The TRACE-Seq method tracks recombination alleles and identifies clonal reconstitution dynamics of gene targeted human hematopoietic stem cells

Rajiv Sharma, Daniel P. Dever, Ciaran M. Lee, Armon Azizi, Yidan Pan, Joab Camarena, Thomas Köhnke, Gang Bao (), Matthew H. Porteus () and Ravindra Majeti ()
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Rajiv Sharma: Stanford University
Daniel P. Dever: Stanford University
Ciaran M. Lee: Rice University
Armon Azizi: Stanford University
Yidan Pan: Rice University
Joab Camarena: Stanford University
Thomas Köhnke: Stanford University
Gang Bao: Rice University
Matthew H. Porteus: Stanford University
Ravindra Majeti: Stanford University

Nature Communications, 2021, vol. 12, issue 1, 1-12

Abstract: Abstract Targeted DNA correction of disease-causing mutations in hematopoietic stem and progenitor cells (HSPCs) may enable the treatment of genetic diseases of the blood and immune system. It is now possible to correct mutations at high frequencies in HSPCs by combining CRISPR/Cas9 with homologous DNA donors. Because of the precision of gene correction, these approaches preclude clonal tracking of gene-targeted HSPCs. Here, we describe Tracking Recombination Alleles in Clonal Engraftment using sequencing (TRACE-Seq), a methodology that utilizes barcoded AAV6 donor template libraries, carrying in-frame silent mutations or semi-randomized nucleotides outside the coding region, to track the in vivo lineage contribution of gene-targeted HSPC clones. By targeting the HBB gene with an AAV6 donor template library consisting of ~20,000 possible unique exon 1 in-frame silent mutations, we track the hematopoietic reconstitution of HBB targeted myeloid-skewed, lymphoid-skewed, and balanced multi-lineage repopulating human HSPC clones in mice. We anticipate this methodology could potentially be used for HSPC clonal tracking of Cas9 RNP and AAV6-mediated gene targeting outcomes in translational and basic research settings.

Date: 2021
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DOI: 10.1038/s41467-020-20792-y

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