Type I interferonopathy due to a homozygous loss-of-inhibitory-function mutation in STAT2

International audiencePurpose STAT2 is both an effector and negative regulator of type I interferon (IFN-I) signalling. We describe the characterization of a novel homozygous missense STAT2 substitution in a patient with a type I interferonopathy. Methods Whole-genome sequencing (WGS) was used to identify the genetic basis of disease in a patient with features of enhanced IFN-I signalling. After stable lentiviral reconstitution of STAT2-null human fibrosarcoma U6A cells with STAT2 wild type or p.(A219V), we performed quantitative polymerase chain reaction, western blotting, immunofluorescence, and co-immunoprecipitation to functionally characterize the p.(A219V) variant. Results WGS identified a rare homozygous single nucleotide transition in STAT2 (c.656C > T), resulting in a p.(A219V) substitution, in a patient displaying developmental delay, intracranial calcification, and up-regulation of interferon-stimulated gene (ISG) expression in blood. In vitro studies revealed that the STAT2 p.(A219V) variant retained the ability to transduce an IFN-I stimulus. Notably, STAT2 p.(A219V) failed to support receptor desensitization, resulting in sustained STAT2 phosphorylation and ISG up-regulation. Mechanistically, STAT2 p.(A219V) showed defective binding to ubiquitin specific protease 18 (USP18), providing a possible explanation for the chronic IFN-I pathway activation seen in the patient. Conclusion Our data indicate an impaired negative regulatory role of STAT2 p.(A219V) in IFN-I signalling and that mutations in STAT2 resulting in a type I interferonopathy state are not limited to the previously reported R148 residue. Indeed, structural modelling highlights at least 3 further residues critical to mediating a STAT2-USP18 interaction, in which mutations might be expected to result in defective negative feedback regulation of IFN-I signalling

RNA signature and prediction to treatment response in first episode schizophrenia

International audienceBackground: Despite nearly fifty years of pharmacological research, the treatment of schizophrenia remains a challenge and clinical outcomes are still far from optimal. One of the major shortcomings in the current treatment of schizophrenia is that we have no valid criteria in clinical practice to predict who will respond to antipsychotic treatment and how long the treatment should be maintained before changing therapeutic strategy. The identification of blood-based biological markers of drug response with a good sensitivity and specificity would enable physicians to use these tests prior to choosing the antipsychotic treatment and therefore help the practitioner in his daily clinical practice. Methods: Through a European consortium on Optimization of Treatment and Management of Schizophrenia in Europe (OPTiMiSE) [1], we ran analyses on 214 subjects with first episode schizophrenia, schizophreniform or schizoaffective disorder who were included in a clinical trial. Patients had minimal to no exposure to antipsychotics at inclusion and were all treated for four weeks with amisulpride. Blood samples were collected at inclusion and after treatment. DNA and RNA were extracted. Using RNA-Seq, we analysed transcriptome for each patient before and after treatment as well as according to treatment outcome defined as remitter versus non-remitter following remission criteria of Andreasen [2]. The detection of differentially expressed genes and pathways have been achieved using the combination of the DESeq2 package [3] and the Panther’s ontology-based pathway database [4], with the aim of predicting remission before treatment. Genotypic data have been generated for each subject using DNA array containing more than 900,000 probes, and genotypes have been used to detect single nucleotide polymorphisms (SNPs) that have an effect on gene expression (eQTL, expression quantitative trait loci). Results: From almost 11,000 genes expressed in peripheral blood mononuclear cells, we detected significantly more differentially expressed genes in remitted patients than in non-remitted subjects after 4-week treatment with amisulpride ( p = 0.01). A subgroup of these genes was already differentially expressed before treatment between remitted and non-remitted patients and may help predicting treatment response. Among differentially expressed genes after amisulpride treatment, we identified genes for which expression was correlated with clinical symptom improvement. Pathway analyses revealed enrichment of the GABA-B receptor II signalling pathway, including genes that have already been associated with psychiatric disorders in previous studies. In addition, association studies using cis eQTL identified genetic variations, which were both associated with gene expression and treatment response, suggesting they may be used to predict remission before treatment. Conclusion: We demonstrated here that amisulpride affects gene expression in peripheral blood mononuclear cells, mainly in patients who are in remission after four weeks of treatment. Genes and pathway analyses identified molecular mechanisms that were associated with symptom improvement and should help both in the identification of biological signatures of treatment response as well as in the development of new therapeutic strategie

Performance of a multi-species-plant illumina beadchip

Since mid-2005, Illumina Infinium® genotyping arrays provide data with good accuracy for thousands of SNPs (single nucleotide polymorphism) in thousands individuals for many organisms including plants. These extensive data used in large studies gave new insight in population and molecular genetics. Nevertheless, flexible high density genotyping tools at reasonable costs are still to be developed. Low cost genotyping assays would allow many applications including control of individuals, marker assisted management and genetic approaches in species where molecular developments have a comparatively low value relative to the cost of SNP arrays. The initial cost and/or the minimum sample number requirement are limiting factors for developing a new genotyping tool. An add-on option on already existing product gives a first opportunity to reduce the cost of a beadchip. Designing a multi-species array could be another alternative to increase the number of SNPs and decrease the minimum number of samples for each species, reaching lower genotyping cost assay per species

RNA Signature of treatment response in first-episode psychosis

International audienceDespite nearly fifty years of pharmacological research, the treatment of schizophrenia remains a challenge and clinical outcomes are still far from optimal. One of the major shortcomings in the current treatment of schizophrenia is that we have no valid criteria in clinical practice to predict who will respond to antipsychotic treatment and how long the treatment should be maintained before changing therapeutic strategy. The identification of blood-based biological markers of drug response with a good sensitivity and specificity would enable physicians to use these tests prior to choosing the antipsychotic treatment and therefore help the practitioner in his daily clinical practice. Methods Through a European consortium on Optimization of Treatment and Management of Schizophrenia in Europe (OPTiMiSE), we conducted a transcriptome analysis on 163 subjects with first episode psychosis. Patients were all treated for four weeks with amisulpride. Blood samples were collected at inclusion and after treatment and total RNA was analyzed by RNA-Seq for each patient before and after treatment as well as according to treatment outcome. After quality control, the detection of differentially expressed genes have been achieved using the DESeq. 2 package and in regards to biological processes and symptom improvement, with the aim of characterizing a biological signature of treatment response in first-episode psychosis. Results The transcription level of 10,683 expressed genes has been analyzed in peripheral blood mononuclear cells. We detected 499 and 84 genes that were differentially expressed after 4-week treatment with amisulpride in remitted and non-remitted patients, respectively, showing enrichment in differentially expressed genes in remitters when compared to non-remitters (p=0.02). We also found that for some of these genes, the expression level was significantly correlated with clinical outcome. A second analysis revealed that 39 of the 499 differentially expressed genes had a different expression level before amisulpride treatment between patients who will be in remission after 4-week treatment, suggesting these genes may help in predicting treatment response. Discussion We demonstrated here that amisulpride treatment affects gene expression in peripheral blood mononuclear cells, mainly in patients who will be in remission after four weeks of treatment, and that gene expression may be associated with symptom improvement. Further replications on independent samples are needed to confirm molecular mechanisms associated with clinical outcome and should help both in the identification of biological signatures of treatment response as well as in the development of new therapeutic strategies

Combining differential gene expression analysis and genetic data predict treatment response in first-episode psychosis

International audienceBackground: Despite nearly fifty years of pharmacological research, the treatment of schizophrenia remains a challenge and clinical outcomes are still far from optimal. One of the major shortcomings in the current treatment of schizophrenia is that we have no valid criteria in clinical practice to predict who will respond to antipsychotic treatment and how long the treatment should be maintained before changing therapeutic strategy. The identification of blood-based biological markers of drug response with a good sensitivity and specificity would enable physicians to use these tests prior to choosing the antipsychotic treatment and therefore help the practitioner in his daily clinical practice. Methods: Through a European consortium on Optimization of Treatment and Management of Schizophrenia in Europe (OPTiMiSE), we investigated treatment response in 188 individuals with first episode psychoses. Using RNA sequencing, we characterized changes in gene expression after 4-week treatment with amisulpride according to treatment outcome. In addition, we genotyped subjects with DNA array to identify eQTLs, and used this eQTLs to propose a polygenic score to predict treatment outcome. Results: Out of the 16,264 genes expressed in peripheral blood mononuclear cells, we showed an enrichment in differentially expressed genes in subjects who will be in remission after 4-week amilsupride treatment, when compared with non-remitted patients. We thus demonstrated that 10% of differentially expressed genes had a change in the expression level, which was correlated with clinical outcome. We identified many eQTLs that may explain transcriptional variations between responders and non-responders to treatment. The combination of these eQTLs in a polygenic score allowed the prediction of clinical improvement with an accuracy of 0.7 on the discovery sample of 135 individuals and 0.6 on an independent sample of 129 subjects. Discussion: We demonstrated here that amisulpride treatment affects gene expression in peripheral blood mononuclear cells, mainly in patients who will be in remission after four-week treatment, and that gene expression was associated with symptom improvement. We also showed that combining transcription and genetic data might help in the identification of biological signature to predict treatment response in first episode psychosis

Risperidone response in patients with schizophrenia drives DNA methylation changes in immune and neuronal systems

International audienceBackground: The choice of efficient antipsychotic therapy for schizophrenia relies on a time-consuming trial-and-error approach, whereas the social and economic burdens of the disease call for faster alternatives. Material & methods: In a search for predictive biomarkers of antipsychotic response, blood methylomes of 28 patients were analyzed before and 4 weeks into risperidone therapy. Results: Several CpGs exhibiting response-specific temporal dynamics were identified in otherwise temporally stable methylomes and noticeable global response-related differences were observed between good and bad responders. These were associated with genes involved in immunity, neurotransmission and neuronal development. Polymorphisms in many of these genes were previously linked with schizophrenia etiology and antipsychotic response. Conclusion: Antipsychotic response seems to be shaped by both stable and medication-induced methylation differences

Gene expression and response prediction to amisulpride in the OPTiMiSE first episode psychoses

International audienceA fundamental shortcoming in the current treatment of schizophrenia is the lack of valid criteria to predict who will respond to antipsychotic treatment. The identification of blood-based biological markers of the therapeutic response would enable clinicians to identify the subgroup of patients in whom conventional antipsychotic treatment is ineffective and offer alternative treatments. As part of the Optimisation of Treatment and Management of Schizophrenia in Europe (OPTiMiSE) programme, we conducted an RNA-Seq analysis on 188 subjects with first episode psychosis, all of whom were subsequently treated with amisulpride for 4 weeks. We compared gene expression on total RNA from patients' blood before and after treatment and identified 32 genes for which the expression changed after treatment in good responders only. These findings were replicated in an independent sample of 24 patients with first episode psychosis. Six genes showed a significant difference in expression level between good and poor responders before starting treatment, allowing to predict treatment outcome with a predictive value of 93.8% when combined with clinical features. Collectively, these findings identified new mechanisms to explain symptom improvement after amisulpride medication and highlight the potential of combining gene expression profiling with clinical data to predict treatment response in first episode psychoses

Modifier genes in NF1: results of the first Genome-Wide Association Study in 1,333 patients

International audienc