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Steinbeck BJ, Gao XD, McElroy AN, Pandey S, Doman JL, Riddle MJ, Xia L, Chen W, Eide CR, Lengert AH, Han SW, Blazar BR, Wandall HH, Dabelsteen S, Liu DR, Tolar J, Osborn MJ. Twin prime editing mediated exon skipping/reinsertion for restored collagen VII expression in recessive dystrophic epidermolysis bullosa. J Invest Dermatol 2024:S0022-202X(24)00372-5. [PMID: 38763174 DOI: 10.1016/j.jid.2024.04.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 04/12/2024] [Accepted: 04/26/2024] [Indexed: 05/21/2024]
Abstract
Gene editing nucleases, base editors, and prime editors are potential locus specific genetic treatment strategies for recessive dystrophic epidermolysis bullosa (RDEB); however, many RDEB COL7A1 mutations are unique, making the development of personalized editing reagents challenging. 270 of the ∼320 COL7A1 EB mutations reside in exons that can be skipped, and antisense oligonucleotides (ASO) and gene editing nucleases have been used to create in-frame deletions. ASOs are transient and nucleases generate deleterious double stranded DNA breaks (DSB) and uncontrolled mixtures of allele products. We developed a twin prime editing (twinPE) strategy using the PEmax and recently evolved PE6 prime editors and dual prime editing guide RNAs flanking COL7A1 exon five. Prime editing-mediated deletion of exon 5 with a homozygous premature stop codon was achieved in RDEB fibroblasts, keratinocytes, and iPSC with minimal DSBs, and collagen type VII (C7) protein was restored. TwinPE can replace the target exon with recombinase attachment sequences, and we exploited this to re-insert a normal copy of exon 5 using the Bxb1 recombinase. These findings demonstrate that twinPE can facilitate locus-specific, predictable, in-frame deletions and sequence replacement with few DSBs as a strategy that may enable a single therapeutic agent to treat multiple RDEB patient cohorts.
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Affiliation(s)
- Benjamin J Steinbeck
- Department of Pediatrics, Division of Blood and Marrow Transplant and Cellular Therapy, University of Minnesota, Minneapolis, MN, USA
| | - Xin D Gao
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of Harvard and MIT, Cambridge, MA, USA; Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA; Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - Amber N McElroy
- Department of Pediatrics, Division of Blood and Marrow Transplant and Cellular Therapy, University of Minnesota, Minneapolis, MN, USA
| | - Smriti Pandey
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of Harvard and MIT, Cambridge, MA, USA; Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA; Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - Jordan L Doman
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of Harvard and MIT, Cambridge, MA, USA; Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA; Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - Megan J Riddle
- Department of Pediatrics, Division of Blood and Marrow Transplant and Cellular Therapy, University of Minnesota, Minneapolis, MN, USA
| | - Lily Xia
- Department of Pediatrics, Division of Blood and Marrow Transplant and Cellular Therapy, University of Minnesota, Minneapolis, MN, USA
| | - Weili Chen
- Department of Pediatrics, Division of Blood and Marrow Transplant and Cellular Therapy, University of Minnesota, Minneapolis, MN, USA
| | - Cindy R Eide
- Department of Pediatrics, Division of Blood and Marrow Transplant and Cellular Therapy, University of Minnesota, Minneapolis, MN, USA
| | - Andre H Lengert
- Universidade Federal de Sao Paulo Escola Paulista de Medicina: Sao Paulo, SP, BR
| | - Sang Won Han
- Universidade Federal de Sao Paulo Escola Paulista de Medicina: Sao Paulo, SP, BR
| | - Bruce R Blazar
- Department of Pediatrics, Division of Blood and Marrow Transplant and Cellular Therapy, University of Minnesota, Minneapolis, MN, USA
| | - Hans H Wandall
- University of Copenhagen, Centre for Glycomics, Department of Cellular and Molecular Medicine, Copenhagen, Denmark
| | - Sally Dabelsteen
- University of Copenhagen, Centre for Glycomics, Department of Cellular and Molecular Medicine, Copenhagen, Denmark
| | - David R Liu
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of Harvard and MIT, Cambridge, MA, USA; Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA; Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - Jakub Tolar
- Department of Pediatrics, Division of Blood and Marrow Transplant and Cellular Therapy, University of Minnesota, Minneapolis, MN, USA
| | - Mark J Osborn
- Department of Pediatrics, Division of Blood and Marrow Transplant and Cellular Therapy, University of Minnesota, Minneapolis, MN, USA.
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2
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Ivanenko AV, Evtushenko NA, Gurskaya NG. Genome Editing in Therapy of Genodermatoses. Mol Biol 2022. [DOI: 10.1134/s0026893322060085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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3
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Ham KA, Aung-Htut MT, Fletcher S, Wilton SD. Nonsequential Splicing Events Alter Antisense-Mediated Exon Skipping Outcome in COL7A1. Int J Mol Sci 2020; 21:ijms21207705. [PMID: 33081018 PMCID: PMC7590164 DOI: 10.3390/ijms21207705] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 10/06/2020] [Accepted: 10/14/2020] [Indexed: 11/16/2022] Open
Abstract
The COL7A1 gene encodes homotrimer fibrils essential for anchoring dermal and epidermal layers, and pathogenic mutations in COL7A1 can cause recessive or dominant dystrophic epidermolysis bullosa. As a monogenic disease gene, COL7A1 constitutes a potential target for antisense oligomer-mediated exon skipping, a therapy applicable to a growing number of other genetic disorders. However, certain characteristics of COL7A1: many exons, low average intron size, and repetitive and guanine-cytosine rich coding sequence, present challenges to the design of specific and effective antisense oligomers. While targeting COL7A1 exons 10 and 73 for excision from the mature mRNA, we discovered that antisense oligomers comprised of 2′-O-methyl modified bases on a phosphorothioate backbone and phosphorodiamidate morpholino oligomers produced similar, but distinctive, splicing patterns including excision of adjacent nontargeted exons and/or retention of nearby introns in some transcripts. We found that the nonsequential splicing of certain introns may alter pre-mRNA processing during antisense oligomer-mediated exon skipping and, therefore, additional studies are required to determine if the order of intron removal influences multiexon skipping and/or intron retention in processing of the COL7A1 pre-mRNA.
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Affiliation(s)
- Kristin A. Ham
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, Murdoch 6150, Australia; (K.A.H.); (M.T.A.-H.); (S.F.)
- Perron Institute for Neurological and Translational Science, Centre for Neuromuscular and Neurological Disorders, The University of Western Australia, Nedlands 6009, Australia
| | - May Thandar Aung-Htut
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, Murdoch 6150, Australia; (K.A.H.); (M.T.A.-H.); (S.F.)
- Perron Institute for Neurological and Translational Science, Centre for Neuromuscular and Neurological Disorders, The University of Western Australia, Nedlands 6009, Australia
| | - Sue Fletcher
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, Murdoch 6150, Australia; (K.A.H.); (M.T.A.-H.); (S.F.)
| | - Steve D. Wilton
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, Murdoch 6150, Australia; (K.A.H.); (M.T.A.-H.); (S.F.)
- Perron Institute for Neurological and Translational Science, Centre for Neuromuscular and Neurological Disorders, The University of Western Australia, Nedlands 6009, Australia
- Correspondence:
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4
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Jin L, Li Z, Xin C, Tang L, Zhang X, Zhang B, Yang S. A novel mutation of COL7A1 in a Chinese DEB‐Pt family and review of the literature. J Cosmet Dermatol 2019; 19:1508-1512. [PMID: 31709745 DOI: 10.1111/jocd.13172] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2019] [Revised: 09/05/2019] [Accepted: 09/06/2019] [Indexed: 11/28/2022]
Affiliation(s)
- Ling Jin
- Institute of Dermatology and Department of Dermatology The First Affiliated Hospital Anhui Medical University Hefei Anhui China
- Key Laboratory of Dermatology Ministry of Education Anhui Medical University Hefei Anhui China
| | - Zhi Li
- Institute of Dermatology and Department of Dermatology The First Affiliated Hospital Anhui Medical University Hefei Anhui China
- Key Laboratory of Dermatology Ministry of Education Anhui Medical University Hefei Anhui China
| | - Cong Xin
- Institute of Dermatology and Department of Dermatology The First Affiliated Hospital Anhui Medical University Hefei Anhui China
- Key Laboratory of Dermatology Ministry of Education Anhui Medical University Hefei Anhui China
| | - Lili Tang
- Institute of Dermatology and Department of Dermatology The First Affiliated Hospital Anhui Medical University Hefei Anhui China
- Key Laboratory of Dermatology Ministry of Education Anhui Medical University Hefei Anhui China
| | - Xuejun Zhang
- Institute of Dermatology and Department of Dermatology The First Affiliated Hospital Anhui Medical University Hefei Anhui China
- Key Laboratory of Dermatology Ministry of Education Anhui Medical University Hefei Anhui China
| | - Bo Zhang
- Department of Oncology The Second Affiliated Hospital Anhui Medical University Hefei Anhui China
| | - Sen Yang
- Institute of Dermatology and Department of Dermatology The First Affiliated Hospital Anhui Medical University Hefei Anhui China
- Key Laboratory of Dermatology Ministry of Education Anhui Medical University Hefei Anhui China
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5
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Bremer J, van der Heijden EH, Eichhorn DS, Meijer R, Lemmink HH, Scheffer H, Sinke RJ, Jonkman MF, Pasmooij AMG, Van den Akker PC. Natural Exon Skipping Sets the Stage for Exon Skipping as Therapy for Dystrophic Epidermolysis Bullosa. MOLECULAR THERAPY. NUCLEIC ACIDS 2019; 18:465-475. [PMID: 31670143 PMCID: PMC6831832 DOI: 10.1016/j.omtn.2019.09.009] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Revised: 09/10/2019] [Accepted: 09/10/2019] [Indexed: 02/04/2023]
Abstract
Dystrophic epidermolysis bullosa (DEB) is a devastating blistering disease affecting skin and mucous membranes. It is caused by pathogenic variants in the COL7A1 gene encoding type VII collagen, and can be inherited dominantly or recessively. Recently, promising proof-of-principle has been shown for antisense oligonucleotide (AON)-mediated exon skipping as a therapeutic approach for DEB. However, the precise phenotypic effect to be anticipated from exon skipping, and which patient groups could benefit, is not yet clear. To answer these questions, we studied new clinical and molecular data on seven patients from the Dutch EB registry and reviewed the literature on COL7A1 exon skipping variants. We found that phenotypes associated with dominant exon skipping cannot be distinguished from phenotypes caused by other dominant DEB variants. Recessive exon skipping phenotypes are generally relatively mild in the spectrum of recessive DEB. Therefore, for dominant DEB, AON-mediated exon skipping is unlikely to ameliorate the phenotype. In contrast, the overall severity of phenotypes associated with recessive natural exon skipping pivots toward the milder end of the spectrum. Consequently, we anticipate AON-mediated exon skipping for recessive DEB caused by bi-allelic null variants should lead to a clinically relevant improvement of this devastating phenotype.
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Affiliation(s)
- Jeroen Bremer
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands; Department of Dermatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands.
| | - Elisabeth H van der Heijden
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Daryll S Eichhorn
- Department of Dermatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Rowdy Meijer
- Department of Human Genetics, Radboud University Nijmegen Medical Centre, Nijmegen, the Netherlands
| | - Henny H Lemmink
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Hans Scheffer
- Department of Human Genetics, Radboud University Nijmegen Medical Centre, Nijmegen, the Netherlands
| | - Richard J Sinke
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Marcel F Jonkman
- Department of Dermatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Anna M G Pasmooij
- Department of Dermatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Peter C Van den Akker
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands; Department of Dermatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
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6
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Abstract
The size and relatively high GC content of cDNAs are challenges for efficient targeted engineering of large collagens. There are both basic biological and therapeutic interests in the ability to modify collagens, as this would allow for studies precisely describing interactions of collagens with specific interaction partners, addressing consequences of individual disease-causing mutations, and assessing therapeutic applicability of precision medicine approaches. Using collagen VII as an example, we will here describe a strategy for rapid and simple modification of cDNAs encoding large collagens. The method is flexible and can be used for the creation of point mutations, small or large deletions, and insertion of DNA.
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Affiliation(s)
- Olivier Bornert
- Department of Dermatology, Faculty of Medicine, Medical Center, University of Freiburg, Freiburg, Germany
| | - Alexander Nyström
- Department of Dermatology, Faculty of Medicine, Medical Center, University of Freiburg, Freiburg, Germany.
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7
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Mu YZ, Du ZC, Zhang ZZ, Yang H, Chen X, Wang YB, Liu LL. The clinical phenotype and a novel COL7A1
mutation in a Chinese family with dystrophic epidermolysis bullosa pruriginosa. J Eur Acad Dermatol Venereol 2018; 32:e372-e373. [PMID: 29512192 DOI: 10.1111/jdv.14917] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Y.-Z. Mu
- Department of Dermatology; The Affiliated Hospital of North Sichuan Medical College; Nanchong Sichuan Province China
| | - Z.-C. Du
- Department of Dermatology; The Affiliated Hospital of North Sichuan Medical College; Nanchong Sichuan Province China
| | - Z.-Z. Zhang
- Department of Dermatology; The Affiliated Hospital of North Sichuan Medical College; Nanchong Sichuan Province China
| | - H. Yang
- Department of Dermatology; The Affiliated Hospital of North Sichuan Medical College; Nanchong Sichuan Province China
| | - X. Chen
- Department of Dermatology; The Affiliated Hospital of North Sichuan Medical College; Nanchong Sichuan Province China
| | - Y.-B. Wang
- Department of Dermatology; The Affiliated Hospital of North Sichuan Medical College; Nanchong Sichuan Province China
| | - L.-L. Liu
- Department of Dermatology; Suining Central Hospital; Suining Sichuan Province China
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8
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Bornert O, Kühl T, Bremer J, van den Akker PC, Pasmooij AM, Nyström A. Analysis of the functional consequences of targeted exon deletion in COL7A1 reveals prospects for dystrophic epidermolysis bullosa therapy. Mol Ther 2016; 24:1302-11. [PMID: 27157667 DOI: 10.1038/mt.2016.92] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Accepted: 05/03/2016] [Indexed: 12/18/2022] Open
Abstract
Genetically evoked deficiency of collagen VII causes dystrophic epidermolysis bullosa (DEB)-a debilitating disease characterized by chronic skin fragility and progressive fibrosis. Removal of exons carrying frame-disrupting mutations can reinstate protein expression in genetic diseases. The therapeutic potential of this approach is critically dependent on gene, protein, and disease intrinsic factors. Naturally occurring exon skipping in COL7A1, translating collagen VII, suggests that skipping of exons containing disease-causing mutations may be feasible for the treatment of DEB. However, despite a primarily in-frame arrangement of exons in the COL7A1 gene, no general conclusion of the aptitude of exon skipping for DEB can be drawn, since regulation of collagen VII functionality is complex involving folding, intra- and intermolecular interactions. To directly address this, we deleted two conceptually important exons located at both ends of COL7A1, exon 13, containing recurrent mutations, and exon 105, predicted to impact folding. The resulting recombinantly expressed proteins showed conserved functionality in biochemical and in vitro assays. Injected into DEB mice, the proteins promoted skin stability. By demonstrating functionality of internally deleted collagen VII variants, our study provides support of targeted exon deletion or skipping as a potential therapy to treat a large number of individuals with DEB.
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Affiliation(s)
- Olivier Bornert
- Department of Dermatology, Medical Center - University of Freiburg, Freiburg, Germany
| | - Tobias Kühl
- Department of Dermatology, Medical Center - University of Freiburg, Freiburg, Germany
| | - Jeroen Bremer
- Department of Dermatology, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Peter C van den Akker
- Department of Dermatology, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands.,Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Anna Mg Pasmooij
- Department of Dermatology, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Alexander Nyström
- Department of Dermatology, Medical Center - University of Freiburg, Freiburg, Germany
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9
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Kitazawa T, Kawakami T, Matsuoka M, Kimura S, Soma Y, Nakano H. Splicing mutation in the COL7A1 gene mRNA exon 71 in a female patient with pretibial epidermolysis bullosa. J Dermatol 2016; 41:1018-9. [PMID: 25346305 DOI: 10.1111/1346-8138.12648] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
- Tomoko Kitazawa
- Department of Dermatology, St Marianna University School of Medicine, Kawasaki, Japan
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10
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Abstract
Genetic skin fragility manifests with diminished resistance of the skin and mucous membranes to external mechanical forces and with skin blistering, erosions, and painful wounds as clinical features. Skin fragility disorders, collectively called epidermolysis bullosa, are caused by mutations in 18 distinct genes that encode proteins involved in epidermal integrity and dermal-epidermal adhesion. The genetic spectrum, along with environmental and genetic modifiers, creates a large number of clinical phenotypes, spanning from minor localized lesions to severe generalized blistering, secondary skin cancer, or early demise resulting from extensive loss of the epidermis. Laboratory investigations of skin fragility have greatly augmented our understanding of genotype-phenotype correlations in epidermolysis bullosa and have also advanced skin biology in general. Current translational research concentrates on the development of biologically valid treatments with therapeutic genes, cells, proteins, or small-molecule compounds in preclinical settings or human pilot trials.
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Affiliation(s)
- Cristina Has
- Department of Dermatology, Medical Center-University of Freiburg, Freiburg 79104, Germany;
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11
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Liu YH, Shang X, Li ZT, Wu YM, Li LF, Xu XM. A novel COL7A1 gene mutation causing pretibial epidermolysis bullosa: report of a Chinese family with intra-familial phenotypical diversity. Gene 2013; 524:377-80. [PMID: 23624125 DOI: 10.1016/j.gene.2013.03.143] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2012] [Revised: 02/20/2013] [Accepted: 03/31/2013] [Indexed: 10/26/2022]
Abstract
Pretibial epidermolysis bullosa (PEB) is an extremely rare subtype of dominant dystrophic epidermolysis bullosa (DDEB) caused by mutation of the COL7A1 gene. More than 730 mutations have been identified in patients with DDEB, but only five mutations have been found to be related to PEB. In this study, a novel heterozygous nucleotide G>T transition at position 6101 in exon 73 of COL7A1 was detected, which resulted in a glycine to valine substitution (G2034V) in the triple-helical domain of type-VII collagen. This is the first report to show that one mutation caused a broad range of severity of disease in one family with PEB. These data suggest that c.6101G>T may influence the phenotype of PEB. They also contribute to the expanding database on COL7A1 mutations.
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Affiliation(s)
- Yan-Hui Liu
- Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong, People's Republic of China
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12
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Brick K, Hand JL, Frankel AS, Siegel DH, Thomas KB, El-Azhary R, Krol A. Epidermolysis bullosa pruriginosa: further clarification of the phenotype. Pediatr Dermatol 2012; 29:732-7. [PMID: 23106673 DOI: 10.1111/j.1525-1470.2012.01786.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
A defect in type VII collagen causes dystrophic epidermolysis bullosa (DEB). The pruriginosa variant (DEB-Pr) is unique because its initial presentation may be delayed until adolescence or adulthood, and its predominant feature is scarring and pruritus without the characteristic skin fragility of DEB. We describe three families with multiple affected members in which DEB-Pr shows an autosomal-dominant inheritance pattern. All affected individuals were examined, and three previously unreported COL7A1 mutations were identified.
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Affiliation(s)
- Katherine Brick
- Department of Dermatology, Mayo Clinic, Rochester, Minnesota 55905, USA
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