The pancreatic adenocarcinoma proteome

Pancreatic cancer is the 11th most common cancer globally and is associated with poor prognosis. Estimated 5- year survival rate is less than 5% and pancreatic cancer accounts for 4% of all deaths that occur worldwide each year. The risk of pancreatic cancer increases with age and the tumor is slightly more common in women than in men. Most patients suffering from pancreatic cancer are above 50 years of age and pain, jaundice and weight loss are the most common symptoms. The cause of pancreatic cancer is unknown. However, pancreatic cancer is more common in people with diabetes and chronic pancreatitis (persistent inflammation in the pancreas) as well as in tobacco smokers.

Pancreatic exocrine tumors are the most common form of pancreatic cancer, accounting for 95% of cases, with ductal adenocarcinoma being the most prevalent exocrine cancer. Pancreatic endocrine tumors constitute the remaining 5% of reported cases. Due to diffuse symptoms, pancreatic cancer is often detected at such a late stage of the disease that curative surgery is not possible. In addition to local spread in the pancreas and surrounding tissues, pancreatic cancer often spreads to regional lymph nodes and to the liver. Over 80% of all patients have metastasis at the time of diagnosis.

Here, we explore the pancreatic adenocarcinoma proteome using TCGA transcriptomics data and antibody-based protein data. 2436 genes are suggested as prognostic based on transcriptomics data from 176 patients; 1794 genes are associated with unfavorable prognosis and 662 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, with 80 female patients and 96 male patients. 84 patients were alive and 92 patients were deceased at the time of data collection. The stage distribution was stage i) 21 patients, stage ii) 145 patients, stage iii) 3 patients, stage iv) 4 patients and 3 patients with missing stage information.

Unfavorable prognostic genes in pancreatic adenocarcinoma

For unfavorable genes, higher relative expression levels at diagnosis give significantly lower overall survival for the patients. There are 1794 genes associated with an unfavorable prognosis in pancreatic adenocarcinoma, among these potential prognostic genes there are 134 genes that were validated in a separate study. In Table 1, the top 20 most significant genes related to an unfavorable prognosis are listed.

MUC1 is a gene associated with unfavorable prognosis in pancreatic adenocarcinoma. The best separation is achieved by an expression cutoff at 348 TPM which divides the patients into two groups with 17% 5-year survival for patients with high expression versus 58% for patients with low expression, p-value: 4.44e-4. MUC1 encodes the protein Mucin 1, a cell surface associated protein. It creates a barrier on the surface of epithelial cells to serve as protection against pathogens and harmful molecules. A tumor-associated form is overexpressed in epithelial cancers and plays an important role in tumor progression. Unlike normal cells, cancer cells lack cell-polarity and therefore this protein is distributed in the cytoplasm of cancer cells. Immunohistochemical staining using an antibody targeting MUC1 (CAB000036) shows a differential expression pattern in pancreatic adenocarcinoma samples.

p<0.001
MUC1 - survival analysis
MUC1 - high expression
MUC1 - low expression

ITGA2 is another gene associated with an unfavorable prognosis in pancreatic adenocarcinoma in two separate independent cohorts. The best separation is achieved by an expression cutoff at 13 TPM which divides the patients into two groups with 14% 5-year survival for patients with high expression versus 53% for patients with low expression, p-value: 5.59e-5. The TCGA data analysis was validated in a separate study with the p-value: 7.65e-4. Immunohistochemical staining using an antibody targeting ITGA2 (HPA063556) shows a differential expression pattern in pancreatic adenocarcinoma samples.

p<0.001
ITGA2 - survival analysis
ITGA2 - high expression
ITGA2 - low expression

Table 1. The 20 genes with highest significance associated with an unfavorable prognosis in pancreatic adenocarcinoma.

Favorable prognostic genes in pancreatic adenocarcinoma

For favorable genes, higher relative expression levels at diagnosis give significantly higher overall survival for the patients. There are 662 genes associated with a favorable prognosis in pancreatic adenocarcinoma, among these potential prognostic genes there are 4 genes that were validated in a separate study. In Table 2, the top 20 most significant genes related to a favorable prognosis are listed.

PELP1 is a gene associated with a favorable prognosis in pancreatic adenocarcinoma. The best separation is achieved by an expression cutoff at 17 TPM which divides the patients into two groups with 49% 5-year survival for patients with high expression versus 11% for patients with low expression, p-value: 1.73e-4. The PELP1 gene encodes the Proline, glutamic acid- and leucine-rich protein 1. It is involved in transcription regulation by interacting with nuclear hormone receptors and transcription factors. These genes include estrogen alpha and also genes implicated in tumor development, invasiveness and metastasis. Immunohistochemical staining using an antibody targeting PELP1 (HPA060760) shows a differential expression pattern in pancreatic adenocarcinoma samples.

p<0.001
PELP1 - survival analysis
PELP1 - high expression
PELP1 - low expression

CFAP410 is another gene associated with a favorable prognosis in pancreatic adenocarcinoma in two separate independent cohorts. The best separation is achieved by an expression cutoff at 13 TPM which divides the patients into two groups with 59% 5-year survival for patients with high expression versus 13% for patients with low expression, p-value: 3.80e-5. The TCGA data analysis was validated in a separate study with the p-value: 1.23e-4. Immunohistochemical staining using an antibody targeting CFAP410 (HPA030284) shows a differential expression pattern in pancreatic adenocarcinoma samples.

p<0.001
CFAP410 - survival analysis
CFAP410 - high expression
CFAP410 - low expression

Table 2. The 20 genes with highest significance associated with a favorable prognosis in pancreatic adenocarcinoma.

CPTAC relative protein expression data

Proteins that are significantly down- or upregulated in pancreatic adenocarcinoma 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 145 tumor samples and 90 normal samples.

In pancreatic adenocarcinoma, 2227 and 2293 genes are down- (blue) and upregulated (red) compared to normal tissue, respectively. In Table 3, the top 20 most significant genes are listed.

Table 3. The 20 genes with the highest significance associated with a downregulated or upregulated protein expression in pancreatic adenocarcinoma compared to normal tissue.

The pancreatic adenocarcinoma transcriptome

The transcriptome analysis shows that 71% (n=14320) of all human genes (n=20162) are expressed in pancreatic adenocarcinoma. All genes were classified according to the pancreatic adenocarcinoma-specific expression into one of five different categories, based on the ratio between mRNA levels in pancreatic adenocarcinoma 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 pancreatic adenocarcinoma as well as in all other cancer tissues.

242 genes show some level of elevated expression in pancreatic adenocarcinoma 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 pancreatic adenocarcinoma.

Additional information

Most patients with pancreatic cancer displayed diffuse symptoms which poses a major obstacle for early detection. Moreover, imaging techniques and biopsy often give inconclusive results due to malign lesions being indistinguishable from chronic pancreatitis or benign cysts. There is a great need for biomarkers to facilitate early detection and help the establishment of a diagnosis. The only currently available treatment for pancreatic cancer is surgical resection. However, less than 25% of all patients have tumors that are eligible for resection at the time of diagnosis.

Ductal adenocarcinomas are poorly differentiated tumors that are characterized by atypical cells forming irregular, often complex tubular or glandular structures, embedded in dense tumor stroma. Two-thirds of tumors arise in the head of the pancreas. This type of pancreatic cancer grows rapidly and has often spread beyond the pancreas at the time of diagnosis. It is often accompanied by chronic pancreatitis showing infiltrates of inflammatory cells, fibrosis and atrophy of normal exocrine pancreatic structures. Tumor cells vary in shape and size of nuclei, often with distinct nucleoli. Ductal carcinomas are classified as well, moderately or poorly differentiated dependent on morphology. The degree of differentiation may vary within a tumor so that occasional anaplastic foci of the tumor can be present within an otherwise well-differentiated ductal carcinoma. The differentiation grade has not proven helpful for predicting prognosis and likewise has staging only limited value since the vast majority of patients have an advanced stage of the disease when diagnosed. Immunohistochemical analysis shows that most cases of ductal adenocarcinomas show expression of CK7 and are also positive for CK8, CK17, CK18, CK19, CEA, CA19-9, Dupan-2, MUC1, MUC4 and MUC5AC.

Pancreatic endocrine tumors (PETs) are categorized clinically as either "functioning" or "non-function" depending on whether there are any symptoms indicating elevated hormone production. Around 40 % of PETs are classified as "non-functioning" and these tumors may still produce hormones detectable by immunohistochemistry or blood samples despite lack of symptoms. These lesions are often noticed by clinicians once they have reached a size that affects other organs in the vicinity or when they metastasize. These tumors are classified according to WHO classification into three categories based on size, mitotic count, Ki-67 proliferation index, angioinvasion and metastasis. Cells in PETs are typically round with granular pattern in cytoplasm and chromatin pattern in nuclei. Synaptophysin and chromogranin are used for identifying neuroendocrine differentiation in cancers.

In addition to the typical ductal carcinoma, there are uncommon variants of pancreatic cancer, including adenosquamous carcinoma, mucinous carcinoma, papillary carcinoma and acinar cell carcinoma. Mucinous cystadenocarcinoma and tumors corresponding to the endocrine compartment of the pancreas also exist with various symptoms, microscopical features and often less severe prognosis.

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

Danielsson A et al., The human pancreas proteome defined by transcriptomics and antibody-based profiling. PLoS One. (2014)
PubMed: 25546435 DOI: 10.1371/journal.pone.0115421

Histology dictionary - Pancreatic cancer