Single Cell Sequencing for Autologous Hematopoietic Stem Cell Gene Therapy

Bulk sequencing is the standard way to read out hematopoietic stem cell (HSC) gene therapy. But an average across millions of cells can’t show how edits are spread from one cell to the next. That gap can change how engraftment, editing efficiency and therapeutic benefit are interpreted.

In this 36-minute webinar, Dr. Stefan Radtke, a senior scientist in the Stem Cell and Gene Therapy Program at Fred Hutchinson Cancer Center, presents data from nonhuman primate studies. His team used single-cell DNA and protein sequencing on the Tapestri® platform. The studies paired a therapeutic edit for sickle cell disease with a protective CD33 edit, and the single-cell readouts changed the interpretation of the results.

Topics include:

• Why bulk vector copy number and allelic editing efficiency don’t reflect engraftment or replacement
• Mono- and biallelic editing measured across thousands of cells and individual blood lineages
• Stacked genotypes pointing to near-complete marrow replacement, where bulk data suggested roughly half
• How the spread of HBG promoter edits across cells explained fetal hemoglobin levels above the therapeutic threshold
• What multiplex therapeutic and protective editing means for in vivo selection strategies
• Long-term follow-up from small blood samples, with room to add off-target and clonal tracking

This session is for researchers working on HSC transplantation, gene editing and in vivo gene therapy who want a closer look at what happens in each cell.