Survival in uveal melanoma patients is linked to genetic variation at HERC2 SNP rs12913832.

PURPOSE: Uveal melanoma (UM) is a rare disease, with the highest incidence in people with a fair skin and light eyes. Eye colour is largely genetically determined and defined by a set of single nucleotide polymorphisms (SNPs). We set out to determine whether we could identify a SNP that is related to prognosis. DESIGN: We sequenced DNA from peripheral blood mononuclear cells of 392 patients with UM and obtained the genotype of six common eye colour-related SNPs. Clinical and histopathologic tumour characteristics, tumour chromosome status, and patient survival were compared among patients with different genotypes. SUBJECTS: 392 patients who underwent enucleation for UM at the Leiden University Medical Center, Leiden, The Netherlands. METHODS: We isolated DNA from peripheral blood leukocytes of 392 patients with UM and performed sequencing, using six eye colour SNPs from the HIrisPlex-S assay. The genotypes extracted from the sequencing data were uploaded onto the Hirisplex webtool (https://hirisplex.erasmusmc.nl/) for eye colour prediction. We tested the association of eye colour SNPs with tumour characteristics and chromosome aberrations using Pearson's chi-square test and Mann-Whitney U test and survival with Kaplan-Meier curves with log-rank test and Cox regression. MAIN OUTCOME MEASURES: UM-related survival. RESULTS: Of the total cohort of 392 patients with analysable genotype data, 307 (78%) were assigned to have blue eyes, 74 (19%) brown eyes and 11 (3%) could not be assigned to either blue or brown. Patients with a genetically-blue eye colour had a worse survival (p = 0.04). This was related to one genotype: patients with the G/G genotype of rs12913832 (HERC2) which codes for blue eye colour had a worse prognosis (p = 0.017), which was related to more often having high-risk tumours (monosomy of chromosome 3, p = 0.04) than patients with an A/G or A/A genotype. CONCLUSION: The G/G genotype of rs12913832 (HERC2), which is related to blue eye colour, is not only a genetic factor related to the risk to develop a UM, but is also linked to a worse prognosis, due to an association with a higher risk of developing a high-risk UM (carrying monosomy of chromosome 3).

Mitochondrial Transport from Mesenchymal Stromal Cells to Chondrocytes Increases DNA Content and Proteoglycan Deposition In Vitro in 3D Cultures.

OBJECTIVE: Allogeneic mesenchymal stromal cells (MSCs) are used in the 1-stage treatment of articular cartilage defects. The aim of this study is to investigate whether transport of mitochondria exists between chondrocytes and MSCs and to investigate whether the transfer of mitochondria to chondrocytes contributes to the mechanism of action of MSCs. DESIGN: Chondrocytes and MSCs were stained with MitoTracker, and CellTrace was used to distinguish between cell types. The uptake of fluorescent mitochondria was measured in cocultures using flow cytometry. Transport was visualized using fluorescence microscopy. Microvesicles were isolated and the presence of mitochondria was assessed. Mitochondria were isolated from MSCs and transferred to chondrocytes using MitoCeption. Pellets of chondrocytes, chondrocytes with transferred MSC mitochondria, and cocultures were cultured for 28 days. DNA content and proteoglycan content were measured. Mitochondrial DNA of cultured pellets and of repair cartilage tissue was quantified. RESULTS: Mitochondrial transfer occurred bidirectionally within the first 4 hours until 16 hours of coculture. Transport took place via tunneling nanotubes, direct cell-cell contact, and extracellular vesicles. After 28 days of pellet culture, DNA content and proteoglycan deposition were higher in chondrocyte pellets to which MSC mitochondria were transferred than the control groups. No donor mitochondrial DNA was traceable in the biopsies, whereas an increase in MSC mitochondrial DNA was seen in the pellets. CONCLUSIONS: These results suggest that mitochondrial transport plays a role in the chondroinductive effect of MSCs on chondrocytes in vitro. However, in vivo no transferred mitochondria could be traced back after 1 year.

Taxonomic classification and abundance estimation using 16S and WGS-A comparison using controlled reference samples.

The assessment of microbiome biodiversity is the most common application of metagenomics. While 16S sequencing remains standard procedure for taxonomic profiling of metagenomic data, a growing number of studies have clearly demonstrated biases associated with this method. By using Whole Genome Shotgun sequencing (WGS) metagenomics, most of the known restrictions associated with 16S data are alleviated. However, due to the computationally intensive data analyses and higher sequencing costs, WGS based metagenomics remains a less popular option. Selecting the experiment type that provides a comprehensive, yet manageable amount of information is a challenge encountered in many metagenomics studies. In this work, we created a series of artificial bacterial mixes, each with a different distribution of skin-associated microbial species. These mixes were used to estimate the resolution of two different metagenomic experiments - 16S and WGS - and to evaluate several different bioinformatics approaches for taxonomic read classification. In all test cases, WGS approaches provide much more accurate results, in terms of taxa prediction and abundance estimation, in comparison to those of 16S. Furthermore, we demonstrate that a 16S dataset, analysed using different state of the art techniques and reference databases, can produce widely different results. In light of the fact that most forensic metagenomic analysis are still performed using 16S data, our results are especially important.