Caractérisation de la SERPINA1, une antiprotéase différentiellement exprimée dans le cancer épithélial de l’ovaire

Le cancer épithélial de l’ovaire est le cancer gynécologique le plus létal. La survie à 5 ans est de 30-40% chez les patientes atteintes d’une tumeur invasive (TOV), comparativement à 95% chez les patientes diagnostiquées pour une tumeur à faible potentiel de malignité ou borderline (LMP). Au laboratoire, l’analyse de l’expression des gènes de la micropuce à ADN U133 d’Affymetrix a révélé que la SERPINA1 est un gène dont l’expression varie entre les tumeurs LMP et TOV. La validation par Q-PCR nous a confirmé que cette antiprotéase est majoritairement surexprimée dans les tumeurs LMP, par rapport aux tumeurs bénignes (BOV) et aux tumeurs TOV. Nous avons donc surexprimé la SERPINA1 dans les lignées cellulaires invasives TOV 112D et TOV 1946 du cancer de l’ovaire et dérivé des clones stables. Les résultats obtenus nous indiquent que la surexpression de la SERPINA1 a un effet sur la capacité d’invasion et de migration cellulaire et non au niveau de la croissance cellulaire et la formation de structures tridimensionnelles. Les résultats issus de l’étude in vivo dans les souris SCID nous permettront de déterminer si la surexpression de la SERPINA1 a un effet sur la tumorigénèse ovarienne. Ainsi, la SERPINA1 demeure à notre avis un candidat d’intérêt pour tenter de mieux comprendre les différences biologiques entre les tumeurs LMP et TOV, ainsi que le rôle des protéases et de leurs inhibiteurs dans la progression tumorale du cancer de l’ovaire.

The orphan nuclear receptor, liver receptor homolog-1 (LRH-1, NR5A2) regulates decidualization

La période de réceptivité endométriale chez l’humain coïncide avec la différentiation des cellules stromales de l’endomètre en cellules hautement spécifiques, les cellules déciduales, durant le processus dit de décidualisation. Or, on sait qu’une transformation anormale des cellules endométriales peut être à l’origine de pertes récurrentes de grossesses. LRH-1 est un récepteur nucléaire orphelin et un facteur de transcription régulant de nombreux évènements relatif à la reproduction et comme tout récepteur, son activation promouvoit l’activité transcriptionnelle de ses gènes cibles. Nous avons déjà montré que LRH-1 et son activité sont essentiels pour la décidualisation au niveau de l’utérus chez la souris et nous savons qu’il est présent dans l’utérus chez l’humain au moment de la phase de prolifération mais aussi de sécrétion du cycle menstruel, et que son expression augmente dans des conditions de décidualisation in vitro. Notre hypothèse est alors la suivante : LRH-1 est indispensable à la décidualisation du stroma endométrial, agissant par le biais de la régulation transcriptionnelle de gènes requis pour la transformation de cellules stromales en cellules déciduales. Afin d’explorer le mécanisme moléculaire impliqué dans la régulation transcriptionnelle effectuée par l’intermédiaire de ce récepteur, nous avons mis en place un modèle de décidualisation in vitro utilisant une lignée de cellules stromales de l’endomètre, cellules humaines et immortelles (hESC). Notre modèle de surexpression développé en transfectant les dites cellules avec un plasmide exprimant LRH-1, résulte en l’augmentation, d’un facteur 5, de l’abondance du transcriptome de gènes marqueurs de la décidualisation que sont la prolactine (PRL) et l’insulin-like growth factor binding protein-1 (IGFBP-1). En outre, la sous-régulation de ce récepteur par l’intermédiaire de petits ARN interférents (shRNA) abolit la réaction déciduale, d’un point de vue morphologique mais aussi en terme d’expression des deux gènes marqueurs cités ci-dessus. Une analyse par Chromatin ImmunoPrécipitation (ou ChIP) a démontré que LRH-1 se lie à des régions génomiques se trouvant en aval de certains gènes importants pour la décidualisation comme PRL, WNT 4, WNT 5, CDKN1A ou encore IL-24, et dans chacun de ces cas cités, cette capacité de liaison augmente dans le cadre de la décidualisation in vitro. Par ailleurs, des études structurelles ont identifié les phospholipides comme des ligands potentiels pour LRH-1. Nous avons donc choisi d’orienter notre travail de façon à explorer les effets sur les ligands liés à LRH-1 de traitements impliquant des agonistes et antagonistes à notre récepteur nucléaire. Les analyses par q-PCR et Western blot ont montré que la modulation de l’activité de LRH-1 par ses ligands influait aussi sur la réaction déciduale. Enfin, des études récentes de Salker et al (Salker, Teklenburg et al. 2010) ont mis en évidence que les cellules stromales humaines décidualisées sont de véritables biocapteurs de la qualité embryonnaire et qu’elles ont la capacité de migrer en direction de l’embryon. La série d’expériences que nous avons réalisée à l’aide de cellules hESC placées en co-culture avec des embryons de souris confirme que la migration cellulaire est bien dirigée vers les embryons. Cette propriété quant à l’orientation de la migration cellulaire est notoirement diminuée dans le cas où l’expression de LRH-1 est déplétée par shRNA dans les hESC. Nos données prouvent donc que LRH-1 régule non seulement la transcription d’un ensemble de gènes impliqués dans le processus de décidualisation mais agit aussi sur la motilité directionnelle de ces cellules hESC décidualisées in vitro.

Untersuchungen zur Verbreitung von Klasse II-Transposons wie Tn21, Tn501 und Tn3 in terrestrischen Habitaten

Mobile genetische Elementen wie Transposons wurden in unbelasteten Böden nachgewiesen. Hierzu wurden unterschiedliche Ansätze gewählt: Verschiedene, unbelastete Böden wurden mittels PCR auf das Vorhandensein von Markergenen, in diesem Fall Transposasen vom Typ Tn3, Tn21 und Tn501, hin untersucht. Hierzu wurde ein System entwickelt, welches es ermöglichte die Gesamt-DNA aus verschiedensten Böden mit einem System einfach und reproduzierbar zu extrahieren und anschließend mittels PCR zu untersuchen. Die mittlere Nachweisgrenze dieses Systems lag bei 9 x 10 *3 Templates / g Boden. Ein paralleler Ansatz erfolgte, indem aus den gleichen, unbelasteten Böden Bakterien mittels Selektivmedien isoliert wurden. Diese Isolate wurden anschließend auf genetische Marker hin untersucht. Transposons, bzw. Transposasen konnten in den unbelasteten Böden in weitaus geringerer Zahl als aus belasteten Böden bekannt nachgewiesen werden. Jedoch verhielten sich die unterschiedlichen Elemente in der Verteilung wie aus belasteten Böden bekannt. Am häufigsten wurde Tn21 dann Tn501 nachgewiesen. Tn3, nach dem auch gescreent wurde, konnte nicht nachgewiesen werden. Anschließend wurden diese Böden mittels Bodensäulen unter Laborbedingungen auf die Übertragung von potentiell transponierbaren Elementen aus der autochthonen Flora hin untersucht. Mittels dieses Experimentes konnte kein transponierbares Element nachgewiesen werden. Weiterhin wurden vorhandene Boden-Bakterienkollektive auf das Vorhandensein von Transposons mittels Gensondentechnik und PCR auf Transposasen hin gescreent. Auch hier konnten wiederum Signale zu Tn21, Tn501 und in diesem Falle auch Tn3 erhalten werden. Einige dieser Isolate wurden mittels Southern-Blot und Sequenzierung näher charakterisiert. Bei den Sequenzvergleichen einer so erhaltenen 2257 bp langen Sequenz wurde diese als Transposase der Tn21-Familie mit großer Homologie zur Transposase von Tn5060 bestimmt.

A process for analysis of microarray comparative genomics hybridisation studies for bacterial genomes

Background: Microarray based comparative genomic hybridisation (CGH) experiments have been used to study numerous biological problems including understanding genome plasticity in pathogenic bacteria. Typically such experiments produce large data sets that are difficult for biologists to handle. Although there are some programmes available for interpretation of bacterial transcriptomics data and CGH microarray data for looking at genetic stability in oncogenes, there are none specifically to understand the mosaic nature of bacterial genomes. Consequently a bottle neck still persists in accurate processing and mathematical analysis of these data. To address this shortfall we have produced a simple and robust CGH microarray data analysis process that may be automated in the future to understand bacterial genomic diversity. Results: The process involves five steps: cleaning, normalisation, estimating gene presence and absence or divergence, validation, and analysis of data from test against three reference strains simultaneously. Each stage of the process is described and we have compared a number of methods available for characterising bacterial genomic diversity, for calculating the cut-off between gene presence and absence or divergence, and shown that a simple dynamic approach using a kernel density estimator performed better than both established, as well as a more sophisticated mixture modelling technique. We have also shown that current methods commonly used for CGH microarray analysis in tumour and cancer cell lines are not appropriate for analysing our data. Conclusion: After carrying out the analysis and validation for three sequenced Escherichia coli strains, CGH microarray data from 19 E. coli O157 pathogenic test strains were used to demonstrate the benefits of applying this simple and robust process to CGH microarray studies using bacterial genomes.

High genetic diversity in field isolates of Trypanosoma theileri assessed by analysis of cathepsin L-like sequences disclosed multiple and new genotypes infecting cattle in Thailand

In this study, we describe the first survey in Thailand of Trypanosoma theileri, a widespread and prevalent parasite of cattle that is transmitted by tabanid flies. Investigation of 210 bovine blood samples of Thai cattle from six farms by hematocrit centrifuge technique (HCT) revealed 14 samples with trypanosomes morphologically compatible to T. theileri. Additional animals were positive for T. theileri by PCR based on the Cathepsin L-like sequence (TthCATL-PCR) despite negative by HCT, indicating cryptic infections. Results revealed a prevalence of 26 +/- 15% (95% CI) of T. theileri infection. Additionally, 12 samples positive for T. theileri were detected in cattle from other 11 farms. From a total of 30 blood samples positive by HCT and/or PCR from 17 farms, seven were characterized to evaluate the genetic polymorphism of T. theileri through sequence analysis of PCR-amplified CATL DNA sequences. All CATL sequences of T. theileri from Thai cattle clustered with sequences of the previously described phylogenetic lineages TthI and TthII, supporting only two major lineages of T. theileri in cattle around the world. However, 11 of the 29 CATL sequences analyzed showed to be different, disclosing an unexpectedly large polymorphic genetic repertoire, with multiple genotypes of T. theileri not previously described in other countries circulating in Thai cattle. (C) 2011 Elsevier B.V. All rights reserved.

Multi-objective clustering ensemble for gene expression data analysis

In this paper, we present an algorithm for cluster analysis that integrates aspects from cluster ensemble and multi-objective clustering. The algorithm is based on a Pareto-based multi-objective genetic algorithm, with a special crossover operator, which uses clustering validation measures as objective functions. The algorithm proposed can deal with data sets presenting different types of clusters, without the need of expertise in cluster analysis. its result is a concise set of partitions representing alternative trade-offs among the objective functions. We compare the results obtained with our algorithm, in the context of gene expression data sets, to those achieved with multi-objective Clustering with automatic K-determination (MOCK). the algorithm most closely related to ours. (C) 2009 Elsevier B.V. All rights reserved.

Determinação de prevalência de bactérias na efusão da orelha média de crianças submetidas à mmiringotomia

Introdução: A etiologia da otite média com efusão ainda não está completamente estabelecida, mas agentes infecciosos podem contribuir para sua patogênese. Demonstrou-se que a reação em cadeia da polimerase (PCR) é superior ao exame cultural para detectar espécies bacterianas. O conhecimento sobre a epidemiologia bacteriana da otite média com efusão em áreas geográficas distintas é essencial para a implementação de tratamentos racionais, quando necessários. Objetivos: Determinar a prevalência do Streptococcus pneumoniae, Haemophilus influenzae, Moraxella catarrhalis e Alloiococcus otitidis nas efusões de orelha média de crianças com otite média recorrente e otite média com efusão crônica que foram submetidas à miringotomia, comparar os resultados obtidos por cultura e PCR, comparar os achados bacteriológicos em crianças menores e maiores de dois anos e determinar o perfil de resistência à penicilina dos germes isolados. Métodos: Analisaram-se 128 amostras de efusões de orelha média de 75 crianças entre 11 meses e 9 anos e 4 meses de idade (média = 34,7 meses). Pacientes com otite média recorrente tinham efusão documentada por ≥ 6 semanas e aqueles com otite média com efusão crônica, por ≥3 meses. Os pacientes não tinham sinais de otite média aguda ou infecção do trato respiratório e não estavam sob antibioticoterapia no momento do procedimento. A aspiração do material foi realizada por timpanocentese, utilizando-se um coletor de Alden-Senturia. Os estudos bacteriológicos foram iniciados em menos de 15 minutos após a obtenção da efusão e uma parte da amostra foi armazenada a -20oC para análise posterior pela PCR. Utilizou-se um método de PCR simultânea para a detecção de quatro patógenos. A análise estatística foi efetivada com o teste χ2 de McNemar, teste χ2 com correção de Yates e teste exato de Fisher, quando apropriados. Resultados: Cultivaram-se bactérias em 32 (25,1%) das 128 amostras e os patógenos principais foram encontrados em 25 (19,6%). O A. otitidis não foi isolado em cultura. A PCR identificou bactérias em 110 (85,9%) das amostras, e os resultados positivos foram: 67 (52,3%) para A. otitidis, 50 (39,1%) para H. influenzae, 16 (12,5%) para S. pneumoniae e 13 (10,2%) para M. catarrhalis. Todas as amostras positivas por cultura foram positivas pela PCR, mas 85 (77,2%) das efusões com resultado positivo pela PCR foram negativas por cultura, para os germes estudados. A PCR foi significativamente mais sensível que a cultura (P<0,001). O S. pneumoniae foi encontrado mais freqüentemente em otite média recorrente do que em otite média com efusão crônica (P=0,038) e o H. influenzae foi encontrado mais vezes em crianças menores de dois anos (P=0,049). Quanto ao perfil de resistência, 100% das M. catarrhalis, 62,5% dos S. pneumoniae e 23% dos H. influenzae eram resistentes à penicilina. Conclusões: A prevalência das bactérias na otite média com efusão em um grupo de crianças brasileiras é semelhante àquelas relatadas em outros países, sendo o H. influenzae o mais encontrado dentre os patógenos principais da orelha média. Essa prevalência sugere que bactérias podem desempenhar um papel na patogênese da otite média com efusão. Os resultados mostram que a PCR é mais sensível na detecção de bactérias na efusão da orelha média, comparada com cultura, e é essencial para a identificação do A. otitidis. O elevado percentual de detecção do A. otitidis sugere mais investigações sobre sua atuação no início e no prolongamento de doenças da orelha média. O S. pneumoniae foi mais freqüente em otite média recorrente do que em otite média com efusão crônica e o H. influenzae foi mais encontrado em crianças menores de dois anos. A resistência à penicilina por parte do pneumococo e da moraxela é semelhante à relatada em outros países, ao passo que a produção de β-lactamase pelo hemófilo é mais baixa que aquela referida em bactérias isoladas em amostras de efusões de otite média com efusão.

Disparity between Multilocus Enzyme Electrophoresis, Microsatellite Markers and Pulsed-Field Gel Electrophoresis in epidemiological tracking of Candida albicans

Various molecular systems are available for epidemiological, genetic, evolutionary, taxonomic and systematic studies of innumerable fungal infections, especially those caused by the opportunistic pathogen C. albicans. A total of 75 independent oral isolates were selected in order to compare Multilocus Enzyme Electrophoresis (MLEE), Electrophoretic Karyotyping (EK) and Microsatellite Markers (Simple Sequence Repeats - SSRs), in their abilities to differentiate and group C. albicans isolates (discriminatory power), and also, to evaluate the concordance and similarity of the groups of strains determined by cluster analysis for each fingerprinting method. Isoenzyme typing was performed using eleven enzyme systems: Adh, Sdh, M1p, Mdh, Idh, Gdh, G6pdh, Asd, Cat, Po, and Lap (data previously published). The EK method consisted of chromosomal DNA separation by pulsed-field gel electrophoresis using a CHEF system. The microsatellite markers were investigated by PCR using three polymorphic loci: EF3, CDC3, and HIS3. Dendrograms were generated by the SAHN method and UPGMA algorithm based on similarity matrices (S(SM)). The discriminatory power of the three methods was over 95%, however a paired analysis among them showed a parity of 19.7-22.4% in the identification of strains. Weak correlation was also observed among the genetic similarity matrices (S(SM)(MLEE) x S(SM)(EK) x S(SM)(SSRs)). Clustering analyses showed a mean of 9 +/- 12.4 isolates per cluster (3.8 +/- 8 isolates/taxon) for MLEE, 6.2 +/- 4.9 isolates per cluster (4 +/- 4.5 isolates/taxon) for SSRs, and 4.1 +/- 2.3 isolates per cluster (2.6 +/- 2.3 isolates/taxon) for EK. A total of 45 (13%), 39(11.2%), 5 (1.4%) and 3 (0.9%) clusters pairs from 347 showed similarity (Si) of 0.1-10%, 10.1-20%, 20.1-30% and 30.1-40%, respectively. Clinical and molecular epidemiological correlation involving the opportunistic pathogen C. albicans may be attributed dependently of each method of genotyping (i.e., MLEE, EK, and SSRs) supplemented with similarity and grouping analysis. Therefore, the use of genotyping systems that give results which offer minimum disparity, or the combination of the results of these systems, can provide greater security and consistency in the determination of strains and their genetic relationships. (C) 2010 Elsevier B.V. All rights reserved.

Searching for molecular markers in head and neck squamous cell carcinomas (HNSCC) by statistical and bioinformatic analysis of larynx-derived SAGE libraries

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Hypothalamic melanin-concentrating hormone is induced by cold exposure and participates in the control of energy expenditure in rats

Short-term cold exposure of homeothermic animals leads to higher thermogenesis and food consumption accompanied by weight loss. An analysis of cDNA-macroarray was employed to identify candidate mRNA species that encode proteins involved in thermogenic adaptation to cold. A cDNA-macroarray analysis, confirmed by RT-PCR, immunoblot, and RIA, revealed that the hypothalamic expression of melanin-concentrating hormone (MCH) is enhanced by exposure of rats to cold environment. The blockade of hypothalamic MCH expression by antisense MCH oligonucleotide in cold-exposed rats promoted no changes in feeding behavior and body temperature. However, MCH blockade led to a significant drop in body weight, which was accompanied by decreased liver glycogen, increased relative body fat, increased absolute and relative interscapular brown adipose tissue mass, increased uncoupling protein 1 expression in brown adipose tissue, and increased consumption of lean body mass. Thus, increased hypothalamic MCH expression in rats exposed to cold may participate in the process that allows for efficient use of energy for heat production during thermogenic adaptation to cold.

RAPD genomic fingerprinting differentiates Thiobacillus ferrooxidans strains

The PCR-based technique, involving the random amplification of polymorphic DNA (RAPD), was optimized and used for assessing genomic variability among eight Thiobacillus ferrooxidans strains. RAPD fingerprints presented variation for the thirty primers used, giving a total of 269 polymorphic bands. Similarity coefficients between the strains were calculated, and UPGMA cluster analysis was used to generate a dendrogram showing relationships among them. Most primers divided T. ferrooxidans strains in two distinct groups - Group 1: S, SSP, V3, AMF and Group 2: CMV, FG-460, I-35, LR. We observed that the T. ferrooxidans strains used in this work have a high degree of genomic diversity and that RAPD is a powerful method to differentiate them.

Increased Levels of NOTCH1, NF-kappa B, and Other Interconnected Transcription Factors Characterize Primitive Sets of Hematopoietic Stem Cells

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

rDNA-RFLP identification of Candida species in immunocompromised and seriously diseased patients

PCR was used to amplify a targeted region of the ribosomal DNA of 76 Candida spp. isolates from immunocompromised and seriously diseased patients. Thirty-seven strains isolated from different anatomical sites of 11 patients infected with HIV (Vitória, ES, Brazil), 26 isolates from patients under treatment at Odilon Behrens Hospital and 13 isolates from skin and urine samples from São Marcos Clinical Analysis Laboratory (Belo Horizonte, Brazil) were scored. Fragments of rDNA were amplified using primer pairs ITS1-ITS4, for the amplification of ITS1 and ITS2 regions, including the gene for the 5.8s subunit. Amplification resulted in fragments ranging in size from 350 to 950 bp. Amplicons were digested with eight restriction enzymes. A pattern of species-specificity among the different medically important Candida species could be identified following restriction digestion of the PCR products. Candida albicans was the species most frequently observed, except for the group of newborns under treatment at the Odilon Behrens Hospital and for the isolates from the clinical analysis laboratory. C. parapsilosis was the species most frequently observed in these two groups.

An Integrative Genomic and Transcriptomic Analysis Reveals Potential Targets Associated with Cell Proliferation in Uterine Leiomyomas

Background: Uterine Leiomyomas (ULs) are the most common benign tumours affecting women of reproductive age. ULs represent a major problem in public health, as they are the main indication for hysterectomy. Approximately 40-50% of ULs have non-random cytogenetic abnormalities, and half of ULs may have copy number alterations (CNAs). Gene expression microarrays studies have demonstrated that cell proliferation genes act in response to growth factors and steroids. However, only a few genes mapping to CNAs regions were found to be associated with ULs. Methodology: We applied an integrative analysis using genomic and transcriptomic data to identify the pathways and molecular markers associated with ULs. Fifty-one fresh frozen specimens were evaluated by array CGH (JISTIC) and gene expression microarrays (SAM). The CONEXIC algorithm was applied to integrate the data. Principal Findings: The integrated analysis identified the top 30 significant genes (P<0.01), which comprised genes associated with cancer, whereas the protein-protein interaction analysis indicated a strong association between FANCA and BRCA1. Functional in silico analysis revealed target molecules for drugs involved in cell proliferation, including FGFR1 and IGFBP5. Transcriptional and protein analyses showed that FGFR1 (P = 0.006 and P<0.01, respectively) and IGFBP5 (P = 0.0002 and P = 0.006, respectively) were up-regulated in the tumours when compared with the adjacent normal myometrium. Conclusions: The integrative genomic and transcriptomic approach indicated that FGFR1 and IGFBP5 amplification, as well as the consequent up-regulation of the protein products, plays an important role in the aetiology of ULs and thus provides data for potential drug therapies development to target genes associated with cellular proliferation in ULs. © 2013 Cirilo et al.

Reação de 16 porta-enxertos sob laranjeira 'Valência' ao agente causal, Candidatus Liberibacter asiaticus

Pós-graduação em Agronomia (Genética e Melhoramento de Plantas) - FCAV