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Biswas M, Sawajan N, Rungrotmongkol T, Sanachai K, Ershadian M, Sukasem C. Pharmacogenetics and Precision Medicine Approaches for the Improvement of COVID-19 Therapies. Front Pharmacol 2022; 13:835136. [PMID: 35250581 PMCID: PMC8894812 DOI: 10.3389/fphar.2022.835136] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 01/24/2022] [Indexed: 01/18/2023] Open
Abstract
Many drugs are being administered to tackle coronavirus disease 2019 (COVID-19) pandemic situations without establishing clinical effectiveness or tailoring safety. A repurposing strategy might be more effective and successful if pharmacogenetic interventions are being considered in future clinical studies/trials. Although it is very unlikely that there are almost no pharmacogenetic data for COVID-19 drugs, however, from inferring the pharmacokinetic (PK)/pharmacodynamic(PD) properties and some pharmacogenetic evidence in other diseases/clinical conditions, it is highly likely that pharmacogenetic associations are also feasible in at least some COVID-19 drugs. We strongly mandate to undertake a pharmacogenetic assessment for at least these drug–gene pairs (atazanavir–UGT1A1, ABCB1, SLCO1B1, APOA5; efavirenz–CYP2B6; nevirapine–HLA, CYP2B6, ABCB1; lopinavir–SLCO1B3, ABCC2; ribavirin–SLC28A2; tocilizumab–FCGR3A; ivermectin–ABCB1; oseltamivir–CES1, ABCB1; clopidogrel–CYP2C19, ABCB1, warfarin–CYP2C9, VKORC1; non-steroidal anti-inflammatory drugs (NSAIDs)–CYP2C9) in COVID-19 patients for advancing precision medicine. Molecular docking and computational studies are promising to achieve new therapeutics against SARS-CoV-2 infection. The current situation in the discovery of anti-SARS-CoV-2 agents at four important targets from in silico studies has been described and summarized in this review. Although natural occurring compounds from different herbs against SARS-CoV-2 infection are favorable, however, accurate experimental investigation of these compounds is warranted to provide insightful information. Moreover, clinical considerations of drug–drug interactions (DDIs) and drug–herb interactions (DHIs) of the existing repurposed drugs along with pharmacogenetic (e.g., efavirenz and CYP2B6) and herbogenetic (e.g., andrographolide and CYP2C9) interventions, collectively called multifactorial drug–gene interactions (DGIs), may further accelerate the development of precision COVID-19 therapies in the real-world clinical settings.
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Affiliation(s)
- Mohitosh Biswas
- Division of Pharmacogenomics and Personalized Medicine, Department of Pathology, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
- Laboratory for Pharmacogenomics, Somdech Phra Debaratana Medical Center (SDMC), Ramathibodi Hospital, Bangkok, Thailand
- Department of Pharmacy, University of Rajshahi, Rajshahi, Bangladesh
| | - Nares Sawajan
- Division of Pharmacogenomics and Personalized Medicine, Department of Pathology, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
- Laboratory for Pharmacogenomics, Somdech Phra Debaratana Medical Center (SDMC), Ramathibodi Hospital, Bangkok, Thailand
- Department of Pathology, School of Medicine, Mae Fah Luang University, Chiang Rai, Thailand
| | - Thanyada Rungrotmongkol
- Structural and Computational Biology Research Unit, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
- Program in Bioinformatics and Computational Biology, Graduate School, Chulalongkorn University, Bangkok, Thailand
| | - Kamonpan Sanachai
- Structural and Computational Biology Research Unit, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | - Maliheh Ershadian
- Division of Pharmacogenomics and Personalized Medicine, Department of Pathology, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
- Laboratory for Pharmacogenomics, Somdech Phra Debaratana Medical Center (SDMC), Ramathibodi Hospital, Bangkok, Thailand
| | - Chonlaphat Sukasem
- Division of Pharmacogenomics and Personalized Medicine, Department of Pathology, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
- Laboratory for Pharmacogenomics, Somdech Phra Debaratana Medical Center (SDMC), Ramathibodi Hospital, Bangkok, Thailand
- Pharmacogenomics and Precision Medicine, The Preventive Genomics and Family Check-up Services Center, Bumrungrad International Hospital, Bangkok, Thailand
- MRC Centre for Drug Safety Science, Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, United Kingdom
- *Correspondence: Chonlaphat Sukasem,
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Li W. Association of APOE E2 and low-density lipoprotein with depressive symptoms in Chinese senile schizophrenia inpatients: A cross-sectional study. SCHIZOPHRENIA RESEARCH-COGNITION 2020; 23:100193. [PMID: 33294393 PMCID: PMC7689319 DOI: 10.1016/j.scog.2020.100193] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Accepted: 11/15/2020] [Indexed: 11/23/2022]
Abstract
Background Schizophrenia is considered to occur due to both environmental and genetic factors. Depressive symptoms and apolipoprotein E (APOE) gene polymorphisms are involved in the pathogenesis of schizophrenia. However, the effect of APOE gene polymorphism on depressive symptoms has never been investigated among Chinese elderly schizophrenia patients. Objective This cross-sectional study aimed to determine the effect of APOE gene polymorphism on blood lipid metabolism and depressive symptoms among elderly schizophrenia patients. Method A total of 301 elderly schizophrenia patients (161 males, age ranges from 60 to 92 years, with an average age of 67.31 ± 6.667) were included in the study. Depressive symptoms were assessed using the Geriatric Depression Scale (GDS). APOE gene polymorphisms were determined by polymerase chain reaction (PCR). Correlations between GDS and serum low-density lipoprotein (LDL) levels with APOE genotypes were assessed. Results The concentration of LDL in the APOE E2 group was significantly lower than those in the APOE E3 and APOE E4 groups, and the GDS scores in the APOE E2 and APOE E3 groups were higher than those in the APOE E4 group. Using partial correlation analysis and controlling the duration of disease and hyperlipidemia, we found that GDS scores were significantly correlated with LDL (r = −0.179, p = 0.025). Conclusions The APOE E2 genotype is associated with more depressive symptoms and lower serum LDL in elderly Chinese schizophrenia patients, and there is a negative correlation between depressive symptoms and LDL.
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Affiliation(s)
- Wei Li
- Department of Geriatric Psychiatry, Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Alzheimer's Disease and Related Disorders Center, Shanghai Jiao Tong University, Shanghai, China
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The Genetic Variability of APOE in Different Human Populations and Its Implications for Longevity. Genes (Basel) 2019; 10:genes10030222. [PMID: 30884759 PMCID: PMC6471373 DOI: 10.3390/genes10030222] [Citation(s) in RCA: 85] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 03/01/2019] [Accepted: 03/12/2019] [Indexed: 12/11/2022] Open
Abstract
Human longevity is a complex phenotype resulting from the combinations of context-dependent gene-environment interactions that require analysis as a dynamic process in a cohesive ecological and evolutionary framework. Genome-wide association (GWAS) and whole-genome sequencing (WGS) studies on centenarians pointed toward the inclusion of the apolipoprotein E (APOE) polymorphisms ε2 and ε4, as implicated in the attainment of extreme longevity, which refers to their effect in age-related Alzheimer's disease (AD) and cardiovascular disease (CVD). In this case, the available literature on APOE and its involvement in longevity is described according to an anthropological and population genetics perspective. This aims to highlight the evolutionary history of this gene, how its participation in several biological pathways relates to human longevity, and which evolutionary dynamics may have shaped the distribution of APOE haplotypes across the globe. Its potential adaptive role will be described along with implications for the study of longevity in different human groups. This review also presents an updated overview of the worldwide distribution of APOE alleles based on modern day data from public databases and ancient DNA samples retrieved from literature in the attempt to understand the spatial and temporal frame in which present-day patterns of APOE variation evolved.
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Shatwan IM, Winther KH, Ellahi B, Elwood P, Ben-Shlomo Y, Givens I, Rayman MP, Lovegrove JA, Vimaleswaran KS. Association of apolipoprotein E gene polymorphisms with blood lipids and their interaction with dietary factors. Lipids Health Dis 2018; 17:98. [PMID: 29712557 PMCID: PMC5928585 DOI: 10.1186/s12944-018-0744-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2017] [Accepted: 04/13/2018] [Indexed: 01/21/2023] Open
Abstract
BACKGROUND Several candidate genes have been identified in relation to lipid metabolism, and among these, lipoprotein lipase (LPL) and apolipoprotein E (APOE) gene polymorphisms are major sources of genetically determined variation in lipid concentrations. This study investigated the association of two single nucleotide polymorphisms (SNPs) at LPL, seven tagging SNPs at the APOE gene, and a common APOE haplotype (two SNPs) with blood lipids, and examined the interaction of these SNPs with dietary factors. METHODS The population studied for this investigation included 660 individuals from the Prevention of Cancer by Intervention with Selenium (PRECISE) study who supplied baseline data. The findings of the PRECISE study were further replicated using 1238 individuals from the Caerphilly Prospective cohort (CaPS). Dietary intake was assessed using a validated food-frequency questionnaire (FFQ) in PRECISE and a validated semi-quantitative FFQ in the CaPS. Interaction analyses were performed by including the interaction term in the linear regression model adjusted for age, body mass index, sex and country. RESULTS There was no association between dietary factors and blood lipids after Bonferroni correction and adjustment for confounding factors in either cohort. In the PRECISE study, after correction for multiple testing, there was a statistically significant association of the APOE haplotype (rs7412 and rs429358; E2, E3, and E4) and APOE tagSNP rs445925 with total cholesterol (P = 4 × 10- 4 and P = 0.003, respectively). Carriers of the E2 allele had lower total cholesterol concentration (5.54 ± 0.97 mmol/L) than those with the E3 (5.98 ± 1.05 mmol/L) (P = 0.001) and E4 (6.09 ± 1.06 mmol/L) (P = 2 × 10- 4) alleles. The association of APOE haplotype (E2, E3, and E4) and APOE SNP rs445925 with total cholesterol (P = 2 × 10- 6 and P = 3 × 10- 4, respectively) was further replicated in the CaPS. Additionally, significant association was found between APOE haplotype and APOE SNP rs445925 with low density lipoprotein cholesterol in CaPS (P = 4 × 10- 4 and P = 0.001, respectively). After Bonferroni correction, none of the cohorts showed a statistically significant SNP-diet interaction on lipid outcomes. CONCLUSION In summary, our findings from the two cohorts confirm that genetic variations at the APOE locus influence plasma total cholesterol concentrations, however, the gene-diet interactions on lipids require further investigation in larger cohorts.
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Affiliation(s)
- Israa M Shatwan
- Hugh Sinclair Unit of Human Nutrition and Institute for Cardiovascular and Metabolic Research (ICMR), Department of Food and Nutritional Sciences, University of Reading, Whiteknights, PO Box 226, Reading, RG6 6AP, UK.,Food and Nutrition Department, Faculty of Home Economics, King Abdulaziz University, Jeddah, Saudi Arabia
| | | | - Basma Ellahi
- Faculty of Health and Social Care, University of Chester, Chester, CH1 1SL, UK
| | - Peter Elwood
- Department of Epidemiology, Statistics and Public Health, Cardiff University, University Hospital of Wales, Heath Park, Cardiff, CF14 4XW, UK
| | - Yoav Ben-Shlomo
- Population Health Sciences, University of Bristol, Bristol, BS8 2PS, UK
| | - Ian Givens
- Institute for Food, Nutrition and Health, University of Reading, Earley Gate, Reading, RG6 6AR, UK
| | - Margaret P Rayman
- Department of Nutritional Sciences Faculty of Health and Medical Sciences, University of Surrey, Guildford, GU2 7XH, UK
| | - Julie A Lovegrove
- Hugh Sinclair Unit of Human Nutrition and Institute for Cardiovascular and Metabolic Research (ICMR), Department of Food and Nutritional Sciences, University of Reading, Whiteknights, PO Box 226, Reading, RG6 6AP, UK
| | - Karani S Vimaleswaran
- Hugh Sinclair Unit of Human Nutrition and Institute for Cardiovascular and Metabolic Research (ICMR), Department of Food and Nutritional Sciences, University of Reading, Whiteknights, PO Box 226, Reading, RG6 6AP, UK.
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Ang HX, Chan SL, Sani LL, Quah CB, Brunham LR, Tan BOP, Winther MD. Pharmacogenomics in Asia: a systematic review on current trends and novel discoveries. Pharmacogenomics 2017; 18:891-910. [DOI: 10.2217/pgs-2017-0009] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
While early pharmacogenomic studies have primarily been carried out in Western populations, there has been a notable increase in the number of Asian studies over the past decade. We systematically reviewed all pharmacogenomic studies conducted in Asia published before 2016 to highlight trends and identify research gaps in Asia. We observed that pharmacogenomic research in Asia was dominated by larger developed countries, notably Japan and Korea, and mainly driven by local researchers. Studies were focused on drugs acting on the CNS, chemotherapeutics and anticoagulants. Significantly, several novel pharmacogenomic associations have emerged from Asian studies. These developments are highly encouraging for the strength of regional scientific and clinical community and propound the importance of discovery studies in different populations.
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Affiliation(s)
- Hazel Xiaohui Ang
- Genome Institute of Singapore, Agency for Science, Technology & Research, Singapore
| | - Sze Ling Chan
- Translational Laboratory in Genetic Medicine, Agency for Science, Technology & Research, Singapore
| | - Levana L Sani
- Genome Institute of Singapore, Agency for Science, Technology & Research, Singapore
| | | | - Liam R Brunham
- Translational Laboratory in Genetic Medicine, Agency for Science, Technology & Research, Singapore
- Department of Medicine, Centre for Heart Lung Innovation, University of British Columbia, Vancouver, BC, Canada
| | - Boon Ooi Patrick Tan
- Genome Institute of Singapore, Agency for Science, Technology & Research, Singapore
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
- Cancer & Stem Cell Biology Program, Duke-NUS Graduate Medical School, Singapore
- Division of Cellular & Molecular Research, National Cancer Centre Singapore, Singapore
| | - Michael D Winther
- Genome Institute of Singapore, Agency for Science, Technology & Research, Singapore
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Pérez-Matute P, Iñiguez M, Recio-Fernández E, Oteo JA. Deciphering the molecular mechanisms involved in HIV-associated lipoatrophy by transcriptomics: a pilot study. J Physiol Biochem 2017; 73:431-443. [PMID: 28074419 DOI: 10.1007/s13105-016-0547-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Accepted: 12/26/2016] [Indexed: 01/11/2023]
Abstract
HIV-associated lipoatrophy (LA) has considerable implications for risk of metabolic diseases, quality of life, and adherence to treatments. Although it has decreased in high-income countries, it is still very common in resource-limited countries. Understanding the pathophysiological mechanisms of LA can open the possibility to explore new ways to treat or prevent this condition. To identify new markers for an accurate and quick diagnosis will be also of interest. Thus, we aimed to examine functional classes of genes implicated in LA and to identify potential new markers for an accurate/quick diagnosis of LA and future complications. Eighteen participants were recruited: seven healthy volunteers, five non-LA-HIV patients, and six LA-HIV subjects. Clinical lipoatrophy was considered when changes in fat volume in the cheeks next to the nose, lateral aspect of the face, legs, arms, and buttocks were observed by the physicians. mRNA was isolated from peripheral blood mononuclear cells (PBMCs) to perform a transcriptomic and Gene Ontology analysis. To confirm RNA sequencing results, qPCRs were developed. A total of 55 genes were differentially expressed between LA and non-LA patients. Thirty-seven genes were overexpressed, whereas 18 genes were repressed. Functional analysis showed that overexpressed genes were involved in lymphocyte/neutrophil activation, inflammation, and atherogenesis. Several lymphoma markers and members of the lipocalin and aquaporin families were also found more expressed in LA patients. In contrast, most of the genes found less expressed in LA subjects were involved in angiogenesis and protection against myocardial infarction. Our results demonstrated a distinct transcriptomic signature in PBMCs of LA patients in comparison with non-LA-HIV subjects and, therefore, provided novel insights to the pathogenesis of HIV-associated lipoatrophy. Our study also highlights the potential usage of some of these genes as early markers of future complications.
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Affiliation(s)
- Patricia Pérez-Matute
- HIV and Associated Metabolic Alterations Unit, Infectious Diseases Department, Center for Biomedical Research of La Rioja (CIBIR)-Hospital San Pedro, Piqueras 98, 26006, Logroño, Spain.
| | - María Iñiguez
- Genomics Core Facility, Center for Biomedical Research of La Rioja (CIBIR), Piqueras 98, 26006, Logroño, Spain
| | - Emma Recio-Fernández
- HIV and Associated Metabolic Alterations Unit, Infectious Diseases Department, Center for Biomedical Research of La Rioja (CIBIR)-Hospital San Pedro, Piqueras 98, 26006, Logroño, Spain
| | - José-Antonio Oteo
- HIV and Associated Metabolic Alterations Unit, Infectious Diseases Department, Center for Biomedical Research of La Rioja (CIBIR)-Hospital San Pedro, Piqueras 98, 26006, Logroño, Spain
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Marino RB, Kingsley LA, Hussain SK, Bream JH, Penogonda S, Duggal P, Martinson JJ. Lipid levels in HIV-positive men receiving anti-retroviral therapy are not associated with copy number variation of reverse cholesterol transport pathway genes. BMC Res Notes 2015; 8:697. [PMID: 26590594 PMCID: PMC4654814 DOI: 10.1186/s13104-015-1665-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2014] [Accepted: 11/02/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The exacerbation of HIV-1 associated dyslipidemia seen in a subset of patients receiving anti-retroviral therapy suggests that genetic factors put these individuals at greater risk of cardiovascular disease. Single nucleotide polymorphisms (SNPs) within genes of and influencing the reverse cholesterol transport (RCT) pathway are associated with lipid levels but little is known regarding their copy number variation (CNV). This form of quantitative genetic variation has the potential to alter the amount of gene product made, thereby also influencing lipid metabolism. RESULTS To examine if CNV in RCT pathway genes was associated with altered serum lipid profiles in HIV-positive individuals receiving therapy, we designed a custom multiplex ligation-dependent probe amplification assay to screen 16 RCT genes within a subset of individuals from the Multicenter AIDS Cohort Study who show extreme lipid phenotypes. Verification of CNV was performed using a custom NanoString assay, and the Illumina HT-12 mRNA expression microarray was used to determine the influence of copy number on gene expression. Among the RCT genes, CNV was observed to be extremely rare. The only CNV seen was in the CETP gene, which showed a loss of copy in 1 of the 320 samples (0.3%) in our study. The genes in our study showed little variation in expression between individuals, and the variation seen was not related to any detected CNV. CONCLUSIONS Whole gene CNV is uncommon in RCT pathway genes, and not a major factor in the development of highly active antiretroviral therapy (HAART) associated dyslipidemia.
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Affiliation(s)
- Rebecca B Marino
- Department of Infectious Diseases and Microbiology, Graduate School of Public Health, University of Pittsburgh, 130 De Soto St, Pittsburgh, PA, 15261, USA.
| | - Lawrence A Kingsley
- Department of Infectious Diseases and Microbiology, Graduate School of Public Health, University of Pittsburgh, 130 De Soto St, Pittsburgh, PA, 15261, USA.
| | - Shehnaz K Hussain
- Division of Hematology/Oncology, Department of Medicine, Cedars-Sinai Medical Center, 8700 Beverly Blvd, Los Angeles, CA, 90048, USA.
| | - Jay H Bream
- Bloomberg School of Public Health, Johns Hopkins University, 615 Wolfe St, Baltimore, MD, 21205, USA.
| | - Sudhir Penogonda
- Feinberg School of Medicine, Northwestern University, 645 N Michigan Avenue, Chicago, IL, 60611, USA.
| | - Priya Duggal
- Bloomberg School of Public Health, Johns Hopkins University, 615 Wolfe St, Baltimore, MD, 21205, USA.
| | - Jeremy J Martinson
- Department of Infectious Diseases and Microbiology, Graduate School of Public Health, University of Pittsburgh, 130 De Soto St, Pittsburgh, PA, 15261, USA.
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Abstract
PURPOSE OF REVIEW Lipoprotein metabolism and the role of apolipoprotein E in the pathogenesis of dysbetalipoproteinemia. RECENT FINDINGS Remnant lipoproteins, modulated by lifestyle and genetic factors, are atherogenic. Dysbetalipoproteinemia could be viewed as a monogenic disorder of remnant metabolism. SUMMARY Elevated plasma triglyceride and cholesterol concentrations (mixed hyperlipidemias) are commonly encountered and dysbetaliproteinemia should be considered in this setting. Dysbetalipoproteinemia (remnant clearance disease, Fredrickson type III hyperlipidemia) is an uncommon dyslipoproteinemia related to mutations in apolipoprotein E that disrupt the clearance of remnants of triglyceride-rich lipoproteins; it may be overlooked because xanthomata of the skin and/or tendons occur in a minority of patients. The diagnosis ideally requires the demonstration of remnant lipoprotein accumulation and a genetic cause. Genotyping for apolipoprotein E2 may not prove the diagnosis as it may be associated with low plasma lipid values. The recent association of remnant lipoproteins with atherosclerosis along with many factors that modulate remnant lipoprotein metabolism underscores the importance of recognising dysbetalipoproteinemia as an extreme state of remnant lipoprotein accumulation. Although there may be some differences between remnants in the general population and dysbetalipoproteinemia, it is clear that remnants promote atherosclerosis. Current treatment strategies are adequate but new strategies could also be of benefit in dysbetalipoproteinemia.
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Affiliation(s)
- David Marais
- Chemical Pathology, University of Cape Town Health Science Faculty, National Health Laboratory Service and Medical Research Council Cape Heart Group, Cape Town, South Africa
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