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Gonçalves M, Santos JI, Coutinho MF, Matos L, Alves S. Development of Engineered-U1 snRNA Therapies: Current Status. Int J Mol Sci 2023; 24:14617. [PMID: 37834063 PMCID: PMC10572768 DOI: 10.3390/ijms241914617] [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: 08/17/2023] [Revised: 09/22/2023] [Accepted: 09/25/2023] [Indexed: 10/15/2023] Open
Abstract
Splicing of pre-mRNA is a crucial regulatory stage in the pathway of gene expression. The majority of human genes that encode proteins undergo alternative pre-mRNA splicing and mutations that affect splicing are more prevalent than previously thought. Targeting aberrant RNA(s) may thus provide an opportunity to correct faulty splicing and potentially treat numerous genetic disorders. To that purpose, the use of engineered U1 snRNA (either modified U1 snRNAs or exon-specific U1s-ExSpeU1s) has been applied as a potentially therapeutic strategy to correct splicing mutations, particularly those affecting the 5' splice-site (5'ss). Here we review and summarize a vast panoply of studies that used either modified U1 snRNAs or ExSpeU1s to mediate gene therapeutic correction of splicing defects underlying a considerable number of genetic diseases. We also focus on the pre-clinical validation of these therapeutic approaches both in vitro and in vivo, and summarize the main obstacles that need to be overcome to allow for their successful translation to clinic practice in the future.
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Affiliation(s)
- Mariana Gonçalves
- Research and Development Unit, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge, INSA I.P., Rua Alexandre Herculano, 321, 4000-055 Porto, Portugal; (M.G.); (J.I.S.); (M.F.C.); (L.M.)
- Center for the Study of Animal Science, Institute of Sciences, Technologies and Agro-Environment, CECA-ICETA, University of Porto, Praça Gomes Teixeira, Apartado 55142, 4051-401 Porto, Portugal
- Associate Laboratory for Animal and Veterinary Sciences, AL4AnimalS, Faculty of Veterinary Medicine, University of Lisboa, Avenida da Universidade Técnica, 1300-477 Lisboa, Portugal
- Centre for the Research and Technology of Agro-Environmental and Biological Sciences, CITAB, Inov4Agro, University of Trás-os-Montes and Alto Douro, 5000-801 Vila Real, Portugal
| | - Juliana Inês Santos
- Research and Development Unit, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge, INSA I.P., Rua Alexandre Herculano, 321, 4000-055 Porto, Portugal; (M.G.); (J.I.S.); (M.F.C.); (L.M.)
- Center for the Study of Animal Science, Institute of Sciences, Technologies and Agro-Environment, CECA-ICETA, University of Porto, Praça Gomes Teixeira, Apartado 55142, 4051-401 Porto, Portugal
- Associate Laboratory for Animal and Veterinary Sciences, AL4AnimalS, Faculty of Veterinary Medicine, University of Lisboa, Avenida da Universidade Técnica, 1300-477 Lisboa, Portugal
- Biology Department, Faculty of Sciences, University of Porto, Rua do Campo Alegre, 4169-007 Porto, Portugal
| | - Maria Francisca Coutinho
- Research and Development Unit, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge, INSA I.P., Rua Alexandre Herculano, 321, 4000-055 Porto, Portugal; (M.G.); (J.I.S.); (M.F.C.); (L.M.)
- Center for the Study of Animal Science, Institute of Sciences, Technologies and Agro-Environment, CECA-ICETA, University of Porto, Praça Gomes Teixeira, Apartado 55142, 4051-401 Porto, Portugal
- Associate Laboratory for Animal and Veterinary Sciences, AL4AnimalS, Faculty of Veterinary Medicine, University of Lisboa, Avenida da Universidade Técnica, 1300-477 Lisboa, Portugal
| | - Liliana Matos
- Research and Development Unit, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge, INSA I.P., Rua Alexandre Herculano, 321, 4000-055 Porto, Portugal; (M.G.); (J.I.S.); (M.F.C.); (L.M.)
- Center for the Study of Animal Science, Institute of Sciences, Technologies and Agro-Environment, CECA-ICETA, University of Porto, Praça Gomes Teixeira, Apartado 55142, 4051-401 Porto, Portugal
- Associate Laboratory for Animal and Veterinary Sciences, AL4AnimalS, Faculty of Veterinary Medicine, University of Lisboa, Avenida da Universidade Técnica, 1300-477 Lisboa, Portugal
| | - Sandra Alves
- Research and Development Unit, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge, INSA I.P., Rua Alexandre Herculano, 321, 4000-055 Porto, Portugal; (M.G.); (J.I.S.); (M.F.C.); (L.M.)
- Center for the Study of Animal Science, Institute of Sciences, Technologies and Agro-Environment, CECA-ICETA, University of Porto, Praça Gomes Teixeira, Apartado 55142, 4051-401 Porto, Portugal
- Associate Laboratory for Animal and Veterinary Sciences, AL4AnimalS, Faculty of Veterinary Medicine, University of Lisboa, Avenida da Universidade Técnica, 1300-477 Lisboa, Portugal
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Persico I, Fontana G, Faleschini M, Zanchetta ME, Ammeti D, Cappelli E, Corsolini F, Mosa C, Guarina A, Bogliolo M, Surrallés J, Dufour C, Farruggia P, Savoia A, Bottega R. A self-repair history: compensatory effect of a de novo variant on the FANCA c.2778+83C>G splicing mutation. Front Genet 2023; 14:1209138. [PMID: 37547463 PMCID: PMC10397729 DOI: 10.3389/fgene.2023.1209138] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 07/05/2023] [Indexed: 08/08/2023] Open
Abstract
Introduction: Fanconi anemia (FA) is a genome instability condition that drives somatic mosaicism in up to 25% of all patients, a phenomenon now acknowledged as a good prognostic factor. Herein, we describe the case of P1, a FA proband carrying a splicing variant, molecularly compensated by a de novo insertion. Methods and Results: Targeted next-generation sequencing on P1's peripheral blood DNA detected the known FANCA c.2778 + 83C > G intronic mutation and suggested the presence of a large deletion on the other allele, which was then assessed by MLPA and RT-PCR. To determine the c.2778 + 83C > G splicing effect, we performed a RT-PCR on P1's lymphoblastoid cell line (LCL) and on the LCL of another patient (P2) carrying the same variant. Although we confirmed the expected alternative spliced form with a partial intronic retention in P2, we detected no aberrant products in P1's sample. Sequencing of P1's LCL DNA allowed identification of the de novo c.2778 + 86insT variant, predicted to compensate 2778 + 83C > G impact. Albeit not found in P1's bone marrow (BM) DNA, c.2778 + 86insT was detected in a second P1's LCL established afterward, suggesting its occurrence at a low level in vivo. Minigene assay recapitulated the c.2778 + 83C > G effect on splicing and the compensatory role of c.2778 + 86insT in re-establishing the physiological mechanism. Accordingly, P1's LCL under mitomycin C selection preserved the FA pathway activity in terms of FANCD2 monoubiquitination and cell survival. Discussion: Our findings prove the role of c.2778 + 86insT as a second-site variant capable of rescuing c.2778 + 83C > G pathogenicity in vitro, which might contribute to a slow hematopoietic deterioration and a mild hematologic evolution.
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Affiliation(s)
- Ilaria Persico
- Department of Medical Sciences, University of Trieste, Trieste, Italy
- Department of Genetics and Microbiology, Universitat Autònoma de Barcelona, Barcelona, Spain
- Genomic Instability DNA Repair Syndromes Group, Joint Research Unit in Genomic Medicine UAB-IR Sant Pau, Sant Pau Biomedical Research Institute (IIB Sant Pau), Barcelona, Spain
| | - Giorgia Fontana
- Institute for Maternal and Child Health—IRCCS “Burlo Garofolo”, Trieste, Italy
| | - Michela Faleschini
- Institute for Maternal and Child Health—IRCCS “Burlo Garofolo”, Trieste, Italy
| | | | - Daniele Ammeti
- Institute for Maternal and Child Health—IRCCS “Burlo Garofolo”, Trieste, Italy
| | - Enrico Cappelli
- Hematology Unit, IRCCS Istituto “G. Gaslini”—Genoa, Genova, Italy
| | - Fabio Corsolini
- LABSIEM—Laboratory for the Study of Inborn Errors of Metabolism—Pediatric Clinic and Endocrinology—IRCCS Istituto “G. Gaslini”—Genoa, Genova, Italy
| | - Clara Mosa
- Pediatric Onco-Hematology, ARNAS Civico Hospital, Palermo, Italy
| | - Angela Guarina
- Pediatric Onco-Hematology, ARNAS Civico Hospital, Palermo, Italy
| | - Massimo Bogliolo
- Department of Genetics and Microbiology, Universitat Autònoma de Barcelona, Barcelona, Spain
- Genomic Instability DNA Repair Syndromes Group, Joint Research Unit in Genomic Medicine UAB-IR Sant Pau, Sant Pau Biomedical Research Institute (IIB Sant Pau), Barcelona, Spain
| | - Jordi Surrallés
- Department of Genetics and Microbiology, Universitat Autònoma de Barcelona, Barcelona, Spain
- Genomic Instability DNA Repair Syndromes Group, Joint Research Unit in Genomic Medicine UAB-IR Sant Pau, Sant Pau Biomedical Research Institute (IIB Sant Pau), Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Carlos III Health Institute, Madrid, Spain
| | - Carlo Dufour
- Hematology Unit, IRCCS Istituto “G. Gaslini”—Genoa, Genova, Italy
| | - Piero Farruggia
- Pediatric Onco-Hematology, ARNAS Civico Hospital, Palermo, Italy
| | - Anna Savoia
- Department of Neurosciences, Biomedicine and Movement Sciences, University of Verona, Verona, Italy
| | - Roberta Bottega
- Institute for Maternal and Child Health—IRCCS “Burlo Garofolo”, Trieste, Italy
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SLC4A11 mutations causative of congenital hereditary endothelial dystrophy (CHED) progressing to Harboyan syndrome in consanguineous Pakistani families. Mol Biol Rep 2021; 48:7467-7476. [PMID: 34637099 DOI: 10.1007/s11033-021-06765-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Accepted: 08/17/2021] [Indexed: 10/20/2022]
Abstract
BACKGROUND Autosomal recessive corneal hereditary endothelial dystrophy (CHED) is a rare congenital disorder of cornea. Mutations in SLC4A11 gene are associated with CHED phenotype. CHED is also an early feature of Harboyan syndrome. The aim of the present study was to identify genetic mutations in the SLC4A11 gene in CHED cases belonging to inbred Pakistani families. Furthermore, all homozygous mutation carriers were investigated for hearing deficit. METHODS AND RESULTS This study included consanguineous CHED families presented at Al-Shifa Trust Eye Hospital, Rawalpindi, Pakistan from June 2018 to September 2018. DNA was extracted from blood samples. Direct sequencing of SLC4A11 gene was performed. All identified variants were evaluated by in silico programs i.e., SIFT, PolyPhen-2, and MutationTaster. Pathogenicity of the two identified splice site variants was analyzed by Human Splicing Finder and MaxEnt Scan. Screening of five CHED families revealed a total of three previously un reported (p.Arg128Gly, c.2241-2A > T and c.1898-2A > C in family CHED19, CHED22 and CHED26 respectively) and two already reported homozygous disease causing variants (p.Arg869Cys and p.Val824Met in family CHED24 and CHED25 respectively) as predicted by mutation taster. All of these variants segregated with disease phenotype and were not detected in controls. CONCLUSION Affected individuals of the five CHED families screened in this study had the disease due to SLC4A11 mutations and progressing to Harboyan syndrome. Identification of previously unreported mutations aid to heterogeneity of SLC4A11 and CHED pathogenesis as well as helped to provide genetic counseling to affected families.
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Takafuji S, Mori T, Nishimura N, Yamamoto N, Uemura S, Nozu K, Terui K, Toki T, Ito E, Muramatsu H, Takahashi Y, Matsuo M, Yamamura T, Iijima K. Usefulness of functional splicing analysis to confirm precise disease pathogenesis in Diamond-Blackfan anemia caused by intronic variants in RPS19. Pediatr Hematol Oncol 2021; 38:515-527. [PMID: 33622161 DOI: 10.1080/08880018.2021.1887984] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Diamond-Blackfan anemia (DBA) is mainly caused by pathogenic variants in ribosomal proteins and 22 responsible genes have been identified to date. The most common causative gene of DBA is RPS19 [NM_001022.4]. Nearly 180 RPS19 variants have been reported, including three deep intronic variants outside the splicing consensus sequence (c.72-92A > G, c.356 + 18G > C, and c.411 + 6G > C). We also identified one case with a c.412-3C > G intronic variant. Without conducting transcript analysis, the pathogenicity of these variants is unknown. However, it is difficult to assess transcripts because of their fragility. In such cases, in vitro functional splicing assays can be used to assess pathogenicity. Here, we report functional splicing analysis results of four RPS19 deep intronic variants identified in our case and in previously reported cases. One splicing consensus variant (c.411 + 1G > A) was also examined as a positive control. Aberrant splicing with a 2-bp insertion between exons 5 and 6 was identified in the patient samples and minigene assay results also identified exon 6 skipping in our case. The exon 6 skipping transcript was confirmed by further evaluation using quantitative RT-PCR. Additionally, minigene assay analysis of three reported deep intronic variants revealed that none of them showed aberrant splicing and that these variants were not considered to be pathogenic. In conclusion, the minigene assay is a useful method for functional splicing analysis of inherited disease.
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Affiliation(s)
- Satoru Takafuji
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Takeshi Mori
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Noriyuki Nishimura
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Nobuyuki Yamamoto
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Suguru Uemura
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Kandai Nozu
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Kiminori Terui
- Department of Pediatrics, Hirosaki University Graduate School of Medicine, Hirosaki, Japan
| | - Tsutomu Toki
- Department of Pediatrics, Hirosaki University Graduate School of Medicine, Hirosaki, Japan
| | - Etsuro Ito
- Department of Pediatrics, Hirosaki University Graduate School of Medicine, Hirosaki, Japan
| | - Hideki Muramatsu
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yoshiyuki Takahashi
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Masafumi Matsuo
- Locomotion Biology Research Center, Kobe Gakuin University, Kobe, Japan
| | - Tomohiko Yamamura
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Kazumoto Iijima
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Japan
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Donegà S, Rogalska ME, Pianigiani G, Igreja S, Amaral MD, Pagani F. Rescue of common exon-skipping mutations in cystic fibrosis with modified U1 snRNAs. Hum Mutat 2020; 41:2143-2154. [PMID: 32935393 DOI: 10.1002/humu.24116] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 08/31/2020] [Accepted: 09/07/2020] [Indexed: 01/22/2023]
Abstract
In cystic fibrosis (CF), the correction of splicing defects represents an interesting therapeutic approach to restore normal CFTR function. In this study, we focused on 10 common mutations/variants 711+3A>G/C, 711+5G>A, TG13T3, TG13T5, TG12T5, 1863C>T, 1898+3A>G, 2789+5G>A, and 3120G>A that induce skipping of the corresponding CFTR exons 5, 10, 13, 16, and 18. To rescue the splicing defects we tested, in a minigene assay, a panel of modified U1 small nuclear RNAs (snRNAs), named Exon Specific U1s (ExSpeU1s), that was engineered to bind to intronic sequences downstream of each defective exon. Using this approach, we show that all 10 splicing mutations analyzed are efficiently corrected by specific ExSpeU1s. Using complementary DNA-splicing competent minigenes, we also show that the ExspeU1-mediated splicing correction at the RNA level recovered the full-length CFTR protein for 1863C>T, 1898+3A>G, 2789+5G>A variants. In addition, detailed mutagenesis experiments performed on exon 13 led us to identify a novel intronic regulatory element involved in the ExSpeU1-mediated splicing rescue. These results provide a common strategy based on modified U1 snRNAs to correct exon skipping in a group of disease-causing CFTR mutations.
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Affiliation(s)
- Stefano Donegà
- Human Molecular Genetics, ICGEB - International Center for Genetic Engineering and Biotechnology, Trieste, Italy
| | - Malgorzata Ewa Rogalska
- Human Molecular Genetics, ICGEB - International Center for Genetic Engineering and Biotechnology, Trieste, Italy
| | - Giulia Pianigiani
- Human Molecular Genetics, ICGEB - International Center for Genetic Engineering and Biotechnology, Trieste, Italy
| | - Susana Igreja
- BioISI - Biosystems and Integrative Sciences Institute, Faculty of Sciences, University of Lisbon, Lisbon, Portugal
| | - Margarida Duarte Amaral
- BioISI - Biosystems and Integrative Sciences Institute, Faculty of Sciences, University of Lisbon, Lisbon, Portugal
| | - Franco Pagani
- Human Molecular Genetics, ICGEB - International Center for Genetic Engineering and Biotechnology, Trieste, Italy
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Suñé-Pou M, Limeres MJ, Moreno-Castro C, Hernández-Munain C, Suñé-Negre JM, Cuestas ML, Suñé C. Innovative Therapeutic and Delivery Approaches Using Nanotechnology to Correct Splicing Defects Underlying Disease. Front Genet 2020; 11:731. [PMID: 32760425 PMCID: PMC7373156 DOI: 10.3389/fgene.2020.00731] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Accepted: 06/16/2020] [Indexed: 12/11/2022] Open
Abstract
Alternative splicing of pre-mRNA contributes strongly to the diversity of cell- and tissue-specific protein expression patterns. Global transcriptome analyses have suggested that >90% of human multiexon genes are alternatively spliced. Alterations in the splicing process cause missplicing events that lead to genetic diseases and pathologies, including various neurological disorders, cancers, and muscular dystrophies. In recent decades, research has helped to elucidate the mechanisms regulating alternative splicing and, in some cases, to reveal how dysregulation of these mechanisms leads to disease. The resulting knowledge has enabled the design of novel therapeutic strategies for correction of splicing-derived pathologies. In this review, we focus primarily on therapeutic approaches targeting splicing, and we highlight nanotechnology-based gene delivery applications that address the challenges and barriers facing nucleic acid-based therapeutics.
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Affiliation(s)
- Marc Suñé-Pou
- Drug Development Service (SDM), Faculty of Pharmacy, University of Barcelona, Barcelona, Spain
| | - María J Limeres
- Institute of Research in Microbiology and Medical Parasitology (IMPaM), Faculty of Medicine, University of Buenos Aires-CONICET, Buenos Aires, Argentina
| | - Cristina Moreno-Castro
- Department of Molecular Biology, Institute of Parasitology and Biomedicine "López-Neyra" (IPBLN-CSIC), Granada, Spain
| | - Cristina Hernández-Munain
- Department of Cell Biology and Immunology, Institute of Parasitology and Biomedicine "López-Neyra" (IPBLN-CSIC), Granada, Spain
| | - Josep M Suñé-Negre
- Drug Development Service (SDM), Faculty of Pharmacy, University of Barcelona, Barcelona, Spain
| | - María L Cuestas
- Institute of Research in Microbiology and Medical Parasitology (IMPaM), Faculty of Medicine, University of Buenos Aires-CONICET, Buenos Aires, Argentina
| | - Carlos Suñé
- Department of Molecular Biology, Institute of Parasitology and Biomedicine "López-Neyra" (IPBLN-CSIC), Granada, Spain
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Coutinho MF, Matos L, Santos JI, Alves S. RNA Therapeutics: How Far Have We Gone? ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1157:133-177. [PMID: 31342441 DOI: 10.1007/978-3-030-19966-1_7] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
In recent years, the RNA molecule became one of the most promising targets for therapeutic intervention. Currently, a large number of RNA-based therapeutics are being investigated both at the basic research level and in late-stage clinical trials. Some of them are even already approved for treatment. RNA-based approaches can act at pre-mRNA level (by splicing modulation/correction using antisense oligonucleotides or U1snRNA vectors), at mRNA level (inhibiting gene expression by siRNAs and antisense oligonucleotides) or at DNA level (by editing mutated sequences through the use of CRISPR/Cas). Other RNA approaches include the delivery of in vitro transcribed (IVT) mRNA or the use of oligonucleotides aptamers. Here we review these approaches and their translation into clinics trying to give a brief overview also on the difficulties to its application as well as the research that is being done to overcome them.
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Affiliation(s)
- Maria Francisca Coutinho
- Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge, Porto, Portugal
| | - Liliana Matos
- Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge, Porto, Portugal
| | - Juliana Inês Santos
- Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge, Porto, Portugal
| | - Sandra Alves
- Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge, Porto, Portugal.
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Afzal R, Firasat S, Kaul H, Ahmed B, Siddiqui SN, Zafar SN, Shahzadi M, Afshan K. Mutational analysis of the CYP1B1 gene in Pakistani primary congenital glaucoma patients: Identification of four known and a novel causative variant at the 3' splice acceptor site of intron 2. Congenit Anom (Kyoto) 2019; 59:152-161. [PMID: 30270463 DOI: 10.1111/cga.12312] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Revised: 09/25/2018] [Accepted: 09/25/2018] [Indexed: 01/06/2023]
Abstract
Primary congenital glaucoma (PCG) causes blindness in early age. It has an autosomal recessive pattern of inheritance, hence is more prevalent in populations with frequent consanguineous marriages that occur in the Pakistani population. Mutations in the CYP1B1 gene are commonly associated with PCG. The aim of the present study was to identify genetic mutations in the CYP1B1 gene in PCG cases belonging to 38 Pakistani families. DNA was extracted using blood samples collected from all enrolled patients, their available unaffected family members and controls. Direct sequencing of the CYP1B1 gene revealed a novel 3' splice acceptor site causative variant segregating in an autosomal recessive manner in a large consanguineous family with four PCG-affected individuals. The novel variant was not detected in 93 ethnically matched controls. Furthermore, four already reported mutations, including p.G61E, p.R355X, p.R368H, and p.R390H were also detected in patients belonging to nine different families. All identified causative variants were evaluated by computational programs, that is, SIFT, PolyPhen-2, and MutationTaster. Pathogenicity of the novel splice site variant identified in this study was analyzed by Human Splicing Finder and MaxEntScan. Ten out of 38 families with PCG had the disease due to CYP1B1 mutations, suggesting CYP1B1 was contributing to PCG in these Pakistani patients. Identification of this novel 3' splice acceptor site variant in intron 2 is the first report for the CYP1B1 gene contributing to genetic heterogeneity of disease.
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Affiliation(s)
- Rabia Afzal
- Department of Animal Sciences, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Sabika Firasat
- Department of Animal Sciences, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Haiba Kaul
- Genetics Division, Department of Livestock Production, University of Veterinary and Animal Sciences, Pattoki, Pakistan
| | - Bashir Ahmed
- Department of Animal Sciences, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Sorath N Siddiqui
- Department of Pediatric Ophthalmology and Strabismus, Al-Shifa Trust Eye Hospital, Rawalpindi, Pakistan
| | - Saemah N Zafar
- Department of Pediatric Ophthalmology and Strabismus, Al-Shifa Trust Eye Hospital, Rawalpindi, Pakistan
| | - Misbah Shahzadi
- Department of Animal Sciences, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Kiran Afshan
- Department of Animal Sciences, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
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Engel NW, Schliffke S, Schüller U, Frenzel C, Bokemeyer C, Kubisch C, Lessel D. Fatal Myelotoxicity Following Palliative Chemotherapy With Cisplatin and Gemcitabine in a Patient With Stage IV Cholangiocarcinoma Linked to Post Mortem Diagnosis of Fanconi Anemia. Front Oncol 2019; 9:420. [PMID: 31192125 PMCID: PMC6540739 DOI: 10.3389/fonc.2019.00420] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Accepted: 05/03/2019] [Indexed: 12/16/2022] Open
Abstract
Unrecognized genome instability syndromes can potentially impede the rational treatment of cancer in rare patients. Identification of cancer patients with a hereditary condition is a compelling necessity for oncologists, giving varying hypersensitivities to various chemotherapeutic agents or radiation, depending on the underlying genetic cause. Omission of genetic testing in the setting of an overlooked hereditary syndrome may lead to unexpected and unbearable toxicity from oncological standard approaches. We present a case of a 33-year-old man with an early-onset stage IV intrahepatic cholangiocarcinoma, who experienced unusual bone marrow failure and neutropenic fever syndrome as a consequence of palliative chemotherapy containing cisplatin and gemcitabine, leading to a fatal outcome on day 25 of his first chemotherapeutic cycle. The constellation of bone marrow failure after exposure to the platinum-based agent cisplatin, the presence of an early-onset solid malignancy and the critical appraisal of further phenotypical features raised suspicion of a hereditary genome instability syndrome. Whole-exome sequencing from buccal swab DNA enabled the post mortem diagnosis of Fanconi anemia, most likely linked to the fatal outcome due to utilization of the DNA crosslinking agent cisplatin. The patient's phenotype was exceptional, as he never displayed significant hematologic abnormalities, which is the hallmark of Fanconi anemia. As such, this case stresses the importance to at least question the possibility of a hereditary basis in cases of relatively early-onset malignancy before defining an oncological treatment strategy.
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Affiliation(s)
- Nils W Engel
- Department of Oncology, Haematology and Bone Marrow Transplantation with Section Pneumology, Hubertus Wald Tumorzentrum, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Simon Schliffke
- Department of Oncology, Haematology and Bone Marrow Transplantation with Section Pneumology, Hubertus Wald Tumorzentrum, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Ulrich Schüller
- Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.,Department of Pediatric Hematology and Oncology, University Medical Center, Hamburg-Eppendorf, Germany.,Research Institute Children's Cancer Center Hamburg, Hamburg, Germany
| | - Christian Frenzel
- Department of Oncology, Haematology and Bone Marrow Transplantation with Section Pneumology, Hubertus Wald Tumorzentrum, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Carsten Bokemeyer
- Department of Oncology, Haematology and Bone Marrow Transplantation with Section Pneumology, Hubertus Wald Tumorzentrum, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Christian Kubisch
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Davor Lessel
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
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Brahami N, Subramaniam S, Al-Ddafari MS, Elkaim C, Harmand PO, Sari BE, Lefranc G, Aribi M. Facial cutaneo-mucosal venous malformations can develop independently of mutation of TEK gene but may be associated with excessive expression of Src and p-Src. J Negat Results Biomed 2017; 16:9. [PMID: 28316284 PMCID: PMC5357811 DOI: 10.1186/s12952-017-0072-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Accepted: 02/16/2017] [Indexed: 12/11/2022] Open
Abstract
We aimed to search for mutations in the germline and somatic DNA of the TEK gene and to analyze the expression level of Src and phospho-Src (p-Src) in tumor and healthy tissues from patients with facial cutaneo-mucosal venous malformations (VMCM). Eligible patients from twelve families and thirty healthy controls were recruited respectively at the Departments of Stomatology and Oral Surgery, and Transfusion Medicine of Tlemcen University Medical Centre. Immunoblot analyses of Src and p-Src were performed after direct DNA sequencing. No somatic or germline mutations were found in all the 23 exons and their 5’ and 3’ intronic flanking regions, except for one case in which a c.3025+20-3025+22 del mutation was highlighted at the intron 15, both in the germline and somatic DNA. Additionally, elevated expression levels of Src and p-Src were observed only in the patient with such mutation. However, when normalized to β-actin, the overall relative expression levels of both Src and p-Src were significantly increased in VMCM tissues when compared to healthy tissues (for both comparisons, p <0.001). In conclusion, we confirm the outcomes of our previous work suggesting that VMCM can develop independently of mutation of the TEK gene. Additionally, the results for Src activity are of particular interest in the context of specific targeted therapies and biological diagnosis. Nevertheless, such a conclusion should be confirmed through a mechanistic study and/or in a satisfactory number of patients.
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Affiliation(s)
- Nabila Brahami
- Laboratory of Applied Molecular Biology and Immunology, University of Tlemcen, Imama-Mansourah, Rocade # 2, PO Box: 262, Tlemcen, 13000, Algeria
| | | | - Moudjahed Saleh Al-Ddafari
- Laboratory of Applied Molecular Biology and Immunology, University of Tlemcen, Imama-Mansourah, Rocade # 2, PO Box: 262, Tlemcen, 13000, Algeria
| | - Cecile Elkaim
- Laboratory of Cell and Hormonal Biology, Arnaud de Villeneuve Hospital, 34295, Montpellier, France
| | - Pierre-Olivier Harmand
- Laboratory of Cell and Hormonal Biology, Arnaud de Villeneuve Hospital, 34295, Montpellier, France
| | - Badr-Eddine Sari
- Laboratory of Applied Molecular Biology and Immunology, University of Tlemcen, Imama-Mansourah, Rocade # 2, PO Box: 262, Tlemcen, 13000, Algeria.,Stomatology and Oral Surgery Department of Tlemcen, University Medical Centre, 13000, Tlemcen, Algeria
| | - Gérard Lefranc
- Laboratoire d'Immunogénétique Moléculaire, Institut de Génétique Humaine, CNRS UPR 1142, et Université de Montpellier, Montpellier, 34095, Cedex 5, France
| | - Mourad Aribi
- Laboratory of Applied Molecular Biology and Immunology, University of Tlemcen, Imama-Mansourah, Rocade # 2, PO Box: 262, Tlemcen, 13000, Algeria.
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11
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Sasai H, Aoyama Y, Otsuka H, Abdelkreem E, Nakama M, Hori T, Ohnishi H, Turner L, Fukao T. Single-nucleotide substitution T to A in the polypyrimidine stretch at the splice acceptor site of intron 9 causes exon 10 skipping in the ACAT1 gene. Mol Genet Genomic Med 2017; 5:177-184. [PMID: 28361105 PMCID: PMC5370231 DOI: 10.1002/mgg3.275] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2016] [Revised: 01/03/2017] [Accepted: 12/20/2016] [Indexed: 02/05/2023] Open
Abstract
Background β‐ketothiolase (T2, gene symbol ACAT1) deficiency is an autosomal recessive disorder, affecting isoleucine and ketone body metabolism. We encountered a patient (GK03) with T2 deficiency whose T2 mRNA level was <10% of the control, but in whom a previous routine cDNA analysis had failed to find any mutations. Genomic PCR‐direct sequencing showed homozygosity for c.941‐9T>A in the polypyrimidine stretch at the splice acceptor site of intron 9 of ACAT1. Initially, we regarded this variant as not being disease‐causing by a method of predicting the effect of splicing using in silico tools. However, based on other findings of exon 10 splicing, we eventually hypothesized that this mutation causes exon 10 skipping. Methods cDNA analysis was performed using GK03's fibroblasts treated with/without cycloheximide (CHX), since exon 10 skipping caused a frameshift and nonsense‐mediated mRNA decay (NMD). Minigene splicing experiment was done to confirm aberrant splicing. Results cDNA analysis using fibroblasts cultured with cycloheximide indeed showed the occurrence of exon 10 skipping. A minigene splicing experiment clearly showed that the c.941‐9T>A mutant resulted in transcripts with exon 10 skipping. There are few reports describing that single‐nucleotide substitutions in polypyrimidine stretches of splice acceptor sites cause aberrant splicing. Conclusion We showed that c.941‐9T>A induces aberrant splicing in the ACAT1 gene. Our ability to predict the effects of mutations on splicing using in silico tools is still limited. cDNA analysis and minigene splicing experiments remain useful alternatives to reveal splice defects.
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Affiliation(s)
- Hideo Sasai
- Department of Pediatrics Graduate School of Medicine Gifu University Gifu Japan
| | - Yuka Aoyama
- Department of PediatricsGraduate School of MedicineGifu UniversityGifuJapan; Department of Biomedical SciencesCollege of Life and Health SciencesChubu UniversityKasugaiJapan
| | - Hiroki Otsuka
- Department of Pediatrics Graduate School of Medicine Gifu University Gifu Japan
| | - Elsayed Abdelkreem
- Department of PediatricsGraduate School of MedicineGifu UniversityGifuJapan; Department of PediatricsFaculty of MedicineSohag UniversitySohagEgypt
| | - Mina Nakama
- Division of Clinical Genetics Gifu University Hospital Gifu Japan
| | - Tomohiro Hori
- Department of Pediatrics Graduate School of Medicine Gifu University Gifu Japan
| | - Hidenori Ohnishi
- Department of Pediatrics Graduate School of Medicine Gifu University Gifu Japan
| | - Lesley Turner
- Discipline of Genetics Memorial University of Newfoundland St John's NF Canada
| | - Toshiyuki Fukao
- Department of PediatricsGraduate School of MedicineGifu UniversityGifuJapan; Division of Clinical GeneticsGifu University HospitalGifuJapan
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12
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Matos L, Canals I, Dridi L, Choi Y, Prata MJ, Jordan P, Desviat LR, Pérez B, Pshezhetsky AV, Grinberg D, Alves S, Vilageliu L. Therapeutic strategies based on modified U1 snRNAs and chaperones for Sanfilippo C splicing mutations. Orphanet J Rare Dis 2014; 9:180. [PMID: 25491247 PMCID: PMC4279800 DOI: 10.1186/s13023-014-0180-y] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2014] [Accepted: 11/04/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Mutations affecting RNA splicing represent more than 20% of the mutant alleles in Sanfilippo syndrome type C, a rare lysosomal storage disorder that causes severe neurodegeneration. Many of these mutations are localized in the conserved donor or acceptor splice sites, while few are found in the nearby nucleotides. METHODS In this study we tested several therapeutic approaches specifically designed for different splicing mutations depending on how the mutations affect mRNA processing. For three mutations that affect the donor site (c.234 + 1G > A, c.633 + 1G > A and c.1542 + 4dupA), different modified U1 snRNAs recognizing the mutated donor sites, have been developed in an attempt to rescue the normal splicing process. For another mutation that affects an acceptor splice site (c.372-2A > G) and gives rise to a protein lacking four amino acids, a competitive inhibitor of the HGSNAT protein, glucosamine, was tested as a pharmacological chaperone to correct the aberrant folding and to restore the normal trafficking of the protein to the lysosome. RESULTS Partial correction of c.234 + 1G > A mutation was achieved with a modified U1 snRNA that completely matches the splice donor site suggesting that these molecules may have a therapeutic potential for some splicing mutations. Furthermore, the importance of the splice site sequence context is highlighted as a key factor in the success of this type of therapy. Additionally, glucosamine treatment resulted in an increase in the enzymatic activity, indicating a partial recovery of the correct folding. CONCLUSIONS We have assayed two therapeutic strategies for different splicing mutations with promising results for the future applications.
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Affiliation(s)
- Liliana Matos
- Department of Human Genetics, Research and Development Unit, INSA, Porto, Portugal. .,Department of Biology, Faculty of Sciences, Porto, Portugal.
| | - Isaac Canals
- Departament de Genètica, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain. .,CIBER de Enfermedades Raras (CIBERER), Madrid, Spain. .,Institut de Biomedicina de la Universitat de Barcelona (IBUB), Barcelona, Spain.
| | - Larbi Dridi
- Department of Medical Genetics, Sainte-Justine University Hospital Centre, University of Montreal, Montreal, Canada.
| | - Yoo Choi
- Department of Medical Genetics, Sainte-Justine University Hospital Centre, University of Montreal, Montreal, Canada.
| | - Maria João Prata
- Department of Biology, Faculty of Sciences, Porto, Portugal. .,IPATIMUP, Porto, Portugal.
| | - Peter Jordan
- Department of Human Genetics, Research and Development Unit, INSA, Lisbon, Portugal.
| | - Lourdes R Desviat
- CIBER de Enfermedades Raras (CIBERER), Madrid, Spain. .,Centro de Diagnóstico de Enfermedades Moleculares, Centro de Biología Molecular Severo Ochoa, UAM-CSIC, Universidad Autónoma de Madrid, Madrid, Spain.
| | - Belén Pérez
- CIBER de Enfermedades Raras (CIBERER), Madrid, Spain. .,Centro de Diagnóstico de Enfermedades Moleculares, Centro de Biología Molecular Severo Ochoa, UAM-CSIC, Universidad Autónoma de Madrid, Madrid, Spain.
| | - Alexey V Pshezhetsky
- Department of Medical Genetics, Sainte-Justine University Hospital Centre, University of Montreal, Montreal, Canada. .,Department of Anatomy and Cell Biology, Faculty of Medicine, McGill University, Montreal, Canada.
| | - Daniel Grinberg
- Departament de Genètica, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain. .,CIBER de Enfermedades Raras (CIBERER), Madrid, Spain. .,Institut de Biomedicina de la Universitat de Barcelona (IBUB), Barcelona, Spain.
| | - Sandra Alves
- Department of Human Genetics, Research and Development Unit, INSA, Porto, Portugal.
| | - Lluïsa Vilageliu
- Departament de Genètica, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain. .,CIBER de Enfermedades Raras (CIBERER), Madrid, Spain. .,Institut de Biomedicina de la Universitat de Barcelona (IBUB), Barcelona, Spain.
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13
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Van Neste L, Van Criekinge W. We are all individuals... bioinformatics in the personalized medicine era. Cell Oncol (Dordr) 2014; 38:29-37. [PMID: 25204962 DOI: 10.1007/s13402-014-0195-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/26/2014] [Indexed: 12/16/2022] Open
Abstract
The medical landscape is evolving at a rapid pace, creating the opportunity for more personalized patient treatment and shifting the way healthcare is approached and thought about. With the availability of (epi)genome-wide, transcriptomic and proteogenomic profiling techniques detailed characterization of a disease at the level of the individual is now possible, offering the opportunity for truly tailored approaches for treatment and patient care. While improvements are still expected, the techniques and the basic analytical tools have reached a state that these can be efficiently deployed in both routine research and clinical practice. Still, some major challenges remain. Notably, holistic approaches, integrating data from several sources, e.g. genomic and epigenomic, will increase the understanding of the underlying biological concepts and provide insight into the causes, effects and effective solutions. However, creating and validating such a knowledge base, potentially for different levels of expertise, and integrating several data points into meaningful information is not trivial.
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Affiliation(s)
- Leander Van Neste
- Department of Pathology, School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, The Netherlands,
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