Targeting single neuronal networks for gene expression and cell labeling in vivo

Abstract

To understand fine-scale structure and function of single mammalian neuronal networks, we developed and validated a strategy to genetically target and trace monosynaptic inputs to a single neuron in vitro and in vivo. The strategy independently targets a neuron and its presynaptic network for specific gene expression and fine-scale labeling, using single-cell electroporation of DNA to target infection and monosynaptic retrograde spread of a genetically modifiable rabies virus. The technique is highly reliable, with transsynaptic labeling occurring in every electroporated neuron infected by the virus. Targeting single neocortical neuronal networks in vivo, we found clusters of both spiny and aspiny neurons surrounding the electroporated neuron in each case, in addition to intricately labeled distal cortical and subcortical inputs. This technique, broadly applicable for probing and manipulating single neuronal networks with single-cell resolution in vivo, may help shed new light on fundamental mechanisms underlying circuit development and information processing by neuronal networks throughout the brain.

Figure 1. Single Cell Tracing Strategy

(A) A single neuron is electroporated with plasmids (colored circles) coding for a fluorescent marker (e.g., pCAG-mCherry), the TVA receptor (pCMMP-TVA800), and the rabies glycoprotein (pHCMV-RabiesG). (B) After 1–3 days, SADΔG-XFP(EnvA) virus is applied to the tissue, and infects only the electroporated neuron, since no other cells express the EnvA receptor, TVA (red indicates electroporated marker expression; black symbols, TVA and rabies glycoprotein (G)). As the virus replicates in the host neuron, it expresses XFP from the rabies genome, labeling the neuron (green in (C); merge yellow with electroporated marker). (C) After 3–6 days, the tissue is fixed with paraformaldehyde after time has elapsed for transsynaptic infection (dotted arrow) and expression of the rabies virus and the tissue is visualized with fluorescence microscopy. The virus only transsynaptically infects and labels direct monosynaptic, presynaptic inputs (green) to the original host neuron, and not secondary connections (red crosses) because rabies glycoprotein, which is necessary for transsynaptic spread, is expressed only in the electroporated neuron. The schematic shows the timeline and gene constructs used for the experiment in Figure 4.

Figure 2. Tracing the Monosynaptic Inputs to Single Neurons in Rat Cortical Slice Culture

(A) Twenty-one neurons were electroporated one by one with plasmids encoding venusYFP, TVA and rabies glycoprotein in a single slice. Two days later, SADΔG-mCherry(EnvA) was applied to the slice. After an additional six days, the slice was fixed in paraformaldehyde. Thirteen neurons expressed venusYFP from the electroporation transfection (green or yellow), and 8 neurons were confirmed to show co-expression of both the electroporated and rabies markers (yellow). Approximately 1000 neurons were infected transsynaptically by the virus and expressed mCherry (red). (B) Higher magnification of box in (A) showing 5 out of the 13 transfected neurons (green or yellow) surrounded by a dense cluster of mCherry expressing neurons (red). Four of these five neurons also showed mCherry expression (yellow). One neuron (white arrow, green) showed low expression of venusYFP and did not show expression of mCherry. (C) A different slice in which only one neuron (yellow) was electroporated with plasmids encoding venusYFP, TVA and rabies glycoprotein in a single slice. Two days later, SADΔG-mCherry(EnvA) was applied directly to the slice. After four additional days, the slice was fixed in paraformaldehyde. The electroporated neuron expressed both venusYFP (green) and mCherry (red) indicating successful transfection and virus infection (merged = yellow). Dozens of neurons were infected transsynaptically by the virus and expressed mCherry, displayed in red (n = 36; some not shown here, see supplementary Figure S1 which shows more transsynaptically labeled neurons and the extent of axonal labeling of the same electroporated neuron). Scale bars: 500 μm in (A), 50 μm in (B), 100 μm in (C).

Figure 3. In Vivo Single Cell Electroporation Visualized by Two-Photon Imaging

(A) Schematic of shadow imaging using a pipette containing Alexa dye and plasmid DNA (green circle) in intracellular solution. Positive pressure applied to the back of the pipette fills the extracellular space with fluorescent dye but does not fill neurons; they appear as dark shadows in the negative image. (B₁) In vivo two-photon fluorescent images of a pipette containing pCAG-YTB and Alexa dye in intracellular solution approaching a neuron, and dimpling its membrane in (B₂). (B₃) The neuron filled with Alexa 594 dye immediately after electroporation (See also Movie S1). (C) An average z-projection of the same neuron imaged under two-photon microscopy in vivo five days later. The neuron is green due to expression of venusYFP from the electroporated pCAG-YTB plasmid. Scale bars are 15 μm in (B₁), (B₂), and (B₃) (same scale) and 25 μm in (C).

Figure 4. Tracing the Monosynaptic Inputs to a Single Mammalian Neuron In Vivo

(A) A single layer 2/3 neuron (yellow neuron indicated by white arrow) in mouse visual cortex was targeted for the single cell tracing strategy using the parameters and reagents schematically represented in Figure 1. Transfection of electroporated plasmids was confirmed by expression of mCherry in the neuron (inset) and by infection of the neuron by SADΔG-EGFP(EnvA), and glycoprotein mediated transsynaptic spread of rabies virus to presynaptic neurons, where the virus expressed EGFP (green). A cluster of a variety of interneuron cell types and pyramidal cells was found surrounding the electroporated neuron shown in (A) and extending onto adjacent 40 μm sections (for example (B), some sections not shown). Many other neurons were also found throughout the brain, located several hundred microns to over a centimeter away from the host neuron (C–G). Regardless of distance from the host neuron, the morphology of neurons was labeled in intricate detail, and it was possible to characterize the cell type of labeled neurons based on morphology. A total of 97 neurons were labeled transsynaptically by the virus in this experiment. All panels in this figure are from the same animal. Blue is NeuN staining of neuronal nuclei. (B) Adjacent medial section to (A). Dendrites from the electroporated neuron (yellow) can be seen extending onto this section, as well as the neuron’s descending axon (indicated by white arrow). (C) Higher magnification image of the pyramidal neuron indicated by the lower white box in (A). This neuron was located over 400 μm caudal to the host neuron, in the same lateral-medial plane. The detailed morphology of the neuron is clearly visible, with complete filling of the neuron’s dendritic spines and axon. This image only shows a small fraction of the elaboration of the neuron’s processes. Some of these features are visible in (B, similar location to in (A)). (D) Higher magnification image of the interneuron indicated by the upper white box in (A). This neuron was located over 200 μm caudal to the host neuron, in the same lateral-medial plane. The complete filling of the neuron’s dendritic tree permitted characterization of the neuron as a layer 2/3 multipolar inhibitory neuron (more dendrites visible in (B)). Dozens of other interneurons were found in this experiment, representing a variety of cell types. (E) A projection neuron found several hundred microns away from the host neuron in retrosplenial cortex. (F) A neuron transsynaptically labeled in hypothalamus. Despite the over 1 cm distance from the host neuron, the brightness of label in this cell was comparable to the other neurons labeled throughout the brain. (G) A visual cortical projection neuron labeled in complete detail, located over 200 μm lateral to the host neuron. Scale bars: 100 μm in (A), (B), 25 μm inset in (A) and (C)–(G).