Tissue-Specific Evolution of Protein Coding Genes in Human and Mouse.

Protein-coding genes evolve at different rates, and the influence of different parameters, from gene size to expression level, has been extensively studied. While in yeast gene expression level is the major causal factor of gene evolutionary rate, the situation is more complex in animals. Here we investigate these relations further, especially taking in account gene expression in different organs as well as indirect correlations between parameters. We used RNA-seq data from two large datasets, covering 22 mouse tissues and 27 human tissues. Over all tissues, evolutionary rate only correlates weakly with levels and breadth of expression. The strongest explanatory factors of purifying selection are GC content, expression in many developmental stages, and expression in brain tissues. While the main component of evolutionary rate is purifying selection, we also find tissue-specific patterns for sites under neutral evolution and for positive selection. We observe fast evolution of genes expressed in testis, but also in other tissues, notably liver, which are explained by weak purifying selection rather than by positive selection.

NLRP3 Inflammasome Is Expressed and Functional in Mouse Brain Microglia but Not in Astrocytes.

Neuroinflammation is the local reaction of the brain to infection, trauma, toxic molecules or protein aggregates. The brain resident macrophages, microglia, are able to trigger an appropriate response involving secretion of cytokines and chemokines, resulting in the activation of astrocytes and recruitment of peripheral immune cells. IL-1β plays an important role in this response; yet its production and mode of action in the brain are not fully understood and its precise implication in neurodegenerative diseases needs further characterization. Our results indicate that the capacity to form a functional NLRP3 inflammasome and secretion of IL-1β is limited to the microglial compartment in the mouse brain. We were not able to observe IL-1β secretion from astrocytes, nor do they express all NLRP3 inflammasome components. Microglia were able to produce IL-1β in response to different classical inflammasome activators, such as ATP, Nigericin or Alum. Similarly, microglia secreted IL-18 and IL-1α, two other inflammasome-linked pro-inflammatory factors. Cell stimulation with α-synuclein, a neurodegenerative disease-related peptide, did not result in the release of active IL-1β by microglia, despite a weak pro-inflammatory effect. Amyloid-β peptides were able to activate the NLRP3 inflammasome in microglia and IL-1β secretion occurred in a P2X7 receptor-independent manner. Thus microglia-dependent inflammasome activation can play an important role in the brain and especially in neuroinflammatory conditions.

Dendritic Cells Cause Bone Lesions in a New Mouse Model of Histiocytosis.

Langerhans cell histiocytosis (LCH) is a rare disease caused by the clonal accumulation of dendritic Langerhans cells, which is often accompanied by osteolytic lesions. It has been reported that osteoclast-like cells play a major role in the pathogenic bone destruction seen in patients with LCH and these cells are postulated to originate from the fusion of DCs. However, due to the lack of reliable animal models the pathogenesis of LCH is still poorly understood. In this study, we have established a mouse model of histiocytosis- recapitulating human disease for osteolytic lesions seen in LCH patients. At 12 weeks after birth, severe bone lesions were observed in our multisystem histiocytosis (Mushi) model, when CD8α conventional dendritic cells (DCs) are transformed (MuTuDC) and accumulate. Most importantly, our study demonstrates that bone loss in LCH can be accounted for the transdifferentiation of MuTuDCs into functional osteoclasts both in vivo and in vitro. Moreover, we have shown that injected MuTuDCs reverse the osteopetrotic phenotype of oc/oc mice in vivo. In conclusion, our results support a crucial role of DCs in bone lesions in histiocytosis patients. Furthermore, our new model of LCH based on adoptive transfer of MuTuDC lines, leading to bone lesions within 1-2 weeks, will be an important tool for investigating the pathophysiology of this disease and ultimately for evaluating the potential of anti-resorptive drugs for the treatment of bone lesions.

Innate Immune Sensing of Fusarium culmorum by Mouse Dendritic Cells.

Chronic inhalation of grain dust is associated with asthma and chronic bronchitis in grain worker populations. Exposure to fungal particles was postulated to be an important etiologic agent of these pathologies. Fusarium species frequently colonize grain and straw and produce a wide array of mycotoxins that impact human health, necessitating an evaluation of risk exposure by inhalation of Fusarium and its consequences on immune responses. Data showed that Fusarium culmorum is a frequent constituent of aerosols sampled during wheat harvesting in the Vaud region of Switzerland. The aim of this study was to examine cytokine/chemokine responses and innate immune sensing of F. culmorum in bone-marrow-derived dendritic cells and macrophages. Overall, dendritic cells and macrophages responded to F. culmorum spores but not to its secreted components (i.e., mycotoxins) by releasing large amounts of macrophage inflammatory protein (MIP)-1α, MIP-1β, MIP-2, monocyte chemoattractant protein (MCP)-1, RANTES, and interleukin (IL)-12p40, intermediate amounts of tumor necrosis factor (TNF), IL-6, IL-12p70, IL-33, granulocyte colony-stimulating factor (G-CSF), and interferon gamma-induced protein (IP-10), but no detectable amounts of IL-4 and IL-10, a pattern of mediators compatible with generation of Th1 or Th17 antifungal protective immune responses rather than with Th2-dependent allergic responses. The sensing of F. culmorum spores by dendritic cells required dectin-1, the main pattern recognition receptor involved in β-glucans detection, but likely not MyD88 and TRIF-dependent Toll-like receptors. Taken together, our results indicate that F. culmorum stimulates potently innate immune cells in a dectin-1-dependent manner, suggesting that inhalation of F. culmorum from grain dust may promote immune-related airway diseases in exposed worker populations.

Controlling complexity: the clinical relevance of mouse complex genetics.

Experimental animal models are essential to obtain basic knowledge of the underlying biological mechanisms in human diseases. Here, we review major contributions to biomedical research and discoveries that were obtained in the mouse model by using forward genetics approaches and that provided key insights into the biology of human diseases and paved the way for the development of novel therapeutic approaches.

Meeting report of the European mouse complex genetics network SYSGENET.

The second scientific meeting of the European systems genetics network for the study of complex genetic human disease using genetic reference populations (SYSGENET) took place at the Center for Cooperative Research in Biosciences in Bilbao, Spain, December 10-12, 2012. SYSGENET is funded by the European Cooperation in the Field of Scientific and Technological Research (COST) and represents a network of scientists in Europe that use mouse genetic reference populations (GRPs) to identify complex genetic factors influencing disease phenotypes (Schughart, Mamm Genome 21:331-336, 2010). About 50 researchers working in the field of systems genetics attended the meeting, which consisted of 27 oral presentations, a poster session, and a management committee meeting. Participants exchanged results, set up future collaborations, and shared phenotyping and data analysis methodologies. This meeting was particularly instrumental for conveying the current status of the US, Israeli, and Australian Collaborative Cross (CC) mouse GRP. The CC is an open source project initiated nearly a decade ago by members of the Complex Trait Consortium to aid the mapping of multigenetic traits (Threadgill, Mamm Genome 13:175-178, 2002). In addition, representatives of the International Mouse Phenotyping Consortium were invited to exchange ongoing activities between the knockout and complex genetics communities and to discuss and explore potential fields for future interactions.

Assessing Recent Selection and Functionality at Long Noncoding RNA Loci in the Mouse Genome.

Long noncoding RNAs (lncRNAs) are one of the most intensively studied groups of noncoding elements. Debate continues over what proportion of lncRNAs are functional or merely represent transcriptional noise. Although characterization of individual lncRNAs has identified approximately 200 functional loci across the Eukarya, general surveys have found only modest or no evidence of long-term evolutionary conservation. Although this lack of conservation suggests that most lncRNAs are nonfunctional, the possibility remains that some represent recent evolutionary innovations. We examine recent selection pressures acting on lncRNAs in mouse populations. We compare patterns of within-species nucleotide variation at approximately 10,000 lncRNA loci in a cohort of the wild house mouse, Mus musculus castaneus, with between-species nucleotide divergence from the rat (Rattus norvegicus). Loci under selective constraint are expected to show reduced nucleotide diversity and divergence. We find limited evidence of sequence conservation compared with putatively neutrally evolving ancestral repeats (ARs). Comparisons of sequence diversity and divergence between ARs, protein-coding (PC) exons and lncRNAs, and the associated flanking regions, show weak, but significantly lower levels of sequence diversity and divergence at lncRNAs compared with ARs. lncRNAs conserved deep in the vertebrate phylogeny show lower within-species sequence diversity than lncRNAs in general. A set of 74 functionally characterized lncRNAs show levels of diversity and divergence comparable to PC exons, suggesting that these lncRNAs are under substantial selective constraints. Our results suggest that, in mouse populations, most lncRNA loci evolve at rates similar to ARs, whereas older lncRNAs tend to show signals of selection similar to PC genes.

Micrornas involvement in cortical plasticity in adult mouse barrel cortex

In rodents, sensory experience alters the whisker representation in layer IV of the barrel cortex (Woolsey and Van der Loos, 1970). Excitatory and inhibitory interneurons, together with the astrocytic network, modify the functional representation in an integrated manner. Our group showed that continuous whisker stimulation induces structural and functional changes in the corresponding barrel. These modifications include the depression of neuronal responses and an insertion of new inhibitory synapses on dendritic spines (Knott et al., 2002; Genoud et al., 2006; Quairiaux et al., 2007). This form of cortical plasticity is controlled by several gene regulatory mechanisms including the activation of genetic programs controlling the expression of microRNAs (miRNAs). The transitory and localized expression of miRNAs in dendrites and their capacity to respond in an activity-dependent manner make them ideal candidates for the fine tuning of gene expression associated with neural plasticity. In a previous study of our group (Johnston- Wenger, 2010) using microarray analysis on laser-dissected barrels in order to compare the gene expression levels in stimulated and non-stimulated barrels after whisker stimulation, 261 genes were found significantly regulated, among these genes there were two miRNAs (miR- 132 and miR-137). In this study I tested the initial observation on the up-regulation of miR-132 and miR-137 after whisker stimulation and the possible involvement of two other miRNAs (miR-138 and miR-125b) that are known play a role in other form of synaptic plasticity. I used in situ hybridization (ISH) after unilateral stimulation of three whiskers (Cl-3) in the adult mouse. We found that sensory stimulation increases the expression, of miR-132 after 3hours of stimulation (p<0.01) and miR-137 (pO.Ol; 24 hrs of stim.), whereas it reduces the level of miR-125b (pO.Ol; 9 hrs of stim.). No significant difference was detected for miR-138. We further determined a correlation between the level of expression of the four selected miRNAs in the cortical barrels (measured by ISH) and in blood plasma (measured by qPCR). In addition to this quantitative comparison, we combined miRNAs ISH and immunolabeling for various neuronal markers that were chosen for the localization in both excitatory and inhibitory circuits as well as in astrocytes. Analysis of three-dimensional confocal acquisitions showed that stimulation alters significantly the degree of co-localization in the stimulated barrel of miR-132 with GAD65/67 and VGLUT2; miR-125b with GAD65/67 and parvalbumin; miR-138 with parvalbumin, VGLUT1 and PSD95; and miR-137 with VGLUT1 and astrocytic markers (GS; GFAP and SlOOß). To conclude, using increased neuronal activity in the whisker-to-barrel pathway; our results suggest that miRNAs can be regulated in an activity-dependent manner and they may regulate local mRNA translation to shape neuronal responses. These findings motivate further investigation of the different modes in which miRNAs may regulate cortical plasticity. -- Chez les rongeurs, l'expérience sensorielle modifie la représentation des vibrisses au niveau du cortex somatosensoriel primaire (Woolsey and Van der Loos, 1970). Les interneurones excitateurs et inhibiteurs, en collaboration avec le réseau astrocytaire, modifient la représentation fonctionnelle d'une manière intégrée. Notre groupe a montré que la stimulation continue des vibrisses induit des changements structuraux et fonctionnels dans le tonneau correspondant. Ces modifications incluent la dépression des réponses neuronales et une insertion de nouvelles synapses inhibitrices sur les épines dendritiques (Knott et al., 2002 ; Genoud et al., 2006 ; Quairiaux et al., 2007). Cette forme de plasticité corticale est contrôlée par plusieurs mécanismes de régulation génique dont l'activation des programmes géniques contrôlant l'expression des microARNs (miARNs). Par leur expression transitoire et localisée dans les dendrites et leur capacité à réagir d'une manière dépendante de l'activité, les miARNs sont des candidats idéaux pour le réglage fin de l'expression des gènes associée à la plasticité neuronale. Afin de comparer le niveau d'expression des gènes dans les tonneaux stimulés et non-stimulés après stimulation des vibrisses, une étude antérieure dans notre groupe (Johnston-Wenger, 2010), utilisant l'analyse par microarray sur des tonneaux disséqués par laser, a montré l'altération significative de 261 gènes. Parmi ces gènes, il y avait deux miARNs (miR-132 et miR-137). Dans la présente étude, j'ai testé l'observation initiale sur la régulation de miR-132 et miR-137 après stimulation des vibrisses et la possible implication de deux autres miARNs (miR-138 et miR-125b) connus avoir jouer un rôle important dans d'autres formes de plasticité synaptique. J'ai utilisé l'hybridation in situ (ISH) après stimulation unilatérale de trois vibrisses (Cl-3) chez la souris adulte. J'ai trouvé que la stimulation sensorielle augmente l'expression, de miR-132 après 3 heures de stimulation (p < 0.01) et miR-137 (p < 0.01 ; 24 hrs de stim.), alors qu'elle réduit le niveau de miR-125b (p < 0.01; 9 hrs de stim.). Aucune différence significative n'a été détectée pour miR-138. J'ai aussi déterminé une corrélation entre le niveau d'expression des quatre miARNs sélectionnés dans les tonneaux (mesurés par ISH) et dans le plasma sanguin (mesuré par qPCR). En plus de cette comparaison quantitative, j'ai combiné le miR-ISH et l'immunomarquage pour divers marqueurs neuronaux qui ont été choisis pour étudier la localisation dans les circuits excitateurs et inhibiteurs, ainsi que dans les astrocytes. Les acquisitions tridimensionnelles montrent que la stimulation modifie considérablement le degré de co-localisation dans le tonneau stimulé de miR-132 avec GAD65/67 et VGLUT2; miR-125b avec GAD65/67 et parvalbumine; miR-138 avec parvalbumine, VGLUT1 et PSD95; et miR-137 avec VGLUT1 et les marqueurs astrocytaires (GS ; GFAP et SlOOß). En conclusion, à l'aide de l'activité neuronale accrue dans la voie de vibrisses-au-baril; les résultats suggèrent que les miARNs peuvent être régulé d'une manière dépendante de l'activité et peuvent résulter la stabilité des ARNm et la traduction pour façonner les réponses neuronales ultérieures. Ces résultats incitent d'investiguer davantage les voies importantes par lesquels les miARNs peuvent réguler la plasticité corticale.

Targeted Therapy for Patients with BRAF-Mutant Lung Cancer: Results from the European EURAF Cohort.

INTRODUCTION: Approximately 2% of lung adenocarcinomas have BRAF (v-Raf murine sarcoma viral oncogene homolog B) mutations, including V600E and other types. Vemurafenib, dabrafenib, and sorafenib as BRAF inhibitors are currently tested in clinical trials, but access for patients is limited. The aim of this study was to document the clinical course of patients treated outside of clinical trials. METHODS: We conducted a retrospective multicenter cohort study in Europe of patients with advanced BRAF-mutant lung cancer treated with known BRAF inhibitors. Data were anonymized and centrally assessed for age, gender, smoking, histology, stage, local molecular diagnostic results, systemic therapies, and survival. Best response was assessed locally by RECIST1.1. RESULTS: We documented 35 patients treated in 17 centers with vemurafenib, dabrafenib, or sorafenib. Median age was 63 years (range 42-85); gender was balanced; 14 (40%) were never smokers; all (100%) had adenocarcinoma; 29 (83%) had V600E; 6 (17%) had other mutations; one of them had a concomitant KRAS mutation. Thirty (86%) patients had chemotherapy in the first line. Overall survival with first-line therapy was 25.3 months for V600E and 11.8 months for non-V600E. Thirty-one patients received one BRAF inhibitor, and four received a second inhibitor. Overall response rate with BRAF therapy was 53%, and disease control rate was 85%. Median progression-free survival with BRAF therapy was 5.0 months, and overall survival was 10.8 months. CONCLUSIONS: These results confirm the activity of targeted therapy in patients with BRAF-mutant lung adenocarcinoma. Further trials are warranted to study combination therapies and drug resistance mechanisms.

Characterization and genetic mapping of eceriferum-ym (cer-ym), a cutin deficient barley mutant with impaired leaf water retention capacity.

The cuticle covers the aerial parts of land plants, where it serves many important functions, including water retention. Here, a recessive cuticle mutant, eceriferum-ym (cer-ym), of Hordeum vulgare L. (barley) showed abnormally glossy spikes, sheaths, and leaves. The cer-ym mutant plant detached from its root system was hypersensitive to desiccation treatment compared with wild type plants, and detached leaves of mutant lost 41.8% of their initial weight after 1 h of dehydration under laboratory conditions, while that of the wild type plants lost only 7.1%. Stomata function was not affected by the mutation, but the mutant leaves showed increased cuticular permeability to water, suggesting a defective leaf cuticle, which was confirmed by toluidine blue staining. The mutant leaves showed a substantial reduction in the amounts of the major cutin monomers and a slight increase in the main wax component, suggesting that the enhanced cuticle permeability was a consequence of cutin deficiency. cer-ym was mapped within a 0.8 cM interval between EST marker AK370363 and AK251484, a pericentromeric region on chromosome 4H. The results indicate that the desiccation sensitivity of cer-ym is caused by a defect in leaf cutin, and that cer-ym is located in a chromosome 4H pericentromeric region.

Missense mutations in TENM4, a regulator of axon guidance and central myelination, cause essential tremor.

Essential tremor (ET) is a common movement disorder with an estimated prevalence of 5% of the population aged over 65 years. In spite of intensive efforts, the genetic architecture of ET remains unknown. We used a combination of whole-exome sequencing and targeted resequencing in three ET families. In vitro and in vivo experiments in oligodendrocyte precursor cells and zebrafish were performed to test our findings. Whole-exome sequencing revealed a missense mutation in TENM4 segregating in an autosomal-dominant fashion in an ET family. Subsequent targeted resequencing of TENM4 led to the discovery of two novel missense mutations. Not only did these two mutations segregate with ET in two additional families, but we also observed significant over transmission of pathogenic TENM4 alleles across the three families. Consistent with a dominant mode of inheritance, in vitro analysis in oligodendrocyte precursor cells showed that mutant proteins mislocalize. Finally, expression of human mRNA harboring any of three patient mutations in zebrafish embryos induced defects in axon guidance, confirming a dominant-negative mode of action for these mutations. Our genetic and functional data, which is corroborated by the existence of a Tenm4 knockout mouse displaying an ET phenotype, implicates TENM4 in ET. Together with previous studies of TENM4 in model organisms, our studies intimate that processes regulating myelination in the central nervous system and axon guidance might be significant contributors to the genetic burden of this disorder.