Beyond phenotypic markers: rethinking dopaminergic identity in iPSC-derived neurons

Abstract

Human pluripotent stem cell-derived dopaminergic neurons have become central platforms for Parkinson’s disease (PD) modeling and regenerative medicine. Current differentiation systems can efficiently generate TH+/FOXA2+/LMX1A+ ventral midbrain-like populations. Although canonical markers remain important components of dopaminergic validation, the field increasingly complements them with single-cell profiling, developmental reference mapping, functional assessment, and transplantation-based evaluation. Nevertheless, marker-positive phenotypic resemblance alone may inadequately capture the full multidimensional identity of substantia nigra pars compacta neurons. Recent single-cell, developmental, and organoid studies indicate that human dopaminergic neurons exist across highly specialized multidimensional states shaped by developmental trajectory, epigenetic regulation, metabolic adaptation, biological aging, and ecosystem-level interactions. On the basis of these observations, we hypothesize that some current in vitro systems may generate neurons with incomplete or context-dependent identity because of accelerated differentiation, strong exogenous patterning, resetting of age-associated features, incomplete metabolic maturation, and the absence of supporting cells and tissue-derived signals. We distinguish these experimentally observed limitations from their conceptual interpretation and propose a testable framework for evaluating dopaminergic identity across developmental, molecular, metabolic, functional, aging-related, and environmental dimensions. This framework identifies improved maturation, representation of biological age, metabolic resilience, and multicellular context as priorities for PD modeling and regenerative neuroscience.