Skeletal Site-Related Variation in Human Trabecular Bone Transcriptome and Signaling

BACKGROUND: The skeletal site-specific influence of multiple genes on bone morphology is recognised, but the question as to how these influences may be exerted at the molecular and cellular level has not been explored. METHODOLOGY: To address this question, we have compared global gene expression profiles of human trabecular bone from two different skeletal sites that experience vastly different degrees of mechanical loading, namely biopsies from iliac crest and lumbar spinal lamina. PRINCIPAL FINDINGS: In the lumbar spine, compared to the iliac crest, the majority of the differentially expressed genes showed significantly increased levels of expression; 3406 transcripts were up- whilst 838 were down-regulated. Interestingly, all gene transcripts that have been recently demonstrated to be markers of osteocyte, as well as osteoblast and osteoclast-related genes, were markedly up-regulated in the spine. The transcriptome data is consistent with osteocyte numbers being almost identical at the two anatomical sites, but suggesting a relatively low osteocyte functional activity in the iliac crest. Similarly, osteoblast and osteoclast expression data suggested similar numbers of the cells, but presented with higher activity in the spine than iliac crest. This analysis has also led to the identification of expression of a number of transcripts, previously known and novel, which to our knowledge have never earlier been associated with bone growth and remodelling. CONCLUSIONS AND SIGNIFICANCE: This study provides molecular evidence explaining anatomical and micro-architectural site-related changes in bone cell function, which is predominantly attributable to alteration in cell transcriptional activity. A number of novel signaling molecules in critical pathways, which have been hitherto not known to be expressed in bone cells of mature vertebrates, were identified

Feature selection for microRNA prediction

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miRBoost: Boosting support vector machines for microRNA precursor classification

International audienceIdentification of microRNAs (miRNAs) is an important step toward understanding post-transcriptional gene regulation and miRNA-related pathology. Difficulties in identifying miRNAs through experimental techniques combined with the huge amount of data from new sequencing technologies have made in silico discrimination of bona fide miRNA precursors from non-miRNA hairpin-like structures an important topic in bioinformatics. Among various techniques developed for this classification problem, machine learning approaches have proved to be the most promising. However these approaches require the use of training data, which is problematic due to an imbalance in the number of miRNAs (positive data) and non-miRNAs (negative data), which leads to a degradation of their performance. In order to address this issue, we present an ensemble method that uses a boosting technique with support vector machine components to deal with imbalanced training data. Classification is performed following a feature selection on 187 novel and existing features. The algorithm, miRBoost, performed better in comparison with state-of-the-art methods on imbalanced human and cross-species data. It also showed the highest ability among the tested methods for discovering novel miRNA precursors. In addition, miRBoost was over 1400 times faster than the second most accurate tool tested and was significantly faster than most of the other tools. miRBoost thus provides a good compromise between prediction efficiency and execution time, making it highly suitable for use in genome-wide miRNA precursor prediction. The software miRBoost is available on our web server http://EvryRNA.ibisc.univ-evry.fr

Recognition and cleavage of related to ubiquitin 1 (Rub1) and Rub1-ubiquitin chains by components of the ubiquitin-proteasome system

Of all ubiquitin-like proteins, Rub1 (Nedd8 in mammals) is the closest kin of ubiquitin. We show via NMR that structurally, Rub1 and ubiquitin are fundamentally similar as well. Despite these profound similarities, the prevalence of Rub1/Nedd8 and of ubiquitin as modifiers of the proteome is starkly different, and their attachments to specific substrates perform different functions. Recently, some proteins, including p53, p73, EGFR, caspase-7, and Parkin, have been shown to be modified by both Rub1/Nedd8 and ubiquitin within cells. To understand whether and how it might be possible to distinguish among the same target protein modified by Rub1 or ubiquitin or both, we examined whether ubiquitin receptors can differentiate between Rub1 and ubiquitin. Surprisingly, Rub1 interacts with proteasome ubiquitin-shuttle proteins comparably to ubiquitin but binds more weakly to a proteasomal ubiquitin receptor Rpn10. We identified Rub1-ubiquitin heteromers in yeast and Nedd8-Ub heteromers in human cells. We validate that in human cells and in vitro, human Rub1 (Nedd8) forms chains with ubiquitin where it acts as a chain terminator. Interestingly, enzymatically assembled K48-linked Rub1-ubiquitin heterodimers are recognized by various proteasomal ubiquitin shuttles and receptors comparably to K48-linked ubiquitin homodimers. Furthermore, these heterologous chains are cleaved by COP9 signalosome or 26S proteasome. A derubylation function of the proteasome expands the repertoire of its enzymatic activities. In contrast, Rub1 conjugates may be somewhat resilient to the actions of other canonical deubiquitinating enzymes. Taken together, these findings suggest that once Rub1/Nedd8 is channeled into ubiquitin pathways, it is recognized essentially like ubiquitin

Protracted systemic changes in bone biology after segmented unloading in the rat

To investigate whether the decreased bone formation observed in most experimental situations of disuse was caused by an increased inhibition by the bone microenvironment of osteoblast (OB) proliferation, we studied the inhibiting power on ROS 17/2.8 proliferation of the bone marrow extracellular fluid (IPEF) in loaded and unloaded bones of rats submitted to two situations of partial disuse: tail suspension (TS) for 3 days to 2 weeks and around the knee tenectomy (KT) for 2-10 weeks. Histomorphometric parameters and osteoblast precursors dynamics were studied in parallel. Bone volume was lost in the unloaded bones, but not in loaded bones, in both experimental situations. Bone formation was low at early times (7-14 days) in TS rats. However, in KT at later times (4-10 weeks), the osteoblastic index of the unloaded tibia was increased. IPEF was not increased in the unloaded bones 3-7 days after TS. It was decreased later in the course of unloading (after 2 weeks of TS and 2-10 weeks after KT). This decrease was observed in the loaded bones as well. Unexpectedly, we also found that the number of FCFUs was decreased in both loaded and unloaded limbs in TS and KT, and that the yield of cells obtained in primary culture from tibial metaphysis was decreased in both tibiae from KT animals. These data show that an increased IPEF does not play a role in the early inhibition of bone formation responsible for the loss of bone after unloading in the TS model. Its later decrease could be permissive for the increased osteoblastic index observed in the KT model. They also show that, contrary to the usual assumptions, bone biology is changed all over the skeleton after partial unloading, even if the changes result in bone loss in the unloaded bones only. Thus, as yet, unidentified systemic factors probably superimpose on the local factors that control bone volume.Journal ArticleResearch Support, Non-U.S. Gov'tinfo:eu-repo/semantics/publishe

Effects of high-phosphorus and/or low-calcium diets on bone tissue in trained male rats

International audiencePURPOSE: The aim of the present study was to investigate if wheel running exercise could offset the detrimental influences of independent or combined high-phosphorus and low-calcium diets on bone tissue in rats. METHODS: Forty male dark Agouti rats were randomly assigned to eight groups of five animals. Four sedentary groups (SED) and four voluntary trained groups (TR) were fed over 6 wk of either a standard food or a modified diet, namely, high phosphorus (HP), low calcium (LCa), or high phosphorus combined with low calcium (HP/LCa). After sacrifice, blood samples were collected to determine parathyroid hormone, Ca(2+), and Pi levels. Both tibiae were removed for bone mass determination and extended histomorphometric analyses. RESULTS: In SED rats, all unbalanced diets induced a sizeable bone volume decrease, up to 56%. Interestingly, steady training partially compensates for this bone volume loss, regardless of the considered modified diets. At the cellular level, only independent LCa diet induced a 38% decrease in osteoblastic surface in both SED and TR rat groups, generating thereby a reduction in bone neosynthesis. In terms of osteoclastic surface, an increase in this parameter was evidenced only in HP diets (both HP and HP-LCa), implying heightened bone resorption. The major effects of unbalanced diets are mainly observed on bone tissue because serum parameters (parathyroid hormone, Ca(2+), and Pi levels) remained only slightly modified. CONCLUSIONS: Training induced a positive effect on unbalanced diet-altered bone tissue formation but remained inadequate to reach standard bone mass measured in SED rats fed with balanced food. Further, we suggest that the nature of the diet influences the balance between bone formation and resorption: LCa diet decreases bone formation, whereas HP and HP-LCa increase bone resorption