**2.1 Genetic variation in enzymes involved in lipid metabolism and HDL-C levels**

Perhaps, the most notable gene in the HDL-C synthesis and metabolism pathways, whose variants have been consistently associated with HDL-C, is the cholesterol ester transfer protein (CETP), which is a key plasma protein that mediates the transfer of esterfied cholesterol from HDL to APOB containing particles in exchange for TG. Although complete loss of CETP function is rare and can yield HDL-C levels up to five times higher than normal (Klos and Kullo, 2007), three common polymorphisms (Table 1: TaqIB (rs708272); -

LPL rs325 0.89 (T) E 17723 p= 7.8×10-25 (Waterworth

rs17145738 0.12 (T) EA 25,167 p=1.64E-05 (Dumitrescu et

0.30 (G) W 1232 (P) W: +0.1 /+2.3

0.67 B 554 -5.4 /- 6.7 mg/dl

0.29 (R) Hu 738 (P) -3.1 mg/dl /- 3.1

261 CVD, Co

(CVD)

(CVD)

mg/dl (1/2 copies) ; p=0.041

> (1/2 copies) ; p=0.008

mg/dl (1/2 copies) ; p=0.001

M: +1.5 /+2.7 mg/dl (1/2 copies) ; p=0.035


1/2 copies;p=0.006

+2.3 /+1.9 mg/dl (1/2 copies); p=0.03

MLXIP L

SCARB 1

SCARB 1

PON1 Q192R rs662 =

g

PON1 rs662 =

PON1 rs662 =

Exon 8 C>T

(2009) with permission from Elsevier.

PON1 Gln192Ar

rs60480675

rs662 = rs60480675

rs60480675

rs60480675

PON1 C -107T rs705379 0.48 (C) W 710

C1050T rs5888 0.49 (T) W 546

0.36 (R) W-

Bra

PON1 Leu55M rs85456 0.20 (T) MA 741 p=0.02 (Chang et al.

Table 1. Genetic Polymorphisms Associated With HDL-C. MAF=Minor Allele Frequency; Ethn.: A=Asians; AA=African Americans; Am=Amish; A-I=Asian Indian; B=Blacks; C=Chinese; CH=Caribbean Hispanics; In=Inuit; Ma= Malays; N=Netherlands; NHW=Non-Hispanic Whites; H=Hispanics; Hu=Hutteries; Tu=Turks; UK=United Kingdom; W-Bra=Caucasian Brazilians; W= Whites; Va=Various; Non-DM C0=Non diabetic control subjects; MI=Myocardial infarction; NGT=Normal glucose tolerance; DM= Diabetes mellitus; Ho Sta= Hospital staff; HBP= Hypertensive patients; He Ex=Health examination;

Cor Ang=coronary angiography; hyperCH=hypercholesterolemia patients; CVD= Cardiovascular Disease; Co=Controls; Ho Co=Hospital based controls; GP=General Population; Meta= Meta Analysis; P=Population based; M= Males; F= females; + =increase; - = decrease; n.s.=not significant; see text for full gene names. Adapted from Boes et al.

**2.1 Genetic variation in enzymes involved in lipid metabolism and HDL-C levels**  Perhaps, the most notable gene in the HDL-C synthesis and metabolism pathways, whose variants have been consistently associated with HDL-C, is the cholesterol ester transfer protein (CETP), which is a key plasma protein that mediates the transfer of esterfied cholesterol from HDL to APOB containing particles in exchange for TG. Although complete loss of CETP function is rare and can yield HDL-C levels up to five times higher than normal (Klos and Kullo, 2007), three common polymorphisms (Table 1: TaqIB (rs708272); -

rs5888 0.44 (T) W 865 (P) +1.9/2.7 mg/dl

et al. 2010)

al. 2011)

(Srinivasan et al. 2004)

"

(Hegele et al. 1995)

(Rios et al. 2007)

(Blatter Garin et al. 2006)

2010)

(Morabia et al. 2004)

(Boekholdt et al. 2006)

629C>A (rs1800775); Ile405Val (rs5882)) can all modestly inhibit CETP activity and have been consistently associated with higher HDL-C levels (Bernstein et al., 2003; Blankenberg et al., 2004; Boekholdt et al., 2005; Boekholdt and Thompson, 2003; Borggreve et al., 2005; Eiriksdottir et al., 2001; Freeman et al., 2003; Kathiresan et al., 2008a; Klerkx et al., 2003; Tai et al., 2003b; Thompson et al., 2008). The CETP gene is located on chromosome 16 (16q21).

Lipoprotein lipase (LPL) is an enzyme involved in lipolysis of TG-containing lipoproteins such as VLDL and chlyomicrons (Miller and Zhan, 2004), which generate free fatty acids (FFA) that can be taken up by the liver, muscle and adipose tissues (Kwan et al., 2007). Thus, LPL affects LDL levels directly (see Section 3.2) may only affect HDL-C levels indirectly (Lewis and Rader, 2005). The human LPL gene is located on chromosome 8 (8p22). Several LPL SNPs have been associated with HDL-C (Table 1) (Ahn et al., 1993; Corella et al., 2002; Holmer et al., 2000; Klos and Kullo, 2007; Klos et al., 2006; Komurcu-Bayrak et al., 2007; Lee et al., 2004; Nettleton et al., 2007; Senti et al., 2001; Wittrup et al., 1999); however, many of them are in strong linkage disequilibrium with each other (e.g., rs320, rs326, rs13702, rs10105606) (Boes et al., 2009; Heid et al., 2008).

Hepatic lipase (HL; LIPC) is a glycoprotein that is synthesized by liver cells (hepatocytes) and catalyzes the hydrolysis of TG and phospholipids (Miller et al., 2003). For example, after hydrolysis of TG by LPL, VLDL particles are reduced to IDL particles and can be further hydrolyzed by HL/LIPC to LDL or taken up by the liver (Kwan et al., 2007). The human HL/LIPC gene is located on chromosome 15 (15q21). Several HL/LIPC SNPs have been associated with HDL-C levels (Table 1) (Andersen et al., 2003; Costanza et al., 2005; de Andrade et al., 2004; Fang and Liu, 2002; Grarup et al., 2008; Iijima et al., 2008; Isaacs et al., 2007; Kathiresan et al., 2008b; Ko et al., 2004; McCaskie et al., 2006; Nettleton et al., 2007; Tai et al., 2003a; Talmud et al., 2002b; Whiting et al., 2005; Yamada et al., 2007). However, the most consistent associations have been observed for rs1800588 and rs2070895 and, several SNPs in the promoter region are in strong LD (Boes et al., 2009).

Endothelial lipase (EL; LIPG) is an enzyme expressed in endothelial cells that, in the presence of HL/LIPC, metabolizes larger (HDL3) to smaller (HDL2) HDL-C particles and increases the catabolism of APOA-I (see Section 2.3) (Jaye and Krawiec, 2004). EL/LIPG plays a role in the dyslipidemia component and, possibly, the yet to be established, proinflammatrory component of MetSyn (Lamarche and Paradis, 2007) (see Section 5.0). The human EL/LIPG gene is located on chromosome 18 (18q21.1). Several polymorphisms in EL/LPIG have been associated with HDL-C levels (Table 1) (Hutter et al., 2006; Ma et al., 2003; Mank-Seymour et al., 2004; Paradis et al., 2003; Tang et al., 2008; Yamakawa-Kobayashi et al., 2003). However, most of these SNPs have not been as well studied as those in CETP, LPL and EL; and, only the nonsynonymous SNP, rs2000813, has been consistently associated with HDL-C levels in African-American populations (Hutter et al., 2006; Tang et al., 2008; Yamakawa-Kobayashi et al., 2003).

In the presence of cofactor, APOA-I (see Section 2.3), lecithin-cholesteryl acyltransferase (LCAT), catalyzes the esterification of free cholesterol and, can metabolize larger HDL-C particles to smaller HDL-C particles (Klos and Kullo, 2007; Miller and Zhan, 2004). The human LCAT is located on chromosome 16 (16q22.1). Although mutations leading to complete loss of LCAT and marked (5-10%) reduction in HDL-C levels are rare and can cause cornea opacifications (fish eye disease) and renal disease (Garg and Simha, 2007), several common polymorphisms in LCAT have been associated, albeit inconsistently, with much more modest changes in HDL-C levels (Table 1) (Boekholdt et al., 2006; Miettinen et al., 1998; Pare et al., 2007; Zhang et al., 2004; Zhu et al., 2006).

Dyslipidemia: Genetics and Role in the Metabolic Syndrome 107

human APOA1 gene is located on chromosome 11 (11q23-24). APOA-I is a major constituent of HDL particles and deletions leading to complete APOA-I deficiency are rare but lead to HDL deficiency (HDL-C <10 mg/dl) and sometimes CHD (Garg and Simha, 2007). Several common polymorphisms in APOA-I have been associated with more modest reductions in HDL-C but results across studies are inconsistent (Table 1) (Brown et al., 2006; Kamboh et

Apolipoprotein A-4 (APOA4; APOA-IV) is a potent activator of LCAT and modulates the activation of LPL and transfer of cholestryl esters from HDL to LDL (Kwan et al., 2007). The human APOA4 gene is located on chromosome 11 near APOA1 (11q23) and is part of what is known as the APOA1/C3/A4/A5 gene cluster. Polymorphisms in APOA4 have not been as well studied; however, the nonsynonymous SNP, rs5110 (Gln360His), has recently been associated with reduced HDL-C levels in Brazilian elderly (Ota et al., 2011) and coronary artery calcification (CAC) progression, a marker of subclinical atherosclerosis, in patients with Type I Diabetes Mellitus (T1DM) (Kretowski et al., 2006). The rs675 polymorphism has been associated with reduced HDL-C levels in females with

Apolipoprotein A-5 (APOA5; APOA-V) is located predominantly on TG-rich chylomicrons and VLDL and activates LPL (Hubacek, 2005). The human APOA5 gene is located on chromosome 11 (11q23) in the APOA1/C3/A4/A5 gene cluster. Several APOA5 SNPs have been associated with reduced HDL-C levels; and, perhaps, the most well studied and consistent associations have been observed for rs651821 and rs662799 (Table 1) (Grallert et al., 2007; Hubacek, 2005; Klos et al., 2006; Lai et al., 2003; Qi et al., 2007; Talmud et al., 2002a;

Apolipoprotein C-3 (APOC3; APOC-III) is an inhibitor of LPL and is transferred to HDL during the hydrolysis of TG-rich lipoproteins (Kwan et al., 2007; Miller and Zhan, 2004). The human APOC3 gene is located on chromosome 11 (11q23) in the APOA1/C3/A4/A5 gene cluster. Although several APOC3 SNPs have been identified and investigated, associations between these SNPs and HDL-C levels have been quite inconsistent (Table 1) (Arai and Hirose, 2004; Brown et al., 2006; Corella et al., 2002; Hegele et al., 1995; Kamboh et al., 1999a;

Chylomicron remnants, VLDL and IDL particles are rich in apolipoprotein E (APOE) and APOE is a critical ligand for binding to hepatic receptors that remove these particles from the circulation (Kwan et al., 2007). Mutations in APOE are well known to modify LDL-C levels; however, their independent influence on HDL-C levels remains controversial (Sviridov and Nestel, 2007). Nevertheless, associations between APOE SNPs and HDL-C levels in large scale studies have been fairly consistent (Costanza et al., 2005; Frikke-Schmidt et al., 2000; Gronroos et al., 2008; Kataoka et al., 1996; Srinivasan et al., 1999; Volcik et al.,

Results from genomewide association studies (GWAS) have confirmed associations between polymorphisms in viable candidate genes including CETP, LPL, HL/LIPIC, EL/LIPG, ABCA1, LCAT and the APOA1/C3/A4/A5 gene cluster and HDL-C levels (Boes et al., 2009). GWAS have also identified several novel putative loci, which are discussed in detail

Lahiry et al., 2007; Pallaud et al., 2001; Qi et al., 2007; Russo et al., 2001).

al., 1999b; Larson et al., 2002; Shioji et al., 2004a).

T2DM (Qi et al., 2007).

Yamada et al., 2008; Yamada et al., 2007).

2006; Wilson et al., 1994; Wu et al., 2007).

in a recent review (Teslovich et al., 2010).

**2.4 GWAS and HDL-C Levels** 

Parroxanonase 1 (PON1), inhibits the oxidation of LDL (Mackness et al., 1991) and, therefore, may only indirectly affect antioxidant properties of HDL-C. The human PON1 gene is located on chromosome 7 (7q21.3). Several SNPs in PON1 have been associated with HDL-C levels, most notably, two nonsynonymous SNPs, rs662 and rs3202100, which are in strong LD, but results are inconsistent across studies (Table 1) (Blatter Garin et al., 2006; Hegele et al., 1995; Manresa et al., 2006; Rios et al., 2007; van Aalst-Cohen et al., 2005).
