Genome-wide association study identifies _FUT8_ and _ESR2_ as co-regulators of a bi-antennary N-linked glycan A2 (GlcNAc~2~Man~3~GlcNAc~2~) in human plasma proteins

HPLC analysis of N-glycans quantified levels of the biantennary glycan (A2) in plasma proteins of 924 individuals. Subsequent genome-wide association study (GWAS) using 317,503 single nucleotide polymorphysms (SNP) identified two genetic loci influencing variation in A2: FUT 8 and ESR2. We demonstrate that human glycans are amenable to GWAS and their genetic regulation shows sex-specific effects with _FUT 8_ variants explaining 17.3% of the variance in pre-menopausal women, while _ESR2_ variants explained 6.0% of the variance in post-menopausal women

Contrasting effects of high-starch and high-sugar diets on ruminal function in cattle

The experiment reported in this research paper aimed to determine whether clinical and subclinical effects on cattle were similar if provided with isoenergetic and isonitrogenous challenge diets in which carbohydrate sources were predominantly starch or sugar. The study was a 3 × 3 Latin square using six adult Jersey cows with rumen cannulae, over 9 weeks. In the first 2 weeks of each 3 week experimental period cows were fed with a maintenance diet and, in the last week, each animal was assigned to one of three diets: a control diet (CON), being a continuation of the maintenance diet; a high starch (HSt) or a high sugar (HSu) diet. Reticuloruminal pH and motility were recorded throughout the study period. Blood and ruminal samples were taken on day-1 (TP-1), day-2 (TP-2) and day-7 (TP-7) of each challenge week. Four clinical variables were recorded daily: diarrhoea, inappetence, depression and ruminal tympany. The effects of treatment, hour of day and day after treatment on clinical parameters were analysed using linear mixed effects (LME) models. Although both challenge diets resulted in a decline in pH, an increase in the absolute pH residuals and an increase in the number of minutes per day under pH 5.8, systemic inflammation was only detected with the HSt diet. The challenge diets differentially modified amplitude and period of reticuloruminal contractions compared with CON diet and both were associated with an increased probability of diarrhoea. The HSu diet reduced the probability of an animal consuming its complete allocation. Because the challenge diets were derived from complex natural materials (barley and molasses respectively), it is not possible to assign all the differential effects to the difference in starch and sugar concentration: non-starch components of barley or non-sugar components of molasses might have contributed to some of the observations. In conclusion, substituting much of the starch with sugar caused no substantial reduction in the acidosis load, but inflammatory response was reduced while feed rejection was increased

Genome-Wide Identification of Early-Firing Human Replication Origins by Optical Replication Mapping [preprint]

The timing of DNA replication is largely regulated by the location and timing of replication origin firing. Therefore, much effort has been invested in identifying and analyzing human replication origins. However, the heterogeneous nature of eukaryotic replication kinetics and the low efficiency of individual origins in metazoans has made mapping the location and timing of replication initiation in human cells difficult. We have mapped early-firing origins in HeLa cells using Optical Replication Mapping, a high-throughput single-molecule approach based on Bionano Genomics genomic mapping technology. The single-molecule nature and 290-fold coverage of our dataset allowed us to identify origins that fire with as little as 1% efficiency. We find sites of human replication initiation in early S phase are not confined to well-defined efficient replication origins, but are instead distributed across broad initiation zones consisting of many inefficient origins. These early-firing initiation zones co-localize with initiation zones inferred from Okazaki-fragment-mapping analysis and are enriched in ORC1 binding sites. Although most early-firing origins fire in early-replication regions of the genome, a significant number fire in late-replicating regions, suggesting that the major difference between origins in early and late replicating regions is their probability of firing in early S-phase, as opposed to qualitative differences in their firing-time distributions. This observation is consistent with stochastic models of origin timing regulation, which explain the regulation of replication timing in yeast

Uncovering Networks from Genome-Wide Association Studies via Circular Genomic Permutation

Genome-wide association studies (GWAS) aim to detect single nucleotide polymorphisms (SNP) associated with trait variation. However, due to the large number of tests, standard analysis techniques impose highly stringent significance thresholds, leaving potentially associated SNPs undetected, and much of the trait genetic variation unexplained. Pathway- and network-based methodologies applied to GWAS aim to detect associations missed by standard single-marker approaches. The complex and non-random architecture of the genome makes it a challenge to derive an appropriate testing framework for such methodologies. We developed a rapid and simple permutation approach that uses GWAS SNP association results to establish the significance of pathway associations while accounting for the linkage disequilibrium structure of SNPs and the clustering of functionally related elements in the genome. All SNPs used in the GWAS are placed in a “circular genome” according to their location. Then the complete set of SNP association P values are permuted by rotation with respect to the genomic locations of the SNPs. Once these “simulated” P values are assigned, the joint gene P values are calculated using Fisher’s combination test, and the association of pathways is tested using the hypergeometric test. The circular genomic permutation approach was applied to a human genome-wide association dataset. The data consists of 719 individuals from the ORCADES study genotyped for ∼300,000 SNPs and measured for 51 traits ranging from physical to biochemical measurements. KEGG pathways (n = 225) were used as the sets of pathways to be tested. Our results demonstrate that the circular genomic permutations provide robust association P values. The non-permuted hypergeometric analysis generates ∼1400 pathway-trait combination results with an association P value more significant than P ≤ 0.05, whereas applying circular genomic permutation reduces the number of significant results to a more credible 40% of that value. The circular permutation software (“genomicper”) is available as an R package at http://cran.r-project.org/

Extracardiac septum transversum/proepicardial endothelial cells pattern embryonic coronary arterio–venous connections

Recent reports suggest that mammalian embryonic coronary endothelium (CoE) originates from the sinus venosus and ventricular endocardium. However, the contribution of extracardiac cells to CoE is thought to be minor and nonsignificant for coronary formation. Using classic (Wt1(Cre)) and previously undescribed (G2-Gata4(Cre)) transgenic mouse models for the study of coronary vascular development, we show that extracardiac septum transversum/proepicardium (ST/PE)-derived endothelial cells are required for the formation of ventricular coronary arterio-venous vascular connections. Our results indicate that at least 20% of embryonic coronary arterial and capillary endothelial cells derive from the ST/PE compartment. Moreover, we show that conditional deletion of the ST/PE lineage-specific Wilms' tumor suppressor gene (Wt1) in the ST/PE of G2-Gata4(Cre) mice and in the endothelium of Tie2(Cre) mice disrupts embryonic coronary transmural patterning, leading to embryonic death. Taken together, our results demonstrate that ST/PE-derived endothelial cells contribute significantly to and are required for proper coronary vascular morphogenesi

WT1 expression in breast cancer disrupts the epithelial/mesenchymal balance of tumour cells and correlates with the metabolic response to docetaxel

WT1 is a transcription factor which regulates the epithelial-mesenchymal balance during embryonic development and, if mutated, can lead to the formation of Wilms' tumour, the most common paediatric kidney cancer. Its expression has also been reported in several adult tumour types, including breast cancer, and usually correlates with poor outcome. However, published data is inconsistent and the role of WT1 in this malignancy remains unclear. Here we provide a complete study of WT1 expression across different breast cancer subtypes as well as isoform specific expression analysis. Using in vitro cell lines, clinical samples and publicly available gene expression datasets, we demonstrate that WT1 plays a role in regulating the epithelial-mesenchymal balance of breast cancer cells and that WT1-expressing tumours are mainly associated with a mesenchymal phenotype. WT1 gene expression also correlates with CYP3A4 levels and is associated with poorer response to taxane treatment. Our work is the first to demonstrate that the known association between WT1 expression in breast cancer and poor prognosis is potentially due to cancer-related epithelial-to-mesenchymal transition (EMT) and poor chemotherapy response

Genetic Comparison of a Croatian Isolate and CEPH European Founders

Human isolates have been postulated as a good resource for the identification of QTL due to reduced genetic diversity and a more homogeneous environment. Isolates may also have increased linkage disequilibrium (LD) due to small effective population size and, either loss or increase in frequency of alleles that are rare in the general population from which they originate. Here we investigate the difference in allele and genotype frequencies, LD and homozygous tracts between an isolate—several villages from the island of Vis in Croatia—and an outbred population of European origin: the Hapmap CEPH founders. Using the HumanHap300 v1 Genotyping BeadChip, we show that our population does not differ greatly from the reference CEU outbred population despite having a slightly higher proportion of monomorphic loci, a slightly higher long-range LD, and a greater proportion of individuals with long homozygous tracts. We conclude that genotyping arrays should perform equally well in our isolate as in outbred European populations for disease mapping studies and that SNP–trait associations discovered in our well-characterized Croatian isolate should be valid in the general European population from which they descend. Genet. Epidemiol. 34: 140–145, 2010. © 2009 Wiley-Liss, Inc