Biology subjects

Davenport, C.

Publications and source records attributed to Davenport, C..

4 recordsLinked to original sources

bioRxiv2021

MinION nanopore sequencing provides similar methylation estimates to Sanger bisulfite sequencing in the TRPA1 promoter region

Bisulfite sequencing has long been considered the gold standard for measurement of DNA methylation at single CpG resolution. In the meantime, several new approaches have been developed, which are regarded as less error-prone. Since these errors were shown to be sequence-specific, we aimed to verify the methylation data of a particular region of the TRPA1 promoter obtained from our previous studies. For this purpose, we compared methylation rates obtained via direct bisulfite sequencing and nanopore sequencing. Thus, we were able to confirm our previous findings to a large extent.

molecular biology↗

bioRxiv2020

iPSC culture expansion selects against putatively actionable mutations in the mitochondrial genome

While human induced pluripotent stem cells (iPSCs) offer fascinating prospects for research and clinics, evaluating their genomic stability before applications is of utmost importance. During reprogramming, clonal hiPSC lines derived from the same parental cell population were observed to harbor different mitochondrial DNA (mtDNA) variants and variant heteroplasmy levels. It is unknown to date to which extent this unequal segregation of heteroplasmies between cells arises from mosaicism in the parental cell population, selection on mutated mtDNA molecules on the cellular or organelle level, genetic drift during reduction of mtDNA during reprogramming (genetic bottleneck), or de novo mutations. We analyzed mtDNA variants in 26 clonal iPSC lines by mtDNA sequencing. We did not observe a strong bottleneck or any selection for cells with specific mtDNA variants (clonal eliteness) during reprogramming. iPSC culture expansion, however, selects against putatively actionable mutations in the mitochondrial genome that may affect mitochondrial function and cell metabolism. In contrast, heteroplasmy levels of neutral variants remained stable or increased within clonal iPSC lines during culture expansion. Interestingly, the mtDNA copy number per cell got transiently reduced during targeted differentiation of iPSCs into cardiomyocytes, but mtDNA heteroplasmy levels were not affected. Altogether, our results point towards a scenario in which intra-cellular selection on mtDNA during culture expansion, but not during reprogramming or differentiation, pivotally shapes the mutational landscape of the mitochondrial genome in iPSCs. Other mechanisms such as inter-cellular selection, genetic bottleneck, and genetic drift exert minor impact.

genomics↗

bioRxiv2020

Reprogramming enriches for somatic cell clones with small scale mutations in cancer-associated genes

Recent studies demonstrated that the mutational load in human induced pluripotent stem cells (hiPSCs) is largely derived from their parental cells, but it is still unknown whether reprogramming may enrich for individual mutations. 30 hiPSC lines were analyzed by whole exome sequencing. High accuracy amplicon sequencing showed that all analyzed small scale variants pre-existed in their parental cells and that individual mutations present in small subpopulations of parental cells become enriched among hiPSC clones during reprogramming. Among those, putatively actionable driver mutations affect genes related to cell cycle control, cell death and pluripotency, and may confer a selective advantage during reprogramming. Finally, a shRNA-based experimental approach was applied to provide additional evidence for the individual impact of such genes on the reprogramming efficiency. In conclusion, we show that enriched mutations in curated onco- and tumor suppressor genes may account for an increased tumor risk and impact the clinical value of patient-derived hiPSCs.

genomics↗

bioRxiv2017

Dietary and behavioral inferences from dental pathology and non-masticatory wear on dentitions from a British medieval town

Dental pathology and wear data can provide valuable insights into diet, cultural practices, and the health of populations. In this study, various dental pathologies and types of wear were recorded for 41 individuals (914 permanent teeth), excavated from the medieval cemetery of St. Owens Church in Southgate Street, Gloucester. Teeth were studied macroscopically with a 10x hand lens to confirm the presence of specific pathologies. Relatively high rates of antemortem chipping on the anterior teeth, and the presence of maxillary central incisor notches, suggested that the Gloucester population commonly used their teeth for non-masticatory activities. Abscessing and antemortem tooth loss fell within previously reported ranges for British medieval sites (2.6% and 6% respectively). However, the sample exhibits extremely high levels of carious lesions and calculus. Nearly 24% of teeth have at least one carious lesion, and the presence of calculus was recorded in 74% of teeth within the sample. Overall caries frequency is similar to sites from later time periods. This frequency may reflect Gloucesters location as a large port town. Remains from the same area, but the earlier Roman period, also shows high rates of both caries and calculus, suggesting a continuation of consuming certain cariogenic foods is likely.

pathology↗