Intradermal Testing With COVID-19 mRNA Vaccines Predicts Tolerance

BackgroundThe newly developed mRNA-based COVID-19 vaccines can provoke anaphylaxis, possibly induced by polyethylene glycol (PEG) contained in the vaccine. The management of persons with a history of PEG allergy or with a suspected allergic reaction after the first dose remains to be defined.MethodsIn this real-life study, we defined two cohorts of individuals: one pre-vaccination including 187 individuals with high-risk profiles for developing anaphylaxis and a second post-vaccination including 87 individuals with suspected allergic reactions after the COVID-19 mRNA vaccine. Upon negative skin test with an mRNA vaccine, a two-step (10–90%) vaccination protocol was performed. Positive skin tests were confirmed with the basophil activation test (BAT).ResultsAmong 604,267 doses of vaccine, 87 suspected allergic reactions (5 after the booster) were reported to our division for further investigations: 18/87 (21%) were consistent with anaphylaxis, 78/87 (90%) were female, and 47/87 (54%) received the BNT162b2 mRNA vaccine. Vaccine skin tests were negative in 96% and 76% of the pre- and post-vaccination cohorts, respectively. A two-step vaccination was tolerated in 232/236 (98%) of individuals with negative tests. Four individuals experienced isolated asthmatic reactions during the two-step challenge. Vaccine-positive skin tests were consistently confirmed by BAT; CD63 and CD203c expression was selectively inhibited with ibrutinib, suggesting an IgE-dependent mechanism.ConclusionSensitization to SARS-CoV-2 mRNA vaccines can be detected with intradermal testing. Significantly more individuals were sensitized to mRNA vaccines in the post-vaccination cohort. A two-step 10–90%-vaccination protocol can be safely administered upon negative skin testing

KRAB–Zinc Finger Proteins and KAP1 Can Mediate Long-Range Transcriptional Repression through Heterochromatin Spreading

Krüppel-associated box domain-zinc finger proteins (KRAB–ZFPs) are tetrapod-specific transcriptional repressors encoded in the hundreds by the human genome. In order to explore their as yet ill-defined impact on gene expression, we developed an ectopic repressor assay, allowing the study of KRAB–mediated transcriptional regulation at hundreds of different transcriptional units. By targeting a drug-controllable KRAB–containing repressor to gene-trapping lentiviral vectors, we demonstrate that KRAB and its corepressor KAP1 can silence promoters located several tens of kilobases (kb) away from their DNA binding sites, with an efficiency which is generally higher for promoters located within 15 kb or less. Silenced promoters exhibit a loss of histone H3-acetylation, an increase in H3 lysine 9 trimethylation (H3K9me3), and a drop in RNA Pol II recruitment, consistent with a block of transcriptional initiation following the establishment of silencing marks. Furthermore, we reveal that KRAB–mediated repression is established by the long-range spreading of H3K9me3 and heterochromatin protein 1 β (HP1β) between the repressor binding site and the promoter. We confirm the biological relevance of this phenomenon by documenting KAP1–dependent transcriptional repression at an endogenous KRAB–ZFP gene cluster, where KAP1 binds to the 3′ end of genes and mediates propagation of H3K9me3 and HP1β towards their 5′ end. Together, our data support a model in which KRAB/KAP1 recruitment induces long-range repression through the spread of heterochromatin. This finding not only suggests auto-regulatory mechanisms in the control of KRAB–ZFP gene clusters, but also provides important cues for interpreting future genome-wide DNA binding data of KRAB–ZFPs and KAP1

Development of a multi-scale simulation tool for early radio-induced damage assessment in cells exposed to light ions irradiations (proton and alpha)

Ce travail de thèse, réalisé dans le cadre des projets de recherche ROSIRIS (IRSN) et Geant4-DNA, porte sur la construction d’une simulation multi-échelle dédiée au calcul des dommages radio-induits précoces à l’ADN qui peuvent apparaître suite à l’irradiation d’un noyau cellulaire. L’outil développé s’appuie sur une version modifiée du code de Monte Carlo Geant4-DNA et est capable de simuler dans le détail le transport et les interactions physiques entre l’irradiation ionisante et la matière biologique (étape physique), la création d’espèces chimiques (étape physico-chimique) et les réactions et processus de diffusion de ces dernières (étape chimique). Durant la simulation de ces trois étapes, un modèle géométrique de l’ADN, décrivant l’ensemble du génome humain avec une précision moléculaire, est généré avec un nouveau logiciel développé dans le cadre de cette thèse : DnaFabric. Les premiers résultats obtenus pour des irradiations avec des protons et des ions alpha sont détaillés et comparés à des données de la littérature. Un bon accord est observés avec ces dernières illustrant ainsi la cohérence de l’ensemble de la simulation. L’influence très significative du critère de sélection utilisé pour identifier les dommages à l’ADN est également démontrée.This work was performed in the frame of the ROSIRIS (IRSN) and Geant4-DNA research projects and describes the development of a simulation tool to compute radioinduced early DNA damages in a cell nucleus. The modeling tool is based on a modified version of the Monte Carlo code Geant4-DNA and is able to simulate the physical interactions between ionizing particles and the biological target (physical stage), the creation of chemical species within the cell nucleus (physico-chemical stage) as well as the reactions and diffusion processes of these chemical species (chemical stage). During all the simulation, a geometrical model that describes the DNA content of a human diploid cell nucleus is taken into account. This model was generated with a new software (DnaFabric) developed in the frame of this work and has a molecular level of detail.The first results (in term of DNA strand breaks) obtained with this tool are detailed and compared with experimental data from the literature. The good agreement between the simulation results and those data shows the coherence of our modeling. The significant influence of the selection criteria used to identify the DNA damages is also demonstrated

Development of a multi-scale simulation tool for early radio-induced damage assessment in cells exposed to light ions irradiations (proton and alpha)

Ce travail de thèse, réalisé dans le cadre des projets de recherche ROSIRIS (IRSN) et Geant4-DNA, porte sur la construction d’une simulation multi-échelle dédiée au calcul des dommages radio-induits précoces à l’ADN qui peuvent apparaître suite à l’irradiation d’un noyau cellulaire. L’outil développé s’appuie sur une version modifiée du code de Monte Carlo Geant4-DNA et est capable de simuler dans le détail le transport et les interactions physiques entre l’irradiation ionisante et la matière biologique (étape physique), la création d’espèces chimiques (étape physico-chimique) et les réactions et processus de diffusion de ces dernières (étape chimique). Durant la simulation de ces trois étapes, un modèle géométrique de l’ADN, décrivant l’ensemble du génome humain avec une précision moléculaire, est généré avec un nouveau logiciel développé dans le cadre de cette thèse : DnaFabric. Les premiers résultats obtenus pour des irradiations avec des protons et des ions alpha sont détaillés et comparés à des données de la littérature. Un bon accord est observés avec ces dernières illustrant ainsi la cohérence de l’ensemble de la simulation. L’influence très significative du critère de sélection utilisé pour identifier les dommages à l’ADN est également démontrée.This work was performed in the frame of the ROSIRIS (IRSN) and Geant4-DNA research projects and describes the development of a simulation tool to compute radioinduced early DNA damages in a cell nucleus. The modeling tool is based on a modified version of the Monte Carlo code Geant4-DNA and is able to simulate the physical interactions between ionizing particles and the biological target (physical stage), the creation of chemical species within the cell nucleus (physico-chemical stage) as well as the reactions and diffusion processes of these chemical species (chemical stage). During all the simulation, a geometrical model that describes the DNA content of a human diploid cell nucleus is taken into account. This model was generated with a new software (DnaFabric) developed in the frame of this work and has a molecular level of detail.The first results (in term of DNA strand breaks) obtained with this tool are detailed and compared with experimental data from the literature. The good agreement between the simulation results and those data shows the coherence of our modeling. The significant influence of the selection criteria used to identify the DNA damages is also demonstrated

Développement d'un outil de simulation multi-échelle adapté au calcul des dommages radio-induits précoces dans des cellules exposées à des irradiations d'ions légers (proton et alpha)

This work was performed in the frame of the ROSIRIS (IRSN) and Geant4-DNA research projects and describes the development of a simulation tool to compute radioinduced early DNA damages in a cell nucleus. The modeling tool is based on a modified version of the Monte Carlo code Geant4-DNA and is able to simulate the physical interactions between ionizing particles and the biological target (physical stage), the creation of chemical species within the cell nucleus (physico-chemical stage) as well as the reactions and diffusion processes of these chemical species (chemical stage). During all the simulation, a geometrical model that describes the DNA content of a human diploid cell nucleus is taken into account. This model was generated with a new software (DnaFabric) developed in the frame of this work and has a molecular level of detail.The first results (in term of DNA strand breaks) obtained with this tool are detailed and compared with experimental data from the literature. The good agreement between the simulation results and those data shows the coherence of our modeling. The significant influence of the selection criteria used to identify the DNA damages is also demonstrated.Ce travail de thèse, réalisé dans le cadre des projets de recherche ROSIRIS (IRSN) et Geant4-DNA, porte sur la construction d’une simulation multi-échelle dédiée au calcul des dommages radio-induits précoces à l’ADN qui peuvent apparaître suite à l’irradiation d’un noyau cellulaire. L’outil développé s’appuie sur une version modifiée du code de Monte Carlo Geant4-DNA et est capable de simuler dans le détail le transport et les interactions physiques entre l’irradiation ionisante et la matière biologique (étape physique), la création d’espèces chimiques (étape physico-chimique) et les réactions et processus de diffusion de ces dernières (étape chimique). Durant la simulation de ces trois étapes, un modèle géométrique de l’ADN, décrivant l’ensemble du génome humain avec une précision moléculaire, est généré avec un nouveau logiciel développé dans le cadre de cette thèse : DnaFabric. Les premiers résultats obtenus pour des irradiations avec des protons et des ions alpha sont détaillés et comparés à des données de la littérature. Un bon accord est observés avec ces dernières illustrant ainsi la cohérence de l’ensemble de la simulation. L’influence très significative du critère de sélection utilisé pour identifier les dommages à l’ADN est également démontrée

Genomic Context and KRAB/KAP1-mediated Transcriptional Repression

Chromatin structure and its impact on transcriptional activity represent one of the major revolutions in the biomedical field over the passed decade. The implications concern as much fundamental as clinically-oriented research; diseases and therapeutical strategies are being approached from a new point of view (Mackay et al., 2008; Richman et al., 2009). The current work dissects the different susceptibilities of genes in the human genome and how these react to the changes in chromatin landscape upon the recruitment of a transcriptional corepressor. The KRAB-Zinc finger proteins are the largest family of transcriptional repressors in the human genome. These repressors use the KRAB domain as a docking site for KAP-1 which in turn recruits a macromolecular chromatin-remodelling complex leading to heterochromatin formation. Yet current knowledge of their impact on gene regulation is limited. By artificially recruiting a KRAB-repressor in the context of genes, our lab has previously shown that this repression can act over several tens of kilobases (Groner et al., 2010). Specifically, transcriptional silencing depends on the spreading of repressive marks to the upstream promoter. However, such spreading to the trapped promoter is not systematic, suggesting potential counter-acting influences. To identify the determinants of repression, we designed a high-throughput approach of our experimental system to accumulate thousands of KRAB docking sites for which the trapped promoter is regulable and docking sites for which the promoter is immune to repression. Firstly, our data indicate that KRAB/KAP-1-repression can act efficiently over distances of 20 kb albeit in a very variable fashion, but is limited beyond that. Second, propagation of repression in the transcribed regions was favoured in most open chromatin. Third, we observed that the broader context of genes sustaining repression was that of most euchromatic regions, recapitulating the genetic context of natural targets of KAP1 repression. On the other hand, we have no evidence that barrier elements such as CTCF counteract this KRAB-mediated repression within genes. Finally, work on cases where repression acts over distances greater than 40 kb hints at the regulation of enhancers by our KRAB repressor rather than promoter. In conclusion, this work broadens the knowledge in the emerging field of gene regulation and provides further insight on the complexity of chromatin architecture and its meaning at a functional level

A narrative review of the intermediate category of the antimicrobial susceptibility test: relation with dosing and possible impact on antimicrobial stewardship

The interpretation of 'susceptible (S)' or 'resistant (R)' results of antimicrobial susceptibility testing is easily understood, but the interpretation of the 'intermediate (I)' category can be confusing. This review critically discusses how this categorization (clinical breakpoints) comes into being with the emphasis on the use of pharmacokinetics and pharmacodynamic data. It discusses the differences between the 'I' according to the CLSI and the EUCAST. This review also discusses the recent EUCAST change of the 'I' definition, and the impact of this change from laboratory and clinical points of view

A narrative review of the intermediate category of the antimicrobial susceptibility test: relation with dosing and possible impact on antimicrobial stewardship

The interpretation of 'susceptible (S)' or 'resistant (R)' results of antimicrobial susceptibility testing is easily understood, but the interpretation of the 'intermediate (I)' category can be confusing. This review critically discusses how this categorization (clinical breakpoints) comes into being with the emphasis on the use of pharmacokinetics and pharmacodynamic data. It discusses the differences between the 'I' according to the CLSI and the EUCAST. This review also discusses the recent EUCAST change of the 'I' definition, and the impact of this change from laboratory and clinical points of view