Highly Coordinated Proteome Dynamics during Reprogramming of Somatic Cells to Pluripotency

TLDR

Generation of induced pluripotent stem cells (iPSCs) is a process whose mechanistic underpinnings are only beginning to emerge. The study applies quantitative proteomics to monitor proteome changes during fibroblast reprogramming to iPSCs. In-depth quantitative proteomics was used to track proteome dynamics throughout reprogramming. Proteome analysis revealed a two‑step reset in the first and last 3 days of reprogramming, with coordinated changes in electron‑transport chain stoichiometry, vesicle transport, and an EMT‑like process, and identified the nucleoporin Nup210 as essential for proliferation and MET, providing a stage‑specific protein resource for understanding reprogramming.

Abstract

Generation of induced pluripotent stem cells (iPSCs) is a process whose mechanistic underpinnings are only beginning to emerge. Here, we applied in-depth quantitative proteomics to monitor proteome changes during the course of reprogramming of fibroblasts to iPSCs. We uncover a two-step resetting of the proteome during the first and last 3 days of reprogramming, with multiple functionally related proteins changing in expression in a highly coordinated fashion. This comprised several biological processes, including changes in the stoichiometry of electron transport-chain complexes, repressed vesicle-mediated transport during the intermediate stage, and an EMT-like process in the late phase. In addition, we demonstrate that the nucleoporin Nup210 is essential for reprogramming by its permitting of rapid cellular proliferation and subsequent progression through MET. Along with the identification of proteins expressed in a stage-specific manner, this study provides a rich resource toward an enhanced mechanistic understanding of cellular reprogramming.