Schizophrenia risk from complex variation of complement component 4

Schizophrenia is a heritable brain illness with unknown pathogenic mechanisms. Schizophrenia's strongest genetic association at a population level involves variation in the major histocompatibility complex (MHC) locus, but the genes and molecular mechanisms accounting for this have been challenging to identify. Here we show that this association arises in part from many structurally diverse alleles of the complement component 4 (C4) genes. We found that these alleles generated widely varying levels of C4A and C4B expression in the brain, with each common C4 allele associating with schizophrenia in proportion to its tendency to generate greater expression of C4A. Human C4 protein localized to neuronal synapses, dendrites, axons, and cell bodies. In mice, C4 mediated synapse elimination during postnatal development. These results implicate excessive complement activity in the development of schizophrenia and may help explain the reduced numbers of synapses in the brains of individuals with schizophrenia.

Analysis of RNA-seq data from the interaction of Coffea spp. - Colletotrichum kahawae

Tese de mestrado em Bioinformática e Biologia Computacional (Bioinformática), apresentada à Universidade de Lisboa, através da Faculdade de Ciências, 2014

RT-Bst: an integrated approach for reverse transcription and enrichment of cDNA from viral RNA

The synthesis of cDNA from RNA is challenging due to the inefficiency of reverse transcription (RT). In order to address this, a method was developed known as RT-Bst for sequential RT of RNA and Bst DNA polymerase amplification for enrichment of cDNA in a single tube reaction. Using genomic RNA from bacteriophage MS2, the yield of cDNA produced by RT alone and RT-Bst were compared by analysis of PCR-amplified products. Using random primers a superior performance was observed when amplifying MS2 RNA following RT-Bst compared to RT alone, indicating that greater quantities of cDNA were present after RT-Bst. RT-Bst was also compared with RT alone for their relative ability to produce sufficient cDNA to amplify 8 target regions spanning the respiratory syncytial virus (RSV) genome. Six out of 8 targets were amplified consistently by PCR subsequent to RT-Bst amplification whereas only 3 out of 8 targets could be amplified after RT alone. RSV sequences were selectively amplified using RSV specific primers from a mixed template containing an excess of MS2 RNA in a RT-Bst reaction without amplifying MS2 sequences. This suggests that RT-Bst can be used to amplify RNA sequences non-specifically using random primers and specifically using sequence specific primers and enhances the yield of cDNA when compared to RT alone.

Post-Transcriptional Regulation of BCL2 mRNA by the RNA-Binding Protein ZFP36L1 in Malignant B Cells

The human ZFP36 zinc finger protein family consists of ZFP36, ZFP36L1, and ZFP36L2. These proteins regulate various cellular processes, including cell apoptosis, by binding to adenine uridine rich elements in the 3′ untranslated regions of sets of target mRNAs to promote their degradation. The pro-apoptotic and other functions of ZFP36 family members have been implicated in the pathogenesis of lymphoid malignancies. To identify candidate mRNAs that are targeted in the pro-apoptotic response by ZFP36L1, we reverse-engineered a gene regulatory network for all three ZFP36 family members using the ‘maximum information coefficient’ (MIC) for target gene inference on a large microarray gene expression dataset representing cells of diverse histological origin. Of the three inferred ZFP36L1 mRNA targets that were identified, we focussed on experimental validation of mRNA for the pro-survival protein, BCL2, as a target for ZFP36L1. RNA electrophoretic mobility shift assay experiments revealed that ZFP36L1 interacted with the BCL2 adenine uridine rich element. In murine BCL1 leukemia cells stably transduced with a ZFP36L1 ShRNA lentiviral construct, BCL2 mRNA degradation was significantly delayed compared to control lentiviral expressing cells and ZFP36L1 knockdown in different cell types (BCL1, ACHN, Ramos), resulted in increased levels of BCL2 mRNA levels compared to control cells. 3′ untranslated region luciferase reporter assays in HEK293T cells showed that wild type but not zinc finger mutant ZFP36L1 protein was able to downregulate a BCL2 construct containing the BCL2 adenine uridine rich element and removal of the adenine uridine rich core from the BCL2 3′ untranslated region in the reporter construct significantly reduced the ability of ZFP36L1 to mediate this effect. Taken together, our data are consistent with ZFP36L1 interacting with and mediating degradation of BCL2 mRNA as an important target through which ZFP36L1 mediates its pro-apoptotic effects in malignant B-cells.

A doença pulmonar obstrutiva crónica e o exercício: impacto da doença no declínio funcional e importância do treino de exercício nos benefícios para a saúde

RESUMO: A reabilitação respiratória (RR) é uma intervenção abrangente e interdisciplinar dirigida aos doentes respiratórios crónicos e inclui o treino de exercício, programas de educação e de modificação comportamental, entre outros, desenhados individualmente para melhorar o desempenho físico e psicossocial e promover a adesão a longo prazo a comportamentos promotores de saúde. A doença pulmonar obstrutiva crónica (DPOC) é uma doença comum, afetando cerca de 210 milhões de pessoas em todo o mundo, com elevada mortalidade e com custos económicos significativos decorrentes do agravamento progressivo da doença, das hospitalizações e de reinternamentos frequentes. Apesar do crescente conhecimento da DPOC e do papel da RR nos benefícios para a saúde, existem aspetos ainda não esclarecidos que têm impacto na prática clínica e de investigação e nas decisões das autoridades de saúde. A primeira parte desta tese focou a DPOC e o seu impacto negativo e incluiu: o estudo da prevalência da DPOC em Portugal; os fatores clínicos e funcionais que se associam à mortalidade em doentes com DPOC avançada; a morbilidade, impacto funcional e risco dos doentes se tornarem dependentes para as atividades diárias e a influência da inflamação sistémica. A prevalência estimada da DPOC de 14,2% indica que esta é uma doença comum em Portugal e alerta para a necessidade de uma maior sensibilização da população, dos profissionais de saúde e autoridades de saúde com vista a um diagnóstico precoce e à alocação dos recursos terapêuticos adequados. A elevada taxa de mortalidade em doentes com DPOC avançada - 36,6% em 3 anos - associou-se a insuficiência respiratória, a elevado número de exacerbações, ao cancro do pulmão e a reduzida capacidade funcional para a marcha, salientando a importância da referenciação precoce para RR, a identificação e o tratamento das comorbilidades e a prevenção das exacerbações. A aplicação de um questionário que avaliou as atividades da vida diária básicas e instrumentais, permitiu identificar um marcador clínico do risco de dependência, complementando as avaliações funcionais e associando-se a outros marcadores de mau prognóstico, como as exacerbações. Em doentes com DPOC, com FEV1 médio de 46,76% (desvio padrão: 20,90%), 67% da categoria D do GOLD, verificou-se uma associação positiva entre a expressão de genes inflamatórios avaliada pela reação em cadeia da polimerase (ARN mensageiro de IFNg, IL1b, IL6, IL8, TNFa, TGFb1, iNOS) e o índice de massa corporal em repouso, acentuando-se após o exercício. Este estudo aponta a inflamação como o potencial elo de ligação entre a obesidade e a inflamação sistémica em doentes com DPOC. A segunda parte da tese focou a RR, nomeadamente os seus efeitos em doentes das categorias GOLD A, B, C e D; o impacto das comorbilidades nos resultados da RR e os resultados de diferentes intensidades de treino aeróbio. Após o programa de RR, verificaram-se melhorias significativas na capacidade de exercício funcional e de endurance e no estado geral de saúde dos doentes de todas as categorias GOLD. Esta classificação não distingue os doentes que melhor poderão beneficiar desta intervenção, indicando que devem ser referenciados para RR, os doentes sintomáticos ou com repercussão na qualidade de vida, independentemente da categoria da DPOC a que pertençam. A prevalência das comorbilidades no grupo de doentes com DPOC que é referenciado para RR, é elevada, sendo as mais frequentes, as cardiovasculares, as respiratórias e as psicológicas. Apesar de poderem diminuir o impacto da RR, os resultados desta foram semelhantes independentemente do número de comorbilidades. A identificação e o tratamento sistemáticos das comorbilidades conferem maior segurança clínica a esta intervenção terapêutica a qual, por apresentar bons resultados, não deve limitar a referenciação dos doentes. Com o programa de RR, verificou-se melhoria significativa em todos os resultados centrados no doente para ambas as intensidades de treino aeróbio, a 60% e a 80% da potência aeróbica máxima (Wmax), com melhoria do estado geral de saúde, nos sintomas e na capacidade para o exercício, o que questiona a indicação sistemática de elevadas intensidades de treino em doentes com DPOC para a obtenção de benefícios a curto prazo. Na terceira e última parte da tese foi estudado o papel da atividade física na DPOC, focando os fatores que influenciam a atividade física diária; a evolução da capacidade funcional e o estado de saúde 2 anos após um programa de RR e o papel da telemonitorização na quantificação e monitorização da atividade física. Confirmámos que os doentes com DPOC são marcadamente sedentários e os fatores que se associaram ao sedentarismo nestes doentes foram a dispneia e a distância percorrida na prova de marcha de seis minutos. Este estudo sublinha a importância do controlo sintomático, nomeadamente da dispneia, bem como, mais uma vez, o potencial papel da reabilitação respiratória no aumento da capacidade funcional para o exercício e na aquisição de hábitos de vida fisicamente ativa. Verificámos que, apesar de os doentes com DPOC apresentarem benefícios clinicamente significativos na capacidade funcional para o exercício e no estado geral de saúde com o programa de RR, apenas os que se mantêm ativos, podem, no final dos dois anos de seguimento, manter os efeitos benéficos desse programa. O sistema de telemonitorização que combina a oximetria e a quantificação da atividade física provou ser clinicamente útil na avaliação da necessidade de oxigenoterapia de longa duração (OLD) e na aferição do débito de oxigénio em repouso, no esforço e no sono, podendo contribuir para uma melhor adequação da prescrição da OLD. A monitorização dos níveis de atividade física regular é um importante instrumento de avaliação dos programas de RR e o seu uso potencial na telereabilitação permitirá prolongar a eficácia dos programas e reduzir os custos associados aos cuidados de saúde.---------------------------------------------------------------------------------------------------ABSTRACT: Pulmonary rehabilitation (PR) is a comprehensive interdisciplinary intervention that includes, but is not limited to, exercise training, education, and behavior change, individually designed to improve physical and psychological conditions of people with chronic respiratory disease and to promote long-term adherence to health-enhancing behaviors. Chronic obstructive pulmonary disease (COPD) is a common disease, affecting about 210 million people worldwide, with high mortality and significant health-related costs due to disease progression, hospitalizations and frequent hospital readmissions. Although the increasing knowledge about COPD and benefitial outcomes of PR, some aspects with impact in clinical practice, research and health authorities’ decisions, remain to be clarified. The first part of this thesis focused on COPD and its negative impact, including the study of COPD prevalence in Portugal; clinical and functional factors associated with mortality in advanced COPD patients; morbidity, functional impact and risk of others’ dependance to perform activities of daily living; and the role of systemic inflammation. The evidence of 14.2% estimated COPD prevalence as a common disease in Portugal raises the need of an increasing awareness of population, health care professionals and health authorities towards an earlier diagnosis and apropriate treatment resources allocation. High mortality in patients with advanced COPD – 36.6% in 3 years - was associated with respiratory failure, high frequency of exacerbations, lung cancer and a low functional capacity in walking. This highlightens the importance of an earlier referral to PR, comorbidity identification and treatment, and prevention of exacerbations. A questionnaire evaluated basic and instrumental activities of daily living, and identified a clinical marker of the risk of becoming dependent. This clinical marker complemented other functional evaluations and was associated with prognosis markers such as the number of exacerbations. In COPD patients with a mean FEV1 46.76% (SD 20.90%), 67% belonging to GOLD grade D, we found a positive association between inflammatory gene expression evaluated by polymerase chain reaction (IFNg, IL1b, IL6, IL8, TNFa, TGFb1, iNOS RNA messenger) and body mass index at rest, and a further increase with exercise. This study evidenced obesity as one potential link between COPD and systemic inflammation. The second part of this thesis focused PR, namely its outcomes in patients of GOLD categories A, B, C and D; comorbidities impact in PR outcomes, and the impact of different exercise training intensities in patient related outcomes. xviii With PR intervention, we found significant improvement in functional exercise capacity, endurance exercise capacity and health status in patients of all GOLD categories. This classification did not differentiate which patients would benefit more from PR, hence all symptomatic patients with a negative impact in health status should be referred to PR, regardless of the GOLD category they belong to. There is a high prevalence of comorbidities in COPD patients referred to PR, being cardiovascular, respiratory and psychological, the most prevalent. Although some comorbidities might reduce PR impact, the results were similar regardless of the number of comorbidities. Systematic comorbidities identification and treatment provides safety to PR intervention, and its good results should not preclude patients referral. With PR intervention we found a significant improvement in all patient reported outcomes for exercise training intensities at 60% and 80% maximum work rate (Wmax), namely in health status, symptoms and exercise capacity. These findings challenge the current systematic indication of high exercise training intensities to achieve PR short-term benefits. In the third and last part of the thesis, the role of physical activity in COPD was studied, focusing factors that may influence daily physical activity; the evolution of functional capacity and health status two years after a PR program, and the role of a telemonitoring system in physical activity quantification and monitoring. We confirmed that COPD patients are markedly inactive and factors associated with a sedentary lifestyle are dyspnea and 6 minute walking distance. This study emphasized the importance of symptom control, namely of dyspnea, as well as, once again, the potential role of PR in functional exercise improvement and in integrating physically active habits in daily life. We verified that, although COPD patients improve functional exercise capacity and health status after a PR program, only those who kept physical activity habits were able to maintain those effects after 2 years of follow-up. A telemonitoring system that combines oximetry and physical activity quantification proved to be clinically useful in the evaluation of long-term oxygen therapy (LTOT) indication, as well as in the titration of oxygen levels at rest, exertion, and sleeping, which might contribute to a more adequate LTOT prescription. Monitoring of daily physical activity levels is an important PR evaluation instrument and its potential use in telerehabilitation might allow lengthening programs efficacy, while reducing health-care costs.

Results of An International Study of Quantitative BCR/ABL Assays Using Defined RNA Samples

Molecular monitoring of BCR/ABL transcripts by real time quantitative reverse transcription PCR (qRT-PCR) is an essential technique for clinical management of patients with BCR/ABL-positive CML and ALL. Though quantitative BCR/ABL assays are performed in hundreds of laboratories worldwide, results among these laboratories cannot be reliably compared due to heterogeneity in test methods, data analysis, reporting, and lack of quantitative standards. Recent efforts towards standardization have been limited in scope. Aliquots of RNA were sent to clinical test centers worldwide in order to evaluate methods and reporting for e1a2, b2a2, and b3a2 transcript levels using their own qRT-PCR assays. Total RNA was isolated from tissue culture cells that expressed each of the different BCR/ABL transcripts. Serial log dilutions were prepared, ranging from 100 to 10-5, in RNA isolated from HL60 cells. Laboratories performed 5 independent qRT-PCR reactions for each sample type at each dilution. In addition, 15 qRT-PCR reactions of the 10-3 b3a2 RNA dilution were run to assess reproducibility within and between laboratories. Participants were asked to run the samples following their standard protocols and to report cycle threshold (Ct), quantitative values for BCR/ABL and housekeeping genes, and ratios of BCR/ABL to housekeeping genes for each sample RNA. Thirty-seven (n=37) participants have submitted qRT-PCR results for analysis (36, 37, and 34 labs generated data for b2a2, b3a2, and e1a2, respectively). The limit of detection for this study was defined as the lowest dilution that a Ct value could be detected for all 5 replicates. For b2a2, 15, 16, 4, and 1 lab(s) showed a limit of detection at the 10-5, 10-4, 10-3, and 10-2 dilutions, respectively. For b3a2, 20, 13, and 4 labs showed a limit of detection at the 10-5, 10-4, and 10-3 dilutions, respectively. For e1a2, 10, 21, 2, and 1 lab(s) showed a limit of detection at the 10-5, 10-4, 10-3, and 10-2 dilutions, respectively. Log %BCR/ABL ratio values provided a method for comparing results between the different laboratories for each BCR/ABL dilution series. Linear regression analysis revealed concordance among the majority of participant data over the 10-1 to 10-4 dilutions. The overall slope values showed comparable results among the majority of b2a2 (mean=0.939; median=0.9627; range (0.399 - 1.1872)), b3a2 (mean=0.925; median=0.922; range (0.625 - 1.140)), and e1a2 (mean=0.897; median=0.909; range (0.5174 - 1.138)) laboratory results (Fig. 1-3)). Thirty-four (n=34) out of the 37 laboratories reported Ct values for all 15 replicates and only those with a complete data set were included in the inter-lab calculations. Eleven laboratories either did not report their copy number data or used other reporting units such as nanograms or cell numbers; therefore, only 26 laboratories were included in the overall analysis of copy numbers. The median copy number was 348.4, with a range from 15.6 to 547,000 copies (approximately a 4.5 log difference); the median intra-lab %CV was 19.2% with a range from 4.2% to 82.6%. While our international performance evaluation using serially diluted RNA samples has reinforced the fact that heterogeneity exists among clinical laboratories, it has also demonstrated that performance within a laboratory is overall very consistent. Accordingly, the availability of defined BCR/ABL RNAs may facilitate the validation of all phases of quantitative BCR/ABL analysis and may be extremely useful as a tool for monitoring assay performance. Ongoing analyses of these materials, along with the development of additional control materials, may solidify consensus around their application in routine laboratory testing and possible integration in worldwide efforts to standardize quantitative BCR/ABL testing.

Regulatory RNA binding molecules : implication for diabetes pathogenesis

Le glucose est notre principale source d'énergie. Après un repas, le taux de glucose dans le sang (glycémie) augmente, ce qui entraine la sécrétion d'insuline. L'insuline est une hormone synthétisée au niveau du pancréas par des cellules dites bêta. Elle agit sur différents organes tels que les muscles, le foie ou le tissu adipeux, induisant ainsi le stockage du glucose en vue d'une utilisation future.¦Le diabète est une maladie caractérisée par un taux élevé de glucose dans le sang (hyperglycémie), résultant d'une incapacité de notre corps à utiliser ou à produire suffisamment d'insuline. A long terme, cette hyperglycémie entraîne une détérioration du système cardio-vasculaire ainsi que de nombreuses complications. On distingue principalement deux type de diabète : le diabète de type 1 et le diabète de type 2, le plus fréquent (environ 90% des cas). Bien que ces deux maladies diffèrent sur beaucoup de points, elles partagent quelques similitudes. D'une part, on décèle une diminution de la quantité de cellules bêta. Cette diminution est cependant partielle dans le cas d'un diabète de type 2, et totale dans celui d'un diabète de type 1. D'autre part, la présence dans la circulation de médiateurs de l'inflammation nommés cytokines est décelée aussi bien chez les patients de type 1 que de type 2. Les cytokines sont sécrétées lors d'une inflammation. Elles servent de moyen de communication entre les différents acteurs de l'inflammation et ont pour certaines un effet néfaste sur la survie des cellules bêta.¦L'objectif principal de ma thèse a été d'étudier en détail l'effet de petites molécules régulatrices de l'expression génique, appelées microARNs. Basé sur le fait que de nombreuses publications ont démontré que les microARNs étaient impliqués dans différentes maladies telles que le cancer, j'ai émis l'hypothèse qu'ils pouvaient également jouer un rôle important dans le développement du diabète.¦Nous avons commencé par mettre des cellules bêta en culture en présence de cytokines, imitant ainsi un environnement inflammatoire. Nous avons pu de ce fait identifier les microARNs dont les niveaux d'expression étaient modifiés. A l'aide de méthodes biochimiques, nous avons ensuite observé que la modulation de certains microARNs par les cytokines avaient des effets néfastes sur la cellule bêta : sur sa production et sa sécrétion d'insuline, ainsi que sur sa mort (apoptose). Nous avons en conséquence pu démontrer que ces petites molécules avaient un rôle important à jouer dans le dysfonctionnement des cellules bêta induit par les cytokines, aboutissant au développement du diabète.¦-¦La cellule bêta pancréatique est une cellule endocrine présente dans les îlots de Langerhans, dans le pancréas. L'insuline, une hormone sécrétée par ces cellules, joue un rôle essentiel dans la régulation de la glycémie. Le diabète se développe si le taux d'insuline relâché par les cellules bêta n'est pas suffisant pour couvrir les besoins métaboliques corporels. Le diabète de type 1, qui représente environ 5 à 10% des cas, est une maladie auto-immune qui se caractérise par une réaction inflammatoire déclenchée par notre système immunitaire envers les cellules bêta. La conséquence de cette attaque est une disparition progressive des cellules bêta. Le diabète de type 2 est, quant à lui, largement plus répandu puisqu'il représente environ 90% des cas. Des facteurs à la fois génétiques et environnementaux sont responsables d'une diminution de la sensibilité des tissus métabolisant l'insuline, ainsi que d'une réduction de la sécrétion de l'insuline par les cellules bêta, ce qui a pour conséquence le développement de la maladie. Malgré les différences entre ces deux types de diabète, ils ont pour points communs la présence d'infiltrat immunitaire et la diminution de l'état fonctionnel des cellules bêta.¦Une meilleure compréhension des mécanismes aboutissant à l'altération de la cellule bêta est primordiale, avant de pouvoir développer de nouvelles stratégies thérapeutiques capables de guérir cette maladie. Durant ma thèse, j'ai donc étudié l'implication de petites molécules d'ARN, régulatrices de l'expression génique, appelées microARNs, dans les conditions physiopathologiques qui aboutissent au développement du diabète. J'ai débuté mon étude par l'identification de microARNs dont le niveau d'expression était modifié lorsque les cellules bêta étaient exposées à des conditions favorisant à la fois le développement du diabète de type 1 (cytokines) et celui du diabète de type 2 (palmitate). Nous avons découvert qu'une modification de l'expression des miR-21, -34a et -146a était commune aux deux traitements. Ces changements d'expressions ont également été confirmés dans deux modèles animaux : les souris NOD qui développent un diabète s'apparentant au diabète de type 1 et les souris db/db qui développent plutôt un diabète de type 2. Puis, à l'aide de puces à ADN, nous avons comparé l'expression de microARNs chez des souris NOD pré-diabétiques. Nous avons alors retrouvé des changements au niveau de l'expression des mêmes microARNs mais également au niveau d'une famille de microARNs : les miR-29a, -29b et -29c. De manière artificielle, nous avons ensuite surexprimé ou inhibé en conditions physiopathologiques l'expression de tous ces microARNs et nous nous sommes intéressés à l'impact d'un tel changement sur différentes fonctions de la cellule bêta comme la synthèse et la sécrétion d'insulinè ainsi que leur survie. Nous avons ainsi pu démontrer que les miR-21, -34a, -29a, -29b, -29c avaient un effet délétère sur la sécrétion d'insuline et que la surexpression de tous ces microARNs (excepté le miR-21) favorisait la mort. Finalement, nous avons démontré que la plupart de ces microARNs étaient impliqués dans la régulation d'importantes voies de signalisation responsables de l'apoptose des cellules bêta telles que les voies de NFKB, BCL2 ou encore JNK.¦Par conséquent, nos résultats démontrent que les microARNs ont un rôle important à jouer dans le dysfonctionnement des cellules bêta lors de la mise en place du diabète.

Insulin secretion is regulated by the glucose-dependent production of islet beta cell macrophage migration inhibitory factor.

Macrophage migration inhibitory factor (MIF), originally identified as a cytokine secreted by T lymphocytes, was found recently to be both a pituitary hormone and a mediator released by immune cells in response to glucocorticoid stimulation. We report here that the insulin-secreting beta cell of the islets of Langerhans expresses MIF and that its production is regulated by glucose in a time- and concentration-dependent manner. MIF and insulin colocalize by immunocytochemistry within the secretory granules of the pancreatic islet beta cells, and once released, MIF appears to regulate insulin release in an autocrine fashion. In perifusion studies performed with isolated rat islets, immunoneutralization of MIF reduced the first and second phase of the glucose-induced insulin secretion response by 39% and 31%, respectively. Conversely, exogenously added recombinant MIF was found to potentiate insulin release. Constitutive expression of MIF antisense RNA in the insulin-secreting INS-1 cell line inhibited MIF protein synthesis and decreased significantly glucose-induced insulin release. MIF is therefore a glucose-dependent, islet cell product that regulates insulin secretion in a positive manner and may play an important role in carbohydrate metabolism.

An atlas of human gene expression from massively parallel signature sequencing (MPSS).

We have used massively parallel signature sequencing (MPSS) to sample the transcriptomes of 32 normal human tissues to an unprecedented depth, thus documenting the patterns of expression of almost 20,000 genes with high sensitivity and specificity. The data confirm the widely held belief that differences in gene expression between cell and tissue types are largely determined by transcripts derived from a limited number of tissue-specific genes, rather than by combinations of more promiscuously expressed genes. Expression of a little more than half of all known human genes seems to account for both the common requirements and the specific functions of the tissues sampled. A classification of tissues based on patterns of gene expression largely reproduces classifications based on anatomical and biochemical properties. The unbiased sampling of the human transcriptome achieved by MPSS supports the idea that most human genes have been mapped, if not functionally characterized. This data set should prove useful for the identification of tissue-specific genes, for the study of global changes induced by pathological conditions, and for the definition of a minimal set of genes necessary for basic cell maintenance. The data are available on the Web at http://mpss.licr.org and http://sgb.lynxgen.com.

Phenotypic consequences of copy number variation: insights from Smith-Magenis and Potocki-Lupski syndrome mouse models.

A large fraction of genome variation between individuals is comprised of submicroscopic copy number variation of genomic DNA segments. We assessed the relative contribution of structural changes and gene dosage alterations on phenotypic outcomes with mouse models of Smith-Magenis and Potocki-Lupski syndromes. We phenotyped mice with 1n (Deletion/+), 2n (+/+), 3n (Duplication/+), and balanced 2n compound heterozygous (Deletion/Duplication) copies of the same region. Parallel to the observations made in humans, such variation in gene copy number was sufficient to generate phenotypic consequences: in a number of cases diametrically opposing phenotypes were associated with gain versus loss of gene content. Surprisingly, some neurobehavioral traits were not rescued by restoration of the normal gene copy number. Transcriptome profiling showed that a highly significant propensity of transcriptional changes map to the engineered interval in the five assessed tissues. A statistically significant overrepresentation of the genes mapping to the entire length of the engineered chromosome was also found in the top-ranked differentially expressed genes in the mice containing rearranged chromosomes, regardless of the nature of the rearrangement, an observation robust across different cell lineages of the central nervous system. Our data indicate that a structural change at a given position of the human genome may affect not only locus and adjacent gene expression but also "genome regulation." Furthermore, structural change can cause the same perturbation in particular pathways regardless of gene dosage. Thus, the presence of a genomic structural change, as well as gene dosage imbalance, contributes to the ultimate phenotype.

Alveolar macrophages and lung dendritic cells sense RNA and drive mucosal IgA responses.

The mechanisms regulating systemic and mucosal IgA responses in the respiratory tract are incompletely understood. Using virus-like particles loaded with single-stranded RNA as a ligand for TLR7, we found that systemic vs mucosal IgA responses in mice were differently regulated. Systemic IgA responses following s.c. immunization were T cell independent and did not require TACI or TGFbeta, whereas mucosal IgA production was dependent on Th cells, TACI, and TGFbeta. Strikingly, both responses required TLR7 signaling, but systemic IgA depended upon TLR7 signaling directly to B cells whereas mucosal IgA required TLR7 signaling to lung dendritic cells and alveolar macrophages. Our data show that IgA switching is controlled differently according to the cell type receiving TLR signals. This knowledge should facilitate the development of IgA-inducing vaccines.

PHYTOCHROME KINASE SUBSTRATE4 modulates phytochrome-mediated control of hypocotyl growth orientation

Gravity and light are major factors shaping plant growth. Light perceived by phytochromes leads to seedling deetiolation, which includes the deviation from vertical hypocotyl growth and promotes hypocotyl phototropism. These light responses enhance survival of young seedlings during their emergence from the soil. The PHYTOCHROME KINASE SUBSTRATE (PKS) family is composed of four members in Arabidopsis (Arabidopsis thaliana): PKS1 to PKS4. Here we show that PKS4 is a negative regulator of both phytochrome A- and B-mediated inhibition of hypocotyl growth and promotion of cotyledon unfolding. Most prominently, pks4 mutants show abnormal phytochrome-modulated hypocotyl growth orientation. In dark-grown seedlings hypocotyls change from the original orientation defined by seed position to the upright orientation defined by gravity and light reduces the magnitude of this shift. In older seedlings with the hypocotyls already oriented by gravity, light promotes the deviation from vertical orientation. Based on the characterization of pks4 mutants we propose that PKS4 inhibits changes in growth orientation under red or far-red light. Our data suggest that in these light conditions PKS4 acts as an inhibitor of asymmetric growth. This hypothesis is supported by the phenotype of PKS4 overexpressers. Together with previous findings, these results indicate that the PKS family plays important functions during light-regulated tropic growth responses

Alteration of glucose metabolism in cultured astrocytes after AQP9-small interference RNA application.

Aquaglyceroporin-9 (AQP9) facilitates diffusion of water and energy substrates such as glycerol and monocarboxylates. AQP9 is present in plasma membrane and mitochondria of astrocytes and catecholaminergic neurons, suggesting that it plays a role in the energetic status of these cells. Using specific small interference RNA directed against AQP9 in astrocyte cultures, we showed that glycerol uptake is decreased which is associated with an increase in glucose uptake and oxidative metabolism. Our results not only confirm the presence of AQP9 in astrocytes but also suggest that changes in AQP9 expression alter glial energy metabolism.

Temporal changes in mRNA expression of the brain nutrient transporters in the lithium-pilocarpine model of epilepsy in the immature and adult rat.

The lithium-pilocarpine model mimics most features of human temporal lobe epilepsy. Following our prior studies of cerebral metabolic changes, here we explored the expression of transporters for glucose (GLUT1 and GLUT3) and monocarboxylates (MCT1 and MCT2) during and after status epilepticus (SE) induced by lithium-pilocarpine in PN10, PN21, and adult rats. In situ hybridization was used to study the expression of transporter mRNAs during the acute phase (1, 4, 12 and 24h of SE), the latent phase, and the early and late chronic phases. During SE, GLUT1 expression was increased throughout the brain between 1 and 12h of SE, more strongly in adult rats; GLUT3 increased only transiently, at 1 and 4h of SE and mainly in PN10 rats; MCT1 was increased at all ages but 5-10-fold more in adult than in immature rats; MCT2 expression increased mainly in adult rats. At all ages, MCT1 and MCT2 up-regulation was limited to the circuit of seizures while GLUT1 and GLUT3 changes were more widespread. During the latent and chronic phases, the expression of nutrient transporters was normal in PN10 rats. In PN21 rats, GLUT1 was up-regulated in all brain regions. In contrast, in adult rats GLUT1 expression was down-regulated in the piriform cortex, hilus and CA1 as a result of extensive neuronal death. The changes in nutrient transporter expression reported here further support previous findings in other experimental models demonstrating rapid transcriptional responses to marked changes in cerebral energetic/glucose demand.

The G0/G1 switch gene 2 is a novel PPAR target gene.

PPARs (peroxisome-proliferator-activated receptors) alpha, beta/delta and gamma are a group of transcription factors that are involved in numerous processes, including lipid metabolism and adipogenesis. By comparing liver mRNAs of wild-type and PPARalpha-null mice using microarrays, a novel putative target gene of PPARalpha, G0S2 (G0/G1 switch gene 2), was identified. Hepatic expression of G0S2 was up-regulated by fasting and by the PPARalpha agonist Wy14643 in a PPARalpha-dependent manner. Surprisingly, the G0S2 mRNA level was highest in brown and white adipose tissue and was greatly up-regulated during mouse 3T3-L1 and human SGBS (Simpson-Golabi-Behmel syndrome) adipogenesis. Transactivation, gel shift and chromatin immunoprecipitation assays indicated that G0S2 is a direct PPARgamma and probable PPARalpha target gene with a functional PPRE (PPAR-responsive element) in its promoter. Up-regulation of G0S2 mRNA seemed to be specific for adipogenesis, and was not observed during osteogenesis or myogenesis. In 3T3-L1 fibroblasts, expression of G0S2 was associated with growth arrest, which is required for 3T3-L1 adipogenesis. Together, these data indicate that G0S2 is a novel target gene of PPARs that may be involved in adipocyte differentiation.