A statistical methodology to select covariates in high-dimensional data under dependence. Application to the classification of genetic profiles in oncology.

We propose a new methodology for selecting and ranking covariates associated with a variable of interest in a context of high-dimensional data under dependence but few observations. The methodology successively intertwines the clustering of covariates, decorrelation of covariates using Factor Latent Analysis, selection using aggregation of adapted methods and finally ranking. A simulation study shows the interest of the decorrelation inside the different clusters of covariates. We first apply our method to transcriptomic data of 37 patients with advanced non-small-cell lung cancer who have received chemotherapy, to select the transcriptomic covariates that explain the survival outcome of the treatment. Secondly, we apply our method to 79 breast tumor samples to define patient profiles for a new metastatic biomarker and associated gene network in order to personalize the treatments.

Busulfan-mediated germ cell depletion does not alter gonad differentiation in the urodele amphibian Pleurodeles waltl.

It is not known in urodele amphibians whether germ cells (GCs) are indispensable for gonadal differentiation. In order to address this question in the newt Pleurodeles waltl, we first cloned the ortholog of VASA which is known as a GC marker in many species. Male (ZZ) and female (ZW) larvae were then exposed to the alkylating agent busulfan (25 µg/ml for 3 days) just after hatching (stage 36). In the main body of busulfan-treated larvae, PwVASA mRNA expression decreased before gonad differentiation in both sexes (at stage 50). This suggested GC depletion which was confirmed by histology, with a complete absence of GCs observed slightly earlier in females (stage 54) than in males (stage 54 + 60 days). In busulfan-treated ZW larvae, the presence of the typical central cavity and expression of a high level of aromatase mRNA confirmed the ovarian phenotype. In busulfan-treated ZZ larvae, the presence of a medulla surrounded by a thin cortex and a low level of aromatase mRNA confirmed the testis phenotype. At the juvenile stage, efferent ducts and lobules were present in the first testis lobe. Taken together, these data suggest that GC depletion does not alter gonad differentiation in P. waltl.

Sexual development of the urodele amphibian Pleurodeles waltl.

Pleurodeles waltl is a urodele amphibian that displays a ZZ/ZW genetic mode of sex determination involving a putative W-borne dominant determinant. This determining pathway can be environmentally inhibited since heat treated ZW larvae undergo a functional female to male sex reversal. Moreover, both genetic sexes can be reversed by treatment of larvae with steroid hormones suggesting they are the major players in the differentiation process. Indeed we demonstrated that i) aromatase expression and activity increase just before ovarian differentiation, ii) aromatase inhibitors induce a female to male sex reversal, iii) estrogens induce male to female sex reversal whereas the opposite is obtained with non-aromatizable androgens, iv) steroidogenic factor 1 and estrogen receptor alpha both display a female-enriched expression following the increase in aromatase activity. The role of endogenous hormones was investigated in a parabiosis model. Surprisingly, in ZW/ZZ associations, the ZW gonad could not differentiate suggesting that the ZZ parabiont produces an inhibiting factor, prior to ovarian differentiation. The role of AMH in this process is discussed, keeping in mind that Mullerian ducts are maintained in males. The development of antibodies and new molecular tools in the near future should help us to better understand the sexual development of this vertebrate.

Differential distribution of adipokines between serum and synovial fluid in patients with osteoarthritis. Contribution of joint tissues to their articular production.

OBJECTIVE: To analyze the distribution of leptin, adiponectin and resistin between paired serum and synovial fluid (SF) samples of patients with osteoarthritis (OA) and to determine the potential sources of these adipokines in the joint. The active free form of leptin was also examined by evaluating the level of the soluble leptin receptor (sOb-R). METHODS: Levels of adipokines and sOb-R were measured by a sandwich enzyme-linked immunosorbent assay in serum and SF collected from OA patients. The levels of adipokines were also determined in conditioned media from cultured joint tissues (synovium, infrapatellar fat pad, meniscus, osteophyte, cartilage and bone). RESULTS: The adipokines exhibited different patterns of distribution between the joint and the circulating compartment. Serum levels of resistin and adiponectin exceeded those in the paired SF. Conversely, leptin SF concentrations were similar or higher than those measured in serum counterparts. Leptin and adiponectin in SF may derive from each joint tissue examined, whereas resistin was not detected in conditioned media of cultured explants. Synovium and infrapatellar fat pad were the major sources of adipokines, but osteophytes released also large amounts of leptin. The sOb-R deficiency found in SF further increased the difference in the bioactive leptin levels between serum and SF. A gender-specific difference was observed with women exhibiting the highest level of free leptin in the joint. CONCLUSION: These data demonstrated that adipokines serum levels are not predictive values for SF determination. The joint cavity is a special space where each adipokine undergoes specific regulatory pathways, strengthening the hypothesis that adipokines may have local effects in the joint and may account for the high prevalence of OA in women.

Female-enriched and thermosensitive expression of steroidogenic factor-1 during gonadal differentiation in Pleurodeles waltl.

In the urodele amphibian Pleurodeles waltl, sex differentiation is genetically controlled, that is, ZZ male vs ZW female, but may be influenced by temperature, which induces a female-to-male sex reversal. We investigated whether steroidogenic factor 1 (SF-1) could be involved in Pleurodeles sex differentiation or in temperature-dependent sex reversal by cloning a Pleurodeles SF-1 cDNA and examining its developmental expression. The 468-amino-acid deduced protein is highly conserved in comparison with other species. In ZZ and ZW control larvae, SF-1 mRNA is detected at the first stage of the thermosensitive period (TSP) in the gonad-mesonephros-interrenal complex (GMI). By the end of TSP at stage 55, SF-1 is expressed in the gonad (Gd) and in the mesonephros-interrenal (MI) both in ZZ and ZW larvae. During this stage, a transient, ZW-specific increase of SF-1 transcription occurs not only in Gd but also in MI, this increase starting earlier in Gd than in MI. Therefore, in P. waltl, an SF-1 upregulation occurs after the onset of the ovarian-specific increase of aromatase mRNA expression. At the end of metamorphosis, the SF-1 transcription level in Gd and MI is nearly the same in both ZZ and ZW larvae. Besides, after long-term heat treatment leading to sex reversal, SF-1 mRNA upregulation is not observed in ZW larvae, in either Gd or MI. However, SF-1 expression is not decreased after a 48-h heat shock applied at the end of the TSP, suggesting that temperature has no inhibitory effect by itself in long-term heat treatment. Estradiol benzoate treatments show that, at the end of the TSP, SF-1 gene transcription could be controlled by the estrogen level. This is in accordance with the female-enriched SF-1 expression and the decreased SF-1 expression following long-term, sex-reversing heat treatment, which is known to decrease aromatase expression and activity. Thus, it is unlikely that SF-1 is directly involved in Pleurodeles temperature-dependent sex reversal.

[Is leptin the missing link between osteoarthritis and obesity?]. / La leptine est-elle le maillon manquant entre l'arthrose et l'obésité?

The contribution of leptin, as a possible link between osteoarthritis (OA) and obesity, was studied in cartilage and synovial fluid samples obtained from osteoarthritic patients. Its effect on cartilage was evaluated in rats after intraarticular injections of leptin. Leptin levels were measured in the synovial fluid samples by enzyme linked immunosorbent assay; leptin concentrations were correlated with the body mass index. Leptin was strongly expressed in osteophytes and OA cartilage, while, in normal cartilage, few chondrocytes produced leptin. The level of leptin expression was related to the grade of cartilage destruction and was in good relation with those of growth factors as IGF1 and TGFb. Studies in rats showed that intraarticular leptin injection stimulated anabolic functions of chondrocytes and induced the synthesis of leptin, IGF1 and TGFB in cartilage at both the chondrocytes and induced the synthesis of leptin, IGF1 and TGFB in cartilage at both the mRNA and protein levels. In conclusion, leptin may be a link between osteoarthritis and obesity, and may play a key role in cartilage metabolism. Leptin may contribute to the pathophysiology of OA.

Site specific changes in gene expression and cartilage metabolism during early experimental osteoarthritis.

OBJECTIVES: To characterize the molecular events underlying cartilage injury in the early phase of mono-iodoacetate-induced osteoarthritis (OA) in rats. METHODS: Experimental osteoarthritis was induced by intra-articular injection of 0.03mg mono-iodoacetate (MIA) in Wistar rats. Animals were killed 2, 5, 10, 15 and 20 days post-injection. Synovial tissue and standardized biopsies from different areas of knee cartilage were examined. Proteoglycan synthesis ((35)S incorporation) and gelatinase activities (zymography), semi-quantitative RT-PCR and immunohistochemistry for IL1beta, iNOS, COX2 and PPARgamma, were performed on these samples. RESULTS: Changes in proteoglycan synthesis and gelatinase activities were time and site-dependent. Proteoglycan synthesis inhibition was maximal by day 2 while the highest gelatinase activities were observed at day 5. Central part of patella and posterior plateaus and condyles, i.e. the weight-bearing cartilage areas, were the most affected. IL1beta and iNOS transcripts were induced early in cartilage at time of maximal proteoglycan synthesis inhibition, especially in weight-bearing areas. COX-2 was slightly up-regulated whereas PPARgamma gene expression remained unchanged. Gene expression profile in synovium paralleled that of cartilage, except for PPARgamma which was up-regulated at day 15 and 20. Immunostaining for IL1beta and iNOS showed that proteins were located in diseased cartilage areas at early stage of the experimental OA (day 2). At later time-points (day 20), IL1beta and iNOS were expressed in perilesional areas whereas immunostaining became below control level for COX-2 and PPARgamma. CONCLUSIONS: Time-dependent degradation of cartilage after injection of low dose of MIA (0.03mg) into rat knee joint can be related to early loss of proteoglycan anabolism, increased gelatinase activities and expression of IL1beta and downstream inflammatory genes. Increased susceptibility to MIA in weight-bearing areas of cartilage further indicate that MIA-induced experimental OA is a relevant model to study not only metabolical but also biomechanical aspects of human OA.

[Evolution and development of dopaminergic neurotransmitter systems in vertebrates]. / Evolution et développement des systèmes neuromodulateurs dopaminergiques chez les Vertébrés.

Dopamine is a widespread neurotransmitter which exerts numerous neuromodulatory actions in the vertebrate central nervous system. This pleiotropic activity relies on the organisation of dopamine-synthesizing neuronal pathways and on a multiplicity of specific membrane receptors. A comparative approach has been undertaken to gain clues on the genetic events which took place during evolution to devise the dopamine systems of modern vertebrates. The localisation and phenotype of dopamine-synthesizing neurones is determined by different gene networks in each of the dopaminergic nuclei. However, despite this amazing diversity, the overall organisation of the dopaminergic nuclei is strinkingly conserved in the main vertebrates groups. In sharp contrast, the number of dopamine receptors subtypes has been multiplied by two major steps of gene duplications during vertebrates evolution. The first one occurred in the lineage leading to agnathans, whereas the second was concomitant to the emergence of cartilaginous fish. Accordingly, three subtypes exist in D1 receptor class (D1A, D1B, D1C) in all the jawed vertebrates, with two exceptions: eutherian mammals where only two D1 subtypes are found (D1A, D1B) and archosaurs where a fourth subtype is present (D1D). Comparisons of the pharmacological and biochemical characteristics of the dopamine receptors in vertebrate groups revealed homologous features that define each of the receptor subtypes and that have been fixed after gene duplications. The comparison of the distribution of the D1 receptor transcripts in the brain of teleosts and mammals points to significant conserved or derived expression territories, revealing previously neglected aspects of dopamine physiology in vertebrates.

A large-scale study of Yap1p-dependent genes in normal aerobic and H2O2-stress conditions: the role of Yap1p in cell proliferation control in yeast.

Yeast genes regulated by the transcriptional activator Yap1p were screened by two independent methods: (i) use of a LacZ-fused gene library and (ii) high-density membrane hybridization. Changes in transcriptome profile were examined in the presence and in the absence of Yap1p, as well as under normal and H2O2-mediated stress conditions. Both approaches gave coherent results, leading to the identification of many genes that appear to be directly or indirectly regulated by Yap1p. Promoter sequence analysis of target genes revealed that this regulatory effect is not always dependent upon the presence of a Yap1p binding site. The results show that the regulatory role of Yap1p is not restricted to the activation of stress response but that this factor can act as a positive or a negative regulator, both under normal and oxidative stress conditions. Among the targets, a few genes participating in growth control cascades were detected. In particular, the RPI1 gene, a repressor of the ras-cAMP pathway, was found to be downregulated by Yap1p during the early phase of growth, but upregulated in the stationary phase or after oxidative stress.

Characterization of an AP-1-like transcription factor that mediates an oxidative stress response in Kluyveromyces lactis.

The KlYAP1 gene, encoding the transcription factor Yap1p from Kluyveromyces lactis, was cloned by functional complementation of the cadmium hypersensitivity phenotype of a Saccharomyces cerevisiae strain lacking functional YAP1 and YAP2 genes. The KlYAP1 gene product is 41% identical to Yap1p, the sequence similarity being centered on the bZip domain and extending into the C-terminal portion of both proteins. When expressed in S. cerevisiae, this gene efficiently complements some of the phenotypes associated with both yap1 and yap2 mutations and also mediates AP-1 response element-dependent transcriptional activation in response to H2O2. Gene disruption experiments in K. lactis indicated that the KlYAP1 gene is involved in both the oxidative and cadmium response pathways. We also demonstrate the existence in K. lactis of inducible protective stress responses to both peroxides and superoxides and investigate the role of the Klyap1p protein in these responses.