OO001 - GENERATION OF A COHORT OF FULLY REPROGRAMMED IPSCS AND A CATALOG OF SINGLE CELL QUANTITATIVE TRAIT LOCI IN IPSC-DERIVED NEURONS (ID 1455)
- Xylena Reed (United States of America)
- Alexandra Beilina (United States of America)
- Sara Saez-Atienzar (United States of America)
- Sultana Solaiman (United States of America)
- J. Raphael Gibbs (United States of America)
- Sonja Scholz (United States of America)
- Mark R. Cookson (United States of America)
Abstract
Aims
Reprogram PBMCs from 100 neurologically healthy individuals to induced Pluripotent Stem Cell (iPSC) lines and assess methylation and telomere length to determine the epigenetic age and efficiency of reprogramming. Differentiate these iPSC lines to forebrain neurons and use single cell sequencing to identify cell type specific expression Quantitative Trail Loci (eQTLs) and chromatin accessibility QTLs (caQTLs).
Methods
PBMCs were collected and reprogrammed using the Cytotune 2.0 kit. The resulting iPSCs were checked for pluripotency using pluritest and Taqman hPSC scorecard. DNA methylation was analyzed in donor PBMCs and iPSCs to determine the epigenetic age of each cell type. Absolute telomere length was determined by qPCR. Genotyped iPSC lines were differentiated to forebrain neurons and dissociated at day 60 for single cell RNA and ATAC sequencing.
Results
These iPSCs lines cluster with known stem cells by pluritest and show expression of self-renewal markers alongside downregulation of germ layer markers. DNA methylation in iPSCs shows a complete reset of the epigenetic clock relative to the corresponding PBMCs. Additionally, absolute telomere length is similar across all lines, irrespective of donor age, suggesting full reprogramming. Differentiation of these iPSCs to forebrain neurons results in a population with variable neuronal maturity. Single cell RNA and ATAC sequencing identifies QTLs in specific neuronal subtypes within the population.
Conclusions
We have generated a large cohort of fully reprogrammed iPSCs from neurologically healthy individuals. Single cell sequencing in iPSC-derived neurons identifies cell type specific eQTLs and caQTLs that may help build regulatory maps and prioritize genes at loci associated with neurodegeneration.
