All Publications

  • Long-term maturation of human cortical organoids matches key early postnatal transitions. Nature neuroscience Gordon, A. n., Yoon, S. J., Tran, S. S., Makinson, C. D., Park, J. Y., Andersen, J. n., Valencia, A. M., Horvath, S. n., Xiao, X. n., Huguenard, J. R., Pașca, S. P., Geschwind, D. H. 2021


    Human stem-cell-derived models provide the promise of accelerating our understanding of brain disorders, but not knowing whether they possess the ability to mature beyond mid- to late-fetal stages potentially limits their utility. We leveraged a directed differentiation protocol to comprehensively assess maturation in vitro. Based on genome-wide analysis of the epigenetic clock and transcriptomics, as well as RNA editing, we observe that three-dimensional human cortical organoids reach postnatal stages between 250 and 300 days, a timeline paralleling in vivo development. We demonstrate the presence of several known developmental milestones, including switches in the histone deacetylase complex and NMDA receptor subunits, which we confirm at the protein and physiological levels. These results suggest that important components of an intrinsic in vivo developmental program persist in vitro. We further map neurodevelopmental and neurodegenerative disease risk genes onto in vitro gene expression trajectories to provide a resource and webtool (Gene Expression in Cortical Organoids, GECO) to guide disease modeling.

    View details for DOI 10.1038/s41593-021-00802-y

    View details for PubMedID 33619405

  • Chromatin accessibility dynamics in a model of human forebrain development Science Trevino, A. *., Sinnott-Armstrong, N. *., Andersen, J. *., Yoon, S., Huber, N., Pritchard, J. K., Chang, H. Y., Greenleaf, W. J., Pasca, S. P. 2020

    View details for DOI 10.1126/science.aay1645

  • Generation of Functional Human 3D Cortico-Motor Assembloids. Cell Andersen, J. n., Revah, O. n., Miura, Y. n., Thom, N. n., Amin, N. D., Kelley, K. W., Singh, M. n., Chen, X. n., Thete, M. V., Walczak, E. M., Vogel, H. n., Fan, H. C., Paşca, S. P. 2020


    Neurons in the cerebral cortex connect through descending pathways to hindbrain and spinal cord to activate muscle and generate movement. Although components of this pathway have been previously generated and studied in vitro, the assembly of this multi-synaptic circuit has not yet been achieved with human cells. Here, we derive organoids resembling the cerebral cortex or the hindbrain/spinal cord and assemble them with human skeletal muscle spheroids to generate 3D cortico-motor assembloids. Using rabies tracing, calcium imaging, and patch-clamp recordings, we show that corticofugal neurons project and connect with spinal spheroids, while spinal-derived motor neurons connect with muscle. Glutamate uncaging or optogenetic stimulation of cortical spheroids triggers robust contraction of 3D muscle, and assembloids are morphologically and functionally intact for up to 10 weeks post-fusion. Together, this system highlights the remarkable self-assembly capacity of 3D cultures to form functional circuits that could be used to understand development and disease.

    View details for DOI 10.1016/j.cell.2020.11.017

    View details for PubMedID 33333020

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

  • Inhibitory Interneurons in Hemimegalencephaly: A Survey of 9 Cases Lummus, S., Andersen, J., Pasca, S., Kleinschmidt-DeMasters, B., Vogel, H. OXFORD UNIV PRESS INC. 2018: 501
  • Assembly of functionally integrated human forebrain spheroids. NATURE Birey, F. *., Andersen, J. *., Makinson, C. *., Islam, S., Wei, W., Huber, N., Fan, H., Cordes Metzler, K. R., Panagiotakos, G., Thom, N., O'Rourke, N. A., Steinmetz, L. M., Bernstein, J. A., Hallmayer, J., Huguenard, J. R., Paşca, S. P. 2017

    View details for DOI 10.1038/nature22330

  • Return to quiescence of mouse neural stem cells by degradation of a proactivation protein SCIENCE Urban, N., van den Berg, D. L., Forget, A., Andersen, J., Demmers, J. A., Hunt, C., Ayrault, O., Guillemot, F. 2016; 353 (6296): 292-295


    Quiescence is essential for long-term maintenance of adult stem cells. Niche signals regulate the transit of stem cells from dormant to activated states. Here, we show that the E3-ubiquitin ligase Huwe1 (HECT, UBA, and WWE domain-containing 1) is required for proliferating stem cells of the adult mouse hippocampus to return to quiescence. Huwe1 destabilizes proactivation protein Ascl1 (achaete-scute family bHLH transcription factor 1) in proliferating hippocampal stem cells, which prevents accumulation of cyclin Ds and promotes the return to a resting state. When stem cells fail to return to quiescence, the proliferative stem cell pool becomes depleted. Thus, long-term maintenance of hippocampal neurogenesis depends on the return of stem cells to a transient quiescent state through the rapid degradation of a key proactivation factor.

    View details for DOI 10.1126/science.aaf4802

    View details for Web of Science ID 000379580800050

    View details for PubMedID 27418510

  • NFIX Regulates Proliferation and Migration Within the Murine SVZ Neurogenic Niche. Cerebral cortex (New York, N.Y. : 1991) Heng, Y. H., Zhou, B. n., Harris, L. n., Harvey, T. n., Smith, A. n., Horne, E. n., Martynoga, B. n., Andersen, J. n., Achimastou, A. n., Cato, K. n., Richards, L. J., Gronostajski, R. M., Yeo, G. S., Guillemot, F. n., Bailey, T. L., Piper, M. n. 2015; 25 (10): 3758–78


    Transcription factors of the nuclear factor one (NFI) family play a pivotal role in the development of the nervous system. One member, NFIX, regulates the development of the neocortex, hippocampus, and cerebellum. Postnatal Nfix(-/-) mice also display abnormalities within the subventricular zone (SVZ) lining the lateral ventricles, a region of the brain comprising a neurogenic niche that provides ongoing neurogenesis throughout life. Specifically, Nfix(-/-) mice exhibit more PAX6-expressing progenitor cells within the SVZ. However, the mechanism underlying the development of this phenotype remains undefined. Here, we reveal that NFIX contributes to multiple facets of SVZ development. Postnatal Nfix(-/-) mice exhibit increased levels of proliferation within the SVZ, both in vivo and in vitro as assessed by a neurosphere assay. Furthermore, we show that the migration of SVZ-derived neuroblasts to the olfactory bulb is impaired, and that the olfactory bulbs of postnatal Nfix(-/-) mice are smaller. We also demonstrate that gliogenesis within the rostral migratory stream is delayed in the absence of Nfix, and reveal that Gdnf (glial-derived neurotrophic factor), a known attractant for SVZ-derived neuroblasts, is a target for transcriptional activation by NFIX. Collectively, these findings suggest that NFIX regulates both proliferation and migration during the development of the SVZ neurogenic niche.

    View details for DOI 10.1093/cercor/bhu253

    View details for PubMedID 25331604

  • A Transcriptional Mechanism Integrating Inputs from Extracellular Signals to Activate Hippocampal Stem Cells NEURON Andersen, J., Urban, N., Achimastou, A., Ito, A., Simic, M., Ullom, K., Martynoga, B., Lebel, M., Goritz, C., Frisen, J., Nakafuku, M., Guillemot, F. 2014; 83 (5): 1085-1097


    The activity of adult stem cells is regulated by signals emanating from the surrounding tissue. Many niche signals have been identified, but it is unclear how they influence the choice of stem cells to remain quiescent or divide. Here we show that when stem cells of the adult hippocampus receive activating signals, they first induce the expression of the transcription factor Ascl1 and only subsequently exit quiescence. Moreover, lowering Ascl1 expression reduces the proliferation rate of hippocampal stem cells, and inactivating Ascl1 blocks quiescence exit completely, rendering them unresponsive to activating stimuli. Ascl1 promotes the proliferation of hippocampal stem cells by directly regulating the expression of cell-cycle regulatory genes. Ascl1 is similarly required for stem cell activation in the adult subventricular zone. Our results support a model whereby Ascl1 integrates inputs from both stimulatory and inhibitory signals and converts them into a transcriptional program activating adult neural stem cells.

    View details for DOI 10.1016/j.neuron.2014.08.004

    View details for Web of Science ID 000341419000012

    View details for PubMedID 25189209

  • Epigenomic enhancer annotation reveals a key role for NFIX in neural stem cell quiescence GENES & DEVELOPMENT Martynoga, B., Mateo, J. L., Zhou, B., Andersen, J., Achimastou, A., Urban, N., van den Berg, D., Georgopoulou, D., Hadjur, S., Wittbrodt, J., Ettwiller, L., Piper, M., Gronostajski, R. M., Guillemot, F. 2013; 27 (16): 1769-1786


    The majority of neural stem cells (NSCs) in the adult brain are quiescent, and this fraction increases with aging. Although signaling pathways that promote NSC quiescence have been identified, the transcriptional mechanisms involved are mostly unknown, largely due to lack of a cell culture model. In this study, we first demonstrate that NSC cultures (NS cells) exposed to BMP4 acquire cellular and transcriptional characteristics of quiescent cells. We then use epigenomic profiling to identify enhancers associated with the quiescent NS cell state. Motif enrichment analysis of these enhancers predicts a major role for the nuclear factor one (NFI) family in the gene regulatory network controlling NS cell quiescence. Interestingly, we found that the family member NFIX is robustly induced when NS cells enter quiescence. Using genome-wide location analysis and overexpression and silencing experiments, we demonstrate that NFIX has a major role in the induction of quiescence in cultured NSCs. Transcript profiling of NS cells overexpressing or silenced for Nfix and the phenotypic analysis of the hippocampus of Nfix mutant mice suggest that NFIX controls the quiescent state by regulating the interactions of NSCs with their microenvironment.

    View details for DOI 10.1101/gad.216804.113

    View details for Web of Science ID 000323416000004

    View details for PubMedID 23964093

  • The Nicotinic Acetylcholine Receptor Partial Agonist Varenicline Increases the Ataxic and Sedative-Hypnotic Effects of Acute Ethanol Administration in C57BL/6J Mice ALCOHOLISM-CLINICAL AND EXPERIMENTAL RESEARCH Kamens, H. M., Andersen, J., Picciotto, M. R. 2010; 34 (12): 2053-2060


    The costs associated with alcohol abuse are staggering, therefore much effort has been put into developing new pharmacologic strategies to decrease alcohol abuse. Recently, the nicotinic acetylcholine receptor (nAChR) partial agonist varenicline has been shown to decrease ethanol consumption in both humans and animal models.We examined the effects of varenicline on the ataxic and sedative-hypnotic effects of ethanol. First, varenicline was administered prior to placement in a locomotor activity chamber to determine whether varenicline influenced baseline locomotor activity. To determine the effect of nicotinic modulation on ethanol-induced motor incoordination, varenicline was administered 30 minutes prior to an acute ethanol injection and then mice were tested on the balance beam, dowel test, or fixed-speed rotarod. To examine ethanol's sedative-hypnotic effects, varenicline was administered 30 minutes prior to 4 g/kg ethanol and the duration of loss of righting reflex (LORR) was measured.Varenicline markedly reduced baseline locomotor activity in C57BL/6J mice. Varenicline increased ethanol-induced ataxia when measured on the balance beam and dowel test but had no effect when measured on the fixed-speed rotarod. Pretreatment with varenicline increased the duration of LORR.These data provide evidence that nAChRs may be involved in the ataxic and sedative effects of ethanol. It is possible that one mechanism that could contribute to the ability of varenicline to decrease ethanol consumption may be through increasing negative behavioral effects of alcohol.

    View details for DOI 10.1111/j.1530-0277.2010.01301.x

    View details for Web of Science ID 000284366100010

    View details for PubMedID 20946306

  • Modulation of ethanol consumption by genetic and pharmacological manipulation of nicotinic acetylcholine receptors in mice PSYCHOPHARMACOLOGY Kamens, H. M., Andersen, J., Picciotto, M. R. 2010; 208 (4): 613-626


    Alcohol and nicotine are commonly co-abused. Genetic correlations between responses to these drugs have been reported, providing evidence that common genes underlie the response to alcohol and nicotine. Nicotinic acetylcholine receptors (nAChRs) in the mesolimbic dopamine system are important in mediating nicotine response, and several studies suggest that alcohol may also interact with these nAChRs.The aim of this study was to examine the role of nAChRs containing α7 or β2 subunits in ethanol consumption.A two-bottle choice paradigm was used to determine ethanol consumption in wild-type and nAChR subunit knockout mice. Challenge studies were performed using the α4β2 nAChR partial agonist varenicline.Mice lacking the β2 subunit consumed a similar amount of ethanol compared to their wild-type siblings in an ethanol-drinking paradigm. In contrast, mice lacking the α7 nAChR receptor subunit consumed significantly less ethanol than wild-type mice but consumed comparable amounts of water, saccharin, and quinine. In C57BL/6J mice, varenicline dose-dependently decreased ethanol consumption with a significant effect of 2 mg/kg, without affecting water or saccharin consumption. This effect of varenicline was not reversed in mice lacking either the α7 or β2 subunit, providing evidence that nAChRs containing one of these subunits are not required for this effect of varenicline.This study provides evidence that α7 nAChRs are involved in ethanol consumption and supports the idea that pharmacological manipulation of nAChRs reduces ethanol intake. Additional nAChRs may also be involved in ethanol intake, and there may be functional redundancy in the nicotinic control of alcohol drinking.

    View details for DOI 10.1007/s00213-009-1759-1

    View details for Web of Science ID 000274100200011

    View details for PubMedID 20072781