Characterization of mouse Dactylaplasia mutations: a model for human ectrodactyly SHFM3

SHFM3 is a limb malformation characterized by the absence of central digits. It has been shown that this condition is associated with tandem duplications of about 500 kb at 10q24. The Dactylaplasia mice display equivalent limb defects and the two corresponding alleles (Dac 1j and Dac 2j ) map in the region syntenic with the duplications in SHFM3. Dac 1j was shown to be associated with an insertion of an unspecified ETn-like mouse endogenous transposon upstream of the Fbxw4 gene. Dac 2j was also thought to be an insertion or a small inversion in intron 5 of Fbxw4, but the breakpoints and the exact molecular lesion have not yet been characterized. Here we report precise mapping and characterization of these alleles. We failed to identify any copy number differences within the SHFM3 orthologous genomic locus between Dac mutant and wild-type littermates, showing that the Dactylaplasia alleles are not associated with duplications of the region, in contrast with the described human SHFM3 cases. We further show that both Dac 1j and Dac 2j are caused by insertions of MusD retroelements that share 98% sequence identity. The differences between the nature of the human and mouse genomic abnormalities argue against models proposed so far that either envisioned SHFM3 as a local trisomy or Dac as a mutant allele of Fbxw4. Instead, both genetic conditions might lead to complex alterations of gene regulation mechanisms that would impair limb morphogenesis. Interestingly, the Dac 2j mutation occurs within a highly conserved element that may represent a regulatory sequence for a neighboring gen

A systematic enhancer screen using lentivector transgenesis identifies conserved and non-conserved functional elements at the olig1 and olig2 locus

Finding sequences that control expression of genes is central to understanding genome function. Previous studies have used evolutionary conservation as an indicator of regulatory potential. Here, we present a method for the unbiased in vivo screen of putative enhancers in large DNA regions, using the mouse as a model. We cloned a library of 142 overlapping fragments from a 200 kb-long murine BAC in a lentiviral vector expressing LacZ from a minimal promoter, and used the resulting vectors to infect fertilized murine oocytes. LacZ staining of E11 embryos obtained by first using the vectors in pools and then testing individual candidates led to the identification of 3 enhancers, only one of which shows significant evolutionary conservation. In situ hybridization and 3C/4C experiments suggest that this enhancer, which is active in the neural tube and posterior diencephalon, influences the expression of the Olig1 and/or Olig2 genes. This work provides a new approach for the large-scale in vivo screening of transcriptional regulatory sequences, and further demonstrates that evolutionary conservation alone seems too limiting a criterion for the identification of enhancers

Multiple mechanisms disrupt the let-7 microRNA family in neuroblastoma

Poor prognosis in neuroblastoma is associated with genetic amplification of MYCN. MYCN is itself a target of let-7, a tumour suppressor family of microRNAs implicated in numerous cancers. LIN28B, an inhibitor of let-7 biogenesis, is overexpressed in neuroblastoma and has been reported to regulate MYCN. Here we show, however, that LIN28B is dispensable in MYCN-amplified neuroblastoma cell lines, despite de-repression of let-7. We further demonstrate that MYCN messenger RNA levels in amplified disease are exceptionally high and sufficient to sponge let-7, which reconciles the dispensability of LIN28B. We found that genetic loss of let-7 is common in neuroblastoma, inversely associated with MYCN amplification, and independently associated with poor outcomes, providing a rationale for chromosomal loss patterns in neuroblastoma. We propose that let-7 disruption by LIN28B, MYCN sponging, or genetic loss is a unifying mechanism of neuroblastoma development with broad implications for cancer pathogenesis.United States. National Institutes of Health (R01GM107536)Alex's Lemonade Stand FoundationHoward Hughes Medical InstituteBoston Children's Hospital. Manton Center for Orphan Disease ResearchNational Institute of General Medical Sciences (U.S.) (T32GM007753

Characterizing the cancer genome in lung adenocarcinoma

Somatic alterations in cellular DNA underlie almost all human cancers(1). The prospect of targeted therapies(2) and the development of high-resolution, genome-wide approaches(3-8) are now spurring systematic efforts to characterize cancer genomes. Here we report a large-scale project to characterize copy-number alterations in primary lung adenocarcinomas. By analysis of a large collection of tumours ( n = 371) using dense single nucleotide polymorphism arrays, we identify a total of 57 significantly recurrent events. We find that 26 of 39 autosomal chromosome arms show consistent large-scale copy-number gain or loss, of which only a handful have been linked to a specific gene. We also identify 31 recurrent focal events, including 24 amplifications and 7 homozygous deletions. Only six of these focal events are currently associated with known mutations in lung carcinomas. The most common event, amplification of chromosome 14q13.3, is found in similar to 12% of samples. On the basis of genomic and functional analyses, we identify NKX2-1 ( NK2 homeobox 1, also called TITF1), which lies in the minimal 14q13.3 amplification interval and encodes a lineage-specific transcription factor, as a novel candidate proto-oncogene involved in a significant fraction of lung adenocarcinomas. More generally, our results indicate that many of the genes that are involved in lung adenocarcinoma remain to be discovered.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/62944/1/nature06358.pd

Somatic mutations affect key pathways in lung adenocarcinoma

Determining the genetic basis of cancer requires comprehensive analyses of large collections of histopathologically well- classified primary tumours. Here we report the results of a collaborative study to discover somatic mutations in 188 human lung adenocarcinomas. DNA sequencing of 623 genes with known or potential relationships to cancer revealed more than 1,000 somatic mutations across the samples. Our analysis identified 26 genes that are mutated at significantly high frequencies and thus are probably involved in carcinogenesis. The frequently mutated genes include tyrosine kinases, among them the EGFR homologue ERBB4; multiple ephrin receptor genes, notably EPHA3; vascular endothelial growth factor receptor KDR; and NTRK genes. These data provide evidence of somatic mutations in primary lung adenocarcinoma for several tumour suppressor genes involved in other cancers - including NF1, APC, RB1 and ATM - and for sequence changes in PTPRD as well as the frequently deleted gene LRP1B. The observed mutational profiles correlate with clinical features, smoking status and DNA repair defects. These results are reinforced by data integration including single nucleotide polymorphism array and gene expression array. Our findings shed further light on several important signalling pathways involved in lung adenocarcinoma, and suggest new molecular targets for treatment.National Human Genome Research InstituteWe thank A. Lash, M.F. Zakowski, M.G. Kris and V. Rusch for intellectual contributions, and many members of the Baylor Human Genome Sequencing Center, the Broad Institute of Harvard and MIT, and the Genome Center at Washington University for support. This work was funded by grants from the National Human Genome Research Institute to E.S.L., R.A.G. and R.K.W.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/62885/1/nature07423.pd

Fondements d'une théorie democratique de la tolérance

Dans Ie monde moralement fragmente de la démocratie contemporaine, la tolérance réalise I'idéal d'un monde politique commun par-delà la différence, ou plut6t dans la différence. Ce monde commun rend possible Ie développement du dissensus et de la conflictualité idéologique. Qu'elle soit comprise comme acception a contrecoeur de la différence ou comme reconnaissance du droit de participer à I'élaboration , d'une culture politique commune, la tolérance accomplit I œuvre d'inclusion qui définit la démocratie authentique. Cet idéal d'inclusion est lie à I'exigence de justification propre aux démocraties libérales dans lesquels les citoyens participent a I'élaboration des normes publiques et a leur interprétation. La tolérance implique alors que toute régie d'exclusion qui ne pourrait pas être justifiée, en des termes acceptables, par la délibération publique, soit rejetée. C'est dans la théorie politique de John Rawls que se manifeste Ie plus clairement cet idéal.PARIS1-BU Pierre Mendès-France (751132102) / SudocSudocFranceF

Dynamique à retard dans un laser à cascade quantique émettant au moyen infra-rouge

International audienceLes lasers à cascade quantique sont des sources semiconductrices basées sur des transitions intersous-bandesau sein de la bande de conduction. Pouvant émettre sur une large plage de longueurs d’onde allantdu moyen infra-rouge au terahertz, ils sont devenus une source privilégiée pour des applications telles que laspectroscopie de gaz, les communications en espace libre ou les contre-mesures optiques [1]. Une analyse temporelledes fluctuations de la puissance optique émise a récemment révélé un comportement chaotique du laser à cascadequantique soumis à une force de rappel optique [3]. Cette étude expérimentale a mis en évidence un scénariode bifurcation impliquant une déstabilisation à la fréquence de cavité externe, puis un chaos sous la forme defluctuations basses fréquences. Ce scénario est typique des lasers à gaz de type classe A [4] mais n’avait jamaisété observé jusqu’alors dans un laser semiconducteur, où la première déstabilisation est basée sur la fréquence desoscillations de relaxation [5]. Ces observations expérimentales ont été validées par une étude numérique exploitantles équations de Lang et Kobayashi [5], en y incorporant les paramètres spécifiques du laser à cascade quantiqueétudié. Cependant, il est important de comprendre si ce scénario de bifurcation peut se reproduire sur d’autresstructures ou dans d’autres conditions expérimentales.L’objectif de ce travail est d’étudier numériquement la dynamique à retard du laser à cascade quantique en fonctionde trois paramètres clés : le courant de pompe, la longueur de la cavité externe et le facteur d’élargissement spectraldu laser (facteur α), intrinsèque à la structure. Les simulations obtenues montrent des déstabilisations proches decelle observée expérimentalement, avec l’apparition d’oscillations à la fréquence de cavité externe. Cependant, sil’on augmente le courant de pompe ou que l’on diminue la valeur du facteur α, la première bifurcation de Hopf, àlaquelle ces oscillations apparaissent, se produit à des taux de réinjection significativement plus élevés, et la zonechaotique tend à disparaître. De plus, si l’on augmente la longueur de cavité externe, la bulle de chaos apparaîtà de plus faibles taux de réinjection, bien que la première bifurcation de Hopf reste à des taux de réinjectionsimilaires, mais cette zone se réduit fortement, et finalement disparait.En conclusion, cette étude numérique montre que le scénario de déstabilisation caractérisée par des fluctuationsbasses fréquences est bien reproductible dans d’autres conditions expérimentales ou sur d’autres types de structuresà cascade quantique. Cependant, le taux de réinjection auquel a lieu la première bifurcation de Hopf ou l’étenduede la zone chaotique peuvent varier, et il est donc fondamental d’étudier chaque cas afin d’éviter une déstabilisationou émission chaotique parasite