The neuronal cell-specific proteome
The function of the brain, defined as the central nervous system, is to receive, process and execute the coordinated higher functions of perception, motion and cognition that signify human life. Retina is an extension of the CNS responsible specifically for vision. The cellular components of the underlying and highly complex network of transmitted signals include neurons and supportive glial cells. Transcriptome analysis shows that 67% (n=13227) of all human proteins (n=19670) are detected in neuronal cells and 2533 of these genes show an elevated expression in any neuronal cells compared to other cell type groups.
The neuronal cell transcriptome
The scRNA-seq-based neuronal cell transcriptome can be analyzed with regard to specificity, illustrating the number of genes with elevated expression in each specific neuronal cell type compared to other cell types (Table 1). Genes with an elevated expression are divided into three subcategories:
Protein expression of genes elevated in neuronal cells
In-depth analysis of the elevated genes in neuronal cells using scRNA-seq and antibody-based protein profiling allowed us to visualize the expression patterns of these proteins in different types of neuronal cells: cone and rod photoreceptor cells, bipolar cells and horizontal cells and other neuronal cells.
Cone photoreceptor cells - eye
As shown in Table 1, 1133 genes are elevated in cone photoreceptor cells compared to other cell types. Cones photoreceptors cells are the less abundant of the two types of photoreceptor cells found in the retina. They register red, green and blue colors and thus allow color vision. Two examples of proteins expressed in cone photoreceptor cells are guanylate cyclase activator 1B (GUCA1B) and arrestin 3 (ARR3). Both are involved in the return of photoreceptor cells to a deactivated state at the end of the phototransduction. GUCA1B is expressed in both cone and rod photoreceptor cells, while arresting ARR3 is active specifically in cone photoreceptor cells.
Rod photoreceptor cells - eye
As shown in Table 1, 943 genes are elevated in rod photoreceptor cells compared to other cell types. There are two types of photoreceptor cells in the retina: rod and cone photoreceptors cells, and out of these rod photoreceptor cells are most abundant. They register the presence of light and allow vision during low light conditions. Two proteins essential for rod function are rhodopsin (RHO) and G protein subunit gamma transducin 1 (GNGT1). They are involved in two different steps of phototransduction, the process of conversion of light to nerve signals.
Bipolar cells - eye
As shown in Table 1, 992 genes are elevated in bipolar cells compared to other cell types. Similarly to horizontal cells, also bipolar cells are located in the inner nuclear layer of the retina. They fine-tune the transmission of nerve signals from photoreceptor cells to ganglion cells in response to phototransduction. Transient receptor potential cation channel subfamily M member 1 (TRPM1) is an example of a protein expressed in bipolar cells. It is a cation channel necessary for the activation of ON-bipolar cells in light conditions.
Horizontal cells - eye
As shown in Table 1, 991 genes are elevated in horizontal cells compared to other cell types. Horizontal cells are located in the inner nuclear layer of the retina. They modulate nerve signaling that is produced during phototransduction by inhibiting or activating signals from photoreceptor cells depending on varying light conditions. Paired box 6 (PAX6) is a transcription factor involved in the development of several tissues, including the eye. In the retina, it is expressed in horizontal cells, as well as other cell types.
Other neuronal cells
The brain includes different cell types and subclasses of the different cells. Neurons are the main signaling units, communicating with each other via synapses. The two main subclasses of neurons are interneurons (local interconnections between neurons) and projection neurons. Neurons are functional entities in the brain and based on morphology and neurotransmitter phenotype originally divided into two main classes, excitatory, glutamatergic pyramidal projection neurons and inhibitory, mostly GABAergic interneurons. The protein ELAV-like protein 3 (ELAVL3) is expressed in all neurons whereas glutamate decarboxylase 1 (GAD1) is an essential enzyme in the biosynthesis of GABA and known to be expressed in the majority of cortical GABAergic interneurons.
Neuronal cell function
Neuronal cells are electrically excitatory cells that communicate through their synapses that connect to other neurons within its neuronal network. There are classes of neurons that serve different functions. Among those are sensory neurons, that receive signals from sensory organs such as skin, eyes and ears when affected by a stimulus, motor neurons that control movement and muscle contraction when receiving signals from the spinal cord and the brain, and interneurons, a network that connects neurons with other neurons and forming a neuronal circuit. The typical neuronal cell consists of an axon, a cell body and dendrites. The signaling in neurons can be inhibitory or excitatory where the signal is driven by a membranous voltage gradient called action potential that generates a pulse that travels through the axon into the synapses.
The histology of organs that contain neuronal cells, including interactive images, is described in the Protein Atlas Histology Dictionary.
Here, the protein-coding genes expressed in neuronal cells are described and characterized, together with examples of immunohistochemically stained tissue sections that visualize corresponding protein expression patterns of genes with elevated expression in different neuronal cell types.
The transcript profiling was based on publicly available genome-wide expression data from scRNA-seq experiments covering 13 different normal tissues, as well as analysis of human peripheral blood mononuclear cells (PBMCs). All datasets (unfiltered read counts of cells) were clustered separately using louvain clustering and the clusters obtained were gathered at the end, resulting in a total of 192 different cell type clusters. The clusters were then manually annotated based on a survey of known tissue and cell type-specific markers. The scRNA-seq data from each cluster of cells was aggregated to average normalized protein-coding transcripts per million (pTPM) and the normalized expression value (nTPM) across all protein-coding genes. A specificity and distribution classification was performed to determine the number of genes elevated in these single cell types, and the number of genes detected in one, several or all cell types, respectively.
It should be noted that since the analysis was limited to datasets from 13 organs only, not all human cell types are represented. Furthermore, some cell types are present only in low amounts, or identified only in mixed cell clusters, which may affect the results and bias the cell type specificity.
Relevant links and publications
Uhlén M et al., Tissue-based map of the human proteome. Science (2015)