[Introduction to human genome sequencing in diagnostics]. / Wprowadzenie do sekwencjonowania ludzkiego genomu w diagnostyce.

The increasing efficiency of genetic analyzers together with the decreasing price of DNA sequencing per single nucleotide read, makes the method of individual genomes sequencing more available for diagnostic laboratories. Nowadays genome sequencing applications are predominantly used for research purposes but in nearest future we will be using them in routine patient evaluation as we are using analytic approaches based on Sanger method now. New generation sequencing is a tool which gives the researchers excellent possibilities for the realization of personalized medicine assumptions. However, before we will be able to make full use of it, there are still some questions to be answered, as for example who should perform the analysis, interpret results and finally who should be responsible for data management.

[Beta-carotene regulates the expression of proapoptotic BAX and CAPN2 in HL-60, U-937 and TF-1 - human acute myeloid leukemia cell lines; microarray, RQ-PCR and Western Blot analysis]. / Wplyw beta-karotenu na ekspresje proapoptotycznych genów BAX i CAPN2 w komórkach linii ostrej bialaczki szpikowej HL-60, U-937 i TF-1; analiza technika mikromacierzy, ilosciowej PCR i Western Blot.

Beta carotene (BC) is a nutritional compound widespread in foods which can influence vital cellular functions--differentiation, proliferation and apoptosis of normal and cancer cells. However its role in the carcinogenesis remains controversial. We performed a microarray expression analysis in three human acute leukemia cell lines (HL-60, U937 and TF-1) exposed to 10mM BC and found that BC stimulated the apoptosis in all studied cell lines. This effect was most evident in the HL-60 cell line and correlated with increased expression of proapoptotic BAX and CAPN2 genes. The micro-array findings were replicated by the quantitative BAX and CAPN2 expression analysis using real-time PCR and by Western Blot on protein level. The biological tests (TUNEL method) for apoptosis showed consistent proapoptotic effects in all studied cell lines. In this paper the stimulatory effect of BC on apoptosis (enhanced expression of proapoptotic genes and proteins) in human acute myeloid leukemia cells was confirmed. The most potent activation of apoptosis in the HL-60 cells is in line with other investigators observations suggesting distinct molecular mechanism of apoptosis stimulation by BC in different human acute myeloid leukemia cells.

Severe dystonic encephalopathy without hyperphenylalaninemia associated with an 18-bp deletion within the proximal GCH1 promoter.

In a recent GCH1 mutation screen, an 18-bp deletion was identified within the proximal promoter in two patients with early-onset Parkinson's disease. The mutation removes cAMP response element critical for adequate GTP cyclohydrolase I activity in selected cell types, including dopaminergic neurons, but its biological significance was unclear as it was also detected in one control individual. We present an 11-year-old boy with infantile-onset severe dystonic encephalopathy without hyperphenylalaninemia whom we found compound heterozygous for the same promoter GCH1 deletion and another common missense mutation associated with classical dopa-responsive dystonia. Extensive diagnostic work up excluded other causes of dystonia, and comprehensive mutation scan did not reveal any additional GCH1 sequence variations, supporting the association between the promoter deletion and disease phenotype.

Evidence for potential functionality of nuclearly-encoded humanin isoforms.

Humanin (HN) is a recently identified neuroprotective and antiapoptotic peptide derived from a portion of the mitochondrial MT-RNR2 gene. We provide bioinformatic and expression data suggesting the existence of 13 MT-RNR2-like nuclear loci predicted to maintain the open reading frames of 15 distinct full-length HN-like peptides. At least ten of these nuclear genes are expressed in human tissues, and respond to staurosporine (STS) and beta-carotene. Sequence comparisons of the nuclear HN isoforms and their homologues in other species reveal two consensus motifs, encompassing residues 5-11 (GFS/NCLLL), and 14-19 (SEIDLP/S). Proline vs serine in position 19 may determine whether the peptide is secreted or not, while threonine in position 13 may be important for cell surface receptor binding. Cytoprotection against the STS-induced apoptosis conferred by the polymorphic HN5 variant, in which threonine in position 13 is replaced with isoleucine, is reduced compared to the wild type HN5 peptide.

Expression of fucosyltransferases contributes to melanoma invasive phenotype.

During carcinogenesis aberrant N-glycosylation may lead to the development of subpopulations of tumor cells with altered adhesion properties and increased invasive potential. Biosynthesis of glycans and oligosaccharides is tissue-specific and developmentally regulated by number of glycosyltransferases of which fucosyl-, sialyl- and N-acetylglucosaminyltransferases often participate in synthesis of tumor type glycans. We analyzed the expression of selected glycosyltransferases (real-time PCR): fucosyltransferases FUT-1 and FUT-4, sialyltransferase SIAT4C and beta 1,6-N-acetylglucosaminyltransferase V (MGAT-5), in human melanoma cell lines: WM35 from primary tumor site and WM239, WM9, A375 from metastatic sites. In parallel their proliferation (crystal violet test) and adhesion to fibronectin and collagen IV (BD Biocoat assay) was assessed. Examined cell lines showed expression of all studied glycosyltransferases. The level of expression of fucosyltransferases was significantly higher in melanoma cell lines from metastatic site than from primary cell line: mRNA expression of FUT-1 was 100 times higher in A375 melanoma cell line from metastatic site (A375, solid tumor) than in WM35 primary cell line. The expression of FUT-4 in cell lines from metastatic sites: WM9 (lymph node) and WM239 (skin) was respectively 80 and 37 times higher than in WM 35 primary cell line. In all melanoma cell lines very low expression of MGAT-5 and high expression of SIAT4C was observed. Melanoma cells bound both to fibronectin and to collagen IV. LTA (Lotus tetragonolobus agglutinin), the lectin that specifically recognizes fucose residue of glycans and 20mM L-fucose by itself significantly reduced adhesion of all studied cell lines, both primary and metastatic, to fibronectin (20-50 %) and to collagen IV (20-50 %). In addition LTA reduced the proliferation (20-30 %) of metastatic cell lines (A375, WM9, WM239) and did not affect the growth of primary cell line (WM35). The results suggest that higher expression of fucosyltransferases (FUT-1, FUT-4) might be an important step in the formation of surface structures that facilitate metastasis of melanoma.

A724A polymorphism of sarco(endo)plasmic reticulum Ca2+-ATPase 2 (SERCA2) in hypertensive patients.

BACKGROUND: Impaired function of calcium ion transporter sarco(endo)plasmic reticulum Ca2+-ATPase2 (SERCA2), encoded by ATP2A2 gene, was observed in hypertension. The aim of this study was to screen for mutations in the ATP2A2 gene, in hypertensive patients compared to healthy controls. METHODS: The frequency of a novel mutation in exon 15 of ATP2A2, coding SERCA2, was studied in 107 hypertensive patients and a control group of 50 healthy volunteers. 24-h ambulatory blood-pressure monitoring (ABPM) was carried out. ATP2A2 genotyping was performed by denaturing HPLC and sequencing. RESULTS: In exon 15 of the ATP2A2 gene, a novel c.2171G>A polymorphism was identified that does not change the amino acid sequence. The frequency of the A allele was significantly higher in normotensive controls than in hypertensive patients (p=0.017). GA genotype carriers demonstrated a tendency towards lower blood pressure values in the doctor's office (p=0.367 systolic, p=0.439 diastolic blood pressure) and measured by ABPM. CONCLUSIONS: Our results suggest a protective role of the A724A (c.2171G>A) polymorphism of ATP2A2 in subjects without hypertension.

Acute myocardial infarction and a new ABCC6 mutation in a 16-year-old boy with pseudoxanthoma elasticum.

Pseudoxanthoma elasticum is caused by mutations of the ABCC6 gene. We hereby report a case of pseudoxanthoma elasticum with clinical features dominated by early coronary involvement in addition to typical skin and ocular abnormalities. A 16-year-old survivor of acute myocardial infarction with 3-vessel coronary artery disease exhibited compound heterozygosity for the well-known nonsense mutation (c.3421C>T; R1141X) in exon 24 and a novel missense mutation (c.3662G>A; R1221H) in exon 26 of the ABCC6 gene.

Bioethics in human nutrigenomics research: European Nutrigenomics Organisation workshop report.

As part of its work on setting standards and establishing guidelines for nutrigenomics research, the European Nutrigenomics Organisation (NuGO) is developing bioethical guidelines for those engaged in human nutrigenomics studies. A NuGO working group developed a set of draft guidelines addressing four areas: (1) information and consenting prior to a nutrigenomics study; (2) the generation and use of genotype information; (3) the establishment and maintenance of biobanks; (4) the exchange of samples and data. NuGO convened a workshop with a panel of invited external experts to assess the draft guidelines. The panel of experts confirmed that these areas are important and that the development of specific bioethical guidelines for nutrigenomics research would therefore enhance the application of established international guidelines in this field of biomedical research.

Different effect of beta-carotene on proliferation of prostate cancer cells.

It was shown that high doses of beta-carotene (>30 microM) decrease proliferation of prostate cancer cells in vitro. However, it is rather doubtful whether such concentration of beta-carotene is really accessible at cellular level. We studied the effect of 3 and 10 microM beta-carotene on proliferation and gene expression in LNCaP and PC-3 prostate cancer cell lines. Beta-carotene--more efficiently absorbed from medium by androgen-sensitive LNCaP cells--increased proliferation of LNCaP cells whereas it had weaker effect on PC-3 cells. Initial global analysis of expression of genes in both cell lines treated with 10 microM beta-carotene (Affymetrix HG-U133A) showed remarkable differences in number of responsive genes. Their recognition allows for conclusion that differences between prostate cancer cell lines in response to beta-carotene treatment are due to various androgen sensitivities of LNCaP and PC-3 cells. Detailed analysis of expression of selected genes in beta-carotene treated LNCaP cells at the level of mRNA and protein indicated that the observed increase of proliferation could have been the result of slight induction of a few genes affecting proliferation (c-myc, c-jun) and apoptosis (bcl-2) with no significant effect on major cell cycle control genes (cdk2, RB, E2F-1).

The effect of beta-carotene and its derivatives on cytotoxicity, differentiation, proliferative potential and apoptosis on the three human acute leukemia cell lines: U-937, HL-60 and TF-1.

The influence of beta-carotene (BC) and its derivatives on differentiation, proliferation and apoptosis in three human acute leukemia cell lines was studied. We investigated: (i) the cellular uptake of BC, (ii) the cytotoxicity, (iii) the effect on cell cycle progression and/or apoptosis. The dose- and time-dependent pattern of cellular BC uptake in all studied cell lines was seen. We did not observe any cytotoxic effect of BC and ATRA in the chosen concentrations. There was only limited effect of BC on gene expression. The microarrray analysis of U-937 cell line exposed to BC for 72 h showed an increased expression of BAX gene. This finding was confirmed by real-time Q-PCR analysis, and supported by a flow cytometry apoptosis tests. We did not observe any influence of studied components on cellular proliferation. The induction of differentiation after incubation with ATRA in HL-60 cells was noted. The induction of cellular apoptosis by BC was seen in all studied cell lines. We demonstrated that BC used in the concentrations achievable in vivo does not affect the proliferation and differentiation process of the studied leukemic cell lines, but can influence and enhance the apoptosis by modulating the expression of the regulatory genes.

The microarray expression analysis identifies BAX as a mediator of beta-carotene effects on apoptosis.

Beta-carotene is a ubiquitous compound rich in foods. However, there are conflicting reports regarding its role in carcinogenesis. We performed a microarray expression analysis in normal [human umbilical vein endothelial cells (HUVECs)] and neoplastic (melanoma A375 and myelomonocytic leukemia U937) actively proliferating cells and found evidence that beta-carotene stimulated vital cellular functions in the former and suppressed them in the latter. These differential effects correlated with the expression of the proapoptotic BCL2-associated X protein (BAX), which was downregulated in HUVECs and upregulated in the two neoplastic cell lines. The quantitative expression analysis using real-time polymerase chain reaction largely confirmed the inhibition of B-cell CLL/lymphoma 2 (BCL2) pathway-mediated apoptosis in HUVECs and its activation in melanoma and leukemic cells. The assays for apoptosis, detecting DNA breaks and caspase activation, showed consistent proapoptotic and antiapoptotic effects in U937 and HUVEC lines, respectively. However, beta-carotene-induced expression changes of BAX and other BCL2 pathway genes did not lead to the predicted induction of apoptosis in the A375 cells.

[Adiponectin--adipocytokine with a broad clinical spectrum]. / Adiponektyna--adipocytokina o szerokim spektrum klinicznym.

Adiponectin (also called AdipoQ, gelatin-binding protein 28, Acrp30) is a novel adipocytokine with important metabolic effects. It is physiologically released from adipose tissue and circulates in serum as a hexamer and larger multimeric structure of high molecular weight. Serum level of the protein correlates with systemic insulin sensitivity. Recently adiponectin receptors AdipoR1 and AdipoR2 have been discovered by expression cloning. AdipoR1 is abundantly expressed in skeletal muscles, whereas AdipoR2 is predominantly expressed in the liver. Marked expression of mRNA for AdipoR1 and AdipoR2 has been lately reported in pancreatic beta cells. Both of the receptors activate AMPK and PPAR alpha metabolic pathways leading to an increase in fatty acid oxidation, glucose uptake and a decreased rate of gluconeogenesis, thus enhancing insulin sensitivity. Moreover effects of adiponectin mimic many metabolic actions of insulin such as augmenting blood flow and glucose disposal in NO-dependent manner. The precise mechanism of regulation of plasma adiponectin level is unknown. Recently the mechanism of transcriptional activation of adiponectin gene via PPAR gamma was described. Its level seems to be decreased by TNFalfa and beta-adrenergic agonists. Furthermore there is increasing evidence that some genetic variants in the adiponectin gene may be associated with its ethnical differences in level as well as its likely clinical consequences. Hipoadiponectynemia is associated with obesity, metabolic syndrome, diabetes type 2, cardiovascular disease, lipodystrophy in AIDS. In patients with chronic renal failure, anorexia nervosa plasma adlponectin level is increased. Weight loss and therapy with thlazolidinediones are proved to enhance endogenous adlponectin production in humans. In summary, the ability of adiponectin to increase insulin sensitivity in conjunction with its anti-inflammatory and antiatherogenic properties have made this novel adipocytokine a promising therapeutic tool for the future, especially in individuals with low plasma levels of adiponectin.

Expression pattern and raft association of NIPSNAP3 and NIPSNAP4, highly homologous proteins encoded by genes in close proximity to the ATP-binding cassette transporter A1.

The highly homologous genes NIPSNAP3 and NIPSNAP4, with 87% amino acid identity, are members of the NIPSNAP family with putative roles in vesicular trafficking. NIPSNAP3 mRNA and NIPSNAP4 mRNA and protein were detected in multiple tissues and cells at varying degrees. Interestingly, NIPSNAP3 is most highly expressed in skeletal muscle, where NIPSNAP4 has a low mRNA abundance. NIPSNAP4 was found associated with membranes and partly localized in rafts. The ubiquitous expression of the highly conserved NIPSNAPs and their association with membranes further support an important cellular function of these proteins probably linked to vesicular trafficking. The NIPSNAP3 and NIPSNAP4 genes are located in close proximity to the 3' end of the ATP-binding cassette transporter A1 (ABCA1), whose mutations cause familial high-density lipoprotein deficiency syndromes. The adjacent genomic location and the finding that ABCA1 is a regulator of vesicular trafficking may indicate a functional relation of these proteins, even though NIPSNAP4 does not interact directly with ABCA1 nor is its expression altered in cells with mutated ABCA1.

[Phenotypes of the cardiovascular system and polymorphisms of the endothelial nitric oxide synthase]. / Wybrane fenotypy ukladu krazenia a zmiennosc genetyczna sródblonkowej syntazy tlenku azotu.

AIM: Reduced nitric oxide (NO) production is associated with pathological changes in the cardiovascular system. In our study we analyzed the relationship between two polymorphisms (Glu298Asp and VNRT in the intron 4) of the endothelial nitric oxide synthase (eNOS) and ambulatory blood pressure (ABP), left ventricular mass index (LVMI) and vascular phenotypes. METHODS: The study population consisted of 127 parents and 167 offspring. All subjects underwent 24 hr ABP monitoring using a SpaceLabs 90207 device. 2D and M-mode echocardiograms were obtained. Pulse wave velocity (PWV) between the common carotid and femoral artery was measured with the Complior device and the carotid intima-media thickness (IMT) was assessed by ultrasound. For statistical analysis co-variables and correlations between relatives were taken into account. RESULTS: There was no relationship between the eNOS gene polymorphisms and ABP or LVMI neither in parents nor their offspring. Among parents, who were carriers of the 298Asp allele higher IMT values were noted as compared with Glu/Glu homozygotes (0.94 vs. 0.70 mm; p = 0.007). Among offspring there was a similar tendency towards higher IMT (0.60 vs. 0.53 mm; p = 0.10), but also higher PWV in carriers of the 298Asp allele as compared with Glu/Glu homozygotes (8.47 vs. 8.17 m/sec; p = 0.14). Polymorphism VNRT in intron 4 was not associated with vascular phenotypes. CONCLUSION: The Glu298Asp polymorphism of eNOS gene identifies patients with larger carotid IMT.