Dr. Neal D. Amin's research findings on gene regulatory mechanisms in the human nervous system have been the basis of articles in top journals, patents, awards, and research funding. He is corresponding author on works identifying cell type-specific RNA processing changes implicated in neurodegeneration. Other products of his research include a sole-author patent on gene delivery, speaking engagements at national and international conferences, and recognition and significant research funding from the NIH and private foundations including the BBRF and the Deeda Blair Research Initiative. His work applies advanced single cell transcriptomics, mice and human brain organoids, and deep learning models to identify gene regulatory network hubs associated with a wide range of diseases.

Dr. Amin is a Clinical Assistant Professor in the Department of Psychiatry at Stanford University where he leads fundamental wet and dry lab research into brain development and disease. He an attending physician in Stanford's Evaluation Clinic where he continues to see patients. He completed the Research Track Psychiatry Residency Program at Stanford University and is a board-certified psychiatrist and his postdoctoral studies with Sergiu Pasca, MD. He earned MD and PhD degrees from the University of California, San Diego with his graduate mentor Samuel L. Pfaff, PhD, at the Salk Institute for Biological Studies in La Jolla, CA. He also holds a Bachelor of Arts from Columbia College, Columbia University.

Academic Appointments

Professional Education

  • Board Certification, American Board of Psychiatry and Neurology, Psychiatry
  • Residency, Stanford University, Psychiatry
  • PhD, UC San Diego, Biomedical Sciences
  • MD, UC San Diego
  • BA, Columbia University, Columbia College

All Publications

  • Single-cell transcriptomic landscape of the developing human spinal cord. Nature neuroscience Andersen, J., Thom, N., Shadrach, J. L., Chen, X., Onesto, M. M., Amin, N. D., Yoon, S. J., Li, L., Greenleaf, W. J., Müller, F., Pașca, A. M., Kaltschmidt, J. A., Pașca, S. P. 2023


    Understanding spinal cord assembly is essential to elucidate how motor behavior is controlled and how disorders arise. The human spinal cord is exquisitely organized, and this complex organization contributes to the diversity and intricacy of motor behavior and sensory processing. But how this complexity arises at the cellular level in the human spinal cord remains unknown. Here we transcriptomically profiled the midgestation human spinal cord with single-cell resolution and discovered remarkable heterogeneity across and within cell types. Glia displayed diversity related to positional identity along the dorso-ventral and rostro-caudal axes, while astrocytes with specialized transcriptional programs mapped into white and gray matter subtypes. Motor neurons clustered at this stage into groups suggestive of alpha and gamma neurons. We also integrated our data with multiple existing datasets of the developing human spinal cord spanning 22 weeks of gestation to investigate the cell diversity over time. Together with mapping of disease-related genes, this transcriptomic mapping of the developing human spinal cord opens new avenues for interrogating the cellular basis of motor control in humans and guides human stem cell-based models of disease.

    View details for DOI 10.1038/s41593-023-01311-w

    View details for PubMedID 37095394

    View details for PubMedCentralID 8353162

  • Generating human neural diversity with a multiplexed morphogen screen in organoids bioRxiv Amin, N. D., Kelley, K. W., Hao, J., Narazaki, G., Li, T., McQueen, P., Kulkarni, S., Pavlov, S., Pasca, S. P. 2023
  • Motor neurons use push-pull signals to direct vascular remodeling critical for their connectivity NEURON Martins, L. F., Brambilla, I., Motta, A., de Pretis, S., Bhat, G., Badaloni, A., Malpighi, C., Amin, N. D., Imai, F., Almeida, R. D., Yoshida, Y., Pfaff, S. L., Bonanomi, D. 2022; 110 (24): 4090-+


    The nervous system requires metabolites and oxygen supplied by the neurovascular network, but this necessitates close apposition of neurons and endothelial cells. We find motor neurons attract vessels with long-range VEGF signaling, but endothelial cells in the axonal pathway are an obstacle for establishing connections with muscles. It is unclear how this paradoxical interference from heterotypic neurovascular contacts is averted. Through a mouse mutagenesis screen, we show that Plexin-D1 receptor is required in endothelial cells for development of neuromuscular connectivity. Motor neurons release Sema3C to elicit short-range repulsion via Plexin-D1, thus displacing endothelial cells that obstruct axon growth. When this signaling pathway is disrupted, epaxial motor neurons are blocked from reaching their muscle targets and concomitantly vascular patterning in the spinal cord is altered. Thus, an integrative system of opposing push-pull cues ensures detrimental axon-endothelial encounters are avoided while enabling vascularization within the nervous system and along peripheral nerves.

    View details for DOI 10.1016/j.neuron.2022.09.021

    View details for Web of Science ID 000921197200001

    View details for PubMedID 36240771

  • Modulating miR-218 in Human Motor Neurons Using Assembloids Amin, N., Kulkarni, S., Pasca, S. WILEY. 2022: S168
  • Maturation and circuit integration of transplanted human cortical organoids. Nature Revah, O., Gore, F., Kelley, K. W., Andersen, J., Sakai, N., Chen, X., Li, M. Y., Birey, F., Yang, X., Saw, N. L., Baker, S. W., Amin, N. D., Kulkarni, S., Mudipalli, R., Cui, B., Nishino, S., Grant, G. A., Knowles, J. K., Shamloo, M., Huguenard, J. R., Deisseroth, K., Pașca, S. P. 2022; 610 (7931): 319-326


    Self-organizing neural organoids represent a promising in vitro platform with which to model human development and disease1-5. However, organoids lack the connectivity that exists in vivo, which limits maturation and makes integration with other circuits that control behaviour impossible. Here we show that human stem cell-derived cortical organoids transplanted into the somatosensory cortex of newborn athymic rats develop mature cell types that integrate into sensory and motivation-related circuits. MRI reveals post-transplantation organoid growth across multiple stem cell lines and animals, whereas single-nucleus profiling shows progression of corticogenesis and the emergence of activity-dependent transcriptional programs. Indeed, transplanted cortical neurons display more complex morphological, synaptic and intrinsic membrane properties than their in vitro counterparts, which enables the discovery of defects in neurons derived from individuals with Timothy syndrome. Anatomical and functional tracings show that transplanted organoids receive thalamocortical and corticocortical inputs, and in vivo recordings of neural activity demonstrate that these inputs can produce sensory responses in human cells. Finally, cortical organoids extend axons throughout the rat brain and their optogenetic activation can drive reward-seeking behaviour. Thus, transplanted human cortical neurons mature and engage host circuits that control behaviour. We anticipate that this approach will be useful for detecting circuit-level phenotypes in patient-derived cells that cannot otherwise be uncovered.

    View details for DOI 10.1038/s41586-022-05277-w

    View details for PubMedID 36224417

  • Mouse embryo models built from stem cells take shape in a dish. Nature Amin, N. D., Pașca, S. P. 2022; 610 (7930): 39-40

    View details for DOI 10.1038/d41586-022-03075-y

    View details for PubMedID 36192499

  • Detecting microRNA-mediated gene regulatory effects in murine neuronal subpopulations. STAR protocols Amin, N. D., Senturk, G., Hayashi, M., Driscoll, S. P., Pfaff, S. L. 2022; 3 (1): 101130


    microRNAs (miRNAs) have unique gene regulatory effects in different neuronal subpopulations. Here, we describe a protocol to identify neuronal subtype-specific effects of a miRNA in murine motor neuron subpopulations. We detail the preparation of primary mouse spinal tissue for single cell RNA sequencing and bioinformatics analyses of pseudobulk expression data. This protocol applies differential gene expression testing approaches to identify miRNA target networks in heterogeneous neuronal subpopulations that cannot otherwise be captured by bulk RNA sequencing approaches. For complete details on the use and execution of this protocol, please refer to Amin et al. (2021).

    View details for DOI 10.1016/j.xpro.2022.101130

    View details for PubMedID 35146446

    View details for PubMedCentralID PMC8801384

  • A hidden threshold in motor neuron gene networks revealed by modulation of miR-218 dose. Neuron Amin, N. D., Senturk, G., Costaguta, G., Driscoll, S., O'Leary, B., Bonanomi, D., Pfaff, S. L. 2021


    Disruption of homeostatic microRNA (miRNA) expression levels is known to cause human neuropathology. However, the gene regulatory and phenotypic effects of altering a miRNA's invivo abundance (rather than its binary gain or loss) are not well understood. By genetic combination, we generated an allelic series of mice expressing varying levels of miR-218, a motor neuron-selective gene regulator associated with motor neuron disease. Titration of miR-218 cellular dose unexpectedly revealed complex, non-ratiometric target mRNA dose responses and distinct gene network outputs. A non-linearly responsive regulon exhibited a steep miR-218 dose-dependent threshold in repression that, when crossed, resulted in severe motor neuron synaptic failure and death. This work demonstrates that a miRNA can govern distinct gene network outputs at different expression levels and that miRNA-dependent phenotypes emerge at particular dose ranges because of hidden regulatory inflection points of their underlying gene networks.

    View details for DOI 10.1016/j.neuron.2021.07.028

    View details for PubMedID 34450025

  • Conserved genetic signatures parcellate cardinal spinal neuron classes into local and projection subsets. Science (New York, N.Y.) Osseward, P. J., Amin, N. D., Moore, J. D., Temple, B. A., Barriga, B. K., Bachmann, L. C., Beltran, F., Gullo, M., Clark, R. C., Driscoll, S. P., Pfaff, S. L., Hayashi, M. 2021; 372 (6540): 385-393


    Motor and sensory functions of the spinal cord are mediated by populations of cardinal neurons arising from separate progenitor lineages. However, each cardinal class is composed of multiple neuronal types with distinct molecular, anatomical, and physiological features, and there is not a unifying logic that systematically accounts for this diversity. We reasoned that the expansion of new neuronal types occurred in a stepwise manner analogous to animal speciation, and we explored this by defining transcriptomic relationships using a top-down approach. We uncovered orderly genetic tiers that sequentially divide groups of neurons by their motor-sensory, local-long range, and excitatory-inhibitory features. The genetic signatures defining neuronal projections were tied to neuronal birth date and conserved across cardinal classes. Thus, the intersection of cardinal class with projection markers provides a unifying taxonomic solution for systematically identifying distinct functional subsets.

    View details for DOI 10.1126/science.abe0690

    View details for PubMedID 33888637

  • Neuronal defects in a human cellular model of 22q11.2 deletion syndrome. Nature medicine Khan, T. A., Revah, O. n., Gordon, A. n., Yoon, S. J., Krawisz, A. K., Goold, C. n., Sun, Y. n., Kim, C. H., Tian, Y. n., Li, M. Y., Schaepe, J. M., Ikeda, K. n., Amin, N. D., Sakai, N. n., Yazawa, M. n., Kushan, L. n., Nishino, S. n., Porteus, M. H., Rapoport, J. L., Bernstein, J. A., O'Hara, R. n., Bearden, C. E., Hallmayer, J. F., Huguenard, J. R., Geschwind, D. H., Dolmetsch, R. E., Paşca, S. P. 2020


    22q11.2 deletion syndrome (22q11DS) is a highly penetrant and common genetic cause of neuropsychiatric disease. Here we generated induced pluripotent stem cells from 15 individuals with 22q11DS and 15 control individuals and differentiated them into three-dimensional (3D) cerebral cortical organoids. Transcriptional profiling across 100 days showed high reliability of differentiation and revealed changes in neuronal excitability-related genes. Using electrophysiology and live imaging, we identified defects in spontaneous neuronal activity and calcium signaling in both organoid- and 2D-derived cortical neurons. The calcium deficit was related to resting membrane potential changes that led to abnormal inactivation of voltage-gated calcium channels. Heterozygous loss of DGCR8 recapitulated the excitability and calcium phenotypes and its overexpression rescued these defects. Moreover, the 22q11DS calcium abnormality could also be restored by application of antipsychotics. Taken together, our study illustrates how stem cell derived models can be used to uncover and rescue cellular phenotypes associated with genetic forms of neuropsychiatric disease.

    View details for DOI 10.1038/s41591-020-1043-9

    View details for PubMedID 32989314

  • 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

  • Building Models of Brain Disorders with Three-Dimensional Organoids NEURON Amin, N. D., Pasca, S. P. 2018; 100 (2): 389–405
  • Speed and segmentation control mechanisms characterized in rhythmically-active circuits created from spinal neurons produced from genetically-tagged embryonic stem cells ELIFE Sternfeld, M. J., Hinckley, C. A., Moore, N. J., Pankratz, M. T., Hilde, K. L., Driscoll, S. P., Hayashi, M., Amin, N. D., Bonanomi, D., Gifford, W. D., Sharma, K., Goulding, M., Pfaff, S. L. 2017; 6


    Flexible neural networks, such as the interconnected spinal neurons that control distinct motor actions, can switch their activity to produce different behaviors. Both excitatory (E) and inhibitory (I) spinal neurons are necessary for motor behavior, but the influence of recruiting different ratios of E-to-I cells remains unclear. We constructed synthetic microphysical neural networks, called circuitoids, using precise combinations of spinal neuron subtypes derived from mouse stem cells. Circuitoids of purified excitatory interneurons were sufficient to generate oscillatory bursts with properties similar to in vivo central pattern generators. Inhibitory V1 neurons provided dual layers of regulation within excitatory rhythmogenic networks - they increased the rhythmic burst frequency of excitatory V3 neurons, and segmented excitatory motor neuron activity into sub-networks. Accordingly, the speed and pattern of spinal circuits that underlie complex motor behaviors may be regulated by quantitatively gating the intra-network cellular activity ratio of E-to-I neurons.

    View details for DOI 10.7554/eLife.21540

    View details for Web of Science ID 000394260700001

    View details for PubMedID 28195039

    View details for PubMedCentralID PMC5308898

  • Loss of motoneuron-specific microRNA-218 causes systemic neuromuscular failure SCIENCE Amin, N. D., Bai, G., Klug, J. R., Bonanomi, D., Pankratz, M. T., Gifford, W. D., Hinckley, C. A., Sternfeld, M. J., Driscoll, S. P., Dominguez, B., Lee, K., Jin, X., Pfaff, S. L. 2015; 350 (6267): 1525-1529


    Dysfunction of microRNA (miRNA) metabolism is thought to underlie diseases affecting motoneurons. One miRNA, miR-218, is abundantly and selectively expressed by developing and mature motoneurons. Here we show that mutant mice lacking miR-218 die neonatally and exhibit neuromuscular junction defects, motoneuron hyperexcitability, and progressive motoneuron cell loss, all of which are hallmarks of motoneuron diseases such as amyotrophic lateral sclerosis and spinal muscular atrophy. Gene profiling reveals that miR-218 modestly represses a cohort of hundreds of genes that are neuronally enriched but are not specific to a single neuron subpopulation. Thus, the set of messenger RNAs targeted by miR-218, designated TARGET(218), defines a neuronal gene network that is selectively tuned down in motoneurons to prevent neuromuscular failure and neurodegeneration.

    View details for DOI 10.1126/science.aad2509

    View details for Web of Science ID 000366591100058

    View details for PubMedID 26680198

    View details for PubMedCentralID PMC4913787

  • Chemical scaffolds with structural similarities to siderophores of nonribosomal peptide-polyketide origin as novel antimicrobials against Mycobacterium tuberculosis and Yersinia pestis BIOORGANIC & MEDICINAL CHEMISTRY LETTERS Ferreras, J. A., Gupta, A., Amin, N. D., Basu, A., Sinha, B. N., Worgall, S., Jayaprakash, V., Quadri, L. N. 2011; 21 (21): 6533–37


    Mycobacterium tuberculosis (Mtb) and Yersinia pestis (Yp) produce siderophores with scaffolds of nonribosomal peptide-polyketide origin. Compounds with structural similarities to these siderophores were synthesized and evaluated as antimicrobials against Mtb and Yp under iron-limiting conditions mimicking the iron scarcity these pathogens encounter in the host and under standard iron-rich conditions. Several new antimicrobials were identified, including some with increased potency in the iron-limiting condition. Our study illustrates the possibility of screening compound libraries in both iron-rich and iron-limiting conditions to identify antimicrobials that may selectively target iron scarcity-adapted bacteria and highlights the usefulness of building combinatorial libraries of compounds having scaffolds with structural similarities to siderophores to feed into antimicrobial screening programs.

    View details for DOI 10.1016/j.bmcl.2011.08.052

    View details for Web of Science ID 000296025900066

    View details for PubMedID 21940166

    View details for PubMedCentralID PMC3210511