Noah Reis

All Publications

• Human neuromodulatory assembloids to study serotonin signaling and disease. bioRxiv : the preprint server for biology Kanton, S., Meng, X., Dong, C., Birey, F., Wang, D., Reis, N., Yoon, S. J., Kim, J. I., McQueen, J. P., Sakai, N., Nishino, S., Huguenard, J. R., Paşca, S. P. 2026

  Abstract

  Neuromodulators influence critical functions of the developing human brain and regulate behavioral states. Dysfunction of neuromodulatory systems is often involved in neuropsychiatric disease and many drugs for these conditions act on these signaling pathways. Recent advances in stem cell biology have made it possible to derive a wide range of cells across the developing human nervous system in regionalized organoids and to functionally integrate them into assembloids, however they currently do not systematically incorporate neuromodulation. Here, we generated human midbrain-hindbrain organoids (hMHO) from human induced pluripotent stem (hiPS) cells and fused them with human cortical organoids (hCO) to form neuromodulatory assembloids (hNMA). We focus on serotonin (5-hydroxytryptamine, 5-HT) as one key neuromodulator and found characteristic gene expression patterns and electrophysiological properties of serotonergic neurons (5-HT neurons) in the hMHO. In hNMA, 5-HT neurons projected into hCO, released 5-HT and modulated cortical network activity. To explore the applicability of this system in human disease, we studied 22q11.2 deletion syndrome (22q11.2DS), a common microdeletion associated with high risk for neuropsychiatric disease and defects in 5-HT signaling. We found aberrant 5-HT dynamics in hNMA from patient hiPS cell lines that were rescued by administration of a selective serotonin reuptake inhibitor (SSRI). Taken together, hNMA can be used to study human 5-HT dynamics and uncover disease phenotypes which could facilitate therapeutic development.

  View details for DOI 10.64898/2026.03.08.710407

  View details for PubMedID 41959100

  View details for PubMedCentralID PMC13060871

• CRISPR screens in human neural organoids and assembloids. Nature protocols Meng, X., Reis, N., Bassik, M. C., Pașca, S. P. 2025

  Abstract

  Studying the molecular mechanisms underlying the assembly of the human nervous system remains a significant challenge. The ability to generate neural cells from pluripotent stem cells, combined with advanced genome-editing techniques, provides unprecedented opportunities to uncover the biology of human neurodevelopment and disease. Organoids and assembloids enable the in vitro modeling of previously inaccessible developmental processes, such as the specification and migration of human neurons, including the integration of cortical interneurons from the ventral into the dorsal forebrain. Here, we present a detailed protocol that combines pooled CRISPR-Cas9 screening with neural organoid and assembloid models and illustrate how it can be applied to map hundreds of disease genes onto cellular pathways and specific aspects of human neural development. Our protocol outlines key steps, from planning and optimizing genetic perturbations to designing readouts for neuronal generation and migration, conducting the screening and validating candidate genes. The screening experiments take ~3 months to complete and require expertise in stem cell culture and neural differentiation, genetic engineering of human induced pluripotent stem cell lines, fluorescence-activated cell sorting and next-generation sequencing and analyses. The integration of genetic screening and human cellular models constitutes a powerful platform for investigating the mechanisms of human brain development and disease, paving the way for the discovery of novel therapeutics.

  View details for DOI 10.1038/s41596-025-01299-6

  View details for PubMedID 41419637

  View details for PubMedCentralID 11688374

• Midline assembloids reveal regulators of human axon guidance. Science (New York, N.Y.) Onesto, M. M., Amin, N. D., Pan, C., Chen, X., Kim, J. I., Reis, N., Kanton, S., Valencia, A. M., Hudacova, Z., McQueen, J. P., Tessier-Lavigne, M., Pașca, S. P. 2025; 389 (6757): 282-289

  Abstract

  Organizers orchestrate cell patterning and axon guidance in the developing nervous system. Although nonhuman models have led to fundamental discoveries about floor plate (FP)-mediated midline organization, an experimental model of the human FP would enable insights into human neurodevelopment and midline connectivity. Here, we developed organoids resembling human FP (hFpOs) and assembled them with human spinal cord organoids (hSpOs) to generate midline assembloids (hMAs). We demonstrate that hFpOs promote ventral patterning, commissural axon guidance, and bilateral connectivity. To investigate midline regulators, we profiled the hFpO secretome, identifying 27 human-enriched genes compared with mouse. In an arrayed CRISPR screen of hMAs, we discovered that loss of GALNT2 and PLD3 impaired FP-mediated guidance of axons. This platform holds promise for revealing aspects of human-specific neurobiology and disease.

  View details for DOI 10.1126/science.adq7934

  View details for PubMedID 40674484

• Generating human neural diversity with a multiplexed morphogen screen in organoids. Cell stem cell Amin, N. D., Kelley, K. W., Kaganovsky, K., Onesto, M., Hao, J., Miura, Y., McQueen, J. P., Reis, N., Narazaki, G., Li, T., Kulkarni, S., Pavlov, S., Pașca, S. P. 2024; 31 (12): 1831-1846.e9

  Abstract

  Morphogens choreograph the generation of remarkable cellular diversity in the developing nervous system. Differentiation of stem cells in vitro often relies upon the combinatorial modulation of these signaling pathways. However, the lack of a systematic approach to understand morphogen-directed differentiation has precluded the generation of many neural cell populations, and the general principles of regional specification and maturation remain incomplete. Here, we developed an arrayed screen of 14 morphogen modulators in human neural organoids cultured for over 70 days. Deconvolution of single-cell-multiplexed RNA sequencing data revealed design principles of brain region specification. We tuned neural subtype diversity to generate a tachykinin 3 (TAC3)-expressing striatal interneuron type within assembloids. To circumvent limitations of in vitro neuronal maturation, we used a neonatal rat transplantation strategy that enabled human Purkinje neurons to develop their hallmark complex dendritic branching. This comprehensive platform yields insights into the factors influencing stem cell-derived neural diversification and maturation.

  View details for DOI 10.1016/j.stem.2024.10.016

  View details for PubMedID 39642864

• Antisense oligonucleotide therapeutic approach for Timothy syndrome. Nature Chen, X., Birey, F., Li, M. Y., Revah, O., Levy, R., Thete, M. V., Reis, N., Kaganovsky, K., Onesto, M., Sakai, N., Hudacova, Z., Hao, J., Meng, X., Nishino, S., Huguenard, J., Pașca, S. P. 2024; 628 (8009): 818-825

  Abstract

  Timothy syndrome (TS) is a severe, multisystem disorder characterized by autism, epilepsy, long-QT syndrome and other neuropsychiatric conditions1. TS type 1 (TS1) is caused by a gain-of-function variant in the alternatively spliced and developmentally enriched CACNA1C exon 8A, as opposed to its counterpart exon 8. We previously uncovered several phenotypes in neurons derived from patients with TS1, including delayed channel inactivation, prolonged depolarization-induced calcium rise, impaired interneuron migration, activity-dependent dendrite retraction and an unanticipated persistent expression of exon 8A2-6. We reasoned that switching CACNA1C exon utilization from 8A to 8 would represent a potential therapeutic strategy. Here we developed antisense oligonucleotides (ASOs) to effectively decrease the inclusion of exon 8A in human cells both in vitro and, following transplantation, in vivo. We discovered that the ASO-mediated switch from exon 8A to 8 robustly rescued defects in patient-derived cortical organoids and migration in forebrain assembloids. Leveraging a transplantation platform previously developed7, we found that a single intrathecal ASO administration rescued calcium changes and in vivo dendrite retraction of patient neurons, suggesting that suppression of CACNA1C exon 8A expression is a potential treatment for TS1. Broadly, these experiments illustrate how a multilevel, in vivo and in vitro stem cell model-based approach can identify strategies to reverse disease-relevant neural pathophysiology.

  View details for DOI 10.1038/s41586-024-07310-6

  View details for PubMedID 38658687

  View details for PubMedCentralID 1149428

• Assembloid CRISPR screens reveal impact of disease genes in human neurodevelopment. Nature Meng, X., Yao, D., Imaizumi, K., Chen, X., Kelley, K. W., Reis, N., Thete, M. V., Arjun McKinney, A., Kulkarni, S., Panagiotakos, G., Bassik, M. C., Pașca, S. P. 2023

  Abstract

  The assembly of cortical circuits involves the generation and migration of interneurons from the ventral to the dorsal forebrain1-3, which has been challenging to study at inaccessible stages of late gestation and early postnatal human development4. Autism spectrum disorder and other neurodevelopmental disorders (NDDs) have been associated with abnormal cortical interneuron development5, but which of these NDD genes affect interneuron generation and migration, and how they mediate these effects remains unknown. We previously developed a platform to study interneuron development and migration in subpallial organoids and forebrain assembloids6. Here we integrate assembloids with CRISPR screening to investigate the involvement of 425 NDD genes in human interneuron development. The first screen aimed at interneuron generation revealed 13 candidate genes, including CSDE1 and SMAD4. We subsequently conducted an interneuron migration screen in more than 1,000 forebrain assembloids that identified 33 candidate genes, including cytoskeleton-related genes and the endoplasmic reticulum-related gene LNPK. We discovered that, during interneuron migration, the endoplasmic reticulum is displaced along the leading neuronal branch before nuclear translocation. LNPK deletion interfered with this endoplasmic reticulum displacement and resulted in abnormal migration. These results highlight the power of this CRISPR-assembloid platform to systematically map NDD genes onto human development and reveal disease mechanisms.

  View details for DOI 10.1038/s41586-023-06564-w

  View details for PubMedID 37758944

  View details for PubMedCentralID 4349583

• Mechanisms of innate and adaptive immunity to the Pfizer-BioNTech BNT162b2 vaccine. Nature immunology Li, C., Lee, A., Grigoryan, L., Arunachalam, P. S., Scott, M. K., Trisal, M., Wimmers, F., Sanyal, M., Weidenbacher, P. A., Feng, Y., Adamska, J. Z., Valore, E., Wang, Y., Verma, R., Reis, N., Dunham, D., O'Hara, R., Park, H., Luo, W., Gitlin, A. D., Kim, P., Khatri, P., Nadeau, K. C., Pulendran, B. 2022

  Abstract

  Despite the success of the BNT162b2 mRNA vaccine, the immunological mechanisms that underlie its efficacy are poorly understood. Here we analyzed the innate and adaptive responses to BNT162b2 in mice, and show that immunization stimulated potent antibody and antigen-specific T cell responses, as well as strikingly enhanced innate responses after secondary immunization, which was concurrent with enhanced serum interferon (IFN)-gamma levels 1d following secondary immunization. Notably, we found that natural killer cells and CD8+ T cells in the draining lymph nodes are the major producers of this circulating IFN-gamma. Analysis of knockout mice revealed that induction of antibody and T cell responses to BNT162b2 was not dependent on signaling via Toll-like receptors 2, 3, 4, 5 and 7 nor inflammasome activation, nor the necroptosis or pyroptosis cell death pathways. Rather, the CD8+ T cell response induced by BNT162b2 was dependent on type I interferon-dependent MDA5 signaling. These results provide insights into the molecular mechanisms by which the BNT162b2 vaccine stimulates immune responses.

  View details for DOI 10.1038/s41590-022-01163-9

  View details for PubMedID 35288714

• Durability of immune responses to the BNT162b2 mRNA vaccine MED Suthar, M. S., Arunachalam, P. S., Hu, M., Reis, N., Trisal, M., Raeber, O., Chinthrajah, S., Davis-Gardner, M. E., Manning, K., Mudvari, P., Boritz, E., Godbole, S., Henry, A. R., Douek, D. C., Halfmann, P., Kawaoka, Y., Boyd, S. D., Davis, M. M., Zarnitsyna, V. I., Nadeau, K., Pulendran, B. 2022; 3 (1): 25-27

  View details for DOI 10.1016/j.medj.2021.12.005

  View details for Web of Science ID 000758831100004