Extended Data Fig. 4: Prime editing in human HSPCs and its adverse impact on HSPCs.

a, Heatmap of normalized read counts for genes belonging to the MMR pathway (KEGG database; hsa03430) in UT CB HSPCs cultured for 1 or 3 days. b, Module score for genes belonging to the MMR pathway in different HSPC subsets from⁵. c, Flow cytometry plots showing the gating strategy for prime edited B2M⁻ mPB HSPCs. d, Representative plot of B2M Sanger sequencing. e, Representative image of capillary electropherogram of prime edited (n = 5) and UT (n = 2) samples. f, Schematics of representative alleles for WT, pPE and iPE outcomes in prime edited samples from Fig. 6e. g, Volcano plot showing significant down- (green) and up- (red) regulated genes after prime editing. h, Schematic representation of the spacer sequence shared between pegRNA and gRNA for Cas9. i, Schematic representation of the probes used for deletions detection. The distances between the target site and the closest primer of the ddPCR amplicons are shown. j, Fold change of APOBEC3H expression over UT 24 hrs after editing (n = 5,5,6). Median with IQR. LME followed by post hoc analysis. k, Representation of TP73 spliced alignment from RNA-Seq reads. l, Fold change of TP73 expression over UT 24 hrs after editing (n = 1). m, Molecular analysis of B2M modification 7 days after prime editing in human mPB HSPCs (n = 5). Median with IQR. n,o, Percentage of human cells engraftment (n) and B2M modified alleles (o) in BM and SPL of mice from Fig. 6p (n = 5,6). Median with IQR. p,q, Lineage composition in BM (p) and SPL (q) of mice from Fig. 6p and Fig. 6q (n = 5,6,3,3). Mean \(\pm\) s.e.m. All statistical tests are two-tailed. n indicate biologically independent experiments except for Extended Data Fig. 4 in which n indicate independent samples and Extended Data Fig. 4n–q in which n indicate independent animals.