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Tollefson MR, Gogal RA, Weaver AM, Schaefer AM, Marini RJ, Azaiez H, Kolbe DL, Wang D, Weaver AE, Casavant TL, Braun TA, Smith RJH, Schnieders MJ. Assessing variants of uncertain significance implicated in hearing loss using a comprehensive deafness proteome. Hum Genet 2023; 142:819-834. [PMID: 37086329 PMCID: PMC10182131 DOI: 10.1007/s00439-023-02559-9] [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: 01/23/2023] [Accepted: 04/11/2023] [Indexed: 04/23/2023]
Abstract
Hearing loss is the leading sensory deficit, affecting ~ 5% of the population. It exhibits remarkable heterogeneity across 223 genes with 6328 pathogenic missense variants, making deafness-specific expertise a prerequisite for ascribing phenotypic consequences to genetic variants. Deafness-implicated variants are curated in the Deafness Variation Database (DVD) after classification by a genetic hearing loss expert panel and thorough informatics pipeline. However, seventy percent of the 128,167 missense variants in the DVD are "variants of uncertain significance" (VUS) due to insufficient evidence for classification. Here, we use the deep learning protein prediction algorithm, AlphaFold2, to curate structures for all DVD genes. We refine these structures with global optimization and the AMOEBA force field and use DDGun3D to predict folding free energy differences (∆∆GFold) for all DVD missense variants. We find that 5772 VUSs have a large, destabilizing ∆∆GFold that is consistent with pathogenic variants. When also filtered for CADD scores (> 25.7), we determine 3456 VUSs are likely pathogenic at a probability of 99.0%. Of the 224 genes in the DVD, 166 genes (74%) exhibit one or more missense variants predicted to cause a pathogenic change in protein folding stability. The VUSs prioritized here affect 119 patients (~ 3% of cases) sequenced by the OtoSCOPE targeted panel. Approximately half of these patients previously received an inconclusive report, and reclassification of these VUSs as pathogenic provides a new genetic diagnosis for six patients.
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Affiliation(s)
- Mallory R Tollefson
- Roy J. Carver Department of Biomedical Engineering, University of Iowa, Iowa City, IA, 52242, USA
- Molecular Otolaryngology and Renal Research Laboratories, Department of Otolaryngology, University of Iowa Hospitals and Clinics, Iowa City, IA, 52242, USA
| | - Rose A Gogal
- Roy J. Carver Department of Biomedical Engineering, University of Iowa, Iowa City, IA, 52242, USA
| | - A Monique Weaver
- Molecular Otolaryngology and Renal Research Laboratories, Department of Otolaryngology, University of Iowa Hospitals and Clinics, Iowa City, IA, 52242, USA
| | - Amanda M Schaefer
- Molecular Otolaryngology and Renal Research Laboratories, Department of Otolaryngology, University of Iowa Hospitals and Clinics, Iowa City, IA, 52242, USA
| | - Robert J Marini
- Molecular Otolaryngology and Renal Research Laboratories, Department of Otolaryngology, University of Iowa Hospitals and Clinics, Iowa City, IA, 52242, USA
| | - Hela Azaiez
- Molecular Otolaryngology and Renal Research Laboratories, Department of Otolaryngology, University of Iowa Hospitals and Clinics, Iowa City, IA, 52242, USA
| | - Diana L Kolbe
- Molecular Otolaryngology and Renal Research Laboratories, Department of Otolaryngology, University of Iowa Hospitals and Clinics, Iowa City, IA, 52242, USA
| | - Donghong Wang
- Molecular Otolaryngology and Renal Research Laboratories, Department of Otolaryngology, University of Iowa Hospitals and Clinics, Iowa City, IA, 52242, USA
| | - Amy E Weaver
- Molecular Otolaryngology and Renal Research Laboratories, Department of Otolaryngology, University of Iowa Hospitals and Clinics, Iowa City, IA, 52242, USA
| | - Thomas L Casavant
- Roy J. Carver Department of Biomedical Engineering, University of Iowa, Iowa City, IA, 52242, USA
| | - Terry A Braun
- Roy J. Carver Department of Biomedical Engineering, University of Iowa, Iowa City, IA, 52242, USA
| | - Richard J H Smith
- Molecular Otolaryngology and Renal Research Laboratories, Department of Otolaryngology, University of Iowa Hospitals and Clinics, Iowa City, IA, 52242, USA.
| | - Michael J Schnieders
- Roy J. Carver Department of Biomedical Engineering, University of Iowa, Iowa City, IA, 52242, USA.
- Department of Biochemistry and Molecular Biology, University of Iowa, Iowa City, IA, 52242, USA.
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2
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Tollefson MR, Gogal RA, Weaver AM, Schaefer AM, Marini RJ, Azaiez H, Kolbe DL, Wang D, Weaver AE, Casavant TL, Braun TA, Smith RJH, Schnieders M. Assessing Variants of Uncertain Significance Implicated in Hearing Loss Using a Comprehensive Deafness Proteome. Res Sq 2023:rs.3.rs-2508462. [PMID: 36778238 PMCID: PMC9915777 DOI: 10.21203/rs.3.rs-2508462/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] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Hearing loss is the leading sensory deficit, affecting ~ 5% of the population. It exhibits remarkable heterogeneity across 223 genes with 6,328 pathogenic missense variants, making deafness-specific expertise a prerequisite for ascribing phenotypic consequences to genetic variants. Deafness-implicated variants are curated in the Deafness Variation Database (DVD) after classification by a genetic hearing loss expert panel and thorough informatics pipeline. However, seventy percent of the 128,167 missense variants in the DVD are "variants of uncertain significance" (VUS) due to insufficient evidence for classification. Here, we use the deep learning protein prediction algorithm, AlphaFold2, to curate structures for all DVD genes. We refine these structures with global optimization and the AMOEBA force field and use DDGun3D to predict folding free energy differences (∆∆G Fold ) for all DVD missense variants. We find that 5,772 VUSs have a large, destabilizing ∆∆G Fold that is consistent with pathogenic variants. When also filtered for CADD scores (> 25.7), we determine 3,456 VUSs are likely pathogenic at a probability of 99.0%. These VUSs affect 119 patients (~ 3% of cases) sequenced by the OtoSCOPE targeted panel. Approximately half of these patients previously received an inconclusive report, and reclassification of these VUSs as pathogenic provides a new genetic diagnosis for six patients.
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3
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Canpolat N, Liu D, Atayar E, Saygili S, Kara NS, Westfall TA, Ding Q, Brown BJ, Braun TA, Slusarski D, Oguz KK, Ozluk Y, Tuysuz B, Ozturk TT, Sever L, Sezerman OU, Topaloglu R, Caliskan S, Attanasio M, Ozaltin F. A splice site mutation in the TSEN2 causes a new syndrome with craniofacial and central nervous system malformations, and atypical hemolytic uremic syndrome. Clin Genet 2022; 101:346-358. [PMID: 34964109 PMCID: PMC10357464 DOI: 10.1111/cge.14105] [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] [Received: 11/19/2021] [Revised: 12/19/2021] [Accepted: 12/26/2021] [Indexed: 07/22/2023]
Abstract
Recessive mutations in the genes encoding the four subunits of the tRNA splicing endonuclease complex (TSEN54, TSEN34, TSEN15, and TSEN2) cause various forms of pontocerebellar hypoplasia, a disorder characterized by hypoplasia of the cerebellum and the pons, microcephaly, dysmorphisms, and other variable clinical features. Here, we report an intronic recessive founder variant in the gene TSEN2 that results in abnormal splicing of the mRNA of this gene, in six individuals from four consanguineous families affected with microcephaly, multiple craniofacial malformations, radiological abnormalities of the central nervous system, and cognitive retardation of variable severity. Remarkably, unlike patients with previously described mutations in the components of the TSEN complex, all the individuals that we report developed atypical hemolytic uremic syndrome (aHUS) with thrombotic microangiopathy, microangiopathic hemolytic anemia, thrombocytopenia, proteinuria, severe hypertension, and end-stage kidney disease (ESKD) early in life. Bulk RNA sequencing of peripheral blood cells of four affected individuals revealed abnormal tRNA transcripts, indicating an alteration of the tRNA biogenesis. Morpholino-mediated skipping of exon 10 of tsen2 in zebrafish produced phenotypes similar to human patients. Thus, we have identified a novel syndrome accompanied by aHUS suggesting the existence of a link between tRNA biology and vascular endothelium homeostasis, which we propose to name with the acronym TRACK syndrome (TSEN2 Related Atypical hemolytic uremic syndrome, Craniofacial malformations, Kidney failure).
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Affiliation(s)
- Nur Canpolat
- Department of Pediatric Nephrology, Istanbul University-Cerrahpasa, Cerrahpasa Faculty of Medicine, Istanbul, Turkey
| | - Dingxiao Liu
- Department of Internal Medicine, Carver College of Medicine, University of Iowa, Iowa City, Iowa, USA
- Department of Vascular Surgery, Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Emine Atayar
- Nephrogenetics Laboratory, Department of Pediatric Nephrology, Hacettepe University, Faculty of Medicine, Ankara, Turkey
| | - Seha Saygili
- Department of Pediatric Nephrology, Istanbul University-Cerrahpasa, Cerrahpasa Faculty of Medicine, Istanbul, Turkey
| | - Nazli Sila Kara
- Biostatistics and Medical Informatics Program, Faculty of Medicine, Graduate School of Health Sciences, Acibadem Mehmet Ali Aydinlar University, Istanbul, Turkey
| | | | - Qiong Ding
- Department of Internal Medicine, Carver College of Medicine, University of Iowa, Iowa City, Iowa, USA
| | - Bartley J. Brown
- Center for Bioinformatics and Computational Biology, University of Iowa, Iowa City, Iowa, USA
| | - Terry A. Braun
- Center for Bioinformatics and Computational Biology, University of Iowa, Iowa City, Iowa, USA
| | - Diane Slusarski
- Center for Bioinformatics and Computational Biology, University of Iowa, Iowa City, Iowa, USA
| | - Kader Karli Oguz
- Department of Radiology, Hacettepe University Faculty of Medicine, Ankara, Turkey
| | - Yasemin Ozluk
- Department of Pathology, Istanbul University Faculty of Medicine, Istanbul, Turkey
| | - Beyhan Tuysuz
- Department of Pediatric Genetics, Istanbul University-Cerrahpasa, Cerrahpasa Faculty of Medicine, Istanbul, Turkey
| | - Tugba Tastemel Ozturk
- Department of Pediatric Nephrology, Hacettepe University Faculty of Medicine, Ankara, Turkey
| | - Lale Sever
- Department of Pediatric Nephrology, Istanbul University-Cerrahpasa, Cerrahpasa Faculty of Medicine, Istanbul, Turkey
| | - Osman Ugur Sezerman
- Biostatistics and Medical Informatics Program, Faculty of Medicine, Graduate School of Health Sciences, Acibadem Mehmet Ali Aydinlar University, Istanbul, Turkey
| | - Rezan Topaloglu
- Department of Pediatric Nephrology, Hacettepe University Faculty of Medicine, Ankara, Turkey
| | - Salim Caliskan
- Department of Pediatric Nephrology, Istanbul University-Cerrahpasa, Cerrahpasa Faculty of Medicine, Istanbul, Turkey
| | - Massimo Attanasio
- Department of Internal Medicine, Carver College of Medicine, University of Iowa, Iowa City, Iowa, USA
| | - Fatih Ozaltin
- Nephrogenetics Laboratory, Department of Pediatric Nephrology, Hacettepe University, Faculty of Medicine, Ankara, Turkey
- Department of Pediatric Nephrology, Hacettepe University Faculty of Medicine, Ankara, Turkey
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4
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Gonzalez Bosquet J, Devor EJ, Newtson AM, Smith BJ, Bender DP, Goodheart MJ, McDonald ME, Braun TA, Thiel KW, Leslie KK. Creation and validation of models to predict response to primary treatment in serous ovarian cancer. Sci Rep 2021; 11:5957. [PMID: 33727600 PMCID: PMC7971042 DOI: 10.1038/s41598-021-85256-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [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: 08/21/2020] [Accepted: 02/24/2021] [Indexed: 01/31/2023] Open
Abstract
Nearly a third of patients with high-grade serous ovarian cancer (HGSC) do not respond to initial therapy and have an overall poor prognosis. However, there are no validated tools that accurately predict which patients will not respond. Our objective is to create and validate accurate models of prediction for treatment response in HGSC. This is a retrospective case–control study that integrates comprehensive clinical and genomic data from 88 patients with HGSC from a single institution. Responders were those patients with a progression-free survival of at least 6 months after treatment. Only patients with complete clinical information and frozen specimen at surgery were included. Gene, miRNA, exon, and long non-coding RNA (lncRNA) expression, gene copy number, genomic variation, and fusion-gene determination were extracted from RNA-sequencing data. DNA methylation analysis was performed. Initial selection of informative variables was performed with univariate ANOVA with cross-validation. Significant variables (p < 0.05) were included in multivariate lasso regression prediction models. Initial models included only one variable. Variables were then combined to create complex models. Model performance was measured with area under the curve (AUC). Validation of all models was performed using TCGA HGSC database. By integrating clinical and genomic variables, we achieved prediction performances of over 95% in AUC. Most performances in the validation set did not differ from the training set. Models with DNA methylation or lncRNA underperformed in the validation set. Integrating comprehensive clinical and genomic data from patients with HGSC results in accurate and robust prediction models of treatment response.
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Affiliation(s)
- Jesus Gonzalez Bosquet
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, University of Iowa Hospitals and Clinics, Iowa City, IA, 52242, USA. .,Holden Comprehensive Cancer Center, University of Iowa Hospitals and Clinics, Iowa City, IA, 52242, USA.
| | - Eric J Devor
- Department of Obstetrics and Gynecology, University of Iowa Hospitals and Clinics, Iowa City, IA, 52242, USA
| | - Andreea M Newtson
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, University of Iowa Hospitals and Clinics, Iowa City, IA, 52242, USA
| | - Brian J Smith
- Holden Comprehensive Cancer Center, University of Iowa Hospitals and Clinics, Iowa City, IA, 52242, USA.,Department of Biostatistics, University of Iowa College of Public Health, Iowa City, IA, 52242, USA
| | - David P Bender
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, University of Iowa Hospitals and Clinics, Iowa City, IA, 52242, USA.,Holden Comprehensive Cancer Center, University of Iowa Hospitals and Clinics, Iowa City, IA, 52242, USA
| | - Michael J Goodheart
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, University of Iowa Hospitals and Clinics, Iowa City, IA, 52242, USA.,Holden Comprehensive Cancer Center, University of Iowa Hospitals and Clinics, Iowa City, IA, 52242, USA
| | - Megan E McDonald
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, University of Iowa Hospitals and Clinics, Iowa City, IA, 52242, USA
| | - Terry A Braun
- Holden Comprehensive Cancer Center, University of Iowa Hospitals and Clinics, Iowa City, IA, 52242, USA.,Coordinated Laboratory for Computational Genomics, University of Iowa Hospitals and Clinics, Iowa City, IA, 52242, USA
| | - Kristina W Thiel
- Department of Obstetrics and Gynecology, University of Iowa Hospitals and Clinics, Iowa City, IA, 52242, USA
| | - Kimberly K Leslie
- Holden Comprehensive Cancer Center, University of Iowa Hospitals and Clinics, Iowa City, IA, 52242, USA.,Department of Obstetrics and Gynecology, University of Iowa Hospitals and Clinics, Iowa City, IA, 52242, USA
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5
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Walls WD, Moteki H, Thomas TR, Nishio SY, Yoshimura H, Iwasa Y, Frees KL, Nishimura CJ, Azaiez H, Booth KT, Marini RJ, Kolbe DL, Weaver AM, Schaefer AM, Wang K, Braun TA, Usami SI, Barr-Gillespie PG, Richardson GP, Smith RJ, Casavant TL. A comparative analysis of genetic hearing loss phenotypes in European/American and Japanese populations. Hum Genet 2020; 139:1315-1323. [PMID: 32382995 DOI: 10.1007/s00439-020-02174-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Accepted: 04/29/2020] [Indexed: 01/04/2023]
Abstract
We present detailed comparative analyses to assess population-level differences in patterns of genetic deafness between European/American and Japanese cohorts with non-syndromic hearing loss. One thousand eighty-three audiometric test results (921 European/American and 162 Japanese) from members of 168 families (48 European/American and 120 Japanese) with non-syndromic hearing loss secondary to pathogenic variants in one of three genes (KCNQ4, TECTA, WFS1) were studied. Audioprofile characteristics, specific mutation types, and protein domains were considered in the comparative analyses. Our findings support differences in audioprofiles driven by both mutation type (non-truncating vs. truncating) and ethnic background. The former finding confirms data that ascribe a phenotypic consequence to different mutation types in KCNQ4; the latter finding suggests that there are ethnic-specific effects (genetic and/or environmental) that impact gene-specific audioprofiles for TECTA and WFS1. Identifying the drivers of ethnic differences will refine our understanding of phenotype-genotype relationships and the biology of hearing and deafness.
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Affiliation(s)
- W Daniel Walls
- Molecular Otolaryngology and Renal Research Labs, Department of Otolaryngology-Head and Neck Surgery, University of Iowa Carver College of Medicine, Iowa City, IA, 52242, USA
| | - Hideaki Moteki
- Department of Otorhinolaryngology, Shinshu University School of Medicine, Matsumoto, Nagano, 390-8621, Japan
| | - Taylor R Thomas
- Molecular Otolaryngology and Renal Research Labs, Department of Otolaryngology-Head and Neck Surgery, University of Iowa Carver College of Medicine, Iowa City, IA, 52242, USA
| | - Shin-Ya Nishio
- Department of Otorhinolaryngology, Shinshu University School of Medicine, Matsumoto, Nagano, 390-8621, Japan
| | - Hidekane Yoshimura
- Department of Otorhinolaryngology, Shinshu University School of Medicine, Matsumoto, Nagano, 390-8621, Japan
| | - Yoichiro Iwasa
- Department of Otorhinolaryngology, Shinshu University School of Medicine, Matsumoto, Nagano, 390-8621, Japan
| | - Kathy L Frees
- Molecular Otolaryngology and Renal Research Labs, Department of Otolaryngology-Head and Neck Surgery, University of Iowa Carver College of Medicine, Iowa City, IA, 52242, USA
| | - Carla J Nishimura
- Molecular Otolaryngology and Renal Research Labs, Department of Otolaryngology-Head and Neck Surgery, University of Iowa Carver College of Medicine, Iowa City, IA, 52242, USA
| | - Hela Azaiez
- Molecular Otolaryngology and Renal Research Labs, Department of Otolaryngology-Head and Neck Surgery, University of Iowa Carver College of Medicine, Iowa City, IA, 52242, USA
| | - Kevin T Booth
- Molecular Otolaryngology and Renal Research Labs, Department of Otolaryngology-Head and Neck Surgery, University of Iowa Carver College of Medicine, Iowa City, IA, 52242, USA.,Department of Neurobiology, Harvard Medical School, Boston, MA, 02215, USA
| | - Robert J Marini
- Molecular Otolaryngology and Renal Research Labs, Department of Otolaryngology-Head and Neck Surgery, University of Iowa Carver College of Medicine, Iowa City, IA, 52242, USA
| | - Diana L Kolbe
- Molecular Otolaryngology and Renal Research Labs, Department of Otolaryngology-Head and Neck Surgery, University of Iowa Carver College of Medicine, Iowa City, IA, 52242, USA
| | - A Monique Weaver
- Molecular Otolaryngology and Renal Research Labs, Department of Otolaryngology-Head and Neck Surgery, University of Iowa Carver College of Medicine, Iowa City, IA, 52242, USA
| | - Amanda M Schaefer
- Molecular Otolaryngology and Renal Research Labs, Department of Otolaryngology-Head and Neck Surgery, University of Iowa Carver College of Medicine, Iowa City, IA, 52242, USA
| | - Kai Wang
- Department of Biostatistics, University of Iowa, Iowa City, IA, 52242, USA
| | - Terry A Braun
- Department of Biomedical Engineering, University of Iowa, Iowa City, IA, 52242, USA
| | - Shin-Ichi Usami
- Department of Otorhinolaryngology, Shinshu University School of Medicine, Matsumoto, Nagano, 390-8621, Japan
| | | | - Guy P Richardson
- Sussex Neuroscience, School of Life Sciences, University of Sussex, Brighton, UK
| | - Richard J Smith
- Molecular Otolaryngology and Renal Research Labs, Department of Otolaryngology-Head and Neck Surgery, University of Iowa Carver College of Medicine, Iowa City, IA, 52242, USA. .,Interdepartmental Ph.D. Program in Genetics, University of Iowa, Iowa City, IA, 52242, USA. .,Department of Molecular Physiology and Biophysics, University of Iowa Carver College of Medicine, Iowa City, IA, 52242, USA.
| | - Thomas L Casavant
- Department of Biomedical Engineering, University of Iowa, Iowa City, IA, 52242, USA.,Center for Bioinformatics and Computational Biology, University of Iowa, Iowa City, IA, 52242, USA.,Department of Electrical and Computer Engineering, University of Iowa, Iowa City, IA, 52242, USA
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6
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Scott AT, Weitz M, Breheny PJ, Ear PH, Darbro B, Brown BJ, Braun TA, Li G, Umesalma S, Kaemmer CA, Maharjan CK, Quelle DE, Bellizzi AM, Chandrasekharan C, Dillon JS, O'Dorisio TM, Howe JR. Gene Expression Signatures Identify Novel Therapeutics for Metastatic Pancreatic Neuroendocrine Tumors. Clin Cancer Res 2020; 26:2011-2021. [PMID: 31937620 PMCID: PMC7165057 DOI: 10.1158/1078-0432.ccr-19-2884] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [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: 09/02/2019] [Revised: 12/19/2019] [Accepted: 01/10/2020] [Indexed: 12/24/2022]
Abstract
PURPOSE Pancreatic neuroendocrine tumors (pNETs) are uncommon malignancies noted for their propensity to metastasize and comparatively favorable prognosis. Although both the treatment options and clinical outcomes have improved in the past decades, most patients will die of metastatic disease. New systemic therapies are needed. EXPERIMENTAL DESIGN Tissues were obtained from 43 patients with well-differentiated pNETs undergoing surgery. Gene expression was compared between primary tumors versus liver and lymph node metastases using RNA-Seq. Genes that were selectively elevated at only one metastatic site were filtered out to reduce tissue-specific effects. Ingenuity pathway analysis (IPA) and the Connectivity Map (CMap) identified drugs likely to antagonize metastasis-specific targets. The biological activity of top identified agents was tested in vitro using two pNET cell lines (BON-1 and QGP-1). RESULTS A total of 902 genes were differentially expressed in pNET metastases compared with primary tumors, 626 of which remained in the common metastatic profile after filtering. Analysis with IPA and CMap revealed altered activity of factors involved in survival and proliferation, and identified drugs targeting those pathways, including inhibitors of mTOR, PI3K, MEK, TOP2A, protein kinase C, NF-kB, cyclin-dependent kinase, and histone deacetylase. Inhibitors of MEK and TOP2A were consistently the most active compounds. CONCLUSIONS We employed a complementary bioinformatics approach to identify novel therapeutics for pNETs by analyzing gene expression in metastatic tumors. The potential utility of these drugs was confirmed by in vitro cytotoxicity assays, suggesting drugs targeting MEK and TOP2A may be highly efficacious against metastatic pNETs. This is a promising strategy for discovering more effective treatments for patients with pNETs.
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Affiliation(s)
- Aaron T Scott
- Department of Surgery, Carver College of Medicine, University of Iowa, Iowa City, IA
| | - Michelle Weitz
- College of Public Health, Department of Biostatistics, University of Iowa, Iowa City, IA
| | - Patrick J Breheny
- College of Public Health, Department of Biostatistics, University of Iowa, Iowa City, IA
- Holden Comprehensive Cancer Center, University of Iowa, Iowa City, IA
| | - Po Hien Ear
- Department of Surgery, Carver College of Medicine, University of Iowa, Iowa City, IA
| | - Benjamin Darbro
- Holden Comprehensive Cancer Center, University of Iowa, Iowa City, IA
- Stead Family Department of Pediatrics, Carver College of Medicine, University of Iowa, Iowa City, IA
| | - Bart J Brown
- Holden Comprehensive Cancer Center, University of Iowa, Iowa City, IA
- Center for Bioinformatics and Computational Biology, College of Engineering, University of Iowa, Iowa City, IA
| | - Terry A Braun
- Holden Comprehensive Cancer Center, University of Iowa, Iowa City, IA
- Center for Bioinformatics and Computational Biology, College of Engineering, University of Iowa, Iowa City, IA
| | - Guiying Li
- Department of Surgery, Carver College of Medicine, University of Iowa, Iowa City, IA
| | - Shaikamjad Umesalma
- Department of Neuroscience and Pharmacology, Carver College of Medicine, University of Iowa, Iowa City, IA
| | - Courtney A Kaemmer
- Department of Neuroscience and Pharmacology, Carver College of Medicine, University of Iowa, Iowa City, IA
| | - Chandra K Maharjan
- Department of Neuroscience and Pharmacology, Carver College of Medicine, University of Iowa, Iowa City, IA
| | - Dawn E Quelle
- Holden Comprehensive Cancer Center, University of Iowa, Iowa City, IA
- Department of Neuroscience and Pharmacology, Carver College of Medicine, University of Iowa, Iowa City, IA
- Department of Pathology, Carver College of Medicine University of Iowa, Iowa City, IA
| | - Andrew M Bellizzi
- Holden Comprehensive Cancer Center, University of Iowa, Iowa City, IA
- Department of Pathology, Carver College of Medicine University of Iowa, Iowa City, IA
| | - Chandrikha Chandrasekharan
- Holden Comprehensive Cancer Center, University of Iowa, Iowa City, IA
- Department of Internal Medicine, Carver College of Medicine, University of Iowa, Iowa City, IA
| | - Joseph S Dillon
- Holden Comprehensive Cancer Center, University of Iowa, Iowa City, IA
- Department of Internal Medicine, Carver College of Medicine, University of Iowa, Iowa City, IA
| | - Thomas M O'Dorisio
- Holden Comprehensive Cancer Center, University of Iowa, Iowa City, IA
- Department of Internal Medicine, Carver College of Medicine, University of Iowa, Iowa City, IA
| | - James R Howe
- Department of Surgery, Carver College of Medicine, University of Iowa, Iowa City, IA.
- Holden Comprehensive Cancer Center, University of Iowa, Iowa City, IA
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7
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Wu VT, Kiriazov B, Koch KE, Gu VW, Beck AC, Borcherding N, Li T, Addo P, Wehrspan ZJ, Zhang W, Braun TA, Brown BJ, Band V, Band H, Kulak MV, Weigel RJ. A TFAP2C Gene Signature Is Predictive of Outcome in HER2-Positive Breast Cancer. Mol Cancer Res 2019; 18:46-56. [PMID: 31619506 DOI: 10.1158/1541-7786.mcr-19-0359] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Revised: 09/05/2019] [Accepted: 10/11/2019] [Indexed: 11/16/2022]
Abstract
The AP-2γ transcription factor, encoded by the TFAP2C gene, regulates the expression of estrogen receptor-alpha (ERα) and other genes associated with hormone response in luminal breast cancer. Little is known about the role of AP-2γ in other breast cancer subtypes. A subset of HER2+ breast cancers with amplification of the TFAP2C gene locus becomes addicted to AP-2γ. Herein, we sought to define AP-2γ gene targets in HER2+ breast cancer and identify genes accounting for physiologic effects of growth and invasiveness regulated by AP-2γ. Comparing HER2+ cell lines that demonstrated differential response to growth and invasiveness with knockdown of TFAP2C, we identified a set of 68 differentially expressed target genes. CDH5 and CDKN1A were among the genes differentially regulated by AP-2γ and that contributed to growth and invasiveness. Pathway analysis implicated the MAPK13/p38δ and retinoic acid regulatory nodes, which were confirmed to display divergent responses in different HER2+ cancer lines. To confirm the clinical relevance of the genes identified, the AP-2γ gene signature was found to be highly predictive of outcome in patients with HER2+ breast cancer. We conclude that AP-2γ regulates a set of genes in HER2+ breast cancer that drive cancer growth and invasiveness. The AP-2γ gene signature predicts outcome of patients with HER2+ breast cancer and pathway analysis predicts that subsets of patients will respond to drugs that target the MAPK or retinoic acid pathways. IMPLICATIONS: A set of genes regulated by AP-2γ in HER2+ breast cancer that drive proliferation and invasion were identified and provided a gene signature that is predictive of outcome in HER2+ breast cancer.
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Affiliation(s)
- Vincent T Wu
- Department of Surgery, University of Iowa, Iowa City, Iowa
| | - Boris Kiriazov
- Department of Surgery, University of Iowa, Iowa City, Iowa
| | - Kelsey E Koch
- Department of Surgery, University of Iowa, Iowa City, Iowa
| | - Vivian W Gu
- Department of Molecular Physiology and Biophysics, University of Iowa, Iowa City, Iowa
| | - Anna C Beck
- Department of Surgery, University of Iowa, Iowa City, Iowa
| | | | - Tiandao Li
- Department of Surgery, University of Iowa, Iowa City, Iowa
| | - Peter Addo
- Department of Surgery, University of Iowa, Iowa City, Iowa
| | | | - Weizhou Zhang
- Department of Pathology, Immunology, and Laboratory Medicine, University of Florida, Gainesville, Florida
| | - Terry A Braun
- Department of Biomedical Engineering, University of Iowa, Iowa City, Iowa
| | - Bartley J Brown
- Department of Biomedical Engineering, University of Iowa, Iowa City, Iowa
| | - Vimla Band
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, Nebraska
| | - Hamid Band
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, Nebraska
| | | | - Ronald J Weigel
- Department of Surgery, University of Iowa, Iowa City, Iowa. .,Department of Molecular Physiology and Biophysics, University of Iowa, Iowa City, Iowa.,Department of Biochemistry, University of Iowa, Iowa City, Iowa
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8
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Tollefson MR, Litman JM, Qi G, O'Connell CE, Wipfler MJ, Marini RJ, Bernabe HV, Tollefson WTA, Braun TA, Casavant TL, Smith RJH, Schnieders MJ. Structural Insights into Hearing Loss Genetics from Polarizable Protein Repacking. Biophys J 2019; 117:602-612. [PMID: 31327459 DOI: 10.1016/j.bpj.2019.06.030] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Revised: 06/10/2019] [Accepted: 06/25/2019] [Indexed: 12/21/2022] Open
Abstract
Hearing loss is associated with ∼8100 mutations in 152 genes, and within the coding regions of these genes are over 60,000 missense variants. The majority of these variants are classified as "variants of uncertain significance" to reflect our inability to ascribe a phenotypic effect to the observed amino acid change. A promising source of pathogenicity information is biophysical simulation, although input protein structures often contain defects because of limitations in experimental data and/or only distant homology to a template. Here, we combine the polarizable atomic multipole optimized energetics for biomolecular applications force field, many-body optimization theory, and graphical processing unit acceleration to repack all deafness-associated proteins and thereby improve average structure MolProbity score from 2.2 to 1.0. We then used these optimized wild-type models to create over 60,000 structures for missense variants in the Deafness Variation Database, which are being incorporated into the Deafness Variation Database to inform deafness pathogenicity prediction. Finally, this work demonstrates that advanced polarizable atomic multipole force fields are efficient enough to repack the entire human proteome.
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Affiliation(s)
- Mallory R Tollefson
- Department of Biomedical Engineering, University of Iowa, Iowa City, Iowa; Molecular Otolaryngology & Renal Research Laboratories, Department of Otolaryngology-Head and Neck Surgery, University of Iowa Hospitals and Clinics, Iowa City, Iowa
| | - Jacob M Litman
- Department of Biochemistry, University of Iowa, Iowa City, Iowa
| | - Guowei Qi
- Department of Biochemistry, University of Iowa, Iowa City, Iowa
| | - Claire E O'Connell
- Department of Biomedical Engineering, University of Iowa, Iowa City, Iowa
| | - Matthew J Wipfler
- Department of Biomedical Engineering, University of Iowa, Iowa City, Iowa
| | - Robert J Marini
- Molecular Otolaryngology & Renal Research Laboratories, Department of Otolaryngology-Head and Neck Surgery, University of Iowa Hospitals and Clinics, Iowa City, Iowa
| | - Hernan V Bernabe
- Department of Biomedical Engineering, University of Iowa, Iowa City, Iowa; Molecular Otolaryngology & Renal Research Laboratories, Department of Otolaryngology-Head and Neck Surgery, University of Iowa Hospitals and Clinics, Iowa City, Iowa
| | | | - Terry A Braun
- Department of Biomedical Engineering, University of Iowa, Iowa City, Iowa
| | - Thomas L Casavant
- Department of Biomedical Engineering, University of Iowa, Iowa City, Iowa
| | - Richard J H Smith
- Molecular Otolaryngology & Renal Research Laboratories, Department of Otolaryngology-Head and Neck Surgery, University of Iowa Hospitals and Clinics, Iowa City, Iowa.
| | - Michael J Schnieders
- Department of Biomedical Engineering, University of Iowa, Iowa City, Iowa; Department of Biochemistry, University of Iowa, Iowa City, Iowa.
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9
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Rendleman MC, Buatti JM, Braun TA, Smith BJ, Nwakama C, Beichel RR, Brown B, Casavant TL. Machine learning with the TCGA-HNSC dataset: improving usability by addressing inconsistency, sparsity, and high-dimensionality. BMC Bioinformatics 2019; 20:339. [PMID: 31208324 PMCID: PMC6580485 DOI: 10.1186/s12859-019-2929-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [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: 09/08/2018] [Accepted: 06/04/2019] [Indexed: 12/15/2022] Open
Abstract
Background In the era of precision oncology and publicly available datasets, the amount of information available for each patient case has dramatically increased. From clinical variables and PET-CT radiomics measures to DNA-variant and RNA expression profiles, such a wide variety of data presents a multitude of challenges. Large clinical datasets are subject to sparsely and/or inconsistently populated fields. Corresponding sequencing profiles can suffer from the problem of high-dimensionality, where making useful inferences can be difficult without correspondingly large numbers of instances. In this paper we report a novel deployment of machine learning techniques to handle data sparsity and high dimensionality, while evaluating potential biomarkers in the form of unsupervised transformations of RNA data. We apply preprocessing, MICE imputation, and sparse principal component analysis (SPCA) to improve the usability of more than 500 patient cases from the TCGA-HNSC dataset for enhancing future oncological decision support for Head and Neck Squamous Cell Carcinoma (HNSCC). Results Imputation was shown to improve prognostic ability of sparse clinical treatment variables. SPCA transformation of RNA expression variables reduced runtime for RNA-based models, though changes to classifier performance were not significant. Gene ontology enrichment analysis of gene sets associated with individual sparse principal components (SPCs) are also reported, showing that both high- and low-importance SPCs were associated with cell death pathways, though the high-importance gene sets were found to be associated with a wider variety of cancer-related biological processes. Conclusions MICE imputation allowed us to impute missing values for clinically informative features, improving their overall importance for predicting two-year recurrence-free survival by incorporating variance from other clinical variables. Dimensionality reduction of RNA expression profiles via SPCA reduced both computation cost and model training/evaluation time without affecting classifier performance, allowing researchers to obtain experimental results much more quickly. SPCA simultaneously provided a convenient avenue for consideration of biological context via gene ontology enrichment analysis.
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Affiliation(s)
- Michael C Rendleman
- Department of Electrical and Computer Engineering, Center for Bioinformatics and Computational Biology, University of Iowa, 5017 Seamans Center, Iowa City, IA, 52242, USA.
| | - John M Buatti
- Department of Radiation Oncology, Carver College of Medicine, University of Iowa Carver College of Medicine, LL-W Pomerantz Family Pavilion, 200 Hawkins Drive, Iowa City, IA, 52242-1089, USA
| | - Terry A Braun
- Department of Biomedical Engineering, Center for Bioinformatics and Computational Biology, University of Iowa, 5017 Seamans Center, Iowa City, IA, 52242, USA
| | - Brian J Smith
- Department of Biostatistics, University of Iowa, 145 N. Riverside Drive, 100 CPHB, Iowa City, IA, 52242, USA
| | - Chibuzo Nwakama
- Department of Electrical and Computer Engineering, Center for Bioinformatics and Computational Biology, University of Iowa, 5017 Seamans Center, Iowa City, IA, 52242, USA
| | - Reinhard R Beichel
- Iowa Institute for Biomedical Imaging, Department of Electrical and Computer Engineering, Department of Internal Medicine, The University of Iowa, Iowa City, 52242, IA, USA.,3312 Seamans Center for the Engineering Arts and Sciences, Iowa City, IA, 52242-1527, USA
| | - Bart Brown
- Center for Bioinformatics and Computational Biology, University of Iowa, 5017 Seamans Center, Iowa City, IA, 52242, USA
| | - Thomas L Casavant
- Department of Electrical and Computer Engineering, Center for Bioinformatics and Computational Biology, University of Iowa, 5017 Seamans Center, Iowa City, IA, 52242, USA.,Department of Biomedical Engineering, Center for Bioinformatics and Computational Biology, University of Iowa, 5017 Seamans Center, Iowa City, IA, 52242, USA
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10
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Umesalma S, Kaemmer CA, Kohlmeyer JL, Letney B, Schab AM, Reilly JA, Sheehy RM, Hagen J, Tiwari N, Zhan F, Leidinger MR, O'Dorisio TM, Dillon J, Merrill RA, Meyerholz DK, Perl AL, Brown BJ, Braun TA, Scott AT, Ginader T, Taghiyev AF, Zamba GK, Howe JR, Strack S, Bellizzi AM, Narla G, Darbro BW, Quelle FW, Quelle DE. RABL6A inhibits tumor-suppressive PP2A/AKT signaling to drive pancreatic neuroendocrine tumor growth. J Clin Invest 2019; 129:1641-1653. [PMID: 30721156 DOI: 10.1172/jci123049] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [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: 06/21/2018] [Accepted: 01/24/2019] [Indexed: 12/15/2022] Open
Abstract
Hyperactivated AKT/mTOR signaling is a hallmark of pancreatic neuroendocrine tumors (PNETs). Drugs targeting this pathway are used clinically, but tumor resistance invariably develops. A better understanding of factors regulating AKT/mTOR signaling and PNET pathogenesis is needed to improve current therapies. We discovered that RABL6A, a new oncogenic driver of PNET proliferation, is required for AKT activity. Silencing RABL6A caused PNET cell-cycle arrest that coincided with selective loss of AKT-S473 (not T308) phosphorylation and AKT/mTOR inactivation. Restoration of AKT phosphorylation rescued the G1 phase block triggered by RABL6A silencing. Mechanistically, loss of AKT-S473 phosphorylation in RABL6A-depleted cells was the result of increased protein phosphatase 2A (PP2A) activity. Inhibition of PP2A restored phosphorylation of AKT-S473 in RABL6A-depleted cells, whereas PP2A reactivation using a specific small-molecule activator of PP2A (SMAP) abolished that phosphorylation. Moreover, SMAP treatment effectively killed PNET cells in a RABL6A-dependent manner and suppressed PNET growth in vivo. The present work identifies RABL6A as a new inhibitor of the PP2A tumor suppressor and an essential activator of AKT in PNET cells. Our findings offer what we believe is a novel strategy of PP2A reactivation for treatment of PNETs as well as other human cancers driven by RABL6A overexpression and PP2A inactivation.
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Affiliation(s)
| | | | | | | | | | | | - Ryan M Sheehy
- Department of Pharmacology.,Free Radical & Radiation Biology Training Program
| | | | | | | | - Mariah R Leidinger
- Department of Pathology, in the College of Medicine, Holden Comprehensive Cancer Center, University of Iowa, Iowa City, Iowa, USA
| | | | | | | | - David K Meyerholz
- Department of Pathology, in the College of Medicine, Holden Comprehensive Cancer Center, University of Iowa, Iowa City, Iowa, USA
| | - Abbey L Perl
- Department of Pharmacology, Case Western Reserve University, Cleveland, Ohio, USA
| | | | | | | | | | - Agshin F Taghiyev
- Pediatrics, Colleges of Medicine, Engineering, or Public Health, University of Iowa, Iowa City, Iowa, USA
| | | | | | | | - Andrew M Bellizzi
- Department of Pathology, in the College of Medicine, Holden Comprehensive Cancer Center, University of Iowa, Iowa City, Iowa, USA
| | - Goutham Narla
- Department of Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Benjamin W Darbro
- Pediatrics, Colleges of Medicine, Engineering, or Public Health, University of Iowa, Iowa City, Iowa, USA
| | | | - Dawn E Quelle
- Department of Pharmacology.,Molecular Medicine Graduate Program.,Free Radical & Radiation Biology Training Program.,Department of Pathology, in the College of Medicine, Holden Comprehensive Cancer Center, University of Iowa, Iowa City, Iowa, USA
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11
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Keck KJ, Breheny P, Braun TA, Darbro B, Li G, Dillon JS, Bellizzi AM, O'Dorisio TM, Howe JR. Changes in gene expression in small bowel neuroendocrine tumors associated with progression to metastases. Surgery 2017; 163:232-239. [PMID: 29154080 DOI: 10.1016/j.surg.2017.07.031] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Revised: 06/13/2017] [Accepted: 07/05/2017] [Indexed: 12/22/2022]
Abstract
BACKGROUND Small bowel neuroendocrine tumors (SBNETs) present frequently with metastases, yet little is known about the molecular basis of this progression. This study sought to identify the serial differential expression of genes between normal small bowel, primary small bowel neuroendocrine tumors, and liver metastases. METHODS RNA isolated from matched normal small bowel tissue, primary small bowel neuroendocrine tumors, and liver metastases in 12 patients was analyzed with whole transcriptome expression microarrays and RNA-Seq. Changes in gene expression between primary small bowel neuroendocrine tumors and normal small bowels, and liver metastases versus primary small bowel neuroendocrine tumors were calculated. Common genes that were differentially expressed serially (increasing or decreasing from normal small bowel to primary small bowel neuroendocrine tumors to liver metastases) were identified, and 10 were validated using qPCR. RESULTS Use of 2 transcriptome platforms allowed for a robust discrimination of genes important in small bowel neuroendocrine tumors progression. Serial differential expression was validated in 7/10 genes, all of which had been described previously in abdominal cancers, and with several interacting with members of the AKT, MYC, or MAPK3 pathways. Liver metastases had consistent underexpression of PMP22, while high expression of SERPINA10 and SYT13 was characteristic of both pSBTs and liver metastases. CONCLUSION Identification of the serial differential expression of genes from normal tissues to primary tumors to metastases lends insight into important pathways for SBNETs progression. Differential expression of various genes, including PMP22, SYT13 and SERPINA10, are associated with the progression of SBNETs and warrant further investigation.
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Affiliation(s)
- Kendall J Keck
- Department of Surgery, University of Iowa Carver College of Medicine, Iowa City, IA
| | - Patrick Breheny
- Department of Biostatistics, University of Iowa College of Public Health, Iowa City, IA
| | - Terry A Braun
- Department of Biomedical Engineering, University of Iowa College of Engineering, Iowa City, IA
| | - Benjamin Darbro
- Department of Pediatrics, University of Iowa Carver College of Medicine, Iowa City, IA
| | - Guiying Li
- Department of Surgery, University of Iowa Carver College of Medicine, Iowa City, IA
| | - Joseph S Dillon
- Department of Internal Medicine, University of Iowa Carver College of Medicine, Iowa City, IA
| | - Andrew M Bellizzi
- Department of Pathology, University of Iowa Carver College of Medicine, Iowa City, IA
| | - Thomas M O'Dorisio
- Department of Internal Medicine, University of Iowa Carver College of Medicine, Iowa City, IA
| | - James R Howe
- Department of Surgery, University of Iowa Carver College of Medicine, Iowa City, IA.
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12
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Bermudez JY, Webber HC, Brown B, Braun TA, Clark AF, Mao W. A Comparison of Gene Expression Profiles between Glucocorticoid Responder and Non-Responder Bovine Trabecular Meshwork Cells Using RNA Sequencing. PLoS One 2017; 12:e0169671. [PMID: 28068412 PMCID: PMC5222504 DOI: 10.1371/journal.pone.0169671] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [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: 05/31/2016] [Accepted: 12/20/2016] [Indexed: 11/23/2022] Open
Abstract
The most common ocular side effect of glucocorticoid (GC) therapy is GC-induced ocular hypertension (OHT) and GC-induced glaucoma (GIG). GC-induced OHT occurs in about 40% of the general population, while the other 60% are resistant. This study aims to determine the genes and pathways involved in differential GC responsiveness in the trabecular meshwork (TM). Using paired bovine eyes, one eye was perfusion-cultured with 100nM dexamethasone (DEX), while the fellow eye was used to establish a bovine TM (BTM) cell strain. Based on maximum IOP change in the perfused eye, the BTM cell strain was identified as a DEX-responder or non-responder strain. Three responder and three non-responder BTM cell strains were cultured, treated with 0.1% ethanol or 100nM DEX for 7 days. RNA and proteins were extracted for RNA sequencing (RNAseq), qPCR, and Western immunoblotting (WB), respectively. Data were analyzed using the human and bovine genome databases as well as Tophat2 software. Genes were grouped and compared using Student’s t-test. We found that DEX induced fibronectin expression in responder BTM cells but not in non-responder cells using WB. RNAseq showed between 93 and 606 differentially expressed genes in different expression groups between responder and non-responder BTM cells. The data generated by RNAseq were validated using qPCR. Pathway analyses showed 35 pathways associated with differentially expressed genes. These genes and pathways may play important roles in GC-induced OHT and will help us to better understand differential ocular responsiveness to GCs.
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Affiliation(s)
- Jaclyn Y. Bermudez
- North Texas Eye Research Institute, University of North Texas Health Science Center, 3500 Camp Bowie Blvd. Fort Worth, TX, United States of America
| | - Hannah C. Webber
- North Texas Eye Research Institute, University of North Texas Health Science Center, 3500 Camp Bowie Blvd. Fort Worth, TX, United States of America
| | - Bartley Brown
- Stephen A. Wynn Institute for Vision Research, University of Iowa, Iowa City, IA, United States of America
- Department of Ophthalmology and Visual Sciences, Carver College of Medicine, University of Iowa, Iowa City, IA, United States of America
- Department of Biomedical Engineering, College of Engineering, University of Iowa, Iowa City, IA, United States of America
| | - Terry A. Braun
- North Texas Eye Research Institute, University of North Texas Health Science Center, 3500 Camp Bowie Blvd. Fort Worth, TX, United States of America
- Stephen A. Wynn Institute for Vision Research, University of Iowa, Iowa City, IA, United States of America
- Department of Ophthalmology and Visual Sciences, Carver College of Medicine, University of Iowa, Iowa City, IA, United States of America
- Department of Biomedical Engineering, College of Engineering, University of Iowa, Iowa City, IA, United States of America
| | - Abbot F. Clark
- North Texas Eye Research Institute, University of North Texas Health Science Center, 3500 Camp Bowie Blvd. Fort Worth, TX, United States of America
| | - Weiming Mao
- North Texas Eye Research Institute, University of North Texas Health Science Center, 3500 Camp Bowie Blvd. Fort Worth, TX, United States of America
- * E-mail:
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13
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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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14
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Bax NM, Sangermano R, Roosing S, Thiadens AAHJ, Hoefsloot LH, van den Born LI, Phan M, Klevering BJ, Westeneng-van Haaften C, Braun TA, Zonneveld-Vrieling MN, de Wijs I, Mutlu M, Stone EM, den Hollander AI, Klaver CCW, Hoyng CB, Cremers FPM. Heterozygous deep-intronic variants and deletions in ABCA4 in persons with retinal dystrophies and one exonic ABCA4 variant. Hum Mutat 2015; 36:43-7. [PMID: 25363634 DOI: 10.1002/humu.22717] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [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: 07/30/2014] [Accepted: 10/18/2014] [Indexed: 11/05/2022]
Abstract
Variants in ABCA4 are responsible for autosomal-recessive Stargardt disease and cone-rod dystrophy. Sequence analysis of ABCA4 exons previously revealed one causative variant in each of 45 probands. To identify the "missing" variants in these cases, we performed multiplex ligation-dependent probe amplification-based deletion scanning of ABCA4. In addition, we sequenced the promoter region, fragments containing five deep-intronic splice variants, and 15 deep-intronic regions containing weak splice sites. Heterozygous deletions spanning ABCA4 exon 5 or exons 20-22 were found in two probands, heterozygous deep-intronic variants were identified in six probands, and a deep-intronic variant was found together with an exon 20-22 deletion in one proband. Based on ophthalmologic findings and characteristics of the identified exonic variants present in trans, the deep-intronic variants V1 and V4 were predicted to be relatively mild and severe, respectively. These findings are important for proper genetic counseling and for the development of variant-specific therapies.
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Affiliation(s)
- Nathalie M Bax
- Department of Ophthalmology, Radboud University Medical Center, Nijmegen, The Netherlands
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15
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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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Sherman SK, Maxwell JE, Qian Q, Bellizzi AM, Braun TA, Iannettoni MD, Darbro BW, Howe JR. Esophageal cancer in a family with hamartomatous tumors and germline PTEN frameshift and SMAD7 missense mutations. Cancer Genet 2014; 208:41-6. [PMID: 25554686 DOI: 10.1016/j.cancergen.2014.11.002] [Citation(s) in RCA: 8] [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] [Received: 05/20/2014] [Revised: 10/29/2014] [Accepted: 11/02/2014] [Indexed: 12/26/2022]
Abstract
Germline mutations in the PTEN tumor-suppressor gene cause autosomal-dominant conditions such as Cowden and Bannayan-Riley-Ruvalcaba syndromes with variable presentations, including hamartomatous gastrointestinal tumors, dermatologic abnormalities, neurologic symptoms, and elevated cancer risk. We describe a father and son with extensive hamartomatous gastrointestinal polyposis who both developed early-onset esophageal cancer. Exome sequencing identified a novel germline PTEN frameshift mutation (c.568_569insC, p.V191Sfs*11). In addition, a missense mutation of SMAD7 (c.115G>A, p.G39R) with an allele frequency of 0.3% in the Exome Variant Server was detected in both affected individuals. Fluorescence in situ hybridization for PTEN in the resected esophageal cancer specimen demonstrated no PTEN copy loss in malignant cells; however, results of an immunohistochemical analysis demonstrated a loss of PTEN protein expression. While the risks of many cancers are elevated in the PTEN hamartoma tumor syndromes, association between esophageal adenocarcinoma and these syndromes has not been previously reported. Esophageal adenocarcinoma and extensive polyposis/ganglioneuromatosis could represent less common features of these syndromes, potentially correlating with this novel PTEN frameshift and early protein termination genotype. Alternatively, because simultaneous disruption of both the PTEN and TGF-β/SMAD4 pathways is associated with development of esophageal cancer in a mouse model and because SMAD4 mutations cause gastrointestinal hamartomas in juvenile polyposis syndrome, the SMAD7 mutation may represent an additional modifier of these individuals' PTEN-mutant phenotype.
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Affiliation(s)
- Scott K Sherman
- Department of General Surgery, University of Iowa Carver College of Medicine, Iowa City, IA, USA
| | - Jessica E Maxwell
- Department of General Surgery, University of Iowa Carver College of Medicine, Iowa City, IA, USA
| | - Qining Qian
- Department of Cytogenetics/Pediatrics, University of Iowa Carver College of Medicine, Iowa City, IA, USA
| | - Andrew M Bellizzi
- Department of Pathology, University of Iowa Carver College of Medicine, Iowa City, IA, USA
| | - Terry A Braun
- Department of Ophthalmology, University of Iowa Carver College of Medicine, Iowa City, IA, USA
| | - Mark D Iannettoni
- Department of Thoracic Surgery, University of Iowa Carver College of Medicine, Iowa City, IA, USA
| | - Benjamin W Darbro
- Department of Cytogenetics/Pediatrics, University of Iowa Carver College of Medicine, Iowa City, IA, USA
| | - James R Howe
- Department of General Surgery, University of Iowa Carver College of Medicine, Iowa City, IA, USA.
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17
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Burnight ER, Wiley LA, Drack AV, Braun TA, Anfinson KR, Kaalberg EE, Halder JA, Affatigato LM, Mullins RF, Stone EM, Tucker BA. CEP290 gene transfer rescues Leber congenital amaurosis cellular phenotype. Gene Ther 2014; 21:662-72. [PMID: 24807808 DOI: 10.1038/gt.2014.39] [Citation(s) in RCA: 93] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2013] [Revised: 03/06/2014] [Accepted: 03/20/2014] [Indexed: 12/17/2022]
Abstract
Mutations in CEP290 are the most common cause of Leber congenital amaurosis (LCA), a severe inherited retinal degenerative disease for which there is currently no cure. Autosomal recessive CEP290-associated LCA is a good candidate for gene replacement therapy, and cells derived from affected individuals give researchers the ability to study human disease and therapeutic gene correction in vitro. Here we report the development of lentiviral vectors carrying full-length CEP290 for the purpose of correcting the CEP290 disease-specific phenotype in human cells. A lentiviral vector containing CMV-driven human full-length CEP290 was constructed. Following transduction of patient-specific, iPSC-derived, photoreceptor precursor cells, reverse transcriptase-PCR analysis and western blotting revealed vector-derived expression. As CEP290 is important in ciliogenesis, the ability of fibroblast cultures from CEP290-associated LCA patients to form cilia was investigated. In cultures derived from these patients, fewer cells formed cilia compared with unaffected controls. Cilia that were formed were shorter in patient-derived cells than in cells from unaffected individuals. Importantly, lentiviral delivery of CEP290 rescued the ciliogenesis defect. The successful construction and viral transfer of full-length CEP290 brings us closer to the goal of providing gene- and cell-based therapies for patients affected with this common form of LCA.
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Affiliation(s)
- E R Burnight
- Department of Opthalmology and Visual Sciences, Stephen A Wynn Institute for Vision Research, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - L A Wiley
- Department of Opthalmology and Visual Sciences, Stephen A Wynn Institute for Vision Research, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - A V Drack
- Department of Opthalmology and Visual Sciences, Stephen A Wynn Institute for Vision Research, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - T A Braun
- 1] Department of Opthalmology and Visual Sciences, Stephen A Wynn Institute for Vision Research, Carver College of Medicine, University of Iowa, Iowa City, IA, USA [2] Biomedical Engineering, University of Iowa, Iowa City, IA, USA
| | - K R Anfinson
- Department of Opthalmology and Visual Sciences, Stephen A Wynn Institute for Vision Research, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - E E Kaalberg
- Department of Opthalmology and Visual Sciences, Stephen A Wynn Institute for Vision Research, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - J A Halder
- Department of Opthalmology and Visual Sciences, Stephen A Wynn Institute for Vision Research, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - L M Affatigato
- Department of Opthalmology and Visual Sciences, Stephen A Wynn Institute for Vision Research, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - R F Mullins
- Department of Opthalmology and Visual Sciences, Stephen A Wynn Institute for Vision Research, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - E M Stone
- 1] Department of Opthalmology and Visual Sciences, Stephen A Wynn Institute for Vision Research, Carver College of Medicine, University of Iowa, Iowa City, IA, USA [2] Howard Hughes Medical Institute, University of Iowa, Iowa City, IA, USA
| | - B A Tucker
- Department of Opthalmology and Visual Sciences, Stephen A Wynn Institute for Vision Research, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
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Sharma TP, McDowell CM, Liu Y, Wagner AH, Thole D, Faga BP, Wordinger RJ, Braun TA, Clark AF. Optic nerve crush induces spatial and temporal gene expression patterns in retina and optic nerve of BALB/cJ mice. Mol Neurodegener 2014; 9:14. [PMID: 24767545 PMCID: PMC4113182 DOI: 10.1186/1750-1326-9-14] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [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: 12/19/2013] [Accepted: 04/18/2014] [Indexed: 12/18/2022] Open
Abstract
Background Central nervous system (CNS) trauma and neurodegenerative disorders trigger a cascade of cellular and molecular events resulting in neuronal apoptosis and regenerative failure. The pathogenic mechanisms and gene expression changes associated with these detrimental events can be effectively studied using a rodent optic nerve crush (ONC) model. The purpose of this study was to use a mouse ONC model to: (a) evaluate changes in retina and optic nerve (ON) gene expression, (b) identify neurodegenerative pathogenic pathways and (c) discover potential new therapeutic targets. Results Only 54% of total neurons survived in the ganglion cell layer (GCL) 28 days post crush. Using Bayesian Estimation of Temporal Regulation (BETR) gene expression analysis, we identified significantly altered expression of 1,723 and 2,110 genes in the retina and ON, respectively. Meta-analysis of altered gene expression (≥1.5, ≤-1.5, p < 0.05) using Partek and DAVID demonstrated 28 up and 20 down-regulated retinal gene clusters and 57 up and 41 down-regulated optic nerve clusters. Regulated gene clusters included regenerative change, synaptic plasticity, axonogenesis, neuron projection, and neuron differentiation. Expression of selected genes (Vsnl1, Syt1, Synpr and Nrn1) from retinal and ON neuronal clusters were quantitatively and qualitatively examined for their relation to axonal neurodegeneration by immunohistochemistry and qRT-PCR. Conclusion A number of detrimental gene expression changes occur that contribute to trauma-induced neurodegeneration after injury to ON axons. Nrn1 (synaptic plasticity gene), Synpr and Syt1 (synaptic vesicle fusion genes), and Vsnl1 (neuron differentiation associated gene) were a few of the potentially unique genes identified that were down-regulated spatially and temporally in our rodent ONC model. Bioinformatic meta-analysis identified significant tissue-specific and time-dependent gene clusters associated with regenerative changes, synaptic plasticity, axonogenesis, neuron projection, and neuron differentiation. These ONC induced neuronal loss and regenerative failure associated clusters can be extrapolated to changes occurring in other forms of CNS trauma or in clinical neurodegenerative pathological settings. In conclusion, this study identified potential therapeutic targets to address two key mechanisms of CNS trauma and neurodegeneration: neuronal loss and regenerative failure.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Abbot F Clark
- North Texas Eye Research Institute, Ft, Worth, TX 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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Tucker BA, Mullins RF, Streb LM, Anfinson K, Eyestone ME, Kaalberg E, Riker MJ, Drack AV, Braun TA, Stone EM. Patient-specific iPSC-derived photoreceptor precursor cells as a means to investigate retinitis pigmentosa. eLife 2013; 2:e00824. [PMID: 23991284 PMCID: PMC3755341 DOI: 10.7554/elife.00824] [Citation(s) in RCA: 149] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2013] [Accepted: 07/24/2013] [Indexed: 12/11/2022] Open
Abstract
Next-generation and Sanger sequencing were combined to identify disease-causing USH2A mutations in an adult patient with autosomal recessive RP. Induced pluripotent stem cells (iPSCs), generated from the patient’s keratinocytes, were differentiated into multi-layer eyecup-like structures with features of human retinal precursor cells. The inner layer of the eyecups contained photoreceptor precursor cells that expressed photoreceptor markers and exhibited axonemes and basal bodies characteristic of outer segments. Analysis of the USH2A transcripts of these cells revealed that one of the patient’s mutations causes exonification of intron 40, a translation frameshift and a premature stop codon. Western blotting revealed upregulation of GRP78 and GRP94, suggesting that the patient’s other USH2A variant (Arg4192His) causes disease through protein misfolding and ER stress. Transplantation into 4-day-old immunodeficient Crb1−/− mice resulted in the formation of morphologically and immunohistochemically recognizable photoreceptor cells, suggesting that the mutations in this patient act via post-developmental photoreceptor degeneration. DOI:http://dx.doi.org/10.7554/eLife.00824.001 Retinitis pigmentosa is an inherited disorder in which the gradual degeneration of light-sensitive cells in the outer retina, known as photoreceptors, causes a progressive loss of sight. Retinitis pigmentosa can also occur as part of a wider syndrome: patients with Usher syndrome, for example, suffer from early-onset deafness and then develop retinitis pigmentosa later in life. Usher syndrome is caused by mutations in any of more than ten genes, but the most commonly affected is USH2A, which encodes a protein called usherin. Mutations in USH2A can also cause retinitis pigmentosa on its own. Clinical trials are underway to determine whether it is possible to treat various forms of inherited retinal degeneration using gene therapy. This involves inserting a functional copy of the gene associated with the disease into an inactivated virus, which is then injected into the eye. The virus carries the target gene to the light-sensitive photoreceptor cells where it can replace the faulty gene. This could be particularly useful for conditions such as Usher syndrome, in which the early-onset deafness makes it possible to diagnose retinitis pigmentosa before substantial numbers of photoreceptor cells have been lost. For gene therapy to become a widely used strategy for the treatment of retinal degenerative disease, identification and functional interrogation of the disease-causing gene/mutations will be critical. This is especially true for large highly polymorphic genes such as USH2A that often have mutations that are difficult to identify by standard sequencing techniques. Likewise, viruses that can carry large amounts of genetic material, or endogenous genome editing approaches, will need to be developed and validated in an efficient patient-specific model system. Tucker et al. might have found a way to address these problems. In their study, they used skin cells from a retinitis pigmentosa patient with mutations in USH2A to produce induced pluripotent stem cells. These are cells that can be made to develop into a wide variety of mature cell types, depending on the exact conditions in which they are cultured. Tucker et al. used these stem cells to generate photoreceptor precursor cells, which they transplanted into the retinas of immune-suppressed mice. The cells developed into normal-looking photoreceptor cells that expressed photoreceptor-specific proteins. These results have several implications. First, they support the idea that stem cell-derived retinal photoreceptor cells, generated from patients with unknown mutations, can be used to identify disease-causing genes and to interrogate disease pathophysiology. This will allow for a more rapid development of gene therapy strategies. Second, they demonstrate that USH2A mutations cause retinitis pigmentosa by affecting photoreceptors later in life rather than by altering their development. This suggests that it should, via early intervention, be possible to treat retinitis pigmentosa in adult patients with this form of the disease. Third, the technique could be used to generate animal models in which to study the effects of specific disease-causing mutations on cellular development and function. Finally, this study suggests that skin cells from adults with retinitis pigmentosa could be used to generate immunologically matched photoreceptor cells that can be transplanted back into the same patients to restore their sight. Many questions remain to be answered before this technique can be moved into clinical trials but, in the meantime, it will provide a new tool for research into this major cause of blindness. DOI:http://dx.doi.org/10.7554/eLife.00824.002
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Affiliation(s)
- Budd A Tucker
- Department of Ophthalmology and Visual Sciences , University of Iowa Carver College of Medicine , Iowa City , United States
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Braun TA, Mullins RF, Wagner AH, Andorf JL, Johnston RM, Bakall BB, Deluca AP, Fishman GA, Lam BL, Weleber RG, Cideciyan AV, Jacobson SG, Sheffield VC, Tucker BA, Stone EM. Non-exomic and synonymous variants in ABCA4 are an important cause of Stargardt disease. Hum Mol Genet 2013; 22:5136-45. [PMID: 23918662 PMCID: PMC3842174 DOI: 10.1093/hmg/ddt367] [Citation(s) in RCA: 127] [Impact Index Per Article: 11.5] [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] [Indexed: 01/07/2023] Open
Abstract
Mutations in ABCA4 cause Stargardt disease and other blinding autosomal recessive retinal disorders. However, sequencing of the complete coding sequence in patients with clinical features of Stargardt disease sometimes fails to detect one or both mutations. For example, among 208 individuals with clear clinical evidence of ABCA4 disease ascertained at a single institution, 28 had only one disease-causing allele identified in the exons and splice junctions of the primary retinal transcript of the gene. Haplotype analysis of these 28 probands revealed 3 haplotypes shared among ten families, suggesting that 18 of the 28 missing alleles were rare enough to be present only once in the cohort. We hypothesized that mutations near rare alternate splice junctions in ABCA4 might cause disease by increasing the probability of mis-splicing at these sites. Next-generation sequencing of RNA extracted from human donor eyes revealed more than a dozen alternate exons that are occasionally incorporated into the ABCA4 transcript in normal human retina. We sequenced the genomic DNA containing 15 of these minor exons in the 28 one-allele subjects and observed five instances of two different variations in the splice signals of exon 36.1 that were not present in normal individuals (P < 10−6). Analysis of RNA obtained from the keratinocytes of patients with these mutations revealed the predicted alternate transcript. This study illustrates the utility of RNA sequence analysis of human donor tissue and patient-derived cell lines to identify mutations that would be undetectable by exome sequencing.
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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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Kim BJ, Braun TA, Wordinger RJ, Clark AF. Progressive morphological changes and impaired retinal function associated with temporal regulation of gene expression after retinal ischemia/reperfusion injury in mice. Mol Neurodegener 2013; 8:21. [PMID: 23800383 PMCID: PMC3695831 DOI: 10.1186/1750-1326-8-21] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.1] [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: 02/14/2013] [Accepted: 06/11/2013] [Indexed: 11/29/2022] Open
Abstract
Retinal ischemia/reperfusion (I/R) injury is an important cause of visual impairment. However, questions remain on the overall I/R mechanisms responsible for progressive damage to the retina. In this study, we used a mouse model of I/R and characterized the pathogenesis by analyzing temporal changes of retinal morphology and function associated with changes in retinal gene expression. Transient ischemia was induced in one eye of C57BL/6 mice by raising intraocular pressure to 120 mmHg for 60 min followed by retinal reperfusion by restoring normal pressure. At various time points post I/R, retinal changes were monitored by histological assessment with H&E staining and by SD-OCT scanning. Retinal function was also measured by scotopic ERG. Temporal changes in retinal gene expression were analyzed using cDNA microarrays and real-time RT-PCR. In addition, retinal ganglion cells and gliosis were observed by immunohistochemistry. H&E staining and SD-OCT scanning showed an initial increase followed by a significant reduction of retinal thickness in I/R eyes accompanied with cell loss compared to contralateral control eyes. The greatest reduction in thickness was in the inner plexiform layer (IPL) and inner nuclear layer (INL). Retinal detachment was observed at days 3 and 7 post- I/R injury. Scotopic ERG a- and b-wave amplitudes and implicit times were significantly impaired in I/R eyes compared to contralateral control eyes. Microarray data showed temporal changes in gene expression involving various gene clusters such as molecular chaperones and inflammation. Furthermore, immunohistochemical staining confirmed Müller cell gliosis in the damaged retinas. The time-dependent changes in retinal morphology were significantly associated with functional impairment and altered retinal gene expression. We demonstrated that I/R-mediated morphological changes the retina closely associated with functional impairment as well as temporal changes in retinal gene expression. Our findings will provide further understanding of molecular pathogenesis associated with ischemic injury to the retina.
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Affiliation(s)
- Byung-Jin Kim
- The North Texas Eye Research Institute, University of North Texas Health Science Center, Fort Worth, TX 76107, USA
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25
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Wagner AH, Taylor KR, DeLuca AP, Casavant TL, Mullins RF, Stone EM, Scheetz TE, Braun TA. Prioritization of retinal disease genes: an integrative approach. Hum Mutat 2013; 34:853-9. [PMID: 23508994 DOI: 10.1002/humu.22317] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2012] [Accepted: 03/07/2013] [Indexed: 02/03/2023]
Abstract
The discovery of novel disease-associated variations in genes is often a daunting task in highly heterogeneous disease classes. We seek a generalizable algorithm that integrates multiple publicly available genomic data sources in a machine-learning model for the prioritization of candidates identified in patients with retinal disease. To approach this problem, we generate a set of feature vectors from publicly available microarray, RNA-seq, and ChIP-seq datasets of biological relevance to retinal disease, to observe patterns in gene expression specificity among tissues of the body and the eye, in addition to photoreceptor-specific signals by the CRX transcription factor. Using these features, we describe a novel algorithm, positive and unlabeled learning for prioritization (PULP). This article compares several popular supervised learning techniques as the regression function for PULP. The results demonstrate a highly significant enrichment for previously characterized disease genes using a logistic regression method. Finally, a comparison of PULP with the popular gene prioritization tool ENDEAVOUR shows superior prioritization of retinal disease genes from previous studies. The java source code, compiled binary, assembled feature vectors, and instructions are available online at https://github.com/ahwagner/PULP.
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Affiliation(s)
- Alex H Wagner
- Department of Biomedical Engineering, University of Iowa, Iowa City, Iowa 52242, USA.
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26
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Wagner AH, Anand VN, Wang WH, Chatterton JE, Sun D, Shepard AR, Jacobson N, Pang IH, Deluca AP, Casavant TL, Scheetz TE, Mullins RF, Braun TA, Clark AF. Exon-level expression profiling of ocular tissues. Exp Eye Res 2013; 111:105-11. [PMID: 23500522 DOI: 10.1016/j.exer.2013.03.004] [Citation(s) in RCA: 84] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2012] [Revised: 02/06/2013] [Accepted: 03/05/2013] [Indexed: 11/25/2022]
Abstract
The normal gene expression profiles of the tissues in the eye are a valuable resource for considering genes likely to be involved with disease processes. We profiled gene expression in ten ocular tissues from human donor eyes using Affymetrix Human Exon 1.0 ST arrays. Ten different tissues were obtained from six different individuals and RNA was pooled. The tissues included: retina, optic nerve head (ONH), optic nerve (ON), ciliary body (CB), trabecular meshwork (TM), sclera, lens, cornea, choroid/retinal pigment epithelium (RPE) and iris. Expression values were compared with publically available Expressed Sequence Tag (EST) and RNA-sequencing resources. Known tissue-specific genes were examined and they demonstrated correspondence of expression with the representative ocular tissues. The estimated gene and exon level abundances are available online at the Ocular Tissue Database.
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Affiliation(s)
- Alex H Wagner
- Department of Biomedical Engineering, University of Iowa, Iowa City, IA 52242, USA
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Scheetz TE, Fingert JH, Wang K, Kuehn MH, Knudtson KL, Alward WLM, Boldt HC, Russell SR, Folk JC, Casavant TL, Braun TA, Clark AF, Stone EM, Sheffield VC. A genome-wide association study for primary open angle glaucoma and macular degeneration reveals novel Loci. PLoS One 2013; 8:e58657. [PMID: 23536807 PMCID: PMC3594156 DOI: 10.1371/journal.pone.0058657] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [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: 09/21/2012] [Accepted: 02/07/2013] [Indexed: 11/22/2022] Open
Abstract
Glaucoma and age-related macular degeneration (AMD) are the two leading causes of visual loss in the United States. We utilized a novel study design to perform a genome-wide association for both primary open angle glaucoma (POAG) and AMD. This study design utilized a two-stage process for hypothesis generation and validation, in which each disease cohort was utilized as a control for the other. A total of 400 POAG patients and 400 AMD patients were ascertained and genotyped at 500,000 loci. This study identified a novel association of complement component 7 (C7) to POAG. Additionally, an association of central corneal thickness, a known risk factor for POAG, was found to be associated with ribophorin II (RPN2). Linked monogenic loci for POAG and AMD were also evaluated for evidence of association, none of which were found to be significantly associated. However, several yielded putative associations requiring validation. Our data suggest that POAG is more genetically complex than AMD, with no common risk alleles of large effect.
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Affiliation(s)
- Todd E Scheetz
- Department of Ophthalmology and Visual Sciences, The University of Iowa, Iowa City, Iowa, United States of America
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Taylor KR, Deluca AP, Shearer AE, Hildebrand MS, Black-Ziegelbein EA, Anand VN, Sloan CM, Eppsteiner RW, Scheetz TE, Huygen PLM, Smith RJH, Braun TA, Casavant TL. AudioGene: predicting hearing loss genotypes from phenotypes to guide genetic screening. Hum Mutat 2013; 34:539-45. [PMID: 23280582 DOI: 10.1002/humu.22268] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2012] [Accepted: 12/18/2012] [Indexed: 12/31/2022]
Abstract
Autosomal dominant nonsyndromic hearing loss (ADNSHL) is a common and often progressive sensory deficit. ADNSHL displays a high degree of genetic heterogeneity and varying rates of progression. Accurate, comprehensive, and cost-effective genetic testing facilitates genetic counseling and provides valuable prognostic information to affected individuals. In this article, we describe the algorithm underlying AudioGene, a software system employing machine-learning techniques that utilizes phenotypic information derived from audiograms to predict the genetic cause of hearing loss in persons segregating ADNSHL. Our data show that AudioGene has an accuracy of 68% in predicting the causative gene within its top three predictions, as compared with 44% for a majority classifier. We also show that AudioGene remains effective for audiograms with high levels of clinical measurement noise. We identify audiometric outliers for each genetic locus and hypothesize that outliers may reflect modifying genetic effects. As personalized genomic medicine becomes more common, AudioGene will be increasingly useful as a phenotypic filter to assess pathogenicity of variants identified by massively parallel sequencing.
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Affiliation(s)
- Kyle R Taylor
- Department of Electrical and Computer Engineering, University of Iowa, Iowa City, IA, USA
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29
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Eppsteiner RW, Shearer AE, Hildebrand MS, Deluca AP, Ji H, Dunn CC, Black-Ziegelbein EA, Casavant TL, Braun TA, Scheetz TE, Scherer SE, Hansen MR, Gantz BJ, Smith RJH. Prediction of cochlear implant performance by genetic mutation: the spiral ganglion hypothesis. Hear Res 2012; 292:51-8. [PMID: 22975204 DOI: 10.1016/j.heares.2012.08.007] [Citation(s) in RCA: 89] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/01/2012] [Revised: 08/16/2012] [Accepted: 08/20/2012] [Indexed: 11/29/2022]
Abstract
BACKGROUND Up to 7% of patients with severe-to-profound deafness do not benefit from cochlear implantation. Given the high surgical implantation and clinical management cost of cochlear implantation (>$1 million lifetime cost), prospective identification of the worst performers would reduce unnecessary procedures and healthcare costs. Because cochlear implants bypass the membranous labyrinth but rely on the spiral ganglion for functionality, we hypothesize that cochlear implant (CI) performance is dictated in part by the anatomic location of the cochlear pathology that underlies the hearing loss. As a corollary, we hypothesize that because genetic testing can identify sites of cochlear pathology, it may be useful in predicting CI performance. METHODS 29 adult CI recipients with idiopathic adult-onset severe-to-profound hearing loss were studied. DNA samples were subjected to solution-based sequence capture and massively parallel sequencing using the OtoSCOPE(®) platform. The cohort was divided into three CI performance groups (good, intermediate, poor) and genetic causes of deafness were correlated with audiometric data to determine whether there was a gene-specific impact on CI performance. RESULTS The genetic cause of deafness was determined in 3/29 (10%) individuals. The two poor performers segregated mutations in TMPRSS3, a gene expressed in the spiral ganglion, while the good performer segregated mutations in LOXHD1, a gene expressed in the membranous labyrinth. Comprehensive literature review identified other good performers with mutations in membranous labyrinth-expressed genes; poor performance was associated with spiral ganglion-expressed genes. CONCLUSIONS Our data support the underlying hypothesis that mutations in genes preferentially expressed in the spiral ganglion portend poor CI performance while mutations in genes expressed in the membranous labyrinth portend good CI performance. Although the low mutation rate in known deafness genes in this cohort likely relates to the ascertainment characteristics (postlingual hearing loss in adult CI recipients), these data suggest that genetic testing should be implemented as part of the CI evaluation to test this association prospectively.
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Affiliation(s)
- Robert W Eppsteiner
- Department of Otolaryngology - Head and Neck Surgery, University of Iowa Hospitals and Clinics, Iowa City, IA 52242, USA
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30
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Eppsteiner RW, Shearer AE, Hildebrand MS, Taylor KR, Deluca AP, Scherer S, Huygen P, Scheetz TE, Braun TA, Casavant TL, Smith RJH. Using the phenome and genome to improve genetic diagnosis for deafness. Otolaryngol Head Neck Surg 2012; 147:975-7. [PMID: 22785243 DOI: 10.1177/0194599812454271] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- Robert W Eppsteiner
- Department of Otolaryngology-Head and Neck Surgery, University of Iowa Hospitals and Clinics, Iowa City, IA, USA
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31
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Levy MA, Freymann JB, Kirby JS, Fedorov A, Fennessy FM, Eschrich SA, Berglund AE, Fenstermacher DA, Tan Y, Guo X, Casavant TL, Brown BJ, Braun TA, Dekker A, Roelofs E, Mountz JM, Boada F, Laymon C, Oborski M, Rubin DL. Informatics methods to enable sharing of quantitative imaging research data. Magn Reson Imaging 2012; 30:1249-56. [PMID: 22770688 DOI: 10.1016/j.mri.2012.04.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2012] [Revised: 04/16/2012] [Accepted: 04/18/2012] [Indexed: 10/28/2022]
Abstract
INTRODUCTION The National Cancer Institute Quantitative Research Network (QIN) is a collaborative research network whose goal is to share data, algorithms and research tools to accelerate quantitative imaging research. A challenge is the variability in tools and analysis platforms used in quantitative imaging. Our goal was to understand the extent of this variation and to develop an approach to enable sharing data and to promote reuse of quantitative imaging data in the community. METHODS We performed a survey of the current tools in use by the QIN member sites for representation and storage of their QIN research data including images, image meta-data and clinical data. We identified existing systems and standards for data sharing and their gaps for the QIN use case. We then proposed a system architecture to enable data sharing and collaborative experimentation within the QIN. RESULTS There are a variety of tools currently used by each QIN institution. We developed a general information system architecture to support the QIN goals. We also describe the remaining architecture gaps we are developing to enable members to share research images and image meta-data across the network. CONCLUSIONS As a research network, the QIN will stimulate quantitative imaging research by pooling data, algorithms and research tools. However, there are gaps in current functional requirements that will need to be met by future informatics development. Special attention must be given to the technical requirements needed to translate these methods into the clinical research workflow to enable validation and qualification of these novel imaging biomarkers.
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Affiliation(s)
- Mia A Levy
- Department of Biomedical Informatics and Medicine, Division of Hematology and Oncology, Vanderbilt University School of Medicine, Nashville, TN 37232-6838, USA.
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32
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Davis LK, Meyer KJ, Schindler EI, Beck JS, Rudd DS, Grundstad AJ, Scheetz TE, Braun TA, Fingert JH, Alward WLM, Kwon YH, Folk JC, Russell SR, Wassink TH, Sheffield VC, Stone EM. Copy number variations and primary open-angle glaucoma. Invest Ophthalmol Vis Sci 2011; 52:7122-33. [PMID: 21310917 DOI: 10.1167/iovs.10-5606] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [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 This study sought to investigate the role of rare copy number variation (CNV) in age-related disorders of blindness, with a focus on primary open-angle glaucoma (POAG). Data are reported from a whole-genome copy number screen in a large cohort of 400 individuals with POAG and 500 age-matched glaucoma-free subjects. METHODS DNA samples from patients and controls were tested for CNVs using a combination of two microarray platforms. The signal intensity data generated from these arrays were then analyzed with multiple CNV detection programs including CNAG version 2.0, PennCNV, and dChip. RESULTS A total of 11 validated CNVs were identified as recurrent in the POAG set and absent in the age-matched control set. This set included CNVs on 5q23.1 (DMXL1, DTWD2), 20p12 (PAK7), 12q14 (C12orf56, XPOT, TBK1, and RASSF3), 12p13.33 (TULP3), and 10q34.21 (PAX2), among others. The CNVs presented here are exceedingly rare and are not found in the Database of Genomic Variants. Moreover, expression data from ocular tissue support the role of these CNV-implicated genes in vision-related processes. In addition, CNV locations of DMXL1 and PAK7 overlap previously identified linkage signals for glaucoma on 5p23.1 and 20p12, respectively. CONCLUSIONS The data are consistent with the hypothesis that rare CNV plays a role in the development of POAG.
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Affiliation(s)
- Lea K Davis
- Department of Psychiatry, University of Illinois, Chicago, Illinois, USA
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Hildebrand MS, Morín M, Meyer NC, Mayo F, Modamio-Hoybjor S, Mencía A, Olavarrieta L, Morales-Angulo C, Nishimura CJ, Workman H, DeLuca AP, del Castillo I, Taylor KR, Tompkins B, Goodman CW, Schrauwen I, Wesemael MV, Lachlan K, Shearer AE, Braun TA, Huygen PLM, Kremer H, Van Camp G, Moreno F, Casavant TL, Smith RJH, Moreno-Pelayo MA. DFNA8/12 caused by TECTA mutations is the most identified subtype of nonsyndromic autosomal dominant hearing loss. Hum Mutat 2011; 32:825-34. [PMID: 21520338 DOI: 10.1002/humu.21512] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2011] [Accepted: 03/31/2011] [Indexed: 12/13/2022]
Abstract
The prevalence of DFNA8/DFNA12 (DFNA8/12), a type of autosomal dominant nonsyndromic hearing loss (ADNSHL), is unknown as comprehensive population-based genetic screening has not been conducted. We therefore completed unbiased screening for TECTA mutations in a Spanish cohort of 372 probands from ADNSHL families. Three additional families (Spanish, Belgian, and English) known to be linked to DFNA8/12 were also included in the screening. In an additional cohort of 835 American ADNSHL families, we preselected 73 probands for TECTA screening based on audiometric data. In aggregate, we identified 23 TECTA mutations in this process. Remarkably, 20 of these mutations are novel, more than doubling the number of reported TECTA ADNSHL mutations from 13 to 33. Mutations lie in all domains of the α-tectorin protein, including those for the first time identified in the entactin domain, as well as the vWFD1, vWFD2, and vWFD3 repeats, and the D1-D2 and TIL2 connectors. Although the majority are private mutations, four of them-p.Cys1036Tyr, p.Cys1837Gly, p.Thr1866Met, and p.Arg1890Cys-were observed in more than one unrelated family. For two of these mutations founder effects were also confirmed. Our data validate previously observed genotype-phenotype correlations in DFNA8/12 and introduce new correlations. Specifically, mutations in the N-terminal region of α-tectorin (entactin domain, vWFD1, and vWFD2) lead to mid-frequency NSHL, a phenotype previously associated only with mutations in the ZP domain. Collectively, our results indicate that DFNA8/12 hearing loss is a frequent type of ADNSHL.
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Affiliation(s)
- Michael S Hildebrand
- Department of Otolaryngology-Head and Neck Surgery, University of Iowa, Iowa City, IA 52242, USA
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Meyer KJ, Davis LK, Schindler EI, Beck JS, Rudd DS, Grundstad AJ, Scheetz TE, Braun TA, Fingert JH, Alward WL, Kwon YH, Folk JC, Russell SR, Wassink TH, Stone EM, Sheffield VC. Genome-wide analysis of copy number variants in age-related macular degeneration. Hum Genet 2010; 129:91-100. [PMID: 20981449 DOI: 10.1007/s00439-010-0904-6] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2010] [Accepted: 10/17/2010] [Indexed: 10/18/2022]
Abstract
Age-related macular degeneration (AMD) is a complex genetic disease, with many loci demonstrating appreciable attributable disease risk. Despite significant progress toward understanding the genetic and environmental etiology of AMD, identification of additional risk factors is necessary to fully appreciate and treat AMD pathology. In this study, we investigated copy number variants (CNVs) as potential AMD risk variants in a cohort of 400 AMD patients and 500 AMD-free controls ascertained at the University of Iowa. We used three publicly available copy number programs to analyze signal intensity data from Affymetrix GeneChip SNP Microarrays. CNVs were ranked based on prevalence in the disease cohort and absence from the control group; high interest CNVs were subsequently confirmed by qPCR. While we did not observe a single-locus "risk CNV" that could account for a major fraction of AMD, we identified several rare and overlapping CNVs containing or flanking compelling candidate genes such as NPHP1 and EFEMP1. These and other candidate genes highlighted by this study deserve further scrutiny as sources of genetic risk for AMD.
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Affiliation(s)
- Kacie J Meyer
- Interdisciplinary Genetics Program, University of Iowa, Iowa City, IA 52242, USA
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O'Leary BM, Davis SG, Smith MF, Brown B, Kemp MB, Almabrazi H, Grundstad JA, Burns T, Leontiev V, Andorf J, Clark AF, Sheffield VC, Casavant TL, Scheetz TE, Stone EM, Braun TA. Transcript annotation prioritization and screening system (TrAPSS) for mutation screening. J Bioinform Comput Biol 2008; 5:1155-72. [PMID: 18172923 DOI: 10.1142/s0219720007003132] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2007] [Revised: 07/31/2007] [Accepted: 08/13/2007] [Indexed: 11/18/2022]
Abstract
When searching for disease-causing mutations with polymerase chain reaction (PCR)-based methods, candidate genes are usually screened in their entirety, exon by exon. Genomic resources (i.e. www.ncbi.nih.gov, www.ensembl.org, and genome.ucsc.edu) largely support this paradigm for mutation screening by making it easy to view and access sequence data associated with genes in their genomic context. However, the administrative burden of conducting mutation screening in potentially hundreds of genes and thousands of exons in thousands of patients is significant, even with the use of public genome resources. For example, the manual design of oligonucleotide primers for all exons of the 10 Leber's congenital amaurosis (LCA) genes (149 exons) represents a significant information management challenge. The Transcript Annotation Prioritization and Screening System (TrAPSS) is designed to accelerate mutation screening by (1) providing a gene-based local cache of candidate disease genes in a genomic context, (2) automating tasks associated with optimizing candidate disease gene screening and information management, and (3) providing the implementation of an algorithmic technique to utilize large amounts of heterogeneous genome annotation (e.g. conserved protein functional domains) so as to prioritize candidate genes.
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Affiliation(s)
- Brian M O'Leary
- Coordinated Laboratory for Computational Genomics, University of Iowa, Iowa City, IA 52242, USA.
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36
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Scheetz TE, Kim KYA, Swiderski RE, Philp AR, Braun TA, Knudtson KL, Dorrance AM, DiBona GF, Huang J, Casavant TL, Sheffield VC, Stone EM. Regulation of gene expression in the mammalian eye and its relevance to eye disease. Proc Natl Acad Sci U S A 2006; 103:14429-34. [PMID: 16983098 PMCID: PMC1636701 DOI: 10.1073/pnas.0602562103] [Citation(s) in RCA: 130] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We used expression quantitative trait locus mapping in the laboratory rat (Rattus norvegicus) to gain a broad perspective of gene regulation in the mammalian eye and to identify genetic variation relevant to human eye disease. Of >31,000 gene probes represented on an Affymetrix expression microarray, 18,976 exhibited sufficient signal for reliable analysis and at least 2-fold variation in expression among 120 F(2) rats generated from an SR/JrHsd x SHRSP intercross. Genome-wide linkage analysis with 399 genetic markers revealed significant linkage with at least one marker for 1,300 probes (alpha = 0.001; estimated empirical false discovery rate = 2%). Both contiguous and noncontiguous loci were found to be important in regulating mammalian eye gene expression. We investigated one locus of each type in greater detail and identified putative transcription-altering variations in both cases. We found an inserted cREL binding sequence in the 5' flanking sequence of the Abca4 gene associated with an increased expression level of that gene, and we found a mutation of the gene encoding thyroid hormone receptor beta2 associated with a decreased expression level of the gene encoding short-wavelength sensitive opsin (Opn1sw). In addition to these positional studies, we performed a pairwise analysis of gene expression to identify genes that are regulated in a coordinated manner and used this approach to validate two previously undescribed genes involved in the human disease Bardet-Biedl syndrome. These data and analytical approaches can be used to facilitate the discovery of additional genes and regulatory elements involved in human eye disease.
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Affiliation(s)
| | | | | | | | | | | | - Anne M. Dorrance
- Department of Physiology, Medical College of Georgia, Augusta, GA 30912
| | | | | | - Thomas L. Casavant
- Departments of Ophthalmology
- Biomedical Engineering
- Electrical Engineering
| | - Val C. Sheffield
- Departments of Ophthalmology
- Pediatrics
- Howard Hughes Medical Institute, University of Iowa, Iowa City, IA 52242; and
| | - Edwin M. Stone
- Departments of Ophthalmology
- Howard Hughes Medical Institute, University of Iowa, Iowa City, IA 52242; and
- To whom correspondence should be addressed. E-mail:
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Braun TA, Shankar SP, Davis S, O'Leary B, Scheetz TE, Clark AF, Sheffield VC, Casavant TL, Stone EM. Prioritizing regions of candidate genes for efficient mutation screening. Hum Mutat 2006; 27:195-200. [PMID: 16395665 DOI: 10.1002/humu.20247] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
The availability of the complete sequence of the human genome has dramatically facilitated the search for disease-causing sequence variations. In fact, the rate-limiting step has shifted from the discovery and characterization of candidate genes to the actual screening of human populations and the subsequent interpretation of observed variations. In this study we tested the hypothesis that some segments of candidate genes are more likely than others to contain disease-causing variations and that these segments can be predicted bioinformatically. A bioinformatic technique, prioritization of annotated regions (PAR), was developed to predict the likelihood that a specific coding region of a gene will harbor a disease-causing mutation based on conserved protein functional domains and protein secondary structures. This method was evaluated by using it to analyze 710 genes that collectively harbor 4,498 previously identified mutations. Nearly 50% of the genes were recognized as disease-associated after screening only 9% of the complete coding sequence. The PAR technique identified 90% of the genes as containing at least one mutation, with less than 40% of the screening resources that traditional approaches would require. These results suggest that prioritization strategies such as PAR can accelerate disease-gene identification through more efficient use of screening resources.
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Affiliation(s)
- Terry A Braun
- Department of Biomedical Engineering, University of Iowa, Iowa City, IA 52242, USA
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Steely HT, Dillow GW, Bian L, Grundstad J, Braun TA, Casavant TL, McCartney MD, Clark AF. Protein expression in a transformed trabecular meshwork cell line: proteome analysis. Mol Vis 2006; 12:372-83. [PMID: 16636656] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/08/2023] Open
Abstract
PURPOSE Characterization of the human trabecular meshwork (TM) proteome is hindered by the small mass of intact tissue and the slow growth of cultured cell strains. We have previously characterized a transformed TM cell strain (GTM3) that demonstrates many of the same protein expression and cell signaling systems of nontransformed cell strains. The aim of this study was to initiate a proteomic survey of GTM3 cells as the initial step toward characterization of the complete human TM proteome. METHODS GTM3 cells were cultured to confluence, harvested and solubilized in urea/Nonidet. The protein extract (600 mug) was focused in immobilized isoelectric focusing (IEF) strips, separated by 10% SDS PAGE, and visualized with colloidal Coomassie Blue. Spots of interest were excised, destained, and the contained proteins subjected to in-gel reduction, derivatization, and tryptic digestion. Tryptic peptides were extracted and analyzed by electrospray LC/MS/MS. Protein identification was made using the TurboSequest search algorithm and a recent version of the nonredundant human protein database downloaded from the National Center for Biotechnology Information (NCBI). RESULTS Eighty-seven (87) primary proteins and 93 variants of these proteins were identified. A website was created (TM proteome) that combines data such as graphic spot location within the gel, peptide sequence, apparent and calculated pI, apparent and calculated mass, percentage of coverage, and protein informatic website links. CONCLUSIONS Proteomic analysis of a transformed human TM cell line has been initiated combining preparative two-dimensional PAGE separation, LC/MS/MS analysis of major proteins, and bioinformatic cataloging of the data. Further investigation of data from the transformed cell strain will be used in a comparative fashion for spot identification of analytical proteomic gels of human TM tissue and cultured normal cells. These initial data will form the base from which the characterization of protein expression in the normal and glaucomatous TM can be accomplished.
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Chiang AP, Beck JS, Yen HJ, Tayeh MK, Scheetz TE, Swiderski RE, Nishimura DY, Braun TA, Kim KYA, Huang J, Elbedour K, Carmi R, Slusarski DC, Casavant TL, Stone EM, Sheffield VC. Homozygosity mapping with SNP arrays identifies TRIM32, an E3 ubiquitin ligase, as a Bardet-Biedl syndrome gene (BBS11). Proc Natl Acad Sci U S A 2006; 103:6287-92. [PMID: 16606853 PMCID: PMC1458870 DOI: 10.1073/pnas.0600158103] [Citation(s) in RCA: 295] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The identification of mutations in genes that cause human diseases has largely been accomplished through the use of positional cloning, which relies on linkage mapping. In studies of rare diseases, the resolution of linkage mapping is limited by the number of available meioses and informative marker density. One recent advance is the development of high-density SNP microarrays for genotyping. The SNP arrays overcome low marker informativity by using a large number of markers to achieve greater coverage at finer resolution. We used SNP microarray genotyping for homozygosity mapping in a small consanguineous Israeli Bedouin family with autosomal recessive Bardet-Biedl syndrome (BBS; obesity, pigmentary retinopathy, polydactyly, hypogonadism, renal and cardiac abnormalities, and cognitive impairment) in which previous linkage studies using short tandem repeat polymorphisms failed to identify a disease locus. SNP genotyping revealed a homozygous candidate region. Mutation analysis in the region of homozygosity identified a conserved homozygous missense mutation in the TRIM32 gene, a gene coding for an E3 ubiquitin ligase. Functional analysis of this gene in zebrafish and expression correlation analyses among other BBS genes in an expression quantitative trait loci data set demonstrate that TRIM32 is a BBS gene. This study shows the value of high-density SNP genotyping for homozygosity mapping and the use of expression correlation data for evaluation of candidate genes and identifies the proteasome degradation pathway as a pathway involved in BBS.
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Affiliation(s)
- Annie P. Chiang
- Departments of *Electrical Engineering
- Howard Hughes Medical Institute, University of Iowa, Iowa City, IA 52242; and
| | - John S. Beck
- Pediatrics
- Howard Hughes Medical Institute, University of Iowa, Iowa City, IA 52242; and
| | - Hsan-Jan Yen
- Pediatrics
- Biological Sciences, and
- Howard Hughes Medical Institute, University of Iowa, Iowa City, IA 52242; and
| | - Marwan K. Tayeh
- Pediatrics
- Biological Sciences, and
- Howard Hughes Medical Institute, University of Iowa, Iowa City, IA 52242; and
| | | | | | | | | | - Kwang-Youn A. Kim
- **Biostatistics
- Howard Hughes Medical Institute, University of Iowa, Iowa City, IA 52242; and
| | | | - Khalil Elbedour
- Genetic Institute, Soroka Medical Center, Ben Gurion University of the Negev, Beer-Sheva, 84105, Israel
| | - Rivka Carmi
- Genetic Institute, Soroka Medical Center, Ben Gurion University of the Negev, Beer-Sheva, 84105, Israel
| | | | - Thomas L. Casavant
- Departments of *Electrical Engineering
- Ophthalmology
- Biomedical Engineering
| | - Edwin M. Stone
- Ophthalmology
- Howard Hughes Medical Institute, University of Iowa, Iowa City, IA 52242; and
| | - Val C. Sheffield
- Pediatrics
- Howard Hughes Medical Institute, University of Iowa, Iowa City, IA 52242; and
- To whom correspondence should be addressed. E-mail:
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Bischof JM, Chiang AP, Scheetz TE, Stone EM, Casavant TL, Sheffield VC, Braun TA. Genome-wide identification of pseudogenes capable of disease-causing gene conversion. Hum Mutat 2006; 27:545-52. [PMID: 16671097 DOI: 10.1002/humu.20335] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Pseudogenes are remnants of gene duplication (nonprocessed pseudogenes) and retrotransposition (processed pseudogenes) events. This study describes methods for identifying gene conversion candidates from predicted pseudogenes. Pseudogenes may accumulate and harbor sequence variations over time that become disease-causing mutations when transferred to genes by gene conversion. A total of 14,476 pseudogenes were identified, including 3,426 nonprocessed pseudogenes. In addition, 1,945 nonprocessed pseudogenes that are localized near their progenitor gene were evaluated for their possible role in gene conversion and disease. All 11 known, human cases of gene conversion (with deleterious effects) involving pseudogenes were successfully identified by these methods. Among the pseudogenes identified is a retinitis pigmentosa 9 (RP9) pseudogene that carries a c.509A>G mutation which produces a p.Asp170Gly substitution that is associated with the RP9 form of autosomal dominant retinitis pigmentosa (adRP). The c.509A>G mutation in RP9 is a previously unrecognized example of gene conversion between the progenitor gene and its pseudogene. Notably, two processed pseudogenes also contain mutations associated with diseases. An inosine monophosphate dehydrogenase 1 (IMPDH1) pseudogene carries a c.676G>A mutation that produces a p.Asp226Asn substitution that causes the retinitis pigmentosa 10 (RP10) form of adRP; and a phosphoglycerate kinase 1 (PGK1) pseudogene (PGK1P1) carries a c.837T>C mutation that produces a p.Ile252Thr substitution that is associated with a phosphoglycerate kinase deficiency. Ranking of nonprocessed pseudogenes as candidates for gene conversion was also performed based on the sequence characteristics of published cases of pseudogene-mediated gene conversion. All results and tools produced by this study are available for download at: http://genome.uiowa.edu/pseudogenes.
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Affiliation(s)
- Jared M Bischof
- Coordinated Laboratory for Computational Genomics, The University of Iowa, Iowa City, Iowa 52240, USA
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Sibenaller ZA, Etame AB, Ali MM, Barua M, Braun TA, Casavant TL, Ryken TC. Genetic characterization of commonly used glioma cell lines in the rat animal model system. Neurosurg Focus 2005; 19:E1. [PMID: 16241103 DOI: 10.3171/foc.2005.19.4.2] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Object
Animal models have been used extensively to discern the molecular biology of diseases and to gain insight into treatments. Nevertheless, discrepancies in the effects of treatments and procedures have been encountered during the transition from these animal models to application of the information to clinical trials in humans. To assess the genetic similarities between human gliomas and four cell lines used routinely in animal models, the authors used microarray technology to characterize the similarities and differences in gene expression.
Methods
To define the changes in gene expression, normal rat astrocytes were compared with four rat glioma cell lines (C6, 9L, F98, and RG2). The data were analyzed using two different methods: fold-change analysis and statistical analysis with t statistics. The gene products that were highlighted after intersecting the lists generated by the two methods of analysis were scrutinized against changes in gene expression reported in the literature. Tumorigenesis involves three major steps: the accumulation of genetic alterations, uncontrolled growth, and selected survival of transformed cells. The discussion of the results focuses attention on genes whose primary function is in pathways involved in glioma proliferation, infiltration, and neovascularization. A comparative microarray analysis of differentially expressed genes for four of the commonly used rat tumor cell lines is presented here.
Conclusions
Due to the variances between the cell lines and results from analyses in humans, caution must be observed in interpreting as well as in the translation of information learned from animal models to its application in human trials.
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Affiliation(s)
- Zita A Sibenaller
- Department of Neurosurgery, University of Iowa Hospitals, Iowa City, Iowa 52242, USA
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Stone EM, Braun TA, Russell SR, Kuehn MH, Lotery AJ, Moore PA, Eastman CG, Casavant TL, Sheffield VC. Missense variations in the fibulin 5 gene and age-related macular degeneration. N Engl J Med 2004; 351:346-53. [PMID: 15269314 DOI: 10.1056/nejmoa040833] [Citation(s) in RCA: 217] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
BACKGROUND Age-related macular degeneration (AMD) is the most common cause of irreversible vision loss in the developed world. The study of a rare mendelian form of macular degeneration implicated fibulin genes in the pathogenesis of more common forms of this disease. We evaluated five fibulin genes in a large series of patients with AMD. METHODS We studied 402 patients with AMD and 429 control subjects from the same clinic population. Patients were examined by means of indirect ophthalmoscopy, slit-lamp microscopy, and fundus photography to establish the presence and phenotypic pattern of AMD. DNA samples were screened for sequence variations in five members of the fibulin gene family. RESULTS Amino acid-altering sequence variations were found in all five fibulin genes, many of which were observed only in patients with AMD. Several of the altered residues have been conserved during evolution. Seven of the 402 patients with AMD had amino acid-altering sequence variations in the fibulin 5 gene, whereas none were observed among 429 control subjects (P<0.01). In addition, these seven patients all had small, circular drusen, which are commonly referred to as basal laminar or cuticular drusen. CONCLUSIONS Missense mutations in the fibulin 5 gene were found in 1.7 percent of patients with AMD. Many variations in other fibulin genes were also found in these patients, and the evolutionary conservation of the affected residues suggests that several of these variations may also be involved in AMD.
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Affiliation(s)
- Edwin M Stone
- Center for Macular Degeneration, University of Iowa, Carver College of Medicine, Iowa City 52242, USA.
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Scheetz TE, Trivedi N, Roberts CA, Kucaba T, Berger B, Robinson NL, Birkett CL, Gavin AJ, O'Leary B, Braun TA, Bonaldo MF, Robinson JP, Sheffield VC, Soares MB, Casavant TL. ESTprep: preprocessing cDNA sequence reads. Bioinformatics 2003; 19:1318-24. [PMID: 12874042 DOI: 10.1093/bioinformatics/btg159] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
MOTIVATION High accuracy of data always governs the large-scale gene discovery projects. The data should not only be trustworthy but should be correctly annotated for various features it contains. Sequence errors are inherent in single-pass sequences such as ESTs obtained from automated sequencing. These errors further complicate the automated identification of EST-related sequencing. A tool is required to prepare the data prior to advanced annotation processing and submission to public databases. RESULTS This paper describes ESTprep, a program designed to preprocess expressed sequence tag (EST) sequences. It identifies the location of features present in ESTs and allows the sequence to pass only if it meets various quality criteria. Use of ESTprep has resulted in substantial improvement in accurate EST feature identification and fidelity of results submitted to GenBank. AVAILABILITY The program is freely available for download from http://genome.uiowa.edu/pubsoft/software.html
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Affiliation(s)
- Todd E Scheetz
- Center for Bioinformatics and Computational Biology, The University of Iowa, Iowa City, IA 52242, USA.
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Gavin AJ, Scheetz TE, Roberts CA, O'Leary B, Braun TA, Sheffield VC, Soares MB, Robinson JP, Casavant TL. Pooled library tissue tags for EST-based gene discovery. Bioinformatics 2002; 18:1162-6. [PMID: 12217907 DOI: 10.1093/bioinformatics/18.9.1162] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.9] [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] [Indexed: 11/14/2022] Open
Abstract
MOTIVATION In gene discovery projects based on EST sequencing, effective post-sequencing identification methods are important in determining tissue sources of ESTs within pooled cDNA libraries. In the past, such identification efforts have been characterized by higher than necessary failure rates due to the presence of errors within the subsequence containing the oligo tag intended to define the tissue source for each EST. RESULTS A large-scale EST-based gene discovery program at The University of Iowa has led to the creation of a unique software method named UITagCreator usable in the creation of large sets of synthetic tissue identification tags. The identification tags provide error detection and correction capability and, in conjunction with automated annotation software, result in a substantial improvement in the accurate identification of the tissue source in the presence of sequencing and base-calling errors. These identification rates are favorable, relative to past paradigms. AVAILABILITY The UITagCreator source code and installation instructions, along with detection software usable in concert with created tag sets, is freely available at http://genome.uiowa.edu/pubsoft/software.html CONTACT tomc@eng.uiowa.edu
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Affiliation(s)
- A J Gavin
- Department of Electrical and Computer Engineering, The University of Iowa, Iowa City, IA 52242, USA
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Barrett S, Beck JC, Bernier R, Bisson E, Braun TA, Casavant TL, Childress D, Folstein SE, Garcia M, Gardiner MB, Gilman S, Haines JL, Hopkins K, Landa R, Meyer NH, Mullane JA, Nishimura DY, Palmer P, Piven J, Purdy J, Santangelo SL, Searby C, Sheffield V, Singleton J, Slager S. An autosomal genomic screen for autism. Collaborative linkage study of autism. Am J Med Genet 1999; 88:609-15. [PMID: 10581478 DOI: 10.1002/(sici)1096-8628(19991215)88:6<609::aid-ajmg7>3.3.co;2-c] [Citation(s) in RCA: 97] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Autism is a severe neurodevelopmental disorder defined by social and communication deficits and ritualistic-repetitive behaviors that are detectable in early childhood. The etiology of idiopathic autism is strongly genetic, and oligogenic transmission is likely. The first stage of a two-stage genomic screen for autism was carried out by the Collaborative Linkage Study of Autism on individuals affected with autism from 75 families ascertained through an affected sib-pair. The strongest multipoint results were for regions on chromosomes 13 and 7. The highest maximum multipoint heterogeneity LOD (MMLS/het) score is 3.0 at D13S800 (approximately 55 cM from the telomere) under the recessive model, with an estimated 35% of families linked to this locus. The next highest peak is an MMLS/het score of 2.3 at 19 cM, between D13S217 and D13S1229. Our third highest MMLS/het score of 2.2 is on chromosome 7 and is consistent with the International Molecular Genetic Study of Autism Consortium report of a possible susceptibility locus somewhere within 7q31-33. These regions and others will be followed up in the second stage of our study by typing additional markers in both the original and a second set of identically ascertained autism families, which are currently being collected. By comparing results across a number of studies, we expect to be able to narrow our search for autism susceptibility genes to a small number of genomic regions. Am. J. Med. Genet. (Neuropsychiatr. Genet.) 88:609-615, 1999.
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Affiliation(s)
- S Barrett
- The Johns Hopkins University School of Medicine, Baltimore, Maryland
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