The prostate cancer proteome


Prostate cancer is one of the most common malignancies in men. In 2015, the incidence of prostate cancer in Sweden was more than 10 000, and in the US 160 000 new cases are estimated in 2017. The vast majority of primary prostate cancer cases are adenocarcinomas, and the cancers often show characteristics such as multifocality and differentiation pattern heterogeneity. The rate of prostate tumor growth varies and is often low. Since the median age at diagnosis is high (65-70 years), most patients, especially those with localized tumors, often die of other complications without ever having suffered significant disability from the cancer. Approximately 15% of patients with prostate cancer are in high-risk of disease-related symptoms and death. However, certain patients may have prolonged survival even after the cancer has metastasized to distant sites. Prostate cancer is often stimulated by hormones (androgens) and anti-hormonal therapies can be effective to limit and slow down tumor growth, while radical prostatectomy is an option for treating localized prostate cancer.

Both normal prostatic glands and prostate cancer cells express the protein PSA (encoded by the gene KLK3) and detection of elevated levels of PSA in the blood is today heavily used as a screening tool to detect the growth of prostate cancer. Prostate cancer can be diagnosed using rectal examination (palpation), and histological examinations of tissue biopsies using the Gleason Grade scoring system, where dominant histological characteristics of the cancer cells are used in order to determine the cancer stage. Immunostaining of relevant molecular markers is also important.

Here, we explore the prostate cancer proteome using TCGA transcriptomics data and antibody based protein data. 159 genes are suggested as prognostic based on transcriptomics data from 494 patients; 134 genes associated with unfavourable prognosis and 25 genes associated with favourable prognosis.

TCGA data analysis


In this metadata study we used data from TCGA where transcriptomics data was available from 494 male patients with prostate adenocarcinoma in total. Most of the patients (484 patients) were still alive at the time of data collection. Information on stage distribution was missing.

Unfavourable prognostic genes in prostate cancer


For unfavourable genes, higher relative expression levels at diagnosis gives significantly lower overall survival for the patients. There are 134 genes associated with unfavourable prognosis in prostate cancer. In Table 1, the top 20 most significant genes related to unfavourable prognosis are listed.

ODF2 is a gene associated with unfavourable prognosis in prostate cancer. The best separation is achieved by an expression cutoff at 10.4 fpkm which divides the patients into two groups with 99% 5-year survival for patients with high expression versus 93% for patients with low expression, p-value: 1.72e-4. The Outer dense fiber protein 2 is encoded by the ODF2 gene and is a major structural component of sperm tail. Previous reports has shown that ODF2 may be a crucial component of the microtubule organizing center. Defects in this gene have been linked to infertility and abnormal sperm morphology. Immunohistochemical staining using an antibody targeting ODF2 (HPA001874) shows differential expression pattern in prostate cancer samples.

ODF2 - survival analysis p<0.001
ODF2 - high expression
ODF2 - low expression

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

Gene Description Predicted localization mRNA (cancer) p-value
MBD1 methyl-CpG binding domain protein 1 Intracellular 7.6 1.70e-6
TEX30 testis expressed 30 Intracellular 1.9 2.10e-6
ZNF330 zinc finger protein 330 Intracellular 11.7 3.66e-6
USP53 ubiquitin specific peptidase 53 Intracellular 2.4 7.54e-6
ZNF654 zinc finger protein 654 Intracellular 3.7 9.97e-6
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Favourable prognostic genes in prostate cancer


For favourable genes, higher relative expression levels at diagnosis gives significantly higher overall survival for the patients. There are 25 genes associated with favourable prognosis in prostate cancer. In Table 2, the top 20 most significant genes related to favourable prognosis are listed.

ATP6V1E1 is a gene associated with favourable prognosis in prostate cancer. The best separation is achieved by an expression cutoff at 33.1 fpkm which divides the patients into two groups with 100% 5- year survival for patients with high expression versus 95% for patients with low expression, p-value: 4.18e-4. The ATP6V1E1 gene encodes a multi-subunit enzyme important for acidification of organelles in eukaryotic cells. This process is deemed necessary for intracellular mechanisms such as protein sorting, zymogen activation and receptor-mediated endocytosis. Immunohistochemical staining using an antibody targeting ATP6V1E1 (HPA029196) shows differential expression pattern in prostate cancer samples.

ATP6V1E1 - survival analysis p<0.001
ATP6V1E1 - high expression
ATP6V1E1 - low expression

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

Gene Description Predicted localization mRNA (cancer) p-value
CRACR2A calcium release activated channel regulator 2A Intracellular 1.6 2.85e-6
TMEM158 transmembrane protein 158 (gene/pseudogene) Membrane 6.7 6.43e-5
EPHX1 epoxide hydrolase 1 Intracellular 73.3 1.32e-4
TSKU tsukushi, small leucine rich proteoglycan Secreted 16.9 1.66e-4
AOC1 amine oxidase, copper containing 1 Secreted 5.7 1.71e-4
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The prostate cancer transcriptome


The transcriptome analysis shows that 69% (n=13484) of all human genes (n=19479) are expressed in prostate cancer. All genes were classified according to the prostate cancer-specific expression into one of five different categories, based on the ratio between mRNA levels in prostate cancer compared to the mRNA levels in the other 16 analyzed cancer tissues. 220 genes show some level of elevated expression in prostate 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 prostate cancer as well as in all other cancer tissues.

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

Category Number of genes Description
Tissue enriched 55 At least five-fold higher mRNA levels in a particular cancer as compared to all other cancers
Group enriched 84 At least five-fold higher mRNA levels in a group of 2-7 cancers
Tissue enhanced 81 At least five-fold higher mRNA levels in a particular cancer as compared to average levels in all cancers
Total 220 Total number of elevated genes in prostate cancer

Additional information


Prostate carcinomas are classified using the Gleason grade (Modified Gleason Grading System). The Gleason grade is a system of characterizing prostate cancer tissue based on the microscopical pattern of growth. The Gleason grade ranges from 1 to 5. Grade 1 is not used in clinical practice as it is impossible to distinguish grade 1 from adenosis and it is considered to lack malignant potential. Gleason grades corresponding to the two dominating growth patterns in a prostate cancer are combined to provide the Gleason score and consequently, Gleason scores range from 4 (2+2) to 10 (5+5). The Gleason score is correlated to the risk of tumor spread and a low Gleason score reflects a more well differentiated tumor, while a high Gleason score corresponds to more poorly differentiated tumors. A tumor with Gleason score of 4 is least likely, and tumor with score of 10 is most likely to spread beyond the prostate.

Grade 1 tumors are small, uniform, well-differentiated, closely packed, and consist of glands in essentially circumscribed masses. In Grade 2 there is a moderate variation in size and shape of glands and more atypia in individual cells. A cribriform pattern may be present - still essentially circumscribed - but more loosely arranged. Grade 3 tumors show marked irregularity in size and shape of glands, with tiny glands/individual cells invading into the stroma. Solid cords and masses (papillary or cribriform), with easily distinguishable glandular differentiation, vary in size and may be quite large, but the essential feature is a smooth and usually rounded edge around all the circumscribed masses of tumor. In Grade 4, tumor cells grow in a diffuse pattern and may show gland formation, however, glands are not single and separate, but coalesce and branch. Grade 5 tumors are poorly differentiated, usually presenting solid masses or diffuse growth with little or no differentiation into glands or with a few tiny glands or signet ring cells.

Immunohistochemistry using antibodies towards PSA can be used to discriminate prostate cancer from other forms of cancer. Immunohistochemistry is also important to delineate the two cell types in benign prostatic ducts and acini. The superficial layer is the secretory epithelium, beneath which there is a layer of continuous basal cells in normal glands. Sparse interspersed endocrine-paracrine cells are also present. The basal cells are useful for histological diagnosis as their presence confirms that the acinus is benign. The basal cells stain positive for p63 and high-molecular weight keratins. Malignant prostatic acini do not display basal cells and are identified using other immunohistochemistry markers such asAMACR/P504S.

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

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

O'Hurley G et al, 2015. Analysis of the Human Prostate-Specific Proteome Defined by Transcriptomics and Antibody-Based Profiling Identifies TMEM79 and ACOXL as Two Putative, Diagnostic Markers in Prostate Cancer. PLoS One.
PubMed: 26237329 DOI: 10.1371/journal.pone.0133449

Histology dictionary - Prostate cancer