Affiliation(s)
- Aaron M Ricca
- Institute for Vision Research, Department of Ophthalmology and Visual Sciences, Carver College of Medicine, University of Iowa, Iowa City, Iowa, USA
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