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Open Access Publications from the University of California

Scholarly Works (5 results)

  • Thesis
  • Peer Reviewed
UC San Francisco Electronic Theses and Dissertations (2022)

Humans are often described as visual creatures as we heavily rely on our vision to perceive and navigate the world around us. Proper visual system function requires that each individual neuron to precisely identify and connect to its respective synaptic partners out of the billions of other neurons in the nervous system. Here, I will present my thesis work using the mouse visual system to understand the developmental organization of synaptic networks and the function of the neural circuits that underlie sight. First, I mapped circuits formed from retinal ganglion cells (RGCs) to the superior colliculus (SC) using a novel sequencing-based circuit discovery technique. The technique, named Trans-Seq, is able to anterogradely map neural circuits from genetically defined starter neurons. I used Trans-Seq to classify SC neuron types innervated by genetically defined RGC types. Alpha-RGCs (αRGCs), but not On-Off Direction-Selective Ganglion Cells (ooDSGCs), were found to connect to Nephronectin-positive wide-field neurons (NPWFs). This connection was validated using genetic labeling, electrophysiology, and retrograde tracing. I then identified the extracellular matrix protein Nephronectin as a determinant for selective synaptic choice from αRGC to NPWFs via binding to Integrin-α8β1. Experiments deleting Npnt in the SC and Itgα8 in RGCs suggested that Itgα8β1 expressed by αRGCs mediates proper αRGC axonal targeting and synapse formation by binding to Npnt deposited in the SC. Next, to generate quantitative molecular circuit maps of retinotectal connectivity, I have built upon Trans-Seq and superimposed anterograde tracing information on top of transcript information from multiplexed error-robust fluorescence in situ hybridization (MERFISH). I have established a limited retinotectal map linking genetically defined RGC types to SC neuron types by revealing the spatial connectivity patterns across multiple retinotectal pairs. Gene imputation additionally revealed rich information surrounding the molecular cues responsible for forming these circuits, offering candidates to test for future mechanistic inquiries. Taken together, these data reveal the architecture of retinotectal circuits and how molecular cues ensure wiring specificity in the visual system.

    Cover page: Deciphering Principles Governing Retinotectal Synaptic Specificity
    • Article
    • Peer Reviewed
    UC San Francisco Previously Published Works (2022)
    In this issue of Neuron, three studies establish new strategies to uncover mediators of retinal neuroprotection and optic nerve regeneration. Tian et al. (2022) carry out a multi-omics screen and identify transcriptional regulators of axon injury signaling leading to cell death; Jacobi et al. (2022) and Li et al. (2022) combine retrograde tracing and single-cell RNA-seq (scRNA-seq) to uncover molecular targets for axon regeneration.
      Cover page: Live, die, or regenerate? New insights from multi-omic analyses
      • Article
      • Peer Reviewed
      UC San Francisco Previously Published Works (2024)
      Maintaining precise synaptic contacts between neuronal partners is critical to ensure the proper functioning of the mammalian central nervous system (CNS). Diverse cell recognition molecules, such as classic cadherins (Cdhs), are part of the molecular machinery mediating synaptic choices during development and synaptic maintenance. Yet, the principles governing neuron-neuron wiring across diverse CNS neuron types remain largely unknown. The retinotectal synapses, connections from the retinal ganglion cells (RGCs) to the superior collicular (SC) neurons, offer an ideal experimental system to reveal molecular logic underlying synaptic choices and formation. This is due to the retina's unidirectional and laminar-restricted projections to the SC and the large databases of presynaptic RGC subtypes and postsynaptic SC neuronal types. Here, we focused on determining the role of Type II Cdhs in wiring the retinotectal synapses. We surveyed Cdhs expression patterns at neuronal resolution and revealed that Cdh13 is enriched in the wide-field neurons in the superficial SC (sSC). In either the Cdh13 null mutant or selective adult deletion within the wide-field neurons, there is a significant reduction of spine densities in the distal dendrites of these neurons in both sexes. Additionally, Cdh13 removal from presynaptic RGCs reduced dendritic spines in the postsynaptic wide-field neurons. Cdh13-expressing RGCs use differential mechanisms than αRGCs and On-Off Direction-Selective Ganglion Cells (ooDSGCs) to form specific retinotectal synapses. The results revealed a selective transneuronal interaction mediated by Cdh13 to maintain proper retinotectal synapses in vivo.
        Cover page: Cadherin-13 Maintains Retinotectal Synapses via Transneuronal Interactions
        • Article
        • Peer Reviewed
        UC San Francisco Previously Published Works (2022)
        The mouse visual system serves as an accessible model to understand mammalian circuit wiring. Despite rich knowledge in retinal circuits, the long-range connectivity map from distinct retinal ganglion cell (RGC) types to diverse brain neuron types remains unknown. In this study, we developed an integrated approach, called Trans-Seq, to map RGCs to superior collicular (SC) circuits. Trans-Seq combines a fluorescent anterograde trans-synaptic tracer, consisting of codon-optimized wheat germ agglutinin fused to mCherry, with single-cell RNA sequencing. We used Trans-Seq to classify SC neuron types innervated by genetically defined RGC types and predicted a neuronal pair from αRGCs to Nephronectin-positive wide-field neurons (NPWFs). We validated this connection using genetic labeling, electrophysiology and retrograde tracing. We then used transcriptomic data from Trans-Seq to identify Nephronectin as a determinant for selective synaptic choice from αRGC to NPWFs via binding to Integrin α8β1. The Trans-Seq approach can be broadly applied for post-synaptic circuit discovery from genetically defined pre-synaptic neurons.
          Cover page: Trans-Seq maps a selective mammalian retinotectal synapse instructed by Nephronectin
          • Article
          • Peer Reviewed
          UC San Francisco Previously Published Works (2020)
          The development of single-cell RNA sequencing (scRNA-seq) has allowed high-resolution analysis of cell-type diversity and transcriptional networks controlling cell-fate specification. To identify the transcriptional networks governing human retinal development, we performed scRNA-seq analysis on 16 time points from developing retina as well as four early stages of retinal organoid differentiation. We identified evolutionarily conserved patterns of gene expression during retinal progenitor maturation and specification of all seven major retinal cell types. Furthermore, we identified gene-expression differences between developing macula and periphery and between distinct populations of horizontal cells. We also identified species-specific patterns of gene expression during human and mouse retinal development. Finally, we identified an unexpected role for ATOH7 expression in regulation of photoreceptor specification during late retinogenesis. These results provide a roadmap to future studies of human retinal development and may help guide the design of cell-based therapies for treating retinal dystrophies.
            Cover page: Single-Cell Analysis of Human Retina Identifies Evolutionarily Conserved and Species-Specific Mechanisms Controlling Development.
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