Study of Transcriptional Effects in Cis at the IFIH1 Locus

Background: The Thr allele at the non-synonymous single-nucleotide polymorphism (nsSNP) Thr946Ala in the IFIH1 gene confers risk for Type 1 diabetes (T1D). The SNP is embedded in a 236 kb linkage disequilibrium (LD) block that includes four genes: IFIH1, GCA, FAP and KCNH7. The absence of common nsSNPs in the other genes makes the IFIH1 SNP the strongest functional candidate, but it could be merely a marker of association, due to LD with a variant regulating expression levels of IFIH1 or neighboring genes. Methodology/Principal Findings: We investigated the effect of the T1D-associated variation on mRNA transcript expression of these genes. Heterozygous mRNA from lymphoblastoid cell lines (LCLs), pancreas and thymus was examined by allelic expression imbalance, to detect effects in cis on mRNA expression. Using single-nucleotide primer extension, we found no difference between mRNA transcripts in 9 LCLs, 6 pancreas and 13 thymus samples, suggesting that GCA and FAP are not involved. On the other hand, KCNH7 was not expressed at a detectable level in all tissues examined. Moreover, the association of the Thr946Ala SNP with T1D is not due to modulation of IFIH1 expression in organs involved in the disease, pointing to the IFIH1 nsSNP as the causal variant. Conclusions/Significance: The mechanism of the association of the nsSNP with T1D remains to be determined, but does not involve mRNA modulation. It becomes necessary to study differential function of the IFIH1 protein alleles at Thr946Al

Correction to:The genetic architecture of Plakophilin 2 cardiomyopathy (Genetics in Medicine, (2021), 23, 10, (1961-1968), 10.1038/s41436-021-01233-7)

Due to a processing error Cynthia James, Brittney Murray, and Crystal Tichnell were assigned to the wrong affiliation. Cynthia James, Brittney Murray, and Crystal Tichnell have as their affiliation 5 Division of Cardiology, Department of Medicine, Johns Hopkins University, Baltimore, MD, USA. In addition Hana Zouk, Megan Hawley, and Birgit Funke were assigned only to affiliation 3; they also have affiliation 4 Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA. The original article has been corrected

Investigation of impulsive-aggressive behaviors in suicide : a clinical and genetic approach

Impulsivity and aggression have been shown to be important behavioral correlates of suicide. Neurobiological and genetic studies, mostly focusing on the serotonergic system, have demonstrated that these behaviors not only have clinical implications in suicide but also play an important biological role in increasing suicide risk. It remains unclear, however, how impulsivity and aggression might mediate suicide risk. The first study presented here was carried out to investigate clinical, behavioral and psychosocial correlates of impulsivity in suicide completers. Impulsive suicides were characterized by a greater psychiatric comorbidity as well as increased levels of aggression, and were more likely to be affected by negative life events. In a separate study, the effect of genetic variants of the 5-HT1B gene on impulsive aggressive behaviors (IABs) in suicide, as well as their contribution to overall suicide risk, was investigated. One 5-HT1B promoter variant significantly influenced levels of aggressive behaviors in suicide completers, suggesting that aggression plays a role as an intermediate phenotype that increases propensity to suicide. Both studies highlight the importance of the role of IABs in mediating suicide at both clinical and biological levels

Functional characterization of novel genetic loci associated with type 1 diabetes

Type 1 diabetes (T1D) is an autoimmune disease that results from the destruction of the insulin producing beta cells by the immune system. A disease of complex etiology, it involves both genetic and environmental factors. Over 40 genetic loci have been shown to increase T1D risk, where allelic variation at several polymorphisms underlies their genetic association. Two of the most important ones map to chromosome 2q24.3, containing functional polymorphisms at the IFIH1 gene, whose role is to bind double stranded (ds) viral RNA and to subsequently induce a type I interferon response, and to chromosome 16p13, encompassing the single CLEC16A gene whose function is unknown. To elucidate the mechanism of these associations, we undertook separate studies to functionally evaluate the role of a T1D-associated IFIH1 polymorphism and to characterize the possible role of CLEC16A in immunity. We began by investigating the role of the T1D-associated coding polymorphism in the IFIH1 gene, Thr946Ala, contained in a linkage disequilibrium (LD) block that encompasses three other genes. Due to the extent of the LD in the region and the possibility of genetic heterogeneity, the Thr946Ala IFIH1 polymorphism could be a marker for a regulatory variant that affects the expression of IFIH1 or the other genes in the IFIH1 block: GCA, KCNH7, and FAP. Upon testing this hypothesis, we observed no significant transcriptional effects at the IFIH1 locus in tissues most relevant to T1D. We also report that protein alleles of the Thr946Ala single nucleotide polymorphism (SNP) had no significant effect on secreted IFN-α levels induced by poly I:C, a dsRNA mimic. Taken together, both studies suggest that the mechanisms of the observed association of the Thr946Ala SNP remains to be determined but does not involve modulation of mRNA or a poly I:C-driven IFN-α response. For the latter, a greater sample size would be needed to confirm this, due to the large observed variability in the IFN response.Our last study focused on the characterization of the CLEC16A protein, whose preferential expression in two antigen presenting cell types points to its potential role in immunity. We thus hypothesized that CLEC16A could be involved in T-cell co-stimulation and activation and assessed this in an antigen-independent model. We found that CLEC16A does not participate in the T-cell co-stimulation pathway, as shown by the lack of effect of the CLEC16A knockdown on T-cell activation and proliferation. We also show subcellular localization of CLEC16A to the rough endoplasmic reticulum (ER). Our results highlight the difficulty in transitioning from T1D genetic associations to functional studies, which are essential in bridging genetic predisposition with biological mechanisms underlying the immune dysregulation associated with T1D. All hypotheses will need to be examined and ruled out one by one until the true mechanism is discovered.Le diabète de type 1 (DT1) est une maladie auto-immune où les cellules bêta, productrices de l'insuline, sont détruites par le système immunitaire. Cette maladie dont l'étiologie est complexe, implique à la fois des facteurs génétiques et environnementaux. Plus de 40 loci génétiques, où il y a une association avec la variation allélique de plusieurs polymorphismes, ont été montré comme augmentant le risque de DT1. Deux de ces régions les plus importantes sont localisés dans la région chromosomique 2q24.3, qui contient des polymorphismes fonctionnels au niveau du gène IFIH1 dont le rôle est de lier l'ARN double brin (DS) viral pour à la suite induire une réponse interféron de type I (IFN), et dans la région chromosomique 16p13, englobant un seul gène nommé CLEC16A dont la fonction est inconnue. Pour élucider le mécanisme de ces associations, nous avons entrepris des études distinctes pour évaluer le rôle fonctionnel d'un polymorphisme de IFIH1 associé au DT1 et de caractériser le rôle possible de CLEC16A dans l'immunité. Nous avons commencé par étudier le rôle d'un polymorphisme codant, Thr946Ala, du gène IFIH1 associé au DT1 et situé dans un bloc de déséquilibre de liaison (DL) qui comprend trois autres gènes. En raison de l'ampleur du DL dans la région ainsi que la possibilité d'une hétérogénéité génétique, le polymorphisme Thr946Ala IFIH1 pourrait être un marqueur pour un variant qui affecte l'expression du gène IFIH1 ou des autres gènes dans le bloc : GCA, KCNH7 et FAP. Lorsque nous avons testé cette hypothèse, nous n'avons observé aucun effet significatif sur la transcription au niveau du locus IFIH1 dans les tissus les plus pertinents pour le DT1. Nous indiquons également que les allèles protéiniques du polymorphisme d'un seul nucléotide (SNP) Thr946Ala n'ont pas d'effets significatifs sur les niveaux l'IFN-α sécrété suite à une stimulation par le poly I:C, un composé imitant l'ARN double brin. Pris ensemble, ces deux études suggèrent que les mécanismes de l'association observée pour le SNP Thr946Ala restent à déterminer, mais n'impliquent pas la modulation de l'ARNm ou la réponse d'IFN-α via le poly I:C. Pour ce dernier, un échantillonnage plus grand serait nécessaire afin de confirmer cette hypothèse en raison de la grande variabilité observée dans la réponse IFN. Notre dernière étude portait sur la caractérisation de la protéine CLEC16A dont l'expression préférentielle par deux types de cellules présentatrice d'antigènes, suggère un rôle potentiel dans l'immunité. Nous avons donc émis l'hypothèse que CLEC16A pourrait être impliqué dans la co-stimulation et l'activation des lymphocytes T et avons évalué celle-ci dans un modèle indépendant d'un antigène. Nous avons constaté que CLEC16A ne participe pas dans la voie de la co-stimulation, comme en témoigne par l'absence d'effets sur l'activation et la prolifération des lymphocytes T lors de la déplétion de CLEC16A. Nous montrons également que la localisation subcellulaire de CLEC16A est dans le réticulum endoplasmique rugueux (RE). Nos résultats mettent en évidence la difficulté qu'est de faire la transition à partir d'associations génétiques avec le DT1 vers des études fonctionnelles, qui sont essentielles pour pouvoir faire le pont entre la prédisposition génétique et les mécanismes biologiques qui sous-tendent le dysfonctionnement immunitaire associé au DT1. Toutes les hypothèses devront être examinées et écartées une par une jusqu'à ce que le mécanisme réel soit découvert

Phenotypes of undiagnosed adults with actionable OTC and GLA variants

Summary: Inherited metabolic disorders (IMDs) are variably expressive, complicating identification of affected individuals. A genotype-first approach can identify individuals at risk for morbidity and mortality from undiagnosed IMDs and can lead to protocols that improve clinical detection, counseling, and management. Using data from 57,340 participants in two hospital biobanks, we assessed the frequency and phenotypes of individuals with pathogenic/likely pathogenic variants (PLPVs) in two IMD genes: GLA, associated with Fabry disease, and OTC, associated with ornithine transcarbamylase deficiency. Approximately 1 in 19,100 participants harbored an undiagnosed PLPV in GLA or OTC. We identified three individuals (2 male, 1 female) with PLPVs in GLA, all of whom were undiagnosed, and three individuals (3 female) with PLPVs in OTC, two of whom were undiagnosed. All three individuals with PLPVs in GLA (100%) had symptoms suggestive of mild Fabry disease, and one individual (14.2%) had an ischemic stroke at age 33, likely indicating the presence of classic disease. No individuals with PLPVs in OTC had documented hyperammonemia despite exposure to catabolic states, but all (100%) had chronic symptoms suggestive of attenuated disease, including mood disorders and migraines. Our findings suggest that GLA and OTC variants identified via a genotype-first approach are of high penetrance and that population screening of these genes can be used to facilitate stepwise phenotyping and appropriate care

The genetic architecture of Plakophilin 2 cardiomyopathy

Purpose The genetic architecture of Plakophilin 2 (PKP2) cardiomyopathy can inform our understanding of its variant pathogenicity and protein function. Methods We assess the gene-wide and regional association of truncating and missense variants in PKP2 with arrhythmogenic cardiomyopathy (ACM), and arrhythmogenic right ventricular cardiomyopathy (ARVC) specifically. A discovery data set compares genetic testing requisitions to gnomAD. Validation is performed in a rigorously phenotyped definite ARVC cohort and non-ACM individuals in the Geisinger MyCode cohort. Results The etiologic fraction (EF) of ACM-related diagnoses from truncating variants in PKP2 is significant (0.85 [0.80,0.88], p < 2 × 10−16), increases for ARVC specifically (EF = 0.96 [0.94,0.97], p < 2 × 10−16), and is highest in definite ARVC versus non-ACM individuals (EF = 1.00 [1.00,1.00], p < 2 × 10−16). Regions of missense variation enriched for ACM probands include known functional domains and the C-terminus, which was not previously known to contain a functional domain. No regional enrichment was identified for truncating variants. Conclusion This multicohort evaluation of the genetic architecture of PKP2 demonstrates the specificity of PKP2 truncating variants for ARVC within the ACM disease spectrum. We identify the PKP2 C-terminus as a potential functional domain and find that truncating variants likely cause disease irrespective of transcript position

Additional file 1 of Genetic sex validation for sample tracking in next-generation sequencing clinical testing

Additional file 1: Table S1. 96-SNP panel design—BCM-HGSC-CL