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The rise of three-dimensional human brain cultures

Pluripotent stem cells show a remarkable ability to self-organize and differentiate in vitro in three-dimensional aggregates, known as organoids or organ spheroids, and to recapitulate aspects of human brain development and function. Region-specific 3D brain cultures can be derived from any individual and assembled to model complex cell–cell interactions and to generate circuits in human brain assembloids. Here I discuss how this approach can be used to understand unique features of the human brain and to gain insights into neuropsychiatric disorders. In addition, I consider the challenges faced by researchers in further improving and developing methods to probe and manipulate patient-derived 3D brain cultures.



Understanding the principles that underlie the assembly of cells into tissues and of tissues into organs is a fundamental goal in biology. Such understanding requires not just observation, but also the ability to construct and deconstruct complex, developing structures. This has been particularly challenging when studying the central nervous system (CNS) in humans, in part because of its complexity, but also because of poor accessibility to all stages of development and lack of functional tissue preparations. In other branches of medicine, such as hematology and oncology, easy access to tissue samples has led to a comprehensive understanding of organ development and substantial therapeutic advances. Therefore, there is a pressing need to develop functional, realistic, and personalized models of the developing human brain so that we can better understand its unique biology and gain mechanistic insights into neuropsychiatric disorders. Several recent conceptual and technological advances are now converging to make human brain tissue more accessible for study. First, the ability to culture pluripotent stem cells, including human embryonic stem (hES) cells, in vitro.


Second, the possibility to reprogram somatic cells into induced pluripotent stem (iPS) cell3 and subsequently to promote their differentiation into neurons, or to shortcut this process and directly derive neurons. Third, progress in building 3D brain cultures as well as advances in biomaterials, CRISPR–Cas9-based genome engineering and highly-parallel single-cell transcriptomics. Combined, these advances open opportunities for understanding the assembly of the human brain and how this may go awry in disease. This review discusses advances in building 3D human brain cultures, such as neural organoids or spheroids, and describes how these cultures may help researchers capture normal and abnormal organogenesis in vitro. While these approaches may bring access to previously inaccessible aspects of human biologies, such as developmental processes in late human gestation, they are still models. As George Box pointed out, “all models are wrong but some are useful, and their value ultimately resides in their ability to provide testable predictions. Therefore, an important goal of this overview will also be to highlight the advantages and disadvantages of the various approaches for engineering in vitro models of the human nervous system1.



Cross-sections through the developing human brain at gestational week 17, showing the cerebral cortex (red), the medial ganglionic eminences (MGE, green) and the thalamus (blue). Interneurons from the MGE migrate tangentially to populate the dorsal pallium. Thalamic neurons project to the cortical subplate and then onto layer 4 cortical neurons, while deep layer cortical neurons project back to the thalamus. a, Pallial–subpallial assembloids show modelling of GABAergic interneuron migration and functional integration into cortical circuits. b, Cortico-thalamic assembloids illustrate projections from deep layer cortical neurons onto thalamic neurons and projections of thalamic neurons onto layer 4 cortical neurons.
Human brain assembloids

  1. Pașca, S. The rise of three-dimensional human brain cultures. Nature553, 437–445 (2018). https://doi.org/10.1038/nature25032

cover photo: https://www.viennabiocenter.org/research/key-discoveries/human-brain-organoids/