Neal Amin
Clinical Assistant Professor, Psychiatry and Behavioral Sciences
Bio
Dr. Amin is a physician-scientist researcher in the Department of Psychiatry at Stanford University. Dr. Amin received a Bachelor of Arts from Columbia College, Columbia University, and earned MD and PhD degrees in the MSTP at 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 uncovered post-transcriptional, RNA regulatory pathways that are remarkably cell type-specific in motor neurons and are essential for mammalian life (Amin et al, Science 2015; Amin et al, Neuron 2021). He completed psychiatry residency training in the Research Track at Stanford University and postdoctoral studies with Sergiu P. Pasca at Stanford University where he developed human stem cell-derived brain organoid technology, enabling the ability to model the immense neurocellular diversity of the human brain and factors affecting stem cell-derived neuronal maturation (Amin and Pasca, Neuron, 2018; Amin*, Kelley* et al, bioRxiv, 2024; Onesto*, Amin* et al, bioRxiv, 2024). The Amin Lab at Stanford University investigates RNA regulatory mechanisms affecting human brain development and the emergence of neuropathology towards the development of novel therapeutics. His work is funded by the NINDS/NIH, Deeda Blair Research Initiative, and the Brain and Behavior Research Foundation. Dr. Amin's research leverages his unique background as a board-certified, practicing Stanford physician and researcher with 20 years of bench research experience spanning mouse genetics, human neuropathology, advanced stem cell models of the brain, and cell type-specific RNA processing pathways.
Academic Appointments
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Clinical Assistant Professor, Psychiatry and Behavioral Sciences
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Member, Wu Tsai Neurosciences Institute
Professional Education
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Board Certification, American Board of Psychiatry and Neurology, Psychiatry
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Residency, Stanford University, Psychiatry
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PhD, UC San Diego, Biomedical Sciences
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MD, UC San Diego
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BA, Columbia University, Columbia College
All Publications
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Midline Assembloids Reveal Regulators of Human Axon Guidance.
bioRxiv : the preprint server for biology
2024
Abstract
Organizers are specialized cell populations that orchestrate cell patterning and axon guidance in the developing nervous system. Although non-human models have led to fundamental discoveries about the organization of the nervous system midline by the floor plate, an experimental model of human floor plate would enable broader insights into regulation of human neurodevelopment and midline connectivity. Here, we have developed stem cell-derived organoids resembling human floor plate (hFpO) and assembled them with spinal cord organoids (hSpO) to generate midline assembloids (hMA). We demonstrate that hFpO promote Sonic hedgehog-dependent ventral patterning of human spinal progenitors and Netrin-dependent guidance of human commissural axons, paralleling non-human models. To investigate evolutionary-divergent midline regulators, we profiled the hFpO secretome and identified 27 evolutionarily divergent genes between human and mouse. Utilizing the hMA platform, we targeted these candidates in an arrayed CRISPR knockout screen and reveal that GALNT2 , a gene involved in O-linked glycosylation, impairs floor plate-mediated guidance of commissural axons in humans. This novel platform extends prior axon guidance discoveries into human-specific neurobiology with implications for mechanisms of nervous system evolution and neurodevelopmental disorders.
View details for DOI 10.1101/2024.06.26.600229
View details for PubMedID 38979350
View details for PubMedCentralID PMC11230451
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Single-cell transcriptomic landscape of the developing human spinal cord.
Nature neuroscience
2023
Abstract
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
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Generating human neural diversity with a multiplexed morphogen screen in organoids
bioRxiv
2023
View details for DOI 10.1101/2023.05.31.541819
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Motor neurons use push-pull signals to direct vascular remodeling critical for their connectivity
NEURON
2022; 110 (24): 4090-+
Abstract
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
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Modulating miR-218 in Human Motor Neurons Using Assembloids
WILEY. 2022: S168
View details for Web of Science ID 000867884200294
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Maturation and circuit integration of transplanted human cortical organoids.
Nature
2022; 610 (7931): 319-326
Abstract
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
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Mouse embryo models built from stem cells take shape in a dish.
Nature
2022; 610 (7930): 39-40
View details for DOI 10.1038/d41586-022-03075-y
View details for PubMedID 36192499
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Detecting microRNA-mediated gene regulatory effects in murine neuronal subpopulations.
STAR protocols
2022; 3 (1): 101130
Abstract
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
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A hidden threshold in motor neuron gene networks revealed by modulation of miR-218 dose.
Neuron
2021
Abstract
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
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Conserved genetic signatures parcellate cardinal spinal neuron classes into local and projection subsets.
Science (New York, N.Y.)
2021; 372 (6540): 385-393
Abstract
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
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Neuronal defects in a human cellular model of 22q11.2 deletion syndrome.
Nature medicine
2020
Abstract
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
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Generation of Functional Human 3D Cortico-Motor Assembloids.
Cell
2020
Abstract
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
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Building Models of Brain Disorders with Three-Dimensional Organoids
NEURON
2018; 100 (2): 389–405
View details for DOI 10.1016/j.neuron.2018.10.007
View details for Web of Science ID 000448288900009
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Speed and segmentation control mechanisms characterized in rhythmically-active circuits created from spinal neurons produced from genetically-tagged embryonic stem cells
ELIFE
2017; 6
Abstract
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
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Loss of motoneuron-specific microRNA-218 causes systemic neuromuscular failure
SCIENCE
2015; 350 (6267): 1525-1529
Abstract
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
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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
2011; 21 (21): 6533–37
Abstract
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