Musunuru K, Strong A, Frank-Kamenetsky M, et al. From noncoding variant to phenotype via SORT1 at the 1p13 cholesterol locus

Cardiovascular Research Center and Center for Human Genetic Research, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts 02114, USA.
Nature (Impact Factor: 41.46). 08/2010; 466(7307):714-9. DOI: 10.1038/nature09266
Source: PubMed


Recent genome-wide association studies (GWASs) have identified a locus on chromosome 1p13 strongly associated with both plasma low-density lipoprotein cholesterol (LDL-C) and myocardial infarction (MI) in humans. Here we show through a series of studies in human cohorts and human-derived hepatocytes that a common noncoding polymorphism at the 1p13 locus, rs12740374, creates a C/EBP (CCAAT/enhancer binding protein) transcription factor binding site and alters the hepatic expression of the SORT1 gene. With small interfering RNA (siRNA) knockdown and viral overexpression in mouse liver, we demonstrate that Sort1 alters plasma LDL-C and very low-density lipoprotein (VLDL) particle levels by modulating hepatic VLDL secretion. Thus, we provide functional evidence for a novel regulatory pathway for lipoprotein metabolism and suggest that modulation of this pathway may alter risk for MI in humans. We also demonstrate that common noncoding DNA variants identified by GWASs can directly contribute to clinical phenotypes.

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Available from: Ludmila Prokunina-Olsson
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    • "Importantly, this GWAS enrichment appeared most significant when the DNAse data was ascertained in a cell type relevant to the phenotype studied (Maurano et al., 2012; Reddy et al., 2012; Schaub et al., 2012). Examples of regulatory DNA mutations that explain differences in disease gene function are increasingly being discovered (e.g., Musunuru et al., 2010) and there is tremendous interest in methods that can predict which non-coding variants are of functional consequence (Schaub et al., 2012; Ward and Kellis, 2012a, 2012b). "
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    ABSTRACT: As exome sequencing gives way to genome sequencing, the need to interpret the function of regulatory DNA becomes increasingly important. To test whether evolutionary conservation of cis-regulatory modules (CRMs) gives insight into human gene regulation, we determined transcription factor (TF) binding locations of four liver-essential TFs in liver tissue from human, macaque, mouse, rat, and dog. Approximately, two thirds of the TF-bound regions fell into CRMs. Less than half of the human CRMs were found as a CRM in the orthologous region of a second species. Shared CRMs were associated with liver pathways and disease loci identified by genome-wide association studies. Recurrent rare human disease causing mutations at the promoters of several blood coagulation and lipid metabolism genes were also identified within CRMs shared in multiple species. This suggests that multi-species analyses of experimentally determined combinatorial TF binding will help identify genomic regions critical for tissue-specific gene control. DOI:
    Full-text · Article · Oct 2014 · eLife Sciences
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    • "Previous eQTL studies in genetically diverse populations suggest that the most significant eQTL tend to be local (Rockman and Kruglyak 2006; Pickrell et al. 2010; Aylor et al. 2011; Lappalainen et al. 2013). Gene prioritization methods are becoming more important in the genome-wide association studies (GWAS) era (Hou and Zhao 2013), and genes with local eQTL are promising candidates for underlying disease-associated regions in human GWAS studies (Knight 2005; Chen et al. 2008; Emilsson et al. 2008; Musunuru et al. 2010; Hou and Zhao 2013; Li et al. 2013). An eQTL may arise from any of several biological mechanisms, including rate of transcription, rate of degredation , or processing of RNA intermediates. "
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    ABSTRACT: Massively parallel RNA sequencing (RNA-seq) has yielded a wealth of new insights into transcriptional regulation. A first step in the analysis of RNA-seq data is the alignment of short sequence reads to a common reference genome or transcriptome. Genetic variants that distinguish individual genomes from the reference sequence can cause reads to be misaligned, resulting in biased estimates of transcript abundance. Fine-tuning of read alignment algorithms does not correct this problem. We have developed Seqnature software to construct individualized diploid genomes and transcriptomes for multiparent populations and have implemented a complete analysis pipeline that incorporates other existing software tools. We demonstrate in simulated and real data sets that alignment to individualized transcriptomes increases read mapping accuracy, improves estimation of transcript abundance, and enables the direct estimation of allele-specific expression. Moreover, when applied to expression QTL mapping we find that our individualized alignment strategy corrects false-positive linkage signals and unmasks hidden associations. We recommend the use of individualized diploid genomes over reference sequence alignment for all applications of high-throughput sequencing technology in genetically diverse populations.
    Full-text · Article · Sep 2014 · Genetics
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    • "Several of the molecules whose trafficking is regulated by sortilin are proteins and enzymes involved in the regulation of lipid and glucose metabolism . Human genome wide association studies (GWAS) have identified an association between a SNP leading to increased hepatic levels of sortilin and reduced levels of serum low-density lipoprotein (LDL) [3]. In contrast to the human studies, double knockout mice for sortilin and LDL receptor display reduced hepatic secretion of LDL, reduced serum LDL and attenuated atherosclerotic lesion formation [4]. "
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    ABSTRACT: Background & aims: Sortilin traffics newly synthesized molecules from the trans-Golgi apparatus along secretory pathways to endosomes, lysosomes or to the cell surface. Sortilin trafficking of acid sphingomyelinase (aSMase) may regulate ceramide levels, a major modulator of insulin signalling. We therefore tested whether sortilin deficiency reduces hepatic and adipose tissue aSMase activity, improving insulin sensitivity in diet-induced obesity (DIO). Methods: DIO in C57BL/6 (WT) and sortilin(-/-) mice was induced by high-fat diet feeding for 10 weeks. Results: Sortilin(-/-) mice gained less body weight and less visceral fat, despite similar food intake compared to WT type mice and had enhanced glucose uptake in insulin tolerance tests, which was further corroborated by enhanced hepatic pAkt expression. Sortilin deficiency led to attenuated hepatic steatosis, reduced expression of genes involved in lipogenesis, ceramide synthesis and inflammatory cytokine production and reduced activity of ceramide synthase 5/6 (CerS5/6). Sortilin(-/-) mice had reduced hepatic aSMase activity under both steady-state and DIO. Likewise, sortilin(-/-) hepatocytes displayed hypersensitivity to insulin, due to enhanced insulin receptor downstream signalling. In adipose tissue, sortilin(-/-) mice exhibited lower expression of inflammatory cytokines and lower expression and activity of CerS5/6. As in liver, adipose tissue displayed increased insulin signalling, accompanied by attenuated aSMase activity. Conclusions: Sortilin deficiency induces a beneficial metabolic phenotype in liver and adipose tissue upon DIO, mediated in part by reduced aSMase activity.
    Full-text · Article · Aug 2014 · Journal of Hepatology
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