The human pathology proteome in endometrial cancer

Endometrial cancer is the fifth most common cancer in women, and one of the most common forms of gynecological cancer in developed countries. The incidence of endometrial cancer is rising which is thought to be related to increased life expectancy and the epidemic of obesity, and the 5-year survival rate in patients without metastatic disease varies from 74% to 91%. Around 80% of endometrial cancers represent endometrioid histology. These are considered hormone dependent and the prognosis of endometrioid cancers is generally favourable. The majority of endometrial cancers are detected at an early stage with the disease restricted to the uterus.

Endometrial cancer originates from the endometrium - the mucosal lining of the uterus. The common form of endometrial cancer, referred to as type 1 or estrogen-related endometrial cancer, usually occurs in younger, premenopausal women and tends to be of lower histologic grade. Type 2, or non-estrogen-related endometrial cancer, occurs in postmenopausal women, and is the more aggressive form of endometrial cancer.

Here, we explore the endometrial cancer proteome using TCGA transcriptomics data and antibody based protein data. 1620 genes are suggested as prognostic based on transcriptomics data from 541 patients; 784 genes associated with unfavourable prognosis and 836 genes associated with favourable prognosis.

TCGA data analysis

In this metadata study we used data from TCGA where transcriptomics data was available from 541 patients in total and dataset included only females . Most of the patients (450 patients) were still alive at the time of data collection. All patients (541) were missing stage information.

Unfavourable prognostic genes in endometrial cancer

For unfavourable genes, higher relative expression levels at diagnosis gives significantly lower overall survival for the patients. There are 784 genes associated with unfavourable prognosis in endometrial cancer. In Table 1, the top 20 most significant genes related to unfavourable prognosis are listed.

ASS1 is a gene associated with unfavourable prognosis in endometrial cancer. The best separation is achieved by an expression cutoff at 45,2 fpkm which divides the patients into two groups with 63% 5-year survival for patients with high expression versus 86% for patients with low expression, p-value: 8,14e-9. Immunohistochemical staining of an antibody targeting ASS1 (HPA020896) shows variable staining intensities in endometrial cancer samples.

Table 1. The 20 genes with highest significance associated with unfavourable prognosis in endometrial cancer.

Gene	Description	Predicted localization	mRNA (cancer)	p-value
L1CAM	L1 cell adhesion molecule	Intracellular,Membrane,Secreted	6.2	8.51e-10
MBOAT2	membrane bound O-acyltransferase domain containing 2	Membrane	2.9	2.13e-9
HIF3A	hypoxia inducible factor 3, alpha subunit	Intracellular	1.4	6.90e-9
ASS1	argininosuccinate synthase 1	Intracellular	59.5	8.14e-9
PTX3	pentraxin 3, long	Secreted	1.3	8.35e-9
FAM110B	family with sequence similarity 110, member B	Intracellular	1.9	3.88e-8
IGSF1	immunoglobulin superfamily, member 1	Membrane,Secreted	1.1	4.25e-8
MGAT4A	mannosyl (alpha-1,3-)-glycoprotein beta-1,4-N-acetylglucosaminyltransferase, isozyme A	Intracellular,Secreted	3.8	6.48e-8
KHK	ketohexokinase (fructokinase)	Intracellular	1.3	7.62e-8
MARK4	MAP/microtubule affinity-regulating kinase 4	Intracellular,Membrane	7.9	8.31e-8
GPRIN2	G protein regulated inducer of neurite outgrowth 2	Intracellular	1.2	8.60e-8
ERBB2	erb-b2 receptor tyrosine kinase 2	Intracellular,Membrane	43.3	8.99e-8
LMO3	LIM domain only 3 (rhombotin-like 2)	Intracellular	1.3	1.10e-7
DAGLA	diacylglycerol lipase, alpha	Membrane	1.2	1.13e-7
ADA	adenosine deaminase	Intracellular	4.3	1.23e-7
MAP1LC3C	microtubule-associated protein 1 light chain 3 gamma	Intracellular	1.2	1.34e-7
CDKN2A	cyclin-dependent kinase inhibitor 2A	Intracellular,Secreted	14.3	1.82e-7
RNF44	ring finger protein 44	Intracellular	12.6	2.57e-7
LRRN2	leucine rich repeat neuronal 2	Membrane	10.6	2.59e-7
TRIM46	tripartite motif containing 46	Intracellular	1.5	2.61e-7

Favourable prognostic genes in endometrial cancer

For favourable genes, higher relative expression levels at diagnosis gives significantly higher overall survival for the patients. There are 836 genes associated with favourable prognosis in endometrial cancer. In Table 2, the top 20 most significant genes related to favourable prognosis are listed.

SCGB2A1 is a gene associated with favourable prognosis in endometrial cancer. The best separation is achieved by an expression cutoff at 36.7 fpkm which divides the patients into two groups with 82% 5-year survival for patients with high expression versus 56% for patient with low expression, p-value: 1,54e-8. Immunohistochemical staining of antibody targeting SCGB2A1 (HPA034584) shows variable staining in endometrial cancer samples.

Table 2. The 20 genes with highest significance associated with favourable prognosis in endometrial cancer.

Gene	Description	Predicted localization	mRNA (cancer)	p-value
B4GALNT3	beta-1,4-N-acetyl-galactosaminyl transferase 3	Intracellular,Secreted	20.8	1.69e-10
P2RX4	purinergic receptor P2X, ligand gated ion channel, 4	Membrane	7.4	6.30e-10
SPDEF	SAM pointed domain containing ETS transcription factor	Intracellular	78.1	9.26e-9
SCGB2A1	secretoglobin, family 2A, member 1	Secreted	971.9	1.54e-8
DHRS7B	dehydrogenase/reductase (SDR family) member 7B	Intracellular,Membrane	8.6	1.98e-8
PLPP2	phospholipid phosphatase 2	Membrane	28.2	3.21e-8
NXNL2	nucleoredoxin-like 2	Intracellular	4.0	3.83e-8
SMDT1	single-pass membrane protein with aspartate-rich tail 1	Membrane	31.4	5.32e-8
SLC47A1	solute carrier family 47 (multidrug and toxin extrusion), member 1	Membrane	14.6	5.54e-8
HEXA	hexosaminidase A (alpha polypeptide)	Secreted	6.8	5.63e-8
PGR	progesterone receptor	Intracellular	11.1	5.76e-8
STX18	syntaxin 18	Intracellular,Membrane	43.1	6.33e-8
ATPIF1	ATPase inhibitory factor 1	Intracellular	76.6	6.38e-8
DRAM1	DNA-damage regulated autophagy modulator 1	Intracellular,Membrane	7.7	6.52e-8
SPAG4	sperm associated antigen 4	Intracellular,Membrane	8.7	9.52e-8
SCGB2A2	secretoglobin, family 2A, member 2	Secreted	35.9	9.57e-8
ZAP70	zeta-chain (TCR) associated protein kinase 70kDa	Intracellular	1.9	9.66e-8
GPR108	G protein-coupled receptor 108	Intracellular,Membrane	21.7	1.04e-7
MSX1	msh homeobox 1	Intracellular	246.3	1.64e-7
SERINC2	serine incorporator 2	Membrane	139.1	1.69e-7

The endometrial cancer transcriptome

The transcriptome analysis shows that 72% (n=14107) of all human genes (n=19571) are expressed in endometrial cancer. All genes were classified according to the endometrial cancer-specific expression into one of five different categories, based on the ratio between mRNA levels in endometrial cancer compared to the mRNA levels in the other 16 analyzed cancer tissues. 198 genes show some level of elevated expression in endometrial cancer compared to other cancers (Figure 1). The elevated category is further subdivided into three categories as shown in Table 3.

Figure 1. The distribution of all genes across the five categories based on transcript abundance in endometrial cancer as well as in all other cancer tissues.

Table 3. Number of genes in the subdivided categories of elevated expression in endometrial cancer

Category	Number of genes	Description
Tissue enriched	15	At least five-fold higher mRNA levels in a particular cancer as compared to all other cancers
Group enriched	74	At least five-fold higher mRNA levels in a group of 2-7 cancers
Tissue enhanced	109	At least five-fold higher mRNA levels in a particular cancer as compared to average levels in all cancers
Total	198	Total number of elevated genes in endometrial cancer

Additional information

High estrogen blood levels stimulate the endometrial mucosa, which may result in excessive endometrial growth and type 1 endometrial cancer. Conditions such as diabetes, infertility, obesity, and polycystic ovarian syndrome (PCOS) are associated with an increased risk to develop type 1 endometrial carcinoma. Infrequent periods, first menstruation before the age of 12, no pregnancies, and entering menopause after the age 50 may is also associated with an increased risk, as is receiving estrogen replacement therapy (without progesterone) or tamoxifen treatment, a common drug for treatment of breast cancer. Factors that predispose for type 2 endometrial cancer are less well known.

Certain correlations exist between the type of endometrial cancer and histology. Type 1 cancers are usually low-grade, have an endometrioid appearance and are associated with hyperplasia in the adjacent endometrium. Type 2 usually consists of high-grade, serous or clear cell tumors and is not associated with endometrial hyperplasia.

Endometrial cancers are popularly staged according to the FIGO (International Federation of Gynaecology and Obstetrics) staging system. Stage I cancers are limited to the uterine corpus (or body). Stage II tumors involve the cervix, while Stage III tumors involve the serosa and/or uterine adnexae, vagina, and pelvic lymph nodes. In Stage IV distant metastases are present.

Histologic grade in endometrial cancers is defined on the basis of tubular differentiation and nuclear pleomorphism. Well-differentiated (Grade 1) endometrial cancers show uniform oval nuclei with evenly dispersed chromatin and a solid tumor growth pattern (without lumen formation) only in a small fraction of the tumor. In poorly differentiated cancers (Grade 3) nuclei with coarse chromatin and prominent nucleoli are observed and more than 50% of the tumor is composed of solid masses.

Immunohistochemistry for estrogen alpha (ER, ESR1) and progesterone receptors (PR, PGR) shows that these hormonal receptors are typically expressed in tumor cells in type 1, but frequently not in type 2 endometrial cancers.

Relevant links and publications

Uhlen M et al, 2017. A pathology atlas of the human cancer transcriptome. Science.
PubMed: 28818916 DOI: 10.1126/science.aan2507

Cancer Genome Atlas Research Network et al, 2013. The Cancer Genome Atlas Pan-Cancer analysis project. Nat Genet.
PubMed: 24071849 DOI: 10.1038/ng.2764