An iPSC-based experimental framework for investigating phenotypic variation associated with Jomon ancestry in the present-day Japanese population

Nakamura, Y.; Watanabe, Y.; Tanabe, H.; Hirai, A.; Higashi, K.; Kurokawa, K.; Toyoda, A.; Kato, T.; Tsukahara, M.; Koganebuchi, K.; Hamazaki, Y.; Takebe, T.; Imamura, M.; Ishida, T.; Ohashi, J.; Oota, H.

doi:10.64898/2026.10.07.756619

bioRxiv · 10.64898/2026.10.07.756619

An iPSC-based experimental framework for investigating phenotypic variation associated with Jomon ancestry in the present-day Japanese population

Nakamura, Y.·Watanabe, Y.·Tanabe, H.·Hirai, A.·Higashi, K.·Kurokawa, K.·Toyoda, A.·Kato, T.·Tsukahara, M.·Koganebuchi, K.·Hamazaki, Y.·Takebe, T.·Imamura, M.·Ishida, T.·Ohashi, J.·Oota, H.

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Abstract

Ancestry-related genomic variation may contribute to phenotypic diversity. However, its cellular consequences remain difficult to evaluate. To address this, we developed a human induced pluripotent stem cell (hiPSC)-based framework for investigating such phenotypes. We used the Japanese population as a model of Jomon-related and continental East Asian ancestry admixture. Jomon ancestry, estimated using the Jomon allele score (JAS), was associated with clinical measures, including renal-related traits and serum triglycerides in 34,152 Tohoku Medical Megabank participants. Peripheral blood mononuclear cell transcriptomics of donors from the upper and lower extremes of the JAS distribution (n = 10) suggested group-level differences in immune-related gene expression. To test whether the serum triglyceride association coincided with hepatic cellular phenotypes, we differentiated hiPSCs from these donors into hepatocyte-like cells. Neither intracellular triglycerides nor lipid-related gene expression differed between groups. These findings highlight the value of a genetically characterized hiPSC-based framework for investigating ancestry-associated phenotypes across cellular contexts.

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Nakamura, Y., Watanabe, Y., Tanabe, H., Hirai, A., Higashi, K., Kurokawa, K., Toyoda, A., Kato, T., Tsukahara, M., Koganebuchi, K., Hamazaki, Y., Takebe, T., Imamura, M., Ishida, T., Ohashi, J., Oota, H.. 2026-10-11. An iPSC-based experimental framework for investigating phenotypic variation associated with Jomon ancestry in the present-day Japanese population. https://doi.org/10.64898/2026.10.07.756619

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