Accounting for linkage disequilibrium in genome scans for selection without individual genotypes: The local score approach

Detecting genomic footprints of selection is an important step in the understanding of evolution. Accounting for linkage disequilibrium in genome scans increases detection power, but haplotype‐based methods require individual genotypes and are not applicable on pool‐sequenced samples. We propose to take advantage of the local score approach to account for linkage disequilibrium in genome scans for selection, cumulating (possibly small) signals from single markers over a genomic segment, to clearly pinpoint a selection signal. Using computer simulations, we demonstrate that this approach detects selection with higher power than several state‐of‐the‐art single‐marker, windowing or haplotype‐based approaches. We illustrate this on two benchmark data sets including individual genotypes, for which we obtain similar results with the local score and one haplotype‐based approach. Finally, we apply the local score approach to Pool‐Seq data obtained from a divergent selection experiment on behaviour in quail and obtain precise and biologically coherent selection signals: while competing methods fail to highlight any clear selection signature, our method detects several regions involving genes known to act on social responsiveness or autistic traits. Although we focus here on the detection of positive selection from multiple population data, the local score approach is general and can be applied to other genome scans for selection or other genomewide analyses such as GWAS.     

The miR-15a-miR-16-1 cluster controls prostate cancer by targeting multiple oncogenic activities

MicroRNAs (miRNAs) are noncoding small RNAs that repress protein translation by targeting specific messenger RNAs. miR-15a and miR-16-1 act as putative tumor suppressors by targeting the oncogene BCL2. These miRNAs form a cluster at the chromosomal region 13q14, which is frequently deleted in cancer. Here, we report that the miR-15a and miR-16-1 cluster targets CCND1 (encoding cyclin D1) and WNT3A, which promotes several tumorigenic features such as survival, proliferation and invasion. In cancer cells of advanced prostate tumors, the miR-15a and miR-16 level is significantly decreased, whereas the expression of BCL2, CCND1 and WNT3A is inversely upregulated. Delivery of antagomirs specific for miR-15a and miR-16 to normal mouse prostate results in marked hyperplasia, and knockdown of miR-15a and miR-16 promotes survival, proliferation and invasiveness of untransformed prostate cells, which become tumorigenic in immunodeficient NOD-SCID mice. Conversely, reconstitution of miR-15a and miR-16-1 expression results in growth arrest, apoptosis and marked regression of prostate tumor xenografts. Altogether, we propose that miR-15a and miR-16 act as tumor suppressor genes in prostate cancer through the control of cell survival, proliferation and invasion. These findings have therapeutic implications and may be exploited for future treatment of prostate cancer.     

The meso-angioblast: a multipotent,self-renewing cell that originates from the dorsal aorta and differentiates into most mesodermal tissues

We have previously reported the origin of a class of skeletal myogenic cells from explants of dorsal aorta. This finding disagrees with the known origin of all skeletal muscle from somites and has therefore led us to investigate the in vivo origin of these cells and, moreover, whether their fate is restricted to skeletal muscle, as observed in vitro under the experimental conditions used. To address these issues, we grafted quail or mouse embryonic aorta into host chick embryos. Donor cells, initially incorporated into the host vessels, were later integrated into mesodermal tissues, including blood, cartilage, bone, smooth, skeletal and cardiac muscle. When expanded on a feeder layer of embryonic fibroblasts, the clonal progeny of a single cell from the mouse dorsal aorta acquired unlimited lifespan, expressed hemo-angioblastic markers (CD34, Flk1 and Kit) at both early and late passages, and maintained multipotency in culture or when transplanted into a chick embryo. We conclude that these newly identified vessel-associated stem cells, the meso-angioblasts, participate in postembryonic development of the mesoderm, and we speculate that postnatal mesodermal stem cells may be derived from a vascular developmental origin.     

Clustering formal concepts to discover biologically relevant knowledge from gene expression data

The production of high-throughput gene expression data has generated a crucial need for bioinformatics tools to generate biologically interesting hypotheses. Whereas many tools are available for extracting global patterns, less attention has been focused on local pattern discovery. We propose here an original way to discover knowledge from gene expression data by means of the so-called formal concepts which hold in derived Boolean gene expression datasets. We first encoded the over-expression properties of genes in human cells using human SAGE data. It has given rise to a Boolean matrix from which we extracted the complete collection of formal concepts, i.e., all the largest sets of over-expressed genes associated to a largest set of biological situations in which their over-expression is observed. Complete collections of such patterns tend to be huge. Since their interpretation is a time-consuming task, we propose a new method to rapidly visualize clusters of formal concepts. This designates a reasonable number of Quasi-Synexpression-Groups (QSGs) for further analysis. The interest of our approach is illustrated using human SAGE data and interpreting one of the extracted QSGs. The assessment of its biological relevancy leads to the formulation of both previously proposed and new biological hypotheses.     

Collagen fibril structure is affected by collagen concentration and decorin

Collagen fibrils were obtained in vitro by aggregation from acid-soluble type I collagen at different initial concentrations and with the addition of decorin core or intact decorin. All specimens were observed by scanning electron microscopy and atomic force microscopy. In line with the findings of other authors, lacking decorin, collagen fibrils undergo an extensive lateral association leading to the formation of a continuous three-dimensional network. The addition of intact decorin or decorin core was equally effective in preventing lateral fusion and restoring the normal fibril appearance. In addition, the fibril diameter was clearly dependent on the initial collagen concentration but not on the presence/absence of proteoglycans. An unusual fibril structure was observed as a result of a very low initial collagen concentration, leading to the formation of huge, irregular superfibrils apparently formed by the lateral coalescence of lesser fibrils, and with a distinctive coil-structured surface. Spots of incomplete fibrillogenesis were occasionally found, where all fibrils appeared made of individual, interwined subfibrils, confirming the presence of a hierarchical association mechanism.     

Transfection efficiency boost by designer multicomponent lipoplexes

Cationic liposome-DNA complexes (lipoplexes) have emerged as leading nonviral gene carriers in worldwide gene therapy clinical trials. Arriving at therapeutic dosages requires the full understanding of the mechanism of transfection. We investigated the correlation between structural evolution of multicomponent lipoplexes when interacting with cellular lipids, the extent of DNA release and the efficiency in transfecting mouse fibroblast (NIH 3T3), ovarian (CHO) and tumoral myofibroblast-like (A17) cell lines. We show, for the first time, that the transfection pattern increases monotonically with the number of lipid components and further demonstrate by means of synchrotron small angle X- ray scattering (SAXS) that structural changes of lipoplexes induced by cellular lipids correlate with the transfection efficiency. Specifically, inefficient lipoplexes either fused too rapidly upon interaction with anionic lipids or, alternatively, are found to be extremely resistant to solubilization. The most efficient lipoplex formulations exhibited an intermediate behaviour. The extent of DNA unbinding (measured by electrophoresis on agarose gel) correlates with structural evolution of the lipoplexes but DNA-release does not scale with the extent of transfection. The general meaning of our results is of broad interest in the field of non-viral gene delivery: rational adjusting of lipoplex composition to generate the proper interaction between lipoplexes and cellular lipids may be the most appropriate strategy in optimizing synthetic lipid transfection agents.     

Osteogenesis imperfecta mutations may probe vital functional domains (e.g. proteoglycan binding sites) of type 1 collagen fibrils

Osteogenesis imperfecta (OI) is a disease characterized by bone malformations caused by mutations in type 1 collagen. Since many of the 338 possible glycine mutations have not been observed in clinical practice, is this due to chance alone? Because only 83 mutations have been reported in 126 patients, we conclude that many mutations are absent from clinical data for non-random causes. Mutations affecting vital intermolecular interactions in the extracellular matrix (e.g. potential collagen binding sites for proteoglycans) may result in non-viable fetuses that do not progress to clinical status. Some mutations may be silent because they do not significantly affect normal function. The total number of clinically active mutations that will be observed may be far fewer than the potential 338 maximum. © 1997 John Wiley & Sons, Ltd.