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Wieben ED, Aleff RA, Basu S, Sarangi V, Bowman B, McLaughlin IJ, Mills JR, Butz ML, Highsmith EW, Ida CM, Ekholm JM, Baratz KH, Fautsch MP. Amplification-free long-read sequencing of TCF4 expanded trinucleotide repeats in Fuchs Endothelial Corneal Dystrophy. PLoS One 2019; 14:e0219446. [PMID: 31276570 PMCID: PMC6611681 DOI: 10.1371/journal.pone.0219446] [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] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2019] [Accepted: 06/24/2019] [Indexed: 11/18/2022] Open
Abstract
Amplification of a CAG trinucleotide motif (CTG18.1) within the TCF4 gene has been strongly associated with Fuchs Endothelial Corneal Dystrophy (FECD). Nevertheless, a small minority of clinically unaffected elderly patients who have expanded CTG18.1 sequences have been identified. To test the hypothesis that the CAG expansions in these patients are protected from FECD because they have interruptions within the CAG repeats, we utilized a combination of an amplification-free, long-read sequencing method and a new target-enrichment sequence analysis tool developed by Pacific Biosciences to interrogate the sequence structure of expanded repeats. The sequencing was successful in identifying a previously described interruption within an unexpanded allele and provided sequence data on expanded alleles greater than 2000 bases in length. The data revealed considerable heterogeneity in the size distribution of expanded repeats within each patient. Detailed analysis of the long sequence reads did not reveal any instances of interruptions to the expanded CAG repeats, but did reveal novel variants within the AGG repeats that flank the CAG repeats in two of the five samples from clinically unaffected patients with expansions. This first examination of the sequence structure of CAG repeats in CTG18.1 suggests that factors other than interruptions to the repeat structure account for the absence of disease in some elderly patients with repeat expansions in the TCF4 gene.
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Affiliation(s)
- Eric D. Wieben
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Ross A. Aleff
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Shubham Basu
- Division of Biostatistics and Bioinformatics and Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Vivekananda Sarangi
- Division of Biostatistics and Bioinformatics and Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Brett Bowman
- Pacific Biosciences of California, Inc., Menlo Park, CA, United States of America
| | - Ian J. McLaughlin
- Pacific Biosciences of California, Inc., Menlo Park, CA, United States of America
| | - John R. Mills
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, United States of America
| | - Malinda L. Butz
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, United States of America
| | - Edward W. Highsmith
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, United States of America
| | - Cristiane M. Ida
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, United States of America
| | - Jenny M. Ekholm
- Pacific Biosciences of California, Inc., Menlo Park, CA, United States of America
| | - Keith H. Baratz
- Department of Ophthalmology, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Michael P. Fautsch
- Department of Ophthalmology, Mayo Clinic, Rochester, Minnesota, United States of America
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Ng PS, Pinto MV, Neff JL, Hasadsri L, Highsmith EW, Fidler ME, Gavrilova RH, Klein CJ. Mitochondrial cerebellar ataxia, renal failure, neuropathy, and encephalopathy (MCARNE). Neurol Genet 2019; 5:e314. [PMID: 31041396 PMCID: PMC6454306 DOI: 10.1212/nxg.0000000000000314] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Accepted: 01/07/2019] [Indexed: 11/25/2022]
Affiliation(s)
- Peng Soon Ng
- Department of Neurology (P.S.N., M.V.P., C.J.K.), Department of Laboratory Genetics and Genomics (J.L.N., L.H., E.W.H.), Department of Anatomic Pathology (J.L.N., M.E.F.), and Department of Clinical Genomics (R.H.G.), Mayo Clinic and Mayo Foundation, Rochester, MN
| | - Marcus V Pinto
- Department of Neurology (P.S.N., M.V.P., C.J.K.), Department of Laboratory Genetics and Genomics (J.L.N., L.H., E.W.H.), Department of Anatomic Pathology (J.L.N., M.E.F.), and Department of Clinical Genomics (R.H.G.), Mayo Clinic and Mayo Foundation, Rochester, MN
| | - Jadee L Neff
- Department of Neurology (P.S.N., M.V.P., C.J.K.), Department of Laboratory Genetics and Genomics (J.L.N., L.H., E.W.H.), Department of Anatomic Pathology (J.L.N., M.E.F.), and Department of Clinical Genomics (R.H.G.), Mayo Clinic and Mayo Foundation, Rochester, MN
| | - Linda Hasadsri
- Department of Neurology (P.S.N., M.V.P., C.J.K.), Department of Laboratory Genetics and Genomics (J.L.N., L.H., E.W.H.), Department of Anatomic Pathology (J.L.N., M.E.F.), and Department of Clinical Genomics (R.H.G.), Mayo Clinic and Mayo Foundation, Rochester, MN
| | - Edward W Highsmith
- Department of Neurology (P.S.N., M.V.P., C.J.K.), Department of Laboratory Genetics and Genomics (J.L.N., L.H., E.W.H.), Department of Anatomic Pathology (J.L.N., M.E.F.), and Department of Clinical Genomics (R.H.G.), Mayo Clinic and Mayo Foundation, Rochester, MN
| | - Mary E Fidler
- Department of Neurology (P.S.N., M.V.P., C.J.K.), Department of Laboratory Genetics and Genomics (J.L.N., L.H., E.W.H.), Department of Anatomic Pathology (J.L.N., M.E.F.), and Department of Clinical Genomics (R.H.G.), Mayo Clinic and Mayo Foundation, Rochester, MN
| | - Ralitza H Gavrilova
- Department of Neurology (P.S.N., M.V.P., C.J.K.), Department of Laboratory Genetics and Genomics (J.L.N., L.H., E.W.H.), Department of Anatomic Pathology (J.L.N., M.E.F.), and Department of Clinical Genomics (R.H.G.), Mayo Clinic and Mayo Foundation, Rochester, MN
| | - Christopher J Klein
- Department of Neurology (P.S.N., M.V.P., C.J.K.), Department of Laboratory Genetics and Genomics (J.L.N., L.H., E.W.H.), Department of Anatomic Pathology (J.L.N., M.E.F.), and Department of Clinical Genomics (R.H.G.), Mayo Clinic and Mayo Foundation, Rochester, MN
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Okumura N, Hayashi R, Nakano M, Yoshii K, Tashiro K, Sato T, Blake DJ, Aleff R, Butz M, Highsmith EW, Wieben ED, Fautsch MP, Baratz KH, Komori Y, Nakahara M, Tourtas T, Schlötzer-Schrehardt U, Kruse F, Koizumi N. Effect of Trinucleotide Repeat Expansion on the Expression of TCF4 mRNA in Fuchs' Endothelial Corneal Dystrophy. Invest Ophthalmol Vis Sci 2019; 60:779-786. [PMID: 30811544 PMCID: PMC6392475 DOI: 10.1167/iovs.18-25760] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [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] [Indexed: 01/04/2023] Open
Abstract
Purpose CTG trinucleotide repeat (TNR) expansion is frequently found in transcription factor 4 (TCF4) in Fuchs' endothelial corneal dystrophy (FECD), though the effect of TNR expansion on FECD pathophysiology remains unclear. The purpose of this study was to evaluate the effect of TNR expansion on TCF4 expression in corneal endothelium of patients with FECD. Methods Peripheral blood DNA and Descemet membrane with corneal endothelium were obtained from 203 German patients with FECD. The CTG TNR repeat length in TCF4 was determined by short tandem repeat (STR) assays and Southern blotting using genomic DNA. Genotyping of rs613872 in TCF4 was performed by PCR. TCF4 mRNA levels in corneal endothelium were evaluated by quantitative PCR using three different probes. Control corneal endothelial samples were obtained from 35 non-FECD subjects. Results The STR assay and Southern blotting showed that 162 of the 203 patients with FECD (80%) harbored CTG trinucleotide repeat lengths larger than 50. Quantitative PCR using all three probes demonstrated that TCF4 mRNA is significantly upregulated in the corneal endothelium of patients with FECD, regardless of the presence of TNR expansion. However, the length of the TNR tended to show a positive correlation with TCF4 expression level. No correlation was shown between the genotype of TCF4 SNP, rs613872, and the level of TCF4 expression. Conclusions Our findings showed that TCF4 mRNA is upregulated in the corneal endothelium of patients with FECD. Further studies on the effects of TCF4 upregulation on corneal endothelial cell function will aid in understanding the pathophysiology of FECD.
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Affiliation(s)
- Naoki Okumura
- Department of Biomedical Engineering, Faculty of Life and Medical Sciences, Doshisha University, Kyotanabe, Japan
| | - Ryosuke Hayashi
- Department of Biomedical Engineering, Faculty of Life and Medical Sciences, Doshisha University, Kyotanabe, Japan
| | - Masakazu Nakano
- Department of Genomic Medical Sciences, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Kengo Yoshii
- Department of Mathematics and Statistics in Medical Sciences, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Kei Tashiro
- Department of Genomic Medical Sciences, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Takahiko Sato
- Department of Ophthalmology, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Derek J Blake
- Division of Psychological Medicine and Clinical Neurosciences, Cardiff University, United Kingdom
| | - Ross Aleff
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, Minnesota, United States
| | - Malinda Butz
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, United States
| | - Edward W Highsmith
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, United States
| | - Eric D Wieben
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, Minnesota, United States
| | - Michael P Fautsch
- Department of Ophthalmology, Mayo Clinic, Rochester, Minnesota, United States
| | - Keith H Baratz
- Department of Ophthalmology, Mayo Clinic, Rochester, Minnesota, United States
| | - Yuya Komori
- Department of Biomedical Engineering, Faculty of Life and Medical Sciences, Doshisha University, Kyotanabe, Japan
| | - Makiko Nakahara
- Department of Biomedical Engineering, Faculty of Life and Medical Sciences, Doshisha University, Kyotanabe, Japan
| | - Theofilos Tourtas
- Department of Ophthalmology, University of Erlangen-Nürnberg, Erlangen, Germany
| | | | - Friedrich Kruse
- Department of Ophthalmology, University of Erlangen-Nürnberg, Erlangen, Germany
| | - Noriko Koizumi
- Department of Biomedical Engineering, Faculty of Life and Medical Sciences, Doshisha University, Kyotanabe, Japan
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Wieben ED, Aleff RA, Tang X, Butz ML, Kalari KR, Highsmith EW, Jen J, Vasmatzis G, Patel SV, Maguire LJ, Baratz KH, Fautsch MP. Trinucleotide Repeat Expansion in the Transcription Factor 4 (TCF4) Gene Leads to Widespread mRNA Splicing Changes in Fuchs' Endothelial Corneal Dystrophy. Invest Ophthalmol Vis Sci 2017; 58:343-352. [PMID: 28118661 PMCID: PMC5270622 DOI: 10.1167/iovs.16-20900] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [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: 11/24/2022] Open
Abstract
Purpose To identify RNA missplicing events in human corneal endothelial tissue isolated from Fuchs' endothelial corneal dystrophy (FECD). Methods Total RNA was isolated and sequenced from corneal endothelial tissue obtained during keratoplasty from 12 patients with FECD and 4 patients undergoing keratoplasty or enucleation for other indications. The length of the trinucleotide repeat (TNR) CTG in the transcription factor 4 (TCF4) gene was determined using leukocyte-derived DNA analyzed by a combination of Southern blotting and Genescan analysis. Commercial statistical software was used to quantify expression of alternatively spliced genes. Validation of selected alternative splicing events was performed by using RT-PCR. Gene sets identified were analyzed for overrepresentation using Web-based analysis system. Results Corneal endothelial tissue from FECD patients containing a CTG TNR expansion sequence in the TCF4 gene revealed widespread changes in mRNA splicing, including a novel splicing event involving FGFR2. Differential splicing of NUMA1, PPFIBP1, MBNL1, and MBNL2 transcripts were identified in all FECD samples containing a TNR expansion. The differentially spliced genes were enriched for products that localize to the cell cortex and bind cytoskeletal and cell adhesion proteins. Conclusions Corneal endothelium from FECD patients harbors a unique signature of mis-splicing events due to CTG TNR expansion in the TCF4 gene, consistent with the hypothesis that RNA toxicity contributes to the pathogenesis of FECD. Changes to the endothelial barrier function, a known event in the development of FECD, was identified as a key biological process influenced by the missplicing events.
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Affiliation(s)
- Eric D Wieben
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, Minnesota, United States
| | - Ross A Aleff
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, Minnesota, United States
| | - Xiaojia Tang
- Division of Biostatistics and Bioinformatics and Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota, United States
| | - Malinda L Butz
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, United States
| | - Krishna R Kalari
- Division of Biostatistics and Bioinformatics and Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota, United States
| | - Edward W Highsmith
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, United States
| | - Jin Jen
- Department of Experimental Pathology and Laboratory Medicine, Mayo Clinic, Rochester, Minnesota, United States
| | - George Vasmatzis
- Department of Molecular Medicine, Mayo Clinic, Rochester, Minnesota, United States
| | - Sanjay V Patel
- Department of Ophthalmology, Mayo Clinic, Rochester, Minnesota, United States
| | - Leo J Maguire
- Department of Ophthalmology, Mayo Clinic, Rochester, Minnesota, United States
| | - Keith H Baratz
- Department of Ophthalmology, Mayo Clinic, Rochester, Minnesota, United States
| | - Michael P Fautsch
- Department of Ophthalmology, Mayo Clinic, Rochester, Minnesota, United States
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Hebert SL, Marquet-de Rougé P, Lanza IR, McCrady-Spitzer SK, Levine JA, Middha S, Carter RE, Klaus KA, Therneau TM, Highsmith EW, Nair KS. Mitochondrial Aging and Physical Decline: Insights From Three Generations of Women. J Gerontol A Biol Sci Med Sci 2015; 70:1409-17. [PMID: 26297939 DOI: 10.1093/gerona/glv086] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2014] [Accepted: 05/22/2015] [Indexed: 02/07/2023] Open
Abstract
Decline in mitochondrial DNA (mtDNA) copy number, function, and accumulation of mutations and deletions have been proposed to contribute to age-related physical decline, based on cross sectional studies in genetically unrelated individuals. There is wide variability of mtDNA and functional measurements in many population studies and therefore we assessed mitochondrial function and physical function in 18 families of grandmothers, mothers, and daughters who share the same maternally inherited mtDNA sequence. A significant age-related decline in mtDNA copy number, mitochondrial protein expression, citrate synthase activity, cytochrome c oxidase content, and VO2 peak were observed. Also, a lower abundance of SIRT3, accompanied by an increase in acetylated skeletal muscle proteins, was observed in grandmothers. Muscle tissue-based full sequencing of mtDNA showed greater than 5% change in minor allele frequency over a lifetime in two locations, position 189 and 408 in the noncoding D-loop region but no changes were noted in blood cells mtDNA. The decline in oxidative capacity and muscle function with age in three generations of women who share the same mtDNA sequence are associated with a decline in muscle mtDNA copy number and reduced protein deacetylase activity of SIRT3.
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Affiliation(s)
| | | | | | | | | | - Sumit Middha
- Department of Health Sciences Research, Division of Biomedical Statistics and Informatics, 200 First Street SW, Joseph 5-194, Rochester, Minnesota 55905
| | - Rickey E Carter
- Department of Health Sciences Research, Division of Biomedical Statistics and Informatics, 200 First Street SW, Joseph 5-194, Rochester, Minnesota 55905
| | | | - Terry M Therneau
- Department of Health Sciences Research, Division of Biomedical Statistics and Informatics, 200 First Street SW, Joseph 5-194, Rochester, Minnesota 55905
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Sethi S, Theis JD, Quint P, Maierhofer W, Kurtin PJ, Dogan A, Highsmith EW. Renal amyloidosis associated with a novel sequence variant of gelsolin. Am J Kidney Dis 2012; 61:161-6. [PMID: 22938848 DOI: 10.1053/j.ajkd.2012.07.016] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2012] [Accepted: 07/25/2012] [Indexed: 11/11/2022]
Abstract
We present a case of a 75-year-old woman who presented with progressive kidney failure. Kidney biopsy performed to determine the cause of kidney failure showed amyloidosis of undetermined type. Laser microdissection of the Congo Red-positive glomeruli followed by mass spectrometry studies showed a large number of spectra matching apolipoprotein E, serum amyloid P component, and gelsolin, consistent with a diagnosis of gelsolin-associated renal amyloidosis. Sequencing of the gelsolin gene revealed a previously undescribed sequence variant, a guanine to adenine substitution at nucleotide 580 of the coding sequence, corresponding to a predicted glycine to arginine mutation at amino acid 194. Gelsolin amyloidosis typically involves the nerves and skin, with only rare reported involvement of the kidney. An atypical finding on electron microscopy was that of a swirling pattern of the amyloid fibrils. The novel gelsolin variant may be responsible for the unusual clinical and pathologic presentation. The report also highlights the usefulness of laser microdissection and mass spectrometry in the typing of difficult cases of amyloidosis.
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Affiliation(s)
- Sanjeev Sethi
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905, USA.
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Castellani C, Macek M, Cassiman JJ, Duff A, Massie J, ten Kate LP, Barton D, Cutting G, Dallapiccola B, Dequeker E, Girodon E, Grody W, Highsmith EW, Kääriäinen H, Kruip S, Morris M, Pignatti PF, Pypops U, Schwarz M, Soller M, Stuhrman M, Cuppens H. Benchmarks for Cystic Fibrosis carrier screening: A European consensus document. J Cyst Fibros 2010; 9:165-78. [DOI: 10.1016/j.jcf.2010.02.005] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2009] [Revised: 02/16/2010] [Accepted: 02/19/2010] [Indexed: 11/28/2022]
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