Study protocol for THINK : a multinational open-label phase I study to assess the safety and clinical activity of multiple administrations of NKR-2 in patients with different metastatic tumour types

Introduction: NKR-2 are autologous T cells genetically modified to express a chimeric antigen receptor (CAR) comprising a fusion of the natural killer group 2D (NKG2D) receptor with the CD3 zeta signalling domain, which associates with the adaptor molecule DNAX-activating protein of 10 kDa (DAP10) to provide co-stimulatory signal upon ligand binding. NKG2D binds eight different ligands expressed on the cell surface of many tumour cells and which are normally absent on non-neoplastic cells. In preclinical studies, NKR-2 demonstrated long-term antitumour activity towards a breadth of tumour indications, with maximum efficacy observed after multiple NKR-2 administrations. Importantly, NKR-2 targeted tumour cells and tumour neovasculature and the local tumour immunosuppressive microenvironment and this mechanism of action of NKR-2 was established in the absence of preconditioning. Methods and analysis: This open-label phase I study will assess the safety and clinical activity of NKR-2 treatment administered three times, with a 2-week interval between each administration in different tumour types. The study will contain two consecutive segments: a dose escalation phase followed by an expansion phase. The dose escalation study involves two arms, one in solid tumours (five specific indications) and one in haematological tumours (two specific indications) and will include three dose levels in each arm: 3x10(8), 1x10(9) and 3x10(9) NKR-2 per injection. On the identification of the recommended dose in the first segment, based on dose-limiting toxicity occurrences, the study will expand to seven different cohorts examining the seven different tumour types separately. Clinical responses will be determined according to standard Response Evaluation Criteria In Solid Tumors (RECIST) criteria for solid tumours or international working group response criteria in haematological tumours. Ethics approval and dissemination: Ethical approval has been obtained at all sites. Written informed consent will be taken from all participants. The results of this study will be disseminated through presentation at international scientific conferences and reported in peer-reviewed scientific journals

L'ambiance est dans l'air : la dimension atmosphérique des ambiances architecturales et urbaines dans les approches environnementalistes

EQUIPEDirection scientifiqueNicolas Tixier, Laboratoire Cresson – UMR CNRS 1563 – ENSA de GrenoblePilotage des travaux de terrain et assistance à la coordination scientifiqueDamien Masson, Laboratoire Cresson – UMR CNRS n°1563 – ENSA de GrenobleResponsable séminaire São-PauloCintia Okamura (CETESB Agence de protection environnementale de São Paulo)Chercheurs impliqués et équipes partenairesPascal Amphoux, Laure Brayer, Sandra Fiori, Guillaume Meigneux, Steven Melemis (Laboratoire Cresson)Gilles Debizet, Jean-Michel Roux (UMR CNRS PACTE)Frédéric Pousin (UMR CNRS Géographie-cités)Carlos Celso do Amaral e Silva (Université de São Paulo)Patricia Mendes, Carolina Rodriguez (Univ. Campinas)Vincent Puig (IRI), Elena Cogato Lanza (EPFL)Partenaires mobilisésPatrice Coindet, Benoît Adeline, Max Montmayeur (Ville de Grenoble)Ana Claudia (CETESB Agence de protection environnementale de São Paulo)Murielle Pezet-Kuhn, Cédric Lomakine (AURG : Agence d’Urbanisme de l’Agglomération Grenobloise)Hélène Poimboeuf (La Métro : Communauté d’agglomération de Grenoble)Naïm Aït Sidhoum, Pierre Bouchon Cesaro, Thibaut Candela (Zoom Architecture)Can an urban cross-section be used to bring together global environmental issues and situated local ambiental ones that take account of the sensorial dimensions of space and city dwellers’ practices? Starting from this assumption of an urban cross-section as a basis for representing and expressing what are usually separate, i.e., built objects, the sensorial world and social practices, we have conducted exploratory research tailored to environmental concerns based on two themes for which we can readily mobilize both researchers and a decent body of research, namely urban heat (City of Grenoble) and solid waste (City of São Paulo).We have dealt with two categories of questions based on existing research and a series of experiments:• Those relating to the different registers of knowledge inherent in ambiance and the environment as understood by technicians, elected representatives, scientists and users. When and how are actors able to articulate (or more effectively articulate) their knowledge of territory, i.e., more implicit user knowledge or the more explicit-type knowledge of scientists?• Those relating to representation / communication / bargaining tools. How and with what representational basis is it possible to “cross-check data” and move from a phase of reflection to a project-based mindset? For both of these questions and realms, we need to ascertain the operational capability of an urban cross-section both for handing environmental issues in local development as well as for its ability to factor the narratives and practices of inhabitants into the whole urban project process. In light of this dual objective, these experiments propose expanding the standard applications of an urban cross-section to a tool that could be used as a practical field instrument, a representation technique, or possibly even as a project basis, namely an urban transect.The transect could then be a process somewhere between a “clinical” profile and a sensorial perspective, drawing upon both techniques in order to “hybridize” them; as a field-based technique, the transect would be produced from drawings, photos, text and video. By rehabilitating the atmospheric dimension in architectural and urban representations and facilitating the incorporation of narratives, the transect could be harnessed to explore and express sensorial space and practical experiences of the fit between analysis and design.The “long-table” analytic approach has been used to debate these issues and to depict and pool representations. It has proved very effective in generating speech, collating ratings and revealing actual experiences – three very useful properties for establishing a shared prospective diagnosis.La coupe urbaine peut-elle être un lieu de rencontre entre les enjeux environnementaux globaux et les enjeux locaux d'ambiances situées prenant en compte les dimensions sensibles de l'espace et les pratiques habitantes ? Sur cette hypothèse de départ de la coupe urbaine comme mode de représentation permettant d'articuler ce qui habituellement est séparé, à savoir les objets construits, le monde sensible et les pratiques sociales, nous avons mené un travail exploratoire appliqué aux préoccupations environnementales, ceci à travers deux thématiques pour lesquelles nous pouvions aisément mobiliser corpus et acteurs, celles des chaleurs urbaines (Ville de Grenoble) et celle des déchets solides (Ville de São Paulo). Deux catégories de questions sont traitées à partir de corpus existants et d'une série d'expérimentations que nous avons menées : * Celles qui concernent les différents registres de connaissance impliqués lorsqu'on parle d'ambiance et d'environnement, ceci entre techniciens, élus, scientifiques et usagers. Quand et comment les acteurs arrivent-ils (ou pourraient-ils mieux arriver) à articuler leurs connaissances du territoire, qu'elles soient principalement implicites (comme dans le cas des usagers) ou plutôt explicite (notamment chez les scientifiques) ? * Celles qui concernent les outils de représentation / communication / négociation. Comment, et grâce à quels moyens de représentation, arrive-t-on à " croiser des données " et à faire le passage du domaine de la réflexion à celui du projet ? Pour ces deux questions et pour ces deux terrains, il s'agissait donc d'éprouver l'opérationnalité de la coupe urbaine tant pour la gestion des enjeux environnementaux dans le développement local que pour sa capacité de prise en compte du récit et des pratiques habitantes dans le processus de projet urbain. A cette double fin, ces expérimentations proposent d'élargir les champs d'applications ordinaires de la coupe urbaine à un outil qui se veut à la fois pratique de terrain, technique de représentation et peut-être même posture de projet, à savoir le transect urbain. Le transect se présente alors comme un dispositif se situant entre la coupe " clinique " et le parcours sensible empruntant à ces deux techniques pour les hybrider ; le transect se construit par le dessin, la photo, le texte, la vidéo autant qu'il se pratique in situ. Réhabilitant de fait la dimension atmosphérique dans les représentations architecturales et urbaines, rendant possible l'inscription des récits, le transect peut devenir alors un mode d'interrogation et d'expression de l'espace sensible et des pratiques vécues à l'articulation entre analyse et conception. Un principe de " table longue " a été mis en place pour débattre de ces enjeux et permettre une mise en situation et un partage des représentations. Ce dispositif s'avère être générateur de paroles, collecteur de notations et révélateur de réalités vécues, trois propriétés utiles à l'établissement d'un diagnostique prospectif partagé

Molecular evolution of HoxA13 and the multiple origins of limbless morphologies in amphibians and reptiles

Developmental processes and their results, morphological characters, are inherited through transmission of genes regulating development. While there is ample evidence that cis-regulatory elements tend to be modular, with sequence segments dedicated to different roles, the situation for proteins is less clear, being particularly complex for transcription factors with multiple functions. Some motifs mediating protein-protein interactions may be exclusive to particular developmental roles, but it is also possible that motifs are mostly shared among different processes. Here we focus on HoxA13, a protein essential for limb development. We asked whether the HoxA13 amino acid sequence evolved similarly in three limbless clades: Gymnophiona, Amphisbaenia and Serpentes. We explored variation in ω (dN/dS) using a maximum-likelihood framework and HoxA13sequences from 47 species. Comparisons of evolutionary models provided low ω global values and no evidence that HoxA13 experienced relaxed selection in limbless clades. Branch-site models failed to detect evidence for positive selection acting on any site along branches of Amphisbaena and Gymnophiona, while three sites were identified in Serpentes. Examination of alignments did not reveal consistent sequence differences between limbed and limbless species. We conclude that HoxA13 has no modules exclusive to limb development, which may be explained by its involvement in multiple developmental processes

Nuclear factor erythroid 2-related factor 2 nuclear translocation induces myofibroblastic dedifferentiation in idiopathic pulmonary fibrosis

AIMS: Oxidants have been implicated in the pathophysiology of idiopathic pulmonary fibrosis (IPF), especially in myofibroblastic differentiation. We aimed at testing the hypothesis that nuclear factor erythroid 2-related factor 2 (Nrf2), the main regulator of endogenous antioxidant enzymes, is involved in fibrogenesis via myofibroblastic differentiation. Fibroblasts were cultured from the lungs of eight controls and eight IPF patients. Oxidants-antioxidants balance, nuclear Nrf2 expression, and fibroblast phenotype (α-smooth muscle actin and collagen I expression, proliferation, migration, and contraction) were studied under basal conditions and after Nrf2 knockdown or activation by Nrf2 or Keap1 siRNA transfection. The effects of sulforaphane (SFN), an Nrf2 activator, on the fibroblast phenotype were tested under basal and pro-fibrosis conditions (transforming growth factor β [TGF-β]). RESULTS: Decreased Nrf2 expression was associated with a myofibroblast phenotype in IPF compared with control fibroblasts. Nrf2 knockdown induced oxidative stress and myofibroblastic differentiation in control fibroblasts. Conversely, Nrf2 activation increased antioxidant defences and myofibroblastic dedifferentation in IPF fibroblasts. SFN treatment decreased oxidants, and induced Nrf2 expression, antioxidants, and myofibroblastic dedifferentiation in IPF fibroblasts. SFN inhibited TGF-β profibrotic deleterious effects in IPF and control fibroblasts and restored antioxidant defences. Nrf2 knockdown abolished SFN antifibrosis effects, suggesting that they were Nrf2 mediated. INNOVATION AND CONCLUSION: Our findings confirm that decreased nuclear Nrf2 plays a role in myofibroblastic differentiation and that SFN induces human pulmonary fibroblast dedifferentiation in vitro via Nrf2 activation. Thus, Nrf2 could be a novel therapeutic target in IPF

Ancient transposable elements transformed the uterine regulatory landscape and transcriptome during the evolution of mammalian pregnancy

A major challenge in biology is determining how evolutionarily novel characters originate; however, mechanistic explanations for the origin of new characters are almost completely unknown. The evolution of pregnancy is an excellent system in which to study the origin of novelties because mammals preserve stages in the transition from egg laying to live birth. To determine the molecular bases of this transition, we characterized the pregnant/gravid uterine transcriptome from tetrapods to trace the evolutionary history of uterine gene expression. We show that thousands of genes evolved endometrial expression during the origins of mammalian pregnancy, including genes that mediate maternal-fetal communication and immunotolerance. Furthermore, thousands of cis-regulatory elements that mediate decidualization and cell-type identity in decidualized stromal cells are derived from ancient mammalian transposable elements (TEs). Our results indicate that one of the defining mammalian novelties evolved from DNA sequences derived from ancient mammalian TEs co-opted into hormone-responsive regulatory elements distributed throughout the genome.Vincent J. Lynch, Mauris C. Nnamani, Aurélie Kapusta, Kathryn Brayer, Silvia L. Plaza, Erik C. Mazur, Deena Emera, Shehzad Z. Sheikh, Frank Grützner, Stefan Bauersachs, Alexander Graf, Steven L. Young, Jason D. Lieb, Francesco J. DeMayo, Cédric Feschotte, Günter P. Wagne

The Case of the Fickle Fingers: How the PRDM9 Zinc Finger Protein Specifies Meiotic Recombination Hotspots in Humans

Recent discoveries have revealed the central role of PRDM9 in mammalian recombination. The precise function of this protein, however, remains poorly understood, as do the causes for its rapid evolution and its role in reproductive isolation

Molecular Dynamics of Mesophilic-Like Mutants of a Cold-Adapted Enzyme: Insights into Distal Effects Induced by the Mutations

Networks and clusters of intramolecular interactions, as well as their “communication” across the three-dimensional architecture have a prominent role in determining protein stability and function. Special attention has been dedicated to their role in thermal adaptation. In the present contribution, seven previously experimentally characterized mutants of a cold-adapted α-amylase, featuring mesophilic-like behavior, have been investigated by multiple molecular dynamics simulations, essential dynamics and analyses of correlated motions and electrostatic interactions. Our data elucidate the molecular mechanisms underlying the ability of single and multiple mutations to globally modulate dynamic properties of the cold-adapted α-amylase, including both local and complex unpredictable distal effects. Our investigation also shows, in agreement with the experimental data, that the conversion of the cold-adapted enzyme in a warm-adapted variant cannot be completely achieved by the introduction of few mutations, also providing the rationale behind these effects. Moreover, pivotal residues, which are likely to mediate the effects induced by the mutations, have been identified from our analyses, as well as a group of suitable candidates for protein engineering. In fact, a subset of residues here identified (as an isoleucine, or networks of mesophilic-like salt bridges in the proximity of the catalytic site) should be considered, in experimental studies, to get a more efficient modification of the features of the cold-adapted enzyme

Tight associations between transcription promoter type and epigenetic variation in histone positioning and modification

Abstract Background Transcription promoters are fundamental genomic cis-elements controlling gene expression. They can be classified into two types by the degree of imprecision of their transcription start sites: peak promoters, which initiate transcription from a narrow genomic region; and broad promoters, which initiate transcription from a wide-ranging region. Eukaryotic transcription initiation is suggested to be associated with the genomic positions and modifications of nucleosomes. For instance, it has been recently shown that histone with H3K9 acetylation (H3K9ac) is more likely to be distributed around broad promoters rather than peak promoters; it can thus be inferred that there is an association between histone H3K9 and promoter architecture. Results Here, we performed a systematic analysis of transcription promoters and gene expression, as well as of epigenetic histone behaviors, including genomic position, stability within the chromatin, and several modifications. We found that, in humans, broad promoters, but not peak promoters, generally had significant associations with nucleosome positioning and modification. Specifically, around broad promoters histones were highly distributed and aligned in an orderly fashion. This feature was more evident with histones that were methylated or acetylated; moreover, the nucleosome positions around the broad promoters were more stable than those around the peak ones. More strikingly, the overall expression levels of genes associated with broad promoters (but not peak promoters) with modified histones were significantly higher than the levels of genes associated with broad promoters with unmodified histones. Conclusion These results shed light on how epigenetic regulatory networks of histone modifications are associated with promoter architecture

The Drosophila Zinc Finger Protein Trade Embargo Is Required for Double Strand Break Formation in Meiosis

Homologous recombination in meiosis is initiated by the programmed induction of double strand breaks (DSBs). Although the Drosophila Spo11 ortholog Mei-W68 is required for the induction of DSBs during meiotic prophase, only one other protein (Mei-P22) has been shown to be required for Mei-W68 to exert this function. We show here that the chromatin-associated protein Trade Embargo (Trem), a C2H2 zinc finger protein, is required to localize Mei-P22 to discrete foci on meiotic chromosomes, and thus to promote the formation of DSBs, making Trem the earliest known function in the process of DSB formation in Drosophila oocytes. We speculate that Trem may act by either directing the binding of Mei-P22 to preferred sites of DSB formation or by altering chromatin structure in a manner that allows Mei-P22 to form foci

MyoMiner: explore gene co-expression in normal and pathological muscle

International audienceBackground: High-throughput transcriptomics measures mRNA levels for thousands of genes in a biological sample. Most gene expression studies aim to identify genes that are differentially expressed between different biological conditions, such as between healthy and diseased states. However, these data can also be used to identify genes that are co-expressed within a biological condition. Gene co-expression is used in a guilt-by-association approach to prioritize candidate genes that could be involved in disease, and to gain insights into the functions of genes, protein relations, and signaling pathways. Most existing gene co-expression databases are generic, amalgamating data for a given organism regardless of tissue-type.Methods: To study muscle-specific gene co-expression in both normal and pathological states, publicly available gene expression data were acquired for 2376 mouse and 2228 human striated muscle samples, and separated into 142 categories based on species (human or mouse), tissue origin, age, gender, anatomic part, and experimental condition. Co-expression values were calculated for each category to create the MyoMiner database.Results: Within each category, users can select a gene of interest, and the MyoMiner web interface will return all correlated genes. For each co-expressed gene pair, adjusted p-value and confidence intervals are provided as measures of expression correlation strength. A standardized expression-level scatterplot is available for every gene pair r-value. MyoMiner has two extra functions: (a) a network interface for creating a 2-shell correlation network, based either on the most highly correlated genes or from a list of genes provided by the user with the option to include linked genes from the database and (b) a comparison tool from which the users can test whether any two correlation coefficients from different conditions are significantly different.Conclusions: These co-expression analyses will help investigators to delineate the tissue-, cell-, and pathology-specific elements of muscle protein interactions, cell signaling and gene regulation. Changes in co-expression between pathologic and healthy tissue may suggest new disease mechanisms and help define novel therapeutic targets. Thus, MyoMiner is a powerful muscle-specific database for the discovery of genes that are associated with related functions based on their co-expression. MyoMiner is freely available at https://www.sys-myo.com/myominer