Contribution of homozygous and compound heterozygous missense mutations in VWA2 to Alzheimer's disease

VWA2 protein molecular mechanism predicts colorectal cancer: Promoting cell invasion and migration by inhibiting NK cell activation

The onset and progression of colorectal cancer is intricately linked to a multitude of factors. Among these, immune cells present within the tumor microenvironment play a pivotal role, particularly natural killer (NK) cells, which are essential for mediating anti-tumor immunity. This study aims to elucidate the mechanism by which the VWA2 protein facilitates the invasion and migration of colorectal cancer cells through the inhibition of NK cell activation. Understanding this molecular mechanism is crucial for deciphering the underlying processes involved in colorectal cancer. To achieve the study's objectives, various methodologies were employed, including cell culture techniques, transgenic technology, and assessments of NK cell functionality. The "limma" bioinformatics tool was utilised to identify differentially expressed genes (DEGs) between samples of colon cancer or polyps and normal tissue through transcriptome sequencing. Subsequent Wien analysis was conducted to pinpoint overlapping genes of interest. The impact of VWA2 on both the invasion and migration of colorectal cancer cell lines was assessed through experiments designed for the overexpression and knockout of VWA2.In addition, flow cytometry was employed to evaluate the activation status of NK cells, enabling an analysis of how VWA2 modulates relevant signaling pathways. The findings revealed that overexpression of VWA2 led to a marked inhibition of NK cell activation, which corresponded with reduced cytotoxic activity against tumor cells. Further examination indicated that VWA2 significantly amplified the migration and invasion capabilities of colorectal cancer cells by upregulating immunosuppressive factors while simultaneously downregulating pro-inflammatory factors. Conversely, the reduction of VWA2 expression was shown to markedly enhance NK cell functionality and decrease the invasive potential of colorectal cancer cells. Thus, the evidence suggests that the VWA2 protein actively promotes the migration and invasion of colorectal cancer cells primarily by suppressing NK cell activation, highlighting its potential role as a significant contributor to tumor progression in colorectal cancer.

Clinical application of whole genome sequencing in young onset dementia: challenges and opportunities

INTRODUCTION

Young onset dementia (YOD) by its nature is difficult to diagnose. Despite involvement of multidisciplinary neurogenetics services, patients with YOD and their families face significant diagnostic delays. Genetic testing for people with YOD currently involves a staggered, iterative approach. There is currently no optimal single genetic investigation that simultaneously identifies the different genetic variants resulting in YOD.

AREAS COVERED

This review discusses the advances in clinical genomic testing for people with YOD. Whole genome sequencing (WGS) can be employed as a 'one stop shop' genomic test for YOD. In addition to single nucleotide variants, WGS can reliably detect structural variants, short tandem repeat expansions, mitochondrial genetic variants as well as capture single nucleotide polymorphisms for the calculation of polygenic risk scores.

EXPERT OPINION

WGS, when used as the initial genetic test, can enhance the likelihood of a precision diagnosis and curtail the time taken to reach this. Finding a clinical diagnosis using WGS can reduce invasive and expensive investigations and could be cost effective. These advances need to be balanced against the limitations of the technology and the genetic counseling needs for these vulnerable patients and their families.

Intervention of next-generation sequencing in diagnosis of Alzheimer's disease: challenges and future prospects

Clinical diagnosis of several neurodegenerative disorders based on clinical phenotype is challenging due to its heterogeneous nature and overlapping disease manifestations. Therefore, the identification of underlying genetic mechanisms is of paramount importance for better diagnosis and therapeutic regimens. With the emergence of next-generation sequencing, it becomes easier to identify all gene variants in the genome simultaneously, with a system-wide and unbiased approach. Presently various bioinformatics databases are maintained on discovered gene variants and phenotypic indications are available online. Since individuals are unique in their genome, evaluation based on their genetic makeup helps evolve the diagnosis, counselling, and treatment process at the personal level. This article aims to briefly summarize the utilization of next-generation sequencing in deciphering the genetic causes of Alzheimer's disease and address the limitations of whole genome and exome sequencing.

Accurate rare variant phasing of whole-genome and whole-exome sequencing data in the UK Biobank

Phasing involves distinguishing the two parentally inherited copies of each chromosome into haplotypes. Here, we introduce SHAPEIT5, a new phasing method that quickly and accurately processes large sequencing datasets and applied it to UK Biobank (UKB) whole-genome and whole-exome sequencing data. We demonstrate that SHAPEIT5 phases rare variants with low switch error rates of below 5% for variants present in just 1 sample out of 100,000. Furthermore, we outline a method for phasing singletons, which, although less precise, constitutes an important step towards future developments. We then demonstrate that the use of UKB as a reference panel improves the accuracy of genotype imputation, which is even more pronounced when phased with SHAPEIT5 compared with other methods. Finally, we screen the UKB data for loss-of-function compound heterozygous events and identify 549 genes where both gene copies are knocked out. These genes complement current knowledge of gene essentiality in the human genome.

Insight into the genetic etiology of Alzheimer's disease: A comprehensive review of the role of rare variants

Early-onset Alzheimer's disease (EOAD) is generally known as a dominant disease due to highly penetrant pathogenic mutations in the amyloid precursor protein, presenilin 1 and 2. However, they explain only a fraction of EOAD patients (5% to 10%). Furthermore, only 10% to 15% of EOAD families present with clear autosomal dominant inheritance. Studies showed that only 35% to 60% of EOAD patients have at least one affected first-degree relative. Parent-offspring concordance in EOAD was estimated to be <10%, indicating that full penetrant dominant alleles are not the sole players in EOAD. We aim to summarize current knowledge of rare variants underlying familial and seemingly sporadic Alzheimer's disease (AD) patients. Genetic findings indicate that in addition to the amyloid beta pathway, other pathways are of importance in AD pathophysiology. We discuss the difficulties in interpreting the influence of rare variants on disease onset and we underline the value of carefully selected ethnicity-matched cohorts in AD genetic research.