Alternative titles; symbols
HGNC Approved Gene Symbol: NPC1L1
Cytogenetic location: 7p13 Genomic coordinates (GRCh38) : 7:44,512,535-44,541,330 (from NCBI)
| Location | Phenotype |
Phenotype MIM number |
Inheritance |
Phenotype mapping key |
|---|---|---|---|---|
| 7p13 | [Ezetimibe, nonresponse to] | 617966 | 3 | |
| [Low density lipoprotein cholesterol level QTL 7] | 617966 | 3 |
NPC1L1 is a 13-transmembrane domain cell surface cholesterol-sensing receptor. It is expressed on the apical surface of intestinal enterocytes and hepatocytes and is responsible for cellular cholesterol absorption and whole-body cholesterol homeostasis (summary by Sainz et al., 2012).
By EST database searching with fragments of the NPC1 (607623) protein sequence, Davies et al. (2000) identified a weakly similar EST that they used to assemble a novel full-length human cDNA, designated NPC1L1. NPC1L1 encodes a deduced 1,359-amino acid protein. Two alternatively spliced transcripts encode truncated proteins, one with 724 amino acids (NPC1L1T) and the other with a 27-amino acid in-frame deletion (NPC1L1delE15). The NPC1L1 protein shares 42% sequence identity with NPC1. Both proteins contain a conserved N-terminal NPC1 domain and a putative sterol-sensing domain, but have different putative intracellular targeting signals. NPC1 has a C-terminal dileucine targeting motif that had been implicated in trafficking to the endosomal/lysosomal system, whereas NPC1L1 has a YQRL motif, which had been shown to function as a plasma membrane to trans-Golgi network transport signal in other proteins. Northern blot analysis detected ubiquitous expression of a major 5-kb and a minor 2.4-kb NPC1L1 transcript, with highest expression in liver, lung, and pancreas.
Altmann et al. (2004) found that in human, mouse, and rat, small intestine showed the highest level of NPC1L1 mRNA expression. They also observed expression in other tissues, including gallbladder, liver, testis, and stomach.
Davis et al. (2004) found that mouse Npc1l1 was highly expressed in small intestinal enterocytes, primarily in proximal jejunum.
Using quantitative RT-PCR, Davies et al. (2005) found that NPC1L1 was predominantly expressed in human liver, with much lower levels in lung, heart, brain, pancreas, kidney, and small intestine. In contrast, in mouse, Npc1l1 was highly expressed in small intestine, with lower levels in lung, heart, brain, testis, skin, liver, muscle, and stomach. Immunofluorescence analysis showed that endogenous and transfected NPC1L1 localized to large vesicular structures in human cells.
Using transfected rat hepatoma cells, Yu et al. (2006) found that human NPC1L1 was N-glycosylated. NPC1L1 localized to the plasma membrane and predominantly to the perinuclear region, likely at the endocytic recycling compartment.
Ge et al. (2011) noted that in humans, NPC1L1 is highly expressed in small intestine and liver, whereas in mouse and rat, it is highly expressed in intestine, but not liver.
Malhotra et al. (2014) showed that Npc1l1 was differentially expressed along the mouse gastrointestinal tract, with very low expression in colon compared with small intestine.
Davies et al. (2000) determined that the NPC1L1 gene contains 20 exons, with an unusually large 1,526-bp exon 2, and spans approximately 29 kb. Its putative promoter region contains a sterol-regulatory element (SRE) for SRE-binding protein (184756), suggesting that NPC1L1 may have a role in subcellular cholesterol homeostasis.
By somatic cell hybrid analysis, Davies et al. (2000) mapped the NPC1L1 gene to chromosome 7. They regionalized the gene to chromosome 7p13 by FISH.
Davies et al. (2000) presented data suggesting that NPC1L1 is involved in subcellular cholesterol trafficking.
Altmann et al. (2004) demonstrated that NPC1L1 protein plays a critical role in the absorption of intestinal cholesterol. NPC1L1 expression was enriched in the small intestine and in the brush border membrane of enterocytes. Although otherwise phenotypically normal, Npc1l1-deficient mice exhibited a substantial reduction in absorbed cholesterol that was unaffected by dietary supplementation of bile acids. Ezetimibe, a drug that inhibits cholesterol absorption, had no effect on Npc1l1-knockout mice, suggesting that NPC1L1 resides in an ezetimibe-sensitive pathway responsible for intestinal cholesterol absorption.
Garcia-Calvo et al. (2005) confirmed that ezetimibe glucuronide binds specifically to a single site in mammalian enterocyte brush border membranes and to human embryonic kidney cells expressing NPC1L1.
Using transfected rat hepatoma cells, Yu et al. (2006) showed that human NPC1L1 trafficked between intracellular compartments and the cell surface, likely through the endocytic recycling pathway. NPC1L1 translocation appeared to be regulated by cholesterol availability in the cells. When cholesterol was depleted, NPC1L1 moved to the cell surface, preferentially to a newly formed apical-like subdomain, resulting in increased uptake of free cholesterol.
FLOT1 (606998) and FLOT2 (131560) are lipid raft proteins. Using a human liver cell line, rat liver cells expressing human NPC1L1, and transgenic mice, Ge et al. (2011) found that NPC1L1 required FLOT1 and FLOT2 for bulk endocytosis of cholesterol-enriched plasma membrane microdomains. NPC1L1 interacted directly with FLOT1 and FLOT2, which functioned upstream of clathrin (see 118955) in NPC1L1 cholesterol uptake. The flotillins had no effect on recycling NPC1L1 to plasma membranes. In addition, ezetimibe disrupted NPC1L1-flotillin interactions, blocking formation of cholesterol-enriched microdomains.
As observed with other hepatitis C virus (HCV; see 609532) entry factors, Sainz et al. (2012) found that NPC1L1 expression was downregulated on a human hepatocyte cell line following HCV infection. Blocking NPC1L1 via small interfering RNA or antibody treatment reduced susceptibility to HCV infection, but not vesicular stomatitis virus infection. Ezetimibe treatment also reduced susceptibility to HCV infection by directly inhibiting viral entry after receptor binding and at or before fusion. Sainz et al. (2012) concluded that NPC1L1 is an HCV cell entry factor and a potential antiviral target.
Malhotra et al. (2014) showed that low expression of Npc1l1 in mouse colon was associated with methylation. The promoter region of the Npc1l1 gene was highly methylated at specific CpG dinucleotides in mouse colon, and DNA demethylation at these sites significantly increased Npc1l1 expression. Similar results were observed by analysis of in vitro methylation of the human NPC1L1 promoter in cultured human intestinal cells. The authors concluded that DNA methylation in the promoter region of the NPC1L1 gene is a major mechanism underlying differential expression of NPC1L1 along the length of the gastrointestinal tract.
Using transfected rat hepatoma cells, Kamishikiryo et al. (2017) found that a substantial amount of NPC1L1 was internalized into cytoplasm when cells were replenished with alpha-tocopherol but depleted of cholesterol. The cholesterol-binding N-terminal domain of NPC1L1 was also essential for alpha-tocopherol-induced NPC1L1 endocytosis, as NPC1L1 mediated uptake of alpha-tocopherol through the same mechanism as cholesterol absorption.
Dog Npc1l1 has a much higher binding affinity for ezetimibe than mouse Npc1l1. Using mass spectrometry to compare ezetimibe binding by recombinant dog and mouse Npc1l1, Weinglass et al. (2008) localized the high-affinity ezetimibe-binding site to a large extracellular domain (loop C) in dog Npc1l1. Mutation analysis revealed residues critical for ezetimibe binding adjacent to a hotspot of human polymorphisms associated with reduced cholesterol absorption. Given that cholesterol binds to the N terminus (loop A) of NPC1, a close homolog of NPC1L1, Weinglass et al. (2008) hypothesized that ezetimibe binding prevents a conformational change in NPC1L1 that is required for translocation of cholesterol across membranes.
Low Density Lipoprotein Cholesterol Level
Chen et al. (2009) screened the NPC1L1 gene in 50 Chinese individuals and identified a genomic -762C-T promoter polymorphism (rs2073548) that was found in 34% of individuals. Luciferase assay in the HepG2 cell line showed that the -762C allele had significantly higher promoter activity than -762T (3.5-fold, p = 0.05), and that NPC1L1 promoter activity was downregulated by cholesterol content in a dose-dependent manner in both genotypes. Association analysis in 224 Chinese individuals revealed that the -762C allele was associated with significantly higher serum total cholesterol and LDL-cholesterol content levels in a recessive model (p less than 0.05).
Teslovich et al. (2010) performed a genomewide association study for plasma lipids in more than 100,000 individuals of European ancestry and reported 95 significantly associated loci (p = less than 5 x 10(-8)), with 59 showing genomewide significant association with lipid traits for the first time. The newly reported associations included SNPs near known lipid regulators (e.g., CYP7A1, 118455; NPC1L1; and SCARB1, 601040) as well as in scores of loci not previously implicated in lipoprotein metabolism. The 95 loci contributed not only to normal variation in lipid traits but also to extreme lipid phenotypes and had an impact on lipid traits in 3 non-European populations (East Asians, South Asians, and African Americans).
The Myocardial Infarction Genetics Consortium Investigators (2014) sequenced the NPC1L1 gene in 7,364 patients with coronary heart disease and 14,728 controls without such disease who were of European, African, and South Asian ancestry and identified 15 distinct inactivating mutations. One in 650 persons was a carrier of such a mutation. Heterozygous carriers of NPC1L1 inactivating mutations had a mean LDL cholesterol level that was 12 mg per deciliter (0.31 mmol per liter) lower than that in noncarriers (p = 0.04). Carrier status was associated with a relative reduction of 53% in the risk of coronary heart disease (odds ratio for carriers, 0.47; 95% confidence interval, 0.25 to 0.87; p = 0.008). In total, only 11 of 29,954 patients with coronary heart disease had an inactivating mutation (carrier frequency, 0.04%) in contrast to 71 of 83,140 controls (carrier frequency, 0.09%). One such inactivating mutation (rs145297799) resulted in replacement of arginine-406 with a stop codon (R406X; 608010.0003). This variant was genotyped in a total of 26,507 patients with coronary heart disease and 75,654 controls. The carrier frequency was 0.02 in CHD patients (6 identified) and 0.06 in participants without CHD (49 identified). The R406X variant was seen only in individuals of European ancestry.
Mirshahi and Carey (2015) followed up on the study of the Myocardial Infarction Genetics Consortium Investigators (2014) by investigating the Geisinger MyCode cohort. They identified 7 R406X carriers, all of European ancestry and none with CHD. They identified no carrier of an inactivating variant of NPC1L1 with CHD, as compared with 1,001 cases among noncarriers. Lipid levels were comparable among carriers and noncarriers, suggesting another cause for the protective effect.
Response to Ezetimibe
Simon et al. (2005) genotyped the NPC1L1 gene in hypercholesterolemic individuals from clinical trial cohorts and healthy individuals and found no association between NPC1L1 SNPs and baseline cholesterol level. Although significant associations of LDL cholesterol response to treatment with ezetimibe were observed in 2 large clinical trials, the authors noted that the SNPs identified in this study were unlikely to represent causal variants because no single SNP was found to support the full magnitude of the effect.
Wang et al. (2004) used the nonresponse phenotype of plasma LDL cholesterol to ezetimibe treatment to ascertain individuals who might have variant NPC1L1. Of 8 nonresponders, 1 was found to be a compound heterozygote for 2 rare nonsynonymous polymorphisms in NPC1L1 (see 608010.0001 and 608010.0002) that were absent in 278 normal controls.
Altmann et al. (2004) characterized Npc1l1-null mice. Deficiency of Npc1l1 appeared to have no effect on development, fertility, or any hematologic or plasma parameters. Intestinal morphology was normal in the null mice, with no lipid accumulation in enterocytes.
Davis et al. (2004) found that intestinal uptake and absorption of cholesterol and sitosterol were significantly reduced in Npc1l1-knockout mice, whereas intestinal triglyceride uptake and its absorption into liver and plasma compartments were not altered. Plasma levels of phytosterols, sitosterol, and campesterol were low in Npc1l1-knockout mice. Both heterozygous and homozygous Npc1l1-knockout mice were completely resistant to a severely hypercholesterolemic diet. Npc1l1-knockout mice on a cholesterol-containing diet had altered liver appearance, lower hepatic cholesterol content, and lower biliary cholesterol levels compared with cholesterol-fed wildtype mice. Intestinal mRNA expression was upregulated for hydroxymethylglutaryl-CoA synthase (HMGCS1; 142940) and downregulated for Abca1 (600046).
Davies et al. (2005) demonstrated that loss of Npc1l1 protected mice against high fat diet-induced hyperlipidemia and led to dramatic morphologic differences in liver and gall bladder compared with wildtype. Npc1l1 -/- cells exhibited aberrant plasma membrane uptake, multiple lipid transport defects, and caveolin (see 601047) mislocalization.
In an individual with hyperlipidemia who did not respond to treatment with ezetimibe (see 617966), Wang et al. (2004) identified compound heterozygosity for 2 rare polymorphisms in the NPC1L1 gene: a 219G-to-T transversion in exon 2, resulting in a val55-to-leu (V55L) substitution; and a 3754T-to-A transversion in exon 18, resulting in an ile1233-to-asn (I1233N) substitution (608010.0002).
For discussion of the ile1233-to-asn (I1233N) mutation in the NPC1L1 gene that was found in compound heterozygous state in a hyperlipidemic patient with nonresponse to ezetimibe (see 617966) by Wang et al. (2004), see 608010.0001.
In a cohort of subjects with or without coronary heart disease (CHD), the Myocardial Infarction Genetics Consortium Investigators (2014) identified an inactivating arg406-to-ter (R406X) mutation in the NPC1L1 gene. By genotyping this variant in a total of 26,507 patients with CHD and 75,654 controls, they found a carrier frequency of 0.02 in CHD patients and 0.06 in controls. The variant, which was found only in individuals of European ancestry, was associated with low LDL-C (617966) and protection against CHD. Heterozygous carriers of this mutation had a mean LDL-C level that was 12 mg per deciliter (0.31 mmol per liter) lower than that in noncarriers (p = 0.04).
Mirshahi and Carey (2015) followed up on the study of the Myocardial Infarction Genetics Consortium Investigators (2014) by investigating the Geisinger MyCode cohort. They identified 7 R406X carriers, all of European ancestry and none with CHD.
Altmann, S. W., Davis, H. R., Jr., Zhu, L., Yao, X., Hoos, L. M., Tetzloff, G., Iyer, S. P. N., Maguire, M., Golovko, A., Zeng, M., Wang, L., Murgolo, N., Graziano, M. P. Niemann-Pick C1 like 1 protein is critical for intestinal cholesterol absorption. Science 303: 1201-1204, 2004. [PubMed: 14976318] [Full Text: https://doi.org/10.1126/science.1093131]
Chen, C.-W., Hwang, J.-J., Tsai, C.-T., Su, Y.-N., Hsueh, C.-H., Shen, M. J., Lai, L.-P. The g.-762T-C polymorphism of the NPC1L1 gene is common in Chinese and contributes to a higher promoter activity and higher serum cholesterol levels. J. Hum. Genet. 54: 242-247, 2009. [PubMed: 19265861] [Full Text: https://doi.org/10.1038/jhg.2009.18]
Davies, J. P., Levy, B., Ioannou, Y. A. Evidence for a Niemann-Pick C (NPC) gene family: identification and characterization of NPC1L1. Genomics 65: 137-145, 2000. [PubMed: 10783261] [Full Text: https://doi.org/10.1006/geno.2000.6151]
Davies, J. P., Scott, C., Oishi, K., Liapis, A., Ioannou, Y. A. Inactivation of NPC1L1 causes multiple lipid transport defects and protects against diet-induced hypercholesterolemia. J. Biol. Chem. 280: 12710-12720, 2005. [PubMed: 15671032] [Full Text: https://doi.org/10.1074/jbc.M409110200]
Davis, H. R., Jr., Zhu, L., Hoos, L. M., Tetzloff, G., Maguire, M., Liu, J., Yao, X., Iyer, S. P. N., Lam, M.-H., Lund, E. G., Detmers, P. A., Graziano, M. P., Altmann, S. W. Niemann-Pick C1 like 1 (NPC1L1) is the intestinal phytosterol and cholesterol transporter and a key modulator of whole-body cholesterol homeostasis. J. Biol. Chem. 279: 33586-33592, 2004. [PubMed: 15173162] [Full Text: https://doi.org/10.1074/jbc.M405817200]
Garcia-Calvo, M., Lisnock, J., Bull, H. G., Hawes, B. E., Burnett, D. A., Braun, M. P., Crona, J. H., Davis, H. R., Jr., Dean, D. C., Detmers, P. A., Graziano, M. P., Hughes, M., and 12 others. The target of ezetimibe is Niemann-Pick C1-like 1 (NPC1L1). Proc. Nat. Acad. Sci. 102: 8132-8137, 2005. [PubMed: 15928087] [Full Text: https://doi.org/10.1073/pnas.0500269102]
Ge, L., Qi, W., Wang, L.-J., Miao, H.-H., Qu, Y.-X., Li, B.-L., Song, B.-L. Flotillins play an essential role in Niemann-Pick C1-like 1-mediated cholesterol uptake. Proc. Nat. Acad. Sci. 108: 551-556, 2011. [PubMed: 21187433] [Full Text: https://doi.org/10.1073/pnas.1014434108]
Kamishikiryo, J., Haraguchi, M., Nakashima, S., Tasaka, Y., Narahara, H., Sugihara, N., Nakamura, T., Morita, T. N-terminal domain of the cholesterol transporter Niemann-Pick C1-like 1 (NPC1L1) is essential for alpha-tocopherol transport. Biochem. Biophys. Res. Commun. 486: 476-480, 2017. [PubMed: 28315682] [Full Text: https://doi.org/10.1016/j.bbrc.2017.03.065]
Malhotra, P., Soni, V., Kumar, A., Anbazhagan, A. N., Dudeja, A., Saksena, S., Gill, R. K., Dudeja, P. K., Alrefai, W. A. Epigenetic modulation of intestinal cholesterol transporter Niemann-Pick C1-like 1 (NPC1L1) gene expression by DNA methylation. J. Biol. Chem. 289: 23132-23140, 2014. [PubMed: 24904062] [Full Text: https://doi.org/10.1074/jbc.M113.546283]
Mirshahi, U. L., Carey, D. J. Mutations in NPC1l1 and coronary heart disease. (Letter) New Eng. J. Med. 372: 881 only, 2015. [PubMed: 25714173] [Full Text: https://doi.org/10.1056/NEJMc1500124]
Myocardial Infarction Genetics Consortium Investigators. Inactivating mutations in NPC1L1 and protection from coronary heart disease. New Eng. J. Med. 371: 2072-2082, 2014. [PubMed: 25390462] [Full Text: https://doi.org/10.1056/NEJMoa1405386]
Sainz, B., Jr., Barretto, N., Martin, D. N., Hiraga, N., Imamura, M., Hussain, S., Marsh, K. A., Yu, X., Chayama, K., Alrefai, W. A., Uprichard, S. L. Identification of the Niemann-Pick C1-like 1 cholesterol absorption receptor as a new hepatitis C virus entry factor. Nature Med. 18: 281-285, 2012. [PubMed: 22231557] [Full Text: https://doi.org/10.1038/nm.2581]
Simon, J. S., Karnoub, M. C., Devlin, D. J., Arreaza, M. G., Qiu, P., Monks, S. A., Severino, M. E., Deutsch, P., Palmisano, J., Sachs, A. B., Bayne, M. L., Plump, A. S., Schadt, E. E. Sequence variation in NPC1L1 and association with improved LDL-cholesterol lowering in response to ezetimibe treatment. Genomics 86: 648-656, 2005. [PubMed: 16297596] [Full Text: https://doi.org/10.1016/j.ygeno.2005.08.007]
Teslovich, T. M., Musunuru, K., Smith, A. V., Edmondson, A. C., Stylianou, I. M., Koseki, M., Pirruccello, J. P., Ripatti, S., Chasman, D. I., Willer, C. J., Johansen, C. T., Fouchier, S. W., and 197 others. Biological, clinical and population relevance of 95 loci for blood lipids. Nature 466: 707-713, 2010. [PubMed: 20686565] [Full Text: https://doi.org/10.1038/nature09270]
Wang, J., Williams, C. M., Hegele, R. A. Compound heterozygosity for two non-synonymous polymorphisms in NPC1L1 in a non-responder to ezetimibe. Clin. Genet. 67: 175-177, 2004. [PubMed: 15679830] [Full Text: https://doi.org/10.1111/j.1399-0004.2004.00388.x]
Weinglass, A. B., Kohler, M., Schulte, U., Liu, J., Nketiah, E. O., Thomas, A., Schmalhofer, W., Williams, B., Bildl, W., McMasters, D. R., Dai, K., Beers, L., McCann, M. E., Kaczorowski, G. J., Garcia, M. L. Extracellular loop C of NPC1L1 is important for binding to ezetimibe. Proc. Nat. Acad. Sci. 105: 11140-11145, 2008. [PubMed: 18682566] [Full Text: https://doi.org/10.1073/pnas.0800936105]
Yu, L., Bharadwaj, S., Brown, J. M., Ma, Y., Du, W., Davis, M. A., Michaely, P., Liu, P., Willingham, M. C., Rudel, L. L. Cholesterol-regulated translocation of NPC1L1 to the cell surface facilitates free cholesterol uptake. J. Biol. Chem. 281: 6616-6624, 2006. [PubMed: 16407187] [Full Text: https://doi.org/10.1074/jbc.M511123200]