The neuronal cell-specific proteome

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:

• Cell type enriched: At least four-fold higher mRNA level in a certain cell type compared to any other cell type.
• Group enriched: At least four-fold higher average mRNA level in a group of 2-10 cell types compared to any other cell type.
• Cell type enhanced: At least four-fold higher mRNA level in a cell certain cell type compared to the average level in all other cell types.

Table 1. Number of genes in the subdivided specificity categories of elevated expression in the analyzed neuronal cell types.

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.

GUCA1B - eye
GUCA1B - eye
GUCA1B - retina

ARR3 - eye
ARR3 - eye
ARR3 - retina

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.

RHO - eye
RHO - eye
RHO - retina

GNGT1 - eye
GNGT1 - eye
GNGT1 - retina

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.

TRPM1 - eye
TRPM1 - eye
TRPM1 - retina

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.

PAX6 - eye
PAX6 - eye
PAX6 - retina

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.

ELAVL3 - cerebral cortex
GAD1 - cerebral cortex

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.

Background

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)
PubMed: 25613900 DOI: 10.1126/science.1260419

Fagerberg L et al., Analysis of the human tissue-specific expression by genome-wide integration of transcriptomics and antibody-based proteomics. Mol Cell Proteomics. (2014)
PubMed: 24309898 DOI: 10.1074/mcp.M113.035600

Sjöstedt E et al., An atlas of the protein-coding genes in the human, pig, and mouse brain. Science. (2020)
PubMed: 32139519 DOI: 10.1126/science.aay5947

Menon M et al., Single-cell transcriptomic atlas of the human retina identifies cell types associated with age-related macular degeneration. Nat Commun. (2019)
PubMed: 31653841 DOI: 10.1038/s41467-019-12780-8