The pigment cell-specific proteome

There are two types of pigment cells, found primarily in the epidermis and eyes. Pigment cells produce melanin which protects against UV radiation and gives the skin, hair and eyes its color. Pigment cells also play a role in the immune system and serve as a blood-retinal barrier. Transcriptome analysis shows that 62% (n=12246) of all human proteins (n=19670) are detected in pigment cells and 394 of these genes show an elevated expression in any pigment cells compared to other cell type groups.

  • 394 elevated genes
  • 36 enriched genes
  • 85 group enriched genes
  • Main function: Melanin production

The pigment cell transcriptome

The scRNA-seq-based pigment cell transcriptome can be analyzed with regard to specificity, illustrating the number of genes with elevated expression in each specific pigment 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 melanocytes.

Cell type Cell type enrichedGroup enrichedCell type enhancedTotal elevated
Melanocytes 36 85 273 394

Protein expression of genes elevated in pigment cells

In-depth analysis of the elevated genes in pigment cells using scRNA-seq and antibody-based protein profiling allowed us to visualize the expression patterns of these proteins in different types of pigment cells: melanocytes and other types of pigment cells.

Melanocytes - skin

As shown in Table 1, 394 genes are elevated in melanocytes compared to other cell types. Melanocytes are mainly located in the basal layer of the epidermis and their primary role is to produce and deliver melanin-pigment to keratinocytes through dendritic processes. Genes with elevated expression in melanocytes include MLANA and DCT, which encode proteins involved in the melanin-synthesis pathways.

MLANA - skin

MLANA - skin

MLANA - skin

DCT - skin

DCT - skin

DCT - skin

Other pigment cells

Retinal pigment cells are found in the eye. Retinal pigment cells produce melanin that protects photoreceptor cells from UV-radiation and they are involved in the transport of nutrients and ions between photoreceptor cells and blood vessels in the choroid. The proteins bestrophin 1 (BEST1) and solute carrier family 16 member 8 (SLC16A8) both play a role in the transport of molecules and have elevated expression in the retina.

BEST1 - retina

SLC16A8 - retina

Pigment cell function

The two pigment cell types are melanocytes and retinal pigment cells. Melanocytes originate from neural crest cells, while retina pigment cells originate from the optic neuroepithelium. The main objective of melanocytes is to produce melanin, which protects the skin against UV-radiation. It is melanin produced by melanocytes in the uveal part of the eye that gives eyes their color. When melanin is exposed to UV-radiation from the sun, it becomes darker to protect the skin from further damage to the tissue. The amount of melanin produced by the melanocytes differs between individuals but the amount of melanocytes is the same. Lack of melanin production can lead to a disease called albinism, where the individual has no pigmentation at all and it will affect both eye and hair pigmentation. Moreover, melanocytes have immune cell qualities such as phagocytosis, antigen presentation capabilities and cytokine production.

Retinal pigment cells form retinal pigment epithelium in the back of the eye, adjacent to the retina. The retinal pigment epithelium works as a retinal-blood barrier and protects the retina. Similarly to melanocytes, retinal pigment cells produce pigment, however instead of protecting the skin, retinal pigment cells protect the retina from UV-radiation. Retinal pigment cells are in constant connection with the photoreceptor cells of the retina and support these cells in various ways. They buffer ions and water between photoreceptor cells and blood. Pigment cells also store 11-cis-retinal, a molecule essential for the transformation of light into visual signals in photoreceptor cells. They can quickly supply photoreceptor cells with 11-cis-retinal, when this molecule is depleted in photoreceptor cells.

The histology of organs that contain pigment cells, including interactive images, is described in the Protein Atlas Histology Dictionary.


Here, the protein-coding genes expressed in pigment 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 pigment 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

UhlĂ©n 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

Solé-Boldo L et al., Single-cell transcriptomes of the human skin reveal age-related loss of fibroblast priming. Commun Biol. (2020)
PubMed: 32327715 DOI: 10.1038/s42003-020-0922-4