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Calling and Phasing of Single-Nucleotide and Structural Variants of the LDLR Gene Using Oxford Nanopore MinION. Int J Mol Sci 2023; 24:ijms24054471. [PMID: 36901902 PMCID: PMC10003201 DOI: 10.3390/ijms24054471] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 01/27/2023] [Accepted: 02/22/2023] [Indexed: 03/12/2023] Open
Abstract
The LDLR locus has clinical significance for lipid metabolism, Mendelian familial hypercholesterolemia (FH), and common lipid metabolism-related diseases (coronary artery disease and Alzheimer's disease), but its intronic and structural variants are underinvestigated. The aim of this study was to design and validate a method for nearly complete sequencing of the LDLR gene using long-read Oxford Nanopore sequencing technology (ONT). Five PCR amplicons from LDLR of three patients with compound heterozygous FH were analyzed. We used standard workflows of EPI2ME Labs for variant calling. All rare missense and small deletion variants detected previously by massively parallel sequencing and Sanger sequencing were identified using ONT. One patient had a 6976 bp deletion (exons 15 and 16) that was detected by ONT with precisely located breakpoints between AluY and AluSx1. Trans-heterozygous associations between mutation c.530C>T and c.1054T>C, c.2141-966_2390-330del, and c.1327T>C, and between mutations c.1246C>T and c.940+3_940+6del of LDLR, were confirmed. We demonstrated the ability of ONT to phase variants, thereby enabling haplotype assignment for LDLR with personalized resolution. The ONT-based method was able to detect exonic variants with the additional benefit of intronic analysis in one run. This method can serve as an efficient and cost-effective tool for diagnosing FH and conducting research on extended LDLR haplotype reconstruction.
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Yin J, Gibbs M, Long C, Rosenthal J, Kim HS, Kim A, Sheng C, Ding P, Javed U, Yuan Q. Transcriptional Regulation of Lipophorin Receptors Supports Neuronal Adaptation to Chronic Elevations of Activity. Cell Rep 2019; 25:1181-1192.e4. [PMID: 30380410 PMCID: PMC6294312 DOI: 10.1016/j.celrep.2018.10.016] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Revised: 08/20/2018] [Accepted: 10/03/2018] [Indexed: 12/18/2022] Open
Abstract
Activity-dependent modifications strongly influence neural development. However, molecular programs underlying their context and circuit-specific effects are not well understood. To study global transcriptional changes associated with chronic elevation of synaptic activity, we performed cell-type-specific transcriptome profiling of Drosophila ventral lateral neurons (LNvs) in the developing visual circuit and identified activity-modified transcripts that are enriched in neuron morphogenesis, circadian regulation, and lipid metabolism and trafficking. Using bioinformatics and genetic analyses, we validated activity-induced isoform-specific upregulation of Drosophila lipophorin receptors LpR1 and LpR2, the homologs of mammalian low-density lipoprotein receptor (LDLR) family proteins. Furthermore, our morphological and physiological studies uncovered critical functions of neuronal lipophorin receptors (LpRs) in maintaining the structural and functional integrities in neurons challenged by chronic elevations of activity. Together, our findings identify LpRs as molecular targets for activity-dependent transcriptional regulation and reveal the functional significance of cell-type-specific regulation of neuronal lipid uptake in experience-dependent plasticity and adaptive responses. Yin et al. highlight Drosophila lipophorin receptors (LpRs) as molecular targets for activity-dependent transcriptional regulation and reveal the functional significance of cell-type-specific regulation of neuronal lipid uptake in experience-dependent plasticity and adaptive responses.
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Affiliation(s)
- Jun Yin
- Dendrite Morphogenesis and Plasticity Unit, National Institute of Neurological Disorders and Stroke, NIH, Bethesda, MD 20892, USA
| | - Mary Gibbs
- Dendrite Morphogenesis and Plasticity Unit, National Institute of Neurological Disorders and Stroke, NIH, Bethesda, MD 20892, USA
| | - Caixia Long
- Dendrite Morphogenesis and Plasticity Unit, National Institute of Neurological Disorders and Stroke, NIH, Bethesda, MD 20892, USA
| | - Justin Rosenthal
- Dendrite Morphogenesis and Plasticity Unit, National Institute of Neurological Disorders and Stroke, NIH, Bethesda, MD 20892, USA
| | - Hyong S Kim
- Dendrite Morphogenesis and Plasticity Unit, National Institute of Neurological Disorders and Stroke, NIH, Bethesda, MD 20892, USA
| | - Anna Kim
- Dendrite Morphogenesis and Plasticity Unit, National Institute of Neurological Disorders and Stroke, NIH, Bethesda, MD 20892, USA
| | - Chengyu Sheng
- Dendrite Morphogenesis and Plasticity Unit, National Institute of Neurological Disorders and Stroke, NIH, Bethesda, MD 20892, USA
| | - Peng Ding
- Neurobiology Department, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Uzma Javed
- Dendrite Morphogenesis and Plasticity Unit, National Institute of Neurological Disorders and Stroke, NIH, Bethesda, MD 20892, USA
| | - Quan Yuan
- Dendrite Morphogenesis and Plasticity Unit, National Institute of Neurological Disorders and Stroke, NIH, Bethesda, MD 20892, USA.
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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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Shimohiro H, Taniguchi SI, Koda M, Sakai C, Yamada S. Association between serum soluble low-density lipoprotein receptor levels and metabolic factors in healthy Japanese individuals. J Clin Lab Anal 2014; 29:52-6. [PMID: 24687274 DOI: 10.1002/jcla.21727] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2013] [Accepted: 11/12/2013] [Indexed: 11/08/2022] Open
Abstract
BACKGROUND Soluble low-density lipoprotein receptor (sLDL-R) is formed by cleavage of the extracellular domain of low-density lipoprotein receptor (LDL-R). It is unclear whether serum sLDL-R is a marker of diseases associated with triglyceride (TG) metabolism. We investigated the association between serum sLDL-R concentrations and other biochemical parameters in healthy Japanese individuals. METHODS Study subjects consisted of 102 healthy adult Japanese volunteers (42 men, 60 women) with body mass index (BMI) < 30 kg/m(2) and serum TGs, LDL cholesterol (LDL-C), aspartate aminotransferase, alanine aminotransferase, γ-glutamyl transpeptidase, and glucose concentrations within normal ranges. Serum sLDL-R concentrations were determined by enzyme-linked immunosorbent assay and their correlations with biochemical parameters were analyzed. RESULTS Mean serum sLDL-R concentration was 120.9 ± 39.9 ng/ml. Serum sLDL-R levels were significantly and positively correlated with BMI (rs = 0.252) and TG (rs = 0.408) and LDL-C (rs = 0.325) concentrations. Multiple regression analysis adjusted for age, gender, and smoking showed that BMI (β = 0.274), TG (β = 0.328), and LDL-C (β = 0.224) were factors independently correlated with sLDL-R levels. CONCLUSION Serum sLDL-R concentration may be a marker of diseases associated with TG metabolism. This is the first report to date describing the clinical relevance of sLDL-R.
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Affiliation(s)
- Hisashi Shimohiro
- Department of Pathobiological Science and Technology, School of Health Science, Faculty of Medicine, Tottori University, Yonago, Japan
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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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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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