Neal Amin

All Publications

• 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

  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

• 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

  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

• 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

  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

• 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

  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

• 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

  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

• Building Models of Brain Disorders with Three-Dimensional Organoids NEURON Amin, N. D., Pasca, S. P. 2018; 100 (2): 389–405

  View details for DOI 10.1016/j.neuron.2018.10.007

  View details for Web of Science ID 000448288900009

• 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

  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

• 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

  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

• 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

  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