From Loci to Biology: Functional Genomics of Genome-Wide Association for Coronary Disease

Circulation Research

Volumn 118, Issue 4, 2016, Pages 586-606

  Nurnberg, Sylvia T ^a   Zhang, Hanrui ^b   Hand, Nicholas J ^c   Bauer, Robert C ^a   Saleheen, Danish ^b   Reilly, Muredach P ^b   Rader, Daniel J ^a,b,c  

^a Division of Translational Medicine and Human Genetics   (United States)

^b UNIVERSITY OF PENNSYLVANIA   (United States)

^c University of Pennsylvania ^*  (United States)

Author keywords

atherosclerosis; coronary artery disease; functional; genome wide; genomics

Indexed keywords

ADAMTS7 PROTEIN; ANTISENSE OLIGONUCLEOTIDE; PARVOVIRUS VECTOR; PROTEIN; SMALL INTERFERING RNA; SORTILIN; TRIBBLES 1; UNCLASSIFIED DRUG; UNTRANSLATED RNA; GENETIC MARKER;

ARTICLE; ATHEROSCLEROSIS; CORONARY ARTERY DISEASE; FUNCTIONAL GENOMICS; GENE; GENE LOCUS; GENE TARGETING; GENETIC ASSOCIATION; HUMAN; NEXT GENERATION SEQUENCING; PHENOTYPE; PRIORITY JOURNAL; QUANTITATIVE TRAIT LOCUS; SINGLE NUCLEOTIDE POLYMORPHISM; TCF21 GENE; ANIMAL; GENETIC MARKER; GENETIC PREDISPOSITION; GENETICS; GENOME-WIDE ASSOCIATION STUDY; PROGNOSIS; RISK ASSESSMENT; RISK FACTOR;

ANIMALS; CORONARY ARTERY DISEASE; GENETIC LOCI; GENETIC MARKERS; GENETIC PREDISPOSITION TO DISEASE; GENOME-WIDE ASSOCIATION STUDY; HUMANS; PHENOTYPE; PROGNOSIS; RISK ASSESSMENT; RISK FACTORS;

EID: 84959048574     PISSN: 00097330     EISSN: 15244571     Source Type: Journal    
DOI: 10.1161/CIRCRESAHA.115.306464     Document Type: Article

References (205)

1. Nikpay M, Goel A, Won HH, CARDIoGRAMplusC4D Consortium A comprehensive 1000 genomes-based genome-wide association meta-analysis of coronary artery disease. Nat Genet 2015 47 1121 1130. doi: 10.1038/ng.3396.
2. Kathiresan S, Voight BF, Purcell S, Myocardial Infarction Genetics Consortium; Wellcome Trust Case Control Consortium Genome-wide association of early-onset myocardial infarction with single nucleotide polymorphisms and copy number variants. Nat Genet 2009 41 334 341. doi: 10.1038/ng.327.
3. Willer CJ, Sanna S, Jackson AU, Newly identified loci that influence lipid concentrations and risk of coronary artery disease. Nat Genet 2008 40 161 169. doi: 10.1038/ng.76.
4. Schunkert H, König IR, Kathiresan S, Cardiogenics; CARDIoGRAM Consortium Large-scale association analysis identifies 13 new susceptibility loci for coronary artery disease. Nat Genet 2011 43 333 338. doi: 10.1038/ng.784.
5. Kathiresan S, Melander O, Guiducci C, Six new loci associated with blood low-density lipoprotein cholesterol, high-density lipoprotein cholesterol or triglycerides in humans. Nat Genet 2008 40 189 197. doi: 10.1038/ng.75.
6. Grallert H, Dupuis J, Bis JC, Eight genetic loci associated with variation in lipoprotein-associated phospholipase A2 mass and activity and coronary heart disease: meta-analysis of genome-wide association studies from five community-based studies. Eur Heart J 2012 33 238 251. doi: 10.1093/eurheartj/ehr372.
7. Deloukas P, Kanoni S, Willenborg C, CARDIoGRAMplusC4D Consortium; DIAGRAM Consortium; CARDIOGENICS Consortium; MuTHER Consortium; Wellcome Trust Case Control Consortium Large-scale association analysis identifies new risk loci for coronary artery disease. Nat Genet 2013 45 25 33. doi: 10.1038/ng.2480.
8. Samani NJ, Erdmann J, Hall AS, WTCCC and the Cardiogenics Consortium Genomewide association analysis of coronary artery disease. N Engl J Med 2007 357 443 453. doi: 10.1056/NEJMoa072366.
9. Erdmann J, Grosshennig A, Braund PS, Italian Atherosclerosis, Thrombosis, and Vascular Biology Working Group; Myocardial Infarction Genetics Consortium; Wellcome Trust Case Control Consortium; Cardiogenics Consortium New susceptibility locus for coronary artery disease on chromosome 3q22.3. Nat Genet 2009 41 280 282. doi: 10.1038/ng.307.
10. Bis JC, Kavousi M, Franceschini N, CARDIoGRAM Consortium Meta-analysis of genome-wide association studies from the CHARGE consortium identifies common variants associated with carotid intima media thickness and plaque. Nat Genet 2011 43 940 947. doi: 10.1038/ng.920.
11. Dichgans M, Malik R, König IR, METASTROKE Consortium; CARDIoGRAM Consortium; C4D Consortium; International Stroke Genetics Consortium Shared genetic susceptibility to ischemic stroke and coronary artery disease: a genome-wide analysis of common variants. Stroke 2014 45 24 36. doi: 10.1161/STROKEAHA.113.002707.
12. Wang F, Xu CQ, He Q, Genome-wide association identifies a susceptibility locus for coronary artery disease in the Chinese Han population. Nat Genet 2011 43 345 349. doi: 10.1038/ng.783.
13. O'Donnell CJ, Kavousi M, Smith AV, CARDIoGRAM Consortium Genome-wide association study for coronary artery calcification with follow-up in myocardial infarction. Circulation 2011 124 2855 2864. doi: 10.1161/CIRCULATIONAHA.110.974899.
14. Debette S, Kamatani Y, Metso TM, International Stroke Genetics Consortium; CADISP group; CADISP group Common variation in PHACTR1 is associated with susceptibility to cervical artery dissection. Nat Genet 2015 47 78 83. doi: 10.1038/ng.3154.
15. Freilinger T, Anttila V, de Vries B, International Headache Genetics Consortium Genome-wide association analysis identifies susceptibility loci for migraine without aura. Nat Genet 2012 44 777 782. doi: 10.1038/ng.2307.
16. Trégouët DA, König IR, Erdmann J, Wellcome Trust Case Control Consortium; Cardiogenics Consortium Genome-wide haplotype association study identifies the SLC22A3-LPAL2-LPA gene cluster as a risk locus for coronary artery disease. Nat Genet 2009 41 283 285. doi: 10.1038/ng.314.
17. Traylor M, Farrall M, Holliday EG, Australian Stroke Genetics Collaborative, Wellcome Trust Case Control Consortium 2 (WTCCC2); International Stroke Genetics Consortium Genetic risk factors for ischaemic stroke and its subtypes (the METASTROKE collaboration): a meta-analysis of genome-wide association studies. Lancet Neurol 2012 11 951 962. doi: 10.1016/S1474-4422(12)70234-X.
18. Coronary Artery Disease (C4D) Genetics Consortium A genome-wide association study in europeans and south asians identifies five new loci for coronary artery disease. Nat Genet 2011 43 339 344. doi: 10.1038/ng.782.
19. Teslovich TM, Musunuru K, Smith AV, Biological, clinical and population relevance of 95 loci for blood lipids. Nature 2010 466 707 713. doi: 10.1038/nature09270.
20. Heit JA, Armasu SM, Asmann YW, Cunningham JM, Matsumoto ME, Petterson TM, De Andrade M., A genome-wide association study of venous thromboembolism identifies risk variants in chromosomes 1q24.2 and 9q. J Thromb Haemost 2012 10 1521 1531. doi: 10.1111/j.1538-7836.2012.04810.x.
21. Yasuno K, Bilguvar K, Bijlenga P, Genome-wide association study of intracranial aneurysm identifies three new risk loci. Nat Genet 2010 42 420 425. doi: 10.1038/ng.563.
22. Levy D, Ehret GB, Rice K, Genome-wide association study of blood pressure and hypertension. Nat Genet 2009 41 677 687. doi: 10.1038/ng.384.
23. Aulchenko YS, Ripatti S, Lindqvist I, ENGAGE Consortium Loci influencing lipid levels and coronary heart disease risk in 16 European population cohorts. Nat Genet 2009 41 47 55. doi: 10.1038/ng.269.
24. Middelberg RP, Ferreira MA, Henders AK, Heath AC, Madden PA, Montgomery GW, Martin NG, Whitfield JB., Genetic variants in LPL, OASL and TOMM40/APOE-C1-C2-C4 genes are associated with multiple cardiovascular-related traits. BMC Med Genet 2011 12 123. doi: 10.1186/1471-2350-12-123.
25. Smith EN, Chen W, Kähönen M, Kettunen J, Lehtimäki T, Peltonen L, Raitakari OT, Salem RM, Schork NJ, Shaw M, Srinivasan SR, Topol EJ, Viikari JS, Berenson GS, Murray SS., Longitudinal genome-wide association of cardiovascular disease risk factors in the Bogalusa heart study. PLoS Genet 2010 6 e1001094. doi: 10.1371/journal.pgen.1001094.
26. Chu AY, Guilianini F, Grallert H, Dupuis J, Ballantyne CM, Barratt BJ, Nyberg F, Chasman DI, Ridker PM., Genome-wide association study evaluating lipoprotein-associated phospholipase A2 mass and activity at baseline and after rosuvastatin therapy. Circ Cardiovasc Genet 2012 5 676 685. doi: 10.1161/CIRCGENETICS.112.963314.
27. Diabetes Genetics Initiative of Broad Institute of Harvard and MIT, Lund University, and Novartis Institutes of BioMedical Research Saxena R, Voight BF, Lyssenko V, Diabetes Genetics Initiative of Broad Institute of Harvard and MIT, Lund University, and Novartis Institutes of BioMedical Research Genome-wide association analysis identifies loci for type 2 diabetes and triglyceride levels. Science 2007 316 1331 1336
28. Kathiresan S, Musunuru K, Orho-Melander M., Defining the spectrum of alleles that contribute to blood lipid concentrations in humans. Curr Opin Lipidol 2008 19 122 127. doi: 10.1097/MOL.0b013e3282f70296.
29. Lettre G, Palmer CD, Young T, Genome-wide association study of coronary heart disease and its risk factors in 8,090 African Americans: the NHLBI CARe Project. PLoS Genet 2011 7 e1001300. doi: 10.1371/journal.pgen.1001300.
30. Jørgensen AB, Frikke-Schmidt R, Nordestgaard BG, Tybjærg-Hansen A., Loss-of-function mutations in APOC3 and risk of ischemic vascular disease. N Engl J Med 2014 371 32 41. doi: 10.1056/NEJMoa1308027.
31. TG and HDL Working Group of the Exome Sequencing Project National Heart, Lung, and Blood Institute Crosby J, Peloso GM, Auer PL, TG and HDL Working Group of the Exome Sequencing Project National Heart, Lung, and Blood Institute Loss-of-function mutations in apoc3, triglycerides, and coronary disease. N Engl J Med 2014 371 22 31. doi: 10.1056/NEJMoa1307095.
32. Do R, Stitziel NO, Won HH, NHLBI Exome Sequencing Project Exome sequencing identifies rare LDLR and APOA5 alleles conferring risk for myocardial infarction. Nature 2015 518 102 106. doi: 10.1038/nature13917.
33. Khetarpal SA, Rader DJ., Triglyceride-rich lipoproteins and coronary artery disease risk: new insights from human genetics. Arterioscler Thromb Vasc Biol 2015 35 e3 e9. doi: 10.1161/ATVBAHA.114.305172.
34. Smemo S, Tena JJ, Kim KH, Obesity-associated variants within FTO form long-range functional connections with IRX3. Nature 2014 507 371 375. doi: 10.1038/nature13138.
35. Giresi PG, Kim J, McDaniell RM, Iyer VR, Lieb JD., FAIRE (Formaldehyde-Assisted Isolation of Regulatory Elements) isolates active regulatory elements from human chromatin. Genome Res 2007 17 877 885. doi: 10.1101/gr.5533506.
36. Boyle AP, Davis S, Shulha HP, Meltzer P, Margulies EH, Weng Z, Furey TS, Crawford GE., High-resolution mapping and characterization of open chromatin across the genome. Cell 2008 132 311 322. doi: 10.1016/j.cell.2007.12.014.
37. Buenrostro JD, Giresi PG, Zaba LC, Chang HY, Greenleaf WJ., Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position. Nat Methods 2013 10 1213 1218. doi: 10.1038/nmeth.2688.
38. Shlyueva D, Stampfel G, Stark A., Transcriptional enhancers: from properties to genome-wide predictions. Nat Rev Genet 2014 15 272 286. doi: 10.1038/nrg3682.
39. Lam MT, Li W, Rosenfeld MG, Glass CK., Enhancer RNAs and regulated transcriptional programs. Trends Biochem Sci 2014 39 170 182. doi: 10.1016/j.tibs.2014.02.007.
40. McDaniell R, Lee BK, Song L, Heritable individual-specific and allele-specific chromatin signatures in humans. Science 2010 328 235 239. doi: 10.1126/science.1184655.
41. McVicker G, van de Geijn B, Degner JF, Cain CE, Banovich NE, Raj A, Lewellen N, Myrthil M, Gilad Y, Pritchard JK., Identification of genetic variants that affect histone modifications in human cells. Science 2013 342 747 749. doi: 10.1126/science.1242429.
42. Consortium GT Human genomics. The genotype-tissue expression (gtex) pilot analysis: Multitissue gene regulation in humans. Science 2015 348 648 660
43. Tang F, Barbacioru C, Wang Y, Nordman E, Lee C, Xu N, Wang X, Bodeau J, Tuch BB, Siddiqui A, Lao K, Surani MA., mRNA-Seq whole-transcriptome analysis of a single cell. Nat Methods 2009 6 377 382. doi: 10.1038/nmeth.1315.
44. Rotem A, Ram O, Shoresh N, Sperling RA, Goren A, Weitz DA, Bernstein BE., Single-cell ChIP-seq reveals cell subpopulations defined by chromatin state. Nat Biotechnol 2015 33 1165 1172. doi: 10.1038/nbt.3383.
45. Boardman-Pretty F, Smith AJ, Cooper J, Functional analysis of a carotid intima-media thickness locus implicates BCAR1 and suggests a causal variant. Circ Cardiovasc Genet 2015 8 696 706. doi: 10.1161/CIRCGENETICS.115.001062.
46. Brem RB, Yvert G, Clinton R, Kruglyak L., Genetic dissection of transcriptional regulation in budding yeast. Science 2002 296 752 755. doi: 10.1126/science.1069516.
47. Rockman MV, Kruglyak L., Genetics of global gene expression. Nat Rev Genet 2006 7 862 872. doi: 10.1038/nrg1964.
48. Schadt EE, Molony C, Chudin E, Mapping the genetic architecture of gene expression in human liver. PLoS Biol 2008 6 e107. doi: 10.1371/journal.pbio.0060107.
49. Innocenti F, Cooper GM, Stanaway IB, Identification, replication, and functional fine-mapping of expression quantitative trait loci in primary human liver tissue. PLoS Genet 2011 7 e1002078. doi: 10.1371/journal.pgen.1002078.
50. Greenawalt DM, Dobrin R, Chudin E, A survey of the genetics of stomach, liver, and adipose gene expression from a morbidly obese cohort. Genome Res 2011 21 1008 1016. doi: 10.1101/gr.112821.110.
51. Zeller T, Wild P, Szymczak S, Genetics and beyond-the transcriptome of human monocytes and disease susceptibility. PLoS One 2010 5 e10693. doi: 10.1371/journal.pone.0010693.
52. Romanoski CE, Che N, Yin F, Mai N, Pouldar D, Civelek M, Pan C, Lee S, Vakili L, Yang WP, Kayne P, Mungrue IN, Araujo JA, Berliner JA, Lusis AJ., Network for activation of human endothelial cells by oxidized phospholipids: a critical role of heme oxygenase 1. Circ Res 2011 109 e27 e41. doi: 10.1161/CIRCRESAHA.111.241869.
53. Albert FW, Kruglyak L., The role of regulatory variation in complex traits and disease. Nat Rev Genet 2015 16 197 212. doi: 10.1038/nrg3891.
54. Brænne I, Civelek M, Vilne B, Leducq Consortium CAD Genomics‡ Prediction of causal candidate genes in coronary artery disease loci. Arterioscler Thromb Vasc Biol 2015 35 2207 2217. doi: 10.1161/ATVBAHA.115.306108.
55. Foroughi Asl H, Talukdar HA, Kindt AS, CARDIoGRAM Consortium Expression quantitative trait Loci acting across multiple tissues are enriched in inherited risk for coronary artery disease. Circ Cardiovasc Genet 2015 8 305 315. doi: 10.1161/CIRCGENETICS.114.000640.
56. Ge B, Pokholok DK, Kwan T, Global patterns of cis variation in human cells revealed by high-density allelic expression analysis. Nat Genet 2009 41 1216 1222. doi: 10.1038/ng.473.
57. Pickrell JK, Marioni JC, Pai AA, Degner JF, Engelhardt BE, Nkadori E, Veyrieras JB, Stephens M, Gilad Y, Pritchard JK., Understanding mechanisms underlying human gene expression variation with RNA sequencing. Nature 2010 464 768 772. doi: 10.1038/nature08872.
58. Lappalainen T, Sammeth M, Friedländer MR, Geuvadis Consortium Transcriptome and genome sequencing uncovers functional variation in humans. Nature 2013 501 506 511. doi: 10.1038/nature12531.
59. Montgomery SB, Sammeth M, Gutierrez-Arcelus M, Lach RP, Ingle C, Nisbett J, Guigo R, Dermitzakis ET., Transcriptome genetics using second generation sequencing in a Caucasian population. Nature 2010 464 773 777. doi: 10.1038/nature08903.
60. Goncalves A, Leigh-Brown S, Thybert D, Stefflova K, Turro E, Flicek P, Brazma A, Odom DT, Marioni JC., Extensive compensatory cis-trans regulation in the evolution of mouse gene expression. Genome Res 2012 22 2376 2384. doi: 10.1101/gr.142281.112.
61. Lagarrigue S, Martin L, Hormozdiari F, Roux PF, Pan C, van Nas A, Demeure O, Cantor R, Ghazalpour A, Eskin E, Lusis AJ., Analysis of allele-specific expression in mouse liver by RNA-Seq: a comparison with Cis-eQTL identified using genetic linkage. Genetics 2013 195 1157 1166. doi: 10.1534/genetics.113.153882.
62. Leung D, Jung I, Rajagopal N, Integrative analysis of haplotype-resolved epigenomes across human tissues. Nature 2015 518 350 354. doi: 10.1038/nature14217.
63. Hughes JR, Roberts N, McGowan S, Hay D, Giannoulatou E, Lynch M, De Gobbi M, Taylor S, Gibbons R, Higgs DR., Analysis of hundreds of cis-regulatory landscapes at high resolution in a single, high-throughput experiment. Nat Genet 2014 46 205 212. doi: 10.1038/ng.2871.
64. Jäger R, Migliorini G, Henrion M, Capture Hi-C identifies the chromatin interactome of colorectal cancer risk loci. Nat Commun 2015 6 6178. doi: 10.1038/ncomms7178.
65. Nagano T, Lubling Y, Stevens TJ, Schoenfelder S, Yaffe E, Dean W, Laue ED, Tanay A, Fraser P., Single-cell Hi-C reveals cell-to-cell variability in chromosome structure. Nature 2013 502 59 64. doi: 10.1038/nature12593.
66. Maurano MT, Humbert R, Rynes E, Systematic localization of common disease-associated variation in regulatory DNA. Science 2012 337 1190 1195. doi: 10.1126/science.1222794.
67. Esteller M., Non-coding RNAs in human disease. Nat Rev Genet 2011 12 861 874. doi: 10.1038/nrg3074.
68. Wagschal A, Najafi-Shoushtari SH, Wang L, Genome-wide identification of microRNAs regulating cholesterol and triglyceride homeostasis. Nat Med 2015 21 1290 1297. doi: 10.1038/nm.3980.
69. Ulitsky I, Bartel DP., lincRNAs: genomics, evolution, and mechanisms. Cell 2013 154 26 46. doi: 10.1016/j.cell.2013.06.020.
70. Ning S, Wang P, Ye J, Li X, Li R, Zhao Z, Huo X, Wang L, Li F, Li X., A global map for dissecting phenotypic variants in human lincRNAs. Eur J Hum Genet 2013 21 1128 1133. doi: 10.1038/ejhg.2013.7.
71. Ning S, Zhao Z, Ye J, Wang P, Zhi H, Li R, Wang T, Li X., LincSNP: a database of linking disease-associated SNPs to human large intergenic non-coding RNAs. BMC Bioinformatics 2014 15 152. doi: 10.1186/1471-2105-15-152.
72. Gong J, Liu W, Zhang J, Miao X, Guo AY., lncRNASNP: a database of SNPs in lncRNAs and their potential functions in human and mouse. Nucleic Acids Res 2015 43 D181 D186. doi: 10.1093/nar/gku1000.
73. Kumar V, Westra HJ, Karjalainen J, Human disease-associated genetic variation impacts large intergenic non-coding RNA expression. PLoS Genet 2013 9 e1003201. doi: 10.1371/journal.pgen.1003201.
74. Morris KV, Mattick JS., The rise of regulatory RNA. Nat Rev Genet 2014 15 423 437. doi: 10.1038/nrg3722.
75. Yoon JH, Abdelmohsen K, Gorospe M., Posttranscriptional gene regulation by long noncoding RNA. J Mol Biol 2013 425 3723 3730. doi: 10.1016/j.jmb.2012.11.024.
76. Augui S, Nora EP, Heard E., Regulation of X-chromosome inactivation by the X-inactivation centre. Nat Rev Genet 2011 12 429 442. doi: 10.1038/nrg2987.
77. Pauli A, Valen E, Lin MF, Garber M, Vastenhouw NL, Levin JZ, Fan L, Sandelin A, Rinn JL, Regev A, Schier AF., Systematic identification of long noncoding RNAs expressed during zebrafish embryogenesis. Genome Res 2012 22 577 591. doi: 10.1101/gr.133009.111.
78. Guttman M, Donaghey J, Carey BW, lincRNAs act in the circuitry controlling pluripotency and differentiation. Nature 2011 477 295 300. doi: 10.1038/nature10398.
79. Ulitsky I, Shkumatava A, Jan CH, Sive H, Bartel DP., Conserved function of lincRNAs in vertebrate embryonic development despite rapid sequence evolution. Cell 2011 147 1537 1550. doi: 10.1016/j.cell.2011.11.055.
80. Qiu MT, Hu JW, Yin R, Xu L., Long noncoding RNA: an emerging paradigm of cancer research. Tumour Biol 2013 34 613 620. doi: 10.1007/s13277-013-0658-6.
81. Ziats MN, Rennert OM., Aberrant expression of long noncoding RNAs in autistic brain. J Mol Neurosci 2013 49 589 593. doi: 10.1007/s12031-012-9880-8.
82. Han P, Li W, Lin CH, A long noncoding RNA protects the heart from pathological hypertrophy. Nature 2014 514 102 106. doi: 10.1038/nature13596.
83. Holdt LM, Beutner F, Scholz M, Gielen S, Gäbel G, Bergert H, Schuler G, Thiery J, Teupser D., ANRIL expression is associated with atherosclerosis risk at chromosome 9p21. Arterioscler Thromb Vasc Biol 2010 30 620 627. doi: 10.1161/ATVBAHA.109.196832.
84. Ishii N, Ozaki K, Sato H, Mizuno H, Saito S, Takahashi A, Miyamoto Y, Ikegawa S, Kamatani N, Hori M, Saito S, Nakamura Y, Tanaka T., Identification of a novel non-coding RNA, MIAT, that confers risk of myocardial infarction. J Hum Genet 2006 51 1087 1099. doi: 10.1007/s10038-006-0070-9.
85. Klattenhoff CA, Scheuermann JC, Surface LE, Bradley RK, Fields PA, Steinhauser ML, Ding H, Butty VL, Torrey L, Haas S, Abo R, Tabebordbar M, Lee RT, Burge CB, Boyer LA., Braveheart, a long noncoding RNA required for cardiovascular lineage commitment. Cell 2013 152 570 583. doi: 10.1016/j.cell.2013.01.003.
86. Wang K, Liu F, Zhou LY, Long B, Yuan SM, Wang Y, Liu CY, Sun T, Zhang XJ, Li PF., The long noncoding RNA CHRF regulates cardiac hypertrophy by targeting miR-489. Circ Res 2014 114 1377 1388. doi: 10.1161/CIRCRESAHA.114.302476.
87. Michalik KM, You X, Manavski Y, Doddaballapur A, Zörnig M, Braun T, John D, Ponomareva Y, Chen W, Uchida S, Boon RA, Dimmeler S., Long noncoding RNA MALAT1 regulates endothelial cell function and vessel growth. Circ Res 2014 114 1389 1397. doi: 10.1161/CIRCRESAHA.114.303265.
88. Wu G, Cai J, Han Y, LincRNA-p21 regulates neointima formation, vascular smooth muscle cell proliferation, apoptosis, and atherosclerosis by enhancing p53 activity. Circulation 2014 130 1452 1465. doi: 10.1161/CIRCULATIONAHA.114.011675.
89. Carpenter S, Aiello D, Atianand MK, Ricci EP, Gandhi P, Hall LL, Byron M, Monks B, Henry-Bezy M, Lawrence JB, O'Neill LA, Moore MJ, Caffrey DR, Fitzgerald KA., A long noncoding RNA mediates both activation and repression of immune response genes. Science 2013 341 789 792. doi: 10.1126/science.1240925.
90. Li Z, Chao TC, Chang KY, Lin N, Patil VS, Shimizu C, Head SR, Burns JC, Rana TM., The long noncoding RNA THRIL regulates TNFα expression through its interaction with hnRNPL. Proc Natl Acad Sci USA 2014 111 1002 1007. doi: 10.1073/pnas.1313768111.
91. Sun L, Goff LA, Trapnell C, Alexander R, Lo KA, Hacisuleyman E, Sauvageau M, Tazon-Vega B, Kelley DR, Hendrickson DG, Yuan B, Kellis M, Lodish HF, Rinn JL., Long noncoding RNAs regulate adipogenesis. Proc Natl Acad Sci USA 2013 110 3387 3392. doi: 10.1073/pnas.1222643110.
92. Hacisuleyman E, Goff LA, Trapnell C, Topological organization of multichromosomal regions by the long intergenic noncoding RNA Firre. Nat Struct Mol Biol 2014 21 198 206. doi: 10.1038/nsmb.2764.
93. Zhao XY, Li S, Wang GX, Yu Q, Lin JD., A long noncoding RNA transcriptional regulatory circuit drives thermogenic adipocyte differentiation. Mol Cell 2014 55 372 382. doi: 10.1016/j.molcel.2014.06.004.
94. Xiao T, Liu L, Li H, Sun Y, Luo H, Li T, Wang S, Dalton S, Zhao RC, Chen R., Long noncoding RNA ADINR regulates adipogenesis by transcriptionally activating C/EBPalpha. Stem cell reports 2015 5 856 865. doi: 10.1016/j.stemcr.2015.09.007.
95. Alvarez-Dominguez JR, Bai Z, Xu D, Yuan B, Lo KA, Yoon MJ, Lim YC, Knoll M, Slavov N, Chen S, Chen P, Lodish HF, Sun L., De novo reconstruction of adipose tissue transcriptomes reveals long non-coding RNA regulators of brown adipocyte development. Cell Metab 2015 21 764 776. doi: 10.1016/j.cmet.2015.04.003.
96. Pasmant E, Sabbagh A, Vidaud M, Bièche I., ANRIL, a long, noncoding RNA, is an unexpected major hotspot in GWAS. FASEB J 2011 25 444 448. doi: 10.1096/fj.10-172452.
97. Burd CE, Jeck WR, Liu Y, Sanoff HK, Wang Z, Sharpless NE., Expression of linear and novel circular forms of an INK4/ARF-associated non-coding RNA correlates with atherosclerosis risk. PLoS Genet 2010 6 e1001233. doi: 10.1371/journal.pgen.1001233.
98. Derrien T, Johnson R, Bussotti G, The GENCODE v7 catalog of human long noncoding RNAs: analysis of their gene structure, evolution, and expression. Genome Res 2012 22 1775 1789. doi: 10.1101/gr.132159.111.
99. Cabili MN, Trapnell C, Goff L, Koziol M, Tazon-Vega B, Regev A, Rinn JL., Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses. Genes Dev 2011 25 1915 1927. doi: 10.1101/gad.17446611.
100. Cong L, Ran FA, Cox D, Lin S, Barretto R, Habib N, Hsu PD, Wu X, Jiang W, Marraffini LA, Zhang F., Multiplex genome engineering using CRISPR/Cas systems. Science 2013 339 819 823. doi: 10.1126/science.1231143.
101. Mali P, Yang L, Esvelt KM, Aach J, Guell M, DiCarlo JE, Norville JE, Church GM., RNA-guided human genome engineering via Cas9. Science 2013 339 823 826. doi: 10.1126/science.1232033.
102. Gaj T, Gersbach CA, Barbas CF III., ZFN, TALEN, and CRISPR/Cas-based methods for genome engineering. Trends Biotechnol 2013 31 397 405. doi: 10.1016/j.tibtech.2013.04.004.
103. Jinek M, Chylinski K, Fonfara I, Hauer M, Doudna JA, Charpentier E., A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity. Science 2012 337 816 821. doi: 10.1126/science.1225829.
104. Gilbert LA, Larson MH, Morsut L, Liu Z, Brar GA, Torres SE, Stern-Ginossar N, Brandman O, Whitehead EH, Doudna JA, Lim WA, Weissman JS, Qi LS., CRISPR-mediated modular RNA-guided regulation of transcription in eukaryotes. Cell 2013 154 442 451. doi: 10.1016/j.cell.2013.06.044.
105. Maeder ML, Linder SJ, Cascio VM, Fu Y, Ho QH, Joung JK., CRISPR RNA-guided activation of endogenous human genes. Nat Methods 2013 10 977 979. doi: 10.1038/nmeth.2598.
106. Perez-Pinera P, Kocak DD, Vockley CM, Adler AF, Kabadi AM, Polstein LR, Thakore PI, Glass KA, Ousterout DG, Leong KW, Guilak F, Crawford GE, Reddy TE, Gersbach CA., RNA-guided gene activation by CRISPR-Cas9-based transcription factors. Nat Methods 2013 10 973 976. doi: 10.1038/nmeth.2600.
107. Mali P, Esvelt KM, Church GM., Cas9 as a versatile tool for engineering biology. Nat Methods 2013 10 957 963. doi: 10.1038/nmeth.2649.
108. Beaudoin M, Gupta RM, Won HH, Lo KS, Do R, Henderson CA, Lavoie-St-Amour C, Langlois S, Rivas D, Lehoux S, Kathiresan S, Tardif JC, Musunuru K, Lettre G., Myocardial infarction-associated SNP at 6p24 interferes with MEF2 binding and associates with PHACTR1 expression levels in human coronary arteries. Arterioscler Thromb Vasc Biol 2015 35 1472 1479. doi: 10.1161/ATVBAHA.115.305534.
109. González F, Zhu Z, Shi ZD, Lelli K, Verma N, Li QV, Huangfu D., An iCRISPR platform for rapid, multiplexable, and inducible genome editing in human pluripotent stem cells. Cell Stem Cell 2014 15 215 226. doi: 10.1016/j.stem.2014.05.018.
110. Kim S, Kim D, Cho SW, Kim J, Kim JS., Highly efficient RNA-guided genome editing in human cells via delivery of purified Cas9 ribonucleoproteins. Genome Res 2014 24 1012 1019. doi: 10.1101/gr.171322.113.
111. Hendel A, Bak RO, Clark JT, Kennedy AB, Ryan DE, Roy S, Steinfeld I, Lunstad BD, Kaiser RJ, Wilkens AB, Bacchetta R, Tsalenko A, Dellinger D, Bruhn L, Porteus MH., Chemically modified guide RNAs enhance CRISPR-Cas genome editing in human primary cells. Nat Biotechnol 2015 33 985 989. doi: 10.1038/nbt.3290.
112. Maruyama T, Dougan SK, Truttmann MC, Bilate AM, Ingram JR, Ploegh HL., Increasing the efficiency of precise genome editing with CRISPR-Cas9 by inhibition of nonhomologous end joining. Nat Biotechnol 2015 33 538 542. doi: 10.1038/nbt.3190.
113. Robert F, Barbeau M, Éthier S, Dostie J, Pelletier J., Pharmacological inhibition of DNA-PK stimulates Cas9-mediated genome editing. Genome Med 2015 7 93. doi: 10.1186/s13073-015-0215-6.
114. Chu VT, Weber T, Wefers B, Wurst W, Sander S, Rajewsky K, Kühn R., Increasing the efficiency of homology-directed repair for CRISPR-Cas9-induced precise gene editing in mammalian cells. Nat Biotechnol 2015 33 543 548. doi: 10.1038/nbt.3198.
115. Miyaoka Y, Chan AH, Judge LM, Yoo J, Huang M, Nguyen TD, Lizarraga PP, So PL, Conklin BR., Isolation of single-base genome-edited human iPS cells without antibiotic selection. Nat Methods 2014 11 291 293. doi: 10.1038/nmeth.2840.
116. Yang H, Wang H, Shivalila CS, Cheng AW, Shi L, Jaenisch R., One-step generation of mice carrying reporter and conditional alleles by CRISPR/Cas-mediated genome engineering. Cell 2013 154 1370 1379. doi: 10.1016/j.cell.2013.08.022.
117. Wang H, Yang H, Shivalila CS, Dawlaty MM, Cheng AW, Zhang F, Jaenisch R., One-step generation of mice carrying mutations in multiple genes by CRISPR/Cas-mediated genome engineering. Cell 2013 153 910 918. doi: 10.1016/j.cell.2013.04.025.
118. Burkhardt R, Toh SA, Lagor WR, Birkeland A, Levin M, Li X, Robblee M, Fedorov VD, Yamamoto M, Satoh T, Akira S, Kathiresan S, Breslow JL, Rader DJ., Trib1 is a lipid-and myocardial infarction-associated gene that regulates hepatic lipogenesis and VLDL production in mice. J Clin Invest 2010 120 4410 4414. doi: 10.1172/JCI44213.
119. Schirle NT, Sheu-Gruttadauria J, MacRae IJ., Structural basis for microRNA targeting. Science 2014 346 608 613. doi: 10.1126/science.1258040.
120. Huntzinger E, Izaurralde E., Gene silencing by microRNAs: contributions of translational repression and mRNA decay. Nat Rev Genet 2011 12 99 110. doi: 10.1038/nrg2936.
121. Miyoshi K, Tsukumo H, Nagami T, Siomi H, Siomi MC., Slicer function of Drosophila Argonautes and its involvement in RISC formation. Genes Dev 2005 19 2837 2848. doi: 10.1101/gad.1370605.
122. Grimm D, Streetz KL, Jopling CL, Storm TA, Pandey K, Davis CR, Marion P, Salazar F, Kay MA., Fatality in mice due to oversaturation of cellular microRNA/short hairpin RNA pathways. Nature 2006 441 537 541. doi: 10.1038/nature04791.
123. Mockenhaupt S, Grosse S, Rupp D, Bartenschlager R, Grimm D., Alleviation of off-target effects from vector-encoded shRNAs via codelivered RNA decoys. Proc Natl Acad Sci USA 2015 112 E4007 E4016. doi: 10.1073/pnas.1510476112.
124. Grimm D, Wang L, Lee JS, Schürmann N, Gu S, Börner K, Storm TA, Kay MA., Argonaute proteins are key determinants of RNAi efficacy, toxicity, and persistence in the adult mouse liver. J Clin Invest 2010 120 3106 3119. doi: 10.1172/JCI43565.
125. Giering JC, Grimm D, Storm TA, Kay MA., Expression of shRNA from a tissue-specific pol II promoter is an effective and safe RNAi therapeutic. Mol Ther 2008 16 1630 1636. doi: 10.1038/mt.2008.144.
126. Wang J, Lu Z, Wientjes MG, Au JL., Delivery of siRNA therapeutics: barriers and carriers. AAPS J 2010 12 492 503. doi: 10.1208/s12248-010-9210-4.
127. Fitzgerald K, Frank-Kamenetsky M, Shulga-Morskaya S, Effect of an RNA interference drug on the synthesis of proprotein convertase subtilisin/kexin type 9 (PCSK9) and the concentration of serum LDL cholesterol in healthy volunteers: a randomised, single-blind, placebo-controlled, phase 1 trial. Lancet 2014 383 60 68. doi: 10.1016/S0140-6736(13)61914-5.
128. Geary RS, Baker BF, Crooke ST., Clinical and preclinical pharmacokinetics and pharmacodynamics of mipomersen (kynamro(®)): a second-generation antisense oligonucleotide inhibitor of apolipoprotein B. Clin Pharmacokinet 2015 54 133 146. doi: 10.1007/s40262-014-0224-4.
129. Lagor WR, Johnston JC, Lock M, Vandenberghe LH, Rader DJ., Adeno-associated viruses as liver-directed gene delivery vehicles: focus on lipoprotein metabolism. Methods Mol Biol 2013 1027 273 307. doi: 10.1007/978-1-60327-369-5-13.
130. Grimm D, Lee JS, Wang L, Desai T, Akache B, Storm TA, Kay MA., In vitro and in vivo gene therapy vector evolution via multispecies interbreeding and retargeting of adeno-associated viruses. J Virol 2008 82 5887 5911. doi: 10.1128/JVI.00254-08.
131. Roche-Molina M, Sanz-Rosa D, Cruz FM, García-Prieto J, López S, Abia R, Muriana FJ, Fuster V, Ibáñez B, Bernal JA., Induction of sustained hypercholesterolemia by single adeno-associated virus-mediated gene transfer of mutant hPCSK9. Arterioscler Thromb Vasc Biol 2015 35 50 59. doi: 10.1161/ATVBAHA.114.303617.
132. Ferreira V, Petry H, Salmon F., Immune responses to AAV-vectors, the glybera example from bench to bedside. Front Immunol 2014 5 82. doi: 10.3389/fimmu.2014.00082.
133. Somanathan S, Jacobs F, Wang Q, Hanlon AL, Wilson JM, Rader DJ., AAV vectors expressing LDLR gain-of-function variants demonstrate increased efficacy in mouse models of familial hypercholesterolemia. Circ Res 2014 115 591 599. doi: 10.1161/CIRCRESAHA.115.304008.
134. Saade S, Cazier JB, Ghassibe-Sabbagh M, FGENTCARD consortium Large scale association analysis identifies three susceptibility loci for coronary artery disease. PLoS One 2011 6 e29427. doi: 10.1371/journal.pone.0029427.
135. Wang AZ, Li L, Zhang B, Shen GQ, Wang QK., Association of SNP rs17465637 on chromosome 1q41 and rs599839 on 1p13.3 with myocardial infarction in an American Caucasian population. Ann Hum Genet 2011 75 475 482. doi: 10.1111/j.1469-1809.2011.00646.x.
136. Musunuru K, Strong A, Frank-Kamenetsky M, From noncoding variant to phenotype via SORT1 at the 1p13 cholesterol locus. Nature 2010 466 714 719. doi: 10.1038/nature09266.
137. Strong A, Ding Q, Edmondson AC, Hepatic sortilin regulates both apolipoprotein B secretion and LDL catabolism. J Clin Invest 2012 122 2807 2816. doi: 10.1172/JCI63563.
138. Ai D, Baez JM, Jiang H, Conlon DM, Hernandez-Ono A, Frank-Kamenetsky M, Milstein S, Fitzgerald K, Murphy AJ, Woo CW, Strong A, Ginsberg HN, Tabas I, Rader DJ, Tall AR., Activation of ER stress and mTORC1 suppresses hepatic sortilin-1 levels in obese mice. J Clin Invest 2012 122 1677 1687. doi: 10.1172/JCI61248.
139. Kjolby M, Andersen OM, Breiderhoff T, Fjorback AW, Pedersen KM, Madsen P, Jansen P, Heeren J, Willnow TE, Nykjaer A., Sort1, encoded by the cardiovascular risk locus 1p13.3, is a regulator of hepatic lipoprotein export. Cell Metab 2010 12 213 223. doi: 10.1016/j.cmet.2010.08.006.
140. Rabinowich L, Fishman S, Hubel E, Thurm T, Park WJ, Pewzner-Jung Y, Saroha A, Erez N, Halpern Z, Futerman AH, Zvibel I., Sortilin deficiency improves the metabolic phenotype and reduces hepatic steatosis of mice subjected to diet-induced obesity. J Hepatol 2015 62 175 181. doi: 10.1016/j.jhep.2014.08.030.
141. Shi J, Kandror KV., Sortilin is essential and sufficient for the formation of Glut4 storage vesicles in 3T3-L1 adipocytes. Dev Cell 2005 9 99 108. doi: 10.1016/j.devcel.2005.04.004.
142. Tsuchiya Y, Hatakeyama H, Emoto N, Wagatsuma F, Matsushita S, Kanzaki M., Palmitate-induced down-regulation of sortilin and impaired GLUT4 trafficking in C2C12 myotubes. J Biol Chem 2010 285 34371 34381. doi: 10.1074/jbc.M110.128520.
143. Li J, Matye DJ, Li T., Insulin resistance induces posttranslational hepatic sortilin 1 degradation in mice. J Biol Chem 2015 290 11526 11536. doi: 10.1074/jbc.M115.641225.
144. Patel KM, Strong A, Tohyama J, Jin X, Morales CR, Billheimer J, Millar J, Kruth H, Rader DJ., Macrophage sortilin promotes LDL uptake, foam cell formation, and atherosclerosis. Circ Res 2015 116 789 796. doi: 10.1161/CIRCRESAHA.116.305811.
145. Willer CJ, Schmidt EM, Sengupta S, Global Lipids Genetics Consortium Discovery and refinement of loci associated with lipid levels. Nat Genet 2013 45 1274 1283. doi: 10.1038/ng.2797.
146. Douvris A, Soubeyrand S, Naing T, Martinuk A, Nikpay M, Williams A, Buick J, Yauk C, McPherson R., Functional analysis of the TRIB1 associated locus linked to plasma triglycerides and coronary artery disease. J Am Heart Assoc 2014 3 e000884. doi: 10.1161/JAHA.114.000884.
147. Rørth P, Szabo K, Texido G., The level of C/EBP protein is critical for cell migration during Drosophila oogenesis and is tightly controlled by regulated degradation. Mol Cell 2000 6 23 30
148. Seher TC, Leptin M., Tribbles, a cell-cycle brake that coordinates proliferation and morphogenesis during Drosophila gastrulation. Curr Biol 2000 10 623 629
149. Grosshans J, Wieschaus E., A genetic link between morphogenesis and cell division during formation of the ventral furrow in Drosophila. Cell 2000 101 523 531
150. Mata J, Curado S, Ephrussi A, Rørth P., Tribbles coordinates mitosis and morphogenesis in Drosophila by regulating string/CDC25 proteolysis. Cell 2000 101 511 522
151. Keeshan K, He Y, Wouters BJ, Shestova O, Xu L, Sai H, Rodriguez CG, Maillard I, Tobias JW, Valk P, Carroll M, Aster JC, Delwel R, Pear WS., Tribbles homolog 2 inactivates C/EBPalpha and causes acute myelogenous leukemia. Cancer Cell 2006 10 401 411. doi: 10.1016/j.ccr.2006.09.012.
152. Dedhia PH, Keeshan K, Uljon S, Xu L, Vega ME, Shestova O, Zaks-Zilberman M, Romany C, Blacklow SC, Pear WS., Differential ability of Tribbles family members to promote degradation of C/EBPalpha and induce acute myelogenous leukemia. Blood 2010 116 1321 1328. doi: 10.1182/blood-2009-07-229450.
153. Keeshan K, Bailis W, Dedhia PH, Vega ME, Shestova O, Xu L, Toscano K, Uljon SN, Blacklow SC, Pear WS., Transformation by Tribbles homolog 2 (Trib2) requires both the Trib2 kinase domain and COP1 binding. Blood 2010 116 4948 4957. doi: 10.1182/blood-2009-10-247361.
154. Yoshida A, Kato JY, Nakamae I, Yoneda-Kato N., COP1 targets C/EBPα for degradation and induces acute myeloid leukemia via Trib1. Blood 2013 122 1750 1760. doi: 10.1182/blood-2012-12-476101.
155. Satoh T, Kidoya H, Naito H, Yamamoto M, Takemura N, Nakagawa K, Yoshioka Y, Morii E, Takakura N, Takeuchi O, Akira S., Critical role of Trib1 in differentiation of tissue-resident M2-like macrophages. Nature 2013 495 524 528. doi: 10.1038/nature11930.
156. Bauer RC, Sasaki M, Cohen DM, Cui J, Smith MA, Yenilmez BO, Steger DJ, Rader DJ., Tribbles-1 regulates hepatic lipogenesis through posttranscriptional regulation of C/EBPα. J Clin Invest 2015 125 3809 3818. doi: 10.1172/JCI77095.
157. Ishizuka Y, Nakayama K, Ogawa A, Makishima S, Boonvisut S, Hirao A, Iwasaki Y, Yada T, Yanagisawa Y, Miyashita H, Takahashi M, Iwamoto S, Jichi Medical University Promotion Team of Large-Scale Human Genome Bank for All over Japan TRIB1 downregulates hepatic lipogenesis and glycogenesis via multiple molecular interactions. J Mol Endocrinol 2014 52 145 158. doi: 10.1530/JME-13-0243.
158. Makishima S, Boonvisut S, Ishizuka Y, Watanabe K, Nakayama K, Iwamoto S., Sin3A-associated protein, 18 kDa, a novel binding partner of TRIB1, regulates MTTP expression. J Lipid Res 2015 56 1145 1152. doi: 10.1194/jlr.M057802.
159. Hanna RN, Shaked I, Hubbeling HG, Punt JA, Wu R, Herrley E, Zaugg C, Pei H, Geissmann F, Ley K, Hedrick CC., NR4A1 (Nur77) deletion polarizes macrophages toward an inflammatory phenotype and increases atherosclerosis. Circ Res 2012 110 416 427. doi: 10.1161/CIRCRESAHA.111.253377.
160. Dastani Z, Hivert MF, Timpson N, DIAGRAM+ Consortium; MAGIC Consortium; GLGC Investigators; MuTHER Consortium; DIAGRAM Consortium; GIANT Consortium; Global B Pgen Consortium; Procardis Consortium; MAGIC investigators; GLGC Consortium Novel loci for adiponectin levels and their influence on type 2 diabetes and metabolic traits: a multi-ethnic meta-analysis of 45,891 individuals. PLoS Genet 2012 8 e1002607. doi: 10.1371/journal.pgen.1002607.
161. Speliotes EK, Yerges-Armstrong LM, Wu J, NASH CRN; GIANT Consortium; MAGIC Investigators; GOLD Consortium Genome-wide association analysis identifies variants associated with nonalcoholic fatty liver disease that have distinct effects on metabolic traits. PLoS Genet 2011 7 e1001324. doi: 10.1371/journal.pgen.1001324.
162. Kraja AT, Chasman DI, North KE, Cross Consortia Pleiotropy Group; Cohorts for Heart and; Aging Research in Genetic Epidemiology; Genetic Investigation of Anthropometric Traits Consortium; Global Lipids Genetics Consortium; Meta-Analyses of Glucose; Insulin-related traits Consortium; Global BPgen Consortium; ADIPOGen Consortium; Women's Genome Health Study; Howard University Family Study Pleiotropic genes for metabolic syndrome and inflammation. Mol Genet Metab 2014 112 317 338. doi: 10.1016/j.ymgme.2014.04.007.
163. ENCODE Project Consortium A user's guide to the encyclopedia of DNA elements (encode). PLoS biology 2011 9 e1001046. doi: 10.1371/journal.pbio.1001046.
164. Miller CL, Anderson DR, Kundu RK, Raiesdana A, Nürnberg ST, Diaz R, Cheng K, Leeper NJ, Chen CH, Chang IS, Schadt EE, Hsiung CA, Assimes TL, Quertermous T., Disease-related growth factor and embryonic signaling pathways modulate an enhancer of TCF21 expression at the 6q23.2 coronary heart disease locus. PLoS Genet 2013 9 e1003652. doi: 10.1371/journal.pgen.1003652.
165. Wild PS, Zeller T, Schillert A, A genome-wide association study identifies LIPA as a susceptibility gene for coronary artery disease. Circ Cardiovasc Genet 2011 4 403 412. doi: 10.1161/CIRCGENETICS.110.958728.
166. Voight BF, Kang HM, Ding J, The metabochip, a custom genotyping array for genetic studies of metabolic, cardiovascular, and anthropometric traits. PLoS Genet 2012 8 e1002793. doi: 10.1371/journal.pgen.1002793.
167. ENCODE Project Consortium An integrated encyclopedia of DNA elements in the human genome. Nature 2012 489 57 74. doi: 10.1038/nature11247.
168. Birney E, Stamatoyannopoulos JA, Dutta A, ENCODE Project Consortium; NISC Comparative Sequencing Program; Baylor College of Medicine Human Genome Sequencing Center; Washington University Genome Sequencing Center; Broad Institute; Children's Hospital Oakland Research Institute Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 2007 447 799 816. doi: 10.1038/nature05874.
169. Anderson RA, Rao N, Byrum RS, Rothschild CB, Bowden DW, Hayworth R, Pettenati M., In situ localization of the genetic locus encoding the lysosomal acid lipase/cholesteryl esterase (LIPA) deficient in Wolman disease to chromosome 10q23.2-q23.3. Genomics 1993 15 245 247. doi: 10.1006/geno.1993.1052.
170. Sando GN, Henke VL., Recognition and receptor-mediated endocytosis of the lysosomal acid lipase secreted by cultured human fibroblasts. J Lipid Res 1982 23 114 123
171. Sheriff S, Du H, Grabowski GA., Characterization of lysosomal acid lipase by site-directed mutagenesis and heterologous expression. J Biol Chem 1995 270 27766 27772
172. Bernstein DL, Hülkova H, Bialer MG, Desnick RJ., Cholesteryl ester storage disease: review of the findings in 135 reported patients with an underdiagnosed disease. J Hepatol 2013 58 1230 1243. doi: 10.1016/j.jhep.2013.02.014.
173. Du H, Schiavi S, Levine M, Mishra J, Heur M, Grabowski GA., Enzyme therapy for lysosomal acid lipase deficiency in the mouse. Hum Mol Genet 2001 10 1639 1648
174. Scott SA, Liu B, Nazarenko I, Martis S, Kozlitina J, Yang Y, Ramirez C, Kasai Y, Hyatt T, Peter I, Desnick RJ., Frequency of the cholesteryl ester storage disease common LIPA E8SJM mutation (c.894G>A) in various racial and ethnic groups. Hepatology 2013 58 958 965. doi: 10.1002/hep.26327.
175. Brown MS, Sobhani MK, Brunschede GY, Goldstein JL., Restoration of a regulatory response to low density lipoprotein in acid lipase-deficient human fibroblasts. J Biol Chem 1976 251 3277 3286
176. Goldstein JL, Dana SE, Faust JR, Beaudet AL, Brown MS., Role of lysosomal acid lipase in the metabolism of plasma low density lipoprotein. Observations in cultured fibroblasts from a patient with cholesteryl ester storage disease. J Biol Chem 1975 250 8487 8495
177. Bowden KL, Bilbey NJ, Bilawchuk LM, Boadu E, Sidhu R, Ory DS, Du H, Chan T, Francis GA., Lysosomal acid lipase deficiency impairs regulation of ABCA1 gene and formation of high density lipoproteins in cholesteryl ester storage disease. J Biol Chem 2011 286 30624 30635. doi: 10.1074/jbc.M111.274381.
178. Choi HY, Karten B, Chan T, Vance JE, Greer WL, Heidenreich RA, Garver WS, Francis GA., Impaired ABCA1-dependent lipid efflux and hypoalphalipoproteinemia in human Niemann-Pick type C disease. J Biol Chem 2003 278 32569 32577. doi: 10.1074/jbc.M304553200.
179. Burton BK, Balwani M, Feillet F, A phase 3 trial of Sebelipase Alfa in lysosomal acid lipase deficiency. N Engl J Med 2015 373 1010 1020. doi: 10.1056/NEJMoa1501365.
180. Du H, Heur M, Duanmu M, Grabowski GA, Hui DY, Witte DP, Mishra J., Lysosomal acid lipase-deficient mice: depletion of white and brown fat, severe hepatosplenomegaly, and shortened life span. J Lipid Res 2001 42 489 500
181. Du H, Schiavi S, Wan N, Levine M, Witte DP, Grabowski GA., Reduction of atherosclerotic plaques by lysosomal acid lipase supplementation. Arterioscler Thromb Vasc Biol 2004 24 147 154. doi: 10.1161/01.ATV.0000107030.22053.1e.
182. Grabowski GA, Du H, Charnas L., Valle D, Beaudet AL, Vogelstein B, Kinzler KW, Antonarakis SE, Ballabio A, Gibson KM, Mitchell G, Lysosomal acid lipase deficiencies: the Wolman disease/cholesteryl ester storage disease spectrum [online]. The Online Metabolic and Molecular Bases of Inherited Disease McGraw-Hill. (June 4, 2015). http://dx.doi.org/10.1036/ommbid.172
183. Zschenker O, Illies T, Ameis D., Overexpression of lysosomal acid lipase and other proteins in atherosclerosis. J Biochem 2006 140 23 38. doi: 10.1093/jb/mvj137.
184. Reilly MP, Li M, He J, Myocardial Infarction Genetics Consortium; Wellcome Trust Case Control Consortium Identification of ADAMTS7 as a novel locus for coronary atherosclerosis and association of ABO with myocardial infarction in the presence of coronary atherosclerosis: two genome-wide association studies. Lancet 2011 377 383 392. doi: 10.1016/S0140-6736(10)61996-4.
185. Wang L, Zheng J, Bai X, Liu B, Liu CJ, Xu Q, Zhu Y, Wang N, Kong W, Wang X., ADAMTS-7 mediates vascular smooth muscle cell migration and neointima formation in balloon-injured rat arteries. Circ Res 2009 104 688 698. doi: 10.1161/CIRCRESAHA.108.188425.
186. Bauer RC, Tohyama J, Cui J, Cheng L, Yang J, Zhang X, Ou K, Paschos GK, Zheng XL, Parmacek MS, Rader DJ, Reilly MP., Knockout of Adamts7, a novel coronary artery disease locus in humans, reduces atherosclerosis in mice. Circulation 2015 131 1202 1213. doi: 10.1161/CIRCULATIONAHA.114.012669.
187. Pu X, Xiao Q, Kiechl S, ADAMTS7 cleavage and vascular smooth muscle cell migration is affected by a coronary-artery-disease-associated variant. Am J Hum Genet 2013 92 366 374. doi: 10.1016/j.ajhg.2013.01.012.
188. Kessler T, Zhang L, Liu Z, ADAMTS-7 inhibits re-endothelialization of injured arteries and promotes vascular remodeling through cleavage of thrombospondin-1. Circulation 2015 131 1191 1201. doi: 10.1161/CIRCULATIONAHA.114.014072.
189. Grundberg E, Small KS, Hedman ÅK, Multiple Tissue Human Expression Resource (MuTHER) Consortium Mapping cis-and trans-regulatory effects across multiple tissues in twins. Nat Genet 2012 44 1084 1089. doi: 10.1038/ng.2394.
190. GTEx Consortium The genotype-tissue expression (gtex) project. Nature genetics 2013 45 580 585. doi: 10.1038/ng.2653.
191. Sazonova O, Zhao Y, Nürnberg S, Miller C, Pjanic M, Castano VG, Kim JB, Salfati EL, Kundaje AB, Bejerano G, Assimes T, Yang X, Quertermous T., Characterization of TCF21 downstream target regions identifies a transcriptional network linking multiple independent coronary artery disease loci. PLoS Genet 2015 11 e1005202. doi: 10.1371/journal.pgen.1005202.
192. Hurskainen TL, Hirohata S, Seldin MF, Apte SS., ADAM-TS5, ADAM-TS6, and ADAM-TS7, novel members of a new family of zinc metalloproteases. General features and genomic distribution of the ADAM-TS family. J Biol Chem 1999 274 25555 25563
193. Somerville RP, Longpré JM, Apel ED, Lewis RM, Wang LW, Sanes JR, Leduc R, Apte SS., ADAMTS7B, the full-length product of the ADAMTS7 gene, is a chondroitin sulfate proteoglycan containing a mucin domain. J Biol Chem 2004 279 35159 35175. doi: 10.1074/jbc.M402380200.
194. Porter S, Clark IM, Kevorkian L, Edwards DR., The ADAMTS metalloproteinases. Biochem J 2005 386 15 27. doi: 10.1042/BJ20040424.
195. Gao W, Zhu J, Westfield LA, Tuley EA, Anderson PJ, Sadler JE., Rearranging exosites in noncatalytic domains can redirect the substrate specificity of ADAMTS proteases. J Biol Chem 2012 287 26944 26952. doi: 10.1074/jbc.M112.380535.
196. Moake JL., Thrombotic microangiopathies. N Engl J Med 2002 347 589 600. doi: 10.1056/NEJMra020528.
197. Dagoneau N, Benoist-Lasselin C, Huber C, Faivre L, Mégarbané A, Alswaid A, Dollfus H, Alembik Y, Munnich A, Legeai-Mallet L, Cormier-Daire V., ADAMTS10 mutations in autosomal recessive Weill-Marchesani syndrome. Am J Hum Genet 2004 75 801 806. doi: 10.1086/425231.
198. Salter RC, Ashlin TG, Kwan AP, Ramji DP., ADAMTS proteases: key roles in atherosclerosis? J Mol Med (Berl) 2010 88 1203 1211. doi: 10.1007/s00109-010-0654-x.
199. Liu CJ, Kong W, Ilalov K, Yu S, Xu K, Prazak L, Fajardo M, Sehgal B, Di Cesare PE., ADAMTS-7: a metalloproteinase that directly binds to and degrades cartilage oligomeric matrix protein. FASEB J 2006 20 988 990. doi: 10.1096/fj.05-3877fje.
200. Quaggin SE, Schwartz L, Cui S, Igarashi P, Deimling J, Post M, Rossant J., The basic-helix-loop-helix protein pod1 is critically important for kidney and lung organogenesis. Development 1999 126 5771 5783
201. Acharya A, Baek ST, Huang G, Eskiocak B, Goetsch S, Sung CY, Banfi S, Sauer MF, Olsen GS, Duffield JS, Olson EN, Tallquist MD., The bHLH transcription factor Tcf21 is required for lineage-specific EMT of cardiac fibroblast progenitors. Development 2012 139 2139 2149. doi: 10.1242/dev.079970.
202. Braitsch CM, Combs MD, Quaggin SE, Yutzey KE., Pod1/Tcf21 is regulated by retinoic acid signaling and inhibits differentiation of epicardium-derived cells into smooth muscle in the developing heart. Dev Biol 2012 368 345 357. doi: 10.1016/j.ydbio.2012.06.002.
203. Miller CL, Haas U, Diaz R, Leeper NJ, Kundu RK, Patlolla B, Assimes TL, Kaiser FJ, Perisic L, Hedin U, Maegdefessel L, Schunkert H, Erdmann J, Quertermous T, Sczakiel G., Coronary heart disease-associated variation in TCF21 disrupts a miR-224 binding site and miRNA-mediated regulation. PLoS Genet 2014 10 e1004263. doi: 10.1371/journal.pgen.1004263.
204. Lu X, Wang L, Chen S, Coronary ARtery DIsease Genome-Wide Replication And Meta-Analysis (CARDIoGRAM) Consortium Genome-wide association study in Han Chinese identifies four new susceptibility loci for coronary artery disease. Nat Genet 2012 44 890 894. doi: 10.1038/ng.2337.
205. Nurnberg ST, Cheng KR, Raiesdana A, Coronary artery disease associated transcription factor tcf21 regulates smooth muscle precursor cells that contribute to the fibrous cap. PLoS genetics 2015 11 e1005155. doi: 10.1371/journal.pgen.1005155.