A genome-wide association study identifies UGT1A1 as a regulator of serum cell-free DNA in young adults: The Cardiovascular Risk in Young Finns Study

Introduction

Circulating cell-free DNA (cf-DNA) is a useful indicator of cell death, and it can also be used to predict outcomes in various clinical disorders. Several innate immune mechanisms are known to be involved in eliminating DNA and chromatin-related material as part of the inhibition of potentially harmful autoimmune responses. However, the exact molecular mechanism underlying the clearance of circulating cf-DNA is currently unclear.

Methods

To examine the mechanisms controlling serum levels of cf-DNA, we carried out a genome-wide association analysis (GWA) in a cohort of young adults (aged 24–39 years; n = 1841; 1018 women and 823 men) participating in the Cardiovascular Risk in Young Finns Study. Genotyping was performed with a custom-built Illumina Human 670 k BeadChip. The Quant-iT^TM high sensitivity DNA assay was used to measure cf-DNA directly from serum.

Results

The results revealed that 110 single nucleotide polymorphisms (SNPs) were associated with serum cf-DNA with genome-wide significance (p<5×10⁻⁸). All of these significant SNPs were localised to chromosome 2q37, near the UDP-glucuronosyltransferase 1 (UGT1) family locus, and the most significant SNPs localised within the UGT1 polypeptide A1 (UGT1A1) gene region.

Conclusion

The UGT1A1 enzyme catalyses the detoxification of several drugs and the turnover of many xenobiotic and endogenous compounds by glucuronidating its substrates. These data indicate that UGT1A1-associated processes are also involved in the regulation of serum cf-DNA concentrations.     

Seasonal movements and habitat use of river whitefish (Coregonus lavaretus) in the Koitajoki River (Finland), as determined by Carlin tagging and acoustic telemetry

In the Koitajoki River, Eastern Finland, there exists a self-sustaining population of river-spawning densely rakered whitefish (Coregonus lavaretus pallasi). The population has been classified as near-threatened due to overexploitation and possible hybridization with the lake-spawning sparsely rakered whitefish form. Thus, knowledge of habitat use, movements, and migrations is important for threat assessment and management decisions. We employed conventional tagging and acoustic telemetry to provide information on movements and home range of the Koitajoki River whitefish. We tagged mature individuals at their spawning areas and followed fish movements by tag recoveries and continuously recording fixed receiving stations. The maximum movement distances were 40–50?km both upstream and downstream from the releasing site. There were indications of a clear seasonal migration pattern and spawning-site fidelity; riverine habitats were mainly occupied for spawning and overwintering, while feeding and growth mainly took place in lacustrine environments within several lakes of the river system. Due to their migratory nature, whitefish is vulnerable to environmental disturbances and overfishing in a large geographic area.     

The effect of progesterone on the localization of progesterone receptors in the nuclei of chick oviduct cells

Summary The location of occupied and unoccupied progesterone receptors (PR) in chick oviduct cells was studied by immuno-electron microscopy with the use of a highly specific polyclonal anti-PR antibody and pre-embedding modifications of the peroxidase-anti-peroxidase-(PAP-) or immunogold-silver methods. Both methods revealed a nuclear localization of the PRs. The location of the PR in the nucleus was studied in detail by means of the immunogold-silver method. The most intense labelling for unoccupied PRs was in the condensed chromatin. After occupation of PRs with progesterone (P), decondensation or dispersion of chromatin was observed. At the same time, the labelling in the border area of condensed and dispersed chromatin, and in the dispersed chromatin, increased. The changes were statistically significant. The results can be explained by conformational changes of the PR-containing chromatin rather than by translocation of PRs from one site to another.     

Intermediate filament proteins and epithelial differentiation in the embryonic ovary of the rat

Abstract. The development and sexual differentiation of gonads in female rat embryos and fetuses between the ages of 11 and 17 days was studied by immunocytochemical analysis of intermediate filament proteins and laminin by light and electron microscopy. In the 11-day-old pregonadal embryo, the surface epithelial cells in the ventral cortex of the mesonephros contained desmin but not cytokeratin or vimentin. The development of the gonad began on the following day by proliferative growth of the mesonephric surface cells, which like the subepithelial cells soon expressed vimentin in addition to desmin. The differentiation continued by formation of separate epithelial cell clusters, which joined into cords, irregular in shape and size. Desmin disappeared from the cord cells and cytokeratins appeared while vimentin remained in all somatic cell types. Desmin was especially abundant in some stromal cells adjacent to the epithelial tissues. After the segration of the basic ovarian tissues, vimentin and desmin decreased and cytokeratins appeared in the surface epithelial cells. New changes in cytokeratin expression appeared with the differentiation of the embryonic cords in a sex-specific manner with gradual decrease of reactivity for cytokeratin 18. No immunoreaction to the neurofilament proteins was found at the present ages, and the germ cells were negative for intermediate filaments. The results show that desmin is expressed in several primitive ovarian and mesonephric cells even though they are not myogenic. The sexual differences emerge after the incipient formation of the genetically female gonad, as different organization of the internal epithelial tissue with different timing of changes in intermediate filament proteins when compared with the male gonad.     

Shading enhances the quality of willow leaves to leaf beetles – but does it matter?

Plant shading is commonly recognised as a factor, which increases susceptibility of plants to attack by herbivorous insects. In this study we experimentally investigated the effect of host plant shading on two willow-feeding leaf beetles, Galerucella lineola feeding upon Salix phylicifolia and Phratora vitellinae feeding upon Salix myrsinifolia . Both beetle species were more abundant on potted willows growing in open habitats than on the same clones placed under the shade of trees. However, in the laboratory the food preference by adults and larval performance showed that the shaded willows are actually better food for both beetle species. On the contrary, when larvae were reared in the field under natural abiotic conditions, we found no difference in larval performance, or if any, even better performance in open habitats. Apparently, higher and more variable daily temperatures in open habitats accelerated the growth of the larvae. When adults were let to emigrate from or immigrate to potted willows, which had been grown in the same conditions but placed either in the open or shady habitats, adults preferred exposed willows. Invertebrate predators were more abundant in open habitats, but we found no differences in leaf beetle mortality by natural enemies between the habitats. Although the larval performance appeared to be approximately equal in the two habitats during the unusually warm study period, we suggest that under suboptimal temperatures the better abiotic conditions of open sites can easily override the better food provided by shaded habitats. The selection of abiotic habitat thus plays a significant role in the adaptive habitat and host plant selection of these beetles within the gradient of shadiness.     

Phenotypic characterization of transgenic mice harboring Nf1+/- or Nf1-/- osteoclasts in otherwise Nf1+/+ background

Skeletal abnormalities in neurofibromatosis type 1 syndrome (NF1) are observed in ～50% of patients. Here, we describe the phenotype of Nf1_Ocl mouse model with Nf1‐deficient osteoclasts. Nf1_Ocl mice with Nf1^+/? or Nf1^?/? osteoclasts in otherwise Nf1^+/+ background were successfully generated by mating parental Nf1flox/flox and TRAP‐Cre mice. Contrary to our original hypothesis, osteoporotic or fragile bone phenotype was not observed. The µCT analysis revealed that tibial bone marrow cavity, trabecular tissue volume, and the perimeter of cortical bone were smaller in Nf1 mice compared to Nf1 control mice. Nf1 mice also a displayed narrowed growth plate in the proximal tibia. In vitro analysis showed increased bone resorption capacity and cytoskeletal changes including irregular cell shape and abnormal actin ring formation in Nf1^?/? osteoclasts. Surprisingly, the size of spleen in Nf1 mice was two times larger than in controls and histomorphometric analysis showed splenic megakaryocytosis. In summary, Nf1Ocl mouse model presented with a mild but specific bone phenotype. This study shows that NF1‐deficiency in osteoclasts may have a role in the development of NF1‐related skeletal abnormalities, but Nf1‐deficiency in osteoclasts in Nf1^+/+ background is not sufficient to induce skeletal abnormalities analogous to those observed in patients with NF1. J. Cell. Biochem. 113: 2136–2146, 2012. © 2012 Wiley Periodicals, Inc.     

Identifying subgroup markers in heterogeneous populations

Traditional methods that aim to identify biomarkers that distinguish between two groups, like Significance Analysis of Microarrays or the t-test, perform optimally when such biomarkers show homogeneous behavior within each group and differential behavior between the groups. However, in many applications, this is not the case. Instead, a subgroup of samples in one group shows differential behavior with respect to all other samples. To successfully detect markers showing such imbalanced patterns of differential signal, a different approach is required. We propose a novel method, specifically designed for the Detection of Imbalanced Differential Signal (DIDS). We use an artificial dataset and a human breast cancer dataset to measure its performance and compare it with three traditional methods and four approaches that take imbalanced signal into account. Supported by extensive experimental results, we show that DIDS outperforms all other approaches in terms of power and positive predictive value. In a mouse breast cancer dataset, DIDS is the only approach that detects a functionally validated marker of chemotherapy resistance. DIDS can be applied to any continuous value data, including gene expression data, and in any context where imbalanced differential signal is manifested.     

Secretion of active membrane type 1 matrix metalloproteinase (MMP-14) into extracellular space in microvesicular exosomes

Membrane type 1 matrix metalloproteinase (MT1-MMP, MMP14) is an efficient extracellular matrix (ECM) degrading enzyme that plays important roles in tissue homeostasis and cell invasion. Like a number of type I membrane proteins, MT1-MMP can be internalized from the cell surface through early and recycling endosomes to late endosomes, and recycled to the plasma membrane. Late endosomes participate in the biogenesis of small (30-100 nm) vesicles, exosomes, which redirect plasma membrane proteins for extracellular secretion. We hypothesized that some of the endosomal MT1-MMP could be directed to exosomes for extracellular release. Using cultured human fibrosarcoma (HT-1080) and melanoma (G361) cells we provide evidence that both the full-length 60 kDa and the proteolytically processed 43 kDa forms of MT1-MMP are secreted in exosomes. The isolated exosomes were identified by their vesicular structure in electron microscopy and by exosomal marker proteins CD9 and tumor susceptibility gene (TSG101). Furthermore, exosomes contained beta1-integrin (CD29). The exosomes were able to activate pro-MMP-2 and degrade type 1 collagen and gelatin, suggesting that the exosomal MT1-MMP was functionally active. The targeting of MT1-MMP in exosomes represents a novel mechanism for cancer cells to secrete membrane type metalloproteolytic activity into the extracellular space.