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Trans-Seq for mammalian retinotectal circuit mapping

ABSTRACT: 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. Here we developed an integrated approach, named Trans-Seq, to map RGC to superior collicular (SC) circuits. Trans-Seq combines a fluorescent anterograde transsynaptic 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 utilized 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 postsynaptic circuit discovery from genetically-defined presynaptic neurons.

ORGANISM(S): Mus musculus

PROVIDER: GSE202257 | GEO | 2022/05/07

REPOSITORIES: GEO

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Project description:Brain circuits are assembled from a large variety of morphologically and functionally diverse cell types. It is not known how the intermingled cell types of individual brain regions differ in their expressed genomes. Here we describe an atlas of cell type transcriptomes of the adult retina. We found that each adult cell type expresses a specific set of genes, including a unique set of transcription factors, forming a “barcode” for cell identity. Cell type transcriptomes carry enough information to categorize cells into corresponding morphological classes and types. Surprisingly, several barcode genes are eye disease-associated genes that we demonstrate to be specifically expressed not only in photoreceptors but also in particular retinal circuit elements such as inhibitory neurons as well as in retinal microglia. Our data suggest that distinct cell types of individual brain regions are characterized by marked differences in their expressed genomes. We assembled a library of 22 transgenic mouse lines in which each line had a group of retinal cells marked with fluorescent proteins. We built up the library with the purpose of having some mouse lines in which single retinal cell types and others in which combinations of types from a single class are labeled. The library had mouse lines with labeled cells representing each of the six retinal cell classes. Retinal cells were characterized by physiological recording and immunohistochemical staining. We isolated 200 fluorescent protein-labeled retinal cells (“cell groups”) from at least three different mice of each mouse line by fluorescence-activated cell sorting. The transcripts of each cell group of these biological triplicates were independently amplified in batches. Each batch contained an internal control cell group from the Arc-line. We performed gene expression analysis of 22 transgenic mouse lines. All experiments were performed in biological triplicates. Gene expression analysis was performed in 3 batches. Arc is the batch control (1st, 2nd, 3rd). B2 was repeated 3 times.

Project description:To investigate the retinal proteins associated with primary and secondary retinal ganglion cell (RGC) degeneration and explore their molecular pathways, SWATH label-free and target-based mass spectrometry was employed to identify the proteomes in various retinal locations in response to localized optic nerve injury. Unilateral partial optic nerve transection (pONT) was performed on adult Wistar rats and their retinas were harvested at 2 weeks later. To confirm the separation of primary and secondary RGC degeneration, immunohistochemistry of RNA binding protein with multiple splicing (RBPMS) and glial fibrillary acidic protein (GFAP) was performed on retinal whole-mounts. Retinal proteomes in the temporal and nasal quadrants were evaluated with high resolution hybrid quadrupole time-of-flight mass spectrometry (QTOF-MS), and SWATH-based acquisition, and their expression was compared to the corresponding retinal quadrant in contralateral control eyes and further validated by multiple reaction monitoring mass spectrometry (MRM-MS). A total of 3641 proteins (p<0.05, FDR<1%) were quantified by SWATH-MS. Bioinformatics data analysis showed that there were 35 up-regulated and 24 down-regulated proteins in the temporal quadrant while 19 and 5 proteins were up-regulated and down-regulated, respectively, in the nasal quadrant respectively (n=4, p<0.05; fold change ≥1.4 fold or ≤0.7). Six proteins were regulated in both the temporal and the nasal quadrants including CLU, GFAP, GNG5, IRF2BPL, L1CAM and CPLX1. Linear regression analysis indicated a strong association between the data obtained by SWATH-MS and MRM-MS (temporal, R2=0.97; nasal, R2=0.96). Gene ontology analysis reveals statistically significant changes in the biological processes and cellular components of primary RGC degeneration. The majority of the significant changes in structural, signaling, and cell death proteins were associated with loss of RGCs in the area of primary RGC degeneration. The combined use of SWATH-MS and MRM-MS methods detects and quantifies regional changes of retinal protein expressions after localized injury. Future investigation with this integrated approach will significantly increase understanding of diverse processes of progressive RGC degeneration from a proteomic prospective.

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Trans-Seq for mammalian retinotectal circuit mapping

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