van der Werf, I. | Search bioRxiv

bioRxiv2024

Accelerated Hematopoietic Stem Cell Aging in Space

Stem cell aging is accelerated by macroenvironmental and microenvironmental stressors, including inflammation. Previously, the NASA Twins study revealed inflammatory cytokine upregulation, chromosomal alterations, and telomere changes suggestive of accelerated aging in low-Earth orbit (LEO). To investigate the effects of spaceflight on human hematopoietic stem and progenitor cell (HSPC) aging, the NASA-supported Integrated Space Stem Cell Orbital Research team performed four independent 30- to 45-day NASA missions with matched flight and ground HSPC nanobioreactors in automated CubeLabs. These experiments revealed loss of HSPC dormancy, reduced self-renewal capacity, mitochondrial DNA amplification, APOBEC3-induced C-to-T mutagenesis, reduced ADAR1p150 expression, and alterations in the expression of repetitive elements. These molecular changes are indicative of accelerated HSPC aging and pre-leukemia stem cell generation in space and may be predictable and preventable.

cancer biology↗

bioRxiv2023

Comprehensive single-cell genome analysis at nucleotide resolution using the PTA Analysis Toolbox

Detection of somatic mutations in single cells has been severely hampered by technical limitations of whole genome amplification. Novel technologies including primary template-directed amplification (PTA) significantly improved the accuracy of single-cell whole genome sequencing (WGS), but still generate hundreds of artefacts per amplification reaction. We developed a comprehensive bioinformatic workflow, called the PTA Analysis Toolkit (PTATO), to accurately detect single base substitutions, small insertions and deletions (indels) and structural variants in PTA-based WGS data. PTATO includes a machine learning approach to distinguish PTA-artefacts from true mutations with high sensitivity (up to 90% for base substitution and 95% for indels), outperforming existing bioinformatic approaches. Using PTATO, we demonstrate that many hematopoietic stem and progenitor cells of patients with Fanconi anemia, which cannot be analyzed using regular WGS technologies, have normal somatic single base substitution burdens, but increased numbers of deletions. Our results show that PTATO enables studying somatic mutagenesis in the genomes of single cells with unprecedented sensitivity and accuracy.

genomics↗