Analyse de données d’expression transcriptomiques rythmées par des gènes-horloge : approche méthodologique et optimisation

Background

In microarray data, wide-scale correlations are numerous and increase the number of genes correlated to a test condition (phenotype, mutation status, etc.) either positively or negatively. Several methods have been developed to limit the effect of such correlations on the false discovery rate, but these may reject too many genes that have a mild or indirect impact on the studied condition. We propose here a simple methodology to correct this spurious effect without eliminating weak but true correlations.

Results

This methodology was applied to a microarray dataset designed to distinguish heterozygous BRCA1 mutation carriers from non-carriers. As our samples were collected at different times in the morning, we evaluated the effect of correlations due to circadian rhythm. The circadian system is a well-known correlation network, regulated by a small number of period genes whose expression varies throughout the day in predictable ways. The downstream effects of this variation on the expression of other genes, however, are incompletely characterized. We used two different strategies to correct this correlation bias, by either dividing or multiplying the expression of correlated genes by the expression of the considered period gene according to the sign of the correlation between the period gene and correlated gene (respectively positive or negative).

Conclusions

We observed a linear relationship between the number of false-positive/negative genes and the strength of the correlation of the candidate gene to the test condition. BRCA1 was highly correlated to the period gene Per1; our correction methodology enabled us to recover genes coding for BRCA1-interacting proteins which were not selected in the initial direct analysis. This methodology may be valuable for other studies and can be applied very easily in case of well-known correlation networks.     

Introduction à l’analyse spectrale des réseaux microvasculaires du mélanome cutané primitif

Cutaneous malignant melanoma represents one of the most dramatic skin cancers because its incidence is steadily growing in White populations. Of note, its metastatic risk and mortality dramatically increase when the primary neoplasm reaches about one millimeter thick. It is believed that angiogenesis and lymphangiogenesis associated with cutaneous melanoma potentially influence the neoplastic progression of the primary tumor and its metastases. In some instances, both the intratumoral and peritumoral microvasculature are correlated to booming of the tumoral growth fraction. In addition, the vascular network serves as a migration path for the intravascular and perivascular neoplastic spread. Hence, the quantification of the microvasculature might help establishing a prognostic factor of evolution. Among the available methods, spectral analysis of immunohistochemical sections highlighting vessels helps defining the microvasculature distribution. The benefit of using spectral analysis is discussed and the modalities of application of this analytical method are scrutinized.     

Candida dubliniensis : méthodes d’identification et implications épidémiologiques

Candida dubliniensis was recently described (1995) associated with oral candidiasis in HIV-positive patients. This organism is very closely related to the pathogenic human yeast, Candida albicans, and share a great number of phenotypic and genotypic characters. This great similarity limits the discrimination between these two species. Several phenotypic and molecular methods were developed. The phenotypic methods are simply used in routine discrimination between these two species and depend on the growth at high temperature, sugar assimilation, growth on special mediums and chlamydospore production…; but these methods are insensitive in discrimination between these two species. The molecular biology methods are highly reliable and able to confirm rapidly the identification of this specie. In this article, we will review the various studies run out concerning the methods deployed for the identification of C. dubliniensis as well as the epidemiological implication of this new pathogen.     

Rôle de la protéine de stress p8 dans la progression tumorale et le développement des métastases

In spite of the great advances made on the knowledge of cancer etiology and the significant breakthroughs in terms of treatment, complete remission is obtained in only around half of cancer patients. In fact, therapies that appear successful for some cancers are totally unfruitful for others, and some cancer types still remain incurables. In order to develop new therapies suitable to these tenacious cancers, we need to renew our view on cancer and to revise some old paradigms and “false friends” that can hide unexpected new therapeutic targets. A good example of these paradigms is the role of the cell stress response in tumor progression. Indeed, a number of studies has been devoted to the pivotal tumor suppressor function of some players of this response, of which the p53 protein is the best example. Nevertheless, during tumor progression and metastasis, the cancer cell faces many stresses imposed by tumor microenvironment and its survival will be conditioned by an efficient cell stress response. This review is consecrated to the role played by a pivotal actor of the cell stress response, the p8 protein, during carcinogenesis. We will recapitulate the data available on its different cell functions and the assets p8 confer to the cancer cell in terms of growth, drugs resistance and metastasis formations.     

Enquête sur les conditions analytiques d’un examen de mycologie médicale auprès des membres de la Société française de mycologie médicale

Aim of the study

The objective of the survey was to describe the practices of clinical laboratories in terms of cultures in medical mycology. We have implemented this project within the members of the French Society for Medical Mycology (SFMM) to evaluate the analytical processes of the mycological examination in our laboratories. This preliminary study would help to suggest the future French guidelines.

Materials and methods

A questionnaire regarding the processing of mycology analysis was sent to the 227 members of the SFMM in 2009. The data involved 21 types of samples, direct microscopic examination with or without colouring and the reagents, the number of culture media, the types of media (Sabouraud, Sabouraud antibiotic, Sabouraud cycloheximide and chromogenic medium), temperature and duration of the incubation (days) and the existence of a first result before the end of the incubation period. The analytical processes were compared to an accredited laboratory according to EN ISO 15189.

Results

A great heterogeneity was observed in the 36 forms from 27 (75%) laboratories belonging to university hospitals among the 38 existing in France. As for deep samples, two microscopic exams were performed, only one was usually done. A more sensitive technique was preferred to the wet–mount for some samples. Routine samples are often inoculated on a chromogenic media. For deep samples two medium are inoculated (chromogenic media, Sabouraud and antibiotics). If the temperature of incubation is unique, 30 °C was chosen. A temperature of 37 °C was preferred for samples where Candida spp. is selected. When there are two temperatures of incubation, 27°C and 37 °C were preferred.

Conclusion

Each biologist can compare his proceedings to the other laboratories and to a laboratory already accredited. The question is to find the best strategies for each medical mycology specimen. They will aid the process of accreditation according to EN ISO 15189, which now applies in all laboratories in Europe.     

Comportement mécanique du rachis cervical : une revue de littérature

Cervical spine is certainly the most complex joint. Biomechanics behaviours of this segment coming from different authors are related in this article. Cervical spine can be divided in two parts: upper cervical spine from occiput to C2 and lower cervical spine from C3 to C7. In vitro biomechanical study shows a strongly non linear behaviour. 60% of the motion of the whole segment takes place at the upper cervical from occiput to C2. Coupling motions are significant, principally in lateral bending and axial rotation. On top of that authors describe a neutral zone with a very little stifness at the center of the behaviour graph. This area represents 60% of whole motion of each intervetebral joint. Finally, authors describe a loss of mobility of 40% with ageing. However weigth and size seem to be non significant on the mechanical behaviour of cervical spine.     

La protoporphyrie érythropoïétique : une maladie,deux gènes et trois mécanismes moléculaires

Erythropoietic protoporphyria (EPP) is an inherited disorder of heme biosynthesis that results from an accumulation of protoporphyrin IX in erythroid cells, plasma, skin and liver. EPP leads to acute photosensitivity and, in about 2% of patients, liver disease. EPP is a complex syndrome in which two genes are independently involved: FECH and ALAS2. More than 96% of unrelated EPP patients have ferrochelatase (FECH) deficiency (MIM 177000). Four percent of them present with autosomal recessive inheritance with two mutated FECH alleles. In dominant cases (95%) the inheritance of a common hypomorphic IVS3-48C FECH allele trans to a deleterious FECH mutation reduces FECH activity below a critical threshold. The frequency of the IVS3-48C allele differs widely from the Japanese (45%), to Black West Africans (< 1%) populations. These differences in the frequency of this single common SNP account for the prevalence of overt EPP in different countries and for the absence of EPP in Black Africans. The phylogenic origin of the IVS3-48C haplotypes strongly suggests that the IVS3-48C allele arose from a single recent mutational event that occurred 60 Kyears ago. Acquired somatic mutation of FECH secondary to myeloid disease may also exceptionally cause EPP (< 1%). Finally, about 4% of unrelated EPP patients have X-linked dominant protoporphyria (XLDPP) (MIM 300752) caused by gain-of-function mutations in the ALAS2 gene leading to an increased erythroid heme biosynthesis and subsequently an accumulation of protoporphyrin without any FECH deficiency.     

Lupus et grossesse : expérience d’un service de médecine interne à propos de 26 cas et revue de la littérature

Objective

To study the maternal and fetal outcomes in women with systemic lupus erythematosus.

Patients and methods

A retrospective study of 26 pregnancies in 15 systemic erythematosus patients diagnosed before or during pregnancy regarding to American College of Rheumatology criteria in a single reference center.

Results

The mean patient age was 31.52 years (24–39 years). The mean interval from the diagnosis of the systemic lupus erythematosus to pregnancy was 4.2 years. Eight pregnancies were planned. The flare rate of lupus during pregnancy was 31%, life birth rate was 65% and fetal loss rate was 35%.

Discussion and conclusion

As an increase in disease activity can occur during pregnancy and because of a higher rate of obstetrical complications in patients with lupus, it is important to carefully plan pregnancy. Pregnancy in lupus patients must be closely monitored by a multispeciality care of the patients.