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Background Genome assembly of viruses with high mutation rates, such as Norovirus and other RNA viruses, or from metagenome samples, poses a challenge for the scientific community due to the coexistence of several viral quasispecies and strains. Furthermore, there is no standard method for obtaining whole-genome sequences in non-related patients. After polyA RNA isolation and sequencing in eight patients with acute gastroenteritis, we evaluated two de Bruijn graph assemblers (SPAdes and MEGAHIT), combined with four different and common pre-assembly strategies, and compared those yielding whole genome Norovirus contigs. Results Reference-genome guided strategies with both host and target virus did not present any advantages compared to the assembly of non-filtered data in the case of SPAdes, and in the case of MEGAHIT, only host genome filtering presented improvements. MEGAHIT performed better than SPAdes in most samples, reaching complete genome sequences in most of them for all the strategies employed. Read binning with CD-HIT improved assembly when paired with different analysis strategies, and more notably in the case of SPAdes. Conclusions Not all metagenome assemblies are equal and the choice in the workflow depends on the species studied and the prior steps to analysis. We may need different approaches even for samples treated equally due to the presence of high intra host variability. We tested and compared different workflows for the accurate assembly of Norovirus genomes and established their assembly capacities for this purpose.

Macronutrients represent risk factors for hyperlipidemia or diabetes. Lipid alterations and type 2 diabetes mellitus are global health problems. Overexpression of sterol regulatory element-binding factor (Srebf2) in transgenic animals is linked to elevated cholesterol levels and diabetes development. We investigated the impact of increased Srebf2 locus expression and the effects of control and high-fat, high-sucrose (HFHS) diets on body weight, glucose and lipid metabolisms in transgenic mice (S-mice). Wild type (WT) and S-mice were fed with both diets for 16 weeks. Plasma glucose, insulin and lipids were assessed (n = 25). Immunostainings were performed in liver, pancreas and fat (N = 10). Expression of Ldlr and Hmgcr in liver was performed by RT-PCR (N = 8). Control diet: S-mice showed reduced weight, insulin, total and HDL cholesterol and triglycerides (TG). HFHS diet widened differences in weight, total and HDL cholesterol, insulin and HOMA index but increased TG in S-mice. In S-mice, adipocyte size was lower while HFHS diet produced lower increase, pancreatic &beta, cell mass was lower with both diets and Srebf2, Ldlr and Hmgcr mRNA levels were higher while HFHS diet produced a rise in Srebf2 and Hmgcr levels. Srebf2 complete gene overexpression seems to have beneficial effects on metabolic parameters and to protect against HFHS diet effects.

// Ana-Barbara Garcia-Garcia 1, 2, * , M. Carmen Gomez-Mateo 3, 7, * , Rebeca Hilario 2 , Pilar Rentero-Garrido 2 , Alvaro Martinez-Domenech 4 , Veronica Gonzalez-Albert 2 , Andres Cervantes 5 , Pablo Marin-Garcia 6 , Felipe Javier Chaves 1, 2 , Antonio Ferrandez-Izquierdo 3 and Luis Sabater 4 1 CIBER of Diabetes and Associated Metabolic Diseases (CIBERDEM), Madrid, Spain 2 Unidad de Genomica y Diagnostico Genetico. Fundacion Investigacion Clinico de Valencia, Instituto de Investigacion Sanitaria Clinico de Valencia (INCLIVA), Valencia, Spain 3 Department of Pathology, Faculty of Medicine and Odontology, University of Valencia and Clinical Hospital of Valencia, and Instituto de Investigacion Sanitaria Clinico de Valencia (INCLIVA), Valencia, Spain 4 Department of Surgery, University of Valencia, Hospital Clinico Universitario, Instituto de Investigacion Sanitaria Clinico de Valencia (INCLIVA), Valencia, Spain 5 Hematology and Medical Oncology Unit, Biomedical Research Institute INCLIVA and Department of Medicine, University of Valencia, Valencia, Spain 6 Bioinformatics Unit. Fundacion Investigacion Clinico de Valencia, Instituto de Investigacion Sanitaria Clinico de Valencia (INCLIVA), Valencia, Spain 7 Current/Present address: Pathology Department, Hospital Universitario Donostia, San Sebastian, Spain * These authors have contributed equally to this work Correspondence to: Felipe Javier Chaves, email: felipe.chaves@uv.es Keywords: pancreatic ductal adenocarcinoma; gene expression; patient survival; microdissected cells; regional lymph node metastases Received: July 22, 2016 Accepted: July 17, 2017 Published: August 03, 2017 ABSTRACT Background: Pancreatic ductal adenocarcinoma (PDAC) is one of the most devastating malignancies in developed countries because of its very poor prognosis and high mortality rates. By the time PDAC is usually diagnosed only 20-25% of patients are candidates for surgery, and the rate of survival for this cancer is low even when a patient with PDAC does undergo surgery. Lymph node invasion is an extremely bad prognosis factor for this disease. Methods: We analyzed the mRNA expression profile in 30 PDAC samples from patients with resectable local disease (stages I and II). Neoplastic cells were isolated by laser-microdissection in order to avoid sample ‘contamination’ by non-tumor cells. Due to important differences in the prognoses of PDAC patients with and without lymph node involvement (stage IIB and stages I-IIA, respectively), we also analyzed the association between the mRNA expression profiles from these groups of patients and their survival. Results: We identified expression profiles associated with patient survival in the whole patient cohort and in each group (stage IIB samples or stage I-IIA samples). Our results indicate that survival-associated genes are different in the groups with and without affected lymph nodes. Survival curves indicate that these expression profiles can help physicians to improve the prognostic classification of patients based on these profiles.

Objectives Oxidative stress can modulate blood pressure levels in different models. Xanthine oxidoreductase is one of the enzymes producing free radicals in the cardiovascular system, and it can contribute to the increment of the oxidative stress and, consequently, blood pressure. We analyzed the association between the - 337GA and 565 + 64CT polymorphisms of the xanthine oxidoreductase gene with blood pressure and oxidative stress levels. Methods These polymorphisms were studied in a case-control study (185 patients with hypertension and 385 normotensive controls), we found that these polymorphisms were related to blood pressure levels. This association was high in patients with hypertension and showed an additive effect but did not increase the risk of developing hypertension. We studied an additional and independent sample of patients with hypertension (n=100) to know the association of these polymorphisms with oxidative stress levels. Results We found that these polymorphisms were related to blood pressure levels. This association was high in hypertensive patients and showed an additive effect, but does not increase the risk of developing hypertension. We have found that the same alleles related with higher blood pressure - 337A and 565 + 64C were related with increased oxidative stress in patients with hypertension. Conclusions Our results suggest that polymorphisms - 337GA and 565 + 64CT of xanthine oxidoreductase gene are related with blood pressure and oxidative stress in hypertension, adding evidence to the role of xanthine oxidoreductase and oxidative stress in blood pressure.

Objetivo Analizar la influencia de parametros antropometricos (tipo y grado de obesidad) sobre el fenotipo lipoproteico y la respuesta terapeutica a atorvastatina en mujeres con Metodos Estudio de intervencion no controlado con 20 mg de atorvastatina al dia (dosis nocturna) en 34 mujeres con hipercolesterolemia familiar heterocigota seleccionadas de forma aleatoria. Resultados El deposito de grasa abdominal influye de forma estadisticamente significativa en los valores de presion arterial y concentraciones plasmaticas basales y postratamiento de los trigliceridos. Existe una interaccion negativa entre el deposito de grasa abdominal y la respuesta terapeutica de cLDL, siendo menores los descensos en mujeres con mayor deposito de grasa abdominal. El indice de masa corporal y la edad no influyen en los valores basales de lipidos y apo B ni en la respuesta terapeutica a atorvastatina. Conclusion El deposito de grasa abdominal en mujeres con hipercolesterolemia familiar y su correccion en los casos en que este aumentado debe realizarse para mejorar su perfil lipidico basal y evitar la interaccion negativa con atorvastatina.

Background Familial hypercholesterolemia (FH) is an autosomal dominant disease caused by mutations in the low-density lipoprotein receptor (LDLR) gene. To date, there has not been a systematic survey of the frequency of gross mutations in the LDLR gene in the Spanish population. The objective of our study was to investigate large rearrangements in the Spanish FH population and the relation between the kind of large rearrangement and the phenotype in carrier families. Material and methods The LDLR gene was screened to detect major rearrangements in a sample of 89 probands. Southern blot, long polymerase chain reaction (PCR), reverse transcription (RT) -PCR and DNA sequencing were used to detect and characterize the mutations. Results Five large rearrangements were found in six probands. Two mutations were due to duplications of internal regions of the gene, whereas the rest were caused by partial deletions, which eliminated the promoter region in two cases. The internal rearrangements, two duplications and one deletion, were apparently caused by recombination between ALU sequences and the study of their mRNA indicated that the reading frame was maintained. The analysis of the lipid profile between patients with similar characteristics (age, sex, body mass index, etc.) but carrying mutations that either eliminated the promoter region or produced internal rearrangements showed significant differences (total cholesterol: 366·6 ± 81·8 vs. 304·6 ± 25·1 P = 0·023, and LDL cholesterol: 317·7 ± 65·1 vs. 249·2 ± 27·4 P = 0·003). Conclusions The frequency of large mutations in a Spanish FH sample was close to 7% and at least four of the mutations found had not been described in other populations. Mutations that eliminate the promoter region originate more severe hypercholesterolemia than defective mutations, which suggests that the absence of the promoter region and transcription of the LDLR gene is worse compensated than the synthesis of a defective LDL receptor.

Aims To assess the relationship of the lipid profile to coronary heart disease in a group of heterozygous familial hypercholesterolaemic subjects with similar age, sex, body mass index, prevalence of angiotensin converting enzyme DD genotype and type of low density lipoprotein receptor mutation. Methods and Results A total of 66 molecularly defined heterozygous familial hypercholesterolaemic subjects, 33 of whom had coronary heart disease, were studied. Clinical features, cardiovascular risk factors and lipid parameters were compared in both groups. Familial hypercholesterolaemic patients with coronary heart disease showed significantly lower values of mean plasma HDL cholesterol and a higher total/HDL cholesterol ratio as compared with familial hypercholesterolaemic subjects free of coronary heart disease. Total and LDL cholesterol concentrations were higher in patients with coronary heart disease, without reaching statistical significance. No differences in plasma lipoprotein(a) levels on absolute and log-transformed values were observed between the two groups. In the whole familial hypercholesterolaemia group, plasma HDL cholesterol levels were related to plasma triglyceride values and to LDL receptor gene ‘null mutations’. Conclusions In familial hypercholesterolaemic subjects of similar age, gender, body mass index, systolic and diastolic blood pressure, and genetic factors that could influence coronary heart disease risk, plasma HDL cholesterol values and total/HDL cholesterol ratios are two important coronary risk factors. Hence, treatment of familial hypercholesterolaemia should focus not only on lowering total and LDL cholesterol levels, but also on increasing HDL cholesterol values for coronary heart disease prevention. More prospective and intervention trials should be conducted to establish the relationship of HDL cholesterol levels and coronary heart disease in familial hypercholesterolaemia.

Background Autosomal dominant hypercholesterolemias (ADHs) are characterised by increased plasma levels of total and LDL cholesterol, predisposing to premature atherosclerosis. ADHs comprise several diseases with undistinguishable phenotype, caused by mutations in different genes: LDLR, APOB and PCSK9. Genetic studies are usually performed in patients with altered cholesterol levels. However, some persons carrying pathogenic mutations are normocholesterolemic and there are no further studies about this subject. We have studied the frequency of families and individuals carrying ADH mutations who do not present the disease in Spanish population. Methods We have analysed genes known to cause ADH by direct sequencing in 24 ADH families (215 members). Functional effect of some LDLR gene mutations was assessed by transfecting cultured cells with plasmids. Results Six families with mutations presented 7 mutation carriers who did not show ADH phenotype: 30% of ADH families presented normocholesterolemic individuals, and 7% of carriers of pathogenic mutations did not show ADH phenotype. We have analysed the effect of some of these mutations and they are responsible for impaired LDL receptor function. We have excluded mutations in APOB and PCSK9 genes that could reduce LDLc levels. Conclusions An important percentage of ADH families presented individuals who do not show an ADH phenotype, but who are able to transmit the pathogenic mutation to their offspring. Genetic study of all subjects in ADH families should be performed in order to identify normocholesterolemic carriers that allow the detection of mutations in their descendants and the prevention of the disease consequences.

Eur J Clin Invest 2010; 40 (2): 89–94 Abstract Background Few data are available on circulating mononuclear cells nuclear factor-kappa B (NF-kB) activity and plasma xanthine oxidase (XO) activity in heterozygous familial hypercholesterolaemia (FH). The goal of the study was to analyse circulating mononuclear cells NF-kB and plasma XO activities in FH patients. Materials and methods Thirty FH index patients and 30 normoglycaemic normocholesterolaemic controls matched by age, gender, body mass index, abdominal circumference and homeostasis model assessment index were studied. Plasma XO and inflammatory markers were measured by standard methods. NF-kB was assayed in circulating mononuclear cells. Results Familial hypercholesterolaemia patients showed a significantly higher NF-kB (75·0 ± 20·7 vs. 42·7 ± 16·8 relative luminiscence units) and XO (0·44 ± 0·13 vs. 0·32 ± 0·09 mU mL–1) activities than controls. In addition, interleukin-1, interleukin-6, high sensitivity C reactive protein (hsCRP) and oxidized LDL (LDL-ox) were also significantly higher in FH patients. In the total group (FH and controls), XO was significantly associated with LDL-cholesterol (LDL-C), apolipoprotein B (apoB), NF-kB and hsCPR, and NF-kB activity was significantly associated with XO, hsCPR, LDL-ox, LDL-C and apoB plasma values. Using multiple regression analysis, XO was independently associated with hsCPR and NF-kB, and NF-kB activity in circulating mononuclear cells was independently associated with apoB and LDL-ox plasma values. Conclusion Familial hypercholesterolaemia patients show increased activities of NF-kB and XO, and higher values of low grade inflammatory markers related to atherosclerosis. NF-kB activity was independently associated with apoB plasma values. These data could explain in part the high cardiovascular disease risk present in these patients.

Autosomal dominant hypercholesterolemia (ADH) is a genetic disorder characterized by increased low-density lipoprotein (LDL)-cholesterol levels, leading to high risk of premature cardiovascular disease. More than 900 mutations in LDL receptor, six in APOB and 10 in PCSK9 have been identified as a cause of the disease in different populations. All known mutations in PCSK9 causing hypercholesterolemia produce an increase in the enzymatic activity of this protease. Up to now, there are data about the implication of PCSK9 in ADH in a low number of populations, not including a Spanish population.The objective of the study was to study the prevalence of PCSK9 mutations in ADH Spanish population.We screened PCSK9 gene in 42 independent ADH patients in whom mutations in LDL receptor and APOB genes had been excluded.None of the known mutations causing ADH was detected in our sample, but we found two variations in the promoter region that could cause ADH, c.-288GA and c.-332CA (each in one proband). The analysis of the effect of these two variations on the transcription activity of the PCSK9 promoter showed that c.-288GA did not modify the transcription, whereas c.-332CA variant caused a 2.5-fold increase when compared with the wild-type sequence, either with or without lovastatin.PCSK9 is a rare cause of ADH in Spanish population and, up to what we know, none of the previously described mutations has been detected. We have identified a new mutation that could cause ADH by increasing the transcription of PCSK9.