Analyse du transcriptome d'une association de lactocoques par affichage différentiel

Les bactéries lactiques contribuent à la qualité des produits laitiers fermentes par leurs activités enzymatiques. Cette activité est reflétée en partie par le transcriptome, qui représente l'ensemble des gènes exprimés en ARN. Le but de cette recherche est donc d'estimer l'activité de Lactococcus lactis ssp. cremoris par suivi de l'expression des gènes lors de l'étape de la fermentation du lait de fromagerie. Pour étudier les transcriptomes, une technique de RAP-PCR fluorescente a été développée puis appliquée à un ferment mixte composé de trois souches de lactocoques. Les résultats de cette technique montrent que le lait UHT présente un bon compromis entre hygiène et altération thermique des constituants. Dans le lait entier, le CO2 interagit avec les ferments en changeant leur profil de transcription, cette influence n'apparait pas dans le lait écrémé pasteurisé. Comparativement à l'ajout d'une base, l'agitation du lait carboné est une bonne méthode pour réduire l'influence du CO2 sur le ferment. Lors d'une fermentation de type Cheddar, le profil de transcription d'un ferment mixte est très influencé par un excès de NaCl et par un manque d'activité de la présure. La RAP-PCR fluorescente peut identifier les souches par leurs profils d'ARN et analyser les particularités d'une association bactérienne. Selon les conditions observées, le ferment mixte composé par trois souches de Lactococcus lactis ssp. cremoris (LL074, LL225 et LL390) est formé d'une association stable de deux souches : LL225 avec LL390 alors que la souche LL074 est éliminée. La souche LL225 apparait la plus réactive en réagissant identiquement par la modulation de certains gènes en présence des souches LL074 ou LL390. Une modulation de la transcription de certains gène de la souche de LL390 apparait en présence de la souche LL225 mais aucune en présence de LL074, LL390 ne faisant que dominer cette souche. L'association des souches LL225 avec LL390 se fait en rapport égal et induit une modulation de leurs gènes aussitôt que les souches sont en présence. Les données ont été validées en analysant la transcription de gènes par RT-PCR en temps réel et par di-sondes FRET adjacentes et sont en adéquation avec les incompatibilités entre souches dues aux types de proteinases de membrane. L'activité d'un ferment mixte lors d'une fabrication de type Cheddar est donc influencée par le type de lait utilisé et par une dynamique d'association entre les souches

Selective time-dependent changes in activity and cell-specific gene expression in human postmortem brain.

As a means to understand human neuropsychiatric disorders from human brain samples, we compared the transcription patterns and histological features of postmortem brain to fresh human neocortex isolated immediately following surgical removal. Compared to a number of neuropsychiatric disease-associated postmortem transcriptomes, the fresh human brain transcriptome had an entirely unique transcriptional pattern. To understand this difference, we measured genome-wide transcription as a function of time after fresh tissue removal to mimic the postmortem interval. Within a few hours, a selective reduction in the number of neuronal activity-dependent transcripts occurred with relative preservation of housekeeping genes commonly used as a reference for RNA normalization. Gene clustering indicated a rapid reduction in neuronal gene expression with a reciprocal time-dependent increase in astroglial and microglial gene expression that continued to increase for at least 24 h after tissue resection. Predicted transcriptional changes were confirmed histologically on the same tissue demonstrating that while neurons were degenerating, glial cells underwent an outgrowth of their processes. The rapid loss of neuronal genes and reciprocal expression of glial genes highlights highly dynamic transcriptional and cellular changes that occur during the postmortem interval. Understanding these time-dependent changes in gene expression in post mortem brain samples is critical for the interpretation of research studies on human brain disorders

Le déficit immunitaire combiné sévère lié l'X (de l'allogreffe de cellules souches hématopoïétiques aux espoirs de la thérapie génique)

Le déficit immunitaire combiné sévère lié à l'X est une pathologie qui entraîne une profonde immunodépression à l'origine d'une susceptibilité accrue aux infections. En l'absence de traitements adaptés, celles-ci sont alors responsable d'une très forte mortalité au cours de la première année d'existence des nourrissons atteints; leur espérance de vie n'excédant pas quelques années, tout au mieux. Actuellement, sa prise en charge repose sur l'allogreffe de cellules souches hématopoïétiques, parfois associée à des injections intraveineuses régulières d'immunoglobulines. Néanmoins, l'extrême limitation de ces traitements, les difficultés à trouver un donneur compatible ainsi que les risques de complications ont nécessité la recherche et la mise au point d'une alternative médicale. Celle-ci réside dans la thérapie génique qui, malgré les débats et la controverse suscités, est sur le point de devenir aujourd'hui la technique de référence de la prise en charge de ce déficit immunitaireLYON1-BU Santé (693882101) / SudocSudocFranceF

Transcriptome profiling of lactococcal mixed culture activity in milk by fluorescent RNA arbitrarily primed-PCR

Thermal treatment of milk is widely used to reduce milk contamination, while CO2 can be used to prevent bacterial growth and maintain milk quality during storage. These treatments applied before or during cheese manufacture could alter the metabolic activity of starter cultures. Changes in gene expression can be evaluated by differential display methods, so that effects on bacterial metabolic activity can be estimated by variation in transcription profiles. The aim of this study was to develop fluorescent RNA arbitrarily primed-polymerase chain reaction (RAP-PCR) as a method to evaluate the influence of milk CO2 acidification as well as rennet and salt concentrations on starter gene expression. Comparison with reference conditions showed that gene transcription was influenced according to the extent of thermal treatment as well as by CO2 acidification followed by different neutralization procedures. Thus, simple acid neutralization after CO2 acidification was not sufficient to regain the reference transcriptome profile. Starter gene transcription profiles showed important modifications following an increase in NaCl concentration or a decrease in rennet activity from standard conditions used in Cheddar cheese making. Increasing rennet activity results in small changes in the starter RNA profile. Fluorescent RAP-PCR is a promising method for obtaining a better understanding of gene expression profiles of mixed cultures during cheese making

Potential for Cell-Mediated Immune Responses in Mouse Models of Pelizaeus-Merzbacher Disease

Although activation of the innate and adaptive arms of the immune system are undoubtedly involved in the pathophysiology of neurodegenerative diseases, it is unclear whether immune system activation is a primary or secondary event. Increasingly, published studies link primary metabolic stress to secondary inflammatory responses inside and outside of the nervous system. In this study, we show that the metabolic stress pathway known as the unfolded protein response (UPR) leads to secondary activation of the immune system. First, we observe innate immune system activation in autopsy specimens from Pelizaeus-Merzbacher disease (PMD) patients and mouse models stemming from PLP1 gene mutations. Second, missense mutations in mildly- and severely-affected Plp1-mutant mice exhibit immune-associated expression profiles with greater disease severity causing an increasingly proinflammatory environment. Third, and unexpectedly, we find little evidence for dysregulated expression of major antioxidant pathways, suggesting that the unfolded protein and oxidative stress responses are separable. Together, these data show that UPR activation can precede innate and/or adaptive immune system activation and that neuroinflammation can be titrated by metabolic stress in oligodendrocytes. Whether or not such activation leads to autoimmune disease in humans is unclear, but the case report of steroid-mitigated symptoms in a PMD patient initially diagnosed with multiple sclerosis lends support

Activity-Dependent Non-Coding RNA MAPK Interactome of the Human Epileptic Brain

The human brain has evolved to have extraordinary capabilities, enabling complex behaviors. The uniqueness of the human brain is increasingly posited to be due in part to the functions of primate-specific, including human-specific, long non-coding RNA (lncRNA) genes, systemically less conserved than protein-coding genes in evolution. Patients who have surgery for drug-resistant epilepsy are subjected to extensive electrical recordings of the brain tissue that is subsequently removed in order to treat their epilepsy. Precise localization of brain tissues with distinct electrical properties offers a rare opportunity to explore the effects of brain activity on gene expression. Here, we identified 231 co-regulated, activity-dependent lncRNAs within the human MAPK signaling cascade. Six lncRNAs, four of which were antisense to known protein-coding genes, were further examined because of their high expression and potential impact on the disease phenotype. Using a model of repeated depolarizations in human neuronal-like cells (Sh-SY5Y), we show that five out of six lncRNAs were electrical activity-dependent, with three of four antisense lncRNAs having reciprocal expression patterns relative to their protein-coding gene partners. Some were directly regulated by MAPK signaling, while others effectively downregulated the expression of the protein-coding genes encoded on the opposite strands of their genomic loci. These lncRNAs, therefore, likely contribute to highly evolved and primate-specific human brain regulatory functions that could be therapeutically modulated to treat epilepsy

Potential for Cell-Mediated Immune Responses in Mouse Models of Pelizaeus-Merzbacher Disease

Although activation of the innate and adaptive arms of the immune system are undoubtedly involved in the pathophysiology of neurodegenerative diseases, it is unclear whether immune system activation is a primary or secondary event. Increasingly, published studies link primary metabolic stress to secondary inflammatory responses inside and outside of the nervous system. In this study, we show that the metabolic stress pathway known as the unfolded protein response (UPR) leads to secondary activation of the immune system. First, we observe innate immune system activation in autopsy specimens from Pelizaeus-Merzbacher disease (PMD) patients and mouse models stemming from PLP1 gene mutations. Second, missense mutations in mildly- and severely-affected Plp1-mutant mice exhibit immune-associated expression profiles with greater disease severity causing an increasingly proinflammatory environment. Third, and unexpectedly, we find little evidence for dysregulated expression of major antioxidant pathways, suggesting that the unfolded protein and oxidative stress responses are separable. Together, these data show that UPR activation can precede innate and/or adaptive immune system activation and that neuroinflammation can be titrated by metabolic stress in oligodendrocytes. Whether or not such activation leads to autoimmune disease in humans is unclear, but the case report of steroid-mitigated symptoms in a PMD patient initially diagnosed with multiple sclerosis lends support