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Dai Z, Wang Y, Li P, Zhang H, Gou X. The association between polymorphism of LDL-R gene and ischemic stroke risk in Chinese population: A meta-analysis. Heliyon 2024; 10:e26314. [PMID: 38390048 PMCID: PMC10881424 DOI: 10.1016/j.heliyon.2024.e26314] [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: 02/05/2024] [Accepted: 02/09/2024] [Indexed: 02/24/2024] Open
Abstract
Objective Low-density lipoprotein receptor (LDL-R) gene polymorphisms have been indicated to be correlated with ischemic cerebrovascular disease including ischemic stroke susceptibility. However, the results from each published study are inconsistent. Methods All eligible case-control studies that met the search terms were retrieved in PubMed, Embase, Wanfang Med Online and Chinese National Knowledge Infrastructure (CNKI) databases. We identified seven independent case-control studies with a total of 10,355 subjects from Chinese population up to May 2023. Summary odds ratios (ORs) and 95% confidence intervals (CIs) were used to evaluate the susceptibility of ischemic stroke. Results Meta-analysis results indicated that rs1122608 polymorphism of LDL-R gene significantly decreased ischemic stroke risk under dominant model (OR = 0.69, 95% CI = 0.54-0.87), heterozygote comparison (OR = 0.69, 95% CI = 0.53-0.92) and allele comparison (OR = 0.74, 95% CI = 0.65-0.84) in overall analysis. Furthermore, pooled analysis showed that significant associations were observed between rs688 polymorphism and ischemic stroke risk in heterozygote carriers (OR = 1.71, 95% CI = 1.07-2.71) and dominant model (OR = 1.67, 95% CI = 1.04-2.68) in Chinese population. Conclusions Our comprehensive meta-analysis on the role of LDL-R gene rs1122608 and rs688 polymorphisms in the risk of ischemic stroke revealed that the rs1122608 polymorphism was associated with a decreased risk, while the rs688 polymorphism was associated with an increased risk of ischemic stroke in Chinese population. Further multicenter studies were needed to confirm the effect on the susceptibility of ischemic stroke.
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Affiliation(s)
- Zhiming Dai
- Anesthesia Operation Center, The First People's Hospital of Xianyang, Xianyang, 712099, PR China
- Department of Anesthesiology, Xi'an Jiaotong University Second Affiliated Hospital, Xi'an, 710004, PR China
| | - Yifan Wang
- Anesthesia Operation Center, The First People's Hospital of Xianyang, Xianyang, 712099, PR China
| | - Peidi Li
- Department of Anesthesiology, Xi'an Jiaotong University Second Affiliated Hospital, Xi'an, 710004, PR China
| | - Huijuan Zhang
- Department of Anesthesiology, Xi'an Jiaotong University Second Affiliated Hospital, Xi'an, 710004, PR China
| | - Xiaohui Gou
- Anesthesia Operation Center, The First People's Hospital of Xianyang, Xianyang, 712099, PR China
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Chen Y, Cai H, Zhang J, Su Y, Wu Y, Lin Z, Zhang Z. Elevated sdLDL level and LDLR rs688 C>T mutation are independent risk factors for ischemic stroke. Med Clin (Barc) 2022; 159:465-469. [PMID: 35337686 DOI: 10.1016/j.medcli.2022.01.016] [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: 10/27/2021] [Revised: 01/11/2022] [Accepted: 01/17/2022] [Indexed: 11/16/2022]
Abstract
PURPOSE To investigate the level of sdLDL and the frequency of LDLR rs688 polymorphisms, as well as the correspondence between them, and to analyze the risk factors for stroke. METHODS Between March 2019 and November 2019, 232 patients diagnosed with stroke and 96 health volunteers were enrolled in Quanzhou First Hospital. Subjects were divided into control group, ischemic stroke group (n=120) and hemorrhagic stroke group (n=112). The level of sdLDL and the genotypes and allele frequencies of LDLR rs688 were compared between groups, the correspondence was analyzed with Spearman method. Risk factors were analyzed with Binary logistic regression. RESULTS The level of sdLDL was highest in ischemic group, followed by hemorrhagic stroke group and lowest control group. The differences of genotypes and allele frequencies of LDLR rs688 were significant in ischemic stroke group (p=0.0000 and 0.0000 respectively), while were not significant in hemorrhagic group (p=0.184 and .0137). There was no obvious correlation between the level of sdLDL and LDLR rs688 genotype by Spearman analysis (p=0.116). CONCLUSION Elevated sdLDL level and the C>T mutation of LDLR rs688 are independent risk factors for ischemic stroke, while they are not correlative to hemorrhagic stroke. The surveillance and regulatory of sdLDL level, the detection of LDLR rs688 gene polymorphisms may contribute to the prevention of ischemic stroke.
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Affiliation(s)
- Yabin Chen
- Clinical Laboratory, Quanzhou First Hospital Affiliated to Fujian Medical University, Quanzhou, Fujian, China
| | - Hehui Cai
- Clinical Laboratory, Quanzhou First Hospital Affiliated to Fujian Medical University, Quanzhou, Fujian, China
| | - Jianming Zhang
- Clinical Laboratory, Quanzhou First Hospital Affiliated to Fujian Medical University, Quanzhou, Fujian, China
| | - Yongfa Su
- Clinical Laboratory, Quanzhou First Hospital Affiliated to Fujian Medical University, Quanzhou, Fujian, China
| | - Yibo Wu
- Clinical Laboratory, Quanzhou First Hospital Affiliated to Fujian Medical University, Quanzhou, Fujian, China
| | - Zhenzhong Lin
- Clinical Laboratory, Quanzhou First Hospital Affiliated to Fujian Medical University, Quanzhou, Fujian, China
| | - Zhishan Zhang
- Clinical Laboratory, Quanzhou First Hospital Affiliated to Fujian Medical University, Quanzhou, Fujian, China.
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Zajac DJ, Green SJ, Johnson LA, Estus S. APOE genetics influence murine gut microbiome. Sci Rep 2022; 12:1906. [PMID: 35115575 PMCID: PMC8814305 DOI: 10.1038/s41598-022-05763-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 01/17/2022] [Indexed: 01/03/2023] Open
Abstract
Apolipoprotein E (APOE) alleles impact pathogenesis and risk for multiple human diseases, making them primary targets for disease treatment and prevention. Previously, we and others reported an association between APOE alleles and the gut microbiome. Here, we evaluated effects of APOE heterozygosity and tested whether these overall results extended to mice maintained under ideal conditions for microbiome analyses. To model human APOE alleles, this study used APOE targeted replacement (TR) mice on a C57Bl/6 background. To minimize genetic drift, homozygous APOE3 mice were crossed to homozygous APOE2 or homozygous APOE4 mice prior to the study, and the resulting heterozygous progeny crossed further to generate the study mice. To maximize environmental homogeneity, mice with mixed genotypes were housed together and used bedding from the cages was mixed and added back as a portion of new bedding. Fecal samples were obtained from mice at 3-, 5- and 7-months of age, and microbiota analyzed by 16S ribosomal RNA gene amplicon sequencing. Linear discriminant analysis of effect size (LefSe) identified taxa associated with APOE status, depicted as cladograms to show phylogenetic relatedness. The influence of APOE status was tested on alpha-diversity (Shannon H index) and beta-diversity (principal coordinate analyses and PERMANOVA). Individual taxa associated with APOE status were identified by classical univariate analysis. Whether findings in the APOE mice were replicated in humans was evaluated by using published microbiome genome wide association data. Cladograms revealed robust differences with APOE in male mice and limited differences in female mice. The richness and evenness (alpha-diversity) and microbial community composition (beta-diversity) of the fecal microbiome was robustly associated with APOE status in male but not female mice. Classical univariate analysis revealed individual taxa that were significantly increased or decreased with APOE, illustrating a stepwise APOE2-APOE3-APOE4 pattern of association with heterozygous animals trending as intermediate in the stepwise pattern. The relative abundance of bacteria from the class Clostridia, order Clostridiales, family Ruminococacceae and related genera increased with APOE2 status. The relative abundance of Erysipelotrichia increased with APOE4 status, a finding that extended to humans. In this study, wherein mice were maintained in an ideal fashion for microbiome studies, gut microbiome profiles were strongly and significantly associated with APOE status in male APOE-TR mice. Erysipelotrichia are increased with APOE4 in both mice and humans. APOE allelic effects appeared generally intermediate in heterozygous animals. Further evaluation of these findings in humans, as well as studies evaluating the impact of the APOE-associated microbiota on disease-relevant phenotypes, will be necessary to determine if alterations in the gut microbiome represent a novel mechanism whereby APOE alleles impact disease.
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Affiliation(s)
- Diana J Zajac
- Department of Physiology and Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY, USA
| | - Stefan J Green
- Genome Research Core, Research Resources Center, University of Illinois at Chicago, Chicago, IL, USA
- Genomics and Microbiome Core Facility, Rush University Medical Center, Chicago, IL, USA
| | - Lance A Johnson
- Department of Physiology and Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY, USA
| | - Steven Estus
- Department of Physiology and Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY, USA.
- Department of Physiology, University of Kentucky, 789 S. Limestone, Rm. 537, Lexington, KY, 40536, USA.
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Buraczynska M, Jacob J, Gwiazda-Tyndel K, Ksiazek A. LDLR gene polymorphism (rs688) affects susceptibility to cardiovascular disease in end-stage kidney disease patients. BMC Nephrol 2021; 22:316. [PMID: 34556050 PMCID: PMC8459523 DOI: 10.1186/s12882-021-02532-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Accepted: 08/14/2021] [Indexed: 11/20/2022] Open
Abstract
Background The low-density lipoprotein receptor (LDLR) plays a significant role in maintaining the cellular cholesterol homeostasis. Mutations in the LDLR gene can lead to a significant rise in plasma LDL levels that may result in an increased risk of atherosclerosis and coronary heart disease. The purpose of this study was to assess the potential association of the LDLR rs688 polymorphism with cardiovascular disease (CVD) in patients with end-stage kidney disease (ESKD) undergoing hemodialysis. Methods In this case-control study the polymorphism was genotyped by the allele specific PCR method in 800 patients with ESKD and 500 healthy controls. The genotype and allele distribution was compared in subgroups of patients with CVD (552) versus those without CVD (248). Results A significant difference was observed in genotype distribution among ESKD patients and healthy controls. The frequencies of the T allele and TT genotype in ESKD group were significantly higher, with OR (95% CI) 2.2 (1.87–2.6), p < 0.0001 and 5.84 (3.94–8.65), p < 0.0001, respectively. In the he ESKD cohort the distribution of the rs688 was compared between CVD+ and CVD- subgroups. A strong association of the polymorphism with the CVD risk was observed in this analysis. The frequencies of the T allele and TT genotype were significantly higher in CVD+ subgroup, with OR (95% CI) 3.4 (2.71–4.26), p < 0.0001 and 13.2 (7.87–22.09), p < 0.0001, respectively. A multivariate logistic regression analysis was performed to estimate the association between rs688 T variant and risk of CVD. After adjustment for age, sex, BMI, hypertension and diabetes, both CT and TT genotypes were associated with an increased risk of developing CVD in the dominant, recessive and codominant models of inheritance. No significant differences in serum LDL cholesterol levels were found when compared between genotypes. Conclusions The present study is the first to demonstrate the association of the LDLR gene polymorphism with increased susceptibility to cardiovascular disease in ESKD patients. This finding needs further investigation to confirm that LDLR rs688 might be a novel genetic risk factor with some prognostic capacity for CVD in ESKD patients.
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Affiliation(s)
- Monika Buraczynska
- Department of Nephrology, Medical University of Lublin, Jaczewskiego 8, 20-950, Lublin, Poland.
| | - Jerry Jacob
- Hope Medical Institute, Newport News, Virginia, USA
| | - Karolina Gwiazda-Tyndel
- Department of Nephrology, Medical University of Lublin, Jaczewskiego 8, 20-950, Lublin, Poland
| | - Andrzej Ksiazek
- Department of Nephrology, Medical University of Lublin, Jaczewskiego 8, 20-950, Lublin, Poland
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Alternative Splicing in Cardiovascular Disease-A Survey of Recent Findings. Genes (Basel) 2021; 12:genes12091457. [PMID: 34573439 PMCID: PMC8469243 DOI: 10.3390/genes12091457] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 09/11/2021] [Accepted: 09/16/2021] [Indexed: 12/22/2022] Open
Abstract
Alternative splicing, a driver of posttranscriptional variance, differs from canonical splicing by arranging the introns and exons of an immature pre-mRNA transcript in a multitude of different ways. Although alternative splicing was discovered almost half a century ago, estimates of the proportion of genes that undergo alternative splicing have risen drastically over the last two decades. Deep sequencing methods and novel bioinformatic algorithms have led to new insights into the prevalence of spliced variants, tissue-specific splicing patterns and the significance of alternative splicing in development and disease. Thus far, the role of alternative splicing has been uncovered in areas ranging from heart development, the response to myocardial infarction to cardiac structural disease. Circular RNAs, a product of alternative back-splicing, were initially discovered in 1976, but landmark publications have only recently identified their regulatory role, tissue-specific expression, and transcriptomic abundance, spurring a renewed interest in the topic. The aim of this review is to provide a brief insight into some of the available findings on the role of alternative splicing in cardiovascular disease, with a focus on atherosclerosis, myocardial infarction, heart failure, dilated cardiomyopathy and circular RNAs in myocardial infarction.
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Ozuynuk AS, Erkan AF, Ekici B, Erginel-Unaltuna N, Coban N. Cholesterol-related gene variants are associated with diabetes in coronary artery disease patients. Mol Biol Rep 2021; 48:3945-3954. [PMID: 34021444 DOI: 10.1007/s11033-021-06393-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2021] [Accepted: 04/29/2021] [Indexed: 11/27/2022]
Abstract
Coronary artery disease (CAD) which is a complex cardiovascular disease is the leading cause of death worldwide. The changing prevalence of the disease in different ethnic groups pointing out the genetic background of CAD. In this study, we aimed to evaluate the contribution of selected cholesterol metabolism-related gene polymorphisms to CAD presence. A total of 493 individuals who underwent coronary angiography were divided into 2 groups: normal coronary arteries (≤ 30% stenosis) and critical disease (≥ 50% stenosis). Individuals were genotyped for APOC1 (rs11568822), APOD (rs1568565), LIPA (rs13500), SORL1 (rs2282649), and LDLR (rs5930) polymorphisms using hydrolysis probes in Real-Time PCR. Blood samples were drawn before coronary angiography and biochemical analyses were done. The results were statistically evaluated. When the study group was stratified according to CAD, the minor allele of APOD polymorphism was found related to decreased risk for T2DM in the non-CAD group. In logistic regression analysis adjusted for several confounders, LDLR rs5930 polymorphism was found associated with T2DM presence in the male CAD group [OR = 0.502, 95%CI (0.259-0.974), p = 0.042]. Besides, APOD and LIPA polymorphisms were shown to affect serum lipid levels in non-CAD T2DM patients (p < 0.05). The minor allele of APOC1 was found associated with triglyceride levels in males independent of CAD status. Besides, LDLR minor allele carrier females had elevated HbA1c and glucose levels independent from CAD status in the whole group. The cholesterol metabolism-related gene polymorphisms were found associated with T2DM and biochemical parameters stratified to sex, CAD, and T2DM status.
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Affiliation(s)
- Aybike Sena Ozuynuk
- Department of Genetics, Istanbul University, Aziz Sancar Institute for Experimental Medicine, Sehremini, Istanbul, 34080, Turkey
- Graduate School of Health Sciences, Istanbul University, Istanbul, Turkey
| | - Aycan Fahri Erkan
- Faculty of Medicine, Department of Cardiology, Ufuk University, Ankara, Turkey
| | - Berkay Ekici
- Faculty of Medicine, Department of Cardiology, Ufuk University, Ankara, Turkey
| | - Nihan Erginel-Unaltuna
- Department of Genetics, Istanbul University, Aziz Sancar Institute for Experimental Medicine, Sehremini, Istanbul, 34080, Turkey
| | - Neslihan Coban
- Department of Genetics, Istanbul University, Aziz Sancar Institute for Experimental Medicine, Sehremini, Istanbul, 34080, Turkey.
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El Marabti E, Abdel-Wahab O. Therapeutic Modulation of RNA Splicing in Malignant and Non-Malignant Disease. Trends Mol Med 2021; 27:643-659. [PMID: 33994320 DOI: 10.1016/j.molmed.2021.04.005] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Revised: 04/11/2021] [Accepted: 04/13/2021] [Indexed: 01/24/2023]
Abstract
RNA splicing is the enzymatic process by which non-protein coding sequences are removed from RNA to produce mature protein-coding mRNA. Splicing is thereby a major mediator of proteome diversity as well as a dynamic regulator of gene expression. Genetic alterations disrupting splicing of individual genes or altering the function of splicing factors contribute to a wide range of human genetic diseases as well as cancer. These observations have resulted in the development of therapies based on oligonucleotides that bind to RNA sequences and modulate splicing for therapeutic benefit. In parallel, small molecules that bind to splicing factors to alter their function or modify RNA processing of individual transcripts are being pursued for monogenic disorders as well as for cancer.
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Affiliation(s)
- Ettaib El Marabti
- Clinical Transplant Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Omar Abdel-Wahab
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Leukemia Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.
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8
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Liu J, Zhou M, Ouyang Y, Du L, Xu L, Li H. Identification of potential biomarkers and their clinical significance in gastric cancer using bioinformatics analysis methods. PeerJ 2020; 8:e9174. [PMID: 33062405 PMCID: PMC7527772 DOI: 10.7717/peerj.9174] [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: 12/19/2019] [Accepted: 04/21/2020] [Indexed: 01/07/2023] Open
Abstract
Background Alternative splicing (AS) is an important mechanism for regulating gene expression and proteome diversity. Tumor-alternative splicing can reveal a large class of new splicing-associated potential new antigens that may affect the immune response and can be used for immunotherapy. Methods The RNA-seq transcriptome data and clinical information of stomach adenocarcinoma (STAD) cohort were downloaded from The Cancer Genome Atlas (TCGA) database data portal, and data of splicing events were obtained from the SpliceSeq database. Predicting genes were validated by Asian cancer research group (ACRG) cohort and Oncomine database. RT-qPCR was used to analysis the expression of ECT2 in STAD. Results A total of 32,166 AS events were identified, among which 2,042 AS events were significantly associated with patients survival. Biological pathway analysis indicated that these genes play an important role in regulating gastric cancer-related processes such as GTPase activity and PI3K-Akt signaling pathway. Next, we derived a risk signature, using alternate acceptor, that is an independent prognostic marker. Moreover, high ECT2 expression was associated with poorer prognosis in STAD. Multivariate survival analysis demonstrated that high ECT2 expression was an independent risk factor for overall survival. Gene set enrichment analysis revealed that high ECT2 expression was enriched for hallmarks of malignant tumors. The ACRG cohort and Oncomine also showed that high ECT2 expression was associated with poorer prognosis in gastric cancer patients. Finally, RT-qPCR showed ECT2 expression was higher in STAD compared to the normal tissues. Conclusion This study excavated the alternative splicing events in gastric cancer, and found ECT2 might be a biomarkers for diagnosis and prognosis.
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Affiliation(s)
- Jie Liu
- Gastroenterology, Jining No.1 People's Hospital, Jining, China
| | - Miao Zhou
- Gastroenterology, Jining No.1 People's Hospital, Jining, China
| | - Yangyang Ouyang
- Gastroenterology, Jining No.1 People's Hospital, Jining, China
| | - Laifeng Du
- General Medicine, Jining Prison Hospital, Jining, China
| | - Lingbo Xu
- Obstetrical, Jining No.1 People's Hospital, Jining, China
| | - Hongyun Li
- Gastroenterology, Jining No.1 People's Hospital, Jining, China
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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: 11] [Impact Index Per Article: 2.8] [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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Interaction between Sex and LDLR rs688 Polymorphism on Hyperlipidemia among Taiwan Biobank Adult Participants. Biomolecules 2020; 10:biom10020244. [PMID: 32033407 PMCID: PMC7072141 DOI: 10.3390/biom10020244] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 01/25/2020] [Accepted: 02/03/2020] [Indexed: 01/04/2023] Open
Abstract
Hyperlipidemia is one of the strong risk factors for ischemic heart disease. Using the Taiwan Biobank (TWB) database, we evaluated the risk of hyperlipidemia and its interaction with sex and rs688 polymorphism on the low-density lipoprotein receptor (LDLR) gene. Data collection in the biobank started in 2008 and is ongoing. Data analysis was performed on the participants’ data collected between 2008 and 2015. In general, 27.92% of the 9237 female participants and 32.65% of the 8690 male participants were identified with hyperlipidemia. Compared to the C/C genotype, C/T and T/T genotypes were not significant risk factors for hyperlipidemia (OR = 1.061, CI: 0.976–1.153 for C/T and OR = 1.052, CI: 0.845–1.309 for T/T genotype) in the general model. However, there was a significant interaction between sex and rs6888 on hyperlipidemia risk (p-interaction = 0.0321). With the male sex/CC genotype being the reference group, only the female sex/CT and T/T genotypes were closely associated with hyperlipidemia, with respective ORs of 1.153 (CI: 1.014–1.311) and 1.423 (CI: 1.056–1.917). Our data indicate that rs688 C/T and T/T genotypes may be associated with increased risk of hyperlipidemia in Taiwanese women. These findings may be relevant in lipid-modification therapy.
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11
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Lunghi B, Bernardi F, Martinelli N, Frusconi S, Branchini A, Linari S, Marchetti G, Castaman G, Morfini M. Functional polymorphisms in the LDLR and pharmacokinetics of Factor VIII concentrates. J Thromb Haemost 2019; 17:1288-1296. [PMID: 31055871 DOI: 10.1111/jth.14473] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Accepted: 04/29/2019] [Indexed: 01/04/2023]
Abstract
BACKGROUND Optimization of factor VIII (FVIII) infusion in hemophilia A would benefit from identification of FVIII pharmacokinetics (PK) determinants. The low-density lipoprotein receptor (LDLR) contains an FVIII-binding site and might influence FVIII clearance. Consistently, LDLR polymorphisms have been associated with FVIII levels. OBJECTIVE To investigate the relationships between individual FVIII PK and functional LDLR polymorphisms. PATIENTS/METHODS Thirty-three hemophilia A patients (FVIII coagulant activity [FVIII:C] ≤2 IU/dL) without inhibitors underwent 85 FVIII single-dose (21.4-51.8 IU/kg) PKs with different FVIII concentrates. Twenty patients underwent repeated PKs (2-6). FVIII C measured up to 72 hours was analyzed by two-compartment model. Parameters were evaluated in relation to F8 mutations, ABO blood-group and LDLR genotypes. RESULTS F8 mutation types were not associated with PK parameters. ABO and LDLR c.1773C/T polymorphism were associated with Alpha, Alpha HL, CLD2, K1-2, and K2-1 parameters, suggesting an influence on the FVIII initial distribution phase. Regression analysis showed an independent association of both ABO and LDLR c.1773C/T with PK parameters (Alpha, β-coefficient -0.311 vs 0.348; CLD2, β-coefficient -0.335 vs 0.318), giving rise to an additive effect in subjects stratified by combined phenotypes. Differently, the LDLR c.81C/T was associated with FVIII clearance and volume of distribution at steady state, which could be related to distinct effects of polymorphisms, potentially linked to LDLR intracellular distribution and FVIII binding behavior. CONCLUSIONS With the limitation of different FVIII concentrates and low number of patients, our data show plausible associations of LDLR polymorphisms with FVIII PK parameters, thus supporting their investigation as candidate functional determinants of FVIII PK.
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Affiliation(s)
- Barbara Lunghi
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
| | - Francesco Bernardi
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
| | | | - Sabrina Frusconi
- Genetic Diagnostics Unit, Laboratory Department, Careggi University Hospital, Florence, Italy
| | - Alessio Branchini
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
| | - Silvia Linari
- Center for Bleeding Disorders, Department of Oncology, Careggi University Hospital, Florence, Italy
| | - Giovanna Marchetti
- Department of Biomedical and Specialty Surgical Sciences, University of Ferrara, Ferrara, Italy
| | - Giancarlo Castaman
- Center for Bleeding Disorders, Department of Oncology, Careggi University Hospital, Florence, Italy
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Steba GS, Koekkoek SM, Tanck MWT, Vanhommerig JW, van der Meer JTM, Kwa D, Brinkman K, Prins M, Berkhout B, Pollakis G, Molenkamp R, Schinkel J, Paxton WA. SNP rs688 within the low-density lipoprotein receptor (LDL-R) gene associates with HCV susceptibility. Liver Int 2019; 39:463-469. [PMID: 30260075 PMCID: PMC6588020 DOI: 10.1111/liv.13978] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Revised: 09/17/2018] [Accepted: 09/19/2018] [Indexed: 02/06/2023]
Abstract
BACKGROUND & AIMS Despite high-risk behaviour, 10%-20% of HCV multiple exposed individuals remain uninfected (MEU), whilst the remainder become infected (MEI). We hypothesize that host factors play a role in HCV susceptibility. We aimed to identify polymorphisms in host genes that encode for proteins involved in viral entry: CD81, Scavenger receptor 1 (SR-1), Low-density lipoprotein receptor (LDL-R), Claudin-1 (CLDN1), Occludin (OCLN) and Niemann-Pick C1-like 1 (NPC1L1). METHODS Multiple exposed infected and MEU from two observational cohorts were selected. From the MSM study of acute infection with HCV (MOSAIC), HIV-1 infected MEU cases (n = 30) and HIV-1 infected MEI controls (n = 32) were selected based on reported high-risk behaviour. From the Amsterdam Cohorts Studies (ACS) injecting drug users (IDU) cohort, MEU cases (n = 40) and MEI controls (n = 22) were selected who injected drugs for ≥2 years, in the nineties, when HCV incidence was high. Selected single nucleotide polymorphisms (SNPs) were determined by sequencing or SNP assays. RESULTS No associations were found for SNPs within genes coding for CD81, SR-1, Claudin-1 or Occludin between the MEU and MEI individuals from either cohort. We did observe a significant association for rs688 within the LDL-R gene with HCV infection (OR: 0.41 P = 0.001), however, LDL cholesterol levels did not vary between individuals carrying the differential SNPs. Additionally, a marginal significant effect was found for rs217434 and rs2072183 (OR: 2.07 P = 0.032 and OR: 1.76 P = 0.039, respectively) within NPC1L1. CONCLUSIONS Our results demonstrate that the rs688 SNP within the LDL-R gene associates with HCV susceptibility through mucosal as well as intravenous exposure.
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Affiliation(s)
- Gaby S. Steba
- Department of Medical Microbiology, Amsterdam UMC, Academic Medical CenterUniversity of AmsterdamAmsterdamThe Netherlands
| | - Sylvie M. Koekkoek
- Department of Medical Microbiology, Amsterdam UMC, Academic Medical CenterUniversity of AmsterdamAmsterdamThe Netherlands
| | - Michael W. T. Tanck
- Department of Clinical Epidemiology, Biostatistics and Bioinformatics (CEBB), Amsterdam UMCAcademic Medical CenterUniversity of AmsterdamAmsterdamThe Netherlands
| | - Joost W. Vanhommerig
- Department of Medical Microbiology, Amsterdam UMC, Academic Medical CenterUniversity of AmsterdamAmsterdamThe Netherlands,Department of Infectious DiseasesPublic Health Service of AmsterdamAmsterdamThe Netherlands
| | - Jan T. M. van der Meer
- Division of Infectious Diseases, Tropical Medicine and AIDS, Department of Internal Medicine, Amsterdam UMC, Academic Medical CenterUniversity of AmsterdamAmsterdamThe Netherlands
| | - David Kwa
- Department of MicrobiologyOnze Lieve Vrouwe GasthuisAmsterdamThe Netherlands
| | - Kees Brinkman
- Department of Internal MedicineOnze Lieve Vrouwe GasthuisAmsterdamThe Netherlands
| | - Maria Prins
- Department of Medical Microbiology, Amsterdam UMC, Academic Medical CenterUniversity of AmsterdamAmsterdamThe Netherlands,Department of Clinical Epidemiology, Biostatistics and Bioinformatics (CEBB), Amsterdam UMCAcademic Medical CenterUniversity of AmsterdamAmsterdamThe Netherlands
| | - Ben Berkhout
- Department of Medical Microbiology, Amsterdam UMC, Academic Medical CenterUniversity of AmsterdamAmsterdamThe Netherlands
| | - Georgios Pollakis
- Department of Clinical Infection, Microbiology and ImmunologyInstitute of Infection and Global HealthUniversity of LiverpoolLiverpoolUK
| | - Richard Molenkamp
- Department of Medical Microbiology, Amsterdam UMC, Academic Medical CenterUniversity of AmsterdamAmsterdamThe Netherlands
| | - Janke Schinkel
- Department of Medical Microbiology, Amsterdam UMC, Academic Medical CenterUniversity of AmsterdamAmsterdamThe Netherlands
| | - William A. Paxton
- Department of Medical Microbiology, Amsterdam UMC, Academic Medical CenterUniversity of AmsterdamAmsterdamThe Netherlands,Department of Clinical Infection, Microbiology and ImmunologyInstitute of Infection and Global HealthUniversity of LiverpoolLiverpoolUK
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13
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LDLR rs688 TT Genotype and T Allele Are Associated with Increased Susceptibility to Coronary Artery Disease-A Case-Control Study. J Cardiovasc Dev Dis 2018; 5:jcdd5020031. [PMID: 29843469 PMCID: PMC6023456 DOI: 10.3390/jcdd5020031] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Revised: 05/21/2018] [Accepted: 05/23/2018] [Indexed: 11/16/2022] Open
Abstract
PURPOSE The low-density lipoprotein receptor is responsible for the binding and uptake of plasma LDL particles and plays a critical role in maintaining cellular cholesterol homeostasis. LDLR gene SNP rs688 has been reported to be associated with increased plasma total and LDL cholesterol in several populations and can lead to elevated plasma LDL levels, resulting in an increased risk for atherosclerosis and coronary artery disease. This study aimed to explore genetic LDLR variant rs688 for its potential roles in coronary artery disease. METHODOLOGY This study recruited 200 coronary artery disease patients and 200 healthy individuals. Genotyping of LDLR-rs688C > T gene variations was performed using the allele specific PCR method. Correlation of LDLR-rs688C > T gene variants with different clinicopathological features of coronary artery disease patients was performed. Pooled odds ratios (ORs) and 95% confidence intervals (CIs) were applied to evaluate the correlation of this microRNA polymorphism with coronary artery disease risk. RESULTS A significant difference was observed in genotype distribution among the coronary artery disease and matched healthy controls (p = 0.003). The frequencies of all three genotypes CC, CT, TT reported in the patient samples were 14%, 65% and 21% and in the healthy controls samples were 18%, 73% and 9%, respectively. The increased risk of developing CAD in Indian patients was found to be associated with LDLR rs688 TT genotype (OR = 3.0, 95% CI, 1.43 × 6.2; p = 0.003) RR 1.87 (1.20⁻2.91) p = 0.0037) and also the increased risk of developing CAD was reported to be associated with LDLR rs688 T allele (OR = 0.74, 95% CI, 1.57⁻0.97; p = 0.03) RR 0.85 (0.73⁻0.99) p = 0.03) compared to the C allele. Therefore, it was observed that more than a 3.0- and 0.74-fold increase risk of developing CAD was associated with TT genotype and T allele in Indian coronary artery disease patients. CONCLUSION The findings indicated that LDLR rs688 TT genotype and T allele are associated with an increased susceptibility to coronary artery disease patients. LDLR-rs688C > T gene variation can be used as a predisposing genetic marker for coronary artery disease. Further studies with larger sample sizes are necessary to confirm our findings.
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14
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Er LK, Teng MS, Wu S, Hsu LA, Tzeng IS, Cheng CF, Chang HI, Chou HH, Ko YL. Combined effect of acid-sensing ion channel 3 and transient receptor potential vanilloid 1 gene polymorphisms on blood pressure variations in Taiwanese. Tzu Chi Med J 2018; 30:29-36. [PMID: 29643714 PMCID: PMC5883834 DOI: 10.4103/tcmj.tcmj_187_17] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Objectives: Both acid-sensing ion channel acid-sensing ion channel 3 (ASIC3) and transient receptor potential vanilloid 1 (TRPV1) have been proposed to be involved in the pathophysiology of hypertension. Common colocalization of ASIC3 and TRPV1 channels in the same sensory neuron has been reported. We aimed to study the combined ASIC3 and TRPV1 gene polymorphisms in the risk of hypertension. Materials and Methods: To test the statistical association between genetic polymorphisms of the ASIC3 and TRPV1 genes and blood pressure (BP) variations in Taiwanese, 551 unrelated individuals (286 men and 265 women) having routine health examinations were recruited. The participants had no history of cardiovascular disease or use of medication for hypertension. Results: Six ASIC3 and four TRPV1 gene polymorphisms were genotyped, and only the ASIC3 rs2288646 polymorphism was associated with variations in BP in the participants. In subgroup analysis, we found participants carrying the combined ASIC3 rs2288646 AA or AG and TRPV1 rs8065080 CC genotypes (combined genotypes) had significantly higher systolic, mean and diastolic BP compared with the other subgroups (P = 0.009, 0.003, and 0.006, respectively, after Bonferroni correction). Interaction analysis also revealed significant gene-gene interaction in the systolic, mean, and diastolic BP in the ASIC3 and TRPV1 genotypes (interaction P = 0.006, 0.002, and 0.002, respectively). A trend of increasing frequencies of the combined genotype was observed in normotensive, prehypertensive, and hypertensive subgroups (P for trend = 0.001), as well as in those with higher systolic and diastolic BPs (P for trend = 9.13 × 10−4 and P for trend = 5.5 × 10−5, respectively). Conclusion: Our data show a combined effect of ASIC3 and TRPV1 gene polymorphisms in BP variations in Taiwanese. These results suggest that the interaction between ASIC3 and TRPV1 is involved in BP regulation.
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Affiliation(s)
- Leay-Kiaw Er
- Division of Endocrinology and Metabolism, Department of Internal Medicine, Taipei Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation, New Taipei, Taiwan
| | - Ming-Sheng Teng
- Department of Research, Taipei Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation, New Taipei, Taiwan
| | - Semon Wu
- Department of Research, Taipei Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation, New Taipei, Taiwan.,Department of Life Science, Chinese Culture University, Taipei, Taiwan
| | - Lung-An Hsu
- First Cardiovascular Division, Department of Internal Medicine, Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Taoyuan, Taiwan
| | - I-Shiang Tzeng
- Department of Research, Taipei Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation, New Taipei, Taiwan
| | - Ching-Feng Cheng
- Department of Pediatrics, Buddhist Tzu Chi General Hospital, Hualien, Taiwan.,School of Medicine, Tzu Chi University, Hualien, Taiwan
| | - Hsin-I Chang
- Division of Cardiology, Department of Internal Medicine and Cardiovascular Medical Center, Taipei Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation, New Taipei, Taiwan
| | - Hsin-Hua Chou
- School of Medicine, Tzu Chi University, Hualien, Taiwan.,Division of Cardiology, Department of Internal Medicine and Cardiovascular Medical Center, Taipei Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation, New Taipei, Taiwan
| | - Yu-Lin Ko
- Department of Research, Taipei Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation, New Taipei, Taiwan.,School of Medicine, Tzu Chi University, Hualien, Taiwan.,Division of Cardiology, Department of Internal Medicine and Cardiovascular Medical Center, Taipei Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation, New Taipei, Taiwan
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Vasquez JB, Simpson JF, Harpole R, Estus S. Alzheimer's Disease Genetics and ABCA7 Splicing. J Alzheimers Dis 2018; 59:633-641. [PMID: 28655137 DOI: 10.3233/jad-170872] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Both common and rare polymorphisms within ABCA7 have been associated with Alzheimer's disease (AD). In particular, the rare AD associated polymorphism rs200538373 was associated with altered ABCA7 exon 41 splicing and an AD risk odds ratio of ∼1.9. To probe the role of this polymorphism in ABCA7 splicing, we used minigene studies and qPCR of human brain RNA. We report aberrant ABCA7 exon 41 splicing in the brain of a carrier of the rs200538373 minor C allele. Moreover, minigene studies show that rs200538373 acts as a robust functional variant in vitro. Lastly, although the ABCA7 isoform with an extended exon 41 is predicted to undergo nonsense mediated RNA decay, this was not supported by qPCR analyses, which showed relatively normal ABCA7 mRNA levels in the carrier of the rs200538373 minor C allele. In summary, rs200538373 is a functional polymorphism that alters ABCA7 exon 41 splicing without grossly altering the level of ABCA7 mRNA.
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Affiliation(s)
- Jared B Vasquez
- Department of Physiology and Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY, USA
| | - James F Simpson
- Department of Physiology and Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY, USA
| | - Ryan Harpole
- Department of Physiology and Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY, USA
| | - Steven Estus
- Department of Physiology and Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY, USA
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16
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Buroker NE, Ning XH, Zhou ZN, Li K, Cen WJ, Wu XF, Zhu WZ, Scott CR, Chen SH. SNPs, linkage disequilibrium, and chronic mountain sickness in Tibetan Chinese. HYPOXIA 2017; 5:67-74. [PMID: 28770234 PMCID: PMC5529112 DOI: 10.2147/hp.s117967] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Chronic mountain sickness (CMS) is estimated at 1.2% in Tibetans living at the Qinghai-Tibetan Plateau. Eighteen single-nucleotide polymorphisms (SNPs) from nine nuclear genes that have an association with CMS in Tibetans have been analyzed by using pairwise linkage disequilibrium (LD). The SNPs included are the angiotensin-converting enzyme (rs4340), the angiotensinogen (rs699), and the angiotensin II type 1 receptor (AGTR1) (rs5186) from the renin-angiotensin system. A low-density lipoprotein apolipoprotein B (rs693) SNP was also included. From the hypoxia-inducible factor oxygen signaling pathway, the endothetal Per-Arnt-Sim domain protein 1 (EPAS1) and the egl nine homolog 1 (ENGL1) (rs480902) SNPs were included in the study. SNPs from the vascular endothelial growth factor (VEGF) signaling pathway included are the v-akt murine thymoma viral oncogene homolog 3 (rs4590656 and rs2291409), the endothelial cell nitric oxide synthase 3 (rs1007311 and rs1799983), and the (VEGFA) (rs699947, rs34357231, rs79469752, rs13207351, rs28357093, rs1570360, rs2010963, and rs3025039). An increase in LD occurred in 40 pairwise comparisons, whereas a decrease in LD was found in 55 pairwise comparisons between the controls and CMS patients. These changes were found to occur within and between signaling pathways, which suggests that there is an interaction between SNP alleles from different areas of the genome that affect CMS.
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Affiliation(s)
| | - Xue-Han Ning
- Department of Pediatrics, University of Washington.,Division of Cardiology, Seattle Children's Hospital Research Foundation, Seattle, WA, USA
| | - Zhao-Nian Zhou
- Laboratory of Hypoxia Physiology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Kui Li
- Lhasa People Hospital, Lhasa, Tibet
| | | | - Xiu-Feng Wu
- Laboratory of Hypoxia Physiology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Wei-Zhong Zhu
- Center for Cardiovascular Biology and Regenerative Medicine, University of Washington, Seattle, WA, USA
| | | | - Shi-Han Chen
- Department of Pediatrics, University of Washington
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17
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Yue YH, Liu LY, Hu L, Li YM, Mao JP, Yang XY, Dila NM. The association of lipid metabolism relative gene polymorphisms and ischemic stroke in Han and Uighur population of Xinjiang. Lipids Health Dis 2017. [PMID: 28623937 PMCID: PMC5474057 DOI: 10.1186/s12944-017-0491-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
Background The present study is aimed to evaluate difference of lipid metabolism related gene single nucleotide polymorphisms (SNPs) with ischemic stroke (IS) in Han and Uighur population of Xinjiang, China. Methods Four hundred eight patients with ischemic stroke and 347 unrelated healthy individuals of age and sex matched were genotyped for Apolipoprotein A5 (ApoA5), lipoprotein lipase (LPL), Cholesteryl ester transfer protein (CETP) and low-density lipoprotein receptor (LDL-R) genes. Their mutation difference was analyzed by SNaP shot techniques. GeneMapper4.1 SPSS20.0 software was used for data management and analysis. Using a single locus analysis, the distribution difference of genotype loci in ischemic stroke cases and controls were detected to assess the genetic risk factors of ischemic stroke. Results Significance differences of genotype distribution in ischemic stroke cases and controls were observed in LDLR rs688 in Han and Uighur population in recessive model from analysis of single gene locus. It also was found that dramatic difference of triglyceride (TG) of LPL rs328 and systolic blood pressure in CETP rs708277 of total population. In binary logistic regression analysis of total studied population, ischemic stroke was observed significantly associated with LDLR rs688 both addictive model (TT/CC, adjusted OR = 1.47, 95% CI = 1.04–2.07) and recessive model (TT/CT + CC, adjusted Odds ratio (OR) = 2.66, 95% Confidence Interval (CI) = 1.37–5.14). In Han population, ischemic stroke was observed significantly associated with rs688 both in addictive model (TT/CC, adjusted OR = 3.27, 95% CI = 1.06–10.05). In Uighur population, no significant association was found between gene polymorphisms and the risk of ischemic stroke. Combined analysis of multiple gene and loci, interaction effects of LDLR rs688 C/T, ApoA5 rs662799 A/G and CETP rs708272 C/T denoted a significant influence on IS susceptibility. Conclusion Single nucleotide polymorphisms of lipid metabolism relative gene were significantly associated with the morbidity of ischemic stroke in Han population. The interaction effects of rs688 C/T with ApoA5 rs662799 A/G and CETP rs708272 C/T promoted the occurrence of IS.
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Affiliation(s)
- Yun-Hua Yue
- Department of Neurology, Yangpu Hospital Tongji University School of Medicine, No. 450 Tengyue Road, Shanghai, 200090, China.
| | - Ling-Yun Liu
- Department of Neurology, Yangpu Hospital Tongji University School of Medicine, No. 450 Tengyue Road, Shanghai, 200090, China
| | - Liang Hu
- Department of Neurology, Yangpu Hospital Tongji University School of Medicine, No. 450 Tengyue Road, Shanghai, 200090, China
| | - You-Mei Li
- Department of Neurology, Yangpu Hospital Tongji University School of Medicine, No. 450 Tengyue Road, Shanghai, 200090, China
| | - Jie-Ping Mao
- Department of Neurology, Friendship Hospital to Urumqi, Urumqi, 830049, China
| | - Xiao-Ying Yang
- Department of Neurology, Friendship Hospital to Urumqi, Urumqi, 830049, China
| | - Na-Mu Dila
- Department of Neurology, Friendship Hospital to Urumqi, Urumqi, 830049, China
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A common polymorphism decreases LRP1 mRNA stability and is associated with increased plasma factor VIII levels. Biochim Biophys Acta Mol Basis Dis 2017; 1863:1690-1698. [DOI: 10.1016/j.bbadis.2017.04.015] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Revised: 03/31/2017] [Accepted: 04/17/2017] [Indexed: 11/18/2022]
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Suñé-Pou M, Prieto-Sánchez S, Boyero-Corral S, Moreno-Castro C, El Yousfi Y, Suñé-Negre JM, Hernández-Munain C, Suñé C. Targeting Splicing in the Treatment of Human Disease. Genes (Basel) 2017; 8:genes8030087. [PMID: 28245575 PMCID: PMC5368691 DOI: 10.3390/genes8030087] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Revised: 02/14/2017] [Accepted: 02/17/2017] [Indexed: 02/07/2023] Open
Abstract
The tightly regulated process of precursor messenger RNA (pre-mRNA) alternative splicing (AS) is a key mechanism in the regulation of gene expression. Defects in this regulatory process affect cellular functions and are the cause of many human diseases. Recent advances in our understanding of splicing regulation have led to the development of new tools for manipulating splicing for therapeutic purposes. Several tools, including antisense oligonucleotides and trans-splicing, have been developed to target and alter splicing to correct misregulated gene expression or to modulate transcript isoform levels. At present, deregulated AS is recognized as an important area for therapeutic intervention. Here, we summarize the major hallmarks of the splicing process, the clinical implications that arise from alterations in this process, and the current tools that can be used to deliver, target, and correct deficiencies of this key pre-mRNA processing event.
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Affiliation(s)
- Marc Suñé-Pou
- Department of Molecular Biology, Institute of Parasitology and Biomedicine "López Neyra" (IPBLN-CSIC), PTS, Granada 18016, Spain.
- Drug Development Service, Department of Pharmacy and Pharmaceutical Technology, Faculty of Pharmacy, University of Barcelona, Avda. Joan XXIII, s/n 08028 Barcelona, Spain.
| | - Silvia Prieto-Sánchez
- Department of Molecular Biology, Institute of Parasitology and Biomedicine "López Neyra" (IPBLN-CSIC), PTS, Granada 18016, Spain.
| | - Sofía Boyero-Corral
- Department of Molecular Biology, Institute of Parasitology and Biomedicine "López Neyra" (IPBLN-CSIC), PTS, Granada 18016, Spain.
| | - Cristina Moreno-Castro
- Department of Molecular Biology, Institute of Parasitology and Biomedicine "López Neyra" (IPBLN-CSIC), PTS, Granada 18016, Spain.
| | - Younes El Yousfi
- Department of Molecular Biology, Institute of Parasitology and Biomedicine "López Neyra" (IPBLN-CSIC), PTS, Granada 18016, Spain.
| | - Josep Mª Suñé-Negre
- Drug Development Service, Department of Pharmacy and Pharmaceutical Technology, Faculty of Pharmacy, University of Barcelona, Avda. Joan XXIII, s/n 08028 Barcelona, Spain.
| | - Cristina Hernández-Munain
- Department of Cell Biology and Immunology, Institute of Parasitology and Biomedicine "López Neyra" (IPBLN-CSIC), PTS, Granada 18016, Spain.
| | - Carlos Suñé
- Department of Molecular Biology, Institute of Parasitology and Biomedicine "López Neyra" (IPBLN-CSIC), PTS, Granada 18016, Spain.
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20
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Fairoozy RH, White J, Palmen J, Kalea AZ, Humphries SE. Identification of the Functional Variant(s) that Explain the Low-Density Lipoprotein Receptor (LDLR) GWAS SNP rs6511720 Association with Lower LDL-C and Risk of CHD. PLoS One 2016; 11:e0167676. [PMID: 27973560 PMCID: PMC5156384 DOI: 10.1371/journal.pone.0167676] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2016] [Accepted: 11/20/2016] [Indexed: 12/02/2022] Open
Abstract
Background The Low-Density Lipoprotein Receptor (LDLR) SNP rs6511720 (G>T), located in intron-1 of the gene, has been identified in genome-wide association studies (GWAS) as being associated with lower plasma levels of LDL-C and a lower risk of coronary heart disease (CHD). Whether or not rs6511720 is itself functional or a marker for a functional variant elsewhere in the gene is not known. Methods The association of LDLR SNP rs6511720 with incidence of CHD and levels of LDL-C was determined by reference to CARDIoGRAM, C4D and Global lipids genetics consortium (GLGC) data. SNP annotation databases were used to identify possible SNP function and prioritization. Luciferase reporter assays in the liver cell line Huh7 were used to measure the effect of variant genotype on gene expression. Electrophoretic Mobility Shift Assays (EMSAs) were used to identify the Transcription Factors (TFs) involved in gene expression regulation. Results The phenotype-genotype analysis showed that the rs6511720 minor allele is associated with lower level of LDL-C [beta = -0.2209, p = 3.85 x10-262], and lower risk of CHD [log (OR) = 0.1155, p = 1.04 x10-7]. Rs6511720 is in complete linkage. Rs6511720 is in complete linkage disequilibrium (LD) with three intron-1 SNPs (rs141787760, rs60173709, rs57217136). Luciferase reporter assays in Huh7 cells showed that the rare alleles of both rs6511720 and rs57217136 caused a significant increase in LDLR expression compared to the common alleles (+29% and +24%, respectively). Multiplex Competitor-EMSAs (MC-EMSA) identified that the transcription factor serum response element (SRE) binds to rs6511720, while retinoic acid receptor (RAR) and signal transducer and activator of transcription 1 (STAT1) bind to rs57217136. Conclusion Both LDLR rs6511720 and rs57217136 are functional variants. Both these minor alleles create enhancer-binding protein sites for TFs and may contribute to increased LDLR expression, which is consequently associated with reduced LDL-C levels and 12% lower CHD risk.
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Affiliation(s)
- Roaa Hani Fairoozy
- Centre for Cardiovascular Genetics, BHF Laboratories, Institute of Cardiovascular Science, University College London, London, United Kingdom
- * E-mail:
| | - Jon White
- University College London Genetics Institute, Department of Genetics, Environment and Evolution, London, United Kingdom
| | - Jutta Palmen
- Centre for Cardiovascular Genetics, BHF Laboratories, Institute of Cardiovascular Science, University College London, London, United Kingdom
| | - Anastasia Z. Kalea
- Centre for Cardiovascular Genetics, BHF Laboratories, Institute of Cardiovascular Science, University College London, London, United Kingdom
| | - Steve E. Humphries
- Centre for Cardiovascular Genetics, BHF Laboratories, Institute of Cardiovascular Science, University College London, London, United Kingdom
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Bien SA, Wojcik GL, Zubair N, Gignoux CR, Martin AR, Kocarnik JM, Martin LW, Buyske S, Haessler J, Walker RW, Cheng I, Graff M, Xia L, Franceschini N, Matise T, James R, Hindorff L, Le Marchand L, North KE, Haiman CA, Peters U, Loos RJF, Kooperberg CL, Bustamante CD, Kenny EE, Carlson CS. Strategies for Enriching Variant Coverage in Candidate Disease Loci on a Multiethnic Genotyping Array. PLoS One 2016; 11:e0167758. [PMID: 27973554 PMCID: PMC5156387 DOI: 10.1371/journal.pone.0167758] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Accepted: 11/18/2016] [Indexed: 11/25/2022] Open
Abstract
Investigating genetic architecture of complex traits in ancestrally diverse populations is imperative to understand the etiology of disease. However, the current paucity of genetic research in people of African and Latin American ancestry, Hispanic and indigenous peoples in the United States is likely to exacerbate existing health disparities for many common diseases. The Population Architecture using Genomics and Epidemiology, Phase II (PAGE II), Study was initiated in 2013 by the National Human Genome Research Institute to expand our understanding of complex trait loci in ethnically diverse and well characterized study populations. To meet this goal, the Multi-Ethnic Genotyping Array (MEGA) was designed to substantially improve fine-mapping and functional discovery by increasing variant coverage across multiple ethnicities at known loci for metabolic, cardiovascular, renal, inflammatory, anthropometric, and a variety of lifestyle traits. Studying the frequency distribution of clinically relevant mutations, putative risk alleles, and known functional variants across multiple populations will provide important insight into the genetic architecture of complex diseases and facilitate the discovery of novel, sometimes population-specific, disease associations. DNA samples from 51,650 self-identified African ancestry (17,328), Hispanic/Latino (22,379), Asian/Pacific Islander (8,640), and American Indian (653) and an additional 2,650 participants of either South Asian or European ancestry, and other reference panels have been genotyped on MEGA by PAGE II. MEGA was designed as a new resource for studying ancestrally diverse populations. Here, we describe the methodology for selecting trait-specific content for use in multi-ethnic populations and how enriching MEGA for this content may contribute to deeper biological understanding of the genetic etiology of complex disease.
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Affiliation(s)
- Stephanie A. Bien
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
- * E-mail: (CSC); (SAB)
| | - Genevieve L. Wojcik
- Department of Genetics, Stanford University, Stanford, California, United States of America
| | - Niha Zubair
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Christopher R. Gignoux
- Department of Genetics, Stanford University, Stanford, California, United States of America
| | - Alicia R. Martin
- Department of Genetics, Stanford University, Stanford, California, United States of America
| | - Jonathan M. Kocarnik
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Lisa W. Martin
- Division of Cardiology, George Washington University School of Medicine and Health Sciences, Washington, DC, United States of America
| | - Steven Buyske
- Department of Genetics, School of Arts and Sciences, Rutgers University, Piscataway, New Jersey, United States of America
| | - Jeffrey Haessler
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Ryan W. Walker
- The Charles Bronfman Institute for Personalized Medicine, The Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- The Department of Preventive Medicine, The Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Iona Cheng
- Cancer Prevention Institute of California, Fremont, California, United States of America
| | - Mariaelisa Graff
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Lucy Xia
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California/Norris Comprehensive Cancer Center, Los Angeles, California, United States of America
| | - Nora Franceschini
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Tara Matise
- Department of Genetics, School of Arts and Sciences, Rutgers University, Piscataway, New Jersey, United States of America
| | - Regina James
- Division of Intramural Research, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Lucia Hindorff
- Division of Genomic Medicine, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Loic Le Marchand
- Department of Epidemiology Program, University of Hawai’i Cancer Center, Honolulu, Hawai’i, United States of America
| | - Kari E. North
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Christopher A. Haiman
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California/Norris Comprehensive Cancer Center, Los Angeles, California, United States of America
| | - Ulrike Peters
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
- Department of Epidemiology, University of Washington, Seattle, Washington, United States of America
| | - Ruth J. F. Loos
- The Charles Bronfman Institute for Personalized Medicine, The Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- The Department of Preventive Medicine, The Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Charles L. Kooperberg
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Carlos D. Bustamante
- Department of Genetics, Stanford University, Stanford, California, United States of America
| | - Eimear E. Kenny
- The Charles Bronfman Institute for Personalized Medicine, The Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- The Department of Preventive Medicine, The Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Christopher S. Carlson
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
- Department of Epidemiology, University of Washington, Seattle, Washington, United States of America
- * E-mail: (CSC); (SAB)
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22
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Makeeva OA, Sleptsov AA, Kulish EV, Barbarash OL, Mazur AM, Prokhorchuk EB, Chekanov NN, Stepanov VA, Puzyrev VP. Genomic Study of Cardiovascular Continuum Comorbidity. Acta Naturae 2015; 7:89-99. [PMID: 26483964 PMCID: PMC4610169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
Comorbidity or a combination of several diseases in the same individual is a common and widely investigated phenomenon. However, the genetic background for non-random disease combinations is not fully understood. Modern technologies and approaches to genomic data analysis enable the investigation of the genetic profile of patients burdened with several diseases (polypathia, disease conglomerates) and its comparison with the profiles of patients with single diseases. An association study featuring three groups of patients with various combinations of cardiovascular disorders and a control group of relatively healthy individuals was conducted. Patients were selected as follows: presence of only one disease, ischemic heart disease (IHD); a combination of two diseases, IHD and arterial hypertension (AH); and a combination of several diseases, including IHD, AH, type 2 diabetes mellitus (T2DM), and hypercholesterolemia (HC). Genotyping was performed using the "My Gene" genomic service (www.i-gene.ru). An analysis of 1,400 polymorphic genetic variants and their associations with the studied phenotypes are presented. A total of 14 polymorphic variants were associated with the phenotype "IHD only," including those in the APOB, CD226, NKX2-5, TLR2, DPP6, KLRB1, VDR, SCARB1, NEDD4L, and SREBF2 genes, and intragenic variants rs12487066, rs7807268, rs10896449, and rs944289. A total of 13 genetic markers were associated with the "IHD and AH" phenotype, including variants in the BTNL2, EGFR, CNTNAP2, SCARB1, and HNF1A genes, and intragenic polymorphisms rs801114, rs10499194, rs13207033, rs2398162, rs6501455, and rs1160312. A total of 14 genetic variants were associated with a combination of several diseases of cardiovascular continuum (CVC), including those in the TAS2R38, SEZ6L, APOA2, KLF7, CETP, ITGA4, RAD54B, LDLR, and MTAP genes, along with intragenic variants rs1333048, rs1333049, and rs6501455. One common genetic marker was identified for the "IHD only" and "IHD and AH" phenotypes: rs4765623 in the SCARB1 gene; two common genetic markers, rs663048 in SEZ6L and intragenic rs6501455, were identified for the "IHD and AH" phenotype and a combination of several diseases (syntropy); there were no common genetic markers for the "syntropy" and "IHD only" phenotypes. Classificatory analysis of the relationships between the associated genes and metabolic pathways revealed that lipid-metabolizing genes are involved in the development of all three CVC variants, whereas immunity-response genes are specific to the "IHD only" phenotype. The study demonstrated that comorbidity presents additional challenges in association studies of disease predisposition, since the genetic profile of combined forms of pathology can be markedly different from those for isolated "single" forms of a disease.
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Affiliation(s)
- O. A. Makeeva
- Research Institute of Medical Genetics, Nab. Ushayki, 10, Tomsk, 634050, Russia
- Research Institute for Complex Issues of Cardiovascular Diseases, Sosnovy Blvd., 6, Kemerovo, 650000, Russia
| | - A. A. Sleptsov
- Research Institute of Medical Genetics, Nab. Ushayki, 10, Tomsk, 634050, Russia
| | - E. V. Kulish
- Research Institute of Medical Genetics, Nab. Ushayki, 10, Tomsk, 634050, Russia
| | - O. L. Barbarash
- Research Institute for Complex Issues of Cardiovascular Diseases, Sosnovy Blvd., 6, Kemerovo, 650000, Russia
| | - A. M. Mazur
- Genoanalitika, Leninskie Gory, 1/77, Off. 102, Moscow, 119234, Russia
| | - E. B. Prokhorchuk
- Genoanalitika, Leninskie Gory, 1/77, Off. 102, Moscow, 119234, Russia
| | - N. N. Chekanov
- Genoanalitika, Leninskie Gory, 1/77, Off. 102, Moscow, 119234, Russia
| | - V. A. Stepanov
- Research Institute of Medical Genetics, Nab. Ushayki, 10, Tomsk, 634050, Russia
| | - V. P. Puzyrev
- Research Institute of Medical Genetics, Nab. Ushayki, 10, Tomsk, 634050, Russia
- Siberian State Medical University, Moskovskiy Trakt, 2, Tomsk, 634050, Russia
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23
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Kim JH, Cheong HS, Kim LH, Shin HJ, Na HS, Chung MW, Shin HD. Direct sequencing for comprehensive screening of LDLR genetic polymorphisms among five ethnic populations. Genes Genomics 2015. [DOI: 10.1007/s13258-014-0244-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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24
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Lee JD, Hsiao KM, Wang TC, Lee TH, Kuo YW, Huang YC, Hsu HL, Lin YH, Wu CY, Huang YC, Lee M, Yang HT, Hsu CY, Pan YT. Mutual Effect of rs688 and rs5925 in Regulating Low-Density Lipoprotein Receptor Splicing. DNA Cell Biol 2014; 33:869-75. [DOI: 10.1089/dna.2014.2577] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Jiann-Der Lee
- Department of Neurology, Chang Gung Memorial Hospital at Chiayi, and School of Traditional Chinese Medicine, College of Medicine, Chang Gung University, Chiayi, Taiwan
- Department of Life Science, National Chung Cheng University, Chiayi, Taiwan
| | - Kuang-Ming Hsiao
- Department of Life Science, National Chung Cheng University, Chiayi, Taiwan
| | - Ting-Chung Wang
- Department of Neurosurgery, Chang Gung Memorial Hospital at Chiayi, Chiayi, Taiwan
| | - Tsong-Hai Lee
- Department of Neurology, Chang Gung Memorial Hospital at Taoyuan, and Chang Gung University, Taoyuan, Taiwan
| | - Ya-Wen Kuo
- Department of Nursing, Asia University, Taichung Taiwan
| | - Yen-Chu Huang
- Department of Neurology, Chang Gung Memorial Hospital at Chiayi, and School of Traditional Chinese Medicine, College of Medicine, Chang Gung University, Chiayi, Taiwan
| | - Huan-Lin Hsu
- Department of Neurology, Chang Gung Memorial Hospital at Chiayi, Chiayi, Taiwan
| | - Ya-Hui Lin
- Department of Neurology, Chang Gung Memorial Hospital at Chiayi, Chiayi, Taiwan
| | - Chih-Ying Wu
- Department of Neurology, Chang Gung Memorial Hospital at Chiayi, Chiayi, Taiwan
| | - Ying-Chih Huang
- Department of Neurology, Chang Gung Memorial Hospital at Chiayi, Chiayi, Taiwan
| | - Meng Lee
- Department of Neurology, Chang Gung Memorial Hospital at Chiayi, and School of Traditional Chinese Medicine, College of Medicine, Chang Gung University, Chiayi, Taiwan
| | - Hsin-Ta Yang
- Department of Neurology, Chang Gung Memorial Hospital at Chiayi, Chiayi, Taiwan
| | - Chia-Yu Hsu
- Department of Neurology, Chang Gung Memorial Hospital at Chiayi, Chiayi, Taiwan
| | - Yi-Ting Pan
- Department of Neurology, Chang Gung Memorial Hospital at Chiayi, Chiayi, Taiwan
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25
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Hussain Y, Ding Q, Connelly PW, Brunt JH, Ban MR, McIntyre AD, Huff MW, Gros R, Hegele RA, Feldman RD. G-protein estrogen receptor as a regulator of low-density lipoprotein cholesterol metabolism: cellular and population genetic studies. Arterioscler Thromb Vasc Biol 2014; 35:213-21. [PMID: 25395619 DOI: 10.1161/atvbaha.114.304326] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
OBJECTIVE Estrogen deficiency is linked with increased low-density lipoprotein (LDL) cholesterol. The hormone receptor mediating this effect is unknown. G-protein estrogen receptor (GPER) is a recently recognized G-protein-coupled receptor that is activated by estrogens. We recently identified a common hypofunctional missense variant of GPER, namely P16L. However, the role of GPER in LDL metabolism is unknown. Therefore, we examined the association of the P16L genotype with plasma LDL cholesterol level. Furthermore, we studied the role of GPER in regulating expression of the LDL receptor and proprotein convertase subtilisin kexin type 9. APPROACH AND RESULTS Our discovery cohort was a genetically isolated population of Northern European descent, and our validation cohort consisted of normal, healthy women aged 18 to 56 years from London, Ontario. In addition, we examined the effect of GPER on the regulation of proprotein convertase subtilisin kexin type 9 and LDL receptor expression by the treatment with the GPER agonist, G1. In the discovery cohort, GPER P16L genotype was associated with a significant increase in LDL cholesterol (mean±SEM): 3.18±0.05, 3.25±0.08, and 4.25±0.33 mmol/L, respectively, in subjects with CC (homozygous for P16), CT (heterozygotes), and TT (homozygous for L16) genotypes (P<0.05). In the validation cohort (n=339), the GPER P16L genotype was associated with a similar increase in LDL cholesterol: 2.17±0.05, 2.34±0.06, and 2.42±0.16 mmol/L, respectively, in subjects with CC, CT, and TT genotypes (P<0.05). In the human hepatic carcinoma cell line, the GPER agonist, G1, mediated a concentration-dependent increase in LDL receptor expression, blocked by either pretreatment with the GPER antagonist G15 or by shRNA-mediated GPER downregulation. G1 also mediated a GPER- and concentration-dependent decrease in proprotein convertase subtilisin kexin type 9 expression. CONCLUSIONS GPER activation upregulates LDL receptor expression, probably at least, in part, via proprotein convertase subtilisin kexin type 9 downregulation. Furthermore, humans carrying the hypofunctional P16L genetic variant of GPER have increased plasma LDL cholesterol. In aggregate, these data suggest an important role of GPER in the regulation of LDL receptor expression and consequently LDL metabolism.
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Affiliation(s)
- Yasin Hussain
- From the Robarts Research Institute (Y.H., Q.D., M.R.B., A.D.M., M.W.H., R.G., R.A.H., R.D.F.) and Departments of Medicine (M.W.H., R.G., R.A.H., R.D.F.), Physiology and Pharmacology (R.G., R.A.H., R.D.F.), and Biochemistry (M.W.H.), Western University, London, Ontario, Canada; Department of Medicine, University of Toronto, Toronto, Ontario, Canada (P.W.C.); and Department of Public Health and Social Policy, University of Victoria, Victoria, British Columbia, Canada (J.H.B.)
| | - Qingming Ding
- From the Robarts Research Institute (Y.H., Q.D., M.R.B., A.D.M., M.W.H., R.G., R.A.H., R.D.F.) and Departments of Medicine (M.W.H., R.G., R.A.H., R.D.F.), Physiology and Pharmacology (R.G., R.A.H., R.D.F.), and Biochemistry (M.W.H.), Western University, London, Ontario, Canada; Department of Medicine, University of Toronto, Toronto, Ontario, Canada (P.W.C.); and Department of Public Health and Social Policy, University of Victoria, Victoria, British Columbia, Canada (J.H.B.)
| | - Philip W Connelly
- From the Robarts Research Institute (Y.H., Q.D., M.R.B., A.D.M., M.W.H., R.G., R.A.H., R.D.F.) and Departments of Medicine (M.W.H., R.G., R.A.H., R.D.F.), Physiology and Pharmacology (R.G., R.A.H., R.D.F.), and Biochemistry (M.W.H.), Western University, London, Ontario, Canada; Department of Medicine, University of Toronto, Toronto, Ontario, Canada (P.W.C.); and Department of Public Health and Social Policy, University of Victoria, Victoria, British Columbia, Canada (J.H.B.)
| | - J Howard Brunt
- From the Robarts Research Institute (Y.H., Q.D., M.R.B., A.D.M., M.W.H., R.G., R.A.H., R.D.F.) and Departments of Medicine (M.W.H., R.G., R.A.H., R.D.F.), Physiology and Pharmacology (R.G., R.A.H., R.D.F.), and Biochemistry (M.W.H.), Western University, London, Ontario, Canada; Department of Medicine, University of Toronto, Toronto, Ontario, Canada (P.W.C.); and Department of Public Health and Social Policy, University of Victoria, Victoria, British Columbia, Canada (J.H.B.)
| | - Matthew R Ban
- From the Robarts Research Institute (Y.H., Q.D., M.R.B., A.D.M., M.W.H., R.G., R.A.H., R.D.F.) and Departments of Medicine (M.W.H., R.G., R.A.H., R.D.F.), Physiology and Pharmacology (R.G., R.A.H., R.D.F.), and Biochemistry (M.W.H.), Western University, London, Ontario, Canada; Department of Medicine, University of Toronto, Toronto, Ontario, Canada (P.W.C.); and Department of Public Health and Social Policy, University of Victoria, Victoria, British Columbia, Canada (J.H.B.)
| | - Adam D McIntyre
- From the Robarts Research Institute (Y.H., Q.D., M.R.B., A.D.M., M.W.H., R.G., R.A.H., R.D.F.) and Departments of Medicine (M.W.H., R.G., R.A.H., R.D.F.), Physiology and Pharmacology (R.G., R.A.H., R.D.F.), and Biochemistry (M.W.H.), Western University, London, Ontario, Canada; Department of Medicine, University of Toronto, Toronto, Ontario, Canada (P.W.C.); and Department of Public Health and Social Policy, University of Victoria, Victoria, British Columbia, Canada (J.H.B.)
| | - Murray W Huff
- From the Robarts Research Institute (Y.H., Q.D., M.R.B., A.D.M., M.W.H., R.G., R.A.H., R.D.F.) and Departments of Medicine (M.W.H., R.G., R.A.H., R.D.F.), Physiology and Pharmacology (R.G., R.A.H., R.D.F.), and Biochemistry (M.W.H.), Western University, London, Ontario, Canada; Department of Medicine, University of Toronto, Toronto, Ontario, Canada (P.W.C.); and Department of Public Health and Social Policy, University of Victoria, Victoria, British Columbia, Canada (J.H.B.)
| | - Robert Gros
- From the Robarts Research Institute (Y.H., Q.D., M.R.B., A.D.M., M.W.H., R.G., R.A.H., R.D.F.) and Departments of Medicine (M.W.H., R.G., R.A.H., R.D.F.), Physiology and Pharmacology (R.G., R.A.H., R.D.F.), and Biochemistry (M.W.H.), Western University, London, Ontario, Canada; Department of Medicine, University of Toronto, Toronto, Ontario, Canada (P.W.C.); and Department of Public Health and Social Policy, University of Victoria, Victoria, British Columbia, Canada (J.H.B.)
| | - Robert A Hegele
- From the Robarts Research Institute (Y.H., Q.D., M.R.B., A.D.M., M.W.H., R.G., R.A.H., R.D.F.) and Departments of Medicine (M.W.H., R.G., R.A.H., R.D.F.), Physiology and Pharmacology (R.G., R.A.H., R.D.F.), and Biochemistry (M.W.H.), Western University, London, Ontario, Canada; Department of Medicine, University of Toronto, Toronto, Ontario, Canada (P.W.C.); and Department of Public Health and Social Policy, University of Victoria, Victoria, British Columbia, Canada (J.H.B.)
| | - Ross D Feldman
- From the Robarts Research Institute (Y.H., Q.D., M.R.B., A.D.M., M.W.H., R.G., R.A.H., R.D.F.) and Departments of Medicine (M.W.H., R.G., R.A.H., R.D.F.), Physiology and Pharmacology (R.G., R.A.H., R.D.F.), and Biochemistry (M.W.H.), Western University, London, Ontario, Canada; Department of Medicine, University of Toronto, Toronto, Ontario, Canada (P.W.C.); and Department of Public Health and Social Policy, University of Victoria, Victoria, British Columbia, Canada (J.H.B.).
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26
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Cymbron T, Mendes P, Ramos A, Raposo M, Kazachkova N, Medeiros AM, Bruges-Armas J, Bourbon M, Lima M. Familial hypercholesterolemia: Molecular characterization of possible cases from the Azores Islands (Portugal). Meta Gene 2014; 2:638-45. [PMID: 25606447 PMCID: PMC4287853 DOI: 10.1016/j.mgene.2014.08.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2014] [Revised: 07/30/2014] [Accepted: 08/15/2014] [Indexed: 01/17/2023] Open
Abstract
Familial hypercholesterolemia (FH) is an autosomal dominant disorder of the cholesterol metabolism, which constitutes a risk factor for coronary arterial disease (CAD). In the Azores Islands (Portugal), where mortality from CAD doubles its rate comparatively to the rest of the country and where a high frequency of dyslipidemia has been reported, the prevalence and distribution of FH remain unknown. The molecular characterization of a group of 33 possible cases of FH of Azorean background was undertaken in this study. A DNA array was initially used to search mutations in the LDLR, APOB and PCSK9 loci in 10 unrelated possible cases of FH. No mutations were detected in the array; after sequencing the full LDLR gene, 18 variants were identified, corresponding to two missense (c.806G > A; c.1171G > A) and sixteen synonymous alterations. Six of the synonymous variants which are consistently described in the literature as associated with altered cholesterol levels were used to build haplotypes. The most frequent haplotype corresponded to TTCGCC (45%), a “risk” haplotype, formed exclusively by alleles that were reported to increase cholesterol levels. Some of the variants detected in the full sequencing of the LDLR gene fell within the ligand-binding domain of this gene, defined by exons 2 to 6. To add information as to the role of such variants, these exons were sequenced in the remaining 23 possible FH cases. Two missense alterations (c.185C > T; c.806G > A) were found in this subset of possible FH cases. The missense alteration c.185C > T, identified in one individual, is novel for the Portuguese population. In silico analysis was not conclusive for this alteration, whose role will have to be further investigated. This study represents the first approach to the establishment of the mutational profile of FH in the Azores Islands.
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Affiliation(s)
- Teresa Cymbron
- Centre of Research in Natural Resources (CIRN), Department of Biology, University of the Azores, 9501-801 Ponta Delgada, Azores, Portugal ; Institute for Molecular and Cell Biology (IBMC), University of Porto, 4150-180 Porto, Portugal
| | - Patrícia Mendes
- The Azores School of New Technologies (ENTA), 9504-540 Ponta Delgada, Azores, Portugal
| | - Amanda Ramos
- Centre of Research in Natural Resources (CIRN), Department of Biology, University of the Azores, 9501-801 Ponta Delgada, Azores, Portugal ; Institute for Molecular and Cell Biology (IBMC), University of Porto, 4150-180 Porto, Portugal
| | - Mafalda Raposo
- Centre of Research in Natural Resources (CIRN), Department of Biology, University of the Azores, 9501-801 Ponta Delgada, Azores, Portugal ; Institute for Molecular and Cell Biology (IBMC), University of Porto, 4150-180 Porto, Portugal
| | - Nadiya Kazachkova
- Centre of Research in Natural Resources (CIRN), Department of Biology, University of the Azores, 9501-801 Ponta Delgada, Azores, Portugal ; Institute for Molecular and Cell Biology (IBMC), University of Porto, 4150-180 Porto, Portugal
| | - Ana Margarida Medeiros
- Grupo de Investigação Cardiovascular, Unidade I&D, Departamento de Promoção da Saúde e Prevenção de Doenças Não Transmissíveis, Instituto Nacional de Saúde Dr. Ricardo Jorge, 1649-040 Lisboa, Portugal ; Centre for Biodiversity, Functional and Integrative Genomics (BioFIG), Faculty of Sciences, University of Lisboa, 1749-016 Lisboa, Portugal
| | - Jácome Bruges-Armas
- Institute for Molecular and Cell Biology (IBMC), University of Porto, 4150-180 Porto, Portugal ; Specialized Service of Epidemiology and Molecular Biology (SEEBMO), Hospital of Santo Espírito, 9700-049 Angra do Heroísmo, Azores, Portugal
| | - Mafalda Bourbon
- Grupo de Investigação Cardiovascular, Unidade I&D, Departamento de Promoção da Saúde e Prevenção de Doenças Não Transmissíveis, Instituto Nacional de Saúde Dr. Ricardo Jorge, 1649-040 Lisboa, Portugal ; Centre for Biodiversity, Functional and Integrative Genomics (BioFIG), Faculty of Sciences, University of Lisboa, 1749-016 Lisboa, Portugal
| | - Manuela Lima
- Centre of Research in Natural Resources (CIRN), Department of Biology, University of the Azores, 9501-801 Ponta Delgada, Azores, Portugal ; Institute for Molecular and Cell Biology (IBMC), University of Porto, 4150-180 Porto, Portugal
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27
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Stormo C, Kringen MK, Lyle R, Olstad OK, Sachse D, Berg JP, Piehler AP. RNA-sequencing analysis of HepG2 cells treated with atorvastatin. PLoS One 2014; 9:e105836. [PMID: 25153832 PMCID: PMC4143339 DOI: 10.1371/journal.pone.0105836] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2013] [Accepted: 07/30/2014] [Indexed: 01/28/2023] Open
Abstract
The cholesterol-lowering drug atorvastatin is among the most prescribed drug in the world. Alternative splicing in a number of genes has been reported to be associated with variable statin response. RNA-seq has proven to be a powerful technique for genome-wide splice variant analysis. In the present study, we sought to investigate atorvastatin responsive splice variants in HepG2 cells using RNA-seq analysis to identify novel candidate genes implicated in cholesterol homeostasis and in the statin response. HepG2 cells were treated with 10 µM atorvastatin for 24 hours. RNA-seq and exon array analyses were performed. The validation of selected genes was performed using Taqman gene expression assays. RNA-seq analysis identified 121 genes and 98 specific splice variants, of which four were minor splice variants to be differentially expressed, 11 were genes with potential changes in their splicing patterns (SYCP3, ZNF195, ZNF674, MYD88, WHSC1, KIF16B, ZNF92, AGER, FCHO1, SLC6A12 and AKAP9), and one was a gene (RAP1GAP) with differential promoter usage. The IL21R transcript was detected to be differentially expressed via RNA-seq and RT-qPCR, but not in the exon array. In conclusion, several novel candidate genes that are affected by atorvastatin treatment were identified in this study. Further studies are needed to determine the biological significance of the atorvastatin responsive splice variants that have been uniquely identified using RNA-seq.
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Affiliation(s)
- Camilla Stormo
- Department of Medical Biochemistry, Oslo University Hospital, Ullevål, Oslo, Norway
| | | | - Robert Lyle
- Department of Medical Genetics, Oslo University Hospital and University of Oslo, Oslo, Norway
| | | | - Daniel Sachse
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Jens P. Berg
- Department of Medical Biochemistry, Oslo University Hospital, Ullevål, Oslo, Norway
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
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28
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Pavlovic Z, Singh RK, Bakovic M. A novel murine CTP:phosphoethanolamine cytidylyltransferase splice variant is a post-translational repressor and an indicator that both cytidylyltransferase domains are required for activity. Gene 2014; 543:58-68. [PMID: 24703999 DOI: 10.1016/j.gene.2014.04.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2013] [Revised: 03/20/2014] [Accepted: 04/01/2014] [Indexed: 11/27/2022]
Abstract
CTP:phosphoethanolamine cytidylyltransferase (Pcyt2) has an important regulatory function in biosynthesis of the membrane phospholipid phosphatidylethanolamine. We previously determined that the full-length Pcyt2α and its splice variant Pcyt2β are the main active isoforms of this enzyme. Here we report that mouse Pcyt2 could be spliced at Introns 7 and 8 to produce a unique third isoform, Pcyt2γ, in which the second cytidylyltransferase domain at the C-terminus becomes deleted. Pcyt2γ is ubiquitously expressed in embryonic and adult mouse tissues, and is the most abundant in the kidney, skeletal muscle and testis. Pcyt2γ splicing mechanism dominates over Pcyt2β exon-skipping mechanism in most examined tissues. Although Pcyt2γ maintains the N-terminal cytidylyltransferase domain as most cytidylyltransferases, the lack of the C-terminal cytidylyltransferase domain causes a complete loss of catalytic activity. However, Pcyt2γ interacts with the active isoform, Pcyt2α, and significantly reduces Pcyt2α homodimerization and activity. The inactive N-domain (H35Y, H35A) and C-domain (H244Y, H244A) mutants of Pcyt2α also reduce Pcyt2α homodimerization and activity. This study revealed the importance of both cytidylyltransferase (35)HYGH and (244)HIGH motifs for the activity of murine Pcyt2α and established that the naturally occurring splice variant Pcyt2γ has a function to restrain the enzyme activity through the formation of unproductive enzyme complexes.
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Affiliation(s)
- Zvezdan Pavlovic
- Department of Human Health and Nutritional Sciences, University of Guelph, 50 Stone Road East, Guelph, Ontario N1G2W1, Canada.
| | - Ratnesh Kumar Singh
- Department of Human Health and Nutritional Sciences, University of Guelph, 50 Stone Road East, Guelph, Ontario N1G2W1, Canada
| | - Marica Bakovic
- Department of Human Health and Nutritional Sciences, University of Guelph, 50 Stone Road East, Guelph, Ontario N1G2W1, Canada
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Gelissen IC, McLachlan AJ. The pharmacogenomics of statins. Pharmacol Res 2013; 88:99-106. [PMID: 24365577 DOI: 10.1016/j.phrs.2013.12.002] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/21/2013] [Revised: 12/06/2013] [Accepted: 12/12/2013] [Indexed: 12/24/2022]
Abstract
The statin class of cholesterol-lowering drugs have been used for decades to successfully lower plasma cholesterol concentrations and cardiovascular risk. Adverse effects of statins are generally considered mild, but increase with age of patients and polypharmacy. One aspect of statin therapy that is still difficult for prescribers to predict is the individual's response to statin therapy. Recent advances in the field of pharmacogenomics have indicated variants of candidate genes that affect statin efficacy and safety. In this review, a number of candidates that affect statin pharmacokinetics and pharmacodynamics are discussed. Some of these candidates, in particular those involved in import and efflux of statins, have now been linked to increased risk of side effects. Furthermore, pharmacogenomic studies continue to reveal new players that are involved in the fine-tuning of the complex regulation of cholesterol homeostasis and response to statins.
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Affiliation(s)
| | - Andrew J McLachlan
- Faculty of Pharmacy, University of Sydney, NSW, Australia; Centre for Education and Research on Ageing, Concord Hospital, Sydney, NSW, Australia
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Vasquez JB, Fardo DW, Estus S. ABCA7 expression is associated with Alzheimer's disease polymorphism and disease status. Neurosci Lett 2013; 556:58-62. [PMID: 24141082 DOI: 10.1016/j.neulet.2013.09.058] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2013] [Revised: 09/24/2013] [Accepted: 09/26/2013] [Indexed: 12/15/2022]
Abstract
Genome-wide association studies (GWAS) have implicated a series of single nucleotide polymorphisms (SNPs) in Alzheimer's disease (AD) risk. Elucidating the function of these SNPs is critical to identify the underlying pathways and, potentially, novel therapeutic agents. SNPs within the gene ATP binding cassette A7 (ABCA7) reached significance in these studies, warranting investigation into their actions. Here, we analyzed ABCA7 expression in a set of human brain samples as a function of AD-associated SNPs and AD status. We report that the rs3764650T allele that decreases AD risk is associated with increased ABCA7 expression. However, ABCA7 expression is increased in AD individuals. We interpret our findings as suggesting a model wherein increased ABCA7 expression reduces AD risk and that the increased ABCA7 observed in AD reflects an inadequate compensatory change.
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Affiliation(s)
- Jared B Vasquez
- Department of Physiology, Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY 40536, United States
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Yu CY, Theusch E, Lo K, Mangravite LM, Naidoo D, Kutilova M, Medina MW. HNRNPA1 regulates HMGCR alternative splicing and modulates cellular cholesterol metabolism. Hum Mol Genet 2013; 23:319-32. [PMID: 24001602 DOI: 10.1093/hmg/ddt422] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
3-hydroxy-3-methylglutaryl-Coenzyme A reductase (HMGCR) encodes the rate-limiting enzyme in the cholesterol biosynthesis pathway and is inhibited by statins, a class of cholesterol-lowering drugs. Expression of an alternatively spliced HMGCR transcript lacking exon 13, HMGCR13(-), has been implicated in the variation of plasma LDL-cholesterol (LDL-C) and is the single most informative molecular marker of LDL-C response to statins. Given the physiological importance of this transcript, our goal was to identify molecules that regulate HMGCR alternative splicing. We recently reported gene expression changes in 480 lymphoblastoid cell lines (LCLs) after in vitro simvastatin treatment, and identified a number of statin-responsive genes involved in mRNA splicing. Heterogeneous nuclear ribonucleoprotein A1 (HNRNPA1) was chosen for follow-up since rs3846662, an HMGCR SNP that regulates exon 13 skipping, was predicted to alter an HNRNPA1 binding motif. Here, we not only demonstrate that rs3846662 modulates HNRNPA1 binding, but also that sterol depletion of human hepatoma cell lines reduced HNRNPA1 mRNA levels, an effect that was reversed with sterol add-back. Overexpression of HNRNPA1 increased the ratio of HMGCR13(-) to total HMGCR transcripts by both directly increasing exon 13 skipping in an allele-related manner and specifically stabilizing the HMGCR13(-) transcript. Importantly, HNRNPA1 overexpression also diminished HMGCR enzyme activity, enhanced LDL-C uptake and increased cellular apolipoprotein B (APOB). rs1920045, an SNP associated with HNRNPA1 exon 8 alternative splicing, was also associated with smaller statin-induced reduction in total cholesterol from two independent clinical trials. These results suggest that HNRNPA1 plays a role in the variation of cardiovascular disease risk and statin response.
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Affiliation(s)
- Chi-Yi Yu
- Children's Hospital Oakland Research Institute, Oakland, CA 94609, USA
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Ellingson MS, Wick MJ, White WM, Raymond KM, Saenger AK, Pichurin PN, Wassif CA, Porter FD, Babovic-Vuksanovic D. Pregnancy in an individual with mild Smith-Lemli-Opitz syndrome. Clin Genet 2013; 85:495-7. [PMID: 23790112 DOI: 10.1111/cge.12209] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2013] [Revised: 05/24/2013] [Accepted: 05/27/2013] [Indexed: 11/29/2022]
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Tang JY, Lee JC, Hou MF, Wang CL, Chen CC, Huang HW, Chang HW. Alternative splicing for diseases, cancers, drugs, and databases. ScientificWorldJournal 2013; 2013:703568. [PMID: 23766705 PMCID: PMC3674688 DOI: 10.1155/2013/703568] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2013] [Accepted: 04/30/2013] [Indexed: 01/05/2023] Open
Abstract
Alternative splicing is a major diversification mechanism in the human transcriptome and proteome. Several diseases, including cancers, have been associated with dysregulation of alternative splicing. Thus, correcting alternative splicing may restore normal cell physiology in patients with these diseases. This paper summarizes several alternative splicing-related diseases, including cancers and their target genes. Since new cancer drugs often target spliceosomes, several clinical drugs and natural products or their synthesized derivatives were analyzed to determine their effects on alternative splicing. Other agents known to have modulating effects on alternative splicing during therapeutic treatment of cancer are also discussed. Several commonly used bioinformatics resources are also summarized.
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Affiliation(s)
- Jen-Yang Tang
- Department of Radiation Oncology, Faculty of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan
- Department of Radiation Oncology, Kaohsiung Medical University Hospital, Kaohsiung 807, Taiwan
- Cancer Center, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 807, Taiwan
| | - Jin-Ching Lee
- Department of Biotechnology, Kaohsiung Medical University, Kaohsiung 807, Taiwan
| | - Ming-Feng Hou
- Cancer Center, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 807, Taiwan
- Institute of Clinical Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan
- Kaohsiung Municipal Ta-Tung Hospital, Kaohsiung 807, Taiwan
| | - Chun-Lin Wang
- Bioresource Collection and Research Center, Food Industry Research and Development Institute, Hsinchu 300, Taiwan
| | - Chien-Chi Chen
- Bioresource Collection and Research Center, Food Industry Research and Development Institute, Hsinchu 300, Taiwan
| | - Hurng-Wern Huang
- Institute of Biomedical Science, National Sun Yat-Sen University, Kaohsiung 807, Taiwan
| | - Hsueh-Wei Chang
- Cancer Center, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 807, Taiwan
- Graduate Institute of Natural Products, Kaohsiung Medical University, Kaohsiung 807, Taiwan
- Department of Biomedical Science and Environmental Biology, Kaohsiung Medical University, Kaohsiung 807, Taiwan
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Wu Y, Waite LL, Jackson AU, Sheu WHH, Buyske S, Absher D, Arnett DK, Boerwinkle E, Bonnycastle LL, Carty CL, Cheng I, Cochran B, Croteau-Chonka DC, Dumitrescu L, Eaton CB, Franceschini N, Guo X, Henderson BE, Hindorff LA, Kim E, Kinnunen L, Komulainen P, Lee WJ, Le Marchand L, Lin Y, Lindström J, Lingaas-Holmen O, Mitchell SL, Narisu N, Robinson JG, Schumacher F, Stančáková A, Sundvall J, Sung YJ, Swift AJ, Wang WC, Wilkens L, Wilsgaard T, Young AM, Adair LS, Ballantyne CM, Bůžková P, Chakravarti A, Collins FS, Duggan D, Feranil AB, Ho LT, Hung YJ, Hunt SC, Hveem K, Juang JMJ, Kesäniemi AY, Kuusisto J, Laakso M, Lakka TA, Lee IT, Leppert MF, Matise TC, Moilanen L, Njølstad I, Peters U, Quertermous T, Rauramaa R, Rotter JI, Saramies J, Tuomilehto J, Uusitupa M, Wang TD, Boehnke M, Haiman CA, Chen YDI, Kooperberg C, Assimes TL, Crawford DC, Hsiung CA, North KE, Mohlke KL. Trans-ethnic fine-mapping of lipid loci identifies population-specific signals and allelic heterogeneity that increases the trait variance explained. PLoS Genet 2013; 9:e1003379. [PMID: 23555291 PMCID: PMC3605054 DOI: 10.1371/journal.pgen.1003379] [Citation(s) in RCA: 101] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2012] [Accepted: 01/19/2013] [Indexed: 12/03/2022] Open
Abstract
Genome-wide association studies (GWAS) have identified ∼100 loci associated with blood lipid levels, but much of the trait heritability remains unexplained, and at most loci the identities of the trait-influencing variants remain unknown. We conducted a trans-ethnic fine-mapping study at 18, 22, and 18 GWAS loci on the Metabochip for their association with triglycerides (TG), high-density lipoprotein cholesterol (HDL-C), and low-density lipoprotein cholesterol (LDL-C), respectively, in individuals of African American (n = 6,832), East Asian (n = 9,449), and European (n = 10,829) ancestry. We aimed to identify the variants with strongest association at each locus, identify additional and population-specific signals, refine association signals, and assess the relative significance of previously described functional variants. Among the 58 loci, 33 exhibited evidence of association at P<1×10−4 in at least one ancestry group. Sequential conditional analyses revealed that ten, nine, and four loci in African Americans, Europeans, and East Asians, respectively, exhibited two or more signals. At these loci, accounting for all signals led to a 1.3- to 1.8-fold increase in the explained phenotypic variance compared to the strongest signals. Distinct signals across ancestry groups were identified at PCSK9 and APOA5. Trans-ethnic analyses narrowed the signals to smaller sets of variants at GCKR, PPP1R3B, ABO, LCAT, and ABCA1. Of 27 variants reported previously to have functional effects, 74% exhibited the strongest association at the respective signal. In conclusion, trans-ethnic high-density genotyping and analysis confirm the presence of allelic heterogeneity, allow the identification of population-specific variants, and limit the number of candidate SNPs for functional studies. Lipid traits are heritable, but many of the DNA variants that influence lipid levels remain unknown. In a genomic region, more than one variant may affect gene expression or function, and the frequencies of these variants can differ across populations. Genotyping densely spaced variants in individuals with different ancestries may increase the chance of identifying variants that affect gene expression or function. We analyzed high-density genotyped variants for association with TG, HDL-C, and LDL-C in African Americans, East Asians, and Europeans. At several genomic regions, we provide evidence that two or more variants can influence lipid traits; across loci, these additional signals increase the proportion of trait variation that can be explained by genes. At some association signals shared across populations, combining data from individuals of different ancestries narrowed the set of likely functional variants. At PCSK9 and APOA5, the data suggest that different variants influence trait levels in different populations. Variants previously reported to alter gene expression or function frequently exhibited the strongest association at those signals. The multiple signals and population-specific characteristics of the loci described here may be shared by genetic loci for other complex traits.
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Affiliation(s)
- Ying Wu
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Lindsay L. Waite
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, United States of America
| | - Anne U. Jackson
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Wayne H-H. Sheu
- Division of Endocrine and Metabolism, Department of Internal Medicine, Taichung Veterans General Hospital, Taichung, Taiwan
- School of Medicine, National Yang-Ming University, Taipei, Taiwan
- College of Medicine, National Defense Medical Center, Taipei, Taiwan
| | - Steven Buyske
- Department of Statistics and Biostatistics, Rutgers University, Piscataway, New Jersey, United States of America
| | - Devin Absher
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, United States of America
| | - Donna K. Arnett
- Department of Epidemiology, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Eric Boerwinkle
- The Human Genetics Center, University of Texas Health Science Center, Houston, Texas, United States of America
| | - Lori L. Bonnycastle
- Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Cara L. Carty
- Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Iona Cheng
- University of Hawaii Cancer Center, Honolulu, Hawaii, United States of America
| | - Barbara Cochran
- The Human Genetics Center, University of Texas Health Science Center, Houston, Texas, United States of America
| | - Damien C. Croteau-Chonka
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Logan Dumitrescu
- Department of Molecular Physiology and Biophysics, Center for Human Genetics Research, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Charles B. Eaton
- Departments of Family Medicine and Epidemiology, Alpert Medical School, Brown University, Providence, Rhode Island, United States of America
| | - Nora Franceschini
- Department of Epidemiology, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Xiuqing Guo
- Medical Genetics Institute, Cedars-Sinai Medical Center, Los Angeles, California, United States of America
| | - Brian E. Henderson
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Lucia A. Hindorff
- Office of Population Genomics, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Eric Kim
- Medical Genetics Institute, Cedars-Sinai Medical Center, Los Angeles, California, United States of America
| | - Leena Kinnunen
- Diabetes Prevention Unit, National Institute for Health and Welfare, Helsinki, Finland
| | | | - Wen-Jane Lee
- Department of Medical Research, Taichung Veterans General Hospital, Taichung, Taiwan
| | - Loic Le Marchand
- University of Hawaii Cancer Center, Honolulu, Hawaii, United States of America
| | - Yi Lin
- Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Jaana Lindström
- Diabetes Prevention Unit, National Institute for Health and Welfare, Helsinki, Finland
| | - Oddgeir Lingaas-Holmen
- HUNT Research Centre, Department of Public Health and General Practice, Norwegian University of Science and Technology, Levanger, Norway
| | - Sabrina L. Mitchell
- Department of Molecular Physiology and Biophysics, Center for Human Genetics Research, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Narisu Narisu
- Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | | | - Fred Schumacher
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Alena Stančáková
- Department of Medicine, University of Eastern Finland and Kuopio University Hospital, Kuopio, Finland
| | - Jouko Sundvall
- National Institute for Health and Welfare, Disease Risk Unit, Helsinki, Finland
| | - Yun-Ju Sung
- Division of Biostatistics, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Amy J. Swift
- Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Wen-Chang Wang
- Division of Biostatistics and Bioinformatics, Institute of Population Health Sciences, National Health Research Institutes, Zhunan, Taiwan
| | - Lynne Wilkens
- University of Hawaii Cancer Center, Honolulu, Hawaii, United States of America
| | - Tom Wilsgaard
- Department of Community Medicine, Faculty of Health Sciences, University of Tromsø, Tromsø, Norway
| | - Alicia M. Young
- Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Linda S. Adair
- Department of Nutrition, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | | | - Petra Bůžková
- Department of Biostatistics, University of Washington, Seattle, Washington, United States of America
| | - Aravinda Chakravarti
- Center for Complex Disease Genomics, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Francis S. Collins
- Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - David Duggan
- Translational Genomics Research Institute, Phoenix, Arizona, United States of America
| | - Alan B. Feranil
- Office of Population Studies Foundation, University of San Carlos, Cebu, Philippines
| | - Low-Tone Ho
- School of Medicine, National Yang-Ming University, Taipei, Taiwan
- Department of Internal Medicine and Department of Medical Research and Education, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Yi-Jen Hung
- Division of Endocrinology and Metabolism, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan
| | - Steven C. Hunt
- Department of Internal Medicine, University of Utah, Salt Lake City, Utah, United States of America
| | - Kristian Hveem
- HUNT Research Centre, Department of Public Health and General Practice, Norwegian University of Science and Technology, Levanger, Norway
| | - Jyh-Ming J. Juang
- Cardiovascular Center and Division of Cardiology, Department of Internal Medicine, National Taiwan University Hospital and National Taiwan University College of Medicine, Taipei, Taiwan
| | - Antero Y. Kesäniemi
- Institute of Clinical Medicine, Department of Medicine, University of Oulu and Clinical Research Center, Oulu University Hospital, Oulu, Finland
| | - Johanna Kuusisto
- Department of Medicine, University of Eastern Finland and Kuopio University Hospital, Kuopio, Finland
| | - Markku Laakso
- Department of Medicine, University of Eastern Finland and Kuopio University Hospital, Kuopio, Finland
| | - Timo A. Lakka
- Kuopio Research Institute of Exercise Medicine, Kuopio, Finland
- Institute of Biomedicine/Physiology, University of Eastern Finland, Kuopio Campus, Kuopio, Finland
| | - I-Te Lee
- Division of Endocrine and Metabolism, Department of Internal Medicine, Taichung Veterans General Hospital, Taichung, Taiwan
- School of Medicine, National Yang-Ming University, Taipei, Taiwan
| | - Mark F. Leppert
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, Utah, United States of America
| | - Tara C. Matise
- Department of Genetics, Rutgers University, Piscataway, New Jersey, United States of America
| | - Leena Moilanen
- Department of Medicine, Kuopio University Hospital, Kuopio, Finland
- Pirkanmaa Hospital District, Tampere, Finland
| | - Inger Njølstad
- Department of Community Medicine, Faculty of Health Sciences, University of Tromsø, Tromsø, Norway
| | - Ulrike Peters
- Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
- School of Public Health, University of Washington, Seattle, Washington, United States of America
| | - Thomas Quertermous
- Department of Medicine, Stanford University School of Medicine, Stanford, California, United States of America
| | - Rainer Rauramaa
- Kuopio Research Institute of Exercise Medicine, Kuopio, Finland
- Department of Clinical Physiology and Nuclear Medicine, Kuopio University Hospital, Kuopio, Finland
| | - Jerome I. Rotter
- Medical Genetics Institute, Cedars-Sinai Medical Center, Los Angeles, California, United States of America
| | | | - Jaakko Tuomilehto
- Diabetes Prevention Unit, National Institute for Health and Welfare, Helsinki, Finland
- South Ostrobothnia Central Hospital, Seinäjoki, Finland
- Red RECAVA Grupo RD06/0014/0015, Hospital Universitario La Paz, Madrid, Spain
- Centre for Vascular Prevention, Danube-University Krems, Krems, Austria
| | - Matti Uusitupa
- Institute of Public Health and Clinical Nutrition, University of Eastern Finland, Kuopio, Finland
- Research Unit, Kuopio University Hospital, Kuopio, Finland
| | - Tzung-Dau Wang
- Cardiovascular Center and Division of Cardiology, Department of Internal Medicine, National Taiwan University Hospital and National Taiwan University College of Medicine, Taipei, Taiwan
| | - Michael Boehnke
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Christopher A. Haiman
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Yii-Der I. Chen
- Medical Genetics Institute, Cedars-Sinai Medical Center, Los Angeles, California, United States of America
| | - Charles Kooperberg
- Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Themistocles L. Assimes
- Department of Medicine, Stanford University School of Medicine, Stanford, California, United States of America
| | - Dana C. Crawford
- Department of Molecular Physiology and Biophysics, Center for Human Genetics Research, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Chao A. Hsiung
- Division of Biostatistics and Bioinformatics, Institute of Population Health Sciences, National Health Research Institutes, Zhunan, Taiwan
| | - Kari E. North
- Department of Epidemiology, University of North Carolina, Chapel Hill, North Carolina, United States of America
- Carolina Center for Genome Sciences, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Karen L. Mohlke
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina, United States of America
- Carolina Center for Genome Sciences, University of North Carolina, Chapel Hill, North Carolina, United States of America
- * E-mail:
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Gao F, Ihn HE, Medina MW, Krauss RM. A common polymorphism in the LDL receptor gene has multiple effects on LDL receptor function. Hum Mol Genet 2013; 22:1424-31. [PMID: 23297366 DOI: 10.1093/hmg/dds559] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
A common synonymous single nucleotide polymorphism in exon 12 of the low-density lipoprotein receptor (LDLR) gene, rs688, has been associated with increased plasma total and LDL cholesterol in several populations. Using immortalized lymphoblastoid cell lines from a healthy study population, we confirmed an earlier report that the minor allele of rs688 is associated with increased exon 12 alternative splicing (P < 0.05) and showed that this triggered nonsense-mediated decay (NMD) of the alternatively spliced LDLR mRNA. However, since synonymous single nucleotide polymorphisms may influence structure and function of the encoded proteins by co-translational effects, we sought to test whether rs688 was also functional in the full-length mRNA. In HepG2 cells expressing LDLR cDNA constructs engineered to contain the major or minor allele of rs688, the latter was associated with a smaller amount of LDLR protein at the cell surface (-21.8 ± 0.6%, P = 0.012), a higher amount in the lysosome fraction (+25.7 ± 0.3%, P = 0.037) and reduced uptake of fluorescently labeled LDL (-24.3 ± 0.7%, P < 0.01). Moreover, in the presence of exogenous proprotein convertase subtilisin/kexin type 9 (PCSK9), a protein that reduces cellular LDL uptake by promoting lysosomal degradation of LDLR, the minor allele resulted in reduced capacity of a PCSK9 monoclonal antibody to increase LDL uptake. These findings are consistent with the hypothesis that rs688, which is located in the β-propeller region of LDLR, has effects on LDLR activity beyond its role in alternative splicing due to impairment of LDLR endosomal recycling and/or PCSK9 binding, processes in which the β-propeller is critically involved.
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Affiliation(s)
- Feng Gao
- Children’s Hospital Oakland Research Institute, 5700 Martin Luther King Jr. Way, Oakland, CA 94609, USA
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36
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Rodrigues AC, Sobrino B, Genvigir FDV, Willrich MAV, Arazi SS, Dorea EL, Bernik MMS, Bertolami M, Faludi AA, Brion MJ, Carracedo A, Hirata MH, Hirata RDC. Genetic variants in genes related to lipid metabolism and atherosclerosis, dyslipidemia and atorvastatin response. Clin Chim Acta 2012; 417:8-11. [PMID: 23247049 DOI: 10.1016/j.cca.2012.11.028] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2012] [Revised: 11/27/2012] [Accepted: 11/27/2012] [Indexed: 01/06/2023]
Abstract
OBJECTIVE Using candidate gene approach, we have investigated the effect of single nucleotide polymorphism (SNP) in genes related to lipid metabolism and atherosclerosis on dyslipidemia and atorvastatin response. METHODS The study included 157 patients treated with atorvastatin and 145 controls. Genomic DNA was isolated and genotyped using SNPlex technology. RESULTS Allele and genotype disease association test revealed that APOB rs693 (OR: 2.2 [1.5-3.2], p=0.0001) and CD36 rs1984112 (OR: 3.7 [1.9-7.0], p=0.0002) SNPs were independent risk factors for hypercholesterolemia. Only APOB rs693 T variant allele was associated with increased LDL cholesterol levels (>160mg/dL). After atorvastatin treatment (10mg/day/4weeks), LIPC -514T allele was positively associated with LDL cholesterol reduction. CONCLUSION The current study reinforces the current knowledge that carrying APOB rs693 is an independent risk factor for dyslipidemia and higher LDL levels. Furthermore, we found that a variant of CD36 was associated with dyslipidemia as a risk (rs1984112) factor. Finally, atorvastatin response could be predicted by LIPC -514C>T SNP and physical activity. In conclusion, our data evidences the contribution of genetic markers and their interaction with environmental factor in the variability of statin response.
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Affiliation(s)
- A C Rodrigues
- Faculdade de Ciências Farmacêuticas, USP, São Paulo, SP, Brazil.
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Ling IF, Bhongsatiern J, Simpson JF, Fardo DW, Estus S. Genetics of clusterin isoform expression and Alzheimer's disease risk. PLoS One 2012; 7:e33923. [PMID: 22506010 PMCID: PMC3323613 DOI: 10.1371/journal.pone.0033923] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2011] [Accepted: 02/21/2012] [Indexed: 01/13/2023] Open
Abstract
The minor allele of rs11136000 within CLU is strongly associated with reduced Alzheimer's disease (AD) risk. The mechanism underlying this association is unclear. Here, we report that CLU1 and CLU2 are the two primary CLU isoforms in human brain; CLU1 and CLU2 share exons 2-9 but differ in exon 1 and proximal promoters. The expression of both CLU1 and CLU2 was increased in individuals with significant AD neuropathology. However, only CLU1 was associated with the rs11136000 genotype, with the minor "protective" rs11136000T allele being associated with increased CLU1 expression. Since CLU1 and CLU2 are predicted to encode intracellular and secreted proteins, respectively, we compared their expression; for both CLU1 and CLU2 transfected cells, clusterin is present in the secretory pathway, accumulates in the extracellular media, and is similar in size to clusterin in human brain. Overall, we interpret these results as indicating that the AD-protective minor rs11136000T allele is associated with increased CLU1 expression. Since CLU1 and CLU2 appear to produce similar proteins and are increased in AD, the AD-protection afforded by the rs11136000T allele may reflect increased soluble clusterin throughout life.
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Affiliation(s)
- I-Fang Ling
- Department of Physiology and Sanders-Brown Center on Aging, University of Kentucky, Lexington, Kentucky, United States of America
| | - Jiraganya Bhongsatiern
- Department of Physiology and Sanders-Brown Center on Aging, University of Kentucky, Lexington, Kentucky, United States of America
| | - James F. Simpson
- Department of Physiology and Sanders-Brown Center on Aging, University of Kentucky, Lexington, Kentucky, United States of America
| | - David W. Fardo
- Department of Biostatistics, University of Kentucky, Lexington, Kentucky, United States of America
| | - Steven Estus
- Department of Physiology and Sanders-Brown Center on Aging, University of Kentucky, Lexington, Kentucky, United States of America
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Lu ZX, Jiang P, Xing Y. Genetic variation of pre-mRNA alternative splicing in human populations. WILEY INTERDISCIPLINARY REVIEWS-RNA 2011; 3:581-92. [PMID: 22095823 DOI: 10.1002/wrna.120] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The precise splicing outcome of a transcribed gene is controlled by complex interactions between cis regulatory splicing signals and trans-acting regulators. In higher eukaryotes, alternative splicing is a prevalent mechanism for generating transcriptome and proteome diversity. Alternative splicing can modulate gene function, affect organismal phenotype and cause disease. Common genetic variation that affects splicing regulation can lead to differences in alternative splicing between human individuals and consequently impact expression level or protein function. In several well-documented examples, such natural variation of alternative splicing has indeed been shown to influence disease susceptibility and drug response. With new microarray and sequencing-based genomic technologies that can analyze eukaryotic transcriptomes at the exon or nucleotide level, it has become possible to globally compare the alternative splicing profiles across human individuals in any tissue or cell type of interest. Recent large-scale transcriptome studies using high-density splicing-sensitive microarray and deep RNA sequencing (RNA-Seq) have revealed widespread genetic variation of alternative splicing in humans. In the future, an extensive catalog of alternative splicing variation in human populations will help elucidate the molecular underpinnings of complex traits and human diseases, and shed light on the mechanisms of splicing regulation in human cells.
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Affiliation(s)
- Zhi-Xiang Lu
- Department of Internal Medicine, University of Iowa, Iowa City, IA, USA
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39
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Smith JD, Moylan JS, Hardin BJ, Chambers MA, Estus S, Telling GC, Reid MB. Prion protein expression and functional importance in skeletal muscle. Antioxid Redox Signal 2011; 15:2465-75. [PMID: 21453198 PMCID: PMC3176344 DOI: 10.1089/ars.2011.3945] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
UNLABELLED Skeletal muscle expresses prion protein (PrP) that buffers oxidant activity in neurons. AIMS We hypothesize that PrP deficiency would increase oxidant activity in skeletal muscle and alter redox-sensitive functions, including contraction and glucose uptake. We used real-time polymerase chain reaction and Western blot analysis to measure PrP mRNA and protein in human diaphragm, five murine muscles, and muscle-derived C2C12 cells. Effects of PrP deficiency were tested by comparing PrP-deficient mice versus wild-type mice and morpholino-knockdown versus vehicle-treated myotubes. Oxidant activity (dichlorofluorescin oxidation) and specific force were measured in murine diaphragm fiber bundles. RESULTS PrP content differs among mouse muscles (gastrocnemius>extensor digitorum longus, EDL>tibialis anterior, TA; soleus>diaphragm) as does glycosylation (di-, mono-, nonglycosylated; gastrocnemius, EDL, TA=60%, 30%, 10%; soleus, 30%, 40%, 30%; diaphragm, 30%, 30%, 40%). PrP is predominantly di-glycosylated in human diaphragm. PrP deficiency decreases body weight (15%) and EDL mass (9%); increases cytosolic oxidant activity (fiber bundles, 36%; C2C12 myotubes, 7%); and depresses specific force (12%) in adult (8-12 mos) but not adolescent (2 mos) mice. INNOVATION This study is the first to directly assess a role of prion protein in skeletal muscle function. CONCLUSIONS PrP content varies among murine skeletal muscles and is essential for maintaining normal redox homeostasis, muscle size, and contractile function in adult animals.
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Affiliation(s)
- Jeffrey D Smith
- Department of Physiology, University of Kentucky, Lexington, 40536, USA
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Worsley-Hunt R, Bernard V, Wasserman WW. Identification of cis-regulatory sequence variations in individual genome sequences. Genome Med 2011; 3:65. [PMID: 21989199 PMCID: PMC3239227 DOI: 10.1186/gm281] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Functional contributions of cis-regulatory sequence variations to human genetic disease are numerous. For instance, disrupting variations in a HNF4A transcription factor binding site upstream of the Factor IX gene contributes causally to hemophilia B Leyden. Although clinical genome sequence analysis currently focuses on the identification of protein-altering variation, the impact of cis-regulatory mutations can be similarly strong. New technologies are now enabling genome sequencing beyond exomes, revealing variation across the non-coding 98% of the genome responsible for developmental and physiological patterns of gene activity. The capacity to identify causal regulatory mutations is improving, but predicting functional changes in regulatory DNA sequences remains a great challenge. Here we explore the existing methods and software for prediction of functional variation situated in the cis-regulatory sequences governing gene transcription and RNA processing.
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Affiliation(s)
- Rebecca Worsley-Hunt
- Centre for Molecular Medicine and Therapeutics at the Child and Family Research Institute, Department of Medical Genetics, University of British Columbia, 950 West 28th Avenue, Vancouver, BC V5Z 4H4, Canada.
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41
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Simmons CR, Zou F, Younkin SG, Estus S. Evaluation of the global association between cholesterol-associated polymorphisms and Alzheimer's disease suggests a role for rs3846662 and HMGCR splicing in disease risk. Mol Neurodegener 2011; 6:62. [PMID: 21867541 PMCID: PMC3180274 DOI: 10.1186/1750-1326-6-62] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2011] [Accepted: 08/25/2011] [Indexed: 01/13/2023] Open
Abstract
BACKGROUND Recent genome-wide association studies (GWAS) have identified single nucleotide polymorphisms (SNP)s that are essentially unequivocally associated with peripheral cholesterol. Since the alleles of the APOE gene, which modulate peripheral cholesterol metabolism, and midlife plasma cholesterol are both associated with Alzheimer's disease (AD) risk, we have evaluated the hypothesis that SNPs associated with plasma cholesterol are also associated with AD. RESULTS Seventeen non-APOE SNPs reproducibly associated with cholesterol per GWAS were tested for association with AD in ~2,000 AD and ~4,000 non-AD subjects. As a group, these SNPs are associated with AD. Two SNPs in particular, rs3846662 and rs1532085, are associated with AD risk and age-of-onset. Additionally, rs3846662 was associated with HMGCR exon 13 splicing in human liver but not brain, possibly obscured by CNS cell-type heterogeneity. However, rs3846662 was associated with HMGCR exon 13 splicing in liver- and brain-derived cell lines. CONCLUSIONS Cholesterol-associated SNPs outside of APOE confer a global risk for AD. Rs3846662 and rs1532085 are associated with both AD risk and age-of-onset. Rs3846662 is associated with HMGCR exon 13 inclusion. Since rs3846662 affects AD risk and age-of-onset as well as statin responsiveness, this SNP may confound clinical trials evaluating the protective effects of statins on AD.
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Affiliation(s)
- Christopher R Simmons
- Department of Physiology, Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY, USA.
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Calandra S, Tarugi P, Speedy HE, Dean AF, Bertolini S, Shoulders CC. Mechanisms and genetic determinants regulating sterol absorption, circulating LDL levels, and sterol elimination: implications for classification and disease risk. J Lipid Res 2011; 52:1885-926. [PMID: 21862702 DOI: 10.1194/jlr.r017855] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
This review integrates historical biochemical and modern genetic findings that underpin our understanding of the low-density lipoprotein (LDL) dyslipidemias that bear on human disease. These range from life-threatening conditions of infancy through severe coronary heart disease of young adulthood, to indolent disorders of middle- and old-age. We particularly focus on the biological aspects of those gene mutations and variants that impact on sterol absorption and hepatobiliary excretion via specific membrane transporter systems (NPC1L1, ABCG5/8); the incorporation of dietary sterols (MTP) and of de novo synthesized lipids (HMGCR, TRIB1) into apoB-containing lipoproteins (APOB) and their release into the circulation (ANGPTL3, SARA2, SORT1); and receptor-mediated uptake of LDL and of intestinal and hepatic-derived lipoprotein remnants (LDLR, APOB, APOE, LDLRAP1, PCSK9, IDOL). The insights gained from integrating the wealth of genetic data with biological processes have important implications for the classification of clinical and presymptomatic diagnoses of traditional LDL dyslipidemias, sitosterolemia, and newly emerging phenotypes, as well as their management through both nutritional and pharmaceutical means.
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Affiliation(s)
- Sebastiano Calandra
- Department of Biomedical Sciences, University of Modena and Reggio Emilia, Modena, Italy.
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Burchett ME, Ling IF, Estus S. FBN1 isoform expression varies in a tissue and development-specific fashion. Biochem Biophys Res Commun 2011; 411:323-8. [PMID: 21726527 DOI: 10.1016/j.bbrc.2011.06.140] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2011] [Accepted: 06/18/2011] [Indexed: 12/17/2022]
Abstract
Mutations in FBN1 cause Marfan syndrome, a heritable disorder of connective tissue. FBN1 encodes the extracellular matrix protein, fibrillin. Our objective was to elucidate the extent that variation in RNA splicing contributes to FBN1 isoforms. To identify FBN1 splice variants, we scanned each of its 64 internal exons in a set of pooled human brain cDNA samples. FBN1 splicing is generally efficient as we identified only two variants. Neither variant has previously been reported in the literature and include (i) an isoform which contains a cryptic 105 basepair exon between exons 54 and 55 (54A-FBN1) and (ii) an isoform which contains a cryptic 62 basepair exon between exons 57 and 58 (57A-FBN1). We compared 57A-FBN1 and FBN1 expression in multiple human tissues, including adult skeletal muscle and brain, as well as fetal skeletal muscle, brain, liver, aorta, lung, skin, and heart. 57A-FBN1 represents 8-44% of FBN1 mRNA and varies in a tissue- and development-specific fashion. In adult brain, 57A-FBN1 represented 39±3 (%, mean±SD) of total FBN1 expression. In contrast, 57A-FBN1 represented 19±2 (%, mean±SD) of FBN1 expression in skeletal muscle. In fetal tissue, the 57A-FBN1 proportion was highest in brain (27%) and low elsewhere, e.g., skin, aorta and lung (9-13%). In summary, a significant proportion of FBN1 is expressed as 57A-FBN1 and this proportion varies in a tissue- and development-specific fashion. Since the 57A insertion creates a premature stop codon that mimics Marfan-associated mutations, the protein encoded by 57A-FBN1 is likely to not be functional. These results suggest that altered splicing may modulate disease severity, regulate FBN1 expression, and potentially represent a therapeutic target.
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Affiliation(s)
- Mary E Burchett
- University of Kentucky College of Medicine, University of Kentucky, Lexington, KY, USA.
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Simmons CR, Zou F, Younkin SG, Estus S. Rheumatoid arthritis-associated polymorphisms are not protective against Alzheimer's disease. Mol Neurodegener 2011; 6:33. [PMID: 21595938 PMCID: PMC3120711 DOI: 10.1186/1750-1326-6-33] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2011] [Accepted: 05/19/2011] [Indexed: 01/29/2023] Open
Abstract
Background Rheumatoid arthritis (RA) and Alzheimer's disease (AD) are inversely associated. To test the hypothesis that genetic elements associated with increased RA risk are associated with decreased AD risk, we evaluated RA genetic risk factors recently identified in genome-wide association studies (GWAS) for their association with AD in a two-stage, case-control analysis. Results In our Stage 1 analysis of ~800 AD and ~1,200 non-AD individuals, three of seventeen RA-associated SNPs were nominally associated with AD (p < 0.05) with one SNP, rs2837960, retaining significance after correction for multiple testing (p = 0.03). The rs2837960_G (minor) allele, which is associated with increased RA risk, was associated with increased AD risk. Analysis of these three SNPs in a Stage 2 population, consisting of ~1,100 AD and ~2,600 non-AD individuals, did not confirm their association with AD. Analysis of Stage 1 and 2 combined suggested that rs2837960 shows a trend for association with AD. When the Stage 2 population was age-matched for the Stage 1 population, rs2837960 exhibited a non-significant trend with AD. Combined analysis of Stage 1 and the age-matched Stage 2 subset showed a significant association of rs2837960 with AD (p = 0.002, OR 1.24) that retained significance following correction for age, sex and APOE (p = 0.02, OR = 1.20). Rs2837960 is near BACE2, which encodes an aspartic protease capable of processing the AD-associated amyloid precursor protein. Testing for an association between rs2837960 and the expression of BACE2 isoforms in human brain, we observed a trend between rs2837960 and the total expression of BACE2 and the expression of a BACE2 transcript lacking exon 7 (p = 0.07 and 0.10, respectively). Conclusions RA-associated SNPs are generally not associated with AD. Moreover, rs2837960_G is associated with increased risk of both RA and, in individuals less than 80 years of age, with AD. Overall, these results contest the hypothesis that genetic variants associated with RA confer protection against AD. Further investigation of rs2837960 is necessary to elucidate the mechanism by which rs2837960 contributes to both AD and RA risk, likely via modulation of BACE2 expression.
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Affiliation(s)
- Christopher R Simmons
- Department of Physiology, Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY, USA.
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Medina MW, Gao F, Naidoo D, Rudel LL, Temel RE, McDaniel AL, Marshall SM, Krauss RM. Coordinately regulated alternative splicing of genes involved in cholesterol biosynthesis and uptake. PLoS One 2011; 6:e19420. [PMID: 21559365 PMCID: PMC3084847 DOI: 10.1371/journal.pone.0019420] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2010] [Accepted: 03/29/2011] [Indexed: 11/18/2022] Open
Abstract
Genes involved in cholesterol biosynthesis and uptake are transcriptionally regulated in response to cellular sterol content in a coordinated manner. A number of these genes, including 3-hydroxy-3-methylglutaryl coenzyme A reductase (HMGCR) and LDL receptor (LDLR), undergo alternative splicing, resulting in reductions of enzyme or protein activity. Here we demonstrate that cellular sterol depletion suppresses, and sterol loading induces, alternative splicing of multiple genes involved in the maintenance of cholesterol homeostasis including HMGCR and LDLR, the key regulators of cellular cholesterol biosynthesis and uptake, respectively. These changes were observed in both in vitro studies of the HepG2 human hepatoma derived cell line, as well as in vivo studies of St. Kitts vervets, also known as African green monkeys, a commonly used primate model for investigating cholesterol metabolism. These effects are mediated in part by sterol regulation of polypyrimidine tract binding protein 1 (PTBP1), since knock-down of PTBP1 eliminates sterol induced changes in alternative splicing of several of these genes. Single nucleotide polymorphisms (SNPs) that influence HMGCR and LDLR alternative splicing (rs3846662 and rs688, respectively), have been associated with variation in plasma LDL-cholesterol levels. Sterol-induced changes in alternative splicing are blunted in carriers of the minor alleles for each of these SNPs, indicating an interaction between genetic and non-genetic regulation of this process. Our results implicate alternative splicing as a novel mechanism of enhancing the robust transcriptional response to conditions of cellular cholesterol depletion or accumulation. Thus coordinated regulation of alternative splicing may contribute to cellular cholesterol homeostasis as well as plasma LDL levels.
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Affiliation(s)
- Marisa Wong Medina
- Department of Atherosclerosis Research, Children's Hospital Oakland Research Institute, Oakland, California, United States of America.
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Pharmacogenomics of the RNA world: structural RNA polymorphisms in drug therapy. Clin Pharmacol Ther 2011; 89:355-65. [PMID: 21289622 DOI: 10.1038/clpt.2010.314] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The use of pharmacogenomic biomarkers can enhance treatment outcomes. Regulatory polymorphisms are promising biomarkers that have proven difficult to uncover. They come in two flavors: those that affect transcription (regulatory single-nucleotide polymorphisms (rSNPs)) and those that affect RNA functions such as splicing, turnover, and translation (termed structural RNA SNPs (srSNPs)). This review focuses on the role of srSNPs in drug metabolism, transport, and response. An understanding of the nature and diversity of srSNPs and rSNPs enables clinical scientists to evaluate genetic biomarkers.
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Lu ZX, Jiang P, Cai JJ, Xing Y. Context-dependent robustness to 5' splice site polymorphisms in human populations. Hum Mol Genet 2010; 20:1084-96. [PMID: 21224255 DOI: 10.1093/hmg/ddq553] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
There has been growing evidence for extensive diversity of alternative splicing in human populations. Genetic variants within the 5' splice site can cause splicing differences among human individuals and constitute an important class of human disease mutations. In this study, we explored whether natural variations of splicing could reveal important signals of 5' splice site recognition. In seven lymphoblastoid cell lines of Asian, European and African ancestry, we identified 1174 single nucleotide polymorphisms (SNPs) within the consensus 5' splice site. We selected 129 SNPs predicted to significantly alter the splice site activity, and quantitatively examined their splicing impact in the seven individuals. Surprisingly, outside of the essential GT dinucleotide position, only ∼14% of the tested SNPs altered splicing. Bioinformatic and minigene analyses identified signals that could modify the impact of 5' splice site polymorphisms, most notably a strong 3' splice site and the presence of intronic motifs downstream of the 5' splice site. Strikingly, we found that the poly-G run, a known intronic splicing enhancer, was the most significantly enriched motif downstream of exons unaffected by 5' splice site SNPs. In TRIM62, the upstream 3' splice site and downstream intronic poly-G runs functioned redundantly to protect an exon from its 5' splice site polymorphism. Collectively, our study reveals widespread context-dependent robustness to 5' splice site polymorphisms in human transcriptomes. Consequently, certain exons are more susceptible to 5' splice site mutations. Additionally, our work demonstrates that genetic diversity of alternative splicing can provide significant insights into the splicing code of mammalian cells.
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Affiliation(s)
- Zhi-xiang Lu
- Department of Internal Medicine, University of Iowa, 3294 CBRB, 285 Newton Rd, Iowa City, IA 52242, USA
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Ling IF, Gopalraj RK, Simpson JF, Estus S. Expression and regulation of a low-density lipoprotein receptor exon 12 splice variant. J Neurochem 2010; 115:614-24. [PMID: 20807319 DOI: 10.1111/j.1471-4159.2010.06972.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
As low-density lipoprotein receptor (LDLR) contributes to cholesterol and amyloid beta homeostasis, insights into LDLR regulation may facilitate our understanding of cardiovascular disease and Alzheimer's disease. Previously, we identified LDLR isoforms that lacked exon 12 or exons 11-12 and that are predicted to encode soluble, dominant negative, LDLR. Moreover, these isoforms were associated with rs688, an exon 12 polymorphism that was associated with LDL-cholesterol and Alzheimer's disease risk. In this study, we present evidence that although the truncated LDLR isoforms are translated in vitro, they represent < 0.1% of CSF proteins. As these LDLR isoforms likely represent a loss of mRNA-encoding functional LDLR, we then focused upon identifying intron-exon boundary and exonic splicing enhancer elements critical to splicing. Exon 12 inclusion is enhanced by altering the 5' splice site in intron 12 towards a consensus splice donor sequence, consistent with its being a weak 5' splice site. Additionally, of the nine evolutionarily conserved putative splicing enhancer regions within exon 12, two regions that flank rs688 were critical to exon 12 inclusion. Overall, these results suggest that LDLR splice variants represent a loss of mRNA encoding functional LDLR and provide insights into the regulatory elements critical for LDLR exon 12 splicing.
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Affiliation(s)
- I-Fang Ling
- Department of Physiology, Sanders-Brown Center on Aging, University of Kentucky, Lexington, Kentucky 40536-0230, USA
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Abstract
Low-density lipoprotein receptor (LDLR) is a major apolipoprotein E (APOE) receptor and thereby is critical to cholesterol homeostasis and, possibly, Alzheimer disease (AD) development. We previously identified a single nucleotide polymorphism (SNP), rs688:C>T, that modulates LDLR exon 12 splicing and is associated with cholesterol levels in premenopausal women and with Alzheimer disease in men. To gain additional insights into LDLR splicing regulation, we seek to identify splicing factors that modulate LDLR splicing efficiency. By using an in vitro minigene study, we first found that ectopic expression of SFRS3 (SRp20), SFRS13A (SRp38), SFRS13A-2 (SRp38-2), and RBMX (hnRNP G) robustly decreased LDLR splicing efficiency. Although SFRS3 and SFRS13A specifically increased the LDLR transcript lacking exon 11, SFRS13A-2 and RBMX primarily increased the LDLR isoform lacking both exons 11 and 12. When we evaluated the relationship between the expression of these splicing factors and LDLR splicing in human brain and liver specimens, we found that overall SFRS13A expression was significantly associated with LDLR splicing efficiency in vivo. We interpret these results as suggesting that SFRS13A regulates LDLR splicing efficiency and may therefore emerge as a modulator of cholesterol homeostasis.
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Affiliation(s)
- I-Fang Ling
- Department of Physiology, Sanders-Brown Center on Aging, University of Kentucky, Lexington, Kentucky 40536-0230, USA
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Polymorphisms at LDLR locus may be associated with coronary artery disease through modulation of coagulation factor VIII activity and independently from lipid profile. Blood 2010; 116:5688-97. [PMID: 20810930 DOI: 10.1182/blood-2010-03-277079] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
High levels of coagulation factor VIII (FVIII) have been associated with cardiovascular disease. Low-density lipoprotein receptor (LDLR) has been recently demonstrated to contribute to FVIII clearance from plasma. The aim of this study was to evaluate 3 single nucleotide polymorphisms in SMARCA4-LDLR gene locus (rs1122608, rs2228671, and rs688) and FVIII coagulant activity (FVIII:c) in subjects with (n = 692) or without (n = 291) angiographically confirmed coronary artery disease (CAD). High FVIII:c levels were an independent risk factor for CAD. The rs688 and rs2228671 genotypes were predictors of FVIII:c with T alleles associated with higher FVIII:c levels. The rs2228671T allele was associated also with reduced total and LDL-cholesterol levels. With respect to the risk of CAD, no association was found for rs2228671. Consistently with higher FVIII:c levels, the rs688T allele was associated with CAD, whereas, consistently with a favorable lipid profile, the rs1122608T allele was associated with a decreased CAD prevalence. After adjustment for classic cardiovascular risk factors, including plasma lipids, rs688 remained associated with CAD (OR for T carriers: 1.67 with 95% confidence interval, 1.10-2.54). Haplotype analysis confirmed such results. Our data suggest that polymorphisms at LDLR locus modulate FVIII:c levels and may be associated with CAD risk independently from plasma lipids.
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