StabilitySort: assessment of protein stability changes on a genome-wide scale to prioritise potentially pathogenic genetic variation

SummaryMissense mutations that change protein stability are strongly associated with human inherited genetic disease. With the recent availability of predicted structures for all human proteins generated using the AlphaFold2 prediction model, genome-wide assessment of the stability effects of genetic variation can, for the first time, be easily performed. This facilitates the interrogation of personal genetic variation for potentially pathogenic effects through the application of stability metrics. Here, we present a novel algorithm to prioritise variants predicted to strongly destabilise essential proteins, available as both a standalone software package and a web-based tool. We demonstrate the utility of this tool by showing that at values of the Stability Sort Z-score above 1.6, pathogenic, protein-destabilising variants from ClinVar are detected at a 58% enrichment, over and above the destabilising (but presumably non-pathogenic) variation already present in the HapMap NA12878 genome.Availability and ImplementationStabilitySort is available as both a web service (http://130.56.244.113/StabilitySort/) and can be deployed as a standalone system (https://gitlab.com/baaron/StabilitySort)[email protected]

Bursaphelenchus xylophilus: An Important Pathogenic Factor of Pine Wilt Disease and Its Relationship With Bursaphelenchus mucronatus

Pine wilt disease is the most devastating pine disease caused by Bursaphelenchus xylophilus. Bursaphelenchus mucronatus is morphologically similar to B. xylophilus and geographically overlaps in its distribution. Although interspecific hybridization of the two nematodes has been performed in vitro, the dynamic regularity of hybrid formation and its risk in forests has not been well evaluated. In this study, a hybrid of B. xylophilus and Bursaphelenchus mucronatus mucronatus was identified in the laboratory and fields by molecular markers. The heterozygosity of ITS-5.8S loci for identification was unstable in the hybrid population, and the allele inherited from B. m. mucronatus was lost over several generations. We also provided evidence that hybrids existed in some new epidemic areas, while old epidemic areas were usually dominated by B. xylophilus. Hybrids could be generated when B. m. mucronatus was invaded by B. xylophilus, and the pathogenicity of the hybrids was similar to that of B. xylophilus. These findings may improve the understanding of the natural hybridization between B. xylophilus and B. m. mucronatus and pathogenic variation in pine wilt disease, providing new insights for future studies on disease detection, transmission, and quarantine.

Cardiac arrest as first presentation of arrhythmogenic left ventricular cardiomyopathy due to Filamin C mutation: a case report

Background Arrhythmogenic left ventricular cardiomyopathy (ALVC) is a rare form of arrhythmogenic cardiomyopathy characterized by fibrofatty replacement of left ventricular myocardium, malignant arrhythmia, and sudden cardiac death. The definition incorporates several genetic causes, including pathogenic variation in the Filamin C gene (FLNC). Although awareness of ALVC has improved, identification remains challenging and diagnostic criteria continue to evolve. Case summary A 50-year-old athletic male was admitted following an out-of-hospital cardiac arrest due to ventricular tachycardia (VT) whilst playing football. Coronary angiography revealed unobstructed epicardial vessels and the diagnosis of ALVC was suggested by cardiovascular magnetic resonance imaging, which demonstrated a mildly dilated and moderately impaired left ventricle with epicardial late gadolinium enhancement in the basal to mid-lateral walls and subendocardial septum. Initial testing with a cardiomyopathy and arrhythmia gene panel was negative but extended testing uncovered a likely pathogenic variant in FLNC. Subsequently, the patient experienced a recurrence of sustained VT necessitating implantable cardioverter-defibrillator (ICD) therapies, ultimately undergoing a combined epicardial and endocardial VT ablation 4 years after presentation. Six months post-ablation, he was asymptomatic and his arrhythmia rendered quiescent. Discussion Arrhythmogenic cardiomyopathy should be considered in the evaluation of an initially unexplained cardiac arrest. This case characterizes the clinical features of a patient with FLNC cardiomyopathy and emphasizes the utility of genetic testing using modern gene panels in patients with comparable phenotypes. We also demonstrate that optimal medical therapy with antiarrhythmic drugs, exercise restriction, ICD insertion, and catheter ablation can be useful in the management of ALVC with positive outcomes

Left Ventricular Myocardial Noncompaction with Advanced Atrioventricular Conduction Disorder and Ventricular Arrhythmias in a Young Patient: Role of MIB1 Gene

Left ventricular noncompaction (LVNC) is a structural abnormality of the left ventricle, usually described as an isolated condition, or sometimes associated with other structural cardiac diseases. LVNC is generally asymptomatic, although it may present conduction disorders, arrhythmias, and heart failure. Here, we present the case of a patient who came to our attention with a severe LVNC phenotype associated with advanced AV conduction disorder, and supraventricular and ventricular arrhythmias at young age, in which a novel MIB1, likely pathogenic, variation has been identified.

Pathogenic and molecular variation of Fusarium species causing head blight on barley landraces

Fusarium head blight (FHB) is consistently one of the most important barley diseases worldwide. This study aimed to evaluate the pathogenicity of 16 isolates of four Fusarium species under controlled conditions and their genetic variability using 22 random amplified polymorphic DNA (RAPD) markers. Pathogenic variation was characterized based on disease development rates and disease index on two Syrian barley landraces with varying resistance to FHB, Arabi Aswad (AS) and Arabi Abiad (AB). Significant differences in intra- and inter-Fusarium species pathogenicity and in susceptibility between the above-mentioned cultivars were highlighted. Overall, the two barley landraces showed moderately susceptible to moderately resistance levels to fungal infection and FHB spread within the head. Quantitative traits showed significant correlation with previous data generated in vitro and under field conditions, suggesting that growth chamber indices can predict fungal pathogenicity and quantitative disease resistance generated under various experimental conditions. Based on PCR amplification with seven different primers, the isolates showed genetic variation. Dendrogram generated by cluster analysis based on RAPD markers data showed two main groups, suggesting that a possible clonal origin could exist in the four Fusarium species. RAPD fingerprints are not useful to distinguish the 16 Fusarium isolates with different levels of pathogenicity.