The uterine corpus endometrial carcinoma proteome

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 and this is believed to be related to increased life expectancy and the epidemic of obesity. 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 favorable. 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 inner cavity 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 uterine corpus endometrial carcinoma proteome using TCGA transcriptomics data and antibody-based protein data. 221 genes are suggested as prognostic based on transcriptomics data from 176 patients; 121 genes are associated with unfavorable prognosis and 100 genes are associated with favorable prognosis.

TCGA data analysis

In this metadata study, we used data from TCGA where transcriptomics data was available from 176 patients in total and dataset included only females . Most of the patients (144 patients) were still alive at the time of data collection. The stage distribution was stage i) 93 patients, stage ii) 24 patients, stage iii) 45 patients and stage iv) 10 patients.

Unfavorable prognostic genes in uterine corpus endometrial carcinoma

For unfavorable genes, higher relative expression levels at diagnosis give significantly lower overall survival for the patients. There are 121 genes associated with an unfavorable prognosis in uterine corpus endometrial carcinoma. In Table 1, the top 20 most significant genes related to an unfavorable prognosis are listed.

CCNE2 is a gene associated with an unfavorable prognosis in uterine corpus endometrial carcinoma. The best separation is achieved by an expression cutoff at 4.2 TPM which divides the patients into two groups with 30% 5-year survival for patients with high expression versus 79% for patients with low expression, p-value: 7.70e-6. Immunohistochemical staining of an antibody targeting CCNE2 (CAB007825) shows variable staining intensities in uterine corpus endometrial carcinoma samples.

p<0.001
CCNE2 - survival analysis
CCNE2 - high expression
CCNE2 - low expression

Table 1. The 20 genes with highest significance associated with an unfavorable prognosis in uterine corpus endometrial carcinoma.

Gene	Description	Predicted location	mRNA (cancer)	p-value	Prognostic
STX1A	Syntaxin 1A	Membrane, Intracellular	5.1	5.05e-7	potential
PIWIL4	Piwi like RNA-mediated gene silencing 4	Intracellular	1.4	8.68e-7	potential
COL22A1	Collagen type XXII alpha 1 chain	Secreted, Intracellular	3.0	3.01e-6	potential
STEAP1B	STEAP family member 1B	Membrane	1.1	3.55e-6	potential
PDE8A	Phosphodiesterase 8A	Intracellular	2.7	4.87e-6	potential
COBLL1	Cordon-bleu WH2 repeat protein like 1	Intracellular	4.3	6.97e-6	potential
ENSG00000285082	Novel protein	Intracellular	2.5	1.53e-5	potential
CELF4	CUGBP Elav-like family member 4	Intracellular	2.4	1.68e-5	potential
PLBD1	Phospholipase B domain containing 1	Intracellular	19.5	1.90e-5	potential
PTX3	Pentraxin 3	Secreted	3.8	2.12e-5	potential
ABCC6	ATP binding cassette subfamily C member 6	Membrane	2.1	2.79e-5	potential
SPATS2L	Spermatogenesis associated serine rich 2 like	Intracellular	50.5	2.86e-5	potential
LMO3	LIM domain only 3	Intracellular	7.2	3.45e-5	potential
TNFAIP6	TNF alpha induced protein 6	Secreted	2.1	3.85e-5	potential
SIX3	SIX homeobox 3	Intracellular	2.3	4.61e-5	potential
DLL3	Delta like canonical Notch ligand 3	Membrane, Intracellular	3.4	4.99e-5	potential
ZNF730	Zinc finger protein 730	Intracellular	1.3	5.02e-5	potential
TAGLN3	Transgelin 3	Intracellular	2.6	5.19e-5	potential
MT1A	Metallothionein 1A	Intracellular	16.0	5.46e-5	potential
EPS15	Epidermal growth factor receptor pathway substrate 15	Intracellular	11.7	5.71e-5	potential
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Favorable prognostic genes in uterine corpus endometrial carcinoma

For favorable genes, higher relative expression levels at diagnosis give significantly higher overall survival for the patients. There are 100 genes associated with a favorable prognosis in uterine corpus endometrial carcinoma. In Table 2, the top 20 most significant genes related to a favorable prognosis are listed.

ACADS is a gene associated with a favorable prognosis in uterine corpus endometrial carcinoma. The best separation is achieved by an expression cutoff at 12 TPM which divides the patients into two groups with 76% 5-year survival for patients with high expression versus 44% for patient with low expression, p-value: 1.09e-4. Immunohistochemical staining of antibody targeting ACADS (HPA022271) shows variable staining in uterine corpus endometrial carcinoma samples.

p<0.001
ACADS - survival analysis
ACADS - high expression
ACADS - low expression

Table 2. The 20 genes with highest significance associated with a favorable prognosis in uterine corpus endometrial carcinoma.

Gene	Description	Predicted location	mRNA (cancer)	p-value	Prognostic
NUDT18	Nudix hydrolase 18	Intracellular	12.3	8.61e-6	potential
CIRBP	Cold inducible RNA binding protein	Intracellular	234.2	1.08e-5	potential
RPAIN	RPA interacting protein	Intracellular	59.7	1.52e-5	potential
SURF6	Surfeit 6	Intracellular	11.2	2.47e-5	potential
NLRX1	NLR family member X1	Intracellular	9.9	2.90e-5	potential
KDM4B	Lysine demethylase 4B	Intracellular	20.1	4.33e-5	potential
ACADS	Acyl-CoA dehydrogenase short chain	Intracellular	22.6	4.58e-5	potential
CPT1B	Carnitine palmitoyltransferase 1B	Membrane	15.8	4.86e-5	potential
DOLK	Dolichol kinase	Membrane	16.4	5.47e-5	potential
WIF1	WNT inhibitory factor 1	Secreted, Intracellular	29.5	6.01e-5	potential
LYRM1	LYR motif containing 1	Intracellular	22.6	6.58e-5	potential
ZNF219	Zinc finger protein 219	Intracellular	25.2	6.68e-5	potential
ANP32B	Acidic nuclear phosphoprotein 32 family member B	Intracellular	267.2	7.53e-5	potential
VAMP2	Vesicle associated membrane protein 2	Membrane	38.8	7.84e-5	potential
ANAPC16	Anaphase promoting complex subunit 16	Intracellular	35.9	9.13e-5	potential
SLC52A3	Solute carrier family 52 member 3	Membrane	14.6	9.70e-5	potential
SCAMP4	Secretory carrier membrane protein 4	Membrane, Intracellular	82.3	1.00e-4	potential
HMGN1	High mobility group nucleosome binding domain 1	Intracellular	530.7	1.30e-4	potential
SPDEF	SAM pointed domain containing ETS transcription factor	Intracellular	84.6	1.60e-4	potential
TMEM250	Transmembrane protein 250	Membrane, Intracellular	25.9	1.62e-4	potential
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CPTAC relative protein expression data

Proteins that are significantly down- or upregulated in uterine corpus endometrial carcinoma compared to normal tissue is illustrated in a vulcano plot using tandem mass tag (TMT) mass spectrometry data from the CPTAC dataset based on the analysis of 104 tumor samples and 49 normal samples.

In uterine corpus endometrial carcinoma, 1976 and 1925 genes are down- (blue) and upregulated (red) compared to normal tissue, respectively. In Table 3, the top 20 most significant genes are listed.

Figure 1. Proteins highlighted in blue are significantly downregulated in cancer tissue, while those in red are significantly upregulated when compared to normal tissue. Gray points represent non-significant proteins based on the log2 (fold change). Wilcox rank test with adjusted p values.

Table 3. The 20 genes with the highest significance associated with a downregulated or upregulated protein expression in uterine corpus endometrial carcinoma compared to normal tissue.

Gene	Description	Predicted location	Log2 fold change	p-value	Regulation
JAM3	Junctional adhesion molecule 3	Secreted, Membrane, Intracellular	-1.58	1.64e-21	Downregulated
ZEB1	Zinc finger E-box binding homeobox 1	Intracellular	-1.36	3.29e-21	Downregulated
HIC1	HIC ZBTB transcriptional repressor 1	Intracellular	-1.5	3.70e-21	Downregulated
CDH13	Cadherin 13	Intracellular	-2.17	5.87e-21	Downregulated
DNM1	Dynamin 1	Intracellular	-0.76	7.10e-21	Downregulated
TCF4	Transcription factor 4	Secreted, Intracellular	-0.83	7.38e-21	Downregulated
ALDH1A2	Aldehyde dehydrogenase 1 family member A2	Intracellular	-1.54	9.64e-21	Downregulated
SNX21	Sorting nexin family member 21	Intracellular	-1.07	1.00e-20	Downregulated
TBL1X	Transducin beta like 1 X-linked	Intracellular	-0.68	1.00e-20	Downregulated
MASP1	MBL associated serine protease 1	Secreted, Intracellular	-1.39	1.08e-20	Downregulated
QKI	QKI, KH domain containing RNA binding	Intracellular	-0.62	1.08e-20	Downregulated
CNRIP1	Cannabinoid receptor interacting protein 1	Intracellular	-1.84	1.21e-20	Downregulated
DNASE2	Deoxyribonuclease 2, lysosomal	Intracellular	0.89	1.47e-20	Upregulated
SERPINA4	Serpin family A member 4	Secreted	-1.23	1.64e-20	Downregulated
FKBP7	FKBP prolyl isomerase 7	Intracellular	-1.1	1.99e-20	Downregulated
RTKN	Rhotekin	Intracellular	0.77	2.06e-20	Upregulated
PALM	Paralemmin	Intracellular	-1.58	2.14e-20	Downregulated
ZCCHC24	Zinc finger CCHC-type containing 24	Intracellular	-1.51	2.14e-20	Downregulated
HOXA11	Homeobox A11	Intracellular	-1.24	2.22e-20	Downregulated
CACNA2D1	Calcium voltage-gated channel auxiliary subunit alpha2delta 1	Membrane, Intracellular	-1.51	2.40e-20	Downregulated
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The uterine corpus endometrial carcinoma transcriptome

The transcriptome analysis shows that 74% (n=15012) of all human genes (n=20162) are expressed in uterine corpus endometrial carcinoma. All genes were classified according to the uterine corpus endometrial carcinoma-specific expression into one of five different categories, based on the ratio between mRNA levels in uterine corpus endometrial carcinoma compared to the mRNA levels in the other 16 analyzed cancer tissues.

Figure 2. The distribution of all genes across the five categories based on transcript abundance in uterine corpus endometrial carcinoma as well as in all other cancer tissues.

361 genes show some level of elevated expression in uterine corpus endometrial carcinoma compared to other cancers (Figure 1). The elevated category is further subdivided into three categories as shown in Table 3.

Table 4. The number of genes in the subdivided categories of elevated expression in uterine corpus endometrial carcinoma.

		Distribution in the 31 cancers
		Detected in single	Detected in some	Detected in many	Detected in all	Total
Specificity	Cancer enriched	12	6	13	5	36
	Group enriched	0	52	35	3	90
	Cancer enhanced	33	85	93	22	233
	Total	45	143	141	30	359

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 of 50 is also associated with an increased risk, as is receiving estrogen replacement therapy (without progesterone) or tamoxifen treatment, a common drug for the 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 adnexa, 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., A pathology atlas of the human cancer transcriptome. Science. (2017)
PubMed: 28818916 DOI: 10.1126/science.aan2507

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

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

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 - Endometrial cancer