The breast-specific proteome

The breast transcriptome

Transcriptome analysis of the breast can be visualized with regard to specificity and distribution of transcribed mRNA molecules (Figure 1). Specificity illustrates the number of genes with elevated or non-elevated expression in the breast compared to other tissues. Elevated expression includes three subcategory types of elevated expression:

• Tissue enriched: At least four-fold higher mRNA level in breast compared to any other tissues.
• Group enriched: At least four-fold higher average mRNA level in a group of 2-5 tissues compared to any other tissue.
• Tissue enhanced: At least four-fold higher mRNA level in breast compared to the average level in all other tissues.

Distribution, on the other hand, visualizes how many genes that have, or do not have, detectable levels (NX≥1) of transcribed mRNA molecules in the breast compared to other tissues. As evident in Table 1, all genes elevated in breast are categorized as:

• Detected in single: Detected in a single tissue
• Detected in some: Detected in more than one but less than one third of tissues
• Detected in many: Detected in at least a third but not all tissues
• Detected in all: Detected in all tissues

Figure 1. (A) The distribution of all genes across the five categories based on transcript specificity in breast as well as in all other tissues. (B) The distribution of all genes across the six categories, based on transcript detection (NX≥1) in breast as well as in all other tissues.

As shown in Figure 1, 187 genes show some level of elevated expression in the breast compared to other tissues. The three categories of genes with elevated expression in breast compared to other organs are shown in Table 1. In Table 2, the 12 genes with the highest enrichment in breast are defined.

Table 1. Number of genes in the subdivided categories of elevated expression in breast.

Table 2. The 12 genes with the highest level of enriched expression in breast. "Tissue distribution" describes the transcript detection (NX≥1) in breast as well as in all other tissues. "mRNA (tissue)" shows the transcript level in breast as NX values. "Tissue specificity score (TS)" corresponds to the fold-change between the expression level in breast and the tissue with second highest expression level.

Protein expression of genes elevated in breast

In-depth analysis of the elevated genes in smooth muscle using antibody-based protein profiling allowed us to visualize the expression patterns of these proteins in different functional compartments.

Mammary glands in the fully developed breast can either be lactating or non-lactating. During pregnancy, non-lactating mammary glands undergo morphological alterations through the influence of hormonal changes in the body to become active and start the lactation process in order to provide milk for infants. Some proteins can therefore only be detected after this transformation. An example of a protein expressed in lactating breast is alpha-lactalbumin (LALBA), a principal protein of milk required for lactose synthesis in the mammary gland.

Figure 2. Immunohistochemical staining of human lactating breast using an antibody toward LALBA.

Examples of proteins specifically expressed during pregnancy are secreted proteins such as CSN1S1, CSN3 and CSN2, which are highly expressed in mammary glands.

Table 3. Following 10 genes have been analyzed in breast.

Gene expression shared between the breast and other tissues

There are 51 group enriched genes expressed in breast. Group enriched genes are defined as genes showing a 4-fold higher average level of mRNA expression in a group of 2-5 tissues, including breast, compared to all other tissues.

In order to illustrate the relation of breast tissue to other tissue types, a network plot was generated, displaying the number of genes with shared expression between different tissue types.

Figure 2. An interactive network plot of the breast enriched and group enriched genes connected to their respective enriched tissues (grey circles). Red nodes represent the number of breast enriched genes and orange nodes represent the number of genes that are group enriched. The sizes of the red and orange nodes are related to the number of genes displayed within the node. Each node is clickable and results in a list of all enriched genes connected to the highlighted edges. The network is limited to group enriched genes in combinations of up to 3 tissues, but the resulting lists show the complete set of group enriched genes in the particular tissue.

Two examples of group enriched genes in breast are Kertatin 15 (KRT15) and Prolactin-inducible protein (PIP).

Keratins are intermediate filament proteins responsible for the structural integrity of epithelial cells. Keratin 15 (KRT15) is expressed in breast, skin and esophagus.

KRT15 - breast
KRT15 - skin
KRT15 - esophagus

Prolactin-induced protein (PIP) is a single polypeptide chain that is secreted by apocrine cells, such as milk, saliva, and seminal fluid which is shown below.

PIP - breast
PIP - salivary gland
PIP - seminal vesicle

Hormone receptors in breast

The function of the breast is dependent on steroid hormones like progesterone, prolactin, placental lactogen and estrogen, which acts through their respective receptors in the mammary epithelium. One example is Estrogen receptor 1, ESR1, a receptor present in female tissues, where it links estrogen hormones and transmit the signal to alter the activity of genes in the nucleus. ESR1 shows distinct nuclear positivity in breast, fallopian tube, cervix and endometrium.

ESR1 - breast
ESR1 - cervix, uterine

ESR1 - fallopian tube
ESR1 - endometrium

Proteins analyzed in extended samples of lactating breast

The standard setup in the Tissue Atlas is based on Tissue Microarray technique (TMA), thus saving valuable tissue material as well as reagents and provides a wide tissue representation for protein profiling. In addition to the standard setup, extended tissue profiling in breast is performed for selected proteins, to give a more complete overview on where the proteins is expressed. The full list of genes used for protein profiling on breast samples is defined in Table 3.

Table 3. Following 10 genes have been analyzed in lactating breast.

Breast function

The primary function of the breast is to provide milk for the newborn infant. The mammary gland is a complex structure that includes a layer of secretory epithelial cells that secrete milk into the ducts and cavities by mechanisms such as exocytosis of secretory vesicles and budding-off of milk fat globules. The milk producing acinar cells are covered in a surrounding layer of myoepithelial cells that eject milk through contraction.

Breast histology

The main components of the human breast consists of the skin, subcutaneous adipose tissue and glandular tissue. Before puberty, the breasts are a very basic construct; a nipple connected to a simple duct system. At puberty the breasts undergo a transformation under the influence of hormones that lead to an increase in adipose tissue and complex branching of the previous basic ductal system. Below the nipple, the collecting ducts dilate to form the lactiferous sinuses. The breast is divided into 15-25 lobes, each based on a branching duct system that leads from the collecting ducts to the terminal duct-lobular units. The terminal duct-lobular units are the functional sites of milk production. Each collecting duct drains a lobe made up of 20-40 lobules. In addition to glandular cells, the lobe is composed chiefly of adipose tissue and fibrous stroma - referred to as the inter- and perilobular connective tissue.

In the nipple, the stratified squamous epithelium from the surface extends into the collecting ducts for a variable short distance. There is then an abrupt change into the glandular epithelium that is present throughout the duct and lobular system. The glandular epithelium is composed of two distinct types of cells, the secretory or luminal cells and myoepithelial cells. In the collecting ducts, the lining cells are usually columnar whereas in the acini they are usually cuboidal.The two types of luminal secretory cells that have been identified are basal cells, which have relatively clear cytoplasm and an oval nucleus lacking a visible nucleolus, and the superficial luminal cells with darker, basophilic cytoplasm. The myoepithelial cells usually form a discontinuous layer between the luminal secretory cells and the basement membrane. The myoepithelial cells appear small, flattened and with dark nuclei.

The histology of human breast including detailed images and information about the different cell types can be viewed in the Protein Atlas Histology Dictionary.

Background

Here, the protein-coding genes expressed in breast are described and characterized, together with examples of immunohistochemically stained tissue sections that visualize corresponding protein expression patterns of genes with elevated expression in breast.

Transcript profiling was based on a combination of three transcriptomics datasets (HPA, GTEx and FANTOM5, corresponding to a total of 483 samples from 37 different human normal tissue types. The final consensus normalized expression (NX) value for each tissue type was used for classification of all genes according to the tissue specific expression into two different categories, based on specificity or distribution.

Relevant links and publications

Uhlén M et al, 2015. Tissue-based map of the human proteome. Science
PubMed: 25613900 DOI: 10.1126/science.1260419

Yu NY et al, 2015. Complementing tissue characterization by integrating transcriptome profiling from the Human Protein Atlas and from the FANTOM5 consortium. Nucleic Acids Res.
PubMed: 26117540 DOI: 10.1093/nar/gkv608

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

Histology dictionary - the breast