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Honors & Awards

  • K99/R00 NIH Pathway to Independence Award, National Institute of Mental Health (2019-2024)
  • AES Postdoctoral Research Fellowship, American Epilepsy Foundation (2018-2019)
  • School of Medicine Dean's Postdoctoral Fellowship, Stanford University School of Medicine (2016-2017)
  • Child Health Research Institue Postdoctoral Award, Child Health Research Institute (CHRI) at Stanford University (2015-2016)
  • Graduate Student Organization Distinguished Travel Award, Stony Brook University (2013)
  • A.T. Kearney Scholarship, Falling Walls Lab (2013)
  • International Society of Neurochemistry Travel Award, International Society of Neurochemistry (2013)
  • John L. Howieson Bioscholarship, University of Kansas (2006-2008)
  • Fulbright Scholarship, Fulbright (2004-2008)

Professional Education

  • Doctor of Philosophy, Stony Brook University, Genetics (2014)
  • Bachelor of Science, University of Kansas (2008)

Stanford Advisors


All Publications

  • Generation and assembly of human brain region-specific three-dimensional cultures. Nature protocols Sloan, S. A., Andersen, J., Pa?ca, A. M., Birey, F., Pa?ca, S. P. 2018


    The ability to generate region-specific three-dimensional (3D) models to study human brain development offers great promise for understanding the nervous system in both healthy individuals and patients. In this protocol, we describe how to generate and assemble subdomain-specific forebrain spheroids, also known as brain region-specific organoids, from human pluripotent stem cells (hPSCs). We describe how to pattern the neural spheroids toward either a dorsal forebrain or a ventral forebrain fate, establishing human cortical spheroids (hCSs) and human subpallial spheroids (hSSs), respectively. We also describe how to combine the neural spheroids in vitro to assemble forebrain assembloids that recapitulate the interactions of glutamatergic and GABAergic neurons seen in vivo. Astrocytes are also present in the human forebrain-specific spheroids, and these undergo maturation when the forebrain spheroids are cultured long term. The initial generation of neural spheroids from hPSCs occurs in <1 week, with regional patterning occurring over the subsequent 5 weeks. After the maturation stage, brain region-specific spheroids are amenable to a variety of assays, including live-cell imaging, calcium dynamics, electrophysiology, cell purification, single-cell transcriptomics, and immunohistochemistry studies. Once generated, forebrain spheroids can also be matured for >24 months in culture.

    View details for PubMedID 30202107

  • Assembly of functionally integrated human forebrain spheroids Nature Birey, F. *., Andersen, J. *., Makinson, C. *., Islam, S., Wei, W., Fan, C. H., Metzler, K. R., Panagiotakos, G., Thom, N., O'Rourke, N. A., Steinmetz, L. M., Bernstein, J. A., Hallmayer, J., Huguenard, J. R., Pasca, S. P. 2017

    View details for DOI 10.1038/nature22330

  • Primate cell fusion disentangles gene regulatory divergence in neurodevelopment. Nature Agoglia, R. M., Sun, D. n., Birey, F. n., Yoon, S. J., Miura, Y. n., Sabatini, K. n., Pa?ca, S. P., Fraser, H. B. 2021


    Among primates, humans display a unique trajectory of development that is responsible for the many traits specific to our species. However, the inaccessibility of primary human and chimpanzee tissues has limited our ability to study human evolution. Comparative in vitro approaches using primate-derived induced pluripotent stem cells have begun to reveal species differences on the cellular and molecular levels1,2. In particular, brain organoids have emerged as a promising platform to study primate neural development in vitro3-5, although cross-species comparisons of organoids are complicated by differences in developmental timing and variability of differentiation6,7. Here we develop a new platform to address these limitations by fusing human and chimpanzee induced pluripotent stem cells to generate a panel of tetraploid hybrid stem cells. We applied this approach to study species divergence in cerebral cortical development by differentiating these cells into neural organoids. We found that hybrid organoids provide a controlled system for disentangling cis- and trans-acting gene-expression divergence across cell types and developmental stages, revealing a signature of selection on astrocyte-related genes. In addition, we identified an upregulation of the human somatostatin receptor 2 gene (SSTR2), which regulates neuronal calcium signalling and is associated with neuropsychiatric disorders8,9. We reveal a human-specific response to modulation of SSTR2 function in cortical neurons, underscoring the potential of this platform for elucidating the molecular basis of human evolution.

    View details for DOI 10.1038/s41586-021-03343-3

    View details for PubMedID 33731928

  • Generation of human striatal organoids and cortico-striatal assembloids from human pluripotent stem cells. Nature biotechnology Miura, Y. n., Li, M. Y., Birey, F. n., Ikeda, K. n., Revah, O. n., Thete, M. V., Park, J. Y., Puno, A. n., Lee, S. H., Porteus, M. H., Pa?ca, S. P. 2020; 38 (12): 1421?30


    Cortico-striatal projections are critical components of forebrain circuitry that regulate motivated behaviors. To enable the study of the human cortico-striatal pathway and how its dysfunction leads to neuropsychiatric disease, we developed a method to convert human pluripotent stem cells into region-specific brain organoids that resemble the developing human striatum and include electrically active medium spiny neurons. We then assembled these organoids with cerebral cortical organoids in three-dimensional cultures to form cortico-striatal assembloids. Using viral tracing and functional assays in intact or sliced assembloids, we show that cortical neurons send axonal projections into striatal organoids and form synaptic connections. Medium spiny neurons mature electrophysiologically following assembly and display calcium activity after optogenetic stimulation of cortical neurons. Moreover, we derive cortico-striatal assembloids from patients with a neurodevelopmental disorder caused by a deletion on chromosome 22q13.3 and capture disease-associated defects in calcium activity, showing that this approach will allow investigation of the development and functional assembly of cortico-striatal connectivity using patient-derived cells.

    View details for DOI 10.1038/s41587-020-00763-w

    View details for PubMedID 33273741

  • Genetically targeted chemical assembly of functional materials in living cells, tissues, and animals. Science (New York, N.Y.) Liu, J. n., Kim, Y. S., Richardson, C. E., Tom, A. n., Ramakrishnan, C. n., Birey, F. n., Katsumata, T. n., Chen, S. n., Wang, C. n., Wang, X. n., Joubert, L. M., Jiang, Y. n., Wang, H. n., Fenno, L. E., Tok, J. B., Pa?ca, S. P., Shen, K. n., Bao, Z. n., Deisseroth, K. n. 2020; 367 (6484): 1372?76


    The structural and functional complexity of multicellular biological systems, such as the brain, are beyond the reach of human design or assembly capabilities. Cells in living organisms may be recruited to construct synthetic materials or structures if treated as anatomically defined compartments for specific chemistry, harnessing biology for the assembly of complex functional structures. By integrating engineered-enzyme targeting and polymer chemistry, we genetically instructed specific living neurons to guide chemical synthesis of electrically functional (conductive or insulating) polymers at the plasma membrane. Electrophysiological and behavioral analyses confirmed that rationally designed, genetically targeted assembly of functional polymers not only preserved neuronal viability but also achieved remodeling of membrane properties and modulated cell type-specific behaviors in freely moving animals. This approach may enable the creation of diverse, complex, and functional structures and materials within living systems.

    View details for DOI 10.1126/science.aay4866

    View details for PubMedID 32193327

  • Nondestructive nanostraw intracellular sampling for longitudinal cell monitoring. Proceedings of the National Academy of Sciences of the United States of America Cao, Y., Hjort, M., Chen, H., Birey, F., Leal-Ortiz, S. A., Han, C. M., Santiago, J. G., Pasca, S. P., Wu, J. C., Melosh, N. A. 2017


    Here, we report a method for time-resolved, longitudinal extraction and quantitative measurement of intracellular proteins and mRNA from a variety of cell types. Cytosolic contents were repeatedly sampled from the same cell or population of cells for more than 5 d through a cell-culture substrate, incorporating hollow 150-nm-diameter nanostraws (NS) within a defined sampling region. Once extracted, the cellular contents were analyzed with conventional methods, including fluorescence, enzymatic assays (ELISA), and quantitative real-time PCR. This process was nondestructive with >95% cell viability after sampling, enabling long-term analysis. It is important to note that the measured quantities from the cell extract were found to constitute a statistically significant representation of the actual contents within the cells. Of 48 mRNA sequences analyzed from a population of cardiomyocytes derived from human induced pluripotent stem cells (hiPSC-CMs), 41 were accurately quantified. The NS platform samples from a select subpopulation of cells within a larger culture, allowing native cell-to-cell contact and communication even during vigorous activity such as cardiomyocyte beating. This platform was applied both to cell lines and to primary cells, including CHO cells, hiPSC-CMs, and human astrocytes derived in 3D cortical spheroids. By tracking the same cell or group of cells over time, this method offers an avenue to understand dynamic cell behavior, including processes such as induced pluripotency and differentiation.

    View details for DOI 10.1073/pnas.1615375114

    View details for PubMedID 28223521

  • Oligodendroglia-lineage cells in brain plasticity, homeostasis and psychiatric disorders. Current opinion in neurobiology Birey, F. n., Kokkosis, A. G., Aguirre, A. n. 2017; 47: 93?103


    Adult oligodendrocyte progenitor cells are uniformly distributed in both gray and white matter, displaying robust proliferative and migratory potential during health and disease. Recently, developments in new experimental approaches have brought about several novel insights about NG2-glia and myelinating oligodendrocytes, indicating a diverse toolkit of functions in experience-dependent myelination and homeostasis in the adult CNS. In this review, we summarize some of the topical studies that highlight newly emerging findings implicating oligodendroglia-lineage cells in brain plasticity, homeostasis and pathophysiology of neuropsychiatric disorders.

    View details for DOI 10.1016/j.conb.2017.09.016

    View details for PubMedID 29073529

  • Human Astrocyte Maturation Captured in 3D Cerebral Cortical Spheroids Derived from Pluripotent Stem Cells. Neuron Sloan, S. A., Darmanis, S. n., Huber, N. n., Khan, T. A., Birey, F. n., Caneda, C. n., Reimer, R. n., Quake, S. R., Barres, B. A., Pa?ca, S. P. 2017; 95 (4): 779?90.e6


    There is significant need to develop physiologically relevant models for investigating human astrocytes in health and disease. Here, we present an approach for generating astrocyte lineage cells in a three-dimensional (3D) cytoarchitecture using human cerebral cortical spheroids (hCSs) derived from pluripotent stem cells. We acutely purified astrocyte-lineage cells from hCSs at varying stages up to 20 months in vitro using immunopanning and cell sorting and performed high-depth bulk and single-cell RNA sequencing to directly compare them to purified primary human brain cells. We found that hCS-derived glia closely resemble primary human fetal astrocytes and that, over time in vitro, they transition from a predominantly fetal to an increasingly mature astrocyte state. Transcriptional changes in astrocytes are accompanied by alterations in phagocytic capacity and effects on neuronal calcium signaling. These findings suggest that hCS-derived astrocytes closely resemble primary human astrocytes and can be used for studying development and modeling disease.

    View details for PubMedID 28817799

  • Age-Dependent Netrin-1 Signaling Regulates NG2(+) Glial Cell Spatial Homeostasis in Normal Adult Gray Matter JOURNAL OF NEUROSCIENCE Birey, F., Aguirre, A. 2015; 35 (17): 6946-6951


    Neuron-glial antigen 2-positive (NG2(+)) glial cells are the most proliferative glia type in the adult CNS, and their tile-like arrangement in adult gray matter is under tight regulation. However, little is known about the cues that govern this unique distribution. To this end, using a NG2(+) glial cell ablation model in mice, we examined the repopulation dynamics of NG2(+) glial cells in the mature and aged mice gray matter. We found that some resident NG2(+) glial cells that escaped depletion rapidly enter the cell cycle to repopulate the cortex with altered spatial distribution. We reveal that netrin-1 signaling is involved in the NG2(+) glial cell early proliferative, late repopulation, and distribution response after ablation in the gray matter. However, ablation of NG2(+) glial cell in older animals failed to stimulate a similar repopulation response, possibly because of a decrease in the sensitivity to netrin-1. Our findings indicate that endogenous netrin-1 plays a role in NG2(+) glial cell homeostasis that is distinct from its role in myelination.

    View details for DOI 10.1523/JNEUROSCI.0356-15.2015

    View details for Web of Science ID 000353647600028

    View details for PubMedID 25926469

  • Genetic and Stress-Induced Loss of NG2 Glia Triggers Emergence of Depressive-like Behaviors through Reduced Secretion of FGF2 Neuron Birey, F., Kloc, M., Chavali, M., Hussein, I., Wilson, M., Christoffel, D. J., Chen, T., Frohman, M. A., Robinson, J. K., Russo, S. J., Maffei, A., Aguirre, A. 2015

    View details for DOI 10.1016/j.neuron.2015

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