Association of lipoprotein lipase S447X, apolipoprotein E exon 4, and apoC3 -455T>C polymorphisms on the susceptibility to diabetic nephropathy

Association of Apolipoprotein E Gene Polymorphism with Type 2 Diabetic Nephropathy in the Southern Chinese Population

Background

Common polymorphisms within the apolipoprotein E (APOE) gene are rs429358 and rs7412, which result in three major alleles (ɛ2, ɛ3, and ɛ4) and six genotypes (E2/E2, E2/E3, E3/E3, E3/E4, E4/E4, and E2/E4). Although APOE gene polymorphisms have been suggested to be associated with the development of diabetic nephropathy (DN), their potential association remains unclear in different regions. This study aims to unveil the genetic effects of APOE gene polymorphisms on DN susceptibility and serum lipid profiles in southern Chinese population.

Methods

A total of 306 DN patients and 483 type 2 diabetic patients as controls were included in the study. The APOE gene polymorphisms were analyzed by polymerase chain reaction (PCR) microarray gene chip. Relevant medical records and information of these participants were collected.

Results

There were statistically significant differences (p < 0.05) in gender, SBP, hypertension, hyperuricemia, UTP, TG and HDL-C between DN patients and controls. DN patients exhibited a higher frequency of the ε2 allele and E2/E3 genotype than controls (p < 0.001). Logistic regression analysis indicated that the ε2 allele and E2/E3 genotype were independent risk factors (adjusted OR: 3.237, 95% CI: 1.789-5.854, p < 0.001; adjusted OR: 3.453, 95% CI: 1.873-6.368, p < 0.001), while the ε3 allele or E3/E3 genotype might serve as protective role (adjusted OR: 0.395, 95% CI: 0.255-0.612, p < 0.001) for development of DN.

Conclusion

Our study indicates a correlation between APOE polymorphisms and DN in the southern Chinese Hakka population. Specifically, individuals carrying the APOE ε2 allele and E2/E3 genotype are at a higher risk of developing DN. Conversely, those with the APOE ε3 allele and E3/E3 genotype have a lower risk of DN in southern Chinese population.

The influence of LPL S447X variants and obesity on lipid profile, oxidative stress, and the risk of T2DM: A case-control study

Aims

The present study aimed to investigate the association between lipoprotein lipase (LPL) S447X polymorphism and type 2 diabetes mellitus (T2DM), obesity, lipid profile, and oxidative stress parameters in a population from the Kurdistan region of Iraq.

Method

We studied 250 adults (51% female and 49% male) aged 45-65 years in four groups, obese and normal body mass index (BMI) diabetic patients versus healthy normal BMI and obese individuals as controls. Lipid profile and oxidative stress parameters were analyzed by colorimetric assay. The LPL S447X genotypes were detected by polymerase chain reaction (PCR)-restriction fragment length polymorphism.

Results

We found that the obese diabetic group had higher levels of triglycerides (TG), cholesterol, and low-density lipoprotein-cholesterol, and lower level of high-density lipoprotein-cholesterol than other groups. Obese diabetic patients had higher anthropometric indices than nonobese diabetic patients, obese and normal BMI controls. The levels of TG and total oxidative status (TOS) were significantly lower and higher, respectively, in normal BMI controls than in obese controls. Obese diabetic patients had a lower level of total antioxidant capacity than nondiabetic obese controls. The level of TOS was lower in nondiabetic controls compared to the patient groups. Obese diabetic patients had the highest TOS and malondialdehyde levels. The LPL SX genotype was associated with decreased the risk of T2DM by 79% (odds ratio [OR] = 0.21; 95% confidence interval [CI]: 0.05-0.81, p = 0.03). Also, the presence of this genotype reduced the risk of obesity by 39% (OR = 0.61; 95% CI: 0.07-4.90, p = 0.6). In all individuals, the presence of the SX genotype was associated with significantly lower levels of fasting blood sugar (FBS) and TOS.

Conclusion

We report the influence of obesity on lipid profile in diabetic and nondiabetic individuals and the effect of LPL SX genotype on decreased risk of T2DM and reduced levels of FBS and TOS.

Does serum kidney injury molecule-1 predict early diabetic nephropathy: A comparative study with microalbuminuria

Introduction:

Diabetic nephropathy (DN) is a multifactorial disease, one of the most common complications of diabetes and a major cause of chronic kidney disease. Kidney injury molecule-1 (KIM-1) is a sensitive and specific marker of kidney injury as well as a predictor of prognosis.

Objective:

The present study aimed to investigate the usefulness of serum KIM-1 as an early marker of DN.

Patients and Methods:

The present study included total 75 participants, among whom 25 nondiabetic participants were chosen as controls. The 50 diabetic participants were divided into two groups according to urine protein/creatinine ratio (UPCR) as participants with normoalbuminuria (T2DM patients without nephropathy) and microalbuminuria (T2DM patients with nephropathy). The complete blood count, blood glucose, HbA1c, serum electrolytes, and creatinine levels were measured using standard laboratory techniques, and serum KIM-1 levels were measured by sandwich enzyme-linked immunosorbent assay.

Results:

There was a significant difference in the mean serum KIM-1 between the control and diabetics without microalbuminuria (P = 0.0001). Patients with longer duration of diabetes had a higher serum KIM-1 values (P = 0.05 in DM without microalbuminuria; P = 0.007 for DM with microalbuminuria). Serum KIM-1 did not correlate with UPCR in controls (P = ‒0.167), in diabetics with microalbuminuria (P = 0.487). However, there was a significant correlation observed between UPCR and serum KIM-1 in diabetics without microalbuminuria (P = 0.04).

Conclusion:

The present study observed significantly increased levels of serum KIM-1 in both the diabetic groups compared to controls. Moreover, serum KIM-1 positively correlated with the duration of diabetes. Therefore, serum KIM-1 may be used as an early diagnostic marker to predict nephropathy among diabetes in our population.

Integrated bioinformatics analysis reveals novel key biomarkers in diabetic nephropathy

Objectives:

The underlying molecular mechanisms of diabetic nephropathy have yet not been investigated clearly. In this investigation, we aimed to identify key genes involved in the pathogenesis and prognosis of diabetic nephropathy.

Methods:

We downloaded next-generation sequencing data set GSE142025 from Gene Expression Omnibus database having 28 diabetic nephropathy samples and nine normal control samples. The differentially expressed genes between diabetic nephropathy and normal control samples were analyzed. Biological function analysis of the differentially expressed genes was enriched by Gene Ontology and REACTOME pathways. Then, we established the protein–protein interaction network, modules, miRNA-differentially expressed gene regulatory network and transcription factor-differentially expressed gene regulatory network. Hub genes were validated by using receiver operating characteristic curve analysis.

Results:

A total of 549 differentially expressed genes were detected including 275 upregulated and 274 downregulated genes. The biological process analysis of functional enrichment showed that these differentially expressed genes were mainly enriched in cell activation, integral component of plasma membrane, lipid binding, and biological oxidations. Analyzing the protein–protein interaction network, miRNA-differentially expressed gene regulatory network and transcription factor-differentially expressed gene regulatory network, we screened hub genes MDFI, LCK, BTK, IRF4, PRKCB, EGR1, JUN, FOS, ALB, and NR4A1 by the Cytoscape software. The receiver operating characteristic curve analysis confirmed that hub genes were of diagnostic value.

Conclusions:

Taken above, using integrated bioinformatics analysis, we have identified key genes and pathways in diabetic nephropathy, which could improve our understanding of the cause and underlying molecular events, and these key genes and pathways might be therapeutic targets for diabetic nephropathy.

Associations of the LPL S447X and Hind III Polymorphism with Type 2 Diabetes Mellitus Risk: A Meta-Analysis

The present study was aimed to evaluate the association of lipoprotein lipase (LPL) gene (S447X and Hind III) polymorphisms and T2DM. Relevant studies were identified through systematic search PubMed, Cochrane Library, Embase, Wanfang, CNKI databases. A total of 22 studies (8 studies for LPL S447X and 14 studies for Hind III) were included. The results showed that the LPL S447X polymorphism was associated with the low risk of T2DM under dominant and allelic genetic models. Subgroup analysis by ethnicity showed that the LPL S447X polymorphism was associated with a decreased risk of T2DM in the Asian population (under dominant, heterozygous and allelic genetic models). In addition, we found that X allele carriers of S447X polymorphism is associated with low levels of TC, TG, and LDL. In subgroup analysis, Hind III polymorphism was associated with low risk of T2DM in Asian populations (under dominant, heterozygote, allele genetic models). Moreover, the carriers of H allele of Hind III have lower levels of TG, and higher levels of HDL-C. This meta-analysis demonstrated that 447X carriers and H allele in LPL gene associated with low risk of T2DM, which may due to in part to the change of serum level of TC, TG, LDL, and HDL.

ε2 allele and ε2-involved genotypes (ε2/ε2, ε2/ε3, and ε2/ε4) may confer the association of APOE genetic polymorphism with risks of nephropathy in type 2 diabetes: a meta-analysis

Background

Diabetic nephropathy (DN) contributes to end-stage renal failure. Microvascular injury resulted from reactive oxygen species is implicated in the pathogenesis of DN. Genetic polymorphism of Apolipoprotein E (APOE) influences the antioxidative properties of the protein. The relationship of APOE polymorphism with the risks of nephropathy in type 2 diabetes (T2DN) remains elusive.

Methods

An up-to-date meta-analysis was conducted on the basis of studies selected from PubMed, WanFang database, Embase, Vip database, Web of Science, Scopus, and CNKI database.

Results

A total of 33 studies conferring 3266 cases and 3259 controls were selected on the basis of criteria of inclusion and exclusion in this meta-analysis. For APOE alleles, the pooled odds ratio (OR) of ε2 vs. ε3 was 1.89 (95% confidence intervals [95% CI]: 1.49–2.38, P < 0.0001). With regard to APOE genotypes, ε2/ε2, ε2/ε3, and ε2/ε4 increased the risk of T2DN (ε2/ε2 vs. ε3/ε3: OR = 2.32, 95% CI: 1.52–3.56, P = 0.0001; ε2/ε3 vs. ε3/ε3: OR = 1.97, 95% CI: 1.50–2.59, P<0.0001; ε2/ε4 vs. ε3/ε3: OR = 1.69, 95% CI: 1.18–2.44, P = 0.0046).

Conclusions

This meta-analysis found that the APOE ε2 allele and the ε2-involved genotypes (ε2/ε2, ε2/ε3, and ε2/ε4) are the risk factors of T2DN.

The apolipoprotein E (APOE) gene and the risk of diabetic nephropathy (DN): a meta-analysis in East Asian populations

Background: Several studies have examined the association between DN and the APOE gene, but the results have been inconsistent. Objective: Determine whether APOE is a risk factor for DN by a meta-analysis. Methods: A meta-analysis was performed using all findings of 16 similar case-control studies in East Asian to evaluate the effect of APOE as a risk factor for DN. Several electronic databases were searched for relevant articles up to 2009. After data collection, a meta-analysis was used to assess heterogeneity, combine results and evaluate variations by using software STATA SE 9.0. Publication bias was examined by the Egger’s linear regression test and fail-safe number. Results: The meta-analysis showed that the ε2 allele almost doubled the risk of DN in East Asians (pooled ORs [95% CI]: 1.85 [1.49-2.29]). In contrast, studies relating the ε4 allele to DN risk were very heterogeneous and the pooled ORs were 1.05 [95% CI: 0.72-1.52]. In the subgroup meta-analysis, ε4 was substantially related to an increased risk for DN in studies conducted in China (pooled ORs [95% CI]: 1.51 [1.11-2.06]), which was different from previous results. However, the higher risk of DN associated with ε4 was not found in Japanese or Korean populations (pooled ORs [95% CI]: 0.46 [0.27-0.80] and 0.58 [0.09-3.55], respectively). Conclusion: The ε2 allele conferred a higher risk of DN in East Asians, and no significant result was obtained with the ε4 allele.

Effects of Apolipoprotein E Isoforms in Diabetic Nephropathy of Chinese Type 2 Diabetic Patients

Diabetic nephropathy (DN) is one of the major chronic complications of diabetes. Genetic polymorphism of Apolipoprotein E (ApoE) has been proposed to participating in DN. The purpose of the study was to evaluate the relationship between ApoE genetic polymorphism and the presence of DN in Chinese type 2 diabetic patients. We studied 845 diabetic patients who were divided into DN group (n = 429) and control group (n = 416). ApoE genotype was determined by ApoE genotyping chip and the plasmatic biochemical characterization was performed on all subjects. There were differences (P < 0.001) in HbA1c, creatinine, and urinary albumin between the two groups. The ApoE ε2 allelic frequency was 7.69% in DN group versus 3.49% in control group (OR = 2.22, 95% CI = 1.41-3.47, and P < 0.05), as expected, ApoE E2/E2 and E2/E3 genotype frequency were higher in DN group (13.75% versus 6.49%, P < 0.05). The ApoE ε4 allelic frequency was 7.93% in DN group versus 11.54% in control group (OR = 0.70, 95% CI = 0.50-0.97, and P < 0.05), and DN group presented a lower frequency of ApoE E3/E4 and E4/E4 genotype frequency (14.91% versus 19.96%, P < 0.05). These results suggest ApoE ε2 allele may be a risk factor; however ApoE ε4 allele may play a protective role of DN in Chinese type 2 diabetic patients.

Identifying Common Genetic Risk Factors of Diabetic Neuropathies

Type 2 diabetes mellitus (T2DM) is a global public health problem of epidemic proportions, with 60-70% of affected individuals suffering from associated neurovascular complications that act on multiple organ systems. The most common and clinically significant neuropathies of T2DM include uremic neuropathy, peripheral neuropathy, and cardiac autonomic neuropathy. These conditions seriously impact an individual's quality of life and significantly increase the risk of morbidity and mortality. Although advances in gene sequencing technologies have identified several genetic variants that may regulate the development and progression of T2DM, little is known about whether or not the variants are involved in disease progression and how these genetic variants are associated with diabetic neuropathy specifically. Significant missing heritability data and complex disease etiologies remain to be explained. This article is the first to provide a review of the genetic risk variants implicated in the diabetic neuropathies and to highlight potential commonalities. We thereby aim to contribute to the creation of a genetic-metabolic model that will help to elucidate the cause of diabetic neuropathies, evaluate a patient's risk profile, and ultimately facilitate preventative and targeted treatment for the individual.

Apo E gene polymorphism affects development of type 2 diabetic nephropathy in Asian populations, especially in East Asians: an updated meta-analysis

BACKGROUND

Many studies have determined the correlation between the Apolipoprotein E (APO E) gene polymorphisms and diabetic nephropathy, but their results are inconclusive.

MATERIAL/METHODS

With the aim to confirm this correlation, we performed a meta-analysis of 16 studies. The dichotomous data are presented as the odds ratio (OR) with a 95% confidence interval (CI).

RESULTS

The results of our study indicate that APO ε2 allele among the pooled Asian populations were more likely to show high risk of DN development (2 allele vs. ε3 allele: pooled OR =1.629, 95% CI=1.010-2.628, P=0.045). For further analysis, the APO e2 allele was associated with progress of DN in the group with duration >10 years, but not in the group with duration <10 years (ε2 allele vs. ε3 allele: pooled OR=1.920, 95% CI=1.338-2.754, P<0.001). The APO e2 polymorphism increased the susceptibility to DN in Asian population compared with healthy people (ε2 allele vs. ε3 allele: pooled OR=1.629, 95% CI=1.010-2.628, P=0.045).

CONCLUSIONS

Development of DN is associated with APO E polymorphisms in Asian populations, especially in East Asians.

Influence of apolipoprotein E gene polymorphism on development of type 2 diabetes mellitus in Chinese Han population: a meta-analysis of 29 studies

OBJECTIVES

Published data regarding the association between apolipoprotein E (ApoE) gene polymorphism and type 2 diabetes mellitus (T2DM) risk in Chinese Han population were inconclusive. To derive a more precise estimation of the relationship between this variant and T2DM risk in Chinese Han population, we performed this meta-analysis.

DESIGN AND METHODS

A computerized literature search was conducted to identify the relevant studies from PubMed, EMbase, Web of Science, CBMdisc, CNKI, and Google Scholar. Additionally, hand searching of the references of identified articles was performed. All the statistical tests were performed using Stata 11.0.

RESULTS

A total of 29 articles with 4615 T2DM cases and 2867 controls were included in the present meta-analysis. The results showed evidence for significant association between ApoE gene polymorphism and T2DM risk (for ε2/ε3 vs. ε3/ε3: OR=1.37, 95% CI=1.12-1.68, P<0.01; for ε3/ε4 vs. ε3/ε3: OR=1.53, 95% CI=1.23-1.91, P<0.01; for ε4/ε4 vs. ε3/ε3: OR=1.86, 95% CI=1.22-2.84, P<0.01; for ε2 allele vs. ε3 allele: OR=1.28, 95% CI=1.08-1.52, P=0.01; for ε4 allele vs. ε3 allele: OR=1.43, 95% CI=1.22-1.68, P<0.01). In addition, significant association was also found between ApoE gene polymorphism and diabetic nephropathy (DN) risk.

CONCLUSIONS

The results of this meta-analysis suggest that the ApoE ε2 and ε4 alleles may be associated with increased risks of T2DM and DN in Chinese Han population. Additional well-designed genome-wide association studies are required to confirm these results.

Meta-based association of the lipoprotein lipase gene S447X variant with hypertension and blood pressure variation

Association of the lipoprotein lipase (LPL) gene S447X variant with hypertension has been investigated extensively, whereas the results are often irreproducible. We therefore conducted a meta-analysis to examine whether S447X variant was associated with hypertension and blood pressure variation. Case-control reports published in English language and humans were identified from MEDLINE, EMBASE and Web of Science search engines as of 10 December 2009. Fixed-effects model was applied to pool data in the absence of between-studies heterogeneity, and random-effects model otherwise. A total of five studies (960 cases and 1145 controls) for hypertension and four studies (n=2777) for blood pressure were included. Compared with 447SS homogeneous carriers, those with 447X variant had a lower risk of hypertension (odds ratio (OR)=0.78; 95% confidence interval (CI): 0.62-0.98; P=0.03), and this effect reached significance under the fixed-effects model (I(2)=30% and P=0.22). Similarly, compared with 447S allele carriers, those with 447X allele carriers also had a lower risk of hypertension (OR=0.79; 95% CI: 0.64-0.98; P=0.03). In case of pregnancy-induced hypertension, no significance was observed (P>0.05). As for blood pressure association, there was no significant difference between 447X variant and 447SS homogeneous carriers for both systolic and diastolic blood pressure in the whole population, even stratified by gender (P>0.05). The Egger test told no publication bias for all associations. This meta-analysis demonstrated that LPL gene S447X variant was significantly associated with hypertension and showed no obvious relation with pregnancy-induced hypertension and blood pressure variation.

Genetic diversity of the apolipoprotein E gene and diabetic nephropathy: a meta-analysis

In the past decade, a number of case-control studies have been carried out to investigate the relationship between the ApoE polymorphism and diabetic nephropathy. However, the results have been inconclusive. To investigate this inconsistency, we performed a meta-analysis of all available studies dealing with the relationship between the ApoE polymorphism and DN. The 23 studies in the meta- analysis included 6,012 diabetic patients with (n = 2,979) and without (n = 3,033) DN. The ApoE ε2 allele was significantly associated with DN (OR = 1.64, 95% CI: 1.26-2.13; P(Z) = 0.00027), whereas the ε4 allele was non-significantly associated with DN (OR = 0.93, 95% CI: 0.78-1.11; P(Z) = 0.418). However, significant heterogeneity was detected. In further subgroup analyses, genotyping methods, outcome of cases and duration of diabetes in controls were found to explain some of the heterogeneity. Genotypic analysis also found a strong association between the ε2 carriers and DN (OR = 1.61, 95% CI: 1.22-2.13; P(Z) = 0.001) and indicated that ε4 tended to have a marginally significant protective effect for DN (OR = 0.82, 95% CI: 0.65-1.03; P(Z) = 0.085). The results of our meta-analysis support a genetic association between the ApoE polymorphism and DN. ε2 increases the risk of DN in diabetes patients, while ε4 trends to be protective. These findings may have implications for therapeutic intervention in diabetic nephropathy.

Apolipoprotein epsilon4 allele is associated with psoriasis severity

Many reports provided strong evidence of the influence of genetic factors in the pathogenesis of psoriasis (Ps). A higher prevalence of lipid disorders in psoriatic patients has been reported. Because apolipoprotein E (apoE) is involved in lipid metabolism, APOE gene variants could be candidates to influence Ps-risk. However, data about the potential influence of the APOE genotypes in Ps are inconclusive. Our objective was to investigate the relationship between the common APOE-epsilon2/epsilon3/epsilon4 variation and Ps in a Caucasian population. Our study involved 331 unrelated Ps-patients and 400 healthy controls. Patients and controls were genotyped for the APOE-epsilon2/epsilon3/epsilon4 polymorphism, and allele and genotype frequencies were statistically compared between the two groups and between patients according to disease severity. Mean lipid values were also compared between the APOE genotypes. Allele and genotype frequencies did not differ between patients and controls. APOE-epsilon4 carriers were significantly more frequent in patients with severe Ps compared to controls (P = 0.003) and to non-severe Ps (P = 0.017). No significant difference in mean lipid values was found between the APOE genotypes. The APOE-epsilon4 allele could be a risk factor for developing a severe form of psoriasis.

Phenotype-genotype interactions on renal function in type 2 diabetes: an analysis using structural equation modelling

AIMS/HYPOTHESIS

Cardiovascular and renal diseases share common risk factors. We used structural equation modelling (SEM) to evaluate the independent and combined effects of phenotypes and genotypes implicated in cardiovascular diseases on renal function in type 2 diabetes.

METHODS

1,188 type 2 diabetic patients were stratified into high-risk and low-risk groups according to bimodal distributions of the logarithmically transformed (log(e)) urinary albumin:creatinine ratio and plasma creatinine levels. Models for these groups, comprising continuous and non-ranking categorical data, were developed separately to evaluate the inter-relationships among measured variables and latent factors using non-linear SEMs, Bayesian estimation and model selection as assessed by a goodness-of-fit statistic.

RESULTS

Inter-correlated measured variables (obesity, glycaemia, lipid, blood pressure) and variants of the genes encoding endothelial nitric oxide synthase (NOS), beta-adrenergic receptor (ADRB), components of the renin-angiotensin system (RAS) and lipid metabolism were loaded onto their respective latent factors of phenotypes and genotypes. In addition to direct and indirect effects, latent factors of obesity, lipid and BP interacted with latent factors of ADRB and RAS genotypes to influence renal function. Together with variants of the genes encoding peroxisome proliferator-activated receptor gamma, atrial natriuretic peptide, adducin, G protein beta(3) subunit, epithelial sodium channel alpha subunit and matrix metallopeptidase 3, these parameters explained 39-80% of the variance in renal function in the high-risk and low-risk models.

CONCLUSIONS/INTERPRETATION

SEM is a useful tool for confirming and quantifying multiple interactions of biological pathways with genetic determinants. The combined and interactive effects of blood pressure, lipid and obesity on renal function may have therapeutic implications, especially in type 2 diabetic individuals with genetic risk factors.

Apolipoprotein E polymorphism and expression in type 2 diabetic patients with nephropathy: clinicopathological correlation

BACKGROUND

Diabetic nephropathy represents a heterogeneous group of renal pathologies that may be associated with genetic susceptibility. There have been clinical reports on the risk association of diabetic nephropathy with an apolipoprotein E (ApoE) exon 4 polymorphism although its correlations with renal histopathological changes have not been explored.

METHODS

A total of 213 adult autopsies with type 2 diabetes and 111 non-diabetic control cases were analysed. Genomic DNA samples were obtained from spleen tissues. The ApoE genotype was determined by PCR-LDR analysis. Histopathological examination of kidney sections was performed in a subset of 51 diabetic and 111 control cases. ApoE protein expression in diabetic carriers with similar clinical status was examined by immunohistochemical staining.

RESULTS

In type 2 diabetes, epsilon2 carriers (P = 0.04; odds ratio = 5.42; 95% CI: 1.10-26.8) and epsilon3/epsilon4 (P = 0.04; odds ratio = 22.5; 95% CI: 1.11-454.90) genotype carriers were more likely to have glomerular hypertrophy than were epsilon3/epsilon3 carriers. The epsilon2 carriers showed an increase in glomerular ApoE protein expression. A correlation between ApoE genotype and nodular glomerulosclerosis was not found.

CONCLUSIONS

Our findings confirm the risk association of the ApoE polymorphism with diabetic nephropathy in clinical studies and is the first study demonstrating the correlations between ApoE genotypes, protein expression and structural changes in diabetic nephropathy.

Association of lipoprotein lipase (LPL) single nucleotide polymorphisms with type 2 diabetes mellitus

The etiology and pathogenesis of type 2 diabetes mellitus (T2DM) are not completely understood although it is often associated with other conditions such as obesity, hypertension, and dyslipidemia. Lipoprotein lipase (LPL) is a key enzyme in human lipid metabolism that facilitates the removal of triglyceride-rich lipoproteins from the bloodstream. LPL hydrolyzes the core of triglyceride-rich lipoproteins (chylomicrons and very low density lipoprotein) into free fatty acids and monoacylglycerol. To gain insight into the possible role of LPL in T2DM, nine single nucleotide polymorphisms (SNPs) of LPL were analyzed for the association with T2DM using 944 unrelated Koreans, including 474 T2DM subjects and 470 normal healthy controls. Of the nine LPL SNPs we analyzed, a significant association with multiple tests by the false discovery rate (FDR) was observed between T2DM and SNP rs343 (+13836C>A in intron 3). SNP rs343 was also marginally associated with some of T2DM-related phenotypes including total cholesterol, high density lipoprotein cholesterol (HDLc), and log transformed glycosylated hemoglobin in 470 normal controls, although no significant association was detected by multiple tests. In total, our results suggest that the control of lipid level by LPL in the bloodstream might be an important factor in T2DM pathogenesis in the Korean population.

Type 2 diabetes mellitus and its renal complications in relation to apolipoprotein E gene polymorphism

The apolipoprotein E (APOE) epsilon2 allele is reported to be associated with greater risk of renal impairment in type 2 diabetes. Relationships among APOE polymorphisms, renal impairment, and biochemical parameters were explored. A prospective study of 405 consenting Chinese type 2 diabetic patients [mean age +/- standard deviation (SD): 59.2 +/- 10.3 years] without advanced complications at entry was conducted. APOE genotyping and measurement of plasma biomarkers of oxidative stress and antioxidants were performed at entry. HbA1C, plasma glucose, lipids, creatinine, urine albumin/creatinine, and blood pressure were measured at entry and at up to 4 years of follow-up. APOE allelic frequencies were in Hardy-Weinberg equilibrium. Odds ratios of albuminuria at entry and/or during follow-up for different APOE groups were not significantly different. The non-epsilon2 (epsilon3/3, epsilon3/4, epsilon4/4) group had significantly greater plasma ascorbate (51.6 +/- 20.1 mumol/L) than the epsilon2 (epsilon2/2, epsilon2/3) group (44.5 +/- 16.2 mumol/L, P = 0.021), but higher plasma ascorbate levels did not seem to decrease the risk of renal impairment in the non-epsilon2 group. Baseline plasma lipid-standardized alpha-tocopherol levels were least in epsilon2 subjects with persistent albuminuria (3.6 +/- 1.1 mumol/mmol of total cholesterol plus triglycerides, P = 0.008) compared with epsilon2 subjects who had no albuminuria at entry or during follow-up (4.5 +/- 0.8 mumol/mmol of total cholesterol plus triglycerides). The APOE epsilon2 allele does not seem to be associated with increased risk of renal impairment in Chinese type 2 diabetic patients. Plasma lipid-standardized alpha-tocopherol may play a role in determining risk of renal dysfunction in type 2 diabetes.

Ontology-guided data preparation for discovering genotype-phenotype relationships

Background

Complexity and amount of post-genomic data constitute two major factors limiting the application of Knowledge Discovery in Databases (KDD) methods in life sciences. Bio-ontologies may nowadays play key roles in knowledge discovery in life science providing semantics to data and to extracted units, by taking advantage of the progress of Semantic Web technologies concerning the understanding and availability of tools for knowledge representation, extraction, and reasoning.

Results

This paper presents a method that exploits bio-ontologies for guiding data selection within the preparation step of the KDD process. We propose three scenarios in which domain knowledge and ontology elements such as subsumption, properties, class descriptions, are taken into account for data selection, before the data mining step. Each of these scenarios is illustrated within a case-study relative to the search of genotype-phenotype relationships in a familial hypercholesterolemia dataset. The guiding of data selection based on domain knowledge is analysed and shows a direct influence on the volume and significance of the data mining results.

Conclusions

The method proposed in this paper is an efficient alternative to numerical methods for data selection based on domain knowledge. In turn, the results of this study may be reused in ontology modelling and data integration.

Expression of lipoprotein lipase associated with lung adenocarcinoma tissues

Lipoprotein lipase (LPL) plays a key role in the lipid metabolism and transporting. It can catalyze the hydrolysis of chylomicron and very low-density lipoprotein triglyceride. Moreover, the abnormality of LPL associates with many pathophysiological conditions. Herein cDNA microarray and Northern blots analysis were used to study the expression of lipoprotein lipase in lung adenocarcinoma tissues. There were 113 genes of all tested blots in cDNA microarray expressed lowly. LPL gene is expressed lowly at the average ratio 0.26 (Cy5/Cy3) in lung adenocarcinoma tissues over controls. Northern blots confirmed those changes detected from the cDNA microarray and suggested that low expression of LPL may play an important role in the lung adenocarcinoma development.