1
|
Ma Y, Zhang Y, Chen F, Liu S, Wang D, Lu Z, Zhang D, Liang R. The COL7A1/PI3K/AKT axis regulates the progression of cholangiocarcinoma. Heliyon 2024; 10:e37361. [PMID: 39309925 PMCID: PMC11415666 DOI: 10.1016/j.heliyon.2024.e37361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Revised: 08/07/2024] [Accepted: 09/02/2024] [Indexed: 09/25/2024] Open
Abstract
Background The role and molecular mechanisms of collagen type VII (COL7A1) in cholangiocarcinoma (CCA) remain unknown. Methods We analyzed the expression of COL7A1 in CCA and its relationship with patient prognosis using bioinformatic techniques. Expression levels of COL7A1 in CCA cells and tissues were detected using reverse transcription-quantitative PCR, western blotting, and immunohistochemistry. The effects of COL7A1 expression on the proliferation, migration, and invasion of CCA cells were assessed using CCK-8, colony formation, and Transwell assays. Bioinformatics and luciferase reporter gene assays were performed to examine the binding of KLF4 to COL7A1, and cytological experiments further verified the role of KLF4 in regulating the CCA phenotype through COL7A1. Xenograft mouse models were established to investigate the effects of COL7A1 on CCA tumor growth in vivo. Results CCA tissues exhibited higher COL7A1 expression than normal bile duct tissues. There was no significant correlation between high or low COL7A1 expression and the survival time of patients with CCA. COL7A1 knockdown inhibited CCA cell proliferation, migration, and invasion. Furthermore, COL7A1 knockdown suppressed the activation of the PI3K/AKT signaling pathway. KLF4 can bind to COL7A1 and regulate COL7A1 expression, which in turn regulates the PI3K/AKT signaling pathway and impacts the proliferation and metastasis of CCA cells. Conclusion Our findings suggest that KLF4 regulates CCA cell proliferation, migration, and invasion via the COL7A1/PI3K/AKT axis.
Collapse
Affiliation(s)
- Yang Ma
- Department of General Surgery, The First Affiliated Hospital of BengBu Medical College, NO. 287, Changhuai Road, Longzihu district, Bengbu, 233000, Anhui, China
| | - Yanfang Zhang
- Department of General Surgery, The First Affiliated Hospital of BengBu Medical College, NO. 287, Changhuai Road, Longzihu district, Bengbu, 233000, Anhui, China
| | - Fangfang Chen
- Department of General Surgery, The First Affiliated Hospital of BengBu Medical College, NO. 287, Changhuai Road, Longzihu district, Bengbu, 233000, Anhui, China
| | - Sihua Liu
- Department of General Surgery, The First Affiliated Hospital of BengBu Medical College, NO. 287, Changhuai Road, Longzihu district, Bengbu, 233000, Anhui, China
| | - Dongdong Wang
- Department of General Surgery, The First Affiliated Hospital of BengBu Medical College, NO. 287, Changhuai Road, Longzihu district, Bengbu, 233000, Anhui, China
| | - Zheng Lu
- Department of General Surgery, The First Affiliated Hospital of BengBu Medical College, NO. 287, Changhuai Road, Longzihu district, Bengbu, 233000, Anhui, China
| | - Dengyong Zhang
- Department of General Surgery, The First Affiliated Hospital of BengBu Medical College, NO. 287, Changhuai Road, Longzihu district, Bengbu, 233000, Anhui, China
| | - Rui Liang
- Department of General Surgery, The First Affiliated Hospital of BengBu Medical College, NO. 287, Changhuai Road, Longzihu district, Bengbu, 233000, Anhui, China
| |
Collapse
|
2
|
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; however, many recessive dystrophic epidermolysis bullosa COL7A1 pathogenic nucleotide variations (PNVs) are unique, making the development of personalized editing reagents challenging. A total of 270 of the ∼320 COL7A1 epidermolysis bullosa PNVs reside in exons that can be skipped, and antisense oligonucleotides and gene editing nucleases have been used to create in-frame deletions. Antisense oligonucleotides are transient, and nucleases generate deleterious double-stranded DNA breaks and uncontrolled mixtures of allele products. We developed a twin prime editing strategy using the PEmax and recently evolved PE6 prime editors and dual prime editing guide RNAs flanking COL7A1 exon 5. Prime editing-mediated deletion of exon 5 with a homozygous premature stop codon was achieved in recessive dystrophic epidermolysis bullosa fibroblasts, keratinocytes, and induced pluripotent stem cells with minimal double-stranded DNA breaks, and collagen type VII protein was restored. Twin prime editing can replace the target exon with recombinase attachment sequences, and we exploited this to reinsert a normal copy of exon 5 using the Bxb1 recombinase. These findings demonstrate that twin prime editing can facilitate locus-specific, predictable, in-frame deletions and sequence replacement with few double-stranded DNA breaks as a strategy that may enable a single therapeutic agent to treat multiple recessive dystrophic epidermolysis bullosa patient cohorts.
Collapse
Affiliation(s)
- Benjamin J Steinbeck
- Division of Pediatric Blood and Marrow Transplantation & Cellular Therapy, Department of Pediatrics, University of Minnesota, Minneapolis, Minnesota, USA
| | - Xin D Gao
- Merkin Institute of Transformative Technologies in Healthcare, The Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA; Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts, USA; Howard Hughes Medical Institute, Harvard University, Cambridge, Massachusetts, USA
| | - Amber N McElroy
- Division of Pediatric Blood and Marrow Transplantation & Cellular Therapy, Department of Pediatrics, University of Minnesota, Minneapolis, Minnesota, USA
| | - Smriti Pandey
- Merkin Institute of Transformative Technologies in Healthcare, The Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA; Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts, USA; Howard Hughes Medical Institute, Harvard University, Cambridge, Massachusetts, USA
| | - Jordan L Doman
- Merkin Institute of Transformative Technologies in Healthcare, The Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA; Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts, USA; Howard Hughes Medical Institute, Harvard University, Cambridge, Massachusetts, USA
| | - Megan J Riddle
- Division of Pediatric Blood and Marrow Transplantation & Cellular Therapy, Department of Pediatrics, University of Minnesota, Minneapolis, Minnesota, USA
| | - Lily Xia
- Division of Pediatric Blood and Marrow Transplantation & Cellular Therapy, Department of Pediatrics, University of Minnesota, Minneapolis, Minnesota, USA
| | - Weili Chen
- Division of Pediatric Blood and Marrow Transplantation & Cellular Therapy, Department of Pediatrics, University of Minnesota, Minneapolis, Minnesota, USA
| | - Cindy R Eide
- Division of Pediatric Blood and Marrow Transplantation & Cellular Therapy, Department of Pediatrics, University of Minnesota, Minneapolis, Minnesota, USA
| | - Andre H Lengert
- Escola Paulista de Medicina, Universidade Federal de Sao Paulo, Sao Paulo, Brazil
| | - Sang Won Han
- Escola Paulista de Medicina, Universidade Federal de Sao Paulo, Sao Paulo, Brazil
| | - Bruce R Blazar
- Division of Pediatric Blood and Marrow Transplantation & Cellular Therapy, Department of Pediatrics, University of Minnesota, Minneapolis, Minnesota, USA
| | - Hans H Wandall
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Sally Dabelsteen
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - David R Liu
- Merkin Institute of Transformative Technologies in Healthcare, The Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA; Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts, USA; Howard Hughes Medical Institute, Harvard University, Cambridge, Massachusetts, USA
| | - Jakub Tolar
- Division of Pediatric Blood and Marrow Transplantation & Cellular Therapy, Department of Pediatrics, University of Minnesota, Minneapolis, Minnesota, USA
| | - Mark J Osborn
- Division of Pediatric Blood and Marrow Transplantation & Cellular Therapy, Department of Pediatrics, University of Minnesota, Minneapolis, Minnesota, USA.
| |
Collapse
|
3
|
Cale JM, Ham KA, Li D, McIntosh CS, Watts GF, Wilton SD, Aung-Htut MT. Induced alternative splicing an opportunity to study PCSK9 protein isoforms at physiologically relevant concentrations. Sci Rep 2023; 13:19725. [PMID: 37957262 PMCID: PMC10643364 DOI: 10.1038/s41598-023-47005-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Accepted: 11/07/2023] [Indexed: 11/15/2023] Open
Abstract
Splice modulating antisense oligomers (AOs) are increasingly used to modulate RNA processing. While most are investigated for their use as therapeutics, AOs can also be used for basic research. This study examined their use to investigate internally and terminally truncated proprotein convertase subtilisin/kexin type 9 (PCSK9) protein isoforms. Previous studies have used plasmid or viral-vector-mediated protein overexpression to study different PCSK9 protein isoforms, creating an artificial environment within the cell. Here we designed and tested AOs to remove specific exons that encode for PCSK9 protein domains and produced protein isoforms at more physiologically relevant levels. We evaluated the isoforms' expression, secretion, and subsequent impact on the low-density lipoprotein (LDL) receptor and its activity in Huh-7 cells. We found that modifying the Cis-His-rich domain by targeting exons 10 or 11 negatively affected LDL receptor activity and hence did not enhance LDL uptake although the levels of LDL receptor were increased. On the other hand, removing the hinge region encoded by exon 8, or a portion of the prodomain encoded by exon 2, have the potential as therapeutics for hypercholesterolemia. Our findings expand the understanding of PCSK9 isoforms and their impact on the LDL receptor and its activity at physiologically relevant concentrations.
Collapse
Affiliation(s)
- Jessica M Cale
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, 90 South Street, Murdoch, WA, 6150, Australia
| | - Kristin A Ham
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, 90 South Street, Murdoch, WA, 6150, Australia
- Perron Institute for Neurological and Translational Science, Perth, WA, 6009, Australia
| | - Dunhui Li
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, 90 South Street, Murdoch, WA, 6150, Australia
- Perron Institute for Neurological and Translational Science, Perth, WA, 6009, Australia
| | - Craig S McIntosh
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, 90 South Street, Murdoch, WA, 6150, Australia
- Perron Institute for Neurological and Translational Science, Perth, WA, 6009, Australia
| | - Gerald F Watts
- School of Medicine, Faculty of Health and Medical Sciences, University of Western Australia, Perth, WA, 6009, Australia
- Cardiometabolic Clinic, Departments of Cardiology and Internal Medicine, Royal Perth Hospital, Perth, WA, 6000, Australia
| | - Steve D Wilton
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, 90 South Street, Murdoch, WA, 6150, Australia
- Perron Institute for Neurological and Translational Science, Perth, WA, 6009, Australia
| | - May T Aung-Htut
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, 90 South Street, Murdoch, WA, 6150, Australia.
- Perron Institute for Neurological and Translational Science, Perth, WA, 6009, Australia.
| |
Collapse
|
4
|
Choquet K, Baxter-Koenigs AR, Dülk SL, Smalec BM, Rouskin S, Churchman LS. Pre-mRNA splicing order is predetermined and maintains splicing fidelity across multi-intronic transcripts. Nat Struct Mol Biol 2023; 30:1064-1076. [PMID: 37443198 PMCID: PMC10653200 DOI: 10.1038/s41594-023-01035-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 06/13/2023] [Indexed: 07/15/2023]
Abstract
Combinatorially, intron excision within a given nascent transcript could proceed down any of thousands of paths, each of which would expose different dynamic landscapes of cis-elements and contribute to alternative splicing. In this study, we found that post-transcriptional multi-intron splicing order in human cells is largely predetermined, with most genes spliced in one or a few predominant orders. Strikingly, these orders were conserved across cell types and stages of motor neuron differentiation. Introns flanking alternatively spliced exons were frequently excised last, after their neighboring introns. Perturbations to the spliceosomal U2 snRNA altered the preferred splicing order of many genes, and these alterations were associated with the retention of other introns in the same transcript. In one gene, early removal of specific introns was sufficient to induce delayed excision of three proximal introns, and this delay was caused by two distinct cis-regulatory mechanisms. Together, our results demonstrate that multi-intron splicing order in human cells is predetermined, is influenced by a component of the spliceosome and ensures splicing fidelity across long pre-mRNAs.
Collapse
Affiliation(s)
- Karine Choquet
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | | | - Sarah-Luisa Dülk
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Brendan M Smalec
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Silvi Rouskin
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - L Stirling Churchman
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA.
| |
Collapse
|
5
|
Roshandel D, Semnani F, Rayati Damavandi A, Masoudi A, Baradaran-Rafii A, Watson SL, Morgan WH, McLenachan S. Genetic predisposition to ocular surface disorders and opportunities for gene-based therapies. Ocul Surf 2023; 29:150-165. [PMID: 37192706 DOI: 10.1016/j.jtos.2023.05.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 04/24/2023] [Accepted: 05/09/2023] [Indexed: 05/18/2023]
Abstract
The ocular surface, comprised of the corneal and conjunctival epithelium, innervation system, immune components, and tear-film apparatus, plays a key role in ocular integrity as well as comfort and vision. Gene defects may result in congenital ocular or systemic disorders with prominent ocular surface involvement. Examples include epithelial corneal dystrophies, aniridia, ectrodactyly-ectodermal dysplasia-clefting (EEC) syndrome, xeroderma pigmentosum (XP), and hereditary sensory and autonomic neuropathy. In addition, genetic factors may interact with environmental risk factors in the development of several multifactorial ocular surface disorders (OSDs) such as autoimmune disorders, allergies, neoplasms, and dry eye disease. Advanced gene-based technologies have already been introduced in disease modelling and proof-of-concept gene therapies for monogenic OSDs. For instance, patient-derived induced pluripotent stem cells have been used for modelling aniridia-associated keratopathy (AAK), XP, and EEC syndrome. Moreover, CRISPR/Cas9 genome editing has been used for disease modelling and/or gene therapy for AAK and Meesmann's epithelial corneal dystrophy. A better understanding of the role of genetic factors in OSDs may be helpful in designing personalized disease models and treatment approaches. Gene-based approaches in monogenic OSDs and genetic predisposition to multifactorial OSDs such as immune-mediated disorders and neoplasms with known or possible genetic risk factors has been seldom reviewed. In this narrative review, we discuss the role of genetic factors in monogenic and multifactorial OSDs and potential opportunities for gene therapy.
Collapse
Affiliation(s)
- Danial Roshandel
- Lions Eye Institute, Perth, WA, Australia; Centre for Ophthalmology and Visual Science, The University of Western Australia, Perth, WA, Australia
| | - Farbod Semnani
- School of Public Health, Tehran University of Medical Sciences (TUMS), Tehran, Iran; School of Medicine, Tehran University of Medical Sciences (TUMS), Tehran, Iran
| | - Amirmasoud Rayati Damavandi
- School of Public Health, Tehran University of Medical Sciences (TUMS), Tehran, Iran; School of Medicine, Tehran University of Medical Sciences (TUMS), Tehran, Iran
| | - Ali Masoudi
- Stein Eye Institute, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Alireza Baradaran-Rafii
- Department of Ophthalmology, Research Institute for Ophthalmology and Vision Science, Shahid Beheshti University of Medical Sciences, Tehran, Iran; Department of Ophthalmology, Morsani College of Medicine, University of South Florida, Tampa, FL, USA
| | - Stephanie L Watson
- The University of Sydney, Save Sight Institute, Discipline of Ophthalmology, Sydney Medical School, Sydney, New South Wales, Australia
| | - William H Morgan
- Lions Eye Institute, Perth, WA, Australia; Centre for Ophthalmology and Visual Science, The University of Western Australia, Perth, WA, Australia
| | - Samuel McLenachan
- Lions Eye Institute, Perth, WA, Australia; Centre for Ophthalmology and Visual Science, The University of Western Australia, Perth, WA, Australia.
| |
Collapse
|
6
|
Hou PC, del Agua N, Lwin SM, Hsu CK, McGrath JA. Innovations in the Treatment of Dystrophic Epidermolysis Bullosa (DEB): Current Landscape and Prospects. Ther Clin Risk Manag 2023; 19:455-473. [PMID: 37337559 PMCID: PMC10277004 DOI: 10.2147/tcrm.s386923] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 06/02/2023] [Indexed: 06/21/2023] Open
Abstract
Dystrophic epidermolysis bullosa (DEB) is one of the major types of EB, a rare hereditary group of trauma-induced blistering skin disorders. DEB is caused by inherited pathogenic variants in the COL7A1 gene, which encodes type VII collagen, the major component of anchoring fibrils which maintain adhesion between the outer epidermis and underlying dermis. DEB can be subclassified into dominant (DDEB) and recessive (RDEB) forms. Generally, DDEB has a milder phenotype, while RDEB patients often have more extensive blistering, chronic inflammation, skin fibrosis, and a propensity for squamous cell carcinoma development, collectively impacting on daily activities and life expectancy. At present, best practice treatments are mostly supportive, and thus there is a considerable burden of disease with unmet therapeutic need. Over the last 20 years, considerable translational research efforts have focused on either trying to cure DEB by direct correction of the COL7A1 gene pathology, or by modifying secondary inflammation to lessen phenotypic severity and improve patient symptoms such as poor wound healing, itch, and pain. In this review, we provide an overview and update on various therapeutic innovations for DEB, including gene therapy, cell-based therapy, protein therapy, and disease-modifying and symptomatic control agents. We outline the progress and challenges for each treatment modality and identify likely prospects for future clinical impact.
Collapse
Affiliation(s)
- Ping-Chen Hou
- Department of Dermatology, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Nathalie del Agua
- Institute of Clinical Medicine, College of Medicine, National Cheng Kung University, Tainan, Taiwan
- International Center for Wound Repair and Regeneration (iWRR), National Cheng Kung University, Tainan, Taiwan
| | - Su M Lwin
- St John’s Institute of Dermatology, School of Basic and Medical Biosciences, King’s College London, London, UK
| | - Chao-Kai Hsu
- Department of Dermatology, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan
- Institute of Clinical Medicine, College of Medicine, National Cheng Kung University, Tainan, Taiwan
- International Center for Wound Repair and Regeneration (iWRR), National Cheng Kung University, Tainan, Taiwan
| | - John A McGrath
- Department of Dermatology, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan
- International Center for Wound Repair and Regeneration (iWRR), National Cheng Kung University, Tainan, Taiwan
- St John’s Institute of Dermatology, School of Basic and Medical Biosciences, King’s College London, London, UK
| |
Collapse
|
7
|
Antisense RNA Therapeutics: A Brief Overview. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2022; 2434:33-49. [PMID: 35213008 DOI: 10.1007/978-1-0716-2010-6_2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Nucleic acid therapeutics is a growing field aiming to treat human conditions that has gained special attention due to the successful development of mRNA vaccines against SARS-CoV-2. Another type of nucleic acid therapeutics is antisense oligonucleotides, versatile tools that can be used in multiple ways to target pre-mRNA and mRNA. While some years ago these molecules were just considered a useful research tool and a curiosity in the clinical market, this has rapidly changed. These molecules are promising strategies for personalized treatments for rare genetic diseases and they are in development for very common disorders too. In this chapter, we provide a brief description of the different mechanisms of action of these RNA therapeutic molecules, with clear examples at preclinical and clinical stages.
Collapse
|
8
|
Zhang J, Shen Y, Yang Z, Yang F, Li Y, Yu B, Chen W, Gan J. A splicing variation in NPRL2 causing familial focal epilepsy with variable foci: additional cases and literature review. J Hum Genet 2022; 67:79-85. [PMID: 34376795 PMCID: PMC8786660 DOI: 10.1038/s10038-021-00969-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 07/23/2021] [Accepted: 07/26/2021] [Indexed: 01/31/2023]
Abstract
NPRL2 (nitrogen permease regulator like 2) is a component of the GATOR1(GAP activity towards rags complex 1) proteins, which is an inhibitor of the amino acid-sensing branch of the mTORC1 pathway. GATOR1 complex variations were reported to correlate with familial focal epilepsy with variable foci (FFEVF). However, FFEVF caused by NPRL2 variants has not been widely explored. Here, we describe a variant, 339+2T>C, in NPRL2 identified by trio whole-exome sequencing (WES) in a family. This splicing variant that occurred at the 5' end of exon 3 was confirmed by minigene assays, which affected alternative splicing and led to exon 3 skipping in NPRL2. Our cases presented multiple seizure types (febrile seizures, infantile spasms, focal seizures, or focal to generalized tonic-clonic seizures). Electroencephalogram (EEG) showed frequent discharges in the left frontal and central regions. A favorable prognosis was achieved in response to vitamin B6 and topiramate when the patient was seven months old. Our study expands the phenotype and genotype spectrum of FFEVF and provides solid diagnostic evidence for FFEVF.
Collapse
Affiliation(s)
- Jia Zhang
- Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Obstetrics & Gynecologic and Pediatric Diseases and Birth Defects of the Ministry of Education, Sichuan University, Chengdu, Sichuan, China
| | - Yajun Shen
- Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Obstetrics & Gynecologic and Pediatric Diseases and Birth Defects of the Ministry of Education, Sichuan University, Chengdu, Sichuan, China
| | | | | | - Yang Li
- Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Obstetrics & Gynecologic and Pediatric Diseases and Birth Defects of the Ministry of Education, Sichuan University, Chengdu, Sichuan, China
| | - Bo Yu
- Department of Pediatrics, The City Central Hospital of Wanyuan, Wanyuan, Sichuan, China
| | - Wanlin Chen
- Department of Pediatrics, The City Central Hospital of Wanyuan, Wanyuan, Sichuan, China
| | - Jing Gan
- Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu, China.
- Key Laboratory of Obstetrics & Gynecologic and Pediatric Diseases and Birth Defects of the Ministry of Education, Sichuan University, Chengdu, Sichuan, China.
| |
Collapse
|
9
|
McIntosh CS, Watts GF, Wilton SD, Aung-Htut MT. Splice correction therapies for familial hypercholesterolemic patients with low-density lipoprotein receptor mutations. Curr Opin Lipidol 2021; 32:355-362. [PMID: 34653074 PMCID: PMC8631153 DOI: 10.1097/mol.0000000000000793] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
PURPOSE OF REVIEW Antisense oligomers (ASOs) have been available for decades: however, only recently have these molecules been applied clinically. This review aims to discuss the possible development of antisense-mediated splice correction therapies as precision medicines for familial hypercholesterolemic patients carrying mutations that compromise normal splicing of the low-density lipoprotein receptor (LDLR) gene transcript. RECENT FINDINGS Three antisense drugs are currently being assessed in ongoing clinical trials for dyslipidemias, aiming to lower the plasma concentrations of lipoproteins that lead to end-organ damage, principally coronary artery disease. Although a handful of drugs may be applicable to many patients with familial hypercholesterolemia (FH), mutation-specific personalised antisense drugs may be even more effective in selected patients. Currently, there is no therapy that effectively addresses mutations in the LDLR, the major cause of FH. Many mutations in the LDLR that disrupt normal pre-mRNA processing could be applicable to splice correction therapy to restore receptor activity. SUMMARY Precision medicine could provide long-term economic and social benefits if they can be implemented effectively and sustainably. Many mutations found in the LDLR gene could be amendable to therapeutic splice correction and we should consider developing a therapeutic ASO platform for these mutations.
Collapse
Affiliation(s)
- Craig S. McIntosh
- Perron Institute for Neurological and Translational Science, Nedlands, Western Australia, Australia
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, Murdoch, Western Australia, Australia
| | - Gerald F. Watts
- School of Medicine, University of Western Australia
- Lipid Disorders Clinic, Department of Cardiology, Royal Perth Hospital, Perth, Western Australia, Australia
| | - Steve D. Wilton
- Perron Institute for Neurological and Translational Science, Nedlands, Western Australia, Australia
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, Murdoch, Western Australia, Australia
| | - May T. Aung-Htut
- Perron Institute for Neurological and Translational Science, Nedlands, Western Australia, Australia
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, Murdoch, Western Australia, Australia
| |
Collapse
|
10
|
Therapeutic Prospects of Exon Skipping for Epidermolysis Bullosa. Int J Mol Sci 2021; 22:ijms222212222. [PMID: 34830104 PMCID: PMC8621297 DOI: 10.3390/ijms222212222] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 11/03/2021] [Accepted: 11/08/2021] [Indexed: 12/12/2022] Open
Abstract
Epidermolysis bullosa is a group of genetic skin conditions characterized by abnormal skin (and mucosal) fragility caused by pathogenic variants in various genes. The disease severity ranges from early childhood mortality in the most severe types to occasional acral blistering in the mildest types. The subtype and severity of EB is linked to the gene involved and the specific variants in that gene, which also determine its mode of inheritance. Current treatment is mainly focused on symptomatic relief such as wound care and blister prevention, because truly curative treatment options are still at the preclinical stage. Given the current level of understanding, the broad spectrum of genes and variants underlying EB makes it impossible to develop a single treatment strategy for all patients. It is likely that many different variant-specific treatment strategies will be needed to ultimately treat all patients. Antisense-oligonucleotide (ASO)-mediated exon skipping aims to counteract pathogenic sequence variants by restoring the open reading frame through the removal of the mutant exon from the pre-messenger RNA. This should lead to the restored production of the protein absent in the affected skin and, consequently, improvement of the phenotype. Several preclinical studies have demonstrated that exon skipping can restore protein production in vitro, in skin equivalents, and in skin grafts derived from EB-patient skin cells, indicating that ASO-mediated exon skipping could be a viable strategy as a topical or systemic treatment. The potential value of exon skipping for EB is supported by a study showing reduced phenotypic severity in patients who carry variants that result in natural exon skipping. In this article, we review the substantial progress made on exon skipping for EB in the past 15 years and highlight the opportunities and current challenges of this RNA-based therapy approach. In addition, we present a prioritization strategy for the development of exon skipping based on genomic information of all EB-involved genes.
Collapse
|
11
|
McIntosh CS, Li D, Wilton SD, Aung-Htut MT. Polyglutamine Ataxias: Our Current Molecular Understanding and What the Future Holds for Antisense Therapies. Biomedicines 2021; 9:1499. [PMID: 34829728 PMCID: PMC8615177 DOI: 10.3390/biomedicines9111499] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 10/13/2021] [Accepted: 10/14/2021] [Indexed: 02/07/2023] Open
Abstract
Polyglutamine (polyQ) ataxias are a heterogenous group of neurological disorders all caused by an expanded CAG trinucleotide repeat located in the coding region of each unique causative gene. To date, polyQ ataxias encompass six disorders: spinocerebellar ataxia types 1, 2, 3, 6, 7, and 17 and account for a larger group of disorders simply known as polyglutamine disorders, which also includes Huntington's disease. These diseases are typically characterised by progressive ataxia, speech and swallowing difficulties, lack of coordination and gait, and are unfortunately fatal in nature, with the exception of SCA6. All the polyQ spinocerebellar ataxias have a hallmark feature of neuronal aggregations and share many common pathogenic mechanisms, such as mitochondrial dysfunction, impaired proteasomal function, and autophagy impairment. Currently, therapeutic options are limited, with no available treatments that slow or halt disease progression. Here, we discuss the common molecular and clinical presentations of polyQ spinocerebellar ataxias. We will also discuss the promising antisense oligonucleotide therapeutics being developed as treatments for these devastating diseases. With recent advancements and therapeutic approvals of various antisense therapies, it is envisioned that some of the studies reviewed may progress into clinical trials and beyond.
Collapse
Affiliation(s)
- Craig S. McIntosh
- Molecular Therapy Laboratory, Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute Murdoch University, Discovery Way, Murdoch, WA 6150, Australia; (C.S.M.); (D.L.); (S.D.W.)
- Perron Institute for Neurological and Translational Science, Centre for Neuromuscular and Neurological Disorders, The University of Western Australia, Nedlands, WA 6009, Australia
| | - Dunhui Li
- Molecular Therapy Laboratory, Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute Murdoch University, Discovery Way, Murdoch, WA 6150, Australia; (C.S.M.); (D.L.); (S.D.W.)
- Perron Institute for Neurological and Translational Science, Centre for Neuromuscular and Neurological Disorders, The University of Western Australia, Nedlands, WA 6009, Australia
| | - Steve D. Wilton
- Molecular Therapy Laboratory, Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute Murdoch University, Discovery Way, Murdoch, WA 6150, Australia; (C.S.M.); (D.L.); (S.D.W.)
- Perron Institute for Neurological and Translational Science, Centre for Neuromuscular and Neurological Disorders, The University of Western Australia, Nedlands, WA 6009, Australia
| | - May T. Aung-Htut
- Molecular Therapy Laboratory, Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute Murdoch University, Discovery Way, Murdoch, WA 6150, Australia; (C.S.M.); (D.L.); (S.D.W.)
- Perron Institute for Neurological and Translational Science, Centre for Neuromuscular and Neurological Disorders, The University of Western Australia, Nedlands, WA 6009, Australia
| |
Collapse
|
12
|
Ham KA, Keegan NP, McIntosh CS, Aung-Htut MT, Zaw K, Greer K, Fletcher S, Wilton SD. Induction of cryptic pre-mRNA splice-switching by antisense oligonucleotides. Sci Rep 2021; 11:15137. [PMID: 34302060 PMCID: PMC8302632 DOI: 10.1038/s41598-021-94639-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Accepted: 07/14/2021] [Indexed: 11/09/2022] Open
Abstract
Antisense oligomers (AOs) are increasingly being used to modulate RNA splicing in live cells, both for research and for the development of therapeutics. While the most common intended effect of these AOs is to induce skipping of whole exons, rare examples are emerging of AOs that induce skipping of only part of an exon, through activation of an internal cryptic splice site. In this report, we examined seven AO-induced cryptic splice sites in six genes. Five of these cryptic splice sites were discovered through our own experiments, and two originated from other published reports. We modelled the predicted effects of AO binding on the secondary structure of each of the RNA targets, and how these alterations would in turn affect the accessibility of the RNA to splice factors. We observed that a common predicted effect of AO binding was disruption of the exon definition signal within the exon's excluded segment.
Collapse
Affiliation(s)
- Kristin A Ham
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, Perth, WA, 6150, Australia.,Perron Institute for Neurological and Translational Science, Centre for Neuromuscular and Neurological Disorders, The University of Western Australia, Perth, WA, 6009, Australia
| | - Niall P Keegan
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, Perth, WA, 6150, Australia.,Perron Institute for Neurological and Translational Science, Centre for Neuromuscular and Neurological Disorders, The University of Western Australia, Perth, WA, 6009, Australia
| | - Craig S McIntosh
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, Perth, WA, 6150, Australia.,Perron Institute for Neurological and Translational Science, Centre for Neuromuscular and Neurological Disorders, The University of Western Australia, Perth, WA, 6009, Australia
| | - May T Aung-Htut
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, Perth, WA, 6150, Australia.,Perron Institute for Neurological and Translational Science, Centre for Neuromuscular and Neurological Disorders, The University of Western Australia, Perth, WA, 6009, Australia
| | - Khine Zaw
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, Perth, WA, 6150, Australia.,Perron Institute for Neurological and Translational Science, Centre for Neuromuscular and Neurological Disorders, The University of Western Australia, Perth, WA, 6009, Australia.,Department of Biochemistry, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand
| | - Kane Greer
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, Perth, WA, 6150, Australia.,Perron Institute for Neurological and Translational Science, Centre for Neuromuscular and Neurological Disorders, The University of Western Australia, Perth, WA, 6009, Australia
| | - Sue Fletcher
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, Perth, WA, 6150, Australia.,Perron Institute for Neurological and Translational Science, Centre for Neuromuscular and Neurological Disorders, The University of Western Australia, Perth, WA, 6009, Australia
| | - Steve D Wilton
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, Perth, WA, 6150, Australia. .,Perron Institute for Neurological and Translational Science, Centre for Neuromuscular and Neurological Disorders, The University of Western Australia, Perth, WA, 6009, Australia.
| |
Collapse
|
13
|
Matsuo M. Antisense Oligonucleotide-Mediated Exon-skipping Therapies: Precision Medicine Spreading from Duchenne Muscular Dystrophy. JMA J 2021; 4:232-240. [PMID: 34414317 PMCID: PMC8355726 DOI: 10.31662/jmaj.2021-0019] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2021] [Accepted: 04/13/2021] [Indexed: 11/12/2022] Open
Abstract
In 1995, we were the first to propose antisense oligonucleotide (ASO)-mediated exon-skipping therapy for the treatment of Duchenne muscular dystrophy (DMD), a noncurable, progressive muscle-wasting disease. DMD is caused by deletion mutations in one or more exons of the DMD gene that shift the translational reading frame and create a premature stop codon, thus prohibiting dystrophin production. The therapy aims to correct out-of-frame mRNAs to produce in-frame transcripts by removing an exon during splicing, with the resumption of dystrophin production. As this treatment is recognized as the most promising, many extensive studies have been performed to develop ASOs that induce the skipping of DMD exons. In 2016, an ASO designed to skip exon 51 was first approved by the Food and Drug Administration, which accelerated studies on the use of ASOs to treat other monogenic diseases. The ease of mRNA editing by ASO-mediated exon skipping has resulted in the further application of exon-skipping therapy to nonmonogenic diseases, such as diabetes mellites. Recently, this precision medicine strategy was drastically transformed for the emergent treatment of only one patient with one ASO, which represents a future aspect of ASO-mediated exon-skipping therapy for extremely rare diseases. Herein, the invention of ASO-mediated exon-skipping therapy for DMD and the current applications of ASO-mediated exon-skipping therapies are reviewed, and future perspectives on this therapeutic strategy are discussed. This overview will encourage studies on ASO-mediated exon-skipping therapy and will especially contribute to the development of treatments for noncurable diseases.
Collapse
Affiliation(s)
- Masafumi Matsuo
- KNC Department of Nucleic Acid Drug Discovery, Department of Physical Rehabilitation and Research Center for Locomotion Biology, Kobe Gakuin University, Kobe, Japan
| |
Collapse
|
14
|
Chiba S, Lim KRQ, Sheri N, Anwar S, Erkut E, Shah MNA, Aslesh T, Woo S, Sheikh O, Maruyama R, Takano H, Kunitake K, Duddy W, Okuno Y, Aoki Y, Yokota T. eSkip-Finder: a machine learning-based web application and database to identify the optimal sequences of antisense oligonucleotides for exon skipping. Nucleic Acids Res 2021; 49:W193-W198. [PMID: 34104972 PMCID: PMC8265194 DOI: 10.1093/nar/gkab442] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 04/18/2021] [Accepted: 05/12/2021] [Indexed: 01/13/2023] Open
Abstract
Exon skipping using antisense oligonucleotides (ASOs) has recently proven to be a powerful tool for mRNA splicing modulation. Several exon-skipping ASOs have been approved to treat genetic diseases worldwide. However, a significant challenge is the difficulty in selecting an optimal sequence for exon skipping. The efficacy of ASOs is often unpredictable, because of the numerous factors involved in exon skipping. To address this gap, we have developed a computational method using machine-learning algorithms that factors in many parameters as well as experimental data to design highly effective ASOs for exon skipping. eSkip-Finder (https://eskip-finder.org) is the first web-based resource for helping researchers identify effective exon skipping ASOs. eSkip-Finder features two sections: (i) a predictor of the exon skipping efficacy of novel ASOs and (ii) a database of exon skipping ASOs. The predictor facilitates rapid analysis of a given set of exon/intron sequences and ASO lengths to identify effective ASOs for exon skipping based on a machine learning model trained by experimental data. We confirmed that predictions correlated well with in vitro skipping efficacy of sequences that were not included in the training data. The database enables users to search for ASOs using queries such as gene name, species, and exon number.
Collapse
Affiliation(s)
- Shuntaro Chiba
- HPC- and AI-driven Drug Development Platform Division, RIKEN Center for Computational Science, Yokohama 230-0045, Japan
| | - Kenji Rowel Q Lim
- Department of Medical Genetics, University of Alberta Faculty of Medicine and Dentistry, 8613-114 St, Edmonton, AB, Canada
| | - Narin Sheri
- Department of Medical Genetics, University of Alberta Faculty of Medicine and Dentistry, 8613-114 St, Edmonton, AB, Canada
| | - Saeed Anwar
- Department of Medical Genetics, University of Alberta Faculty of Medicine and Dentistry, 8613-114 St, Edmonton, AB, Canada
| | - Esra Erkut
- Department of Medical Genetics, University of Alberta Faculty of Medicine and Dentistry, 8613-114 St, Edmonton, AB, Canada
| | - Md Nur Ahad Shah
- Department of Medical Genetics, University of Alberta Faculty of Medicine and Dentistry, 8613-114 St, Edmonton, AB, Canada
| | - Tejal Aslesh
- Department of Medical Genetics, University of Alberta Faculty of Medicine and Dentistry, 8613-114 St, Edmonton, AB, Canada
| | - Stanley Woo
- Department of Medical Genetics, University of Alberta Faculty of Medicine and Dentistry, 8613-114 St, Edmonton, AB, Canada
| | - Omar Sheikh
- Department of Medical Genetics, University of Alberta Faculty of Medicine and Dentistry, 8613-114 St, Edmonton, AB, Canada
| | - Rika Maruyama
- Department of Medical Genetics, University of Alberta Faculty of Medicine and Dentistry, 8613-114 St, Edmonton, AB, Canada
| | - Hiroaki Takano
- HPC- and AI-driven Drug Development Platform Division, RIKEN Center for Computational Science, Yokohama 230-0045, Japan
| | - Katsuhiko Kunitake
- Department of Molecular Therapy, National Institute of Neuroscience, National Center of Neurology and Psychiatry (NCNP), Kodaira, Tokyo 187-8551, Japan
| | - William Duddy
- Northern Ireland Center for Stratified Medicine, Biomedical Sciences Research Institute, C-TRIC, Altnagelvin Hospital Campus, Ulster University, Londonderry BT47 6SB, UK
| | - Yasushi Okuno
- HPC- and AI-driven Drug Development Platform Division, RIKEN Center for Computational Science, Yokohama 230-0045, Japan.,Department of Biomedical Data Intelligence, Graduate School of Medicine, Kyoto University, Kyoto 606-8507, Japan
| | - Yoshitsugu Aoki
- Department of Molecular Therapy, National Institute of Neuroscience, National Center of Neurology and Psychiatry (NCNP), Kodaira, Tokyo 187-8551, Japan
| | - Toshifumi Yokota
- Department of Medical Genetics, University of Alberta Faculty of Medicine and Dentistry, 8613-114 St, Edmonton, AB, Canada
| |
Collapse
|