Induced pluripotent stem (iPS) cells carry the genome of their donor, enabling human in vitro models that reveal the mechanisms of genetic disease and potential autologous cell therapies. Combined with CRISPR-Cas9 genome editing, the effects of natural genetic variations on human characteristics including disease predisposition and severity can be functionally tested in iPS cell-derived tissues. Moreover, we can re-create combinations of genetic variants found only in ancient genomes, or variants which improve the efficacy or safety of therapeutic cells.

The Woltjen Lab has developed gene editing strategies that manipulate DNA repair pathways to create precise single-nucleotide variations and small deletions in human iPS cells. Using these strategies, we generated models for the APRT*J allele which predates 300 BC and is prevalent in Japanese patients with urolithiasis leading to kidney failure, and ALDH2 variants differing between the Yayoi and Jomon lineages that determine the efficiency of aldehyde breakdown following alcohol consumption. More recently, we are studying how polymorphisms in variable number tandem repeats (VNTRs) may shape our genomes and define ethnicity. Towards therapies, we created a disease-associated mutation in EPOR which enhances differentiation and reduces the cost of red blood cell production from iPS cells in vitro.

In this seminar, I will review modern and ancient genetic variants, gene editing technologies used to engineer them, and applications in functional genomics and enhanced cell therapies.

1. Martínez-Gálvez, G., Lee, S., Niwa, R. & Woltjen, K. On the edge of deletion: Using natural and engineered microhomology to edit the human genome. Gene and Genome Editing 7, 100033 (2024).

2. Niwa, R. et al. Enrichment of Allelic Editing Outcomes by Prime Editing in Induced Pluripotent Stem Cells. The CRISPR Journal 7, 293–304 (2024).

3. Maurissen, T. L. & Woltjen, K. Synergistic gene editing in human iPS cells via cell cycle and DNA repair modulation. Nat Commun 11, 2876 (2020).

4. Grajcarek, J. et al. Genome-wide microhomologies enable precise template-free editing of biologically relevant deletion mutations. Nat Commun 10, 4856 (2019).

東京大学大学院理学系研究科・生物科学専攻・ゲノム人類学研究室