Morphogen-guided neocortical organoids recapitulate regional areal identity and model neurodevelopmental disorder pathology

  • bioRxiv. 2025 Sep 3:2025.09.02.672952. doi: 10.1101/2025.09.02.672952.
Yuan-Chen Tsai  1 ,  Hajime Ozaki  1 ,  Xinyi Wang  2 ,  Axel A Almet  2  3 ,  Isabel Fleming  1 ,  Kaori Shiraiwa  1 ,  Matthew Jung Min Noh  1 ,  Caihao Nie  1 ,  Sunnyana Trejo  1 ,  Bret Kiyoshi Sugita  1 ,  Jiya Dalal  1 ,  Ruben Alberto Gonzalez  1 ,  Briana De Jesus  1 ,  Gregory Li-Min Chen  1 ,  Michael J Gandal  4 ,  Qing Nie  2  3  5 ,  Momoko Watanabe  1  5  6
Affiliations
  • 1. Department of Anatomy and Neurobiology, School of Medicine, University of California, Irvine, Irvine, CA, USA.
  • 2. Department of Mathematics, School of Physical Sciences, University of California, Irvine, Irvine, CA, USA.
  • 3. NSF-Simons Center for Multiscale Cell Fate Research, University of California, Irvine, Irvine, CA, USA.
  • 4. Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
  • 5. Department of Developmental & Cell Biology, School of Biological Sciences, University of California, Irvine, Irvine, CA USA.
  • 6. Sue & Bill Gross Stem Cell Research Center, School of Medicine, University of California, Irvine, Irvine, CA, USA.
PMID: 40950130 DOI: 10.1101/2025.09.02.672952
Abstract

The human neocortex exhibits characteristic regional patterning (arealization) critical for higher-order cognitive function. Disrupted arealization is strongly implicated in neurodevelopmental disorders (NDDs), but current neocortical Organoid models largely fail to recapitulate this patterning, limiting mechanistic understanding. Here, we establish a straightforward method for generating arealized organoids through short-term early exposure to anterior (FGF8) or posterior (BMP4/CHIR-99021) morphogens. These treatments created distinct anterior and posterior signaling centers, supporting long-lasting polarization, which we validated with single-cell RNA Sequencing that revealed area-specific molecular signatures matching prenatal human cortex. To demonstrate the utility of this platform, we modeled Fragile X Syndrome (FXS) in organoids with distinct anterior and posterior regional identities. FXS organoids showed highly disrupted SOX4/SOX11 expression gradients along the anterior-posterior axis, consistent with alterations found in autism spectrum disorder (ASD) and demonstrate how regional patterning defects may contribute to NDD pathology. Together, our study provides a robust platform for generating neocortical organoids with anterior-posterior molecular signatures and highlights the importance of modeling NDDs using experimental platforms with neuroanatomic specificity.

Keywords
autism spectrum disorder; brain organoids; neocortical areal signatures.
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