Table 1. Dissection of West Nile virus (WNV)-induced coordinated transcriptional shifts at the protein marker and cell morphology/ topology/function levels.
| Biological process | Enriched GO terms | Protein marker IR* | Cellular morphology/topology/function | Representative images |
|---|---|---|---|---|
| Reactive astrocytosis | glial cell activation (GO:0061900); regulation of cell migration (GO:0030334) | GFAP ↑ | Astrocytes: hypertrophy of somata and processes; neuron-centripetal migration; perineuronal topology | Figure 6a |
| Microglia/macrophage activation and migration | innate immune response (GO:0045087); glial cell activation (GO:0061900); regulation of cell migration (GO:0030334); regulation of microglial cell activation (GO:1903978); macrophage activation (GO:0042116); regulation of macrophage chemotaxis (GO:0010758); phagocytosis (GO:0006909); lysosome (GO:0005764) | CD68 ↑ | Microglial cells: hypertrophy of somata and processes; neuron-centripetal migration; perineuronal topology; phagocytic activity | Figure 6b |
| Lymphocytic activation, migration, and infiltration | adaptive immune response (GO:0002250); lymphocyte activation (GO:0046649); lymphocyte migration (GO:0072676); B cell mediated immunity (GO:0019724); regulation of T cell mediated immunity (GO:0002709); regulation of CD4-positive, alpha-beta T cell activation (GO:2000514); regulation of CD8-positive, alpha-beta T cell activation (GO:2001185) | CD20 ↑ | B cells: leptomeningeal infiltration in the cerebellar cortex; perivascular infiltration if the spinal cord gray matter; no parenchymal migration | Figure 6c |
| CD4 ↑ | T helper cells: leptomeningeal infiltration; perivascular infiltration; minimal parenchymal migration | Figure 6c | ||
| CD8 ↑ | Cytotoxic T lymphocytes: leptomeningeal infiltration; perivascular infiltration; parenchymal infiltration; neuron-centripetal migration; perineuronal topology | Figure 6c | ||
| Virus infection of specific neuronal cell types | negative regulation of viral process (GO:0048525); regulation of viral entry into host cell (GO:0046596) | WNV-Ag positivity |
Purkinje cells (PCs; CALB-positive): presence of viral antigens in neuronal perikarya and processes Spinal motor neurons (SMNs; ChAT-positive): presence of viral antigens in neuronal perikarya and processes |
Figure 7a and b
Figure 7c and d |
| Disruption of structural integrity and function of infected neurons | neuronal cell body (GO:0043025); somatodendritic compartment (GO:0036477); dendrite (GO:0030425); regulation of cytosolic calcium ion concentration (GO:0051480); cellular calcium ion homeostasis (GO:0006874); calcium ion-regulated exocytosis of neurotransmitter (GO:0048791); neurotransmitter secretion (GO:0007269); synapse (GO:0045202); neuron to neuron synapse (GO:0098984); presynapse (GO:0098793); asymmetric synapse (GO:0032279); distal axon (GO:0150034); glutamatergic synapse (GO:0098978); GABA-ergic synapse (GO:0098982); synapse organization (GO:0050808); synaptic signaling (GO:0099536); chemical synaptic transmission (GO:0007268) | CALB ↓ | Purkinje cells: decrease of CALB-IR in somatodendritic compartments of WNV-infected PCs; disturbance of cellular calcium homeostasis in infected PCs | Figure 7b |
| ChAT ↓ | Spinal motor neurons: decrease of ChAT-IR in SMN cytoplasm and synapses innervating SMNs; disruption of neurotransmitter secretion in SMNs and their afferent innervation | Figure 7d | ||
| SYP ↓ | Decrease in IR for structural constituent of synaptic vesicles (SYP-IR) in the cerebellar cortex and spinal cord. Disruption of structural integrity of presynaptic compartments. Cerebellar cortex: putatively affected synapses innervating PCs: CF-PC and PF-PC (asymmetric-glutamatergic) in ML; BC-PC (GABA-ergic) in ML and PCL; and SC-PC (GABA-ergic) in ML Spinal gray matter: putatively affected synapses innervating SMNs: cholinergic C- boutons (ChAT-IR); asymmetric-glutamatergic synapses from descending tracts; and inhibitory synapses from local inhibitory neuron networks |
Figure 8a and c
Figure 8a Figure 7d and Figure 8c |
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| neuronal cell body (GO:0043025); somatodendritic compartment (GO:0036477); dendrite (GO:0030425); postsynapse (GO:0098794); microtubule cytoskeleton organization (GO:0000226) | MAP2 ↓ | Cerebellar cortex and spinal gray matter: loss of postsynaptic cellular targets for asymmetric (axodendritic) and symmetric (axosomatic) synapses; disruption of integrity of microtubule cytoskeleton | Figure 8b and d |
*IR, immunoreactivity. ↑ - increased compared to mock. ↓ - decreased compared to mock. GFAP, glial fibrillary acidic protein. WNV-Ag, WNV antigens. CALB, calbindin D28k. ChAT, choline acetyltransferase. SYP, synaptophysin. MAP2, microtubule associated protein 2. ML. molecular layer. PCL, Purkinje cell (PC) layer. CF-PC, climbing fiber to PC synapses. PF-PC, parallel fiber to PC synapses. BC-PC basket cell to PC synapses. SC-PC, stellate cell to PC synapses.