The endometrium-specific proteome

The endometrial mucosa lines the inner wall of the uterus and maintains the patency of the uterine cavity by preventing adhesion between the opposed uterine walls. It also serves as a medium for implantation of the blastocyst (fertilized egg) during pregnancy. In fertile women the endometrium undergoes hormone-driven cyclic regeneration, coarsely divided into the menstrual, proliferative and secretory phase. Transcriptome analysis shows that 69% (n=13898) of all human proteins (n=20090) are expressed in the endometrium and 92 of these genes show an elevated expression in the endometrium compared to other tissue types.

  • 92 elevated genes
  • 2 enriched genes
  • 13 group enriched genes
  • Endometrium has most group enriched gene expression in common with cervix

The endometrium transcriptome

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

  • Tissue enriched: At least four-fold higher mRNA level in endometrium 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 endometrium compared to the average level in all other tissues.

Distribution, on the other hand, visualizes how many genes have, or do not have, detectable levels (nTPM≥1) of transcribed mRNA molecules in the endometrium compared to other tissues. As evident in Table 1, all genes elevated in endometrium 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

A. Specificity

B. Distribution

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

As shown in Figure 1, 92 genes show some level of elevated expression in the endometrium compared to other tissues. The three categories of genes with elevated expression in endometrium compared to other organs are shown in Table 1. In Table 2, the 2 enriched genes are defined.

Table 1. The number of genes in the subdivided categories of elevated expression in endometrium.

Distribution in the 36 tissues
Detected in singleDetected in someDetected in manyDetected in all Total
Tissue enriched 1010 2
Group enriched 0760 13
Tissue enhanced 09626 77
Total 116696 92

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

Gene Description Tissue distribution mRNA (tissue) Tissue specificity score
MMP10 matrix metallopeptidase 10 Detected in many 265.4 34
MMP26 matrix metallopeptidase 26 Detected in single 13.1 24

Protein expression of genes elevated in the endometrium

In-depth analysis of the elevated genes in endometrium using antibody-based protein profiling allowed us to create a map of where these proteins are expressed within the endometrium, including glandular cells, stroma cells and with respect to differences dependent on the menstrual cycle.

Proteins expressed during the proliferative phase

Proteins expressed during the proliferative phase include female sex hormone receptors progesterone receptor (PGR) and estrogen receptor 1 (ESR1), which are expressed in the nucleus of both glandular and stromal cells, and play a central role in regulation of reproductive events.



Proteins specifically expressed during the secretory phase

Proteins expressed during the secretory phase include PAEP, a glycoprotein expressed in glandular cells with an essential role in regulating uterine environment suitable for pregnancy and C1QTNF6, a complement C1q tumor necrosis factor-related protein expressed in stromal cells with unknown function.



Proteins specifically expressed during secretory and proliferative phase

Proteins expressed during both the proliferative and secretory phase include the transcription factor HOXA11, which is involved in the regulation of uterine development and is required for female fertility. Also expressed in stroma cells, is HOXA11 while SFRP4, a modulator of Wnt signaling with a role in regulating cell growth and differentiation in specific cell types, is expressed both in stroma and glandular cells.



Proteins expressed during the menstruation

Matrix metalloproteinases (MMP) have an important role in the cyclic remodeling of the human endometrium. The expression of MMPs increases dramatically at the onset of the menstrual phase to facilitate extracellular matrix breakdown and shedding of the endometrial superficial functional layer. At the proliferative and secretory phases, MMP mRNA levels are significantly lower. This is exemplified by MMP10 and MMP11 below where expression in glandular cells and stroma are presented, respectively.



Gene expression shared between the endometrium and other tissues

There are 13 group enriched genes expressed in endometrium. 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 endometrium, compared to all other tissues.

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

Figure 2. An interactive network plot of the endometrium enriched and group enriched genes connected to their respective enriched tissues (grey circles). Red nodes represent the number of endometrium 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 5 tissues, but the resulting lists show the complete set of group enriched genes in the particular tissue.

The endometrium shares group enriched gene expression of few genes with several other tissues but has most shared group enriched gene expression with other female tissues, including uterine cervix, fallopian tube and placenta, as well as smooth muscle and brain.

Endometrium function

The endometrium is the inner mucous membrane of the uterus and consists of endometrial glands and endometrial stroma. It functions as a lining for the uterus, preventing adhesions between opposing walls of the myometrium, thereby maintaining the patency of the uterine cavity.

Menstrual cycle The endometrial lining undergoes cyclic regeneration. The menstrual cycle in the uterine can be divided into menstruation, proliferative phase, and secretory phase and is controlled by the endocrine system.

During the proliferative phase, as a response to increasing amounts of estrogen, the lining of the endometrium grows to a thick, blood vessel-rich, glandular tissue layer. Under complex hormonal interplay, follicles in the ovary start to develop. As they mature, the ovarian follicles secrete increasing amounts of estrogens which initiate the formation of a new layer of endometrium in the uterus. Histologically, this layer is identified as the proliferative endometrium. When fully developed, the dominant ovarian follicle releases an ovum (egg), whereas the non-dominant follicles will atrophy and die.

During the secretory phase, pituitary hormones cause the remaining parts of the dominant follicle to transform into the corpus luteum, which produces progesterone. After ovulation and a rise in progesterone levels by the corpus luteum, the endometrium changes to prepare for implantation of the blastocyst (fertilized egg). If implantation does not occur within approximately two weeks, the levels of progesterone and estrogen drops causing the uterus to shed its lining and egg in menstruation.

During pregnancy, the glands and blood vessels in the endometrium continue to increase in size and number. Under the influence of progesterone, in a process called decidualization, the vascular spaces fuse and become interconnected. This results in the formation of the maternal part of the placenta, the decidua, which supplies oxygen and nutrition to the fetus.

Figure 3. The ovaries, fallopian tubes and uterus. The menstrual cycle can be described both by the ovarian cycle and the uterine cycle which consists of menstruation, proliferative phase, and secretory phase. During the proliferative phase the lining of the uterus grow, or proliferate, and follicles in the ovary start to mature. During ovulation the dominant follicle releases an ovum (egg) via the fallopian tube. After ovulation and during the secretory phase the remaining parts of the follicle transforms into the corpus luteum. The corpus luteum produces hormones that support the early stages of pregnancy but, if the ovum is not fertilized these hormones will instead lead to atrophy of the unfertilized egg. Subsequently this leads to falling levels of hormones. This drop in hormone levels initiates female menstruation after which a new cycle begins. If the ovum is fertilized it develops into a blastocyst and implants itself in the uterus. This is made possible through changes in both the blastocyst and endometrial wall. Implantation allows for the next step in embryogenesis which includes the formation of the placenta.

Endometrium histology

The inactive, prepubertal endometrium shows a low single layer of cuboidal epithelium that lines the surface and the underlying glands. Both prepubertal and postmenopausal endometrium does not exhibit any hormone dependent proliferative or secretory changes. The appearance of prepubertal endometrium therefore greatly resembles the inactive endometrium seen in postmenopausal women. The endometrium in the reproductive female can be divided into a deeper basal layer and a superficial functional layer. The functional layer is subdivided into two strata - the compactum (towards the surface) and the spongiosum (towards the basalis).

The histology of human endometrium including detailed images and information can be viewed in the Protein Atlas Histology Dictionary.


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

Transcript profiling was based on a combination of two transcriptomics datasets (HPA and GTEx), corresponding to a total of 14590 samples from 54 different human normal tissue types. The final consensus normalized expression (nTPM) value for each tissue type was used for the 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., Tissue-based map of the human proteome. Science (2015)
PubMed: 25613900 DOI: 10.1126/science.1260419

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

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

Zieba A et al., The Human Endometrium-Specific Proteome Defined by Transcriptomics and Antibody-Based Profiling. OMICS. (2015)
PubMed: 26488136 DOI: 10.1089/omi.2015.0115

Histology dictionary - the endometrium