Biology subjects

Trypsteen, W.

Publications and source records attributed to Trypsteen, W..

2 recordsLinked to original sources

bioRxiv2020

Recurrent chromosomal imbalances provide selective advantage to human embryonic stem cells under enhanced replicative stress conditions

Human embryonic stem cells (hESCs) and embryonal tumors share a number of common features including a compromised G1/S checkpoint. Consequently, these rapidly dividing hESCs and cancer cells undergo elevated levels of replicative stress which is known to induce genomic instability causing chromosomal imbalances. In this context, it is of interest that long-term in vitro cultured hESCs exhibit a remarkable high incidence of segmental DNA copy number gains, some of which are also highly recurrent in certain malignancies such as 17q gain (17q+). The selective advantage of DNA copy number changes in these cells has been attributed to several underlying processes including enhanced proliferation. We hypothesized that these recurrent chromosomal imbalances become rapidly embedded in the cultured hESCs through a replicative stress driven Darwinian selection process. To this end, we compared the effect of hydroxyurea induced replicative stress versus normal growth conditions in an equally-mixed cell population of isogenic euploid and 17q+ hESCs. We could show that 17q+ hESCs rapidly overtook normal hESCs. Our data suggest that recurrent chromosomal segmental gains provide a proliferative advantage to hESCs under increased replicative stress, a process that may also explain the highly recurrent nature of certain imbalances in cancer.

cancer biology↗

bioRxiv2020

When DNA gets in the way in RNA-seq experiments, a sequel

Using a newly developed method dubbed SILVER-Seq--enabling extracellular RNA sequencing (exRNA-seq) directly from a small volume of human serum or plasma-- Yan et al. recently reported in Current Biology a potential exRNA biomarker for the early diagnosis of Alzheimers disease [1]. After the publication of the initial paper describing the SILVER-Seq method [2], we reported our concern regarding potential DNA contamination in their datasets [3]. Although the authors replied they were able to successfully treat RNA samples with DNase to avoid such contamination, they did not address our observations of the majority of reads without evidence of being derived from RNA, nor documented verified absence of DNA after DNase treatment [4]. To assess whether the newly data generated may suffer from DNA contamination, we downloaded the publicly available sequencing data and evaluated two quality control metrics (i.e., fraction of exonic and splice reads), which were not reported in the paper. We found that both quality metrics were much lower than expected for RNA-seq data (6.28% exonic and 0.478% splice reads), in line with our previous findings on the first SILVER-Seq paper. These observations suggest the data and results presented by Yan et al. are affected by DNA contamination, an issue that may be inherent to the SILVER-Seq technology.

molecular biology↗