Comparing RNA extraction methods to face the variations in RNA quality using two human biological matrices

BACKGROUND

Nucleic acids, RNA among them, are widely used in biomedicine and Biotechnology. Because of their susceptibility to degradation by RNases, the handling and extraction process of RNA from cells and tissues require specialized personnel and standardized methods to guarantee high purity and integrity. Due to the diversity of techniques found in the market, a comparative study between different RNA extraction methods is useful to facilitate the best choice for the researcher or in research service platforms such as biobanks to see the traceability of the samples.

METHODS AND RESULTS

In this study, we have compared seven different RNA extraction methods: manual (TRIzol™), semiautomated (QIAGEN™, Bio-Rad, Monarch®, and Canvax™), and fully automated (QIAcube™ and Maxwell®) processes, from two biological matrices: human Jurkat T cells and peripheral blood mononuclear cells (PBMC). Results showed marked differences in the RNA quality and functionality according to the method employed for RNA extraction and the matrix used.

DISCUSSION

QIAcube™ and semi-automated extraction methods were perceived as the best options because of their lower variability, good functionality, and lower cost (P < 0.001). These data contribute to facilitating researchers or research service platforms (Biobanks) in decision-making practices and emphasize the relevance of the selection of the RNA extraction method in each experimental procedure or traceability study to guarantee both quality standards and its reproducibility.

Measurement of yield and quality of DNA in human buffy coat is extraction method dependent

During the last few years, an important element in the improvement of the molecular biology techniques has been the necessity for availability of high quality and functionality DNA. Several DNA extraction procedures with different results in both performance and quality, have been proposed. In this study our objective was to determine the most reliable extraction method that balances DNA quantity, and to assess the sample quantification of the fluorometric DNA quantification methods. For this, blood extracted by venopunction from 20 healthy volunteers was used to obtain DNA from buffy coat, and 4 commercial DNA extraction kits were assessed as well as two fluorometric DNA quantification methods with protocols of different complexity. Results suggest that manual methods achieve higher quality and larger yields of DNA. DNA purity obtained with the 4 extraction kits evaluated through the 260/280 and 260/230 ratio showed that the Qiacube kit fulfilled the criteria established in this work, followed very close by the Flexigene kit. On the other hand, the fluorometric DNA methods used in the samples quantification showed a higher variability when using QuantiFlour method, obtaining better results probably due to the simplicity of this protocol.

Characterization of two novel HLA-A null alleles: A*11:210N and A*26:107N

Two new HLA-A null alleles were characterized, A*11:210N and A*26:107N.

Anti-oxidized low-density lipoprotein antibody levels are associated with the development of type 2 diabetes mellitus

BACKGROUND

Anti-oxidized low-density lipoprotein (LDL) antibodies are associated with the oxidative capacity of plasma, but whether they protect or promote diabetes is unknown. We undertook a prospective study to determine the predictive capacity of anti-oxidized LDL antibodies for the onset of type 2 diabetes mellitus (T2DM).

MATERIALS AND METHODS

We selected 391 non-diabetic women aged 18-65 years. The subjects were classified as being normal (oral glucose test tolerance normal, OGTT-N), or having impaired glucose tolerance (IGT), impaired fasting glucose (IFG) or T2DM according to their baseline glucose levels and after an OGTT. The same subjects were studied six years later. The levels of anti-oxidized LDL antibodies were classified as above or below the 50th percentile.

RESULTS

Of the women who were OGTT-N at the start of the study and who had anti-oxidized LDL antibody levels below the 50th percentile, only 65.1% were still OGTT-N after 6 years versus 79.5% of those who had anti-oxidized LDL antibody levels above the 50th percentile (P = 0.015). Women who had IGT or IFG at the start of the study whose anti-oxidized LDL antibody levels were below the 50th percentile had a relative risk of 9.79 (95% confidence interval, 1.40-68.45) of developing diabetes (P < 0.001). Logistic regression analysis showed that the variables predicting the development of a carbohydrate metabolism disorder in the women after 6 years were body mass index (P < 0.001) and the levels of anti-oxidized LDL antibodies (P = 0.042).

CONCLUSIONS

Levels of anti-oxidized LDL antibodies are independent predictors for the development of T2DM in women.

Effect of long-term administration of cross-sex hormone therapy on serum and urinary uric acid in transsexual persons

BACKGROUND

Transsexual persons afford a very suitable model to study the effect of sex steroids on uric acid metabolism.

DESIGN

This was a prospective study to evaluate the uric acid levels and fractional excretion of uric acid (FEUA) in a cohort of 69 healthy transsexual persons, 22 male-to-female transsexuals (MFTs) and 47 female-to-male transsexuals (FMTs). The subjects were studied at baseline and 1 and 2 yr after starting cross-sex hormone treatment.

RESULTS

The baseline levels of uric acid were higher in the MFT group. Compared with baseline, uric acid levels had fallen significantly after 1 yr of hormone therapy in the MFT group and had risen significantly in the FMT group. The baseline FEUA was greater in the FMT group. After 2 yr of cross-sex hormone therapy, the FEUA had increased in MFTs (P = 0.001) and fallen in FMTs (P = 0.004). In MFTs, the levels of uric acid at 2 yr were lower in those who had received higher doses of estrogens (P = 0.03), and the FEUA was higher (P = 0.04). The FEUA at 2 yr was associated with both the estrogen dose (P = 0.02) and the serum levels of estradiol-17beta (P =0.03). In MFTs, a correlation was found after 2 yr of therapy between the homeostasis model assessment of insulin resistance and the serum uric acid (r = 0.59; P = 0.01).

CONCLUSIONS

Serum levels of uric acid and the FEUA are altered in transsexuals as a result of cross-sex hormone therapy. The results concerning the MFT group support the hypothesis that the lower levels of uric acid in women are due to estrogen-induced increases in FEUA.

Monounsaturatedn-9 fatty acids and adipocyte lipolysis in rats

To investigate the role of the monounsaturatedn-9 fatty acids (MUFA) in the lipolytic activity of adipocytes, a study was carried out in which an increase in MUFA was produced in the tissues by two different methods; by the dietary enrichment of oleic acid or by producing an essential fatty acid deficiency syndrome. For this, forty-five male Sprague–Dawley rats were fed with a normal-energy diet and were subdivided into three groups. The diets varied in the type of dietary fat; palmitic acid, olive oil, or soyabean oil+palmitic acid. At the end of the study measurements were taken of weight, plasma leptin, tissue concentration of fatty acids, fat-cell size in the epididymal and the omental adipose tissues, adipocyte lipolytic activity of both tissues after stimulation with adrenaline, and the capacity of insulin to inhibit lipolysis. The baseline and adrenaline-stimulated lipolytic activity were greater and the anti-lipolytic capacity of insulin lower in the animals undergoing an increase in MUFA in the tissues (palmitic-acid and olive-oil diets). The area under the curve of glycerol, used as an indicator of lipolytic activity, was positively correlated with the concentration of MUFA and negatively with polyunsaturated fatty acids in the adipose tissues. It is concluded that an increase in tissue MUFA, however obtained, induces an increase in lipolytic activity.

Association between MspI polymorphism of the APO AI gene and Type 2 diabetes mellitus

AIMS

Genes of the Apo AI/CIII/AIV cluster on chromosome 11 have been related to plasma lipid patterns. The close relationship between carbohydrate metabolism and lipid metabolism warrants investigation of the association between this cluster and Type 2 diabetes mellitus. We therefore examined the possible association between polymorphisms of this cluster and Type 2 diabetes mellitus as part of a study of the prevalence of diabetes and the metabolic syndrome in southern Spain.

METHODS

A total of 1224 persons were selected randomly from the town of Pizarra in the province of Malaga, southern Spain. The sample errors for the prevalence of Type 2 diabetes mellitus and the three polymorphisms studied were all < or = 4%. All subjects underwent phenotyping after an oral glucose tolerance test (75 g) (WHO 1998 criteria) and the XmnI and MspI polymorphisms of Apo AI and the SstI polymorphism of Apo CIII were genotyped.

RESULTS

Those subjects with the mutated AA genotype of the MspI polymorphism (-75 G-->A) of Apo AI had a greater risk of impaired glucose tolerance [odds ratio (OR) = 1.95, CI = 1.02-3.8, P = 0.05], Type 2 diabetes mellitus, both known (OR = 7.38, CI = 1.3-39.7, P = 0.02) and unknown (OR = 3.7, CI = 1.4-9.9, P = 0.009). This risk was independent of age, sex, obesity, triglyceride level, HDL cholesterol and pattern of insulin resistance.

CONCLUSIONS

Pending confirmation in prospective studies, the AA genotype of the MspI polymorphism of the Apo AI gene, within the Apo A-I/C-III/A-IV cluster, seems to be a risk factor for Type 2 diabetes mellitus.

Dietary palmitic acid influences LDL-mediated lymphocyte proliferation differently to other mono- and polyunsaturated fatty acids in rats

Recent studies suggest that the biological effects of saturated fatty acids depend on the length of their chain. We compared the effect of diets containing different fatty acids on plasma lipids and lymphocyte proliferation in the presence of lovastatin and with increasing amounts of LDL. Lymphocytes from rats fed with a diet rich in palmitic acid had a greater lymphocyte proliferation capacity than those from rats fed with diets rich in oleic acid, linoleic acid, or fish oil. This effect was maintained when small amounts of polyunsaturatwed fatty acids (PUFA; sunflower oil) were added to the palmitic acid diet. LDL receptor activity, measured by the capacity of lovastatin to revert the inhibition of lymphocyte proliferation with increasing amounts of LDL in the medium, was greater in the rats fed with palmitic acid, and was similar to the other groups when small amounts of PUFA were added. All the groups had similar levels of plasma cholesterol, but the LDL levels were significantly lower in the group fed with palmitic acid plus PUFA. The highest HDL-cholesterol (HDLc) levels were found in the palmitic acid group and the lowest LDL-cholesterol (LDLc)/HDLc ratio in the palmitic acid plus PUFA group. These results suggest that diets rich in palmitic acid do not raise total cholesterol, but reduce LDLc or keep it normal, and raise HDLc levels. This effect may be partly due to an increase in LDL receptor activity. The inclusion of small amounts of PUFA in the diet rich in palmitic acid substantially modified the LDL receptor response in the lymphocytes, suggesting that the proportion of different families of dietary fatty acids may be more important than the individual amount of each in absolute terms to explain their effects on plasma lipids and lipoproteins.

Patterns of insulin resistance in the general population of southeast Spain

The aim of this study was to evaluate patterns of insulin resistance in the general population. The study was cross sectional. Clinical, anthropometric, and lipid measurements were made in 1226 persons aged 18-65 years. An oral glucose tolerance test (OGTT) was performed in 1020 subjects, with insulin levels determined at baseline and after 2 h. The homeostasis model assessment insulin resistance index (HOMA IR) and HOMA beta-cell function were calculated. Compared with subjects with normal glucose tolerance, the groups with abnormal OGTT had different baseline insulinemia, 2 h post OGTT insulinemia, HOMA IR and HOMA beta-cell indices. Serum insulin levels at baseline and 2 h after OGTT showed a characteristic pattern for each category of glucose tolerance, resulting from the different insulin responses. In the subjects with normal glucose tolerance, the pattern of the relationships between both types of serum insulin levels was exactly the same, so that it was possible to determine risk groups according to the ratio of baseline serum insulin/2 h insulin. HOMA IR and HOMA beta-cell were significantly associated with the risk of impaired fasting glucose, previously unknown diabetes mellitus, and known diabetes mellitus. These results support the rationale for introducing preventive measures against insulin resistance in the general population.

Association of biological markers of activity of systemic lupus erythematosus with levels of anti-oxidized low-density lipoprotein antibodies

OBJECTIVES

To study the levels of anti-oxidized low-density lipoprotein (LDL) antibodies in patients with systemic lupus erythematosus (SLE) at two different points during the disease, and evaluate their relation with markers of SLE activity in serial blood samples. To investigate the correlations at two points in time between anti-oxidized LDL antibodies and anti-beta2-glycoprotein-I antibodies, leucocytes, immunoglobulin G, anti-deoxyribonucleic acid, complement 3, complement 4 and the disease activity index.

METHODS

A total of 49 patients with SLE according to ACR criteria were studied at two points, 3 to 4 months apart, Time 1 and Time 2.

RESULTS

There were ostensible changes in levels of anti-oxidized LDL antibodies between Times 1 and 2, which correlated significantly with disease activity markers. The association between levels of anti-oxidized LDL antibodies and complement system activation remained after multiple regression analysis with stepwise adjustment.

CONCLUSIONS

Antibody levels against oxidized LDL vary with time and are closely related to the degree of SLE activity. There is an association between levels of autoantibodies to oxidized LDL and complement system activation.

Oleic acid from cooking oils is associated with lower insulin resistance in the general population (Pizarra study)

AIM

To evaluate the relation between type of dietary fatty acid and degree of insulin resistance.

DESIGN

A cross-sectional study.

METHODS

Anthropometrical data were measured in 538 subjects, aged 18-65 Years, selected randomly from the municipal census of Pizarra (Spain). An oral glucose tolerance test (OGTT) was given to all subjects and measurements were made of glycemia, insulinemia and the proportion of fatty acids in plasma phospholipids. Insulin resistance (IR) was estimated by homeostasis model assessment. Samples of cooking oil being used were obtained from the kitchens. The strength of association between variables was measured by calculating the odds ratio (OR) from logistic models, and the relationships were measured by linear correlation coefficients.

RESULTS

Insulin resistance was significantly less in people who used olive oil compared with those who used sunflower oil or a mixture. Statistical significance remained in the group of people with normal OGTT after adjusting for obesity. In the whole sample, IR correlated negatively with the concentration of oleic acid (r=-0.11; P=0.02) and positively with that of linoleic acid (r=0.10; P=0.02) from the cooking oil. In subjects with normal OGTT, IR correlated negatively with oleic acid from cooking oil (r=-0.17; P=0.004) and from plasma phospholipids (r=-0.11; P=0.01) and positively with the concentration of linoleic acid in cooking oil (r=0.18; P=0.004) and plasma phospholipids (r=0.12; P=0.005). The risk (OR) of having raised IR was significantly lower in people who consumed olive oil, either alone (OR=0.50) or mixed (OR=0.52) compared with those who consumed only sunflower oil.

CONCLUSION

There is an association between the intake of oleic acid, the composition of oleic acid in plasma phospholipids and peripheral insulin action.

Dietary fatty acids modify insulin secretion of rat pancreatic islet cells in vitro

The type of dietary fat affects the action of insulin by changes induced in the fatty acid composition of cell membranes. Little is known, however, about the effects of dietary fatty acids on insulin secretion or the possible relation between the fatty acid composition of the membrane phospholipids and insulin secretion. We therefore studied the effects of dietary fatty acids on insulin secretion stimulated by glucose, forskolin and arginine, and on the insulin content of isolated pancreatic islets, as well as on the fatty acid composition of muscle phospholipids, which were used as markers of the diet-induced modifications in the cell membranes. Five groups of rats were fed for one month with diets varying only in their fat composition: olive oil, sunflower oil, soybean oil, fish oil and palmitic acid (16:0) + soybean oil (SAT). The SAT group had higher insulin secretion, independently of the secretagogue used. No significant differences were found in insulin content between the groups. The dietary fatty acids modified the fatty acid composition of the muscle phospholipids, both in endogenously synthesized fatty acids and in those which were unable to be synthesized by the organism. No statistically significant relation was found between insulin secretion and the content of certain fatty acids in the muscle phospholipids.

Increased levels of anti-oxidized low-density lipoprotein antibodies are associated with reduced levels of cholesterol in the general population

Autoantibodies against epitopes of oxidized low-density lipoprotein (LDL), initially shown in human sera, were later related with the atherosclerotic process, although recent studies have questioned this association. Moreover, their association with total cholesterol and plasma LDL, or with the other lipoproteins, is not clear. We studied the relation between the levels of autoantibodies to oxidized LDL and lipoproteins in a population of 400 subjects from the lower Guadalhorce area in Malaga, Spain. Anti-oxidized LDL antibodies were measured by enzyme-linked immunosorbent assay (ELISA), and total cholesterol, triglycerides, high-density lipoprotein (HDL) cholesterol, and lipoprotein(a) [Lp(a)] were measured with commercial kits. Subjects who were positive for anti-oxidized LDL antibodies had significantly lower levels of total cholesterol (P <.01) and LDL cholesterol (P <.01). There was a negative correlation between titers of anti-oxidized LDL antibodies and levels of total cholesterol (P =.007) and LDL cholesterol (P =.024). This inverse relation between the levels of anti-oxidized LDL antibodies and the levels of total cholesterol and LDL cholesterol in a large population study, together with the discordances already published, suggests that the relation between anti-oxidized LDL antibodies, arteriosclerosis, and lipids is more complex than initially thought.

Varying incorporation of fatty acids into phospholipids from muscle, adipose and pancreatic exocrine tissues and thymocytes in adult rats fed with diets rich in different fatty acids

Despite numerous studies, the importance which the tissue or the composition of the diet may have in the biological distribution of each fatty acid is not well known. To determine the importance of tissue origin and dietary fatty acids in the fatty acid composition of cell phospholipids, 54 male adult rats were fed isocaloric diets for one month varying only in their fatty acid compositions. The fat component of the six experimental groups was derived from olive oil, sunflower oil, fish oil, soybean oil, palmitic acid, or 82% palmitic acid plus 18% soybean oil, supplying the essential fatty acid. The fatty acid composition of phospholipids from thymocytes, pancreatic exocrine, muscle and adipose tissues was studied by gas-chromatography. The tissue of origin was a more important source of variation than diet in the fatty acid content of the cell phospholipids except for palmitic acid (16:0), eicosapentaenoic acid (20:5 n-3), and docosahexaenoic acid (22:6 n-3). This study points out the complexity of the interrelations between different families of fatty acids and of the specificity of each tissue to changes in the composition of dietary fatty acids, as well as the inconvenience of speaking from the dietary point of view of groups of fatty acid families based on the position of the double bond, since their individual behaviour, including saturated fatty acids, is very different in the face of dietary manipulation. The study also highlights the different behaviour of each of the fatty acids in relation to the others in the diet in each of the tissues, a circumstance which should be taken into account when evaluating the biological effects in both epidemiological and experimental studies.

Serum leptin and habitual fatty acid dietary intake in patients with type 1 diabetes mellitus

OBJECTIVE

To study the contribution of a normal intake of nutrients to the variability of serum leptin concentrations in persons with type 1 diabetes mellitus.

DESIGN

We studied the relation between serum leptin and nutrient intake in a cross-sectional study.

METHODS

Serum leptin measured by radioimmunoassay, nutritional data determined by a self-administered 7-day nutritional questionnaire, and the fatty acid composition of the serum phospholipids (measured by thin layer chromatography and gas chromatography) were determined in 60 patients with type 1 diabetes mellitus. Correlation and regression analyses were performed between serum leptin and dietary fatty acids and serum phospholipid fatty acids.

RESULTS

In the prediction models for the concentrations of serum leptin in men with type 1 diabetes mellitus, the dietary fatty acids displaced the anthropometric variables, and were independent of the serum testosterone concentrations. This fact remained when the prediction was made on the basis of indirect markers of the intake, such as the serum phospholipid fatty acids. In the women, the fatty acids from the diet or from the serum phospholipids also partly explained the variation in serum leptin, although not displacing the anthropometric variables.

CONCLUSIONS

Our data suggest that, in non-experimental conditions, the concentrations of serum leptin in men with type 1 diabetes mellitus and, to a lesser extent, those in women with diabetes, may be influenced by the composition of the habitual diet, especially the type of dietary fat.

Autoantibodies against malondialdehyde-modified lipoprotein(a) in antiphospholipid syndrome

OBJECTIVE

To demonstrate the existence of antibodies that react against malondialdehyde (MDA)-modified lipoprotein(a) (MDA-Lp[a]), a molecule that exhibits behavioral similarities to MDA-modified low-density lipoprotein (MDA-LDL), and to assess the possible relationship of these antibodies (anti-MDA-Lp[a]) to anti-MDA-LDL antibodies (anti-MDA-LDL) in the antiphospholipid syndrome (APS).

METHODS

We studied 104 patients with APS (61 with primary APS and 43 with APS secondary to systemic lupus erythematosus) and 106 healthy controls. Anti-MDA-Lp(a) were measured by enzyme-linked immunosorbent assay (ELISA) using MDA-Lp(a) as antigen. Plasma levels of Lp(a) were determined. Anti-MDA-LDL, anticardiolipin antibodies (aCL), and anti-beta2-glycoprotein I antibodies (anti-beta2GPI) were also measured by ELISA. Inhibition assays were performed to determine the presence of cross-reactivity between anti-MDA-Lp(a) and anti-MDA-LDL.

RESULTS

Anti-MDA-Lp(a) were detected in 38 of 104 patients (37%) but in only 6 of 106 controls (6%) (chi2 = 28, P<0.0001). Levels of anti-MDA-Lp(a) were also higher in patients than in controls (P<0.0001). Titers of these antibodies did not correlate with plasma levels of Lp(a). The presence of anti-MDA-Lp(a) was significantly associated with that of anti-MDA-LDL (chi2 = 22.09, P<0.0001). There was a strong correlation between the titers of anti-MDA-Lp(a) and anti-MDA-LDL (r = 0.59, P<0.0001), and inhibition assays showed significant cross-reactivity between the 2 populations of antibodies. Anticardiolipin antibodies and anti-beta2GPI were present in sera from 67 patients (64%) and 48 patients (46%), respectively. No correlation was found between the titer of anti-MDA-Lp(a) and titers of either aCL or anti-beta2GPI.

CONCLUSION

We report for the first time the existence of autoantibodies against MDA-Lp(a). The presence of antibodies reacting not only against MDA-LDL but also against MDA-Lp(a) supports the hypothesis of a role for oxidative phenomena in the pathogenesis of APS and atherosclerosis.

Antiphospholipid, anti-beta 2-glycoprotein-I and anti-oxidized-low-density-lipoprotein antibodies in antiphospholipid syndrome

Antiphospholipid antibodies (aPL), anti-beta 2-glycoprotein I (anti-beta 2-GPI) and anti-oxidized-low-density lipoprotein (LDL) antibodies are all implicated in the pathogenesis of antiphospholipid syndrome. To investigate whether different autoantibodies or combinations thereof produced distinct effects related to their antigenic specificities, we examined the frequencies of antiphospholipid syndrome (APS)-related features in the presence of different antibodies [aPL, beta 2-GPI, anti-oxidized low density lipoprotein (LDL)] in 125 patients with APS. Median follow-up was 72 months: 58 patients were diagnosed as primary APS and 67 as APS plus systemic lupus erythematosus (SLE). Anticardiolipin antibodies (aCL), anti-beta 2-GPI and anti-oxidized LDL antibodies were determined by ELISA; lupus anticoagulant (LA) by standard coagulometric methods. Univariate analysis showed that patients positive for anti-beta 2-GPI had a higher risk of recurrent thrombotic events (OR = 3.64, 95% CI, p = 0.01) and pregnancy loss (OR = 2.99, 95% CI, p = 0.004). Patients positive for anti-oxidized LDL antibodies had a 2.24-fold increase in the risk of arterial thrombosis (2.24, 95% CI, p = 0.03) and lower risk of thrombocytopenia (OR = 0.41 95% CI, p = 0.04). Patients positive for aCL antibodies had a higher risk of pregnancy loss (OR = 4.62 95% CI, p = 0.001). When these data were tested by multivariate logistic regression, the association between anti-beta 2-GPI and pregnancy loss and the negative association between anti-oxidized LDL antibodies and thrombocytopenia disappeared.