CYR61 and alphaVbeta5 integrin cooperate to promote invasion and metastasis of tumors growing in preirradiated stroma.

Radiotherapy is widely used to treat human cancer. Patients locally recurring after radiotherapy, however, have increased risk of metastatic progression and poor prognosis. The clinical management of postradiation recurrences remains an unresolved issue. Tumors growing in preirradiated tissues have an increased fraction of hypoxic cells and are more metastatic, a condition known as tumor bed effect. The transcription factor hypoxia inducible factor (HIF)-1 promotes invasion and metastasis of hypoxic tumors, but its role in the tumor bed effect has not been reported. Here, we show that tumor cells derived from SCCVII and HCT116 tumors growing in a preirradiated bed, or selected in vitro through repeated cycles of severe hypoxia, retain invasive and metastatic capacities when returned to normoxia. HIF activity, although facilitating metastatic spreading of tumors growing in a preirradiated bed, is not essential. Through gene expression profiling and gain- and loss-of-function experiments, we identified the matricellular protein CYR61 and alphaVbeta5 integrin as proteins cooperating to mediate these effects. The anti-alphaV integrin monoclonal antibody 17E6 and the small molecular alphaVbeta3/alphaVbeta5 integrin inhibitor EMD121974 suppressed invasion and metastasis induced by CYR61 and attenuated metastasis of tumors growing within a preirradiated field. These results represent a conceptual advance to the understanding of the tumor bed effect and identify CYR61 and alphaVbeta5 integrin as proteins that cooperate to mediate metastasis. They also identify alphaV integrin inhibition as a potential therapeutic approach for preventing metastasis in patients at risk for postradiation recurrences.

Using environmental niche modeling to understand biological invasions in a changing world

L'activité humaine affecte particulièrement la biodiversité, qui décline à une vitesse préoccupante. Parmi les facteurs réduisant la biodiversité, on trouve les espèces envahissantes. Symptomatiques d'un monde globalisé où l'échange se fait à l'échelle de la planète, certaines espèces, animales ou végétales, sont introduites, volontairement ou accidentellement par l'activité humaine (par exemple lors des échanges commerciaux ou par les voyageurs). Ainsi, ces espèces atteignent des régions qu'elles n'auraient jamais pu coloniser naturellement. Une fois introduites, l'absence de compétiteur peut les rendre particulièrement nuisibles. Ces nuisances sont plus ou moins directes, allant de problèmes sanitaires (p. ex. les piqûres très aigües des fourmis de feu, originaires d'Amérique du Sud et colonisant à une vitesse fulgurante les USA, l'Australie ou la Chine) à des nuisances sur la biodiversité (p. ex. les ravages de la perche du Nil sur la diversité unique des poissons Cichlidés du Lac Victoria). Il est donc important de pouvoir prévenir de telles introductions. De plus, pour le biologiste, ces espèces représentent une rare occasion de pouvoir comprendre les mécanismes évolutifs et écologiques qui expliquent le succès des envahissantes dans un monde où les équilibres sont bouleversés. Les modèles de niche environnementale sont un outil particulièrement utile dans le cadre de cette problématique. En reliant des observations d'espèces aux conditions environnementales où elles se trouvent, ils peuvent prédire la distribution potentielle des envahissantes, permettant d'anticiper et de mieux limiter leur impact. Toutefois, ils reposent sur des hypothèses pas évidentes à démontrer. L'une d'entre elle étant que la niche d'une espèce reste constante dans le temps, et dans l'espace. Le premier objectif de mon travail est de comparer si la niche d'une espèce envahissante diffère entre sa distribution d'origine native et celle d'origine introduite. En étudiant 50 espèces de plantes et 168 espèces de Mammifères, je démontre que c'est le cas et que par corolaire, il est possible de prédire leurs distributions. La deuxième partie de mon travail consiste à comprendre quelles seront les interactions entre le changement climatiques et les envahissantes, afin d'estimer leur impact sous un climat réchauffé. En étudiant la distribution de 49 espèces de plantes envahissantes, je démontre que les montagnes, régions relativement préservée par ce problème, deviendront bien plus exposées aux risques d'invasions biologiques. J'expose aussi comment les interactions entre l'activité humaine, le réchauffement climatique et les espèces envahissantes menacent la vigne sauvage en Europe et propose des zones géographiques particulièrement adaptée pour sa conservation. Enfin, à une échelle beaucoup plus locale, je montre qu'il est possible d'utiliser ces modèles de niches le long d'une rivière à une échelle extrêmement fine (1 mètre), potentiellement utile pour rationnaliser des mesures de conservations sur le terrain. - Biodiversity is significantly negatively affected by human activity. Invasive species are one of the most important factors causing biodiversity's decline. Intimately linked to the era of global trade, some plant or animal species can be accidentally or casually introduced with human activity (e.g. trade or travel). In this way, these species reach areas they could never reach through natural dispersal. Once naturalized, the lack of competitors can make these species highly noxious. Their effect is more or less direct, from sanitary problems (e.g. the harmful sting of Fire Ants, originating from South America and now spreading throughout USA, China and Australia) or can affect biodiversity (e.g. the Nile perch, devastating the one of the richest hotspot of Cichlid fishes diversity in Lake Victoria). It is thus important to prevent such harmful introductions. Moreover, invasive species represent for biologists one of the rare occasions to understand the evolutionary and ecological mechanisms behind the success of invaders in a world where natural equilibrium is already disturbed. Environmental niche models are particularly useful to tackle this problematic. By relating species observation to the environmental conditions where they occur, they can predict the potential distribution of invasive species, allowing a better anticipation and thus limiting their impact. However, they rely on strong assumption, one of the most important being that the modeled niche remains constant through space and time. The first aim of my thesis is to quantify the difference between the native and the invaded niche. By investigating 50 plant and 168 mammal species, I show that the niche is at least partially conserved, supporting for reliable predictions of invasive' s potential distributions. The second aim of my thesis is to understand the possible interactions between climate change and invasive species, such as to assess their impact under a warmer climate. By studying 49 invasive plant species, I show that mountain areas, which were relatively preserved, will become more suitable for biological invasions. Additionally, I show how interactions between human activity, global warming and invasive species are threatening the wild grapevine in Europe and propose geographical areas particularly adapted for conservation measures. Finally, at a much finer scale where conservation plannings ultimately take place, I show that it is possible to model the niche at very high resolution (1 meter) in an alluvial area allowing better prioritizations for conservation.

Value of PET/CT versus contrast-enhanced CT in identifying chest wall invasion (T3) by NSCLC [B-671]

Purpose: To determine the diagnostic value of 18F-FDG PET/CT versus contrastenhanced CT in identifying chest wall invasion by NSCLC. Methods and Materials: The primary selection criterion was a peripheral tumor of any size with contact to the chest wall. A total of 25 patients with pathologically proven NSCLC satisfied these criteria. Chest wall invasion was interpreted upon PET/CT when a frank costal or intercostal 18F-FDG uptake was identified with or without concomitant morphologic alterations. On the other hand, the existence of periosteal rib reaction/erosion, chest wall thickening or obliteration of the pleural fat layer either separately or combined were considered essential diagnostic criteria for disease extension into the chest wall upon contrast-enhanced CT. The results were correlated with the final histological analysis. Results: Among the studied cohort, 13/25 (52%) patients had chest wall invasion consistent with T3 disease. Both PET/CT and contrast-enhanced CT successfully identified 12/13 (92%) of these patients. The single false-negative result was due to parietal pleural invasion. On the other hand, one false-positive result was encountered by PET/CT in a dyspneic patient; whereas, CT analysis revealed false-positive results in six patients. In these patients, periosteal rib reaction (n = 2) or asymmetric enlargement of adjacent chest wall muscles (n = 1) were identified along with an obliterated pleural fat layer (n = 6). The sensitivity, specificity, and accuracy of PET/CT and contrast-enhanced CT were 92, 91 and 92% versus 92, 50 and 72%. Conclusion: 18F-FDG PET/CT is an accurate diagnostic modality in identifying.

gcodeml: A Grid-enabled Tool for Detecting Positive Selection in Biological Evolution

One of the important questions in biological evolution is to know if certain changes along protein coding genes have contributed to the adaptation of species. This problem is known to be biologically complex and computationally very expensive. It, therefore, requires efficient Grid or cluster solutions to overcome the computational challenge. We have developed a Grid-enabled tool (gcodeml) that relies on the PAML (codeml) package to help analyse large phylogenetic datasets on both Grids and computational clusters. Although we report on results for gcodeml, our approach is applicable and customisable to related problems in biology or other scientific domains.

Contrasting spatio-temporal climatic niche dynamics during the eastern and western invasions of spotted knapweed in North America

Aim The spotted knapweed (Centaurea stoebe), a plant native to south-east and central Europe, is highly invasive in North America. We investigated the spatio-temporal climatic niche dynamics of the spotted knapweed in North America along two putative eastern and western invasion routes. We then considered the patterns observed in the light of historical, ecological and evolutionary factors. Location Europe and North America. Methods The niche characteristics of the east and west invasive populations of spotted knapweed in North America were determined from documented occurrences over 120 consecutive years (1890-2010). The 2.5 and 97.5 percentiles of values along temperature and precipitation gradients, as given by the two first axes of a principal component axis (PCA), were then calculated. We additionally measured the climatic dissimilarity between invaded and native niches using a multivariate environmental similarity surface (MESS) analysis. Results Along both invasion routes, the species established in regions with climatic conditions that were similar to those in the native range in Europe. An initial spread in ruderal habitats always preceded spread in (semi-)natural habitats. In the east, the niche gradually increased over time until it reached limits similar to the native niche. Conversely, in the west the niche abruptly expanded after an extended time lag into climates not occupied in the native range; only the native cold niche limit was conserved. Main conclusions Our study reveals that different niche dynamics have taken place during the eastern and western invasions. This pattern indicates different combinations of historical, ecological and evolutionary factors in the two ranges. We hypothesize that the lack of a well-developed transportation network in the west at the time of the introduction of spotted knapweed confined the species to a geographically and climatically isolated region. The invasion of dry rangelands may have been favoured during the agricultural transition in the 1930s by release from natural enemies, local adaptation and less competitive vegetation, but further experimental and molecular studies are needed to explain these contrasting niche patterns fully. Our study illustrates the need and benefit of applying large-scale, temporally explicit approaches to understanding biological invasions.

Host-parasite relationships during a biologic invasion: 75 years postinvasion, cane toads and sympatric Australian frogs retain separate lungworm faunas.

Invasive species may carry with them parasites from their native range, differing from parasite taxa found in the invaded range. Host switching by parasites (either from the invader to native fauna or from native fauna to the invader) may have important consequences for the viability of either type of host (e.g., their survivorship, fecundity, dispersal ability, or geographic distribution). Rhabdias pseudosphaerocephala (Nematoda) is a common parasite of cane toads (Rhinella marina) in the toad's native range (South and Central America) and also in its introduced Australian range. This lungworm can depress host viability and is capable of infecting Australian frogs in laboratory trials. Despite syntopy between toads and frogs for up to 75 yr, our analyses, based on DNA sequence data of lungworms from 80 frogs and 56 toads, collected from 2008 to 2011, did not reveal any cases of host switching in nature: toads and native frogs retain entirely different lungworm faunas. All lungworms in cane toads were the South and Central American species Rhabdias pseudosphaerocephala, whereas Australian frogs contained at least four taxa (mostly undescribed and currently lumped under the name Rhabdias cf. hylae). General patterns of prevalence and intensity, based on the dissection of 1,315 frogs collected between 1989 and 2011 across the toads' Australian range, show that these Australian endemic Rhabdias spp. are widely distributed geographically and across host taxa but are more common in some frog species (especially, large-bodied species) than they are in others.

Sequencing and characterizing the genome of Estrella lausannensis as an undergraduate project: training students and biological insights.

With the widespread availability of high-throughput sequencing technologies, sequencing projects have become pervasive in the molecular life sciences. The huge bulk of data generated daily must be analyzed further by biologists with skills in bioinformatics and by "embedded bioinformaticians," i.e., bioinformaticians integrated in wet lab research groups. Thus, students interested in molecular life sciences must be trained in the main steps of genomics: sequencing, assembly, annotation and analysis. To reach that goal, a practical course has been set up for master students at the University of Lausanne: the "Sequence a genome" class. At the beginning of the academic year, a few bacterial species whose genome is unknown are provided to the students, who sequence and assemble the genome(s) and perform manual annotation. Here, we report the progress of the first class from September 2010 to June 2011 and the results obtained by seven master students who specifically assembled and annotated the genome of Estrella lausannensis, an obligate intracellular bacterium related to Chlamydia. The draft genome of Estrella is composed of 29 scaffolds encompassing 2,819,825 bp that encode for 2233 putative proteins. Estrella also possesses a 9136 bp plasmid that encodes for 14 genes, among which we found an integrase and a toxin/antitoxin module. Like all other members of the Chlamydiales order, Estrella possesses a highly conserved type III secretion system, considered as a key virulence factor. The annotation of the Estrella genome also allowed the characterization of the metabolic abilities of this strictly intracellular bacterium. Altogether, the students provided the scientific community with the Estrella genome sequence and a preliminary understanding of the biology of this recently-discovered bacterial genus, while learning to use cutting-edge technologies for sequencing and to perform bioinformatics analyses.

TACI, an enigmatic BAFF/APRIL receptor, with new unappreciated biochemical and biological properties.

BAFF is a B cell survival factor that binds to three receptors BAFF-R, TACI and BCMA. BAFF-R is the receptor triggering naïve B cell survival and maturation while BCMA supports the survival of plasma cells in the bone marrow. Excessive BAFF production leads to autoimmunity, presumably as the consequence of inappropriate survival of self-reactive B cells. The function of TACI has been more elusive with TACI(-/-) mice revealing two sides of this receptor, a positive one driving T cell-independent immune responses and a negative one down-regulating B cell activation and expansion. Recent work has revealed that the regulation of TACI expression is intimately linked to the activation of innate receptors on B cells and that TACI signalling in response to multimeric BAFF and APRIL provides positive signals to plasmablasts. How TACI negatively regulates B cells remains elusive but may involve an indirect control of BAFF levels. The discovery of TACI mutations associated with common variable immunodeficiency (CVID) in humans not only reinforces its important role for humoral responses but also suggests a more complex role than first anticipated from knockout animals. TACI is emerging as an unusual TNF receptor-like molecule with a sophisticated mode of action.

Allergo-immunologie. 2. Faut-il se méfier des agents biologiques [Allergy-immunology. Do we have to be afraid of biological agents?].

Biologicals are now fully part of our daily therapeutic strategies. However, even if their high specificity seems to induce less risk compared to older or classical immunosuppressive drugs, there are not harmless especially regarding infectious but also immunological and allergic issues. Recent attempts to better characterize the different types of reactions to biologicals should be reported, allowing us better understanding of the risk to maintain these therapies or defining how to improve the methods to use them.

Synthesis and Biological Evaluation of S-Neofucopeptides as E- and P-Selectin Inhibitors.

The synthesis of /-L-fucosylated cysteamine, 3-thiopropionic acid, and 3-thioacetic acid derivatives as building blocks for the preparation of S-neofucopeptides is shown. These compounds were used in the synthesis of new thiofucosides derivatives (8, 9, 9, 10, 22, 22, 24, 26) that show affinity towards E- and P-selectins. They constitute a new series of hydrolytically stable and low-molecular-weight mimetics of the natural SLex tetrasaccharide.

MRI newsletter 8: Georeferenced biological databases - A tool for understanding mountain biodiversity

The Mountain Research Initiative invited Dr Eva Spehn, Director of the Global Mountain Biodiversity Assessment (GMBA), and Dr Antoine Guisan, head of the Spatial Ecology Group at the University of Lausanne, to introduce the reader to their coordinated efforts to advance understanding and prediction of mountain biodiversity. Antoine Guisan's EUROMONT project is one of the many scientific projects that may potentially provide data for the new GMBA initiative for a GIS mountain biodiversity database.

Characterization of N-cadherin association to lipid rafts in melanoma

RESUME La peau est un organe complex composé de deux parties distinctes: l'épiderme et le derme, séparé par une membrane basale. Dans la couche basale de l'épiderme, les melanocytes synthétisent la mélanine dans des mélanosomes. Les mélanosomes sont ensuite transportés des mélanocytes vers les kératinocytes, protégeant ainsi la peau des dégâts dus aux radiations U.V. La E-cadhérine assure l'adhésion entre les mélanocytes et les kératinocytes. Au cours de la transformation du mélanocyte en cellule malignes, les mélanocytes perdent l'expression de la E-cadhérine et, simultanément, se mettent à exprimer la N-cadhérine, ce phénomène est nommé « cadherin switch ». La perte de l'expression de la E-cadhérine permet au mélanocytes d'échapper au contrôle des kératinocytes, tandis que l'expression de la N-cadhérine promeut l'invasion métastasique des cellules de mélanome. Préalablement, nous avons trouvé qu'une fraction de la N-cadhérine était localisée les microdomaines membranaires spécialisés, enrichi en cholestérol et en glycosphingolipides, appelés « lipid rafts ». Une des particularité des « lipid rafts » est qu'ils sont riches en molécules permettant la transmission de signaux d'activation. De plus, des travaux récents rapportent qu'un sous-type de « lipid rafts » appelé caveolae pourrai contribuer à la progression tumorale. S'appuyant sur le rôle prépondérant de la N-cadhérine dans la progression du mélanome ainsi que sur sa présence dans les « lipid rafts », nous avons émis l'hypothèse que l'association de la N-cadhérine avec les « lipid rafts » pourrai contribuer à la progression du mélanome. Le but de ce projet à été de caractériser l'association de la Ncadhérine avec les « lipid rafts » au cours de la progression du mélanome. Au moyen de lignées cellulaires humaines, dérivées de mélanomes à différents stades de progression, nous avons trouvé que (1) la N-cadhérine est partiellement associée aux «lipid rafts » dans six lignées dérivées de mélanome en phase avancée de progression et dans des tumeurs expérimentales, mais pas dans deux lignées dérivées de mélanome à un stade plus précoce ; (2) l'association de la N-cadhérine dans les « lipid rafts » ne dépent pas de son niveau d'expression ; (3) la E-cadhérine n'est pas présente dans les « lipid rafts »d'une lignée de cellule de mélanome ayant conservé l'expression de la E-cadhérine ; (4) la localisation de la N-cadhérine dans les « lipid rafts »n'est pas modulée par les facteurs de croissance bFGF, IGF-I, et HRG1-β1, ni par des voies de signalisation impliquant MEK, PKA, les kinases de la famille Src, et PI3K ; (5) l'association de la N-cadhérine avec les « lipid rafts » n'est pas requise pour la stabilisation des jonctions adhérentes et n'est pas perturbée par la destruction de ces dernières ; (6) la N-cadhérine dans les « lipid rafts » forme un complexe avec β-caténine, p 120ctn et α-caténine. En conclusion, cette étude originale montre pour la première fois que dans des cellules de mélanome agressifs, une fraction de la N-cadhérine est localisée dans les « lipid rafts » en association avec β-caténine, p 120ctn et α-caténine. Comme la présence de la N-cadhérine dans les « lipid rafts » ne contribue pas à la formation de jonction adhérentes, cette étude suggère une nouvelle fonction pour la N-cadhérine dans les « lipid rafts ». SUMMARY Human skin is a complex organ composed of two layers separated by a basement membrane: the epidermis and the dermis. In the basal layer of the epidermis, the melanin-producing cells of the skin, the melanocytes deliver melanin-containing melanosomes to keratinocytes, thereby protecting the epidermis and the dermis from the deleterious effects of ultraviolet light. Melanocytes physically interact with keratinocytes through E-cadherin-mediated adhesion. During malignant transformation into melanoma cells, melanocytes lose E-cadherin expression and concomitantly gain expression of N-cadherin, a phenomenon referred to as "cadherin switch". Loss of E-cadherin allows melanocytes to escape the regulatory effects of neighbouring keratinocytes, while gain of N-cadherin expression promotes migration, invasion and metastatic abilities of melanoma cells. In preliminary experiments, we found that a fraction of N-cadherin localized to specialized membrane microdomains enriched in cholesterol- and glycosphingolipid, called lipid rafts. One particular feature of lipid rafts is that they are rich in signalling molecules and they possibly modulate transmembrane signalling events. Moreover, recent reports suggested that a specialized type of rafts called caveolae might contribute to tumor progression. Based on the documented role of N-cadherin in melanoma progression and its presence in lipid rafts of melanoma cells, we raised the hypothesis that the association of N-cadherin with lipid rafts might be relevant to melanoma progression. The aim of this project was to characterize N-cadherin associated to lipid rafts during melanoma progression. Using human melanoma cell lines derived from melanoma at different stages of progression, we found that (1) N-cadherin is partly associated to lipid rafts in six cell lines derived from melanomas at late stages of progression and in experimental tumors, but not in two melanoma cell lines derived from early stages; (2) N-cadherin targeting to lipid rafts does not depend on its expression level; (3) E-cadherin is not localized in lipid rafts of a melanoma cell line that retained E-cadherin expression; (4) N-cadherin localization to lipid rafts is not modulated by the growth factors bFGF, IGF-I, and HRG1-β1, nor by MEK-, PKA-, Src family kinases-, and PI3K-mediated signalling events; (5) the association of N-cadherin with lipid rafts is not required for adherens junctions stability nor it is perturbed by adherens junctions disruption; (6) N-cadherin in lipid rafts is in complex with β-catenin, p 120ctm and α-catenin. In conclusion, this study provides original evidence that in aggressive melanoma cells a pool of N-cadherin is localized in lipid rafts in association with β-catenin, p 120 and α-catenin. The presence of N-cadherin in lipid rafts independently of its involvement in adherens junctions formation, suggests a possible new role for N-cadherin recruited to lipid rafts. Further studies investigating the biological meaning of this localization promise to uncover new properties of this molecule.

Research involving biological material from forensic autopsies: legal and ethical issues.

Recommendations and laws do not always contain specific and clear provisions on the use of cadaveric material in research, and even more rarely do they address explicitly the ethical issues related to research on material obtained during forensic autopsy. In this article we analyse existing legal frameworks in Europe by comparing the legal provisions in 2 European Countries which are member states of the Council of Europe, the UK and Switzerland. They were chosen because they have distinct legal frameworks that make comparisons interesting. In addition, the detailed laws of the UK and a specific law project and national ethical recommendations in Switzerland permit us to define more clearly the legal range of options for researchers using cadaveric material obtained during forensic investigations. The Human Tissue Act 2004 in England, Wales and Northern Ireland, its Scottish equivalent with the same title (2006) and the national ethical guidelines in Switzerland all require consent from the deceased person, an appropriate relative or a person with power of attorney for healthcare decisions before cadaveric biological material can be obtained and used for research. However, if the purpose of the autopsy is purely forensic, no such authorization will be sought to carry out the autopsy and related analyses, which might include genetic testing. In order to be allowed to carry out future research projects, families need to be approached for informed consent, unless the deceased person had left written directives including permission to use his or her tissues for research.