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developed for in vivo studies of brain development As organoids advance toward maturation, the emergence
(Figure 3). These markers are essential for identifying the of distinct neuronal and glial subtypes can be assessed using
developmental stage and functional identity of various a repertoire of layer- and lineage-specific markers. Deep-
neural and glial populations within organoids. During layer cortical neurons (Layers V–VI) are identified by the
early developmental phases, NPCs dominate and are expression of TBR1, CTIP2 (BCL11B), and FOXP2, which
typically localized in the VZ and SVZ. VZ progenitors’ collectively contribute to corticothalamic and corticospinal
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express transcription factors such as PAX6, which governs connectivity. In contrast, upper-layer neurons (Layers
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neural stem cell identity and early fate decisions, and SOX2, II–IV) express SATB2 and CUX1, both of which regulate
which maintains pluripotency and self-renewal capacity. callosal projection development and intracortical
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SVZ progenitors are marked by EOMES (TBR2), a key connectivity. General neuronal maturation is marked by
regulator of intermediate progenitor proliferation and RBFOX3 (NeuN) and TUBB3 (βIII-tubulin), indicative
neuronal commitment. In addition, migrating and of axonal development and neuronal identity. These
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differentiating neuroblasts express doublecortin (DCX), markers enable the delineation of neuronal maturation
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which is indispensable for early cortical lamination. These stages and the establishment of cortical layer identities.
spatial and temporal markers enhance the resolution of In parallel, glial populations emerge, including astrocytes
developmental mapping, thereby improving the precision expressing ALDH1L1 and GFAP, which reflect metabolic
and reproducibility of cellular characterization. Despite and structural support functions. Oligodendrocyte
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their utility, organoid systems face significant challenges lineage cells are identified by OLIG2 and MBP, both
in fully recapitulating the spatial and temporal fidelity of essential for myelination, while microglia are marked by
in vivo differentiation processes. Structural heterogeneity Iba1, denoting their immunological roles. However,
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is particularly evident in early neuroepithelial rosettes, challenges persist in achieving robust and functionally
and cortical lamination often diverges from canonical complete glial diversification within current organoid
in vivo patterns, complicating direct comparisons. 10,179-181 models, thereby limiting their translational fidelity. The
Moreover, even among organoids derived from the same complexity of developmental trajectories necessitates the
hPSC line, intrinsic developmental variability hinders the use of multiple markers for accurate cell type identification.
reproducibility of results. Furthermore, the lack of standardized protocols across

Figure 3. Cell type-specific markers in brain organoids

Volume 1 Issue 3 (2025) 11 doi: 10.36922/OR025100010