Whole-exome sequencing in the clinical setting: Establishing a foothold for precision medicine in genodermatoses and other diseases

@#The concept of “precision medicine” has been a mainstay in discourses about the future of medicine, although it was not until the completion of the Human Genome Project that genetic associations to Mendelian diseases have risen dramatically. Since genetic variations in most (85%) monogenic or oligogenic diseases reside in exons, whole-exome sequencing (WES) serves as a pivotal tool in the identification of causative variants in genodermatoses and other diseases, leading to efficient and timely diagnosis. Here, we share our current diagnosis protocol for genodermatoses using WES as a first-tier solution. Two cases are presented to demonstrate the process of identifying germline variants and one case for a somatic variant. In the first case, a germline missense mutation in COL7A1 (exon73:c.G6127A) was identified for a patient that presented with clinical symptoms of dystrophic epidermolysis bullosa (DEB). Immunofluorescence study revealed decreased collagen VII expression in the dermal-epidermal junction. In case 2, we detected a germline missense mutation in KRT16 (exon1:c.374A>G) in a patient with palmoplantar keratoderma (PPK) and congenital pachyonychia. Sanger sequencing and segregation analysis confirmed the variant detected in WES. For case 3, a patient with linear nevus comedonicus was found to have a somatic missense mutation in NEK9 (exon4:c.500T>C), which was only detected in the lesional DNA sample. Thus, WES shows great potential as a diagnostic tool for monogenic or oligogenic genodermatoses. Since omics is a technology-driven tool, we expect that reaching precision medicine is ever closer.

Comparative transcriptomic analysis reveals adriamycin-induced apoptosis via p53 signaling pathway in retinal pigment epithelial cells / 浙江大学学报（英文版）（B辑：生物医学和生物技术）

OBJECTIVE@#This paper applied a transcriptomic approach to investigate the mechanisms of adriamycin (ADR) in treating proliferative vitreoretinopathy (PVR) using ARPE-19 cells.@*METHODS@#The growth inhibitory effects of ADR on ARPE-19 cells were assessed by sulforhodamine B (SRB) assay and propidium iodide (PI) staining using flow cytometry. The differentially expressed genes between ADR-treated ARPE-19 cells and normal ARPE-19 cells and the signaling pathways involved were investigated by microarray analysis. Mitochondrial function was detected by JC-1 staining using flow cytometry and the Bcl-2/Bax protein family. The phosphorylated histone H2AX (γ-H2AX), phosphorylated checkpoint kinase 1 (p-CHK1), and phosphorylated checkpoint kinase 2 (p-CHK2) were assessed to detect DNA damage and repair.@*RESULTS@#ADR could significantly inhibit ARPE-19 cell proliferation and induce caspase-dependent apoptosis in vitro. In total, 4479 differentially expressed genes were found, and gene ontology items and the p53 signaling pathway were enriched. A protein-protein interaction analysis indicated that the TP53 protein molecules regulated by ADR were related to DNA damage and oxidative stress. ADR reduced mitochondrial membrane potential and the Bcl-2/Bax ratio. p53-knockdown restored the activation of c-caspase-3 activity induced by ADR by regulating Bax expression, and it inhibited ADR-induced ARPE-19 cell apoptosis. Finally, the levels of the γ-H2AX, p-CHK1, and p-CHK2 proteins were up-regulated after ADR exposure.@*CONCLUSIONS@#The mechanism of ARPE-19 cell death induced by ADR may be caspase-dependent apoptosis, and it may be regulated by the p53-dependent mitochondrial dysfunction, activating the p53 signaling pathway through DNA damage.