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Patil SV, Kaipa BR, Ranshing S, Sundaresan Y, Millar JC, Nagarajan B, Kiehlbauch C, Zhang Q, Jain A, Searby CC, Scheetz TE, Clark AF, Sheffield VC, Zode GS. Lentiviral mediated delivery of CRISPR/Cas9 reduces intraocular pressure in a mouse model of myocilin glaucoma. Sci Rep 2024; 14:6958. [PMID: 38521856 PMCID: PMC10960846 DOI: 10.1038/s41598-024-57286-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Accepted: 03/16/2024] [Indexed: 03/25/2024] Open
Abstract
Mutations in myocilin (MYOC) are the leading known genetic cause of primary open-angle glaucoma, responsible for about 4% of all cases. Mutations in MYOC cause a gain-of-function phenotype in which mutant myocilin accumulates in the endoplasmic reticulum (ER) leading to ER stress and trabecular meshwork (TM) cell death. Therefore, knocking out myocilin at the genome level is an ideal strategy to permanently cure the disease. We have previously utilized CRISPR/Cas9 genome editing successfully to target MYOC using adenovirus 5 (Ad5). However, Ad5 is not a suitable vector for clinical use. Here, we sought to determine the efficacy of adeno-associated viruses (AAVs) and lentiviruses (LVs) to target the TM. First, we examined the TM tropism of single-stranded (ss) and self-complimentary (sc) AAV serotypes as well as LV expressing GFP via intravitreal (IVT) and intracameral (IC) injections. We observed that LV_GFP expression was more specific to the TM injected via the IVT route. IC injections of Trp-mutant scAAV2 showed a prominent expression of GFP in the TM. However, robust GFP expression was also observed in the ciliary body and retina. We next constructed lentiviral particles expressing Cas9 and guide RNA (gRNA) targeting MYOC (crMYOC) and transduction of TM cells stably expressing mutant myocilin with LV_crMYOC significantly reduced myocilin accumulation and its associated chronic ER stress. A single IVT injection of LV_crMYOC in Tg-MYOCY437H mice decreased myocilin accumulation in TM and reduced elevated IOP significantly. Together, our data indicates, LV_crMYOC targets MYOC gene editing in TM and rescues a mouse model of myocilin-associated glaucoma.
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Affiliation(s)
- Shruti V Patil
- Department of Pharmacology and Neuroscience, North Texas Eye Research Institute, University of North Texas Health Science Center at Fort Worth, Fort Worth, TX, 76107, USA
| | - Balasankara Reddy Kaipa
- Department of Ophthalmology and Center for Translational Vision Research, University of California, 829 Health Sciences Rd, Irvine, CA, 92617, USA
| | - Sujata Ranshing
- Department of Pharmacology and Neuroscience, North Texas Eye Research Institute, University of North Texas Health Science Center at Fort Worth, Fort Worth, TX, 76107, USA
| | - Yogapriya Sundaresan
- Department of Ophthalmology and Center for Translational Vision Research, University of California, 829 Health Sciences Rd, Irvine, CA, 92617, USA
| | - J Cameron Millar
- Department of Pharmacology and Neuroscience, North Texas Eye Research Institute, University of North Texas Health Science Center at Fort Worth, Fort Worth, TX, 76107, USA
| | - Bhavani Nagarajan
- Department of Pharmacology and Neuroscience, North Texas Eye Research Institute, University of North Texas Health Science Center at Fort Worth, Fort Worth, TX, 76107, USA
| | - Charles Kiehlbauch
- Department of Pharmacology and Neuroscience, North Texas Eye Research Institute, University of North Texas Health Science Center at Fort Worth, Fort Worth, TX, 76107, USA
| | - Qihong Zhang
- Department of Pediatrics, University of Iowa, Iowa City, IA, 52242, USA
| | - Ankur Jain
- Department of Pediatrics, University of Iowa, Iowa City, IA, 52242, USA
| | - Charles C Searby
- Department of Pediatrics, University of Iowa, Iowa City, IA, 52242, USA
| | - Todd E Scheetz
- Department of Ophthalmology and Visual Sciences, University of Iowa, Iowa City, IA, 52242, USA
| | - Abbot F Clark
- Department of Pharmacology and Neuroscience, North Texas Eye Research Institute, University of North Texas Health Science Center at Fort Worth, Fort Worth, TX, 76107, USA
| | - Val C Sheffield
- Department of Pediatrics, University of Iowa, Iowa City, IA, 52242, USA
- Department of Ophthalmology and Visual Sciences, University of Iowa, Iowa City, IA, 52242, USA
| | - Gulab S Zode
- Department of Ophthalmology and Center for Translational Vision Research, University of California, 829 Health Sciences Rd, Irvine, CA, 92617, USA.
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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:S0161-6420(24)00096-4. [PMID: 38309476 DOI: 10.1016/j.ophtha.2024.01.035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [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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Patil SV, Kaipa BR, Ranshing S, Sundaresan Y, Millar JC, Nagarajan B, Kiehlbauch C, Zhang Q, Jain A, Searby CC, Scheetz TE, Clark AF, Sheffield VC, Zode GS. Lentiviral mediated delivery of CRISPR/Cas9 reduces intraocular pressure in a mouse model of myocilin glaucoma. Res Sq 2023:rs.3.rs-3740880. [PMID: 38196579 PMCID: PMC10775399 DOI: 10.21203/rs.3.rs-3740880/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2024]
Abstract
Mutations in myocilin (MYOC) are the leading known genetic cause of primary open-angle glaucoma, responsible for about 4% of all cases. Mutations in MYOC cause a gain-of-function phenotype in which mutant myocilin accumulates in the endoplasmic reticulum (ER) leading to ER stress and trabecular meshwork (TM) cell death. Therefore, knocking out myocilin at the genome level is an ideal strategy to permanently cure the disease. We have previously utilized CRISPR/Cas9 genome editing successfully to target MYOC using adenovirus 5 (Ad5). However, Ad5 is not a suitable vector for clinical use. Here, we sought to determine the efficacy of adeno-associated viruses (AAVs) and lentiviruses (LVs) to target the TM. First, we examined the TM tropism of single-stranded (ss) and self-complimentary (sc) AAV serotypes as well as LV expressing GFP via intravitreal (IVT) and intracameral (IC) injections. We observed that LV_GFP expression was more specific to the TM injected via the IVT route. IC injections of Trp-mutant scAAV2 showed a prominent expression of GFP in the TM. However, robust GFP expression was also observed in the ciliary body and retina. We next constructed lentiviral particles expressing Cas9 and guide RNA (gRNA) targeting MYOC (crMYOC) and transduction of TM cells stably expressing mutant myocilin with LV_crMYOC significantly reduced myocilin accumulation and its associated chronic ER stress. A single IVT injection of LV_crMYOC in Tg-MYOCY437H mice decreased myocilin accumulation in TM and reduced elevated IOP significantly. Together, our data indicates, LV_crMYOC targets MYOC gene editing in TM and rescues a mouse model of myocilin-associated glaucoma.
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Affiliation(s)
- Shruti V Patil
- University of North Texas Health Science Center at Fort Worth
| | | | - Sujata Ranshing
- University of North Texas Health Science Center at Fort Worth
| | | | | | | | | | | | | | | | | | - Abbot F Clark
- University of North Texas Health Science Center at Fort Worth
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DeLuca AP, Whitmore SS, Tatro NJ, Andorf JL, Faga BP, Faga LA, Colins MM, Luse MA, Fenner BJ, Stone EM, Scheetz TE. Using Goldmann Visual Field Volume to Track Disease Progression in Choroideremia. Ophthalmol Sci 2023; 3:100397. [PMID: 38025158 PMCID: PMC10630671 DOI: 10.1016/j.xops.2023.100397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/18/2023] [Revised: 08/31/2023] [Accepted: 09/06/2023] [Indexed: 12/01/2023]
Abstract
Purpose Choroideremia is an X-linked choroidopathy caused by pathogenic variants in the CHM gene. It is characterized by the early appearance of multiple scotomas in the peripheral visual field that spread and coalesce, usually sparing central vision until late in the disease. These features make quantitative monitoring of visual decline particularly challenging. Here, we describe a novel computational approach to convert Goldmann visual field (GVF) data into quantitative volumetric measurements. With this approach, we analyzed visual field loss in a longitudinal, retrospective cohort of patients with choroideremia. Design Single-center, retrospective, cohort study. Participants We analyzed data from 238 clinic visits of 56 molecularly-confirmed male patients with choroideremia from 41 families (range, 1-27 visits per patient). Patients had a median follow up of 4 years (range, 0-56 years) with an age range of 5 to 76 years at the time of their visits. Methods Clinical data from molecularly-confirmed patients with choroideremia, including GVF data, were included for analysis. Goldmann visual field records were traced using a tablet-based application, and the 3-dimensional hill of vision was interpolated for each trace. This procedure allowed quantification of visual field loss from data collected over decades with differing protocols, including different or incomplete isopters. Visual acuity (VA) data were collected and converted to logarithm of the minimum angle of resolution values. A delayed exponential mixed-effects model was used to evaluate the loss of visual field volume over time. Main Outcome Measures Visual acuity and GVF volume. Results The estimated mean age at disease onset was 12.6 years (standard deviation, 9.1 years; 95% quantile interval, 6.5-36.4 years). The mean field volume loss was 6.8% per year (standard deviation, 4.5%; 95% quantile interval, 1.9%-18.8%) based on exponential modeling. Field volume was more strongly correlated between eyes (r2 = 0.935) than best-corrected VA (r2 = 0.285). Conclusions Volumetric analysis of GVF data enabled quantification of peripheral visual function in patients with choroideremia and evaluation of disease progression. The methods presented here may facilitate the analysis of historical GVF data from patients with inherited retinal disease and other diseases associated with visual field loss. This work informs the creation of appropriate outcome measures in choroideremia therapeutic trials, particularly in trial designs. Financial Disclosures Proprietary or commercial disclosure may be found in the Footnotes and Disclosures at the end of this article.
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Affiliation(s)
- Adam P. DeLuca
- The University of Iowa Institute for Vision Research & Department of Ophthalmology and Visual Sciences, Carver College of Medicine, The University of Iowa, Iowa City, Iowa
| | - S. Scott Whitmore
- The University of Iowa Institute for Vision Research & Department of Ophthalmology and Visual Sciences, Carver College of Medicine, The University of Iowa, Iowa City, Iowa
| | - Nicole J. Tatro
- The University of Iowa Institute for Vision Research & Department of Ophthalmology and Visual Sciences, Carver College of Medicine, The University of Iowa, Iowa City, Iowa
| | - Jeaneen L. Andorf
- The University of Iowa Institute for Vision Research & Department of Ophthalmology and Visual Sciences, Carver College of Medicine, The University of Iowa, Iowa City, Iowa
| | - Ben P. Faga
- The University of Iowa Institute for Vision Research & Department of Ophthalmology and Visual Sciences, Carver College of Medicine, The University of Iowa, Iowa City, Iowa
| | - Laurel A. Faga
- The University of Iowa Institute for Vision Research & Department of Ophthalmology and Visual Sciences, Carver College of Medicine, The University of Iowa, Iowa City, Iowa
| | - Malia M. Colins
- The University of Iowa Institute for Vision Research & 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 & Department of Ophthalmology and Visual Sciences, Carver College of Medicine, The University of Iowa, Iowa City, Iowa
| | - Beau J. Fenner
- The University of Iowa Institute for Vision Research & Department of Ophthalmology and Visual Sciences, Carver College of Medicine, The University of Iowa, Iowa City, Iowa
- Department of Medical Retina, Singapore National Eye Centre, Singapore
- Singapore Eye Research Institute, Singapore
- Ophthalmology and Visual Sciences Academic Clinical Programme, SingHealth Duke-NUS Academic Medical Centre, Duke-NUS Graduate Medical School, Singapore
| | - Edwin M. Stone
- The University of Iowa Institute for Vision Research & 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 & Department of Ophthalmology and Visual Sciences, Carver College of Medicine, The University of Iowa, Iowa City, Iowa
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5
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Boese EA, Alward WLM, Kwon YH, Roos BR, Stone EM, Scheetz TE, Fingert JH. Thrombospondin Mutations and Patients With Primary Congenital Glaucoma in a United States Population. J Glaucoma 2023; 32:e156-e160. [PMID: 37327471 DOI: 10.1097/ijg.0000000000002254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 06/02/2023] [Indexed: 06/18/2023]
Abstract
Mutations in the thrombospondin 1 ( THBS1 ) gene have been previously reported in primary congenital glaucoma (PCG) pedigrees that exhibit autosomal dominant inheritance with low penetrance. We sought to determine the role of THBS1 mutations in a cohort of 20 patients with PCG and 362 normal controls from Iowa using a combination of Sanger sequencing and whole exome sequencing. We detected 16 different THBS1 variants, including 4 rare, nonsynonymous variants (p.Thr611Met, p.Asn708Lys, p.Gln1089His, and p.Glu1166Lys). However, none of these variants were judged to be disease-causing mutations based on: 1) prevalence in cases and controls from Iowa, 2) prevalence in the public database gnomAD, 3) mutation analysis algorithms, and 4) THBS1 DNA sequence conservation. These results indicate THBS1 mutations are not a common cause of PCG in patients from Iowa and may be a rare cause of PCG overall.
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Affiliation(s)
- Erin A Boese
- Institute for Vision Research
- Department of Ophthalmology and Visual Sciences, Carver College of Medicine, University of Iowa, Iowa City, IA
| | - Wallace L M Alward
- Institute for Vision Research
- Department of Ophthalmology and Visual Sciences, Carver College of Medicine, University of Iowa, Iowa City, IA
| | - Young H Kwon
- Institute for Vision Research
- Department of Ophthalmology and Visual Sciences, Carver College of Medicine, University of Iowa, Iowa City, IA
| | - Ben R Roos
- Institute for Vision Research
- Department of Ophthalmology and Visual Sciences, Carver College of Medicine, University of Iowa, Iowa City, IA
| | - Edwin M Stone
- Institute for Vision Research
- Department of Ophthalmology and Visual Sciences, Carver College of Medicine, University of Iowa, Iowa City, IA
| | - Todd E Scheetz
- Institute for Vision Research
- Department of Ophthalmology and Visual Sciences, Carver College of Medicine, University of Iowa, Iowa City, IA
| | - John H Fingert
- Institute for Vision Research
- Department of Ophthalmology and Visual Sciences, Carver College of Medicine, University of Iowa, Iowa City, IA
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Tejan-Kamara AZ, Boese EA, Pouw AE, Sears NC, Roos BR, Stone EM, Scheetz TE, Fingert JH. Mutations in EFEMP1 in Patients with Juvenile Open-Angle Glaucoma. Ophthalmol Glaucoma 2023; 6:668-670. [PMID: 37224920 DOI: 10.1016/j.ogla.2023.05.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 04/27/2023] [Accepted: 05/16/2023] [Indexed: 05/26/2023]
Affiliation(s)
- Aminatta Z Tejan-Kamara
- Institute for Vision Research, University of Iowa, Iowa City, Iowa; Des Moines University, Des Moines, Iowa
| | - Erin A Boese
- Institute for Vision Research, University of Iowa, Iowa City, Iowa; Department of Ophthalmology and Visual Sciences, Carver College of Medicine, University of Iowa, Iowa City, Iowa
| | - Andrew E Pouw
- Institute for Vision Research, University of Iowa, Iowa City, Iowa; Department of Ophthalmology and Visual Sciences, Carver College of Medicine, University of Iowa, Iowa City, Iowa
| | - Nathan C Sears
- Institute for Vision Research, University of Iowa, Iowa City, Iowa; Department of Ophthalmology and Visual Sciences, Carver College of Medicine, University of Iowa, Iowa City, Iowa
| | - Ben R Roos
- Institute for Vision Research, University of Iowa, Iowa City, Iowa; Department of Ophthalmology and Visual Sciences, Carver College of Medicine, University of Iowa, Iowa City, Iowa
| | - Edwin M Stone
- Institute for Vision Research, University of Iowa, Iowa City, Iowa; Department of Ophthalmology and Visual Sciences, Carver College of Medicine, University of Iowa, Iowa City, Iowa
| | - Todd E Scheetz
- Institute for Vision Research, University of Iowa, Iowa City, Iowa; Department of Ophthalmology and Visual Sciences, Carver College of Medicine, University of Iowa, Iowa City, Iowa
| | - John H Fingert
- Institute for Vision Research, University of Iowa, Iowa City, Iowa; Department of Ophthalmology and Visual Sciences, Carver College of Medicine, University of Iowa, Iowa City, Iowa.
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Voigt AP, Mullin NK, Navratil EM, Flamme-Wiese MJ, Lin LC, Scheetz TE, Han IC, Stone EM, Tucker BA, Mullins RF. Gene Expression Within a Human Choroidal Neovascular Membrane Using Spatial Transcriptomics. Invest Ophthalmol Vis Sci 2023; 64:40. [PMID: 37878301 PMCID: PMC10615143 DOI: 10.1167/iovs.64.13.40] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 10/07/2023] [Indexed: 10/26/2023] Open
Abstract
Purpose Macular neovascularization is a relatively common and potentially visually devastating complication of age-related macular degeneration. In macular neovascularization, pathologic angiogenesis can originate from either the choroid or the retina, but we have limited understanding of how different cell types become dysregulated in this dynamic process. Methods To study how gene expression is altered in focal areas of pathology, we performed spatial RNA sequencing on a human donor eye with macular neovascularization as well as a healthy control donor. We performed differential expression to identify genes enriched within the area of macular neovascularization and used deconvolution algorithms to predict the originating cell type of these dysregulated genes. Results Within the area of neovascularization, endothelial cells demonstrated increased expression of genes related to Rho family GTPase signaling and integrin signaling. Likewise, VEGF and TGFB1 were identified as potential upstream regulators that could drive the observed gene expression changes produced by endothelial and retinal pigment epithelium cells in the macular neovascularization donor. These spatial gene expression profiles were compared to previous single-cell gene expression experiments in human age-related macular degeneration as well as a model of laser-induced neovascularization in mice. As a secondary aim, we investigated regional gene expression patterns within the macular neural retina and between the macular and peripheral choroid. Conclusions Overall, this study spatially analyzes gene expression across the retina, retinal pigment epithelium, and choroid in health and describes a set of candidate molecules that become dysregulated in macular neovascularization.
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Affiliation(s)
- Andrew P. Voigt
- Department of Ophthalmology and Visual Sciences, the University of Iowa Carver College of Medicine, Iowa City, Iowa, United States
- Institute for Vision Research, the University of Iowa, Iowa City, Iowa, United States
| | - Nathaniel K. Mullin
- Department of Ophthalmology and Visual Sciences, the University of Iowa Carver College of Medicine, Iowa City, Iowa, United States
- Institute for Vision Research, the University of Iowa, Iowa City, Iowa, United States
| | - Emma M. Navratil
- Department of Ophthalmology and Visual Sciences, the University of Iowa Carver College of Medicine, Iowa City, Iowa, United States
- Institute for Vision Research, the University of Iowa, Iowa City, Iowa, United States
| | - Miles J. Flamme-Wiese
- Department of Ophthalmology and Visual Sciences, the University of Iowa Carver College of Medicine, Iowa City, Iowa, United States
- Institute for Vision Research, the University of Iowa, Iowa City, Iowa, United States
| | - Li-Chun Lin
- University of Iowa Neuroscience Institute, the University of Iowa Carver College of Medicine, Iowa City, Iowa, United States
| | - Todd E. Scheetz
- Department of Ophthalmology and Visual Sciences, the University of Iowa Carver College of Medicine, Iowa City, Iowa, United States
- Institute for Vision Research, the University of Iowa, Iowa City, Iowa, United States
| | - Ian C. Han
- Department of Ophthalmology and Visual Sciences, the University of Iowa Carver College of Medicine, Iowa City, Iowa, United States
- Institute for Vision Research, the University of Iowa, Iowa City, Iowa, United States
| | - Edwin M. Stone
- Department of Ophthalmology and Visual Sciences, the University of Iowa Carver College of Medicine, Iowa City, Iowa, United States
- Institute for Vision Research, the University of Iowa, Iowa City, Iowa, United States
| | - Budd A. Tucker
- Department of Ophthalmology and Visual Sciences, the University of Iowa Carver College of Medicine, Iowa City, Iowa, United States
- Institute for Vision Research, the University of Iowa, Iowa City, Iowa, United States
| | - Robert F. Mullins
- Department of Ophthalmology and Visual Sciences, the University of Iowa Carver College of Medicine, Iowa City, Iowa, United States
- Institute for Vision Research, the University of Iowa, Iowa City, Iowa, United States
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8
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Boese EA, Drack AV, Roos BR, Alward WLM, Tollefson MR, Schnieders MJ, Scheetz TE, Boldt HC, Stone EM, Fingert JH. GJA3 Genetic Variation and Autosomal Dominant Congenital Cataracts and Glaucoma Following Cataract Surgery. JAMA Ophthalmol 2023; 141:872-879. [PMID: 37589989 PMCID: PMC10436186 DOI: 10.1001/jamaophthalmol.2023.3535] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Accepted: 06/16/2023] [Indexed: 08/18/2023]
Abstract
Importance The p.Asp67Tyr genetic variant in the GJA3 gene is responsible for congenital cataracts in a family with a high incidence of glaucoma following cataract surgery. Objective To describe the clinical features of a family with a strong association between congenital cataracts and glaucoma following cataract surgery secondary to a genetic variant in the GJA3 gene (NM_021954.4:c.199G>T, p.Asp67Tyr). Design, Setting, and Participants This was a retrospective, observational, case series, genetic association study from the University of Iowa spanning 61 years. Examined were the ophthalmic records from 1961 through 2022 of the family members of a 4-generation pedigree with autosomal dominant congenital cataracts. Main Outcomes and Measures Frequency of glaucoma following cataract surgery and postoperative complications among family members with congenital cataract due to the p.Asp67Tyr GJA3 genetic variant. Results Medical records were available from 11 of 12 family members (7 male [63.6%]) with congenital cataract with a mean (SD) follow-up of 30 (21.7) years (range, 0.2-61 years). Eight of 9 patients with congenital cataracts developed glaucoma, and 8 of 8 patients who had cataract surgery at age 2 years or younger developed glaucoma following cataract surgery. The only family member with congenital cataracts who did not develop glaucoma had delayed cataract surgery until 12 and 21 years of age. Five of 11 family members (45.5%) had retinal detachments after cataract extraction and vitrectomy. No patients developed retinal detachments after prophylactic 360-degree endolaser. Conclusions and Relevance The GJA3 genetic variant, p.Asp67Tyr, was identified in a 4-generation congenital cataract pedigree from Iowa. This report suggests that patients with congenital cataract due to some GJA3 genetic variants may be at especially high risk for glaucoma following cataract surgery. Retinal detachments after cataract extraction in the first 2 years of life were also common in this family, and prophylactic retinal endolaser may be indicated at the time of surgery.
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Affiliation(s)
- Erin A. Boese
- Department of Ophthalmology and Visual Sciences, Carver College of Medicine, University of Iowa, Iowa City
- Institute for Vision Research, Carver College of Medicine, University of Iowa, Iowa City
| | - Arlene V. Drack
- Department of Ophthalmology and Visual Sciences, Carver College of Medicine, University of Iowa, Iowa City
- Institute for Vision Research, Carver College of Medicine, University of Iowa, Iowa City
| | - Benjamin R. Roos
- Department of Ophthalmology and Visual Sciences, Carver College of Medicine, University of Iowa, Iowa City
- Institute for Vision Research, Carver College of Medicine, University of Iowa, Iowa City
| | - Wallace L. M. Alward
- Department of Ophthalmology and Visual Sciences, Carver College of Medicine, University of Iowa, Iowa City
- Institute for Vision Research, Carver College of Medicine, University of Iowa, Iowa City
| | - Mallory R. Tollefson
- Institute for Vision Research, Carver College of Medicine, University of Iowa, Iowa City
- Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City
| | - Michael J. Schnieders
- Institute for Vision Research, Carver College of Medicine, University of Iowa, Iowa City
- Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City
| | - Todd E. Scheetz
- Department of Ophthalmology and Visual Sciences, Carver College of Medicine, University of Iowa, Iowa City
- Institute for Vision Research, Carver College of Medicine, University of Iowa, Iowa City
| | - H. Culver Boldt
- Department of Ophthalmology and Visual Sciences, Carver College of Medicine, University of Iowa, Iowa City
- Institute for Vision Research, Carver College of Medicine, University of Iowa, Iowa City
| | - Edwin M. Stone
- Department of Ophthalmology and Visual Sciences, Carver College of Medicine, University of Iowa, Iowa City
- Institute for Vision Research, Carver College of Medicine, University of Iowa, Iowa City
| | - John H. Fingert
- Department of Ophthalmology and Visual Sciences, Carver College of Medicine, University of Iowa, Iowa City
- Institute for Vision Research, Carver College of Medicine, University of Iowa, Iowa City
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9
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Voigt AP, Mullin NK, Navratil EM, Flamme-Wiese MJ, Lin LC, Scheetz TE, Han IC, Stone EM, Tucker BA, Mullins RF. GENE EXPRESSION WITHIN A HUMAN CHOROIDAL NEOVASCULAR MEMBRANE USING SPATIAL TRANSCRIPTOMICS. bioRxiv 2023:2023.06.16.544770. [PMID: 37398429 PMCID: PMC10312719 DOI: 10.1101/2023.06.16.544770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Macular neovascularization is a relatively common and potentially visually devastating complication of age-related macular degeneration. In macular neovascularization, pathologic angiogenesis can originate from either the choroid or the retina, but we have limited understanding of how different cell types become dysregulated in this dynamic process. In this study, we performed spatial RNA sequencing on a human donor eye with macular neovascularization as well as a healthy control donor. We identified genes enriched within the area of macular neovascularization and used deconvolution algorithms to predict the originating cell type of these dysregulated genes. Within the area of neovascularization, endothelial cells were predicted to increase expression of genes related to Rho family GTPase signaling and integrin signaling. Likewise, VEGF and TGFB1 were identified as potential upstream regulators that could drive the observed gene expression changes produced by endothelial and retinal pigment epithelium cells in the macular neovascularization donor. These spatial gene expression profiles were compared to previous single-cell gene expression experiments in human age-related macular degeneration as well as a model of laser-induced neovascularization in mice. As a secondary aim, we also investigated spatial gene expression patterns within the macular neural retina and between the macular and peripheral choroid. We recapitulated previously described regional-specific gene expression patterns across both tissues. Overall, this study spatially analyzes gene expression across the retina, retinal pigment epithelium, and choroid in health and describes a set of candidate molecules that become dysregulated in macular neovascularization.
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Affiliation(s)
- Andrew P. Voigt
- Department of Ophthalmology and Visual Sciences, the University of Iowa Carver College of Medicine, Iowa City, IA, 52242
- Institute for Vision Research, the University of Iowa, Iowa City, IA, 52242
| | - Nathaniel K. Mullin
- Department of Ophthalmology and Visual Sciences, the University of Iowa Carver College of Medicine, Iowa City, IA, 52242
- Institute for Vision Research, the University of Iowa, Iowa City, IA, 52242
| | - Emma M. Navratil
- Department of Ophthalmology and Visual Sciences, the University of Iowa Carver College of Medicine, Iowa City, IA, 52242
- Institute for Vision Research, the University of Iowa, Iowa City, IA, 52242
| | - Miles J. Flamme-Wiese
- Department of Ophthalmology and Visual Sciences, the University of Iowa Carver College of Medicine, Iowa City, IA, 52242
- Institute for Vision Research, the University of Iowa, Iowa City, IA, 52242
| | - Li-Chun Lin
- University of Iowa Neuroscience Institute, the University of Iowa Carver College of Medicine, Iowa City, IA, 52242
| | - Todd E. Scheetz
- Department of Ophthalmology and Visual Sciences, the University of Iowa Carver College of Medicine, Iowa City, IA, 52242
- Institute for Vision Research, the University of Iowa, Iowa City, IA, 52242
| | - Ian C. Han
- Department of Ophthalmology and Visual Sciences, the University of Iowa Carver College of Medicine, Iowa City, IA, 52242
- Institute for Vision Research, the University of Iowa, Iowa City, IA, 52242
| | - Edwin M. Stone
- Department of Ophthalmology and Visual Sciences, the University of Iowa Carver College of Medicine, Iowa City, IA, 52242
- Institute for Vision Research, the University of Iowa, Iowa City, IA, 52242
| | - Budd A. Tucker
- Department of Ophthalmology and Visual Sciences, the University of Iowa Carver College of Medicine, Iowa City, IA, 52242
- Institute for Vision Research, the University of Iowa, Iowa City, IA, 52242
| | - Robert F. Mullins
- Department of Ophthalmology and Visual Sciences, the University of Iowa Carver College of Medicine, Iowa City, IA, 52242
- Institute for Vision Research, the University of Iowa, Iowa City, IA, 52242
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10
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Voigt AP, Mullin NK, Mulfaul K, Lozano LP, Wiley LA, Flamme-Wiese MJ, Boese EA, Han IC, Scheetz TE, Stone EM, Tucker BA, Mullins RF. Choroidal endothelial and macrophage gene expression in atrophic and neovascular macular degeneration. Hum Mol Genet 2022; 31:2406-2423. [PMID: 35181781 PMCID: PMC9307320 DOI: 10.1093/hmg/ddac043] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2021] [Revised: 01/22/2022] [Accepted: 02/06/2022] [Indexed: 11/22/2022] Open
Abstract
The human choroid is a heterogeneous, highly vascular connective tissue that dysfunctions in age-related macular degeneration (AMD). In this study, we performed single-cell RNA sequencing on 21 human choroids, 11 of which were derived from donors with early atrophic or neovascular AMD. Using this large donor cohort, we identified new gene expression signatures and immunohistochemically characterized discrete populations of resident macrophages, monocytes/inflammatory macrophages and dendritic cells. These three immune populations demonstrated unique expression patterns for AMD genetic risk factors, with dendritic cells possessing the highest expression of the neovascular AMD-associated MMP9 gene. Additionally, we performed trajectory analysis to model transcriptomic changes across the choroidal vasculature, and we identified expression signatures for endothelial cells from choroidal arterioles and venules. Finally, we performed differential expression analysis between control, early atrophic AMD, and neovascular AMD samples, and we observed that early atrophic AMD samples had high expression of SPARCL1, a gene that has been shown to increase in response to endothelial damage. Likewise, neovascular endothelial cells harbored gene expression changes consistent with endothelial cell damage and demonstrated increased expression of the sialomucins CD34 and ENCM, which were also observed at the protein level within neovascular membranes. Overall, this study characterizes the molecular features of new populations of choroidal endothelial cells and mononuclear phagocytes in a large cohort of AMD and control human donors.
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Affiliation(s)
- Andrew P Voigt
- Department of Ophthalmology and Visual Sciences, The University of Iowa Carver College of Medicine, Iowa City, IA 52242, USA
- Institute for Vision Research, The University of Iowa, Iowa City, IA 52242, USA
| | - Nathaniel K Mullin
- Department of Ophthalmology and Visual Sciences, The University of Iowa Carver College of Medicine, Iowa City, IA 52242, USA
- Institute for Vision Research, The University of Iowa, Iowa City, IA 52242, USA
| | - Kelly Mulfaul
- Department of Ophthalmology and Visual Sciences, The University of Iowa Carver College of Medicine, Iowa City, IA 52242, USA
- Institute for Vision Research, The University of Iowa, Iowa City, IA 52242, USA
| | - Lola P Lozano
- Department of Ophthalmology and Visual Sciences, The University of Iowa Carver College of Medicine, Iowa City, IA 52242, USA
- Institute for Vision Research, The University of Iowa, Iowa City, IA 52242, USA
| | - Luke A Wiley
- Department of Ophthalmology and Visual Sciences, The University of Iowa Carver College of Medicine, Iowa City, IA 52242, USA
- Institute for Vision Research, The University of Iowa, Iowa City, IA 52242, USA
| | - Miles J Flamme-Wiese
- Department of Ophthalmology and Visual Sciences, The University of Iowa Carver College of Medicine, Iowa City, IA 52242, USA
- Institute for Vision Research, The University of Iowa, Iowa City, IA 52242, USA
| | - Erin A Boese
- Department of Ophthalmology and Visual Sciences, The University of Iowa Carver College of Medicine, Iowa City, IA 52242, USA
- Institute for Vision Research, The University of Iowa, Iowa City, IA 52242, USA
| | - Ian C Han
- Department of Ophthalmology and Visual Sciences, The University of Iowa Carver College of Medicine, Iowa City, IA 52242, USA
- Institute for Vision Research, The University of Iowa, Iowa City, IA 52242, USA
| | - Todd E Scheetz
- Department of Ophthalmology and Visual Sciences, The University of Iowa Carver College of Medicine, Iowa City, IA 52242, USA
- Institute for Vision Research, The University of Iowa, Iowa City, IA 52242, USA
| | - Edwin M Stone
- Department of Ophthalmology and Visual Sciences, The University of Iowa Carver College of Medicine, Iowa City, IA 52242, USA
- Institute for Vision Research, The University of Iowa, Iowa City, IA 52242, USA
| | - Budd A Tucker
- Department of Ophthalmology and Visual Sciences, The University of Iowa Carver College of Medicine, Iowa City, IA 52242, USA
- Institute for Vision Research, The University of Iowa, Iowa City, IA 52242, USA
| | - Robert F Mullins
- Department of Ophthalmology and Visual Sciences, The University of Iowa Carver College of Medicine, Iowa City, IA 52242, USA
- Institute for Vision Research, The University of Iowa, Iowa City, IA 52242, USA
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11
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Wiley LA, Binkley EM, DeLuca AP, Workalemahu G, Tatro NJ, Luse MA, Kennedy EL, Folk JC, Scheetz TE, Ballas ZK, Tucker BA, Mullins RF, Han IC, Stone EM. AUTOIMMUNE RETINOPATHY MIMICKING HERITABLE RETINAL DEGENERATION IN A PATIENT WITH COMMON VARIABLE IMMUNE DEFICIENCY. Retin Cases Brief Rep 2022; 16:111-117. [PMID: 31764884 PMCID: PMC9211761 DOI: 10.1097/icb.0000000000000941] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
PURPOSE 1) To describe a case of autoimmune retinopathy mimicking heritable photoreceptor degeneration in a patient with common variable immune deficiency and 2) to investigate the humoral and cell-mediated branches of the immune system in this patient to better understand the mechanism of immune-mediated photoreceptor damage in this disease. METHODS Retrospective chart review with evaluation of multimodal imaging, genotype analysis, and investigation of circulating autoantibodies and T-cell response to retinal antigens. RESULTS A 40-year-old woman with bilateral, progressive vision loss was referred for evaluation of a possible inherited retinal degeneration. She was found to have asymmetric peripheral visual field constriction, cystoid macular edema, vitreous cells, and bone spicule-like pigmentary changes in both eyes. An extensive workup for underlying infectious or inflammatory causes was unrevealing, and molecular analysis for heritable retinal degeneration failed to identify a plausible disease-causing genotype. Screening for antiretinal antibodies showed the presence of multiple antiretinal antibodies, consistent with a diagnosis of autoimmune retinopathy. Immunologic workup demonstrated markedly decreased levels of serum IgA and IgG, consistent with common variable immune deficiency. T-cells isolated from the patient showed increased proliferation when stimulated with human retinal proteins, supporting a role for both cell- and humoral-mediated autoimmunity. Treatment with mycophenolate mofetil and intravenous immunoglobin therapy slowed the progression of disease and resulted in preservation of her central vision. CONCLUSION Autoimmune retinopathy can be seen in common variable immune deficiency and has clinical findings similar to heritable photoreceptor degeneration. Both the humoral and cellular immune responses are involved in the pathophysiology. Immune modulatory therapy has stabilized the disease course in this patient and may play an important role in the management of autoimmune retinopathy.
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Affiliation(s)
- Luke A. Wiley
- Institute for Vision Research, University of Iowa, Iowa City, IA
- Department of Ophthalmology and Visual Sciences, University of Iowa, Iowa City, IA
| | - Elaine M. Binkley
- Institute for Vision Research, University of Iowa, Iowa City, IA
- Department of Ophthalmology and Visual Sciences, University of Iowa, Iowa City, IA
| | - Adam P. DeLuca
- Institute for Vision Research, University of Iowa, Iowa City, IA
- Department of Ophthalmology and Visual Sciences, University of Iowa, Iowa City, IA
| | - Grefachew Workalemahu
- Institute for Vision Research, University of Iowa, Iowa City, IA
- Department of Ophthalmology and Visual Sciences, University of Iowa, Iowa City, IA
| | - Nicole J. Tatro
- Institute for Vision Research, University of Iowa, Iowa City, IA
- Department of Ophthalmology and Visual Sciences, University of Iowa, Iowa City, IA
| | - Meagan A. Luse
- Institute for Vision Research, University of Iowa, Iowa City, IA
- Department of Ophthalmology and Visual Sciences, University of Iowa, Iowa City, IA
| | - Elizabeth L. Kennedy
- Institute for Vision Research, University of Iowa, Iowa City, IA
- Department of Ophthalmology and Visual Sciences, University of Iowa, Iowa City, IA
| | - James C. Folk
- Department of Ophthalmology and Visual Sciences, University of Iowa, Iowa City, IA
| | - Todd E. Scheetz
- Institute for Vision Research, University of Iowa, Iowa City, IA
- Department of Ophthalmology and Visual Sciences, University of Iowa, Iowa City, IA
| | - Zuhair K. Ballas
- Department of Internal Medicine, Carver College of Medicine, University of Iowa, Iowa City, IA
| | - Budd A. Tucker
- Institute for Vision Research, University of Iowa, Iowa City, IA
- Department of Ophthalmology and Visual Sciences, University of Iowa, Iowa City, IA
| | - Robert F. Mullins
- Institute for Vision Research, University of Iowa, Iowa City, IA
- Department of Ophthalmology and Visual Sciences, University of Iowa, Iowa City, IA
| | - Ian C. Han
- Institute for Vision Research, University of Iowa, Iowa City, IA
- Department of Ophthalmology and Visual Sciences, University of Iowa, Iowa City, IA
| | - Edwin M. Stone
- Institute for Vision Research, University of Iowa, Iowa City, IA
- Department of Ophthalmology and Visual Sciences, University of Iowa, Iowa City, IA
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12
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Mullin NK, Anfinson KR, Riker MJ, Wieland KL, Tatro NJ, Scheetz TE, Mullins RF, Stone EM, Tucker BA. Sensitive quantification of m.3243A>G mutational proportion in non-retinal tissues and its relationship with visual symptoms. Hum Mol Genet 2021; 31:775-782. [PMID: 34590675 DOI: 10.1093/hmg/ddab289] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 09/22/2021] [Accepted: 09/24/2021] [Indexed: 12/13/2022] Open
Abstract
The m.3243A>G mutation in the mitochondrial genome commonly causes retinal degeneration in patients with maternally inherited diabetes and deafness (MIDD) and mitochondrial encephalopathy, lactic acidosis, and stroke-like episodes (MELAS). Like other mitochondrial mutations, m.3243A>G is inherited from the mother with a variable proportion of wild type and mutant mitochondrial genomes in different cells. The mechanism by which the m.3243A>G variant in each tissue relates to the manifestation of disease phenotype is not fully understood. Using a digital PCR assay we found that the % m.3243G in skin derived dermal fibroblasts was positively correlated with that of blood from the same individual. The % m.3243G detected in fibroblast cultures remained constant over multiple passages and was negatively correlated with mtDNA copy number. Although the % m.3243G present in blood was not correlated with severity of vision loss, as quantified by Goldmann visual field, a significant negative correlation between % m.3243G and the age of onset of visual symptoms was detected. Together, these results indicate that precise measurement of % m.3243G in clinically accessible tissues such as skin and blood may yield information relevant to the management of retinal m.3243A>G associated disease.
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Affiliation(s)
- Nathaniel K Mullin
- University of Iowa Institute for Vision Research, Iowa City, IA, 52242, United States
| | - Kristin R Anfinson
- University of Iowa Institute for Vision Research, Iowa City, IA, 52242, United States
| | - Megan J Riker
- University of Iowa Institute for Vision Research, Iowa City, IA, 52242, United States
| | - Kelsey L Wieland
- University of Iowa Institute for Vision Research, Iowa City, IA, 52242, United States
| | - Nicole J Tatro
- University of Iowa Institute for Vision Research, Iowa City, IA, 52242, United States
| | - Todd E Scheetz
- University of Iowa Institute for Vision Research, Iowa City, IA, 52242, United States
| | - Robert F Mullins
- University of Iowa Institute for Vision Research, Iowa City, IA, 52242, United States
| | - Edwin M Stone
- University of Iowa Institute for Vision Research, Iowa City, IA, 52242, United States
| | - Budd A Tucker
- University of Iowa Institute for Vision Research, Iowa City, IA, 52242, United States
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13
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van der Heide C, Goar W, Meyer KJ, Alward WLM, Boese EA, Sears NC, Roos BR, Kwon YH, DeLuca AP, Siggs OM, Gonzaga-Jauregui C, Sheffield VC, Wang K, Stone EM, Mullins RF, Anderson MG, Fan BJ, Ritch R, Craig JE, Wiggs JL, Scheetz TE, Fingert JH. Exome-based investigation of the genetic basis of human pigmentary glaucoma. BMC Genomics 2021; 22:477. [PMID: 34174832 PMCID: PMC8235805 DOI: 10.1186/s12864-021-07782-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 06/07/2021] [Indexed: 11/18/2022] Open
Abstract
Background Glaucoma is a leading cause of visual disability and blindness. Release of iris pigment within the eye, pigment dispersion syndrome (PDS), can lead to one type of glaucoma known as pigmentary glaucoma. PDS has a genetic component, however, the genes involved with this condition are largely unknown. We sought to discover genes that cause PDS by testing cohorts of patients and controls for mutations using a tiered analysis of exome data. Results Our primary analysis evaluated melanosome-related genes that cause dispersion of iris pigment in mice (TYRP1, GPNMB, LYST, DCT, and MITF). We identified rare mutations, but they were not statistically enriched in PDS patients. Our secondary analyses examined PMEL (previously linked with PDS), MRAP, and 19 other genes. Four MRAP mutations were identified in PDS cases but not in controls (p = 0.016). Immunohistochemical analysis of human donor eyes revealed abundant MRAP protein in the iris, the source of pigment in PDS. However, analysis of MRAP in additional cohorts (415 cases and 1645 controls) did not support an association with PDS. We also did not confirm a link between PMEL and PDS in our cohorts due to lack of reported mutations and similar frequency of the variants in PDS patients as in control subjects. Conclusions We did not detect a statistical enrichment of mutations in melanosome-related genes in human PDS patients and we found conflicting data about the likely pathogenicity of MRAP mutations. PDS may have a complex genetic basis that is not easily unraveled with exome analyses. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07782-0.
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Affiliation(s)
- Carly van der Heide
- Department of Ophthalmology and Visual Sciences, Carver College of Medicine, 3111B Medical Education and Research Facility, University of Iowa, 375 Newton Road, Iowa City, IA52245, USA.,Institute for Vision Research, University of Iowa, Iowa City, IA, USA.,Department of Molecular Physiology and Biophysics, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Wes Goar
- Department of Ophthalmology and Visual Sciences, Carver College of Medicine, 3111B Medical Education and Research Facility, University of Iowa, 375 Newton Road, Iowa City, IA52245, USA.,Institute for Vision Research, University of Iowa, Iowa City, IA, USA
| | - Kacie J Meyer
- Institute for Vision Research, University of Iowa, Iowa City, IA, USA.,Department of Molecular Physiology and Biophysics, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Wallace L M Alward
- Department of Ophthalmology and Visual Sciences, Carver College of Medicine, 3111B Medical Education and Research Facility, University of Iowa, 375 Newton Road, Iowa City, IA52245, USA.,Institute for Vision Research, University of Iowa, Iowa City, IA, USA
| | - Erin A Boese
- Department of Ophthalmology and Visual Sciences, Carver College of Medicine, 3111B Medical Education and Research Facility, University of Iowa, 375 Newton Road, Iowa City, IA52245, USA.,Institute for Vision Research, University of Iowa, Iowa City, IA, USA
| | - Nathan C Sears
- Department of Ophthalmology and Visual Sciences, Carver College of Medicine, 3111B Medical Education and Research Facility, University of Iowa, 375 Newton Road, Iowa City, IA52245, USA.,Institute for Vision Research, University of Iowa, Iowa City, IA, USA
| | - Ben R Roos
- Department of Ophthalmology and Visual Sciences, Carver College of Medicine, 3111B Medical Education and Research Facility, University of Iowa, 375 Newton Road, Iowa City, IA52245, USA.,Institute for Vision Research, University of Iowa, Iowa City, IA, USA
| | - Young H Kwon
- Department of Ophthalmology and Visual Sciences, Carver College of Medicine, 3111B Medical Education and Research Facility, University of Iowa, 375 Newton Road, Iowa City, IA52245, USA.,Institute for Vision Research, University of Iowa, Iowa City, IA, USA
| | - Adam P DeLuca
- Department of Ophthalmology and Visual Sciences, Carver College of Medicine, 3111B Medical Education and Research Facility, University of Iowa, 375 Newton Road, Iowa City, IA52245, USA.,Institute for Vision Research, University of Iowa, Iowa City, IA, USA
| | - Owen M Siggs
- Department of Ophthalmology, Flinders Medical Centre, Adelaide, South Australia, Australia.,Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
| | | | - Val C Sheffield
- Department of Ophthalmology and Visual Sciences, Carver College of Medicine, 3111B Medical Education and Research Facility, University of Iowa, 375 Newton Road, Iowa City, IA52245, USA.,Institute for Vision Research, University of Iowa, Iowa City, IA, USA.,Department of Pediatrics, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Kai Wang
- Institute for Vision Research, University of Iowa, Iowa City, IA, USA.,Department of Biostatistics, College of Public Health, University of Iowa, Iowa City, Iowa, USA
| | - Edwin M Stone
- Department of Ophthalmology and Visual Sciences, Carver College of Medicine, 3111B Medical Education and Research Facility, University of Iowa, 375 Newton Road, Iowa City, IA52245, USA.,Institute for Vision Research, University of Iowa, Iowa City, IA, USA
| | - Robert F Mullins
- Department of Ophthalmology and Visual Sciences, Carver College of Medicine, 3111B Medical Education and Research Facility, University of Iowa, 375 Newton Road, Iowa City, IA52245, USA.,Institute for Vision Research, University of Iowa, Iowa City, IA, USA
| | - Michael G Anderson
- Department of Ophthalmology and Visual Sciences, Carver College of Medicine, 3111B Medical Education and Research Facility, University of Iowa, 375 Newton Road, Iowa City, IA52245, USA.,Institute for Vision Research, University of Iowa, Iowa City, IA, USA.,Department of Molecular Physiology and Biophysics, Carver College of Medicine, University of Iowa, Iowa City, IA, USA.,VA Center for the Prevention and Treatment of Visual Loss, Iowa City VA Healthcare System, Iowa City, IA, USA
| | - Bao Jian Fan
- Department of Ophthalmology, Harvard Medical School, Massachusetts Eye and Ear Boston, Boston, MA, USA
| | - Robert Ritch
- Einhorn Research Center, New York Eye and Ear Infirmary of Mount Sinai, New York, NY, USA
| | - Jamie E Craig
- Department of Ophthalmology, Flinders Medical Centre, Adelaide, South Australia, Australia
| | - Janey L Wiggs
- Department of Ophthalmology, Harvard Medical School, Massachusetts Eye and Ear Boston, Boston, MA, USA
| | - Todd E Scheetz
- Department of Ophthalmology and Visual Sciences, Carver College of Medicine, 3111B Medical Education and Research Facility, University of Iowa, 375 Newton Road, Iowa City, IA52245, USA.,Institute for Vision Research, University of Iowa, Iowa City, IA, USA
| | - John H Fingert
- Department of Ophthalmology and Visual Sciences, Carver College of Medicine, 3111B Medical Education and Research Facility, University of Iowa, 375 Newton Road, Iowa City, IA52245, USA. .,Institute for Vision Research, University of Iowa, Iowa City, IA, USA.
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14
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Lee K, Warren AK, Abràmoff MD, Wahle A, Whitmore SS, Han IC, Fingert JH, Scheetz TE, Mullins RF, Sonka M, Sohn EH. Automated segmentation of choroidal layers from 3-dimensional macular optical coherence tomography scans. J Neurosci Methods 2021; 360:109267. [PMID: 34157370 DOI: 10.1016/j.jneumeth.2021.109267] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 05/29/2021] [Accepted: 06/17/2021] [Indexed: 11/25/2022]
Abstract
BACKGROUND Changes in choroidal thickness are associated with various ocular diseases, and the choroid can be imaged using spectral-domain optical coherence tomography (SD-OCT) and enhanced depth imaging OCT (EDI-OCT). NEW METHOD Eighty macular SD-OCT volumes from 80 patients were obtained using the Zeiss Cirrus machine. Eleven additional control subjects had two Cirrus scans done in one visit along with enhanced depth imaging (EDI-OCT) using the Heidelberg Spectralis machine. To automatically segment choroidal layers from the OCT volumes, our graph-theoretic approach was utilized. The segmentation results were compared with reference standards from two independent graders, and the accuracy of automated segmentation was calculated using unsigned/signed border positioning/thickness errors and Dice similarity coefficient (DSC). The repeatability and reproducibility of our choroidal thicknesses were determined by intraclass correlation coefficient (ICC), coefficient of variation (CV), and repeatability coefficient (RC). RESULTS The mean unsigned/signed border positioning errors for the choroidal inner and outer surfaces are 3.39 ± 1.26 µm (mean ± standard deviation)/- 1.52 ± 1.63 µm and 16.09 ± 6.21 µm/4.73 ± 9.53 µm, respectively. The mean unsigned/signed choroidal thickness errors are 16.54 ± 6.47 µm/6.25 ± 9.91 µm, and the mean DSC is 0.949 ± 0.025. The ICC (95% confidence interval), CV, RC values are 0.991 (0.977-0.997), 2.48%, 14.25 µm for the repeatability and 0.991 (0.977-0.997), 2.49%, 14.30 µm for the reproducibility studies, respectively. COMPARISON WITH EXISTING METHOD(S) The proposed method outperformed our previous method using choroidal vessel segmentation and inter-grader variability. CONCLUSIONS This automated segmentation method can reliably measure choroidal thickness using different OCT platforms.
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Affiliation(s)
- Kyungmoo Lee
- Iowa Institute for Biomedical Imaging, University of Iowa, Iowa City, IA, United States; Department of Electrical and Computer Engineering, University of Iowa, Iowa City, IA, United States
| | - Alexis K Warren
- Department of Ophthalmology and Visual Sciences, University of Iowa Hospitals and Clinics, Iowa City, IA, United States
| | - Michael D Abràmoff
- Iowa Institute for Biomedical Imaging, University of Iowa, Iowa City, IA, United States; Department of Electrical and Computer Engineering, University of Iowa, Iowa City, IA, United States; Department of Ophthalmology and Visual Sciences, University of Iowa Hospitals and Clinics, Iowa City, IA, United States; Department of Biomedical Engineering, University of Iowa, Iowa City, IA, United States; Institute for Vision Research, University of Iowa, Iowa City, IA, United States; Veterans Affairs Medical Center, Iowa City, IA, United States; IDx, Coralville, IA, United States
| | - Andreas Wahle
- Iowa Institute for Biomedical Imaging, University of Iowa, Iowa City, IA, United States; Department of Electrical and Computer Engineering, University of Iowa, Iowa City, IA, United States
| | - S Scott Whitmore
- Department of Ophthalmology and Visual Sciences, University of Iowa Hospitals and Clinics, Iowa City, IA, United States; Institute for Vision Research, University of Iowa, Iowa City, IA, United States
| | - Ian C Han
- Department of Ophthalmology and Visual Sciences, University of Iowa Hospitals and Clinics, Iowa City, IA, United States; Institute for Vision Research, University of Iowa, Iowa City, IA, United States
| | - John H Fingert
- Department of Ophthalmology and Visual Sciences, University of Iowa Hospitals and Clinics, Iowa City, IA, United States; Institute for Vision Research, University of Iowa, Iowa City, IA, United States
| | - Todd E Scheetz
- Iowa Institute for Biomedical Imaging, University of Iowa, Iowa City, IA, United States; Department of Ophthalmology and Visual Sciences, University of Iowa Hospitals and Clinics, Iowa City, IA, United States; Department of Biomedical Engineering, University of Iowa, Iowa City, IA, United States; Institute for Vision Research, University of Iowa, Iowa City, IA, United States
| | - Robert F Mullins
- Department of Ophthalmology and Visual Sciences, University of Iowa Hospitals and Clinics, Iowa City, IA, United States; Institute for Vision Research, University of Iowa, Iowa City, IA, United States
| | - Milan Sonka
- Iowa Institute for Biomedical Imaging, University of Iowa, Iowa City, IA, United States; Department of Electrical and Computer Engineering, University of Iowa, Iowa City, IA, United States; Department of Ophthalmology and Visual Sciences, University of Iowa Hospitals and Clinics, Iowa City, IA, United States
| | - Elliott H Sohn
- Department of Ophthalmology and Visual Sciences, University of Iowa Hospitals and Clinics, Iowa City, IA, United States; Institute for Vision Research, University of Iowa, Iowa City, IA, United States.
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15
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Voigt AP, Mullin NK, Whitmore SS, DeLuca AP, Burnight ER, Liu X, Tucker BA, Scheetz TE, Stone EM, Mullins RF. Human photoreceptor cells from different macular subregions have distinct transcriptional profiles. Hum Mol Genet 2021; 30:1543-1558. [PMID: 34014299 PMCID: PMC8330894 DOI: 10.1093/hmg/ddab140] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Revised: 05/11/2021] [Accepted: 05/13/2021] [Indexed: 12/17/2022] Open
Abstract
The human neural retina is a light sensitive tissue with remarkable spatial and cellular organization. Compared with the periphery, the central retina contains more densely packed cone photoreceptor cells with unique morphologies and synaptic wiring. Some regions of the central retina exhibit selective degeneration or preservation in response to retinal disease and the basis for this variation is unknown. In this study, we used both bulk and single-cell RNA sequencing to compare gene expression within concentric regions of the central retina. We identified unique gene expression patterns of foveal cone photoreceptor cells, including many foveal-enriched transcription factors. In addition, we found that the genes RORB1, PPFIA1 and KCNAB2 are differentially spliced in the foveal, parafoveal and macular regions. These results provide a highly detailed spatial characterization of the retinal transcriptome and highlight unique molecular features of different retinal regions.
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Affiliation(s)
- Andrew P Voigt
- Department of Ophthalmology and Visual Sciences, the University of Iowa Carver College of Medicine, Iowa City, IA 52242, USA.,Institute for Vision Research, the University of Iowa, Iowa City, IA 52242, USA
| | - Nathaniel K Mullin
- Department of Ophthalmology and Visual Sciences, the University of Iowa Carver College of Medicine, Iowa City, IA 52242, USA.,Institute for Vision Research, the University of Iowa, Iowa City, IA 52242, USA
| | - S Scott Whitmore
- Department of Ophthalmology and Visual Sciences, the University of Iowa Carver College of Medicine, Iowa City, IA 52242, USA.,Institute for Vision Research, the University of Iowa, Iowa City, IA 52242, USA
| | - Adam P DeLuca
- Department of Ophthalmology and Visual Sciences, the University of Iowa Carver College of Medicine, Iowa City, IA 52242, USA.,Institute for Vision Research, the University of Iowa, Iowa City, IA 52242, USA
| | - Erin R Burnight
- Department of Ophthalmology and Visual Sciences, the University of Iowa Carver College of Medicine, Iowa City, IA 52242, USA.,Institute for Vision Research, the University of Iowa, Iowa City, IA 52242, USA
| | - Xiuying Liu
- Department of Ophthalmology and Visual Sciences, the University of Iowa Carver College of Medicine, Iowa City, IA 52242, USA.,Institute for Vision Research, the University of Iowa, Iowa City, IA 52242, USA
| | - Budd A Tucker
- Department of Ophthalmology and Visual Sciences, the University of Iowa Carver College of Medicine, Iowa City, IA 52242, USA.,Institute for Vision Research, the University of Iowa, Iowa City, IA 52242, USA
| | - Todd E Scheetz
- Department of Ophthalmology and Visual Sciences, the University of Iowa Carver College of Medicine, Iowa City, IA 52242, USA.,Institute for Vision Research, the University of Iowa, Iowa City, IA 52242, USA
| | - Edwin M Stone
- Department of Ophthalmology and Visual Sciences, the University of Iowa Carver College of Medicine, Iowa City, IA 52242, USA.,Institute for Vision Research, the University of Iowa, Iowa City, IA 52242, USA
| | - Robert F Mullins
- Department of Ophthalmology and Visual Sciences, the University of Iowa Carver College of Medicine, Iowa City, IA 52242, USA.,Institute for Vision Research, the University of Iowa, Iowa City, IA 52242, USA
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16
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Sohn EH, Han IC, Roos BR, Faga B, Luse MA, Binkley EM, Boldt HC, Folk JC, Russell SR, Mullins RF, Fingert JH, Stone EM, Scheetz TE. Genetic Association between MMP9 and Choroidal Neovascularization in Age-Related Macular Degeneration. Ophthalmol Sci 2021; 1:100002. [PMID: 37672224 PMCID: PMC9560657 DOI: 10.1016/j.xops.2020.100002] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Revised: 12/11/2020] [Accepted: 12/11/2020] [Indexed: 11/30/2022]
Abstract
Purpose To evaluate the first association specific to exudative age-related macular degeneration (AMD) located near the matrix metalloproteinase 9 (MMP9) gene. Design Genetic association study. Participants One thousand seven hundred twelve patients with AMD (672 nonexudative, 1040 exudative) of predominantly northern European descent seeking treatment at the University of Iowa Hospitals and Clinics. Methods We reanalyzed the International AMD Genetics Consortium (IAMDGC) data to validate the association of polymorphisms near MMP9 with exudative AMD and to identify additional associated single nucleotide polymorphisms (SNPs), especially MMP9 coding sequence SNPs. We genotyped a cohort of 1712 AMD patients from Iowa with 3 SNPs identified with our analysis of the IAMDGC cohort using commercially available real-time quantitative polymerase chain reaction (PCR) assays. Firth regression was used to measure the association between MMP9 SNP genotypes and exudative AMD in our cohort of patients from Iowa. In addition, we developed a PCR-based assay to genotype the Iowa cohort at a short tandem repeat polymorphism (STRP) at the MMP9 locus. Main Outcome Measures Odds ratios and P values for exudative compared with nonexudative AMD patients in the Iowa cohort for MMP9 SNPs (rs4810482, rs17576, and rs17577) and STRP. Results We identified 3 SNPs in the MMP9 locus (rs4810482, rs17576, and rs17577) that are highly associated with exudative AMD in patient cohorts of the IAMDGC. These MMP9 SNPs also are associated with exudative AMD in the cohort of 1712 AMD patients from Iowa (rs4810482: odds ratio [OR], 0.82; P = 0.010; rs17576: OR, 0.86; P = 0.046; and rs17577: OR, 0.80; P = 0.041). We also genotyped the cohort of AMD patients from Iowa at rs142450006, another MMP9 polymorphism that previously was associated with exudative AMD. We detected a 4bp STRP, (TTTC)n, at the rs142450006 locus that is highly polymorphic and associated significantly with exudative AMD (OR, 0.78; P = 0.016). Conclusions This study independently confirms and expands an association between the MMP9 locus and exudative AMD, further implicating a role for extracellular matrix abnormalities in choroidal neovascularization.
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Affiliation(s)
- Elliott H. Sohn
- Department of Ophthalmology, The University of Iowa, Iowa City, Iowa
- Institute for Vision Research, The University of Iowa, Iowa City, Iowa
| | - Ian C. Han
- Department of Ophthalmology, The University of Iowa, Iowa City, Iowa
- Institute for Vision Research, The University of Iowa, Iowa City, Iowa
| | - Benjamin R. Roos
- Department of Ophthalmology, The University of Iowa, Iowa City, Iowa
- Institute for Vision Research, The University of Iowa, Iowa City, Iowa
| | - Benjamin Faga
- Department of Ophthalmology, The University of Iowa, Iowa City, Iowa
- Institute for Vision Research, The University of Iowa, Iowa City, Iowa
| | - Meagan A. Luse
- Department of Ophthalmology, The University of Iowa, Iowa City, Iowa
- Institute for Vision Research, The University of Iowa, Iowa City, Iowa
| | - Elaine M. Binkley
- Department of Ophthalmology, The University of Iowa, Iowa City, Iowa
- Institute for Vision Research, The University of Iowa, Iowa City, Iowa
| | - H. Culver Boldt
- Department of Ophthalmology, The University of Iowa, Iowa City, Iowa
- Institute for Vision Research, The University of Iowa, Iowa City, Iowa
| | - James C. Folk
- Department of Ophthalmology, The University of Iowa, Iowa City, Iowa
- Institute for Vision Research, The University of Iowa, Iowa City, Iowa
| | - Stephen R. Russell
- Department of Ophthalmology, The University of Iowa, Iowa City, Iowa
- Institute for Vision Research, The University of Iowa, Iowa City, Iowa
| | - Robert F. Mullins
- Department of Ophthalmology, The University of Iowa, Iowa City, Iowa
- Institute for Vision Research, The University of Iowa, Iowa City, Iowa
| | - John H. Fingert
- Department of Ophthalmology, The University of Iowa, Iowa City, Iowa
- Institute for Vision Research, The University of Iowa, Iowa City, Iowa
| | - Edwin M. Stone
- Department of Ophthalmology, The University of Iowa, Iowa City, Iowa
- Institute for Vision Research, The University of Iowa, Iowa City, Iowa
| | - Todd E. Scheetz
- Department of Ophthalmology, The University of Iowa, Iowa City, Iowa
- Institute for Vision Research, The University of Iowa, Iowa City, Iowa
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17
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Voigt AP, Whitmore SS, Lessing ND, DeLuca AP, Tucker BA, Stone EM, Mullins RF, Scheetz TE. Spectacle: An interactive resource for ocular single-cell RNA sequencing data analysis. Exp Eye Res 2020; 200:108204. [PMID: 32910939 DOI: 10.1016/j.exer.2020.108204] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 08/06/2020] [Accepted: 08/25/2020] [Indexed: 12/11/2022]
Abstract
Single-cell RNA sequencing has revolutionized ocular gene expression studies. This technology has enabled researchers to identify expression signatures for rare cell types and characterize how gene expression changes across biological conditions, such as topographic region or disease status. However, sharing single-cell RNA sequencing results remains a major obstacle, particular for individuals without a computational background. To address these limitations, we developed Spectacle, an interactive web-based resource for exploring previously published single-cell RNA sequencing data from ocular studies. Spectacle is powered by a locally developed R package, cellcuratoR, which utilizes the Shiny framework in R to generate interactive visualizations for single-cell expression data. Spectacle contains five pre-processed ocular single-cell RNA sequencing data sets and is accessible via the web at OcularGeneExpression.org/singlecell. With Spectacle, users can interactively identify which cell types express a gene of interest, detect transcriptomic subpopulations within a cell type, and perform highly flexible differential expression analyses. The freely-available Spectacle system reduces the bioinformatic barrier for interacting with rich single-cell RNA sequencing studies from ocular tissues, making it easy to quickly identify cell types that express a gene of interest.
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Affiliation(s)
- Andrew P Voigt
- Departments of Ophthalmology and Visual Sciences, the University of Iowa Carver College of Medicine, Iowa City, IA, 52242, USA; Institute for Vision Research, the University of Iowa, Iowa City, IA, 52242, USA
| | - S Scott Whitmore
- Departments of Ophthalmology and Visual Sciences, the University of Iowa Carver College of Medicine, Iowa City, IA, 52242, USA; Institute for Vision Research, the University of Iowa, Iowa City, IA, 52242, USA
| | - Nicholas D Lessing
- Departments of Ophthalmology and Visual Sciences, the University of Iowa Carver College of Medicine, Iowa City, IA, 52242, USA; Institute for Vision Research, the University of Iowa, Iowa City, IA, 52242, USA
| | - Adam P DeLuca
- Departments of Ophthalmology and Visual Sciences, the University of Iowa Carver College of Medicine, Iowa City, IA, 52242, USA; Institute for Vision Research, the University of Iowa, Iowa City, IA, 52242, USA
| | - Budd A Tucker
- Departments of Ophthalmology and Visual Sciences, the University of Iowa Carver College of Medicine, Iowa City, IA, 52242, USA; Institute for Vision Research, the University of Iowa, Iowa City, IA, 52242, USA
| | - Edwin M Stone
- Departments of Ophthalmology and Visual Sciences, the University of Iowa Carver College of Medicine, Iowa City, IA, 52242, USA; Institute for Vision Research, the University of Iowa, Iowa City, IA, 52242, USA
| | - Robert F Mullins
- Departments of Ophthalmology and Visual Sciences, the University of Iowa Carver College of Medicine, Iowa City, IA, 52242, USA; Institute for Vision Research, the University of Iowa, Iowa City, IA, 52242, USA
| | - Todd E Scheetz
- Departments of Ophthalmology and Visual Sciences, the University of Iowa Carver College of Medicine, Iowa City, IA, 52242, USA; Institute for Vision Research, the University of Iowa, Iowa City, IA, 52242, USA.
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18
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Voigt AP, Whitmore SS, Mulfaul K, Chirco KR, Giacalone JC, Flamme-Wiese MJ, Stockman A, Stone EM, Tucker BA, Scheetz TE, Mullins RF. Bulk and single-cell gene expression analyses reveal aging human choriocapillaris has pro-inflammatory phenotype. Microvasc Res 2020; 131:104031. [PMID: 32531351 DOI: 10.1016/j.mvr.2020.104031] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 06/02/2020] [Accepted: 06/05/2020] [Indexed: 12/17/2022]
Abstract
The human choroidal vasculature is subject to age-related structural and gene expression changes implicated in age-related macular degeneration (AMD). In this study, we performed both bulk and single-cell RNA sequencing on infant (n = 4 for bulk experiments, n = 2 for single-cell experiments) and adult (n = 13 for bulk experiments, n = 6 for single-cell experiments) human donors to characterize how choroidal gene expression changes with age. Differential expression analysis revealed that aged choroidal samples were enriched in genes encoding pro-inflammatory transcription factors and leukocyte transendothelial cell migration adhesion proteins. Such genes were observed to be differentially expressed specifically within choroidal endothelial cells at the single-cell level. Immunohistochemistry experiments support transcriptional findings that CD34 is elevated in infant choriocapillaris endothelial cells while ICAM-1 is enriched in adults. These results suggest several potential drivers of the pro-inflammatory vascular phenotype observed with advancing age.
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Affiliation(s)
- Andrew P Voigt
- Department of Ophthalmology and Visual Sciences, the University of Iowa Carver College of Medicine, Iowa City, IA 52242, United States of America; Institute for Vision Research, the University of Iowa, Iowa City, IA 52242, United States of America
| | - S Scott Whitmore
- Department of Ophthalmology and Visual Sciences, the University of Iowa Carver College of Medicine, Iowa City, IA 52242, United States of America; Institute for Vision Research, the University of Iowa, Iowa City, IA 52242, United States of America
| | - Kelly Mulfaul
- Department of Ophthalmology and Visual Sciences, the University of Iowa Carver College of Medicine, Iowa City, IA 52242, United States of America; Institute for Vision Research, the University of Iowa, Iowa City, IA 52242, United States of America
| | - Kathleen R Chirco
- Department of Ophthalmology and Visual Sciences, the University of Iowa Carver College of Medicine, Iowa City, IA 52242, United States of America; Institute for Vision Research, the University of Iowa, Iowa City, IA 52242, United States of America
| | - Joseph C Giacalone
- Department of Ophthalmology and Visual Sciences, the University of Iowa Carver College of Medicine, Iowa City, IA 52242, United States of America; Institute for Vision Research, the University of Iowa, Iowa City, IA 52242, United States of America
| | - Miles J Flamme-Wiese
- Department of Ophthalmology and Visual Sciences, the University of Iowa Carver College of Medicine, Iowa City, IA 52242, United States of America; Institute for Vision Research, the University of Iowa, Iowa City, IA 52242, United States of America
| | - Adam Stockman
- Department of Ophthalmology and Visual Sciences, the University of Iowa Carver College of Medicine, Iowa City, IA 52242, United States of America; Iowa Lions Eye Bank, Coralville, IA 52241, United States of America
| | - Edwin M Stone
- Department of Ophthalmology and Visual Sciences, the University of Iowa Carver College of Medicine, Iowa City, IA 52242, United States of America; Institute for Vision Research, the University of Iowa, Iowa City, IA 52242, United States of America
| | - Budd A Tucker
- Department of Ophthalmology and Visual Sciences, the University of Iowa Carver College of Medicine, Iowa City, IA 52242, United States of America; Institute for Vision Research, the University of Iowa, Iowa City, IA 52242, United States of America
| | - Todd E Scheetz
- Department of Ophthalmology and Visual Sciences, the University of Iowa Carver College of Medicine, Iowa City, IA 52242, United States of America; Institute for Vision Research, the University of Iowa, Iowa City, IA 52242, United States of America
| | - Robert F Mullins
- Department of Ophthalmology and Visual Sciences, the University of Iowa Carver College of Medicine, Iowa City, IA 52242, United States of America; Institute for Vision Research, the University of Iowa, Iowa City, IA 52242, United States of America.
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19
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Alward WLM, van der Heide C, Khanna CL, Roos BR, Sivaprasad S, Kam J, Ritch R, Lotery A, Igo RP, Cooke Bailey JN, Stone EM, Scheetz TE, Kwon YH, Pasquale LR, Wiggs JL, Fingert JH. Myocilin Mutations in Patients With Normal-Tension Glaucoma. JAMA Ophthalmol 2020; 137:559-563. [PMID: 30816940 DOI: 10.1001/jamaophthalmol.2019.0005] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Importance Mutations in the myocilin (MYOC) gene are the most common molecularly defined cause of primary open-angle glaucoma that typically occurs in patients with high intraocular pressures (IOP). One MYOC mutation, p.Gln368Ter, has been associated with as many as 1.6% of primary open-angle glaucoma cases that had a mean maximum recorded IOP of 30 mm Hg. However, to our knowledge, the role of the p.Gln368Ter mutation in patients with normal-tension glaucoma (NTG) with an IOP of 21 mm Hg or lower has not been investigated. Objective To evaluate the role of the p.Gln368Ter MYOC mutation in patients with NTG. Design, Setting, and Participants In this case-control study of the prevalence of the p.Gln368Ter mutation in patients with NTG, cohort 1 was composed of 772 patients with NTG and 2152 controls from the United States (Iowa, Minnesota, and New York) and England and cohort 2 was composed of 561 patients with NTG and 2606 controls from the Massachusetts Eye and Ear Infirmary and the NEIGHBORHOOD consortium. Genotyping was conducted using real-time polymerase chain reaction that was confirmed with Sanger sequencing, the imputation of genome-wide association study data, or an analysis of whole-exome sequence data. Data analysis occurred between April 2007 and April 2018. Main Outcomes and Measures Comparison of the frequency of the p.Gln368Ter MYOC mutation between NTG cases and controls with the Fisher exact test. Results Of 6091 total participants, 3346 (54.9%) were women and 5799 (95.2%) were white. We detected the p.Gln368Ter mutation in 7 of 772 patients with NTG (0.91%) and 7 of 2152 controls (0.33%) in cohort 1 (P = .03). In cohort 2, we detected the p.Gln368Ter mutation in 4 of 561 patients with NTG (0.71%) and 10 of 2606 controls (0.38%; P = .15). When the cohorts were analyzed as a group, the p.Gln368Ter mutation was associated with NTG (odds ratio, 2.3; 95% CI, 0.98-5.3; P = .04). Conclusions and Relevance In cohorts 1 and 2, the p.Gln368Ter mutation in MYOC was found in patients with IOPs that were 21 mm Hg or lower (NTG), although at a frequency that is lower than previously detected in patients with higher IOP. These data suggest that the p.Gln368Ter mutation may be associated with glaucoma in patients with normal IOPs as well as in patients with IOPs that are greater than 21 mm Hg.
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Affiliation(s)
- Wallace L M Alward
- Department of Ophthalmology and Visual Sciences, Carver College of Medicine, University of Iowa, Iowa City.,Institute for Vision Research, University of Iowa, Iowa City
| | - Carly van der Heide
- Department of Ophthalmology and Visual Sciences, Carver College of Medicine, University of Iowa, Iowa City.,Institute for Vision Research, University of Iowa, Iowa City
| | - Cheryl L Khanna
- Department of Ophthalmology, Mayo Clinic, Rochester, Minnesota
| | - Ben R Roos
- Department of Ophthalmology and Visual Sciences, Carver College of Medicine, University of Iowa, Iowa City.,Institute for Vision Research, University of Iowa, Iowa City
| | - Sobha Sivaprasad
- Moorfields Eye Hospital, London, England.,Kings College Hospital, London, England
| | - Jason Kam
- Kaiser Permanente, Seattle, Washington
| | - Robert Ritch
- Einhorn Clinical Research Center, New York Eye and Ear Infirmary of Mount Sinai, New York
| | - Andrew Lotery
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, England
| | - Robert P Igo
- Department of Population and Quantitative Health Sciences, Case Western Reserve University School of Medicine, Cleveland, Ohio
| | - Jessica N Cooke Bailey
- Department of Population and Quantitative Health Sciences, Case Western Reserve University School of Medicine, Cleveland, Ohio.,Institute for Computational Biology, Case Western Reserve University School of Medicine, Cleveland, Ohio
| | - Edwin M Stone
- Department of Ophthalmology and Visual Sciences, Carver College of Medicine, University of Iowa, Iowa City.,Institute for Vision Research, University of Iowa, Iowa City
| | - Todd E Scheetz
- Department of Ophthalmology and Visual Sciences, Carver College of Medicine, University of Iowa, Iowa City.,Institute for Vision Research, University of Iowa, Iowa City
| | - Young H Kwon
- Department of Ophthalmology and Visual Sciences, Carver College of Medicine, University of Iowa, Iowa City.,Institute for Vision Research, University of Iowa, Iowa City
| | | | - Janey L Wiggs
- Massachusetts Eye and Ear Infirmary, Harvard University, Boston
| | - John H Fingert
- Department of Ophthalmology and Visual Sciences, Carver College of Medicine, University of Iowa, Iowa City.,Institute for Vision Research, University of Iowa, Iowa City
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20
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Voigt AP, Binkley E, Flamme-Wiese MJ, Zeng S, DeLuca AP, Scheetz TE, Tucker BA, Mullins RF, Stone EM. Single-Cell RNA Sequencing in Human Retinal Degeneration Reveals Distinct Glial Cell Populations. Cells 2020; 9:cells9020438. [PMID: 32069977 PMCID: PMC7072666 DOI: 10.3390/cells9020438] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 02/07/2020] [Accepted: 02/07/2020] [Indexed: 12/15/2022] Open
Abstract
Degenerative diseases affecting retinal photoreceptor cells have numerous etiologies and clinical presentations. We clinically and molecularly studied the retina of a 70-year-old patient with retinal degeneration attributed to autoimmune retinopathy. The patient was followed for 19 years for progressive peripheral visual field loss and pigmentary changes. Single-cell RNA sequencing was performed on foveal and peripheral retina from this patient and four control patients, and cell-specific gene expression differences were identified between healthy and degenerating retina. Distinct populations of glial cells, including astrocytes and Müller cells, were identified in the tissue from the retinal degeneration patient. The glial cell populations demonstrated an expression profile consistent with reactive gliosis. This report provides evidence that glial cells have a distinct transcriptome in the setting of human retinal degeneration and represents a complementary clinical and molecular investigation of a case of progressive retinal disease.
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Affiliation(s)
- Andrew P. Voigt
- Department of Ophthalmology and Visual Sciences, The University of Iowa Carver College of Medicine, Iowa City, IA 52242, USA
- Institute for Vision Research, The University of Iowa, Iowa City, IA 52242, USA
| | - Elaine Binkley
- Department of Ophthalmology and Visual Sciences, The University of Iowa Carver College of Medicine, Iowa City, IA 52242, USA
- Institute for Vision Research, The University of Iowa, Iowa City, IA 52242, USA
| | - Miles J. Flamme-Wiese
- Department of Ophthalmology and Visual Sciences, The University of Iowa Carver College of Medicine, Iowa City, IA 52242, USA
- Institute for Vision Research, The University of Iowa, Iowa City, IA 52242, USA
| | - Shemin Zeng
- Department of Ophthalmology and Visual Sciences, The University of Iowa Carver College of Medicine, Iowa City, IA 52242, USA
- Institute for Vision Research, The University of Iowa, Iowa City, IA 52242, USA
| | - Adam P. DeLuca
- Department of Ophthalmology and Visual Sciences, The University of Iowa Carver College of Medicine, Iowa City, IA 52242, USA
- Institute for Vision Research, The University of Iowa, Iowa City, IA 52242, USA
| | - Todd E. Scheetz
- Department of Ophthalmology and Visual Sciences, The University of Iowa Carver College of Medicine, Iowa City, IA 52242, USA
- Institute for Vision Research, The University of Iowa, Iowa City, IA 52242, USA
| | - Budd A. Tucker
- Department of Ophthalmology and Visual Sciences, The University of Iowa Carver College of Medicine, Iowa City, IA 52242, USA
- Institute for Vision Research, The University of Iowa, Iowa City, IA 52242, USA
| | - Robert F. Mullins
- Department of Ophthalmology and Visual Sciences, The University of Iowa Carver College of Medicine, Iowa City, IA 52242, USA
- Institute for Vision Research, The University of Iowa, Iowa City, IA 52242, USA
| | - Edwin M. Stone
- Department of Ophthalmology and Visual Sciences, The University of Iowa Carver College of Medicine, Iowa City, IA 52242, USA
- Institute for Vision Research, The University of Iowa, Iowa City, IA 52242, USA
- Correspondence:
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Voigt AP, Whitmore SS, Flamme-Wiese MJ, Riker MJ, Wiley LA, Tucker BA, Stone EM, Mullins RF, Scheetz TE. Molecular characterization of foveal versus peripheral human retina by single-cell RNA sequencing. Exp Eye Res 2019; 184:234-242. [PMID: 31075224 PMCID: PMC6596422 DOI: 10.1016/j.exer.2019.05.001] [Citation(s) in RCA: 88] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2019] [Revised: 05/02/2019] [Accepted: 05/06/2019] [Indexed: 10/26/2022]
Abstract
The human retina is a complex tissue responsible for detecting photons of light and converting information from these photons into the neurochemical signals interpreted as vision. Such visual signaling not only requires sophisticated interactions between multiple classes of neurons, but also spatially-dependent molecular specialization of individual cell types. In this study, we performed single-cell RNA sequencing on neural retina isolated from both the fovea and peripheral retina in three human donors. We recovered a total of 8,217 cells, with 3,578 cells originating from the fovea and 4,639 cells originating from the periphery. Expression profiles for all major retinal cell types were compiled, and differential expression analysis was performed between cells of foveal versus peripheral origin. Globally, mRNA for the serum iron binding protein transferrin (TF), which has been associated with age-related macular degeneration pathogenesis, was enriched in peripheral samples. Cone photoreceptor cells were of particular interest and formed two predominant clusters based on gene expression. One cone cluster had 96% of cells originating from foveal samples, while the second cone cluster consisted exclusively of peripherally isolated cells. A total of 148 genes were differentially expressed between cones from the fovea versus periphery. Interestingly, peripheral cones were enriched for the gene encoding Beta-Carotene Oxygenase 2 (BCO2). A relative deficiency of this enzyme may account for the accumulation of carotenoids responsible for yellow pigment deposition within the macula. Overall, this data set provides rich expression profiles of the major human retinal cell types and highlights transcriptomic features that distinguish foveal and peripheral cells.
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Affiliation(s)
- A P Voigt
- Departments of Ophthalmology and Visual Sciences, The University of Iowa Carver College of Medicine, Iowa City, IA, 52242, USA; Institute for Vision Research, The University of Iowa, Iowa City, IA, 52242, USA
| | - S S Whitmore
- Departments of Ophthalmology and Visual Sciences, The University of Iowa Carver College of Medicine, Iowa City, IA, 52242, USA; Institute for Vision Research, The University of Iowa, Iowa City, IA, 52242, USA
| | - M J Flamme-Wiese
- Departments of Ophthalmology and Visual Sciences, The University of Iowa Carver College of Medicine, Iowa City, IA, 52242, USA; Institute for Vision Research, The University of Iowa, Iowa City, IA, 52242, USA
| | - M J Riker
- Departments of Ophthalmology and Visual Sciences, The University of Iowa Carver College of Medicine, Iowa City, IA, 52242, USA; Institute for Vision Research, The University of Iowa, Iowa City, IA, 52242, USA
| | - L A Wiley
- Departments of Ophthalmology and Visual Sciences, The University of Iowa Carver College of Medicine, Iowa City, IA, 52242, USA; Institute for Vision Research, The University of Iowa, Iowa City, IA, 52242, USA
| | - B A Tucker
- Departments of Ophthalmology and Visual Sciences, The University of Iowa Carver College of Medicine, Iowa City, IA, 52242, USA; Institute for Vision Research, The University of Iowa, Iowa City, IA, 52242, USA
| | - E M Stone
- Departments of Ophthalmology and Visual Sciences, The University of Iowa Carver College of Medicine, Iowa City, IA, 52242, USA; Institute for Vision Research, The University of Iowa, Iowa City, IA, 52242, USA
| | - R F Mullins
- Departments of Ophthalmology and Visual Sciences, The University of Iowa Carver College of Medicine, Iowa City, IA, 52242, USA; Institute for Vision Research, The University of Iowa, Iowa City, IA, 52242, USA
| | - T E Scheetz
- Departments of Ophthalmology and Visual Sciences, The University of Iowa Carver College of Medicine, Iowa City, IA, 52242, USA; Institute for Vision Research, The University of Iowa, Iowa City, IA, 52242, USA.
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22
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Inamdar SM, Lankford CK, Laird JG, Novbatova G, Tatro N, Whitmore SS, Scheetz TE, Baker SA. Analysis of 14-3-3 isoforms expressed in photoreceptors. Exp Eye Res 2018; 170:108-116. [PMID: 29486162 DOI: 10.1016/j.exer.2018.02.022] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Revised: 02/02/2018] [Accepted: 02/23/2018] [Indexed: 11/18/2022]
Abstract
The 14-3-3 family of proteins has undergone considerable expansion in higher eukaryotes with humans and mice expressing seven isoforms (β, ε, η, γ, θ, ζ, and σ) from seven distinct genes (YWHAB, YWAHE, YWHAH, YWHAG, YWHAQ, YWHAZ, and SFN). Growing evidence indicates that while highly conserved, these isoforms are not entirely functionally redundant as they exhibit unique tissue expression profiles, subcellular localization, and biochemical functions. A key limitation in our understanding of 14-3-3 biology lies in our limited knowledge of cell-type specific 14-3-3 expression. Here we provide a characterization of 14-3-3 expression in whole retina and isolated rod photoreceptors using reverse-transcriptase digital droplet PCR. We find that all 14-3-3 genes with the exception of SFN are expressed in mouse retina with YWHAQ and YWHAE being the most highly expressed. Rod photoreceptors are enriched in YWHAE (14-3-3 ε). Immunohistochemistry revealed that 14-3-3 ε and 14-3-3 ζ exhibit unique distributions in photoreceptors with 14-3-3 ε restricted to the inner segment and 14-3-3 ζ localized to the outer segment. Our data demonstrates that, in the retina, 14-3-3 isoforms likely serve specific functions as they exhibit unique expression levels and cell-type specificity. As such, future investigations into 14-3-3 function in rod photoreceptors should be centered on 14-3-3 ε and 14-3-3 ζ, depending on the subcellular region of question.
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Affiliation(s)
- Shivangi M Inamdar
- Department of Biochemistry, University of Iowa, Iowa City, IA 52242, USA
| | - Colten K Lankford
- Department of Biochemistry, University of Iowa, Iowa City, IA 52242, USA
| | - Joseph G Laird
- Department of Biochemistry, University of Iowa, Iowa City, IA 52242, USA
| | - Gulnara Novbatova
- Department of Biochemistry, University of Iowa, Iowa City, IA 52242, USA
| | - Nicole Tatro
- Department of Ophthalmology & Visual Sciences and Institute for Vision Research, University of Iowa, Iowa City, IA 52242, USA
| | - S Scott Whitmore
- Department of Ophthalmology & Visual Sciences and Institute for Vision Research, University of Iowa, Iowa City, IA 52242, USA
| | - Todd E Scheetz
- Department of Ophthalmology & Visual Sciences and Institute for Vision Research, University of Iowa, Iowa City, IA 52242, USA
| | - Sheila A Baker
- Department of Biochemistry, University of Iowa, Iowa City, IA 52242, USA; Department of Ophthalmology & Visual Sciences and Institute for Vision Research, University of Iowa, Iowa City, IA 52242, USA.
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23
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Chirco KR, Lewis CJ, Scheetz TE, Johnston RM, Tucker BA, Stone EM, Fingert JH, Mullins RF. Evaluation of sFLT1 protein levels in human eyes with the FLT1 rs9943922 polymorphism. Ophthalmic Genet 2017; 39:68-72. [PMID: 28949775 DOI: 10.1080/13816810.2017.1369550] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
PURPOSE Age-related macular degeneration (AMD) is a devastating disease characterized by central vision impairment in individuals with advanced age. Neovascular AMD is a form of end-stage disease in which choroidal vessel outgrowth occurs beneath the retina. While many hypotheses have been raised as to what triggers the formation of pathological choroidal neovascular membranes, the exact mechanism for their initiation remains unresolved. Polymorphisms in the FLT1 gene have previously been associated with neovascular AMD risk, including the rs9943922 single nucleotide polymorphism (SNP). Here, we aimed to determine the association between the high-risk FLT1 genotype and FLT1 protein levels in human retina or retinal pigment epithelium (RPE)/choroid tissue. METHODS Retina and RPE/choroid tissue from 10 human donor eyes was selected from a collection of eyes genotyped for the rs9943922 SNP. Differences in soluble and membrane bound FLT1 protein levels were assessed for retina versus RPE/choroid donor tissue using ELISA and Western blotting analyses. Genotype-associated changes in FLT1 protein levels were also evaluated. RESULTS We found soluble FLT1 levels in the RPE/choroid tissue to be approximately three times higher than that of the retina (p < 0.001), while both samples have similar levels of the membrane bound form. When tissue with the rs9943922 SNP was compared with controls, no significant genotypic differences in FLT1 protein levels were observed. CONCLUSIONS Based on these data, we conclude that the rs9943922 SNP in the FLT1 gene does not result in a large difference in FLT1 protein levels, regardless of whether it is the soluble or the membrane bound form.
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Affiliation(s)
- Kathleen R Chirco
- a The Stephen A. Wynn Institute for Vision Research and the Department of Ophthalmology and Visual Sciences , The University of Iowa , Iowa City , Iowa , USA
| | - Carly J Lewis
- a The Stephen A. Wynn Institute for Vision Research and the Department of Ophthalmology and Visual Sciences , The University of Iowa , Iowa City , Iowa , USA
| | - Todd E Scheetz
- a The Stephen A. Wynn Institute for Vision Research and the Department of Ophthalmology and Visual Sciences , The University of Iowa , Iowa City , Iowa , USA
| | - Rebecca M Johnston
- a The Stephen A. Wynn Institute for Vision Research and the Department of Ophthalmology and Visual Sciences , The University of Iowa , Iowa City , Iowa , USA
| | - Budd A Tucker
- a The Stephen A. Wynn Institute for Vision Research and the Department of Ophthalmology and Visual Sciences , The University of Iowa , Iowa City , Iowa , USA
| | - Edwin M Stone
- a The Stephen A. Wynn Institute for Vision Research and the Department of Ophthalmology and Visual Sciences , The University of Iowa , Iowa City , Iowa , USA
| | - John H Fingert
- a The Stephen A. Wynn Institute for Vision Research and the Department of Ophthalmology and Visual Sciences , The University of Iowa , Iowa City , Iowa , USA
| | - Robert F Mullins
- a The Stephen A. Wynn Institute for Vision Research and the Department of Ophthalmology and Visual Sciences , The University of Iowa , Iowa City , Iowa , USA
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24
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Weihbrecht K, Goar WA, Pak T, Garrison JE, DeLuca AP, Stone EM, Scheetz TE, Sheffield VC. Keeping an Eye on Bardet-Biedl Syndrome: A Comprehensive Review of the Role of Bardet-Biedl Syndrome Genes in the Eye. Med Res Arch 2017; 5. [PMID: 29457131 DOI: 10.18103/mra.v5i9.1526] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Upwards of 90% of individuals with Bardet-Biedl syndrome (BBS) display rod-cone dystrophy with early macular involvement. BBS is an autosomal recessive, genetically heterogeneous, pleiotropic ciliopathy for which 21 causative genes have been discovered to date. In addition to retinal degeneration, the cardinal features of BBS include obesity, cognitive impairment, renal anomalies, polydactyly, and hypogonadism. Here, we review the genes, proteins, and protein complexes involved in BBS and the BBS model organisms available for the study of retinal degeneration. We include comprehensive lists for all known BBS genes, their known phenotypes, and the model organisms available. We also review the molecular mechanisms believed to lead to retinal degeneration. We provide an overview of the mode of inheritance and describe the relationships between BBS genes and Joubert syndrome, Leber Congenital Amaurosis, Senior-Løken syndrome, and non-syndromic retinitis pigmentosa. Finally, we propose ways that new advances in technology will allow us to better understand the role of different BBS genes in retinal formation and function.
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Affiliation(s)
- Katie Weihbrecht
- Department of Pediatrics, University of Iowa; Iowa City, IA 52242, USA.,Department of Ophthalmology and Visual Sciences, University of Iowa; Iowa City, IA 52242, USA.,Stephen A. Wynn Institute for Vision Research, University of Iowa; Iowa City, IA 52242, USA
| | - Wesley A Goar
- Department of Pediatrics, University of Iowa; Iowa City, IA 52242, USA.,Department of Ophthalmology and Visual Sciences, University of Iowa; Iowa City, IA 52242, USA.,Stephen A. Wynn Institute for Vision Research, University of Iowa; Iowa City, IA 52242, USA
| | - Thomas Pak
- Department of Pediatrics, University of Iowa; Iowa City, IA 52242, USA.,Stephen A. Wynn Institute for Vision Research, University of Iowa; Iowa City, IA 52242, USA
| | - Janelle E Garrison
- Department of Pediatrics, University of Iowa; Iowa City, IA 52242, USA.,Stephen A. Wynn Institute for Vision Research, University of Iowa; Iowa City, IA 52242, USA
| | - Adam P DeLuca
- Department of Ophthalmology and Visual Sciences, University of Iowa; Iowa City, IA 52242, USA.,Stephen A. Wynn Institute for Vision Research, University of Iowa; Iowa City, IA 52242, USA
| | - Edwin M Stone
- Department of Ophthalmology and Visual Sciences, University of Iowa; Iowa City, IA 52242, USA.,Stephen A. Wynn Institute for Vision Research, University of Iowa; Iowa City, IA 52242, USA
| | - Todd E Scheetz
- Department of Ophthalmology and Visual Sciences, University of Iowa; Iowa City, IA 52242, USA.,Stephen A. Wynn Institute for Vision Research, University of Iowa; Iowa City, IA 52242, USA
| | - Val C Sheffield
- Department of Pediatrics, University of Iowa; Iowa City, IA 52242, USA.,Department of Ophthalmology and Visual Sciences, University of Iowa; Iowa City, IA 52242, USA.,Stephen A. Wynn Institute for Vision Research, University of Iowa; Iowa City, IA 52242, USA
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25
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Simpson A, Avdic A, Roos BR, DeLuca A, Miller K, Schnieders MJ, Scheetz TE, Alward WL, Fingert JH. LADD syndrome with glaucoma is caused by a novel gene. Mol Vis 2017; 23:179-184. [PMID: 28400699 PMCID: PMC5373035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Accepted: 03/28/2017] [Indexed: 10/30/2022] Open
Abstract
PURPOSE Lacrimo-auriculo-dento-digital (LADD) syndrome is an autosomal dominant disorder displaying variable expression of multiple congenital anomalies including hypoplasia or aplasia of the lacrimal and salivary systems causing abnormal tearing and dry mouth. Mutations in the FGF10, FGFR2, and FGFR3 genes were found to cause some cases of LADD syndrome in prior genetic studies. The goal of this study is to identify the genetic basis of a case of LADD syndrome with glaucoma and thin central corneal thickness (CCT). METHODS Whole exome sequencing was performed, and previously described disease-causing genes (FGF10, FGFR2, and FGFR3) were first evaluated for mutations. Fifty-eight additional prioritized candidate genes were identified by searching gene annotations for features of LADD syndrome. The potential pathogenicity of the identified mutations was assessed by determining their frequency in large public exome databases; through sequence analysis using the Blosum62 matrix, PolyPhen2, and SIFT algorithms; and through homology analyses. A structural analysis of the effects of the top candidate mutation in tumor protein 63 (TP63) was also conducted by superimposing the mutation over the solved crystal structure. RESULTS No mutations were detected in FGF10, FGFR2, or FGFR3. The LADD syndrome patient's exome data was searched for mutations in the 58 candidate genes and only one mutation was detected, an Arg343Trp mutation in the tumor protein 63 (TP63) gene. This TP63 mutation is absent from the gnomAD sequence database. Analysis of the Arg343Trp mutation with Blosum62, PolyPhen2, and SIFT all suggest it is pathogenic. This arginine residue is highly conserved in orthologous genes. Finally, crystal structure analysis showed that the Arg343Trp mutation causes a significant alteration in the structure of TP63's DNA binding domain. CONCLUSIONS We report a patient with no mutations in known LADD syndrome genes (FGF10, FGFR2, and FGFR3). Our analysis provides strong evidence that the Arg343Trp mutation in TP63 caused LADD syndrome in our patient and that TP63 is a fourth gene contributing to this condition. TP63 encodes a transcription factor involved in the development and differentiation of tissues affected by LADD syndrome. These data suggest that TP63 is a novel LADD syndrome gene and may also influence corneal thickness and risk for open-angle glaucoma.
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Affiliation(s)
- Allie Simpson
- Department of Ophthalmology, Carver College of Medicine, University of Iowa, Iowa City, IA,Stephen A. Wynn Institute for Vision Research, University of Iowa, Iowa City, IA
| | - Armin Avdic
- Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, IA
| | - Ben R. Roos
- Department of Ophthalmology, Carver College of Medicine, University of Iowa, Iowa City, IA,Stephen A. Wynn Institute for Vision Research, University of Iowa, Iowa City, IA
| | - Adam DeLuca
- Department of Ophthalmology, Carver College of Medicine, University of Iowa, Iowa City, IA,Stephen A. Wynn Institute for Vision Research, University of Iowa, Iowa City, IA
| | - Kathy Miller
- Department of Ophthalmology, Carver College of Medicine, University of Iowa, Iowa City, IA,Stephen A. Wynn Institute for Vision Research, University of Iowa, Iowa City, IA
| | - Michael J. Schnieders
- Stephen A. Wynn Institute for Vision Research, University of Iowa, Iowa City, IA,Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, IA
| | - Todd E. Scheetz
- Department of Ophthalmology, Carver College of Medicine, University of Iowa, Iowa City, IA,Stephen A. Wynn Institute for Vision Research, University of Iowa, Iowa City, IA
| | - Wallace L.M. Alward
- Department of Ophthalmology, Carver College of Medicine, University of Iowa, Iowa City, IA,Stephen A. Wynn Institute for Vision Research, University of Iowa, Iowa City, IA
| | - John H. Fingert
- Department of Ophthalmology, Carver College of Medicine, University of Iowa, Iowa City, IA,Stephen A. Wynn Institute for Vision Research, University of Iowa, Iowa City, IA
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26
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Gaynor SC, Breen ME, Monson ET, de Klerk K, Parsons M, DeLuca AP, Scheetz TE, Zandi PP, Potash JB, Willour VL. A targeted sequencing study of glutamatergic candidate genes in suicide attempters with bipolar disorder. Am J Med Genet B Neuropsychiatr Genet 2016; 171:1080-1087. [PMID: 27480506 PMCID: PMC5814248 DOI: 10.1002/ajmg.b.32479] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Accepted: 07/11/2016] [Indexed: 11/11/2022]
Abstract
Suicidal behavior has been shown to have a heritable component that is partly driven by psychiatric disorders [Brent and Mann, 2005]. However, there is also an independent factor contributing to the heritability of suicidal behavior. We previously conducted a genome-wide association study (GWAS) of bipolar suicide attempters and bipolar non-attempters to assess this independent factor [Willour et al., 2012]. This GWAS implicated glutamatergic neurotransmission in attempted suicide. In the current study, we have conducted a targeted next-generation sequencing study of the glutamatergic N-methyl-D-aspartate (NMDA) receptor, neurexin, and neuroligin gene families in 476 bipolar suicide attempters and 473 bipolar non-attempters. The goal of this study was to gather sequence information from coding and regulatory regions of these glutamatergic genes to identify variants associated with attempted suicide. We identified 186 coding variants and 4,298 regulatory variants predicted to be functional in these genes. No individual variants were overrepresented in cases or controls to a degree that was statistically significant after correction for multiple testing. Additionally, none of the gene-level results were statistically significant following correction. While this study provides no direct support for a role of the examined glutamatergic candidate genes, further sequencing in expanded gene sets and datasets will be required to ultimately determine whether genetic variation in glutamatergic signaling influences suicidal behavior. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Sophia C. Gaynor
- Department of Psychiatry, University of Iowa Carver College of Medicine, Iowa City, IA, 52242, USA
| | - Marie E. Breen
- Department of Psychiatry, University of Iowa Carver College of Medicine, Iowa City, IA, 52242, USA
| | - Eric T. Monson
- Department of Psychiatry, University of Iowa Carver College of Medicine, Iowa City, IA, 52242, USA
| | - Kelly de Klerk
- Department of Psychiatry, University of Iowa Carver College of Medicine, Iowa City, IA, 52242, USA
| | - Meredith Parsons
- Department of Psychiatry, University of Iowa Carver College of Medicine, Iowa City, IA, 52242, USA
| | - Adam P. DeLuca
- Department of Ophthalmology and Visual Sciences, University of Iowa Carver College of Medicine, Iowa City, IA, 52242, USA
| | - Todd E. Scheetz
- Department of Ophthalmology and Visual Sciences, University of Iowa Carver College of Medicine, Iowa City, IA, 52242, USA,Department of Biomedical Engineering, University of Iowa College of Engineering, Iowa City, IA, 52242, USA
| | - Peter P. Zandi
- Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, 21205, USA
| | - James B. Potash
- Department of Psychiatry, University of Iowa Carver College of Medicine, Iowa City, IA, 52242, USA
| | - Virginia L. Willour
- Department of Psychiatry, University of Iowa Carver College of Medicine, Iowa City, IA, 52242, USA
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27
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Morris SM, Davison J, Carter KT, O'Leary RM, Trobridge P, Knoblaugh SE, Myeroff LL, Markowitz SD, Brett BT, Scheetz TE, Dupuy AJ, Starr TK, Grady WM. Transposon mutagenesis identifies candidate genes that cooperate with loss of transforming growth factor-beta signaling in mouse intestinal neoplasms. Int J Cancer 2016; 140:853-863. [PMID: 27790711 DOI: 10.1002/ijc.30491] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2016] [Revised: 10/06/2016] [Accepted: 10/10/2016] [Indexed: 12/22/2022]
Abstract
Colorectal cancer (CRC) results from the accumulation of gene mutations and epigenetic alterations in colon epithelial cells, which promotes CRC formation through deregulating signaling pathways. One of the most commonly deregulated signaling pathways in CRC is the transforming growth factor β (TGF-β) pathway. Importantly, the effects of TGF-β signaling inactivation in CRC are modified by concurrent mutations in the tumor cell, and these concurrent mutations determine the ultimate biological effects of impaired TGF-β signaling in the tumor. However, many of the mutations that cooperate with the deregulated TGF-β signaling pathway in CRC remain unknown. Therefore, we sought to identify candidate driver genes that promote the formation of CRC in the setting of TGF-β signaling inactivation. We performed a forward genetic screen in mice carrying conditionally inactivated alleles of the TGF-β receptor, type II (Tgfbr2) using Sleeping Beauty (SB) transposon mediated mutagenesis. We used TAPDANCE and Gene-centric statistical methods to identify common insertion sites (CIS) and, thus, candidate tumor suppressor genes and oncogenes within the tumor genome. CIS analysis of multiple neoplasms from these mice identified many candidate Tgfbr2 cooperating genes and the Wnt/β-catenin, Hippo and MAPK pathways as the most commonly affected pathways. Importantly, the majority of candidate genes were also found to be mutated in human CRC. The SB transposon system provides an unbiased method to identify Tgfbr2 cooperating genes in mouse CRC that are functionally relevant and that may provide further insight into the pathogenesis of human CRC.
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Affiliation(s)
- Shelli M Morris
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Jerry Davison
- Public Health Sciences Division, Genomics and Bioinformatics Shared Resource, Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Kelly T Carter
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Rachele M O'Leary
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Patty Trobridge
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Sue E Knoblaugh
- Department of Veterinary Biosciences, The Ohio State University, Columbus, OH
| | - Lois L Myeroff
- Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH
- Department of Medicine, Case Western Reserve University, Cleveland, OH
| | - Sanford D Markowitz
- Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH
- Department of Medicine, Case Western Reserve University, Cleveland, OH
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH
| | - Benjamin T Brett
- Center for Bioinformatics and Computational Biology, University of Iowa, Iowa City, IA
| | - Todd E Scheetz
- Center for Bioinformatics and Computational Biology, University of Iowa, Iowa City, IA
- Department of Ophthalmology and Visual Sciences, Roy J. & Lucille A. Carver College of Medicine, University of Iowa, Iowa City, IA
| | - Adam J Dupuy
- Department of Anatomy and Cell Biology, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, IA
- Department of Pathology, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, IA
| | - Timothy K Starr
- Department of Obstetrics, Gynecology & Women's Health, Masonic Cancer Center, University of Minnesota, Minneapolis, MN
- Department of Genetics, Cell Biology & Development, University of Minnesota, Minneapolis, MN
| | - William M Grady
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA
- Department of Medicine, University of Washington School of Medicine, Seattle, WA
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28
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Scheetz TE, Faga B, Ortega L, Roos BR, Gordon MO, Kass MA, Wang K, Fingert JH. Glaucoma Risk Alleles in the Ocular Hypertension Treatment Study. Ophthalmology 2016; 123:2527-2536. [PMID: 27707548 DOI: 10.1016/j.ophtha.2016.08.036] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2016] [Revised: 08/19/2016] [Accepted: 08/23/2016] [Indexed: 10/20/2022] Open
Abstract
PURPOSE Primary open-angle glaucoma (POAG) is a major cause of blindness and visual disability. Several genetic risk factors for POAG and optic nerve features have been identified. We measured the relative risk for glaucoma that these factors contribute to participants in the Ocular Hypertension Treatment Study (OHTS). DESIGN Comparative series. PARTICIPANTS One thousand fifty-seven of 1636 participants (65%) of the OHTS were enrolled in this genetics ancillary study. METHODS Samples of DNA were available from 1057 OHTS participants. Of these, 209 developed POAG (cases) and 848 did not develop glaucoma (controls) between 1994 and 2009. The frequencies of 13 risk alleles previously associated with POAG or with optic disc features in other cohorts were compared between POAG cases and controls in the OHTS cohort using analyses of variance. The 2 largest subgroups, non-Hispanic whites (n = 752; 70.7%) and blacks (n = 249, 23.7%), also were analyzed separately. The probability of glaucoma developing over the course of the OHTS was compared between participants stratified for transmembrane and coiled-coil domains 1 (TMCO1) risk alleles using Kaplan-Meier and Cox proportional hazards analyses. MAIN OUTCOME MEASURES Association of POAG with known genetic factors. RESULTS No association was detected between the known POAG risk alleles when the OHTS cohort was examined as a whole. However, in the subgroup of non-Hispanic whites, allele frequencies at the TMCO1 locus were statistically different between cases and controls (P = 0.00028). By 13 years, non-Hispanic white participants with TMCO1 risk alleles had a 12% higher cumulative frequency of glaucoma developing than participants with no TMCO1 risk alleles. Moreover, the Cox proportional hazard analysis demonstrated that TMCO1 alleles increased relative risk comparable with that of some previously analyzed clinical measures (i.e., intraocular pressure). CONCLUSIONS The size of the OHTS cohort and its composition of 2 large racial subgroups may limit its power to detect some glaucoma risk factors. However, TMCO1 genotype was found to increase the risk of glaucoma developing among non-Hispanic whites, the largest racial subgroup in the OHTS cohort, at a magnitude similar to clinical predictors of disease that long have been associated with glaucoma.
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Affiliation(s)
- Todd E Scheetz
- Department Ophthalmology and Visual Sciences, University of Iowa, Iowa City, Iowa; Stephen A. Wynn Institute for Vision Research, University of Iowa, Iowa City, Iowa
| | - Ben Faga
- Department Ophthalmology and Visual Sciences, University of Iowa, Iowa City, Iowa; Stephen A. Wynn Institute for Vision Research, University of Iowa, Iowa City, Iowa
| | - Lizette Ortega
- Department of Biostatistics, College of Public Health, University of Iowa, Iowa City, Iowa
| | - Ben R Roos
- Department Ophthalmology and Visual Sciences, University of Iowa, Iowa City, Iowa; Stephen A. Wynn Institute for Vision Research, University of Iowa, Iowa City, Iowa
| | - Mae O Gordon
- Department of Ophthalmology and Visual Sciences, Washington University School of Medicine, St. Louis, Missouri
| | - Michael A Kass
- Department of Ophthalmology and Visual Sciences, Washington University School of Medicine, St. Louis, Missouri
| | - Kai Wang
- Stephen A. Wynn Institute for Vision Research, University of Iowa, Iowa City, Iowa; Department of Biostatistics, College of Public Health, University of Iowa, Iowa City, Iowa
| | - John H Fingert
- Department Ophthalmology and Visual Sciences, University of Iowa, Iowa City, Iowa; Stephen A. Wynn Institute for Vision Research, University of Iowa, Iowa City, Iowa.
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Zarei K, Scheetz TE, Christopher M, Miller K, Hedberg-Buenz A, Tandon A, Anderson MG, Fingert JH, Abràmoff MD. Erratum: Corrigendum: Automated Axon Counting in Rodent Optic Nerve Sections with AxonJ. Sci Rep 2016; 6:34124. [PMID: 27759018 PMCID: PMC5069620 DOI: 10.1038/srep34124] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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Fingert JH, Robin AL, Scheetz TE, Kwon YH, Liebmann JM, Ritch R, Alward WLM. Tank-Binding Kinase 1 ( TBK1) Gene and Open-Angle Glaucomas (An American Ophthalmological Society Thesis). Trans Am Ophthalmol Soc 2016; 114:T6. [PMID: 27881886 PMCID: PMC5113957] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
PURPOSE To investigate the role of TANK-binding kinase 1 (TBK1) gene copy-number variations (ie, gene duplications and triplications) in the pathophysiology of various open-angle glaucomas. METHODS In previous studies, we discovered that copy-number variations in the TBK1 gene are associated with normal-tension glaucoma. Here, we investigated the prevalence of copy-number variations in cohorts of patients with other open-angle glaucomas-juvenile-onset open-angle glaucoma (n=30), pigmentary glaucoma (n=209), exfoliation glaucoma (n=225), and steroid-induced glaucoma (n=79)-using a quantitative polymerase chain reaction assay. RESULTS No TBK1 gene copy-number variations were detected in patients with juvenile-onset open-angle glaucoma, pigmentary glaucoma, or steroid-induced glaucoma. A TBK1 gene duplication was detected in one (0.44%) of the 225 exfoliation glaucoma patients. CONCLUSIONS TBK1 gene copy-number variations (gene duplications and triplications) have been previously associated with normal-tension glaucoma. An exploration of other open-angle glaucomas detected a TBK1 copy-number variation in a patient with exfoliation glaucoma, which is the first example of a TBK1 mutation in a glaucoma patient with a diagnosis other than normal-tension glaucoma. A broader phenotypic range may be associated with TBK1 copy-number variations, although mutations in this gene are most often detected in patients with normal-tension glaucoma.
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Affiliation(s)
- John H Fingert
- Department of Ophthalmology and Visual Sciences, Carver College of Medicine, University of Iowa, Iowa City, Iowa (Dr Fingert, Dr Scheetz, Dr Kwon, Dr Alward); the Stephen A. Wynn Institute for Vision Research, University of Iowa, Iowa City, Iowa (Dr Fingert, Dr Scheetz, Dr Kwon, Dr Alward); the Departments of Ophthalmology and International Health, School of Medicine and the Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland (Dr Robin); the Department of Ophthalmology, University of Maryland, Baltimore, Maryland (Dr Robin); Columbia University Medical Center, New York, New York (Dr Liebmann); the Einhorn Clinical Research Center, New York Eye and Ear Infirmary of Mount Sinai, New York, New York (Dr Ritch)
| | - Alan L Robin
- Department of Ophthalmology and Visual Sciences, Carver College of Medicine, University of Iowa, Iowa City, Iowa (Dr Fingert, Dr Scheetz, Dr Kwon, Dr Alward); the Stephen A. Wynn Institute for Vision Research, University of Iowa, Iowa City, Iowa (Dr Fingert, Dr Scheetz, Dr Kwon, Dr Alward); the Departments of Ophthalmology and International Health, School of Medicine and the Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland (Dr Robin); the Department of Ophthalmology, University of Maryland, Baltimore, Maryland (Dr Robin); Columbia University Medical Center, New York, New York (Dr Liebmann); the Einhorn Clinical Research Center, New York Eye and Ear Infirmary of Mount Sinai, New York, New York (Dr Ritch)
| | - Todd E Scheetz
- Department of Ophthalmology and Visual Sciences, Carver College of Medicine, University of Iowa, Iowa City, Iowa (Dr Fingert, Dr Scheetz, Dr Kwon, Dr Alward); the Stephen A. Wynn Institute for Vision Research, University of Iowa, Iowa City, Iowa (Dr Fingert, Dr Scheetz, Dr Kwon, Dr Alward); the Departments of Ophthalmology and International Health, School of Medicine and the Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland (Dr Robin); the Department of Ophthalmology, University of Maryland, Baltimore, Maryland (Dr Robin); Columbia University Medical Center, New York, New York (Dr Liebmann); the Einhorn Clinical Research Center, New York Eye and Ear Infirmary of Mount Sinai, New York, New York (Dr Ritch)
| | - Young H Kwon
- Department of Ophthalmology and Visual Sciences, Carver College of Medicine, University of Iowa, Iowa City, Iowa (Dr Fingert, Dr Scheetz, Dr Kwon, Dr Alward); the Stephen A. Wynn Institute for Vision Research, University of Iowa, Iowa City, Iowa (Dr Fingert, Dr Scheetz, Dr Kwon, Dr Alward); the Departments of Ophthalmology and International Health, School of Medicine and the Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland (Dr Robin); the Department of Ophthalmology, University of Maryland, Baltimore, Maryland (Dr Robin); Columbia University Medical Center, New York, New York (Dr Liebmann); the Einhorn Clinical Research Center, New York Eye and Ear Infirmary of Mount Sinai, New York, New York (Dr Ritch)
| | - Jeffrey M Liebmann
- Department of Ophthalmology and Visual Sciences, Carver College of Medicine, University of Iowa, Iowa City, Iowa (Dr Fingert, Dr Scheetz, Dr Kwon, Dr Alward); the Stephen A. Wynn Institute for Vision Research, University of Iowa, Iowa City, Iowa (Dr Fingert, Dr Scheetz, Dr Kwon, Dr Alward); the Departments of Ophthalmology and International Health, School of Medicine and the Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland (Dr Robin); the Department of Ophthalmology, University of Maryland, Baltimore, Maryland (Dr Robin); Columbia University Medical Center, New York, New York (Dr Liebmann); the Einhorn Clinical Research Center, New York Eye and Ear Infirmary of Mount Sinai, New York, New York (Dr Ritch)
| | - Robert Ritch
- Department of Ophthalmology and Visual Sciences, Carver College of Medicine, University of Iowa, Iowa City, Iowa (Dr Fingert, Dr Scheetz, Dr Kwon, Dr Alward); the Stephen A. Wynn Institute for Vision Research, University of Iowa, Iowa City, Iowa (Dr Fingert, Dr Scheetz, Dr Kwon, Dr Alward); the Departments of Ophthalmology and International Health, School of Medicine and the Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland (Dr Robin); the Department of Ophthalmology, University of Maryland, Baltimore, Maryland (Dr Robin); Columbia University Medical Center, New York, New York (Dr Liebmann); the Einhorn Clinical Research Center, New York Eye and Ear Infirmary of Mount Sinai, New York, New York (Dr Ritch)
| | - Wallace L M Alward
- Department of Ophthalmology and Visual Sciences, Carver College of Medicine, University of Iowa, Iowa City, Iowa (Dr Fingert, Dr Scheetz, Dr Kwon, Dr Alward); the Stephen A. Wynn Institute for Vision Research, University of Iowa, Iowa City, Iowa (Dr Fingert, Dr Scheetz, Dr Kwon, Dr Alward); the Departments of Ophthalmology and International Health, School of Medicine and the Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland (Dr Robin); the Department of Ophthalmology, University of Maryland, Baltimore, Maryland (Dr Robin); Columbia University Medical Center, New York, New York (Dr Liebmann); the Einhorn Clinical Research Center, New York Eye and Ear Infirmary of Mount Sinai, New York, New York (Dr Ritch)
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Scheetz TE, Roos BR, Solivan-Timpe F, Miller K, DeLuca AP, Stone EM, Kwon YH, Alward WLM, Wang K, Fingert JH. SQSTM1 Mutations and Glaucoma. PLoS One 2016; 11:e0156001. [PMID: 27275741 PMCID: PMC4898711 DOI: 10.1371/journal.pone.0156001] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Accepted: 05/06/2016] [Indexed: 12/14/2022] Open
Abstract
Glaucoma is the most common cause of irreversible blindness worldwide. One subset of glaucoma, normal tension glaucoma (NTG) occurs in the absence of high intraocular pressure. Mutations in two genes, optineurin (OPTN) and TANK binding kinase 1 (TBK1), cause familial NTG and have known roles in the catabolic cellular process autophagy. TKB1 encodes a kinase that phosphorylates OPTN, an autophagy receptor, which ultimately activates autophagy. The sequestosome (SQSTM1) gene also encodes an autophagy receptor and also is a target of TBK1 phosphorylation. Consequently, we hypothesized that mutations in SQSTM1 may also cause NTG. We tested this hypothesis by searching for glaucoma-causing mutations in a cohort of NTG patients (n = 308) and matched controls (n = 157) using Sanger sequencing. An additional 1098 population control samples were also analyzed using whole exome sequencing. A total of 17 non-synonymous mutations were detected which were not significantly skewed between cases and controls when analyzed separately, or as a group (p > 0.05). These data suggest that SQSTM1 mutations are not a common cause of NTG.
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Affiliation(s)
- Todd E. Scheetz
- Department of Ophthalmology and Visual Sciences, Carver College of Medicine, University of Iowa, Iowa City, Iowa, United States of America
- Stephen A. Wynn Institute for Vision Research, University of Iowa, Iowa City, Iowa, United States of America
| | - Ben R. Roos
- Department of Ophthalmology and Visual Sciences, Carver College of Medicine, University of Iowa, Iowa City, Iowa, United States of America
- Stephen A. Wynn Institute for Vision Research, University of Iowa, Iowa City, Iowa, United States of America
| | - Frances Solivan-Timpe
- Department of Ophthalmology and Visual Sciences, Carver College of Medicine, University of Iowa, Iowa City, Iowa, United States of America
- Stephen A. Wynn Institute for Vision Research, University of Iowa, Iowa City, Iowa, United States of America
| | - Kathy Miller
- Department of Ophthalmology and Visual Sciences, Carver College of Medicine, University of Iowa, Iowa City, Iowa, United States of America
- Stephen A. Wynn Institute for Vision Research, University of Iowa, Iowa City, Iowa, United States of America
| | - Adam P. DeLuca
- Department of Ophthalmology and Visual Sciences, Carver College of Medicine, University of Iowa, Iowa City, Iowa, United States of America
- Stephen A. Wynn Institute for Vision Research, University of Iowa, Iowa City, Iowa, United States of America
| | - Edwin M. Stone
- Department of Ophthalmology and Visual Sciences, Carver College of Medicine, University of Iowa, Iowa City, Iowa, United States of America
- Stephen A. Wynn Institute for Vision Research, University of Iowa, Iowa City, Iowa, United States of America
| | - Young H. Kwon
- Department of Ophthalmology and Visual Sciences, Carver College of Medicine, University of Iowa, Iowa City, Iowa, United States of America
- Stephen A. Wynn Institute for Vision Research, University of Iowa, Iowa City, Iowa, United States of America
| | - Wallace L. M. Alward
- Department of Ophthalmology and Visual Sciences, Carver College of Medicine, University of Iowa, Iowa City, Iowa, United States of America
- Stephen A. Wynn Institute for Vision Research, University of Iowa, Iowa City, Iowa, United States of America
| | - Kai Wang
- Stephen A. Wynn Institute for Vision Research, University of Iowa, Iowa City, Iowa, United States of America
- Department of Biostatistics, College of Public Health, University of Iowa, Iowa City, Iowa, United States of America
| | - John H. Fingert
- Department of Ophthalmology and Visual Sciences, Carver College of Medicine, University of Iowa, Iowa City, Iowa, United States of America
- Stephen A. Wynn Institute for Vision Research, University of Iowa, Iowa City, Iowa, United States of America
- * E-mail:
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Zarei K, Scheetz TE, Christopher M, Miller K, Hedberg-Buenz A, Tandon A, Anderson MG, Fingert JH, Abràmoff MD. Automated Axon Counting in Rodent Optic Nerve Sections with AxonJ. Sci Rep 2016; 6:26559. [PMID: 27226405 PMCID: PMC4881014 DOI: 10.1038/srep26559] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2015] [Accepted: 05/05/2016] [Indexed: 01/17/2023] Open
Abstract
We have developed a publicly available tool, AxonJ, which quantifies the axons in optic nerve sections of rodents stained with paraphenylenediamine (PPD). In this study, we compare AxonJ's performance to human experts on 100x and 40x images of optic nerve sections obtained from multiple strains of mice, including mice with defects relevant to glaucoma. AxonJ produced reliable axon counts with high sensitivity of 0.959 and high precision of 0.907, high repeatability of 0.95 when compared to a gold-standard of manual assessments and high correlation of 0.882 to the glaucoma damage staging of a previously published dataset. AxonJ allows analyses that are quantitative, consistent, fully-automated, parameter-free, and rapid on whole optic nerve sections at 40x. As a freely available ImageJ plugin that requires no highly specialized equipment to utilize, AxonJ represents a powerful new community resource augmenting studies of the optic nerve using mice.
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Affiliation(s)
- Kasra Zarei
- Stephen A. Wynn Institute for Vision Research, University of Iowa, Iowa City, IA 52242, USA.,Department of Biomedical Engineering, University of Iowa, Iowa City, IA 52242, USA
| | - Todd E Scheetz
- Stephen A. Wynn Institute for Vision Research, University of Iowa, Iowa City, IA 52242, USA.,Department of Biomedical Engineering, University of Iowa, Iowa City, IA 52242, USA.,Department of Ophthalmology and Visual Sciences, University of Iowa Hospitals and Clinics, 200 Hawkins Drive, Iowa City, IA 52242, USA
| | - Mark Christopher
- Stephen A. Wynn Institute for Vision Research, University of Iowa, Iowa City, IA 52242, USA.,Department of Biomedical Engineering, University of Iowa, Iowa City, IA 52242, USA.,Department of Ophthalmology and Visual Sciences, University of Iowa Hospitals and Clinics, 200 Hawkins Drive, Iowa City, IA 52242, USA
| | - Kathy Miller
- Stephen A. Wynn Institute for Vision Research, University of Iowa, Iowa City, IA 52242, USA.,Department of Ophthalmology and Visual Sciences, University of Iowa Hospitals and Clinics, 200 Hawkins Drive, Iowa City, IA 52242, USA
| | - Adam Hedberg-Buenz
- Stephen A. Wynn Institute for Vision Research, University of Iowa, Iowa City, IA 52242, USA.,Department of Veterans Affairs, Iowa City VA Medical Center, 601 Highway 6 West, Iowa City, IA 55242, USA.,Department of Molecular Physiology and Biophysics, University of Iowa, Iowa City, IA 52242, USA
| | - Anamika Tandon
- Stephen A. Wynn Institute for Vision Research, University of Iowa, Iowa City, IA 52242, USA.,Department of Ophthalmology and Visual Sciences, University of Iowa Hospitals and Clinics, 200 Hawkins Drive, Iowa City, IA 52242, USA
| | - Michael G Anderson
- Stephen A. Wynn Institute for Vision Research, University of Iowa, Iowa City, IA 52242, USA.,Department of Ophthalmology and Visual Sciences, University of Iowa Hospitals and Clinics, 200 Hawkins Drive, Iowa City, IA 52242, USA.,Department of Veterans Affairs, Iowa City VA Medical Center, 601 Highway 6 West, Iowa City, IA 55242, USA.,Department of Molecular Physiology and Biophysics, University of Iowa, Iowa City, IA 52242, USA
| | - John H Fingert
- Stephen A. Wynn Institute for Vision Research, University of Iowa, Iowa City, IA 52242, USA.,Department of Ophthalmology and Visual Sciences, University of Iowa Hospitals and Clinics, 200 Hawkins Drive, Iowa City, IA 52242, USA
| | - Michael David Abràmoff
- Stephen A. Wynn Institute for Vision Research, University of Iowa, Iowa City, IA 52242, USA.,Department of Biomedical Engineering, University of Iowa, Iowa City, IA 52242, USA.,Department of Ophthalmology and Visual Sciences, University of Iowa Hospitals and Clinics, 200 Hawkins Drive, Iowa City, IA 52242, USA.,Department of Veterans Affairs, Iowa City VA Medical Center, 601 Highway 6 West, Iowa City, IA 55242, USA.,Department of Electrical and Computer Engineering, University of Iowa, Iowa City, IA 52242, USA
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Reish O, Aspit L, Zouella A, Roth Y, Polak-Charcon S, Baboushkin T, Benyamini L, Scheetz TE, Mussaffi H, Sheffield VC, Parvari R. A Homozygous Nme7 Mutation Is Associated with Situs Inversus Totalis. Hum Mutat 2016; 37:727-31. [PMID: 27060491 DOI: 10.1002/humu.22998] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2015] [Revised: 02/25/2016] [Accepted: 03/09/2016] [Indexed: 02/06/2023]
Abstract
We investigated the cause of situs inversus totalis (SIT) in two siblings from a consanguineous family. Genotyping and whole-exome analysis revealed a homozygous change in NME7, resulting in deletion of an exon causing an in-frame deletion of 34 amino acids located in the second NDK domain of the protein and segregated with the defective lateralization in the family. NME7 is an important developmental gene, and NME7 protein is a component of the γ-tubulin ring complex. This mutation is predicted to affect the interaction of NME7 protein with this complex as it deletes the amino acids crucial for the binding. SIT associated with homozygous deletion in our patients is in line with Nme7(-/-) mutant mice phenotypes consisting of congenital hydrocephalus and SIT, indicating a novel human laterality patterning role for NME7. Further cases are required to elaborate the full human phenotype associated with NME7 mutations.
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Affiliation(s)
- Orit Reish
- Genetic Institute, Assaf Harofeh Medical Center, Zerifin, Israel.,The Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Liam Aspit
- Shraga Segal Department of Microbiology, Immunology and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Arielle Zouella
- Shraga Segal Department of Microbiology, Immunology and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Yehudah Roth
- The Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel.,Department of Otolaryngology - Head and Neck Surgery, Edith Wolfson Medical Center, Holon, Israel
| | - Sylvie Polak-Charcon
- Department of Pathology, The Sheba Medical Center at Tel Hashomer, Ramat Gan, Israel
| | - Tatiana Baboushkin
- The Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel.,Department of Pathology, The Sheba Medical Center at Tel Hashomer, Ramat Gan, Israel
| | - Lilach Benyamini
- Genetic Institute, Assaf Harofeh Medical Center, Zerifin, Israel
| | - Todd E Scheetz
- Stephen A Wynn Institute for Vision Research and Department of Ophthalmology and Visual Sciences, University of Iowa, Iowa City, Iowa
| | - Huda Mussaffi
- The Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel.,Pediatric Pulmunology Institute, Schneider Children's Medical Center of Israel, Petach Tikva, Israel
| | - Val C Sheffield
- Department of Pediatrics, Division of Medical Genetics, University of Iowa, Iowa City, Iowa
| | - Ruti Parvari
- Shraga Segal Department of Microbiology, Immunology and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel.,National Institute of Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer Sheva, Israel
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Kuehn MH, Lipsett KA, Menotti-Raymond M, Whitmore SS, Scheetz TE, David VA, O'Brien SJ, Zhao Z, Jens JK, Snella EM, Ellinwood NM, McLellan GJ. A Mutation in LTBP2 Causes Congenital Glaucoma in Domestic Cats (Felis catus). PLoS One 2016; 11:e0154412. [PMID: 27149523 PMCID: PMC4858209 DOI: 10.1371/journal.pone.0154412] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2015] [Accepted: 03/31/2016] [Indexed: 01/18/2023] Open
Abstract
The glaucomas are a group of diseases characterized by optic nerve damage that together represent a leading cause of blindness in the human population and in domestic animals. Here we report a mutation in LTBP2 that causes primary congenital glaucoma (PCG) in domestic cats. We identified a spontaneous form of PCG in cats and established a breeding colony segregating for PCG consistent with fully penetrant, autosomal recessive inheritance of the trait. Elevated intraocular pressure, globe enlargement and elongated ciliary processes were consistently observed in all affected cats by 8 weeks of age. Varying degrees of optic nerve damage resulted by 6 months of age. Although subtle lens zonular instability was a common feature in this cohort, pronounced ectopia lentis was identified in less than 10% of cats examined. Thus, glaucoma in this pedigree is attributed to histologically confirmed arrest in the early post-natal development of the aqueous humor outflow pathways in the anterior segment of the eyes of affected animals. Using a candidate gene approach, significant linkage was established on cat chromosome B3 (LOD 18.38, θ = 0.00) using tightly linked short tandem repeat (STR) loci to the candidate gene, LTBP2. A 4 base-pair insertion was identified in exon 8 of LTBP2 in affected individuals that generates a frame shift that completely alters the downstream open reading frame and eliminates functional domains. Thus, we describe the first spontaneous and highly penetrant non-rodent model of PCG identifying a valuable animal model for primary glaucoma that closely resembles the human disease, providing valuable insights into mechanisms underlying the disease and a valuable animal model for testing therapies.
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Affiliation(s)
- Markus H. Kuehn
- Department of Ophthalmology and Visual Sciences, Carver College of Medicine, University of Iowa, Iowa City, Iowa, United States of America
| | - Koren A. Lipsett
- Laboratory of Genomic Diversity, National Cancer Institute, Frederick, Maryland, United States of America
- Department of Chemistry, Gettysburg College, Gettysburg, Pennsylvania, United States of America
| | - Marilyn Menotti-Raymond
- Laboratory of Genomic Diversity, National Cancer Institute, Frederick, Maryland, United States of America
| | - S. Scott Whitmore
- Department of Ophthalmology and Visual Sciences, Carver College of Medicine, University of Iowa, Iowa City, Iowa, United States of America
| | - Todd E. Scheetz
- Department of Ophthalmology and Visual Sciences, Carver College of Medicine, University of Iowa, Iowa City, Iowa, United States of America
| | - Victor A. David
- Laboratory of Genomic Diversity, National Cancer Institute, Frederick, Maryland, United States of America
- Basic Research Laboratory, National Cancer Institute, Frederick, Maryland, United States of America
| | - Stephen J. O'Brien
- Laboratory of Genomic Diversity, National Cancer Institute, Frederick, Maryland, United States of America
- Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg, Russia
- Oceanographic Center, Nova Southeastern University, Fort Lauderdale, Florida, United States of America
| | - Zhongyuan Zhao
- Department of Chemistry, Gettysburg College, Gettysburg, Pennsylvania, United States of America
| | - Jackie K. Jens
- Department of Animal Science, Iowa State University, Ames, Iowa, United States of America
| | - Elizabeth M. Snella
- Department of Animal Science, Iowa State University, Ames, Iowa, United States of America
| | - N. Matthew Ellinwood
- Department of Animal Science, Iowa State University, Ames, Iowa, United States of America
- Department of Veterinary Clinical Sciences, Iowa State University, Ames, Iowa, United States of America
| | - Gillian J. McLellan
- Department of Ophthalmology and Visual Sciences, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Department of Surgical Sciences, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- McPherson Eye Research Institute, Madison, Wisconsin, United States of America
- * E-mail:
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Hedberg-Buenz A, Christopher MA, Lewis CJ, Fernandes KA, Dutca LM, Wang K, Scheetz TE, Abràmoff MD, Libby RT, Garvin MK, Anderson MG. Quantitative measurement of retinal ganglion cell populations via histology-based random forest classification. Exp Eye Res 2016; 146:370-385. [PMID: 26474494 PMCID: PMC4841761 DOI: 10.1016/j.exer.2015.09.011] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2015] [Revised: 09/02/2015] [Accepted: 09/20/2015] [Indexed: 01/27/2023]
Abstract
The inner surface of the retina contains a complex mixture of neurons, glia, and vasculature, including retinal ganglion cells (RGCs), the final output neurons of the retina and primary neurons that are damaged in several blinding diseases. The goal of the current work was two-fold: to assess the feasibility of using computer-assisted detection of nuclei and random forest classification to automate the quantification of RGCs in hematoxylin/eosin (H&E)-stained retinal whole-mounts; and if possible, to use the approach to examine how nuclear size influences disease susceptibility among RGC populations. To achieve this, data from RetFM-J, a semi-automated ImageJ-based module that detects, counts, and collects quantitative data on nuclei of H&E-stained whole-mounted retinas, were used in conjunction with a manually curated set of images to train a random forest classifier. To test performance, computer-derived outputs were compared to previously published features of several well-characterized mouse models of ophthalmic disease and their controls: normal C57BL/6J mice; Jun-sufficient and Jun-deficient mice subjected to controlled optic nerve crush (CONC); and DBA/2J mice with naturally occurring glaucoma. The result of these efforts was development of RetFM-Class, a command-line-based tool that uses data output from RetFM-J to perform random forest classification of cell type. Comparative testing revealed that manual and automated classifications by RetFM-Class correlated well, with 83.2% classification accuracy for RGCs. Automated characterization of C57BL/6J retinas predicted 54,642 RGCs per normal retina, and identified a 48.3% Jun-dependent loss of cells at 35 days post CONC and a 71.2% loss of RGCs among 16-month-old DBA/2J mice with glaucoma. Output from automated analyses was used to compare nuclear area among large numbers of RGCs from DBA/2J mice (n = 127,361). In aged DBA/2J mice with glaucoma, RetFM-Class detected a decrease in median and mean nucleus size of cells classified into the RGC category, as did an independent confirmation study using manual measurements of nuclear area demarcated by BRN3A-immunoreactivity. In conclusion, we have demonstrated that histology-based random forest classification is feasible and can be utilized to study RGCs in a high-throughput fashion. Despite having some limitations, this approach demonstrated a significant association between the size of the RGC nucleus and the DBA/2J form of glaucoma.
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Affiliation(s)
- Adam Hedberg-Buenz
- VA Center for the Prevention and Treatment of Visual Loss, Iowa City VA Health Care System, Iowa City, IA, USA; Department of Molecular Physiology and Biophysics, University of Iowa, Iowa City, IA 52242, USA
| | - Mark A Christopher
- Department of Biomedical Engineering, University of Iowa, Iowa City, IA 52242, USA
| | - Carly J Lewis
- Department of Molecular Physiology and Biophysics, University of Iowa, Iowa City, IA 52242, USA
| | - Kimberly A Fernandes
- Flaum Eye Institute, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Laura M Dutca
- VA Center for the Prevention and Treatment of Visual Loss, Iowa City VA Health Care System, Iowa City, IA, USA; Department of Ophthalmology and Visual Sciences, University of Iowa, Iowa City, IA 52242, USA
| | - Kai Wang
- Department of Biostatistics, University of Iowa, Iowa City, IA 52242, USA
| | - Todd E Scheetz
- Department of Biomedical Engineering, University of Iowa, Iowa City, IA 52242, USA; Department of Ophthalmology and Visual Sciences, University of Iowa, Iowa City, IA 52242, USA
| | - Michael D Abràmoff
- VA Center for the Prevention and Treatment of Visual Loss, Iowa City VA Health Care System, Iowa City, IA, USA; Department of Biomedical Engineering, University of Iowa, Iowa City, IA 52242, USA; Department of Ophthalmology and Visual Sciences, University of Iowa, Iowa City, IA 52242, USA; Department of Electrical and Computer Engineering, University of Iowa, Iowa City, IA 52242, USA
| | - Richard T Libby
- Flaum Eye Institute, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Mona K Garvin
- VA Center for the Prevention and Treatment of Visual Loss, Iowa City VA Health Care System, Iowa City, IA, USA; Department of Electrical and Computer Engineering, University of Iowa, Iowa City, IA 52242, USA
| | - Michael G Anderson
- VA Center for the Prevention and Treatment of Visual Loss, Iowa City VA Health Care System, Iowa City, IA, USA; Department of Molecular Physiology and Biophysics, University of Iowa, Iowa City, IA 52242, USA; Department of Ophthalmology and Visual Sciences, University of Iowa, Iowa City, IA 52242, USA.
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Zeng S, Whitmore SS, Sohn EH, Riker MJ, Wiley LA, Scheetz TE, Stone EM, Tucker BA, Mullins RF. Molecular response of chorioretinal endothelial cells to complement injury: implications for macular degeneration. J Pathol 2015; 238:446-56. [PMID: 26564985 DOI: 10.1002/path.4669] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2015] [Revised: 10/15/2015] [Accepted: 11/04/2015] [Indexed: 12/29/2022]
Abstract
Age-related macular degeneration (AMD) is a common, blinding disease of the elderly in which macular photoreceptor cells, retinal pigment epithelium and choriocapillaris endothelial cells ultimately degenerate. Recent studies have found that degeneration of the choriocapillaris occurs early in this disease and that endothelial cell drop-out is concomitant with increased deposition of the complement membrane attack complex (MAC) at the choroidal endothelium. However, the impact of MAC injury to choroidal endothelial cells is poorly understood. To model this event in vitro, and to study the downstream consequences of MAC injury, endothelial cells were exposed to complement from human serum, compared to heat-inactivated serum, which lacks complement components. Cells exposed to complement components in human serum showed increased labelling with antibodies directed against the MAC, time- and dose-dependent cell death, as assessed by lactate dehydrogenase assay and increased permeability. RNA-Seq analysis following complement injury revealed increased expression of genes associated with angiogenesis including matrix metalloproteinase (MMP)-3 and -9, and VEGF-A. The MAC-induced increase in MMP9 RNA expression was validated using C5-depleted serum compared to C5-reconstituted serum. Increased levels of MMP9 were also established, using western blot and zymography. These data suggest that, in addition to cell lysis, complement attack on choroidal endothelial cells promotes an angiogenic phenotype in surviving cells.
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Affiliation(s)
- Shemin Zeng
- Stephen A Wynn Institute for Vision Research and Department of Ophthalmology and Visual Sciences, University of Iowa, Iowa City, IA, USA
| | - S Scott Whitmore
- Stephen A Wynn Institute for Vision Research and Department of Ophthalmology and Visual Sciences, University of Iowa, Iowa City, IA, USA
| | - Elliott H Sohn
- Stephen A Wynn Institute for Vision Research and Department of Ophthalmology and Visual Sciences, University of Iowa, Iowa City, IA, USA
| | - Megan J Riker
- Stephen A Wynn Institute for Vision Research and Department of Ophthalmology and Visual Sciences, University of Iowa, Iowa City, IA, USA
| | - Luke A Wiley
- Stephen A Wynn Institute for Vision Research and Department of Ophthalmology and Visual Sciences, University of Iowa, Iowa City, IA, USA
| | - Todd E Scheetz
- Stephen A Wynn Institute for Vision Research and Department of Ophthalmology and Visual Sciences, University of Iowa, Iowa City, IA, USA
| | - Edwin M Stone
- Stephen A Wynn Institute for Vision Research and Department of Ophthalmology and Visual Sciences, University of Iowa, Iowa City, IA, USA
| | - Budd A Tucker
- Stephen A Wynn Institute for Vision Research and Department of Ophthalmology and Visual Sciences, University of Iowa, Iowa City, IA, USA
| | - Robert F Mullins
- Stephen A Wynn Institute for Vision Research and Department of Ophthalmology and Visual Sciences, University of Iowa, Iowa City, IA, USA
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Hazlewood RJ, Roos BR, Solivan-Timpe F, Honkanen RA, Jampol LM, Gieser SC, Meyer KJ, Mullins RF, Kuehn MH, Scheetz TE, Kwon YH, Alward WLM, Stone EM, Fingert JH. Heterozygous triplication of upstream regulatory sequences leads to dysregulation of matrix metalloproteinase 19 in patients with cavitary optic disc anomaly. Hum Mutat 2015; 36:369-78. [PMID: 25581579 DOI: 10.1002/humu.22754] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2014] [Accepted: 12/23/2014] [Indexed: 11/06/2022]
Abstract
Patients with a congenital optic nerve disease, cavitary optic disc anomaly (CODA), are born with profound excavation of the optic nerve resembling glaucoma. We previously mapped the gene that causes autosomal-dominant CODA in a large pedigree to a chromosome 12q locus. Using comparative genomic hybridization and quantitative PCR analysis of this pedigree, we report identifying a 6-Kbp heterozygous triplication upstream of the matrix metalloproteinase 19 (MMP19) gene, present in all 17 affected family members and no normal members. Moreover, the triplication was not detected in 78 control subjects or in the Database of Genomic Variants. We further detected the same 6-Kbp triplication in one of 24 unrelated CODA patients and in none of 172 glaucoma patients. Analysis with a Luciferase assay showed that the 6-Kbp sequence has transcription enhancer activity. A 773-bp fragment of the 6-Kbp DNA segment increased downstream gene expression eightfold, suggesting that triplication of this sequence may lead to dysregulation of the downstream gene, MMP19, in CODA patients. Lastly, immunohistochemical analysis of human donor eyes revealed strong expression of MMP19 in optic nerve head. These data strongly suggest that triplication of an enhancer may lead to overexpression of MMP19 in the optic nerve that causes CODA.
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Affiliation(s)
- Ralph J Hazlewood
- Department of Ophthalmology and Visual Sciences, Carver College of Medicine, University of Iowa, Iowa City, Iowa; Stephen A. Wynn Institute for Vision Research, University of Iowa, Iowa City, Iowa
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Taylor KR, Booth KT, Azaiez H, Sloan CM, Kolbe DL, Glanz EN, Shearer AE, DeLuca AP, Anand VN, Hildebrand MS, Simpson AC, Eppsteiner RW, Scheetz TE, Braun TA, Huygen PLM, Smith RJH, Casavant TL. Audioprofile Surfaces: The 21st Century Audiogram. Ann Otol Rhinol Laryngol 2015; 125:361-8. [PMID: 26530094 DOI: 10.1177/0003489415614863] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
OBJECTIVE To present audiometric data in 3 dimensions by considering age as an addition dimension. METHODS Audioprofile surfaces (APSs) were fitted to a set of audiograms by plotting each measurement of an audiogram as an independent point in 3 dimensions with the x, y, and z axes representing frequency, hearing loss in dB, and age, respectively. RESULTS Using the Java-based APS viewer as a standalone application, APSs were pre-computed for 34 loci. By selecting APSs for the appropriate genetic locus, a clinician can compare this APS-generated average surface to a specific patient's audiogram. CONCLUSION Audioprofile surfaces provide an easily interpreted visual representation of a person's hearing acuity relative to others with the same genetic cause of hearing loss. Audioprofile surfaces will support the generation and testing of sophisticated hypotheses to further refine our understanding of the biology of hearing.
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Affiliation(s)
- Kyle R Taylor
- Department of Electrical and Computer Engineering, University of Iowa, Iowa City, Iowa, USA Center for Bioinformatics and Computational Biology, University of Iowa, Iowa City, Iowa, USA
| | - Kevin T Booth
- Department of Otolaryngology, Head and Neck Surgery, University of Iowa, Iowa City, Iowa, USA
| | - Hela Azaiez
- Department of Otolaryngology, Head and Neck Surgery, University of Iowa, Iowa City, Iowa, USA
| | - Christina M Sloan
- Department of Molecular Physiology and Biophysics, University of Iowa Carver, Iowa City, Iowa, USA
| | - Diana L Kolbe
- Department of Otolaryngology, Head and Neck Surgery, University of Iowa, Iowa City, Iowa, USA
| | - Emily N Glanz
- Department of Electrical and Computer Engineering, University of Iowa, Iowa City, Iowa, USA Center for Bioinformatics and Computational Biology, University of Iowa, Iowa City, Iowa, USA
| | - A Eliot Shearer
- Department of Otolaryngology, Head and Neck Surgery, University of Iowa, Iowa City, Iowa, USA
| | - Adam P DeLuca
- Department of Ophthalmology and Visual Sciences, University of Iowa, Iowa City, Iowa, USA
| | - V Nikhil Anand
- Center for Bioinformatics and Computational Biology, University of Iowa, Iowa City, Iowa, USA
| | - Michael S Hildebrand
- Department of Otolaryngology, Head and Neck Surgery, University of Iowa, Iowa City, Iowa, USA
| | - Allen C Simpson
- Department of Otolaryngology, Head and Neck Surgery, University of Iowa, Iowa City, Iowa, USA
| | - Robert W Eppsteiner
- Department of Otolaryngology, Head and Neck Surgery, University of Iowa, Iowa City, Iowa, USA
| | - Todd E Scheetz
- Department of Electrical and Computer Engineering, University of Iowa, Iowa City, Iowa, USA Center for Bioinformatics and Computational Biology, University of Iowa, Iowa City, Iowa, USA Department of Ophthalmology and Visual Sciences, University of Iowa, Iowa City, Iowa, USA
| | - Terry A Braun
- Department of Electrical and Computer Engineering, University of Iowa, Iowa City, Iowa, USA Center for Bioinformatics and Computational Biology, University of Iowa, Iowa City, Iowa, USA
| | - Patrick L M Huygen
- Department of Otorhinolaryngology, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
| | - Richard J H Smith
- Department of Otolaryngology, Head and Neck Surgery, University of Iowa, Iowa City, Iowa, USA Department of Molecular Physiology and Biophysics, University of Iowa Carver, Iowa City, Iowa, USA
| | - Thomas L Casavant
- Department of Electrical and Computer Engineering, University of Iowa, Iowa City, Iowa, USA Center for Bioinformatics and Computational Biology, University of Iowa, Iowa City, Iowa, USA Department of Ophthalmology and Visual Sciences, University of Iowa, Iowa City, Iowa, USA
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Christopher M, Abràmoff MD, Tang L, Gordon MO, Kass MA, Budenz DL, Fingert JH, Scheetz TE. Stereo Photo Measured ONH Shape Predicts Development of POAG in Subjects With Ocular Hypertension. Invest Ophthalmol Vis Sci 2015; 56:4470-9. [PMID: 26193923 DOI: 10.1167/iovs.14-16142] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
PURPOSE To identify objective, quantitative optic nerve head (ONH) structural features and model the contributions of glaucoma. METHODS Baseline stereoscopic optic disc images of 1635 glaucoma-free participants at risk for developing primary open-angle glaucoma (POAG) were collected as part of the Ocular Hypertension Treatment Study. A stereo correspondence algorithm designed for fundus images was applied to extract the three-dimensional (3D) information about the ONH. Principal component analysis was used to identify ONH 3D structural features and the contributions of demographic features, clinical variables, and disease were modeled using linear regression and linear component analysis. The computationally identified features were evaluated based on associations with glaucoma and ability to predict which participants would develop POAG. RESULTS The computationally identified features were significantly associated with future POAG, POAG-related demographics (age, ethnicity), and clinical measurements (horizontal and vertical cup-to-disc ratio, central corneal thickness, and refraction). Models predicting future POAG development using the OHTS baseline data and STEP features achieved an AUC of 0.722 in cross-validation testing. This was a significant improvement over using only demographics (age, sex, and ethnicity), which had an AUC of 0.599. CONCLUSIONS Methods for identifying objective, quantitative measurements of 3D ONH structure were developed using a large dataset. The identified features were significantly associated with POAG and POAG-related variables. Further, these features increased predictive model accuracy in predicting future POAG. The results indicate that the computationally identified features might be useful in POAG early screening programs or as endophenotypes to investigate POAG genetics.
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Affiliation(s)
- Mark Christopher
- Stephen A. Wynn Institute for Vision Research, University of Iowa, Iowa City, Iowa, United States 2Department of Biomedical Engineering, University of Iowa, Iowa City, Iowa, United States
| | - Michael D Abràmoff
- Stephen A. Wynn Institute for Vision Research, University of Iowa, Iowa City, Iowa, United States 2Department of Biomedical Engineering, University of Iowa, Iowa City, Iowa, United States 3Department of Electrical and Computer Engineering, University of I
| | - Li Tang
- Department of Ophthalmology and Visual Sciences, University of Iowa, Iowa City, Iowa, United States
| | - Mae O Gordon
- Division of Biostatistics, Washington University, St. Louis, Missouri, United States 7Department of Ophthalmology and Visual Sciences, Washington University, St. Louis, Missouri, United States
| | - Michael A Kass
- Department of Ophthalmology and Visual Sciences, Washington University, St. Louis, Missouri, United States
| | - Donald L Budenz
- Department of Ophthalmology, University of North Carolina, Chapel Hill, North Carolina, United States
| | - John H Fingert
- Stephen A. Wynn Institute for Vision Research, University of Iowa, Iowa City, Iowa, United States 4Department of Ophthalmology and Visual Sciences, University of Iowa, Iowa City, Iowa, United States
| | - Todd E Scheetz
- Stephen A. Wynn Institute for Vision Research, University of Iowa, Iowa City, Iowa, United States 2Department of Biomedical Engineering, University of Iowa, Iowa City, Iowa, United States 4Department of Ophthalmology and Visual Sciences, University of Iow
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Small KW, DeLuca AP, Whitmore SS, Rosenberg T, Silva-Garcia R, Udar N, Puech B, Garcia CA, Rice TA, Fishman GA, Héon E, Folk JC, Streb LM, Haas CM, Wiley LA, Scheetz TE, Fingert JH, Mullins RF, Tucker BA, Stone EM. North Carolina Macular Dystrophy Is Caused by Dysregulation of the Retinal Transcription Factor PRDM13. Ophthalmology 2015; 123:9-18. [PMID: 26507665 DOI: 10.1016/j.ophtha.2015.10.006] [Citation(s) in RCA: 78] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Revised: 10/07/2015] [Accepted: 10/07/2015] [Indexed: 12/30/2022] Open
Abstract
PURPOSE To identify specific mutations causing North Carolina macular dystrophy (NCMD). DESIGN Whole-genome sequencing coupled with reverse transcription polymerase chain reaction (RT-PCR) analysis of gene expression in human retinal cells. PARTICIPANTS A total of 141 members of 12 families with NCMD and 261 unrelated control individuals. METHODS Genome sequencing was performed on 8 affected individuals from 3 families affected with chromosome 6-linked NCMD (MCDR1) and 2 individuals affected with chromosome 5-linked NCMD (MCDR3). Variants observed in the MCDR1 locus with frequencies <1% in published databases were confirmed using Sanger sequencing. Confirmed variants absent from all published databases were sought in 8 additional MCDR1 families and 261 controls. The RT-PCR analysis of selected genes was performed in stem cell-derived human retinal cells. MAIN OUTCOME MEASURES Co-segregation of rare genetic variants with disease phenotype. RESULTS Five sequenced individuals with MCDR1-linked NCMD shared a haplotype of 14 rare variants spanning 1 Mb of the disease-causing allele. One of these variants (V1) was absent from all published databases and all 261 controls, but was found in 5 additional NCMD kindreds. This variant lies in a DNase 1 hypersensitivity site (DHS) upstream of both the PRDM13 and CCNC genes. Sanger sequencing of 1 kb centered on V1 was performed in the remaining 4 NCMD probands, and 2 additional novel single nucleotide variants (V2 in 3 families and V3 in 1 family) were identified in the DHS within 134 bp of the location of V1. A complete duplication of the PRDM13 gene was also discovered in a single family (V4). The RT-PCR analysis of PRDM13 expression in developing retinal cells revealed marked developmental regulation. Next-generation sequencing of 2 individuals with MCDR3-linked NCMD revealed a 900-kb duplication that included the entire IRX1 gene (V5). The 5 mutations V1 to V5 segregated perfectly in the 102 affected and 39 unaffected members of the 12 NCMD families. CONCLUSIONS We identified 5 rare mutations, each capable of arresting human macular development. Four of these strongly implicate the involvement of PRDM13 in macular development, whereas the pathophysiologic mechanism of the fifth remains unknown but may involve the developmental dysregulation of IRX1.
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Affiliation(s)
- Kent W Small
- Molecular Insight Research Foundation, Glendale, California
| | - Adam P DeLuca
- Department of Ophthalmology and Visual Sciences, Stephen A. Wynn Institute for Vision Research, University of Iowa, Iowa City, Iowa
| | - S Scott Whitmore
- Department of Ophthalmology and Visual Sciences, Stephen A. Wynn Institute for Vision Research, University of Iowa, Iowa City, Iowa
| | - Thomas Rosenberg
- National Eye Clinic, Kennedy Center, Glostrup, Denmark, and Institute of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | | | - Nitin Udar
- Molecular Insight Research Foundation, Glendale, California
| | - Bernard Puech
- Service d'Exploration de la vision et Neuro-ophtalmologie CHRU, Lille, France
| | - Charles A Garcia
- University of Texas Health Science Center at Houston, Houston, Texas
| | - Thomas A Rice
- Byers Eye Institute, Stanford University School of Medicine, Palo Alto, California
| | - Gerald A Fishman
- The Pangere Center for Inherited Retinal Diseases, The Chicago Lighthouse for People Who Are Blind or Visually Impaired, Chicago, Illinois
| | - Elise Héon
- Department of Ophthalmology and Vision Sciences, Programme of Genetics and Genomic Medicine, The Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada
| | - James C Folk
- Department of Ophthalmology and Visual Sciences, Stephen A. Wynn Institute for Vision Research, University of Iowa, Iowa City, Iowa
| | - Luan M Streb
- Department of Ophthalmology and Visual Sciences, Stephen A. Wynn Institute for Vision Research, University of Iowa, Iowa City, Iowa
| | - Christine M Haas
- Department of Ophthalmology and Visual Sciences, Stephen A. Wynn Institute for Vision Research, University of Iowa, Iowa City, Iowa
| | - Luke A Wiley
- Department of Ophthalmology and Visual Sciences, Stephen A. Wynn Institute for Vision Research, University of Iowa, Iowa City, Iowa
| | - Todd E Scheetz
- Department of Ophthalmology and Visual Sciences, Stephen A. Wynn Institute for Vision Research, University of Iowa, Iowa City, Iowa
| | - John H Fingert
- Department of Ophthalmology and Visual Sciences, Stephen A. Wynn Institute for Vision Research, University of Iowa, Iowa City, Iowa
| | - Robert F Mullins
- Department of Ophthalmology and Visual Sciences, Stephen A. Wynn Institute for Vision Research, University of Iowa, Iowa City, Iowa
| | - Budd A Tucker
- Department of Ophthalmology and Visual Sciences, Stephen A. Wynn Institute for Vision Research, University of Iowa, Iowa City, Iowa
| | - Edwin M Stone
- Department of Ophthalmology and Visual Sciences, Stephen A. Wynn Institute for Vision Research, University of Iowa, Iowa City, Iowa.
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DeLuca AP, Whitmore SS, Barnes J, Sharma TP, Westfall TA, Scott CA, Weed MC, Wiley JS, Wiley LA, Johnston RM, Schnieders MJ, Lentz SR, Tucker BA, Mullins RF, Scheetz TE, Stone EM, Slusarski DC. Hypomorphic mutations in TRNT1 cause retinitis pigmentosa with erythrocytic microcytosis. Hum Mol Genet 2015; 25:44-56. [PMID: 26494905 DOI: 10.1093/hmg/ddv446] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2015] [Accepted: 10/19/2015] [Indexed: 02/07/2023] Open
Abstract
Retinitis pigmentosa (RP) is a highly heterogeneous group of disorders characterized by degeneration of the retinal photoreceptor cells and progressive loss of vision. While hundreds of mutations in more than 100 genes have been reported to cause RP, discovering the causative mutations in many patients remains a significant challenge. Exome sequencing in an individual affected with non-syndromic RP revealed two plausibly disease-causing variants in TRNT1, a gene encoding a nucleotidyltransferase critical for tRNA processing. A total of 727 additional unrelated individuals with molecularly uncharacterized RP were completely screened for TRNT1 coding sequence variants, and a second family was identified with two members who exhibited a phenotype that was remarkably similar to the index patient. Inactivating mutations in TRNT1 have been previously shown to cause a severe congenital syndrome of sideroblastic anemia, B-cell immunodeficiency, recurrent fevers and developmental delay (SIFD). Complete blood counts of all three of our patients revealed red blood cell microcytosis and anisocytosis with only mild anemia. Characterization of TRNT1 in patient-derived cell lines revealed reduced but detectable TRNT1 protein, consistent with partial function. Suppression of trnt1 expression in zebrafish recapitulated several features of the human SIFD syndrome, including anemia and sensory organ defects. When levels of trnt1 were titrated, visual dysfunction was found in the absence of other phenotypes. The visual defects in the trnt1-knockdown zebrafish were ameliorated by the addition of exogenous human TRNT1 RNA. Our findings indicate that hypomorphic TRNT1 mutations can cause a recessive disease that is almost entirely limited to the retina.
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Affiliation(s)
- Adam P DeLuca
- The Stephen A. Wynn Institute for Vision Research, Department of Ophthalmology and Visual Sciences
| | - S Scott Whitmore
- The Stephen A. Wynn Institute for Vision Research, Department of Ophthalmology and Visual Sciences
| | | | - Tasneem P Sharma
- The Stephen A. Wynn Institute for Vision Research, Department of Ophthalmology and Visual Sciences
| | | | | | - Matthew C Weed
- The Stephen A. Wynn Institute for Vision Research, Department of Ophthalmology and Visual Sciences
| | - Jill S Wiley
- The Stephen A. Wynn Institute for Vision Research, Department of Ophthalmology and Visual Sciences
| | - Luke A Wiley
- The Stephen A. Wynn Institute for Vision Research, Department of Ophthalmology and Visual Sciences
| | - Rebecca M Johnston
- The Stephen A. Wynn Institute for Vision Research, Department of Ophthalmology and Visual Sciences
| | - Michael J Schnieders
- The Stephen A. Wynn Institute for Vision Research, Department of Biomedical Engineering, Department of Biochemistry, and
| | - Steven R Lentz
- Department of Internal Medicine; The University of Iowa, Iowa City, IA, USA
| | - Budd A Tucker
- The Stephen A. Wynn Institute for Vision Research, Department of Ophthalmology and Visual Sciences
| | - Robert F Mullins
- The Stephen A. Wynn Institute for Vision Research, Department of Ophthalmology and Visual Sciences
| | - Todd E Scheetz
- The Stephen A. Wynn Institute for Vision Research, Department of Ophthalmology and Visual Sciences, Department of Biomedical Engineering
| | - Edwin M Stone
- The Stephen A. Wynn Institute for Vision Research, Department of Ophthalmology and Visual Sciences
| | - Diane C Slusarski
- The Stephen A. Wynn Institute for Vision Research, Department of Biology,
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Khorram D, Choi M, Roos BR, Stone EM, Kopel T, Allen R, Alward WL, Scheetz TE, Fingert JH. Novel TMEM98 mutations in pedigrees with autosomal dominant nanophthalmos. Mol Vis 2015; 21:1017-23. [PMID: 26392740 PMCID: PMC4556162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Accepted: 09/01/2015] [Indexed: 11/17/2022] Open
Abstract
PURPOSE Autosomal dominant nanophthalmos is an inherited eye disorder characterized by a structurally normal but smaller eye. Patients with nanophthalmos have high hyperopia (far-sightedness), a greater incidence of angle-closure glaucoma, and increased risk of surgical complications. In this study, the clinical features and the genetic basis of nanophthalmos were investigated in two large autosomal dominant nanophthalmos pedigrees. METHODS Fourteen members of a Caucasian pedigree from the United States and 15 members of a pedigree from the Mariana Islands enrolled in a genetic study of nanophthalmos and contributed DNA samples. Twenty of 29 family members underwent eye examinations that included measurement of axial eye length and/or refractive error. The genetic basis of nanophthalmos in the pedigrees was studied with linkage analysis, whole exome sequencing, and candidate gene (i.e., TMEM98) sequencing to identify the nanophthalmos-causing gene. RESULTS Nine members of the pedigree from the United States and 11 members of the pedigree from the Mariana Islands were diagnosed with nanophthalmos that is transmitted as an autosomal dominant trait. The patients with nanophthalmos had abnormally short axial eye lengths, which ranged from 15.9 to 18.4 mm. Linkage analysis of the nanophthalmos pedigree from the United States identified nine large regions of the genome (greater than 10 Mbp) that were coinherited with disease in this family. Genes within these "linked regions" were examined for disease-causing mutations using exome sequencing, and a His196Pro mutation was detected in the TMEM98 gene, which was recently reported to be a nanophthalmos gene. Sanger sequencing subsequently showed that all other members of this pedigree with nanophthalmos also carry the His196Pro TMEM98 mutation. Testing the Mariana Islands pedigree for TMEM98 mutations identified a 34 bp heterozygous deletion that spans the 3' end of exon 4 in all affected family members. Neither TMEM98 mutation was detected in public exome sequence databases. CONCLUSIONS A recent report identified a single TMEM98 missense mutation in a nanophthalmos pedigree. Our discovery of two additional TMEM98 mutations confirms the important role of the gene in the pathogenesis of autosomal dominant nanophthalmos.
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Affiliation(s)
- David Khorram
- Marianas Eye Institute, Saipan, Northern Mariana Islands
| | - Michael Choi
- Department of Ophthalmology and Visual Sciences, Carver College of Medicine, University of Iowa,The Wynn Institute for Vision Research, University of Iowa
| | - Ben R. Roos
- Department of Ophthalmology and Visual Sciences, Carver College of Medicine, University of Iowa,The Wynn Institute for Vision Research, University of Iowa
| | - Edwin M. Stone
- Department of Ophthalmology and Visual Sciences, Carver College of Medicine, University of Iowa,The Wynn Institute for Vision Research, University of Iowa
| | - Teresa Kopel
- Department of Ophthalmology and Visual Sciences, Carver College of Medicine, University of Iowa,The Wynn Institute for Vision Research, University of Iowa
| | - Richard Allen
- Department of Ophthalmology and Visual Sciences, Carver College of Medicine, University of Iowa,The Wynn Institute for Vision Research, University of Iowa
| | - Wallace L.M. Alward
- Department of Ophthalmology and Visual Sciences, Carver College of Medicine, University of Iowa,The Wynn Institute for Vision Research, University of Iowa
| | - Todd E. Scheetz
- Department of Ophthalmology and Visual Sciences, Carver College of Medicine, University of Iowa,The Wynn Institute for Vision Research, University of Iowa
| | - John H. Fingert
- Department of Ophthalmology and Visual Sciences, Carver College of Medicine, University of Iowa,The Wynn Institute for Vision Research, University of Iowa
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Hedberg-Buenz A, Christopher MA, Lewis CJ, Meyer KJ, Rudd DS, Dutca LM, Wang K, Garvin MK, Scheetz TE, Abràmoff MD, Harper MM, Anderson MG. RetFM-J, an ImageJ-based module for automated counting and quantifying features of nuclei in retinal whole-mounts. Exp Eye Res 2015; 146:386-392. [PMID: 26283021 DOI: 10.1016/j.exer.2015.07.020] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2015] [Accepted: 07/28/2015] [Indexed: 01/28/2023]
Abstract
The present article introduces RetFM-J, a semi-automated ImageJ-based module that detects, counts, and collects quantitative data on nuclei of the inner retina from H&E-stained whole-mounted retinas. To illustrate performance, computer-derived outputs were analyzed in inbred C57BL/6J mice. Automated characterization yielded computer-derived outputs that closely matched manual counts. As a method using open-source software that is freely available, inexpensive staining reagents that are robust, and imaging equipment that is routine to most laboratories, RetFM-J could be utilized in a wide variety of experiments benefiting from high-throughput, quantitative, uniform analyses of total cellularity in the inner retina.
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Affiliation(s)
- Adam Hedberg-Buenz
- VA Center for the Prevention and Treatment of Visual Loss, Iowa City VA Health Care System, Iowa City, IA, USA; Department of Molecular Physiology and Biophysics, University of Iowa, Iowa City, IA 52242, USA
| | - Mark A Christopher
- Department of Biomedical Engineering, University of Iowa, Iowa City, IA 52242, USA
| | - Carly J Lewis
- Department of Molecular Physiology and Biophysics, University of Iowa, Iowa City, IA 52242, USA
| | - Kacie J Meyer
- Department of Molecular Physiology and Biophysics, University of Iowa, Iowa City, IA 52242, USA
| | - Danielle S Rudd
- VA Center for the Prevention and Treatment of Visual Loss, Iowa City VA Health Care System, Iowa City, IA, USA
| | - Laura M Dutca
- VA Center for the Prevention and Treatment of Visual Loss, Iowa City VA Health Care System, Iowa City, IA, USA; Department of Ophthalmology and Visual Sciences, University of Iowa, Iowa City, IA 52242, USA
| | - Kai Wang
- Department of Biostatistics, University of Iowa, Iowa City, IA 52242, USA
| | - Mona K Garvin
- VA Center for the Prevention and Treatment of Visual Loss, Iowa City VA Health Care System, Iowa City, IA, USA; Department of Electrical and Computer Engineering, University of Iowa, Iowa City, IA 52242, USA
| | - Todd E Scheetz
- Department of Biomedical Engineering, University of Iowa, Iowa City, IA 52242, USA; Department of Ophthalmology and Visual Sciences, University of Iowa, Iowa City, IA 52242, USA
| | - Michael D Abràmoff
- VA Center for the Prevention and Treatment of Visual Loss, Iowa City VA Health Care System, Iowa City, IA, USA; Department of Biomedical Engineering, University of Iowa, Iowa City, IA 52242, USA; Department of Ophthalmology and Visual Sciences, University of Iowa, Iowa City, IA 52242, USA; Department of Electrical and Computer Engineering, University of Iowa, Iowa City, IA 52242, USA
| | - Matthew M Harper
- VA Center for the Prevention and Treatment of Visual Loss, Iowa City VA Health Care System, Iowa City, IA, USA; Department of Ophthalmology and Visual Sciences, University of Iowa, Iowa City, IA 52242, USA
| | - Michael G Anderson
- VA Center for the Prevention and Treatment of Visual Loss, Iowa City VA Health Care System, Iowa City, IA, USA; Department of Molecular Physiology and Biophysics, University of Iowa, Iowa City, IA 52242, USA; Department of Ophthalmology and Visual Sciences, University of Iowa, Iowa City, IA 52242, USA.
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Riordan JD, Drury LJ, Smith RP, Brett BT, Rogers LM, Scheetz TE, Dupuy AJ. Sequencing methods and datasets to improve functional interpretation of sleeping beauty mutagenesis screens. BMC Genomics 2014; 15:1150. [PMID: 25526783 PMCID: PMC4378557 DOI: 10.1186/1471-2164-15-1150] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2014] [Accepted: 12/16/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Animal models of cancer are useful to generate complementary datasets for comparison to human tumor data. Insertional mutagenesis screens, such as those utilizing the Sleeping Beauty (SB) transposon system, provide a model that recapitulates the spontaneous development and progression of human disease. This approach has been widely used to model a variety of cancers in mice. Comprehensive mutation profiles are generated for individual tumors through amplification of transposon insertion sites followed by high-throughput sequencing. Subsequent statistical analyses identify common insertion sites (CISs), which are predicted to be functionally involved in tumorigenesis. Current methods utilized for SB insertion site analysis have some significant limitations. For one, they do not account for transposon footprints - a class of mutation generated following transposon remobilization. Existing methods also discard quantitative sequence data due to uncertainty regarding the extent to which it accurately reflects mutation abundance within a heterogeneous tumor. Additionally, computational analyses generally assume that all potential insertion sites have an equal probability of being detected under non-selective conditions, an assumption without sufficient relevant data. The goal of our study was to address these potential confounding factors in order to enhance functional interpretation of insertion site data from tumors. RESULTS We describe here a novel method to detect footprints generated by transposon remobilization, which revealed minimal evidence of positive selection in tumors. We also present extensive characterization data demonstrating an ability to reproducibly assign semi-quantitative information to individual insertion sites within a tumor sample. Finally, we identify apparent biases for detection of inserted transposons in several genomic regions that may lead to the identification of false positive CISs. CONCLUSION The information we provide can be used to refine analyses of data from insertional mutagenesis screens, improving functional interpretation of results and facilitating the identification of genes important in cancer development and progression.
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Affiliation(s)
| | | | | | | | | | | | - Adam J Dupuy
- Department of Anatomy and Cell Biology, University of Iowa, Iowa City IA 52242, USA.
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Lee A, Wang S, Williams B, Hagen J, Scheetz TE, Haeseleer F. Characterization of Cav1.4 complexes (α11.4, β2, and α2δ4) in HEK293T cells and in the retina. J Biol Chem 2014; 290:1505-21. [PMID: 25468907 DOI: 10.1074/jbc.m114.607465] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
In photoreceptor synaptic terminals, voltage-gated Cav1.4 channels mediate Ca(2+) signals required for transmission of visual stimuli. Like other high voltage-activated Cav channels, Cav1.4 channels are composed of a main pore-forming Cav1.4 α1 subunit and auxiliary β and α2δ subunits. Of the four distinct classes of β and α2δ, β2 and α2δ4 are thought to co-assemble with Cav1.4 α1 subunits in photoreceptors. However, an understanding of the functional properties of this combination of Cav subunits is lacking. Here, we provide evidence that Cav1.4 α1, β2, and α2δ4 contribute to Cav1.4 channel complexes in the retina and describe their properties in electrophysiological recordings. In addition, we identified a variant of β2, named here β2X13, which, along with β2a, is present in photoreceptor terminals. Cav1.4 α1, β2, and α2δ4 were coimmunoprecipitated from lysates of transfected HEK293 cells and mouse retina and were found to interact in the outer plexiform layer of the retina containing the photoreceptor synaptic terminals, by proximity ligation assays. In whole-cell patch clamp recordings of transfected HEK293T cells, channels (Cav1.4 α1 + β2X13) containing α2δ4 exhibited weaker voltage-dependent activation than those with α2δ1. Moreover, compared with channels (Cav1.4 α1 + α2δ4) with β2a, β2X13-containing channels exhibited greater voltage-dependent inactivation. The latter effect was specific to Cav1.4 because it was not seen for Cav1.2 channels. Our results provide the first detailed functional analysis of the Cav1.4 subunits that form native photoreceptor Cav1.4 channels and indicate potential heterogeneity in these channels conferred by β2a and β2X13 variants.
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Affiliation(s)
- Amy Lee
- From the Departments of Molecular Physiology and Biophysics, Otolaryngology Head-Neck Surgery, and Neurology, University of Iowa, Iowa City, Iowa 52242
| | - Shiyi Wang
- From the Departments of Molecular Physiology and Biophysics, Otolaryngology Head-Neck Surgery, and Neurology, University of Iowa, Iowa City, Iowa 52242
| | - Brittany Williams
- From the Departments of Molecular Physiology and Biophysics, Otolaryngology Head-Neck Surgery, and Neurology, University of Iowa, Iowa City, Iowa 52242
| | - Jussara Hagen
- From the Departments of Molecular Physiology and Biophysics, Otolaryngology Head-Neck Surgery, and Neurology, University of Iowa, Iowa City, Iowa 52242
| | - Todd E Scheetz
- the Departments of Ophthalmology and Visual Sciences and Biomedical Engineering, University of Iowa, Iowa City, Iowa 52242, and
| | - Françoise Haeseleer
- the Department of Physiology and Biophysics, University of Washington, Seattle, Washington 98195
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Ephraim SS, Anand N, DeLuca AP, Taylor KR, Kolbe DL, Simpson AC, Azaiez H, Sloan CM, Shearer AE, Hallier AR, Casavant TL, Scheetz TE, Smith RJH, Braun TA. Cordova: web-based management of genetic variation data. Bioinformatics 2014; 30:3438-9. [PMID: 25123904 DOI: 10.1093/bioinformatics/btu539] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
UNLABELLED Cordova is an out-of-the-box solution for building and maintaining an online database of genetic variations integrated with pathogenicity prediction results from popular algorithms. Our primary motivation for developing this system is to aid researchers and clinician-scientists in determining the clinical significance of genetic variations. To achieve this goal, Cordova provides an interface to review and manually or computationally curate genetic variation data as well as share it for clinical diagnostics and the advancement of research. AVAILABILITY AND IMPLEMENTATION Cordova is open source under the MIT license and is freely available for download at https://github.com/clcg/cordova.
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Affiliation(s)
- Sean S Ephraim
- Department of Biomedical Engineering, Department of Ophthalmology and Visual Sciences, Department of Electrical and Computer Engineering, Department of Otolaryngology-Head & Neck Surgery, Carver College of Medicine, Department of Molecular Physiology & Biophysics, Carver College of Medicine, Interdisciplinary Graduate Program in Genetics and Iowa Institute for Human Genetics, Carver College of Medicine, The University of Iowa, Iowa City, IA 52242, USA
| | - Nikhil Anand
- Department of Biomedical Engineering, Department of Ophthalmology and Visual Sciences, Department of Electrical and Computer Engineering, Department of Otolaryngology-Head & Neck Surgery, Carver College of Medicine, Department of Molecular Physiology & Biophysics, Carver College of Medicine, Interdisciplinary Graduate Program in Genetics and Iowa Institute for Human Genetics, Carver College of Medicine, The University of Iowa, Iowa City, IA 52242, USA
| | - Adam P DeLuca
- Department of Biomedical Engineering, Department of Ophthalmology and Visual Sciences, Department of Electrical and Computer Engineering, Department of Otolaryngology-Head & Neck Surgery, Carver College of Medicine, Department of Molecular Physiology & Biophysics, Carver College of Medicine, Interdisciplinary Graduate Program in Genetics and Iowa Institute for Human Genetics, Carver College of Medicine, The University of Iowa, Iowa City, IA 52242, USA
| | - Kyle R Taylor
- Department of Biomedical Engineering, Department of Ophthalmology and Visual Sciences, Department of Electrical and Computer Engineering, Department of Otolaryngology-Head & Neck Surgery, Carver College of Medicine, Department of Molecular Physiology & Biophysics, Carver College of Medicine, Interdisciplinary Graduate Program in Genetics and Iowa Institute for Human Genetics, Carver College of Medicine, The University of Iowa, Iowa City, IA 52242, USA
| | - Diana L Kolbe
- Department of Biomedical Engineering, Department of Ophthalmology and Visual Sciences, Department of Electrical and Computer Engineering, Department of Otolaryngology-Head & Neck Surgery, Carver College of Medicine, Department of Molecular Physiology & Biophysics, Carver College of Medicine, Interdisciplinary Graduate Program in Genetics and Iowa Institute for Human Genetics, Carver College of Medicine, The University of Iowa, Iowa City, IA 52242, USA
| | - Allen C Simpson
- Department of Biomedical Engineering, Department of Ophthalmology and Visual Sciences, Department of Electrical and Computer Engineering, Department of Otolaryngology-Head & Neck Surgery, Carver College of Medicine, Department of Molecular Physiology & Biophysics, Carver College of Medicine, Interdisciplinary Graduate Program in Genetics and Iowa Institute for Human Genetics, Carver College of Medicine, The University of Iowa, Iowa City, IA 52242, USA
| | - Hela Azaiez
- Department of Biomedical Engineering, Department of Ophthalmology and Visual Sciences, Department of Electrical and Computer Engineering, Department of Otolaryngology-Head & Neck Surgery, Carver College of Medicine, Department of Molecular Physiology & Biophysics, Carver College of Medicine, Interdisciplinary Graduate Program in Genetics and Iowa Institute for Human Genetics, Carver College of Medicine, The University of Iowa, Iowa City, IA 52242, USA
| | - Christina M Sloan
- Department of Biomedical Engineering, Department of Ophthalmology and Visual Sciences, Department of Electrical and Computer Engineering, Department of Otolaryngology-Head & Neck Surgery, Carver College of Medicine, Department of Molecular Physiology & Biophysics, Carver College of Medicine, Interdisciplinary Graduate Program in Genetics and Iowa Institute for Human Genetics, Carver College of Medicine, The University of Iowa, Iowa City, IA 52242, USA
| | - A Eliot Shearer
- Department of Biomedical Engineering, Department of Ophthalmology and Visual Sciences, Department of Electrical and Computer Engineering, Department of Otolaryngology-Head & Neck Surgery, Carver College of Medicine, Department of Molecular Physiology & Biophysics, Carver College of Medicine, Interdisciplinary Graduate Program in Genetics and Iowa Institute for Human Genetics, Carver College of Medicine, The University of Iowa, Iowa City, IA 52242, USA Department of Biomedical Engineering, Department of Ophthalmology and Visual Sciences, Department of Electrical and Computer Engineering, Department of Otolaryngology-Head & Neck Surgery, Carver College of Medicine, Department of Molecular Physiology & Biophysics, Carver College of Medicine, Interdisciplinary Graduate Program in Genetics and Iowa Institute for Human Genetics, Carver College of Medicine, The University of Iowa, Iowa City, IA 52242, USA
| | - Andrea R Hallier
- Department of Biomedical Engineering, Department of Ophthalmology and Visual Sciences, Department of Electrical and Computer Engineering, Department of Otolaryngology-Head & Neck Surgery, Carver College of Medicine, Department of Molecular Physiology & Biophysics, Carver College of Medicine, Interdisciplinary Graduate Program in Genetics and Iowa Institute for Human Genetics, Carver College of Medicine, The University of Iowa, Iowa City, IA 52242, USA
| | - Thomas L Casavant
- Department of Biomedical Engineering, Department of Ophthalmology and Visual Sciences, Department of Electrical and Computer Engineering, Department of Otolaryngology-Head & Neck Surgery, Carver College of Medicine, Department of Molecular Physiology & Biophysics, Carver College of Medicine, Interdisciplinary Graduate Program in Genetics and Iowa Institute for Human Genetics, Carver College of Medicine, The University of Iowa, Iowa City, IA 52242, USA
| | - Todd E Scheetz
- Department of Biomedical Engineering, Department of Ophthalmology and Visual Sciences, Department of Electrical and Computer Engineering, Department of Otolaryngology-Head & Neck Surgery, Carver College of Medicine, Department of Molecular Physiology & Biophysics, Carver College of Medicine, Interdisciplinary Graduate Program in Genetics and Iowa Institute for Human Genetics, Carver College of Medicine, The University of Iowa, Iowa City, IA 52242, USA
| | - Richard J H Smith
- Department of Biomedical Engineering, Department of Ophthalmology and Visual Sciences, Department of Electrical and Computer Engineering, Department of Otolaryngology-Head & Neck Surgery, Carver College of Medicine, Department of Molecular Physiology & Biophysics, Carver College of Medicine, Interdisciplinary Graduate Program in Genetics and Iowa Institute for Human Genetics, Carver College of Medicine, The University of Iowa, Iowa City, IA 52242, USA Department of Biomedical Engineering, Department of Ophthalmology and Visual Sciences, Department of Electrical and Computer Engineering, Department of Otolaryngology-Head & Neck Surgery, Carver College of Medicine, Department of Molecular Physiology & Biophysics, Carver College of Medicine, Interdisciplinary Graduate Program in Genetics and Iowa Institute for Human Genetics, Carver College of Medicine, The University of Iowa, Iowa City, IA 52242, USA Department of Biomedical Engineering, Department of Ophthalmology and Visual Sciences, Department of Electrical and Computer Engineering, Department of Otolaryngology-Head & Neck Surgery, Carver College of Medicine, Department of Molecular Physiology & Biophysics, Carver College of Medicine, Interdisciplinary Graduate Program in Genetics and Iowa Institute for Human Genetics, Carver College of Medicine, The University of Iowa, Iowa City, IA 52242, USA Department of Biomedical Engineering, Department of Ophthalmology and Visual Sciences, Department of Electrical and Computer Engineering, Department of Otolaryngology-Head & Neck Surgery, Carver College of Medicine, Department of Molecular Physiology & Biophysics, Carver College of Medicine, Interdisciplinary Graduate Program in Genetics and Iowa Institute for Human Genetics, Carver College of Medicine, The University of Iowa, Iowa City, IA 52242, USA
| | - Terry A Braun
- Department of Biomedical Engineering, Department of Ophthalmology and Visual Sciences, Department of Electrical and Computer Engineering, Department of Otolaryngology-Head & Neck Surgery, Carver College of Medicine, Department of Molecular Physiology & Biophysics, Carver College of Medicine, Interdisciplinary Graduate Program in Genetics and Iowa Institute for Human Genetics, Carver College of Medicine, The University of Iowa, Iowa City, IA 52242, USA
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Brownstein CA, Beggs AH, Homer N, Merriman B, Yu TW, Flannery KC, DeChene ET, Towne MC, Savage SK, Price EN, Holm IA, Luquette LJ, Lyon E, Majzoub J, Neupert P, McCallie D, Szolovits P, Willard HF, Mendelsohn NJ, Temme R, Finkel RS, Yum SW, Medne L, Sunyaev SR, Adzhubey I, Cassa CA, de Bakker PIW, Duzkale H, Dworzyński P, Fairbrother W, Francioli L, Funke BH, Giovanni MA, Handsaker RE, Lage K, Lebo MS, Lek M, Leshchiner I, MacArthur DG, McLaughlin HM, Murray MF, Pers TH, Polak PP, Raychaudhuri S, Rehm HL, Soemedi R, Stitziel NO, Vestecka S, Supper J, Gugenmus C, Klocke B, Hahn A, Schubach M, Menzel M, Biskup S, Freisinger P, Deng M, Braun M, Perner S, Smith RJH, Andorf JL, Huang J, Ryckman K, Sheffield VC, Stone EM, Bair T, Black-Ziegelbein EA, Braun TA, Darbro B, DeLuca AP, Kolbe DL, Scheetz TE, Shearer AE, Sompallae R, Wang K, Bassuk AG, Edens E, Mathews K, Moore SA, Shchelochkov OA, Trapane P, Bossler A, Campbell CA, Heusel JW, Kwitek A, Maga T, Panzer K, Wassink T, Van Daele D, Azaiez H, Booth K, Meyer N, Segal MM, Williams MS, Tromp G, White P, Corsmeier D, Fitzgerald-Butt S, Herman G, Lamb-Thrush D, McBride KL, Newsom D, Pierson CR, Rakowsky AT, Maver A, Lovrečić L, Palandačić A, Peterlin B, Torkamani A, Wedell A, Huss M, Alexeyenko A, Lindvall JM, Magnusson M, Nilsson D, Stranneheim H, Taylan F, Gilissen C, Hoischen A, van Bon B, Yntema H, Nelen M, Zhang W, Sager J, Zhang L, Blair K, Kural D, Cariaso M, Lennon GG, Javed A, Agrawal S, Ng PC, Sandhu KS, Krishna S, Veeramachaneni V, Isakov O, Halperin E, Friedman E, Shomron N, Glusman G, Roach JC, Caballero J, Cox HC, Mauldin D, Ament SA, Rowen L, Richards DR, San Lucas FA, Gonzalez-Garay ML, Caskey CT, Bai Y, Huang Y, Fang F, Zhang Y, Wang Z, Barrera J, Garcia-Lobo JM, González-Lamuño D, Llorca J, Rodriguez MC, Varela I, Reese MG, De La Vega FM, Kiruluta E, Cargill M, Hart RK, Sorenson JM, Lyon GJ, Stevenson DA, Bray BE, Moore BM, Eilbeck K, Yandell M, Zhao H, Hou L, Chen X, Yan X, Chen M, Li C, Yang C, Gunel M, Li P, Kong Y, Alexander AC, Albertyn ZI, Boycott KM, Bulman DE, Gordon PMK, Innes AM, Knoppers BM, Majewski J, Marshall CR, Parboosingh JS, Sawyer SL, Samuels ME, Schwartzentruber J, Kohane IS, Margulies DM. An international effort towards developing standards for best practices in analysis, interpretation and reporting of clinical genome sequencing results in the CLARITY Challenge. Genome Biol 2014; 15:R53. [PMID: 24667040 PMCID: PMC4073084 DOI: 10.1186/gb-2014-15-3-r53] [Citation(s) in RCA: 90] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2013] [Accepted: 03/25/2014] [Indexed: 12/30/2022] Open
Abstract
Background There is tremendous potential for genome sequencing to improve clinical diagnosis and care once it becomes routinely accessible, but this will require formalizing research methods into clinical best practices in the areas of sequence data generation, analysis, interpretation and reporting. The CLARITY Challenge was designed to spur convergence in methods for diagnosing genetic disease starting from clinical case history and genome sequencing data. DNA samples were obtained from three families with heritable genetic disorders and genomic sequence data were donated by sequencing platform vendors. The challenge was to analyze and interpret these data with the goals of identifying disease-causing variants and reporting the findings in a clinically useful format. Participating contestant groups were solicited broadly, and an independent panel of judges evaluated their performance. Results A total of 30 international groups were engaged. The entries reveal a general convergence of practices on most elements of the analysis and interpretation process. However, even given this commonality of approach, only two groups identified the consensus candidate variants in all disease cases, demonstrating a need for consistent fine-tuning of the generally accepted methods. There was greater diversity of the final clinical report content and in the patient consenting process, demonstrating that these areas require additional exploration and standardization. Conclusions The CLARITY Challenge provides a comprehensive assessment of current practices for using genome sequencing to diagnose and report genetic diseases. There is remarkable convergence in bioinformatic techniques, but medical interpretation and reporting are areas that require further development by many groups.
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Whitmore SS, Braun TA, Skeie JM, Haas CM, Sohn EH, Stone EM, Scheetz TE, Mullins RF. Altered gene expression in dry age-related macular degeneration suggests early loss of choroidal endothelial cells. Mol Vis 2013; 19:2274-97. [PMID: 24265543 PMCID: PMC3834599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2013] [Accepted: 11/14/2013] [Indexed: 10/26/2022] Open
Abstract
PURPOSE Age-related macular degeneration (AMD) is a major cause of blindness in developed countries. The molecular pathogenesis of early events in AMD is poorly understood. We investigated differential gene expression in samples of human retinal pigment epithelium (RPE) and choroid from early AMD and control maculas with exon-based arrays. METHODS Gene expression levels in nine human donor eyes with early AMD and nine control human donor eyes were assessed using Affymetrix Human Exon ST 1.0 arrays. Two controls did not pass quality control and were removed. Differentially expressed genes were annotated using the Database for Annotation, Visualization and Integrated Discovery (DAVID), and gene set enrichment analysis (GSEA) was performed on RPE-specific and endothelium-associated gene sets. The complement factor H (CFH) genotype was also assessed, and differential expression was analyzed regarding high AMD risk (YH/HH) and low AMD risk (YY) genotypes. RESULTS Seventy-five genes were identified as differentially expressed (raw p value <0.01; ≥50% fold change, mean log2 expression level in AMD or control ≥ median of all average gene expression values); however, no genes were significant (adj. p value <0.01) after correction for multiple hypothesis testing. Of 52 genes with decreased expression in AMD (fold change <0.5; raw p value <0.01), 18 genes were identified by DAVID analysis as associated with vision or neurologic processes. The GSEA of the RPE-associated and endothelium-associated genes revealed a significant decrease in genes typically expressed by endothelial cells in the early AMD group compared to controls, consistent with previous histologic and proteomic studies. Analysis of the CFH genotype indicated decreased expression of ADAMTS9 in eyes with high-risk genotypes (fold change = -2.61; raw p value=0.0008). CONCLUSIONS GSEA results suggest that RPE transcripts are preserved or elevated in early AMD, concomitant with loss of endothelial cell marker expression. These results are consistent with the notion that choroidal endothelial cell dropout or dedifferentiation occurs early in the pathogenesis of AMD.
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Affiliation(s)
- S. Scott Whitmore
- Department of Ophthalmology and Visual Sciences, The University of Iowa, Iowa City, IA,Stephen A. Wynn Institute for Vision Research, The University of Iowa, Iowa City, IA
| | - Terry A. Braun
- Department of Ophthalmology and Visual Sciences, The University of Iowa, Iowa City, IA,Stephen A. Wynn Institute for Vision Research, The University of Iowa, Iowa City, IA,Department of Biomedical Engineering, The University of Iowa, Iowa City, IA
| | - Jessica M. Skeie
- Department of Ophthalmology and Visual Sciences, The University of Iowa, Iowa City, IA,Stephen A. Wynn Institute for Vision Research, The University of Iowa, Iowa City, IA
| | - Christine M. Haas
- Department of Ophthalmology and Visual Sciences, The University of Iowa, Iowa City, IA,Stephen A. Wynn Institute for Vision Research, The University of Iowa, Iowa City, IA
| | - Elliott H. Sohn
- Department of Ophthalmology and Visual Sciences, The University of Iowa, Iowa City, IA,Stephen A. Wynn Institute for Vision Research, The University of Iowa, Iowa City, IA
| | - Edwin M. Stone
- Department of Ophthalmology and Visual Sciences, The University of Iowa, Iowa City, IA,Stephen A. Wynn Institute for Vision Research, The University of Iowa, Iowa City, IA
| | - Todd E. Scheetz
- Department of Ophthalmology and Visual Sciences, The University of Iowa, Iowa City, IA,Stephen A. Wynn Institute for Vision Research, The University of Iowa, Iowa City, IA,Department of Biomedical Engineering, The University of Iowa, Iowa City, IA
| | - Robert F. Mullins
- Department of Ophthalmology and Visual Sciences, The University of Iowa, Iowa City, IA,Stephen A. Wynn Institute for Vision Research, The University of Iowa, Iowa City, IA
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Christopher M, Scheetz TE, Mullins RF, Abràmoff MD. Selection of Phototransduction Genes in Homo sapiens. Invest Ophthalmol Vis Sci 2013; 54:5489-96. [DOI: 10.1167/iovs.12-11454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Affiliation(s)
- Mark Christopher
- Institute for Vision Research, University of Iowa, Iowa City, Iowa 2Department of Biomedical Engineering, University of Iowa, Iowa City, Iowa
| | - Todd E. Scheetz
- Institute for Vision Research, University of Iowa, Iowa City, Iowa
| | - Robert F. Mullins
- Institute for Vision Research, University of Iowa, Iowa City, Iowa 3Department of Ophthalmology and Visual Sciences, University of Iowa Hospitals and Clinics, Iowa City, Iowa
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Shearer AE, Black-Ziegelbein EA, Hildebrand MS, Eppsteiner RW, Ravi H, Joshi S, Guiffre AC, Sloan CM, Happe S, Howard SD, Novak B, Deluca AP, Taylor KR, Scheetz TE, Braun TA, Casavant TL, Kimberling WJ, Leproust EM, Smith RJH. Advancing genetic testing for deafness with genomic technology. J Med Genet 2013; 50:627-34. [PMID: 23804846 DOI: 10.1136/jmedgenet-2013-101749] [Citation(s) in RCA: 91] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
BACKGROUND Non-syndromic hearing loss (NSHL) is the most common sensory impairment in humans. Until recently its extreme genetic heterogeneity precluded comprehensive genetic testing. Using a platform that couples targeted genomic enrichment (TGE) and massively parallel sequencing (MPS) to sequence all exons of all genes implicated in NSHL, we tested 100 persons with presumed genetic NSHL and in so doing established sequencing requirements for maximum sensitivity and defined MPS quality score metrics that obviate Sanger validation of variants. METHODS We examined DNA from 100 sequentially collected probands with presumed genetic NSHL without exclusions due to inheritance, previous genetic testing, or type of hearing loss. We performed TGE using post-capture multiplexing in variable pool sizes followed by Illumina sequencing. We developed a local Galaxy installation on a high performance computing cluster for bioinformatics analysis. RESULTS To obtain maximum variant sensitivity with this platform 3.2-6.3 million total mapped sequencing reads per sample were required. Quality score analysis showed that Sanger validation was not required for 95% of variants. Our overall diagnostic rate was 42%, but this varied by clinical features from 0% for persons with asymmetric hearing loss to 56% for persons with bilateral autosomal recessive NSHL. CONCLUSIONS These findings will direct the use of TGE and MPS strategies for genetic diagnosis for NSHL. Our diagnostic rate highlights the need for further research on genetic deafness focused on novel gene identification and an improved understanding of the role of non-exonic mutations. The unsolved families we have identified provide a valuable resource to address these areas.
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Affiliation(s)
- A Eliot Shearer
- Department of Otolaryngology-Head and Neck Surgery, Molecular Otolaryngology & Renal Research Labs, University of Iowa Hospitals and Clinics, Iowa City, Iowa, USA
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