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Koko M, Elseed MA, Mohammed IN, Hamed AA, Abd Allah ASI, Yahia A, Siddig RA, Altmüller J, Toliat MR, Elmahdi EO, Amin M, Ahmed EA, Eltazi IZM, Elmugadam FA, Abdelgadir WA, Eltaraifee E, Ibrahim MOM, Ali NMH, Malik HM, Babai AM, Bakhit YH, Nürnberg P, Ibrahim ME, Salih MA, Schubert J, Elsayed LEO, Lerche H. Bi-allelic PRRT2 variants may predispose to Self-limited Familial Infantile Epilepsy. Eur J Hum Genet 2024:10.1038/s41431-024-01541-x. [PMID: 38316952 DOI: 10.1038/s41431-024-01541-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 10/25/2023] [Accepted: 01/10/2024] [Indexed: 02/07/2024] Open
Abstract
Heterozygous PRRT2 variants are frequently implicated in Self-limited Infantile Epilepsy, whereas homozygous variants are so far linked to severe presentations including developmental and epileptic encephalopathy, movement disorders, and intellectual disability. In a study aiming to explore the genetics of epilepsy in the Sudanese population, we investigated several families including a consanguineous family with three siblings diagnosed with self-limited infantile epilepsy. We evaluated both dominant and recessive inheritance using whole exome sequencing and genomic arrays. We identified a pathogenic homozygous splice-site variant in the first intron of PRRT2 [NC_000016.10(NM_145239.3):c.-65-1G > A] that segregated with the phenotype in this family. This work taps into the genetics of epilepsy in an underrepresented African population and suggests that the phenotypes of homozygous PRRT2 variants may include milder epilepsy presentations without movement disorders.
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Affiliation(s)
- Mahmoud Koko
- Department of Neurology and Epileptology, Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany
| | - Maha A Elseed
- Department of Pediatrics, Faculty of Medicine, University of Khartoum, Khartoum, Sudan
| | - Inaam N Mohammed
- Department of Pediatrics, Faculty of Medicine, University of Khartoum, Khartoum, Sudan
| | - Ahlam A Hamed
- Department of Pediatrics, Faculty of Medicine, University of Khartoum, Khartoum, Sudan
| | - Amal S I Abd Allah
- Neurogenetics Research Group, Faculty of Medicine, University of Khartoum, Khartoum, Sudan
| | - Ashraf Yahia
- Department of Biochemistry, Faculty of Medicine, University of Khartoum, Khartoum, Sudan
| | - Rayan A Siddig
- Neurogenetics Research Group, Faculty of Medicine, University of Khartoum, Khartoum, Sudan
| | - Janine Altmüller
- Cologne Center for Genomics, University of Cologne, Cologne, Germany
- Berlin Institute of Health at Charité- Universitätsmedizin Berlin, Berlin, Germany
- Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | | | - Esra O Elmahdi
- Neurogenetics Research Group, Faculty of Medicine, University of Khartoum, Khartoum, Sudan
| | - Mutaz Amin
- Department of Biochemistry, Faculty of Medicine, Al-Neelain University, Khartoum, Sudan
| | - Elhami A Ahmed
- UNESCO Chair on Bioethics, Faculty of Medicine, University of Khartoum, Khartoum, Sudan
| | - Isra Z M Eltazi
- Department of Medicine, Faculty of Medicine, University of Khartoum, Khartoum, Sudan
| | - Fatima A Elmugadam
- Neurogenetics Research Group, Faculty of Medicine, University of Khartoum, Khartoum, Sudan
| | - Wasma A Abdelgadir
- Department of Biochemistry and Molecular Biology, Faculty of Sciences and Technology, Al-Neelain University, Khartoum, Sudan
| | - Esraa Eltaraifee
- Neurogenetics Research Group, Faculty of Medicine, University of Khartoum, Khartoum, Sudan
| | - Mohamed O M Ibrahim
- Department of Biochemistry, Faculty of Medicine, Sudan University of Science and Technology, Khartoum, Sudan
| | - Nabila M H Ali
- Neurogenetics Research Group, Faculty of Medicine, University of Khartoum, Khartoum, Sudan
| | - Hiba M Malik
- Neurogenetics Research Group, Faculty of Medicine, University of Khartoum, Khartoum, Sudan
| | - Arwa M Babai
- Neurogenetics Research Group, Faculty of Medicine, University of Khartoum, Khartoum, Sudan
| | - Yousuf H Bakhit
- Department of Neurology, Neurobiology Division, University Hospital Bonn, Bonn, Germany
| | - Peter Nürnberg
- Cologne Center for Genomics, University of Cologne, Cologne, Germany
| | - Muntaser E Ibrahim
- Department of Molecular Biology, Institute of Endemic Diseases, University of Khartoum, Khartoum, Sudan
| | - Mustafa A Salih
- Division of Pediatric Neurology, Department of Pediatrics, College of Medicine, King Saud University, Riyadh, Saudi Arabia
- Consultant Pediatric Neurologist, Health Sector, King Abdulaziz City for Science and Technology (KACST), Riyadh, Saudi Arabia
| | - Julian Schubert
- Department of Neurology and Epileptology, Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany
| | - Liena E O Elsayed
- Department of Basic Sciences, College of Medicine, Princess Nourah bint Abdulrahman University, P.O.Box 84428, Riyadh, 11671, Saudi Arabia.
| | - Holger Lerche
- Department of Neurology and Epileptology, Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany
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Jang EJ, Kim JS, Choi SA, Yee J, Song TJ, Park J, Gwak HS. Construction of a risk scoring system using clinical factors and RYR2 polymorphisms for bleeding complications in patients on direct oral anticoagulants. Front Pharmacol 2023; 14:1290785. [PMID: 38034995 PMCID: PMC10684747 DOI: 10.3389/fphar.2023.1290785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Accepted: 10/30/2023] [Indexed: 12/02/2023] Open
Abstract
Introduction: Bleeding is one of the most undesirable complications of direct oral anticoagulants (DOACs). While the ryanodine receptor (RYR2) has been related to cardiac diseases, research on bleeding complications is lacking. This study aimed to elucidate the association between RYR2 and bleeding risk to develop the risk scoring system in patients treated with DOACs. Methods: This study was a retrospective analysis of prospectively collected samples. We selected ten SNPs within the RYR2 gene, and two models were constructed (Model I: demographic factors only, Model II: demographic and genetic factors) in multivariable analysis. Independent risk factors for bleeding were used to develop a risk scoring system. Results: A total of 447 patients were included, and 49 experienced either major bleeding or clinically relevant non-major bleeding. In Model I, patients using rivaroxaban and experiencing anemia exhibited an increased bleeding risk after adjusting for covariates. Upon incorporating genetic factors into Model I, a significant association with bleeding was also observed in cases of overdosing on DOACs and in patients with a creatinine clearance (CrCl) < 30 mL/min, in addition to rivaroxaban and anemia (Model II). Among genetic factors, RYR2 rs12594 GG, rs17682073 AA, rs3766871 GG, and rs6678625 T alleles were associated with bleeding complications. The area under the receiver operating characteristic curve (AUROC) of Model I was 0.670, whereas that of Model II increased to 0.803, demonstrating better performance with the inclusion of genetic factors. Using the significant variables in Model II, a risk scoring system was constructed. The predicted bleeding risks for scores of 0, 1-2, 3-4, 5-6, 7-8, and 9-10 points were 0%, 1.2%, 4.6%, 15.7%, 41.7%, and 73.3%, respectively. Conclusion: This study revealed an association between RYR2 and bleeding complications among patients taking DOACs and established a risk scoring system to support individualized DOAC treatment for these patients.
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Affiliation(s)
- Eun Jeong Jang
- College of Pharmacy and Graduate School of Pharmaceutical Sciences, Ewha Womans University, Seoul, Republic of Korea
| | - Jung Sun Kim
- College of Pharmacy and Graduate School of Pharmaceutical Sciences, Ewha Womans University, Seoul, Republic of Korea
| | - Seo A. Choi
- College of Pharmacy and Graduate School of Pharmaceutical Sciences, Ewha Womans University, Seoul, Republic of Korea
| | - Jeong Yee
- College of Pharmacy and Graduate School of Pharmaceutical Sciences, Ewha Womans University, Seoul, Republic of Korea
| | - Tae-Jin Song
- Department of Neurology, Ewha Womans University Seoul Hospital, Ewha Womans University College of Medicine, Seoul, Republic of Korea
| | - Junbeom Park
- Division of Cardiology, Department of Internal Medicine, Ewha Womans University Mokdong Hospital, Ewha Womans University College of Medicine, Seoul, Republic of Korea
| | - Hye Sun Gwak
- College of Pharmacy and Graduate School of Pharmaceutical Sciences, Ewha Womans University, Seoul, Republic of Korea
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Kim JS, Lee S, Yee J, Park K, Jang EJ, Chang BC, Gwak HS. Novel Gene Polymorphisms for Stable Warfarin Dose in a Korean Population: Genome-Wide Association Study. Biomedicines 2023; 11:2308. [PMID: 37626805 PMCID: PMC10452379 DOI: 10.3390/biomedicines11082308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 08/03/2023] [Accepted: 08/16/2023] [Indexed: 08/27/2023] Open
Abstract
Warfarin has a narrow therapeutic window and high intra- and inter-individual variability. Considering that many published papers on genotype-guided dosing are derived from European populations, the aim of this study was to investigate novel genetic variants associated with the variability of stable warfarin dose in the Korean population with cardiac valve replacement, using the GWAS approach. This retrospective cohort study was performed from January 1982 to December 2020 at the Severance Cardiovascular Hospital of Yonsei University College of Medicine. GWAS was performed to identify associations between genotypes and the warfarin maintenance dose, by comparing the allele frequency of genetic variants between individuals. Then, the extent of genetic and non-genetic factors on the dose variability was determined by multivariable regression analysis. The study enrolled 214 participants, and the most robust signal cluster was detected on chromosome 16 around VKORC1. Followed by VKORC1, three novel variants (NKX2-6 rs310279, FRAS1 rs4386623, and FAM201A rs1890109) showed an association with stable warfarin dose requirement in univariate analysis. The algorithm was constructed by using multivariable analysis that includes genetic and non-genetic factors, and it could explain 58.5% of the variations in stable warfarin doses. In this variability, VKORC1 rs9934438 and FRAS1 rs4386623 accounted for 33.0% and 9.9%, respectively. This GWAS analysis identified the fact that three novel variants (NKX2-6 rs310279, FRAS1 rs4386623, and FAM201A rs1890109) were associated with stable warfarin doses. Additional research is necessary to validate the results and establish personalized treatment strategies for the Korean population.
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Affiliation(s)
- Jung Sun Kim
- Graduate School of Pharmaceutical Sciences, College of Pharmacy, Ewha Womans University, Seoul 03760, Republic of Korea; (J.S.K.); (J.Y.); (E.J.J.)
| | - Sak Lee
- Department of Thoracic and Cardiovascular Surgery, Cardiovascular Research Institute, Yonsei University College of Medicine, Seoul 03722, Republic of Korea;
| | - Jeong Yee
- Graduate School of Pharmaceutical Sciences, College of Pharmacy, Ewha Womans University, Seoul 03760, Republic of Korea; (J.S.K.); (J.Y.); (E.J.J.)
| | - Kyemyung Park
- Department of Biomedical Engineering, College of Information and Biotechnology, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea;
| | - Eun Jeong Jang
- Graduate School of Pharmaceutical Sciences, College of Pharmacy, Ewha Womans University, Seoul 03760, Republic of Korea; (J.S.K.); (J.Y.); (E.J.J.)
| | - Byung Chul Chang
- Department of Thoracic and Cardiovascular Surgery, Cardiovascular Research Institute, Yonsei University College of Medicine, Seoul 03722, Republic of Korea;
- Department of Thoracic and Cardiovascular Surgery, Bundang CHA Medical Center, CHA University, Seongnam 13496, Republic of Korea
| | - Hye Sun Gwak
- Graduate School of Pharmaceutical Sciences, College of Pharmacy, Ewha Womans University, Seoul 03760, Republic of Korea; (J.S.K.); (J.Y.); (E.J.J.)
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Kim JS, Kim JW, Yee J, Kim SJ, Chung JE, Gwak HS. Interactive Associations between PPARγ and PPARGC1A and Bisphosphonate-Related Osteonecrosis of the Jaw in Patients with Osteoporosis. Pharmaceuticals (Basel) 2023; 16:1035. [PMID: 37513946 PMCID: PMC10386002 DOI: 10.3390/ph16071035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 07/18/2023] [Accepted: 07/20/2023] [Indexed: 07/30/2023] Open
Abstract
Bisphosphonate-related osteonecrosis of the jaw (BRONJ) is a rare but severe adverse effect that can occur as a result of bisphosphonate treatment. This study aimed to examine the relationship between PPARγ and PPARGC1A polymorphisms and the BRONJ development in female osteoporosis patients undergoing bisphosphonate treatment. We prospectively conducted this nested case-control study at the Ewha Womans University Mokdong Hospital between 2014 and 2018. We assessed five single-nucleotide polymorphisms (SNPs) of PPARγ and six SNPs of PPARGC1A and performed a multivariable logistic regression analysis to determine the independent risk factors for developing BRONJ. There were a total of 123 patients included in this study and 56 patients (45.5%) developed BRONJ. In the univariate analysis, PPARGC1A rs2946385 and rs10020457 polymorphisms were significantly associated with BRONJ (p = 0.034, p = 0.020, respectively), although the results were not statistically significant in the multivariable analysis. Patients with the combined genotypes of GG in both PPARγ rs1151999 and PPARGC1A rs2946385 showed a 3.03-fold higher risk of BRONJ compared to individuals with other genotype combinations after adjusting for confounders (95% confidence interval (CI): 1.01-9.11). Old age (≥70 years) and duration of bisphosphonate use (≥60 months) increased the risk of BRONJ. The area under the receiver operating characteristic curve for the predicted probability was 0.78 (95% CI: 0.69-0.87, p < 0.001), demonstrating a satisfactory level of discriminatory power. Our study elucidated that PPARγ and PPARGC1A polymorphisms were interactively associated with BRONJ development. These results have potential implications for tailoring personalized treatments for females undergoing bisphosphonate therapy for osteoporosis.
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Affiliation(s)
- Jung Sun Kim
- Graduate School of Pharmaceutical Sciences, College of Pharmacy, Ewha Womans University, 52 Ewhayeodae-gil, Seodaemun-gu, Seoul 03760, Republic of Korea
| | - Jin Woo Kim
- Department of Oral and Maxillofacial Surgery, School of Medicine, Ewha Womans University Medical Center, Mokdong Hospital, 1071 Anyangcheon-ro, Yangcheon-gu, Seoul 07985, Republic of Korea
| | - Jeong Yee
- Graduate School of Pharmaceutical Sciences, College of Pharmacy, Ewha Womans University, 52 Ewhayeodae-gil, Seodaemun-gu, Seoul 03760, Republic of Korea
| | - Sun Jong Kim
- Department of Oral and Maxillofacial Surgery, School of Medicine, Ewha Womans University Medical Center, Mokdong Hospital, 1071 Anyangcheon-ro, Yangcheon-gu, Seoul 07985, Republic of Korea
| | - Jee Eun Chung
- Institute of Pharmaceutical Science and Technology, College of Pharmacy, Hanyang University, 55 Hanyangdaehak-ro, Sangnok-gu, Ansan 15588, Republic of Korea
| | - Hye Sun Gwak
- Graduate School of Pharmaceutical Sciences, College of Pharmacy, Ewha Womans University, 52 Ewhayeodae-gil, Seodaemun-gu, Seoul 03760, Republic of Korea
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Kim H, Bae S, Yoon HY, Yee J, Gwak HS. Association of the SLC47A1 Gene Variant With Responses to Metformin Monotherapy in Drug-naive Patients With Type 2 Diabetes. J Clin Endocrinol Metab 2022; 107:2684-2690. [PMID: 35639991 DOI: 10.1210/clinem/dgac333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/19/2021] [Indexed: 11/19/2022]
Abstract
CONTEXT Although metformin is the first-line treatment for type 2 diabetes, the blood sugar-lowering effect of metformin varies among populations. SLC47A1 plays an important role in metformin pharmacokinetics and pharmacodynamics. OBJECTIVE We performed a systematic review and meta-analysis to investigate the association between SLC47A1 rs2289669 (G > A) and the metformin response in drug-naive patients with type 2 diabetes. METHODS Studies published until January 27, 2022, were retrieved from Cochrane CENTRAL, Embase, PubMed, and Web of Science. Two reviewers independently screened titles, abstracts, and full-text articles. Studies conducted in newly diagnosed or drug-naive patients with type 2 diabetes who received metformin monotherapy were included. A total of 6 studies involving 953 patients were included in this meta-analysis. We extracted the study characteristics and changes in glycated hemoglobin (HbA1c) levels before and after treatment according to the SLC47A1 rs2289669 genotype. Changes in HbA1c levels were analyzed using mean differences (MDs) and 95% CIs. SLC47A1 rs2289669 was associated with changes in HbA1c levels (A carrier vs GG; MD = -0.55; 95% CI, -0.91 to - 0.20; I² = 63%). The sensitivity analysis yielded similar results to the main analysis (MD range, -0.64 to -0.37). When comparing all 3 genotypes, there were significant differences in HbA1c level changes between AA vs GG and GA vs GG, but not in GA vs AA. CONCLUSION This meta-analysis showed that SLC47A1 rs2289669 is associated with the glycemic response to metformin in drug-naive patients with type 2 diabetes.
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Affiliation(s)
- Hamin Kim
- College of Pharmacy and Graduate School of Pharmaceutical Sciences, Ewha Womans University, Seoul, Republic of Korea
| | - Suhyun Bae
- College of Pharmacy and Graduate School of Pharmaceutical Sciences, Ewha Womans University, Seoul, Republic of Korea
| | - Ha Young Yoon
- College of Pharmacy and Graduate School of Pharmaceutical Sciences, Ewha Womans University, Seoul, Republic of Korea
| | - Jeong Yee
- College of Pharmacy and Graduate School of Pharmaceutical Sciences, Ewha Womans University, Seoul, Republic of Korea
| | - Hye Sun Gwak
- College of Pharmacy and Graduate School of Pharmaceutical Sciences, Ewha Womans University, Seoul, Republic of Korea
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The pathogenicity classification of PAH gene variants in the Iranian population. Comput Biol Chem 2022; 98:107665. [PMID: 35339094 DOI: 10.1016/j.compbiolchem.2022.107665] [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: 12/23/2021] [Revised: 02/11/2022] [Accepted: 03/10/2022] [Indexed: 12/29/2022]
Abstract
Till now not many studies have been conducted to classify PAH gene variants according to American College of Medical Genetics and Genomics (ACMG-AMP) guidelines. The aim of this study was to collect all PAH gene variants reported among Iranian population and investigate their pathogenicity based on ACMG-AMP guidelines. Systematic collection of PAH gene variants, verification of variants, in silico analysis, and application of ACMG-AMP guidelines were the main steps in performing the present study. A total of 267 unique variants were identified; according to ACMG-AMP guidelines, 90, 40, 71, 14, and 52 variants were classified as pathogenic (P), likely pathogenic (LP), variant of uncertain significance (VUS), likely benign (LB), and benign (B), respectively. The need to pay more attention to synonymous and missense variants with low or no impact on protein function as well as intronic variants, whether they are deep or are close to intron/exon boundaries, was a highlight of this study. Due to the fact that few functional studies are performed on these variants, it is suggested that they be analyzed first using bioinformatics tools, and if positive results are obtained, then functional studies can be designed.
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Wang H, Jiang Y. SRp20: A potential therapeutic target for human tumors. Pathol Res Pract 2021; 224:153444. [PMID: 34126370 DOI: 10.1016/j.prp.2021.153444] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Revised: 04/11/2021] [Accepted: 04/11/2021] [Indexed: 12/12/2022]
Abstract
As an important member of SR protein family, SRp20 plays a crucial role in alternative splicing. It not only participates in cell cycle regulation, export of mRNA, cleaving of primary microRNAs, homologous recombination-mediated DNA repair, cellular senescence and apoptosis, but also gets involved in the integrity and pluripotency of genome. Alternative splicing maintains a strict balance in the body to ensure the normal physiological function of cells. Once the balance is broken, diseases, even tumors, will follow. Through the analysis of SRp20-related articles, we found that Alzheimer's disease, glaucoma, bipolar disorder and other diseases have a certain relationship with SRp20. More importantly, SRp20 is closely related to the occurrence, proliferation, invasion and metastasis of various tumors, as well as chemotherapy resistance. Some SRp20 inhibitors have shown significant anticancer efficacy, suggesting a potential therapeutic strategy for tumors.
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Affiliation(s)
- Han Wang
- Department of Pathology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital & Shenzhen Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Shenzhen, China
| | - Yanxia Jiang
- Department of Pathology, The Affiliated Hospital of Qingdao University, Qingdao, China.
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Yoon HY, Park JY, Yee J, Hwang HS, Chung JE, Lee KE, Kim YJ, Gwak HS. Effects of KCNMB2 gene polymorphisms on ritodrine therapy outcomes in women with preterm labor. Pharmacogenet Genomics 2020; 30:124-130. [PMID: 32371615 DOI: 10.1097/fpc.0000000000000404] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
OBJECTIVE The present prospective follow-up study aimed to evaluate the effects of KCNMB2 gene polymorphisms on ritodrine efficacy and adverse drug events (ADEs) in patients with preterm labor. METHODS A total of 163 preterm labor patients were included in this single-center study. Nine single nucleotide polymorphisms (SNPs) in the KCNMB2 gene (rs10936979, rs7624046, rs7429015, rs7625907, rs6443559, rs9839376, rs9637454, rs11918114, and rs1382045) were assessed. The primary endpoint was time to delivery, and the secondary endpoint was ritodrine-induced ADEs. RESULTS Patients with variant homozygotes of two SNPs (rs7624046 and rs9839376), which were in linkage disequilibrium, showed 2.06 [95% confidence interval (CI), 1.14-3.73] and 2.68 (95% CI, 1.16-6.20) times the hazard of time to delivery compared to wild-type allele carriers, respectively. Among demographic characteristics, gestational age at start of drug therapy and modified Bishop score were significant factors for time to delivery. Regarding safety outcomes, patients with variant homozygotes of rs7625907 had fewer ADEs compared to those with other genotypes (odds ratio, 0.32; 95% CI, 0.13-0.83). CONCLUSION This pharmacogenomic study suggests that ritodrine efficacy and ADEs are associated with KCNMB2 gene polymorphisms in patients with preterm labor.
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Affiliation(s)
- Ha Young Yoon
- College of Pharmacy and Graduate School of Pharmaceutical Sciences, Ewha Womans University
| | - Jin Young Park
- College of Pharmacy and Division of Life & Pharmaceutical Sciences, Ewha Womans University
| | - Jeong Yee
- College of Pharmacy and Division of Life & Pharmaceutical Sciences, Ewha Womans University
| | - Han Sung Hwang
- Department of Obstetrics and Gynecology, Konkuk University Medical Center, Konkuk University School of Medicine, Seoul, Republic of Korea
| | - Jee Eun Chung
- College of Pharmacy and Institute of Pharmaceutical Science and Technology, Hanyang University, Ansan
| | - Kyung Eun Lee
- College of Pharmacy, Chungbuk National University, Chengju, Chungbuk
| | - Young Ju Kim
- Department of Obstetrics and Gynecology, Ewha Womans University School of Medicine, Seoul, Republic of Korea
| | - Hye Sun Gwak
- College of Pharmacy and Graduate School of Pharmaceutical Sciences, Ewha Womans University
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Han JM, Yee J, Chung JE, Lee KE, Park K, Gwak HS. Effects of cytochrome P450 oxidoreductase genotypes on the pharmacokinetics of amlodipine in healthy Korean subjects. Mol Genet Genomic Med 2020; 8:e1201. [PMID: 32134573 PMCID: PMC7216797 DOI: 10.1002/mgg3.1201] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Revised: 02/16/2020] [Accepted: 02/21/2020] [Indexed: 01/26/2023] Open
Abstract
BACKGROUND The aim of this study was to investigate the effects of P450 oxidoreductase (POR) genetic polymorphisms on the pharmacokinetic parameters of amlodipine. METHODS After a single 10-mg dose of amlodipine administration, 25 healthy male subjects completed genotyping for 12 single nucleotide polymorphisms (SNPs) of the POR genes, cytochrome P450 (CYP)3A4 g.25343G>A (CYP3A4*1G), and CYP3A5 g.12083G>A (CYP3A5*3). Stratified analysis and in silico analysis to predict the possible effects of given variants on splicing were performed. RESULTS The maximum blood concentration (Cmax ) of amlodipine in carriers of g.57332T>C and g.56551G>A SNPs of the POR gene was statistically significantly different. In addition, T-allele carriers of g.57332T>C had a 21% higher Cmax than those with the CC genotype (p = .007). Subjects who carried the wild-type g.56551G>A allele also had a 1.12-fold significantly higher Cmax than subjects with mutant-type homozygous carriers (p = .033). In stratified analyses, g.57332T>C was significantly associated with a 1.3-fold increase in Cmax value in T-allele carriers compared with subjects with the CC genotype in CYP3A4 and CYP3A5 expressers. POR g.57332T>C increased the score above the threshold in both ESEfinder 3.0 and HSF 3.1. CONCLUSION This study identified a novel SNP of the POR gene, which affected amlodipine metabolism and may reduce interindividual variation in responses to amlodipine.
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Affiliation(s)
- Ji Min Han
- College of Pharmacy and Graduate School of Pharmaceutical Sciences, Ewha Womans University, Seoul, Republic of Korea
| | - Jeong Yee
- College of Pharmacy and Graduate School of Pharmaceutical Sciences, Ewha Womans University, Seoul, Republic of Korea
| | - Jee Eun Chung
- College of Pharmacy, Hanyang University, Ansan, Republic of Korea
| | - Kyung Eun Lee
- College of Pharmacy, Chungbuk National University, Cheongju-si, Republic of Korea
| | - Kyungsoo Park
- Department of Pharmacology, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Hye Sun Gwak
- College of Pharmacy and Graduate School of Pharmaceutical Sciences, Ewha Womans University, Seoul, Republic of Korea
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Influence of GRK5 gene polymorphisms on ritodrine efficacy and adverse drug events in preterm labor treatment. Sci Rep 2020; 10:1351. [PMID: 31992805 PMCID: PMC6987149 DOI: 10.1038/s41598-020-58348-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Accepted: 01/14/2020] [Indexed: 11/09/2022] Open
Abstract
The present prospective follow-up study aimed to evaluate the effects of GRK5 polymorphisms on ritodrine efficacy and adverse drug events (ADEs) in pregnant women undergoing preterm labor. A total of 162 women undergoing preterm labor were included in the study. Seven single nucleotide polymorphisms (SNPs) in the GRK5 gene (rs915120, rs2230345, rs2230349, rs7923896, rs1020672, rs4752308, and rs4752292) were assessed. Homozygous variant carriers of rs4752292 and rs1020672 had 0.6 times the hazard of delivery compared to wild-type allele carriers (95% confidence interval [CI], 0.41~0.99 and 0.38~0.99, respectively). In addition, homozygous variant carriers of rs4752292 and rs1020672 had 2.4-fold more (95% CI, 1.10~4.98) and 2.3-fold more (95% CI, 1.04~5.06) ADEs compared to those with the wild-type homozygotes, respectively. Among demographic variables, gestational age and modified Bishop score were significant factors associated with time to delivery, while body weight and maximum ritodrine infusion rate were significant factors associated with ADEs. In silico analysis showed that both rs4752292 and rs1020672 had the potential to affect mRNA splicing by alteration of splicing motifs. The present study shows that ritodrine efficacy and ADEs are associated with GRK5 gene polymorphisms in pregnant women undergoing preterm labor.
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11
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Yee J, Hwang HS, Chung JE, Park JY, Lee KE, Kim YJ, Gwak HS. Effects of PDE4 gene polymorphisms on efficacy and adverse drug events of ritodrine therapy in preterm labor patients: a prospective observational study. Eur J Clin Pharmacol 2019; 75:1379-1386. [PMID: 31324945 DOI: 10.1007/s00228-019-02719-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Accepted: 07/11/2019] [Indexed: 11/29/2022]
Abstract
PURPOSE Phosphodiesterase (PDE) terminates the signaling pathway of myometrial relaxation by degradating cAMP to the inactive 5'-AMP. The PDE4 family is one of the most predominant PDE families that display high affinity to cAMP. The objective of this study was to evaluate the effects of PDE4 gene polymorphisms on tocolytic effects and adverse drug events (ADEs) of ritodrine therapy in patients with preterm labor. METHODS A total of 170 preterm labor patients were included in this study. To elucidate the effects of genetic polymorphisms on the inter-individual variability of ritodrine efficacy and ADEs, 8 single nucleotide polymorphisms (SNPs) were genotyped: PDE4D (rs1544791, rs983280, rs1504982, rs10940648, rs829259) and PDE4B2 (rs598961, rs2180335, and rs17128809). Additionally, rs1042719 of the ADRB2 gene was included for multivariate analysis. The primary endpoint of this prospective study was the time to delivery (hr). The secondary endpoint was ritodrine-induced ADEs. RESULTS The mutant-type homozygote carriers of PDE4B2 rs598961 polymorphism showed shorter median time to delivery than those with other genotypes (adjusted hazard ratio 1.6, 95% confidence interval 1.0 to 2.4, P = 0.035). On the other hand, patients with wild-type homozygotes of PDE4B2 rs17128809 showed 2.6~2.9 times higher ADEs compared to those with other genotypes. Among demographic characteristics, gestational age at start of drug therapy and modified Bishop score were significant factors for time to delivery, whereas height, weight, and BSA were significant factors for ritodrine-induced ADEs after adjusting other factors. CONCLUSIONS This pharmacogenomic study suggested that PDE4 genetic polymorphisms impact individual susceptibility to β2-adrenergic receptor targeted therapy in patients with preterm labor.
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Affiliation(s)
- Jeong Yee
- College of Pharmacy and Division of Life & Pharmaceutical Sciences, Ewha Womans University, 52 Ewhayeodae-gil, Seodaemun-gu, Seoul, 03760, Republic of Korea
| | - Han Sung Hwang
- Department of Obstetrics and Gynecology, Konkuk University Medical Center, Konkuk University School of Medicine, Seoul, 05030, South Korea
| | - Jee Eun Chung
- College of Pharmacy and Institute of Pharmaceutical Science and Technology, Hanyang University, Ansan, 15588, South Korea
| | - Jin Young Park
- College of Pharmacy and Division of Life & Pharmaceutical Sciences, Ewha Womans University, 52 Ewhayeodae-gil, Seodaemun-gu, Seoul, 03760, Republic of Korea
| | - Kyung Eun Lee
- College of Pharmacy, Chungbuk National University, Cheongju, Chungbuk, 28644, South Korea
| | - Young Ju Kim
- Department of Obstetrics and Gynecology, Ewha Womans University School of Medicine, 1071 Anyangcheon-ro, Yangcheon-gu, Seoul, 07985, Republic of Korea.
| | - Hye Sun Gwak
- College of Pharmacy and Division of Life & Pharmaceutical Sciences, Ewha Womans University, 52 Ewhayeodae-gil, Seodaemun-gu, Seoul, 03760, Republic of Korea.
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12
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Ye Y, Zeng Y. Whole exome sequencing identifies a novel intron heterozygous mutation in TSC2 responsible for tuberous sclerosis complex. Sci Rep 2019; 9:4456. [PMID: 30872599 PMCID: PMC6418313 DOI: 10.1038/s41598-019-38898-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Accepted: 12/21/2018] [Indexed: 11/09/2022] Open
Abstract
This study was aimed to identify the potentially pathogenic gene variants that contribute to the etiology of the tuberous sclerosis complex. A Chinese pedigree with tuberous sclerosis complex was collected and the exomes of two affected individuals were sequenced using the whole exome sequencing technology. The resulting variants from whole exome sequencing were filtered by basic and advanced biological information analysis and the candidate mutation was verified as heterozygous by sanger sequencing. After basic and advanced biological information analysis, a total of 9 single nucleotide variants were identified, which were all follow the dominant inheritance pattern. Among which, the intron heterozygous mutation c.600-145 C > T transition in TSC2 was identified and validated in the two affected individuals. In silico analysis with human splicing finder (HSF) predicted the effect of the c.600-145 C > T mutations on TSC2 mRNA splicing, and detected the creation of a new exonic cryptic donor site, which would result in a frame-shift, and finally premature termination codon. Our results reported the novel intron heterozygous mutation c.600-145 C > T in TSC2 may contribute to TSC, expanding our understanding of the causally relevant genes for this disorder.
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Affiliation(s)
- Yicong Ye
- Department of Cardiology, Beijing Institute of Heart, Lung and Blood Vessel Diseases, Beijing Anzhen Hospital, Capital Medical University, Beijing, 100029, China.,Department of Cardiology, Chinese Academy of Medical College and Peking Union Medical College Hospital; Peking Union Medical College Hospital, Beijing, 100730, China
| | - Yong Zeng
- Department of Cardiology, Beijing Institute of Heart, Lung and Blood Vessel Diseases, Beijing Anzhen Hospital, Capital Medical University, Beijing, 100029, China. .,Department of Cardiology, Chinese Academy of Medical College and Peking Union Medical College Hospital; Peking Union Medical College Hospital, Beijing, 100730, China.
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13
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Chung JE, Choi SA, Hwang HS, Park JY, Lee KE, Yee J, Kim YJ, Gwak HS. Association between ß2-adrenergic receptor gene polymorphisms and adverse events of ritodrine in the treatment of preterm labor: a prospective observational study. BMC Genet 2017; 18:96. [PMID: 29132297 PMCID: PMC5683230 DOI: 10.1186/s12863-017-0565-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Accepted: 10/31/2017] [Indexed: 11/30/2022] Open
Abstract
Background Ritodrine, a tocolytic β2-agonist, has been used extensively in Europe and Asia despite its safety concerns. This study was designed to identify associations between β2-adrenergic receptor (ADRB2) polymorphisms and adverse drug events (ADEs) in patients with preterm labor treated with ritodrine. Results This follow-up study was prospectively conducted at Ewha Womans University Mokdong Hospital in Korea. Five single nucleotide polymorphisms (SNPs) of the ADRB2 gene (rs1042713, rs1042714, rs1042717, rs1042718, and rs1042719) were analyzed in 186 pregnant women with preterm labor. Patients with the AA genotype of rs1042717 had significantly lower incidence of ADEs compared to those with the G allele (p = 0.009). In multivariate analysis, one of the predictors of ADEs was the maximum infusion rate of ritodrine (AOR 4.47, 95% CI 1.31–15.25). Rs1042719 was also a significant factor for ritodrine-induced ADEs. The CC genotype carriers had 78% decreased risk of ADEs compared to those with other genotypes. Conclusions This study demonstrates that ADEs induced by ritodrine are associated with ADRB2 gene polymorphisms, as well as the infusion rate of ritodrine in pregnant women with preterm labor.
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Affiliation(s)
- Jee Eun Chung
- School of Pharmacy, Sungkyunkwan University, Suwon-si, Gyeonggi-do, 16419, Korea
| | - Soo An Choi
- College of Pharmacy, Korea University, Sejong-Si, 30019, Korea
| | - Han Sung Hwang
- Department of Obstetrics and Gynecology, Konkuk University Medical Center, Konkuk University School of Medicine, Seoul, 05030, Korea
| | - Jin Young Park
- College of Pharmacy and Division of Life & Pharmaceutical Sciences, Ewha Womans University, 52 Ewhayeodae-gil, Seodaemun-gu, Seoul, 03760, Republic of Korea
| | - Kyung Eun Lee
- College of Pharmacy, Chungbuk National University, Cheonju, Chungbuk, 28644, Korea
| | - Jeong Yee
- College of Pharmacy and Division of Life & Pharmaceutical Sciences, Ewha Womans University, 52 Ewhayeodae-gil, Seodaemun-gu, Seoul, 03760, Republic of Korea
| | - Young Ju Kim
- Department of Obstetrics and Gynecology, Ewha Womans University School of Medicine, 1071 Anyangcheon-ro, Yangcheon-gu, Seoul, 07985, Republic of Korea.
| | - Hye Sun Gwak
- College of Pharmacy and Division of Life & Pharmaceutical Sciences, Ewha Womans University, 52 Ewhayeodae-gil, Seodaemun-gu, Seoul, 03760, Republic of Korea.
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14
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Hurst LD, Batada NN. Depletion of somatic mutations in splicing-associated sequences in cancer genomes. Genome Biol 2017; 18:213. [PMID: 29115978 PMCID: PMC5678748 DOI: 10.1186/s13059-017-1337-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Accepted: 10/12/2017] [Indexed: 01/01/2023] Open
Abstract
Background An important goal of cancer genomics is to identify systematically cancer-causing mutations. A common approach is to identify sites with high ratios of non-synonymous to synonymous mutations; however, if synonymous mutations are under purifying selection, this methodology leads to identification of false-positive mutations. Here, using synonymous somatic mutations (SSMs) identified in over 4000 tumours across 15 different cancer types, we sought to test this assumption by focusing on coding regions required for splicing. Results Exon flanks, which are enriched for sequences required for splicing fidelity, have ~ 17% lower SSM density compared to exonic cores, even after excluding canonical splice sites. While it is impossible to eliminate a mutation bias of unknown cause, multiple lines of evidence support a purifying selection model above a mutational bias explanation. The flank/core difference is not explained by skewed nucleotide content, replication timing, nucleosome occupancy or deficiency in mismatch repair. The depletion is not seen in tumour suppressors, consistent with their role in positive tumour selection, but is otherwise observed in cancer-associated and non-cancer genes, both essential and non-essential. Consistent with a role in splicing modulation, exonic splice enhancers have a lower SSM density before and after controlling for nucleotide composition; moreover, flanks at the 5’ end of the exons have significantly lower SSM density than at the 3’ end. Conclusions These results suggest that the observable mutational spectrum of cancer genomes is not simply a product of various mutational processes and positive selection, but might also be shaped by negative selection. Electronic supplementary material The online version of this article (doi:10.1186/s13059-017-1337-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Laurence D Hurst
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath, BA2 7AY, UK
| | - Nizar N Batada
- Institute for Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU, UK.
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15
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Soussi T, Taschner PEM, Samuels Y. Synonymous Somatic Variants in Human Cancer Are Not Infamous: A Plea for Full Disclosure in Databases and Publications. Hum Mutat 2017; 38:339-342. [PMID: 28026089 DOI: 10.1002/humu.23163] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Revised: 11/28/2016] [Accepted: 12/11/2016] [Indexed: 12/12/2022]
Abstract
Single-nucleotide variants (SNVs) are the most frequent genetic changes found in human cancer. Most driver alterations are missense and nonsense variants localized in the coding region of cancer genes. Unbiased cancer genome sequencing shows that synonymous SNVs (sSNVs) can be found clustered in the coding regions of several cancer oncogenes or tumor suppressor genes suggesting purifying selection. sSNVs are currently underestimated, as they are usually discarded during analysis. Furthermore, several public databases do not display sSNVs, which can lead to analytical bias and the false assumption that this mutational event is uncommon. Recent progress in our understanding of the deleterious consequences of these sSNVs for RNA stability and protein translation shows that they can act as strong drivers of cancer, as demonstrated for several cancer genes such as TP53 or BCL2L12. It is therefore essential that sSNVs be properly reported and analyzed in order to provide an accurate picture of the genetic landscape of the cancer genome.
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Affiliation(s)
- Thierry Soussi
- Sorbonne Université, UPMC Univ Paris 06, Paris, F-75005, France.,INSERM, U1138, Centre de Recherche des Cordeliers, Paris, France.,Department of Oncology-Pathology, Karolinska Institutet, Cancer Center Karolinska (CCK) R8:04, Stockholm, SE-171 76, Sweden
| | - Peter E M Taschner
- Generade Centre of Expertise Genomics and University of Applied Sciences Leiden, Leiden, 2333 CL, The Netherlands
| | - Yardena Samuels
- Molecular Cell Biology Department, Weizmann Institute of Science, Rehovot, 76100, Israel
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16
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Di Taranto MD, D'Agostino MN, Fortunato G. Functional characterization of mutant genes associated with autosomal dominant familial hypercholesterolemia: integration and evolution of genetic diagnosis. Nutr Metab Cardiovasc Dis 2015; 25:979-987. [PMID: 26165249 DOI: 10.1016/j.numecd.2015.06.007] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/14/2015] [Accepted: 06/15/2015] [Indexed: 12/18/2022]
Abstract
AIMS Familial Hypercholesterolemia (FH) is one of the most frequent dyslipidemias, the autosomal dominant form of which is primarily caused by mutations in the LDL receptor (LDLR), apolipoprotein B (APOB), and proprotein convertase subtilisin/kexin type 9 (PCSK9) genes, although in around 20% of patients the genetic cause remains unidentified. Genetic testing has notably improved the identification of patients suffering from FH, the most frequent cause of which is the presence of mutations in the LDLR gene. Although more than 1200 different mutations have been identified in this gene, about 80% are recognized to be pathogenic. We aim to overview the current methods used to perform the functional characterization of mutations causing FH and to highlight the conditions requiring a functional characterization of the variant in order to obtain a diagnostic report. DATA SYNTHESIS In the current review, we summarize the different types of functional assays - including their advantages and disadvantages - performed to characterize mutations in the LDLR, APOB and PCSK9 genes helping to better define their pathogenic role. We describe the evaluation of splicing alterations and two major procedures for functional characterization: 1. ex vivo methods, using cells from FH patients; 2. in vitro methods using cell lines. CONCLUSIONS Functional characterization of the LDLR, APOB and PCSK9 mutant genes associated with FH can be considered a necessary integration of its genetic diagnosis.
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Affiliation(s)
| | - M N D'Agostino
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli Federico II, Via Sergio Pansini 5, 80131 Napoli, Italy
| | - G Fortunato
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli Federico II, Via Sergio Pansini 5, 80131 Napoli, Italy; CEINGE Biotecnologie Avanzate S.C.a r.l., Via Gaetano Salvatore 486, 80145 Napoli, Italy.
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17
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Shi Y, Joyner AS, Shadrick W, Palacios G, Lagisetti C, Potter PM, Sambucetti LC, Stamm S, Webb TR. Pharmacodynamic assays to facilitate preclinical and clinical development of pre-mRNA splicing modulatory drug candidates. Pharmacol Res Perspect 2015; 3:e00158. [PMID: 26171237 PMCID: PMC4492733 DOI: 10.1002/prp2.158] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2015] [Accepted: 05/22/2015] [Indexed: 12/29/2022] Open
Abstract
The spliceosome has recently emerged as a new target for cancer chemotherapy and novel antitumor spliceosome targeted agents are under development. Here, we describe two types of novel pharmacodynamic assays that facilitate drug discovery and development of this intriguing class of innovative therapeutics; the first assay is useful for preclinical optimization of small-molecule agents that target the SF3B1 spliceosomal protein in animals, the second assay is an ex vivo validated, gel-based assay for the measurement of drug exposure in human leukocytes. The first assay utilizes a highly specific bioluminescent splicing reporter, based on the skipping of exons 4–11 of a Luc-MDM2 construct, which specifically yields active luciferase when treated with small-molecule spliceosome modulators. We demonstrate that this reporter can be used to monitor alternative splicing in whole cells in vitro. We describe here that cell lines carrying the reporter can be used in vivo for the efficient pharmacodynamic analysis of agents during drug optimization and development. We also demonstrate dose- and time-dependent on-target activity of sudemycin D6 (SD6), which leads to dramatic tumor regression. The second assay relies on the treatment of freshly drawn human blood with SD6 ex vivo treatment. Changes in alternative splicing are determined by RT-PCR using genes previously identified in in vitro experiments. The Luc-MDM2 alternative splicing bioluminescent reporter and the splicing changes observed in human leukocytes should allow for the more facile translation of novel splicing modulators into clinical application.
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Affiliation(s)
- Yihui Shi
- Division of Biosciences, SRI International Menlo Park, California, 94025
| | - Amanda S Joyner
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital Memphis, Tennessee, 38105
| | - William Shadrick
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital Memphis, Tennessee, 38105
| | - Gustavo Palacios
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital Memphis, Tennessee, 38105
| | | | - Philip M Potter
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital Memphis, Tennessee, 38105
| | - Lidia C Sambucetti
- Division of Biosciences, SRI International Menlo Park, California, 94025
| | - Stefan Stamm
- Department of Molecular and Cellular Biochemistry, University of Kentucky 741 South Limestone, Lexington, Kentucky, 40536
| | - Thomas R Webb
- Division of Biosciences, SRI International Menlo Park, California, 94025
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18
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Abstract
![]()
Whole human genome sequencing of
individuals is becoming rapid
and inexpensive, enabling new strategies for using personal genome
information to help diagnose, treat, and even prevent human disorders
for which genetic variations are causative or are known to be risk
factors. Many of the exploding number of newly discovered genetic
variations alter the structure, function, dynamics, stability, and/or
interactions of specific proteins and RNA molecules. Accordingly,
there are a host of opportunities for biochemists and biophysicists
to participate in (1) developing tools to allow accurate and sometimes
medically actionable assessment of the potential pathogenicity of
individual variations and (2) establishing the mechanistic linkage
between pathogenic variations and their physiological consequences,
providing a rational basis for treatment or preventive care. In this
review, we provide an overview of these opportunities and their associated
challenges in light of the current status of genomic science and personalized
medicine, the latter often termed precision medicine.
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Affiliation(s)
- Brett M Kroncke
- †Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, United States.,‡Center for Structural Biology, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - Carlos G Vanoye
- §Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, United States
| | - Jens Meiler
- ‡Center for Structural Biology, Vanderbilt University, Nashville, Tennessee 37232, United States.,∥Departments of Chemistry, Pharmacology, and Bioinformatics, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - Alfred L George
- §Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, United States
| | - Charles R Sanders
- †Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, United States.,‡Center for Structural Biology, Vanderbilt University, Nashville, Tennessee 37232, United States
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19
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Tammaro C, Raponi M, Wilson DI, Baralle D. BRCA1 EXON 11, a CERES (composite regulatory element of splicing) element involved in splice regulation. Int J Mol Sci 2014; 15:13045-59. [PMID: 25056543 PMCID: PMC4139890 DOI: 10.3390/ijms150713045] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2014] [Revised: 06/17/2014] [Accepted: 07/04/2014] [Indexed: 11/16/2022] Open
Abstract
Unclassified variants (UV) of BRCA1 can affect normal pre-mRNA splicing. Here, we investigate the UV c.693G>A, a "silent" change in BRCA1 exon 11, which we have found induces aberrant splicing in patient carriers and in vitro. Using a minigene assay, we show that the UV c.693G>A has a strong effect on the splicing isoform ratio of BRCA1. Systematic site-directed mutagenesis of the area surrounding the nucleotide position c.693G>A induced variable changes in the level of exon 11 inclusion/exclusion in the mRNA, pointing to the presence of a complex regulatory element with overlapping enhancer and silencer functions. Accordingly, protein binding analysis in the region detected several splicing regulatory factors involved, including SRSF1, SRSF6 and SRSF9, suggesting that this sequence represents a composite regulatory element of splicing (CERES).
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Affiliation(s)
- Claudia Tammaro
- Human Development and Health, University of Southampton, Southampton SO16 6YD, UK.
| | - Michela Raponi
- Human Development and Health, University of Southampton, Southampton SO16 6YD, UK.
| | - David I Wilson
- Human Development and Health, University of Southampton, Southampton SO16 6YD, UK.
| | - Diana Baralle
- Human Development and Health, University of Southampton, Southampton SO16 6YD, UK.
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20
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Assessing the residual CFTR gene expression in human nasal epithelium cells bearing CFTR splicing mutations causing cystic fibrosis. Eur J Hum Genet 2013; 22:784-91. [PMID: 24129438 DOI: 10.1038/ejhg.2013.238] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2013] [Revised: 09/06/2013] [Accepted: 09/10/2013] [Indexed: 01/18/2023] Open
Abstract
The major purpose of the present study was to quantify correctly spliced CFTR transcripts in human nasal epithelial cells from cystic fibrosis (CF) patients carrying the splicing mutations c.580-1G>T (712-1G>T) and c.2657+5G>A (2789+5G>A) and to assess the applicability of this model in CFTR therapeutic approaches. We performed the relative quantification of CFTR mRNA by reverse transcription quantitative PCR (RT-qPCR) of these splicing mutations in four groups (wild type, CF-F508del controls, CF patients and CF carriers) of individuals. In addition, in vitro assays using minigene constructs were performed to evaluate the effect of a new CF complex allele c.[2657+5G>A; 2562T>G]. Ex vivo qPCR data show that the primary consequence of both mutations at the RNA level is the skipping of their neighboring exon (6 and 16, respectively). The CFTR minigenes results mimicked the ex vivo data, as exon 16 skipping is the main aberrant transcript, and the correctly spliced transcript level was observed in a similar proportion when the c.2657+5G>A mutation is present. In summary, we provide evidence that ex vivo quantitative transcripts analysis using RT/qPCR is a robust technology that could be useful for measuring the efficacy of therapeutic approaches that attempt to achieve an increase in CFTR gene expression.
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21
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Kelemen O, Convertini P, Zhang Z, Wen Y, Shen M, Falaleeva M, Stamm S. Function of alternative splicing. Gene 2013; 514:1-30. [PMID: 22909801 PMCID: PMC5632952 DOI: 10.1016/j.gene.2012.07.083] [Citation(s) in RCA: 488] [Impact Index Per Article: 44.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2012] [Revised: 07/21/2012] [Accepted: 07/30/2012] [Indexed: 12/15/2022]
Abstract
Almost all polymerase II transcripts undergo alternative pre-mRNA splicing. Here, we review the functions of alternative splicing events that have been experimentally determined. The overall function of alternative splicing is to increase the diversity of mRNAs expressed from the genome. Alternative splicing changes proteins encoded by mRNAs, which has profound functional effects. Experimental analysis of these protein isoforms showed that alternative splicing regulates binding between proteins, between proteins and nucleic acids as well as between proteins and membranes. Alternative splicing regulates the localization of proteins, their enzymatic properties and their interaction with ligands. In most cases, changes caused by individual splicing isoforms are small. However, cells typically coordinate numerous changes in 'splicing programs', which can have strong effects on cell proliferation, cell survival and properties of the nervous system. Due to its widespread usage and molecular versatility, alternative splicing emerges as a central element in gene regulation that interferes with almost every biological function analyzed.
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Affiliation(s)
- Olga Kelemen
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, Kentucky, United States of America
| | - Paolo Convertini
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, Kentucky, United States of America
| | - Zhaiyi Zhang
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, Kentucky, United States of America
| | - Yuan Wen
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, Kentucky, United States of America
| | - Manli Shen
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, Kentucky, United States of America
| | - Marina Falaleeva
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, Kentucky, United States of America
| | - Stefan Stamm
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, Kentucky, United States of America
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22
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Chen L. Statistical and Computational Methods for High-Throughput Sequencing Data Analysis of Alternative Splicing. STATISTICS IN BIOSCIENCES 2012; 5:138-155. [PMID: 24058384 DOI: 10.1007/s12561-012-9064-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The burgeoning field of high-throughput sequencing significantly improves our ability to understand the complexity of transcriptomes. Alternative splicing, as one of the most important driving forces for transcriptome diversity, can now be studied at an unprecedent resolution. Efficient and powerful computational and statistical methods are in urgent need to facilitate the characterization and quantification of alternative splicing events. Here we discuss methods in splice junction read mapping, and methods in exon-centric or isoform-centric quantification of alternative splicing. In addition, we discuss HITS-CLIP and splicing QTL analyses which are novel high-throughput sequencing based approaches in the dissection of splicing regulation.
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Affiliation(s)
- Liang Chen
- Molecular and Computational Biology, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
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23
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Association of the RAVER2 gene with increased susceptibility for ulcerative colitis. Hum Immunol 2012; 73:732-5. [PMID: 22561236 DOI: 10.1016/j.humimm.2012.04.018] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2012] [Revised: 04/11/2012] [Accepted: 04/23/2012] [Indexed: 11/21/2022]
Abstract
Crohn's disease (CD), ulcerative colitis (UC), systemic lupus erythematosus (SLE) and autoimmune polyglandular syndromes (APS) are autoimmune diseases (ADs) that may share common susceptibility pathways. We examined ribonucleo-protein, polypyrimidine tract-binding protein (PTB)-binding 2 (RAVER2) loci for these diseases in a cohort of 39 CD cases, 67 UC cases, 93 SLE cases, 60 APS cases and 162 healthy control subjects of Tunisian origin. We genotyped 3 SNPs of RAVER2 (rs2780814, rs1333739 and rs2780889) and evaluated it genetic association with each ADs, using X2-test. For each association, odds ratio (OR) and 95% CI were calculated. We show that rs2780814 is significantly associated with UC (P = 0.00016, P(corr) = 0.00048, OR = 3.66 (1.82; 7.34)). We also observed a trend of possible association to SLE (P = 0.023, P(corr) = 0.69, OR = 2.19 (1.1; 4.36)). None of these RAVER2 SNPs were associated with CD and APS susceptibility. These findings establish RAVER2 as a new UC genetic susceptibility factor and reveal a genetic heterogeneity of the associated polymorphisms and risk alleles between ADs suggesting different immunopathological roles of RAVER2 in these diseases.
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24
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Abstract
Defects at the level of pre-mRNA splicing represent a common source of disease mutations in almost all known diseases with a genetic aetiology. In general, it is commonly accepted that 15% of all pathogenic mutations are caused by splicing defects. However, this is probably a conservative estimate since clinical practice has only recently begun to routinely assess for this types of abnormalities. Therefore, it is expected that many currently unclassified or apparently harmless genetic variants will really turn out to be splicing-affecting defects. It is also well known that some genes are more susceptible than others to alterations in their splicing processes. Among these genes, one of the most representative is the NF-1 gene. In this gene, almost 50% of all reported disease-causing mutations can be directly attributed to alterations of the pre-mRNA process. In this chapter, we review the splicing process of the NF-1 gene and the most commonly used methods to identify splicing alterations. In particular, we provide practical notes on how to perform this analysis to maximize the chance of correctly identifying aberrant pre-mRNA splicing events in this gene.
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Transcriptional regulation of the human Raver2 ribonucleoprotein gene. Gene 2011; 493:243-52. [PMID: 22146317 DOI: 10.1016/j.gene.2011.11.036] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2011] [Revised: 11/08/2011] [Accepted: 11/16/2011] [Indexed: 01/11/2023]
Abstract
Raver2 is a putative modulator of the activity of the polypyrimidine-tract binding protein (PTB), one of the most intensively studied splicing repressors. Little is known about Raver2 expression, and all current data is from mice where it shows tissue specificity. In the present study, by comparing Raver2 transcript expression in human and mouse tissues, we found that human Raver2 is ubiquitously expressed in adult tissues. In order to investigate human Raver2 transcription regulation, we identified and characterized a putative promoter region in a 1000bp region upstream of the transcription starting site of the gene. Dual luciferase reporter assays demonstrated that this region had promoter activity conferred by the first 160bp. By mutagenic analyses of putative cis-acting regulatory sequences, we identified an individual site that decreased the promoter activity by up to 40% when mutated. Together, our results suggest that regulation of human Raver2 expression involves TATA-less transcriptional activity.
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Fuccio A, Iorio M, Amato F, Elce A, Ingino R, Filocamo M, Castaldo G, Salvatore F, Tomaiuolo R. A novel DHPLC-based procedure for the analysis of COL1A1 and COL1A2 mutations in osteogenesis imperfecta. J Mol Diagn 2011; 13:648-56. [PMID: 21884818 DOI: 10.1016/j.jmoldx.2011.06.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2011] [Revised: 06/13/2011] [Accepted: 06/20/2011] [Indexed: 10/17/2022] Open
Abstract
Approximately 90% of patients with osteogenesis imperfecta (OI) exhibit dominant COL1A1 or COL1A2 mutations; however, molecular analysis is difficult because these genes span 51 and 52 exons, respectively. We devised a PCR-denaturing high-performance liquid chromatography (DHPLC) procedure to analyze the COL1A1 or COL1A2 coding regions and validated it using 130 DNA samples from individuals without OI, 25 DNA samples from two cells to investigate the procedure's potential for preimplantation diagnosis, and DNA samples from 10 patients with OI. Three novel intronic variants in vitro were expressed using a minigene assay to assess their effects on splicing. The procedure is rapid, inexpensive, and reproducible. Analysis of samples from individuals without OI revealed six novel and some known polymorphisms useful for linkage diagnosis because of high heterozygosity. Analysis of two-cell samples confirmed the known genotype in 24 of 25 experiments; DNA failed to amplify in only one case. No incidence of allele dropout was recorded. DHPLC revealed six novel mutations, three of which were intronic, in all patients with OI, and these results were confirmed by means of COL1A1 and COL1A2 direct sequencing. Expression of intronic mutations demonstrated that variant 804 + 2_804 + 3delTG in intron 11 disrupts normal splicing, thereby leading to formation of two alternative products. Variants c.3046-4_3046-5dupCT (COL1A1) and c.891 + 77A>T (COL1A2) did not affect splicing. The described DHPLC protocol combined with the minigene assay may contribute to molecular diagnosis in OI. Moreover, this protocol will aid in counseling about prenatal and preimplantation diagnosis.
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Affiliation(s)
- Antonella Fuccio
- CEINGE-Biotecnologie Avanzate Scarl, Università di Napoli Federico II, Naples, Italy
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Griseri P, Bourcier C, Hieblot C, Essafi-Benkhadir K, Chamorey E, Touriol C, Pagès G. A synonymous polymorphism of the Tristetraprolin (TTP) gene, an AU-rich mRNA-binding protein, affects translation efficiency and response to Herceptin treatment in breast cancer patients. Hum Mol Genet 2011; 20:4556-68. [PMID: 21875902 DOI: 10.1093/hmg/ddr390] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Post-transcriptional regulation plays a central role in cell differentiation and proliferation. Among the regulatory factors involved in this mechanism, Tristetraprolin (ZFP36 or TTP) is the prototype of a family of RNA-binding proteins that bind to adenylate and uridylate (AU)-rich sequences in the 3'UTR of mRNAs, which promotes their physiological decay. Here, we investigated whether TTP correlates with tumor aggressiveness in breast cancer and is a novel prognostic factor for this neoplasia. By immunoblot analysis, we determined the amount of TTP protein in different breast cancer cell lines and found an inverse correlation between aggressiveness and metastatic potential. TTP mRNA levels were very variable among cells lines and did not correlate with protein levels. Interestingly, by sequencing the entire TTP coding region in Hs578T cells that do not express the TTP protein, we identified a synonymous polymorphism (rs3746083) that showed a statistically significant association with a lack of response to Herceptin/Trastuzumab in HER2-positive-breast cancer patients. Even though this genetic change did not modify the corresponding amino acid, we performed functional studies and showed an effect on protein translation associated with the variant allele with respect to the wild-type. These data underline the importance of synonymous variants on gene expression and the potential role of TTP genetic polymorphisms as a prognostic marker for breast cancer.
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Affiliation(s)
- Paola Griseri
- University Nice-Sophia Antipolis Institute of Developmental Biology and Cancer, CNRS UMR 6543, France
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Zago P, Buratti E, Stuani C, Baralle FE. Evolutionary connections between coding and splicing regulatory regions in the fibronectin EDA exon. J Mol Biol 2011; 411:1-15. [PMID: 21663748 DOI: 10.1016/j.jmb.2011.05.031] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2011] [Revised: 05/16/2011] [Accepted: 05/20/2011] [Indexed: 01/03/2023]
Abstract
Research on exonic coding sequences has demonstrated that many substitutions at the amino acid level may also reflect profound changes at the level of splicing regulatory regions. These results have revealed that, for many alternatively spliced exons, there is considerable pressure to strike a balance between two different and sometimes conflicting forces: the drive to improve the quality and production efficiency of proteins and the maintenance of proper exon recognition by the splicing machinery. Up to now, the systems used to investigate these connections have mostly focused on short alternatively spliced exons that contain a high density of splicing regulatory elements. Although this is obviously a desirable feature in order to maximize the chances of spotting connections, it also complicates the process of drawing straightforward evolutionary pathways between different species (because of the numerous alternative pathways through which the same end point can be achieved). The alternatively spliced fibronectin extra domain A exon (also referred to as EDI or EIIIA) does not have these limitations, as its inclusion is already known to depend on a single exonic splicing enhancer element within its sequence. In this study, we have compared the rat and human fibronectin EDA exons with regard to RNA structure, exonic splicing enhancer strengths, and SR protein occupancy. The results gained from these analyses have then been used to perform an accurate evaluation of EDA sequences observed in a wide range of animal species. This comparison strongly suggests the existence of an evolutionary connection between changes at the nucleotide levels and the need to maintain efficient EDA recognition in different species.
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Affiliation(s)
- Paola Zago
- International Center for Genetic Engineering and Biotechnology, Trieste, Italy
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Costantini S, Prandini P, Corradi M, Pasquali A, Contreas G, Pignatti PF, Pinelli L, Trabetti E, Maffeis C. A novel synonymous substitution in the GCK gene causes aberrant splicing in an Italian patient with GCK-MODY phenotype. Diabetes Res Clin Pract 2011; 92:e23-6. [PMID: 21288587 DOI: 10.1016/j.diabres.2011.01.014] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/30/2010] [Accepted: 01/10/2011] [Indexed: 11/15/2022]
Abstract
GCK gene analysis in an Italian MODY patient revealed a novel synonymous substitution in exon 4 (c.459T>G; p.Pro153Pro) resulting in an aberrant transcript lacking the last eight codons of the same exon. Our findings emphazise the importance of not underestimating synonymous variations when screening for disease-causing mutations.
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Affiliation(s)
- Silvia Costantini
- Regional Center for Pediatric Diabetes, ULSS 20 & University of Verona, Department of Life and Reproduction Sciences, Section of Pediatrics, Verona, Italy.
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Barbosa M, Lopes A, Mota C, Martins E, Oliveira J, Alves S, De Bonis P, do Céu Mota M, Dias C, Rodrigues-Santos P, Fortuna AM, Quelhas D, Lacerda L, Bisceglia L, Cardoso ML. Clinical, biochemical and molecular characterization of Cystinuria in a cohort of 12 patients. Clin Genet 2011; 81:47-55. [DOI: 10.1111/j.1399-0004.2011.01638.x] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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