Abstract
Pancreatic cancer accounts for 2.8% of new cancer cases worldwide and is projected to become the second leading cause of cancer-related deaths by 2030. Patients of African ancestry appear to be at an increased risk for pancreatic ductal adenocarcinoma (PDAC), with more severe disease and outcomes. The purpose of this study was to map the proteomic and genomic landscape of a cohort of PDAC patients of African ancestry. Thirty tissues (15 tumours and 15 normal adjacent tissues) were obtained from consenting South African PDAC patients. Optimisation of the sample preparation method allowed for the simultaneous extraction of high-purity protein and DNA for SWATH-MS and OncoArray SNV analyses. We quantified 3402 proteins with 49 upregulated and 35 downregulated proteins at a minimum 2.1 fold change and FDR adjusted p-value (q-value) ≤ 0.01 when comparing tumour to normal adjacent tissue. Many of the upregulated proteins in the tumour samples are involved in extracellular matrix formation (ECM) and related intracellular pathways. In addition, proteins such as EMIL1, KBTB2, and ZCCHV involved in the regulation of ECM proteins were observed to be dysregulated in pancreatic tumours. Downregulation of pathways involved in oxygen and carbon dioxide transport were observed. Genotype data showed missense mutations in some upregulated proteins, such as MYPN, ESTY2 and SERPINB8. Approximately 11% of the dysregulated proteins, including ISLR, BP1, PTK7 and OLFL3, were predicted to be secretory proteins. These findings help in further elucidating the biology of PDAC and may aid in identifying future plausible markers for the disease.
Highlights
Pancreatic ductal adenocarcinoma (PDAC) accounts for 85% of all pancreatic cancers
We have identified significantly dysregulated proteins in resected pancreatic ductal adenocarcinoma tumours obtained from patients of African ancestry using SWATH-mass spectrometry (MS)
Many of these proteins are involved in cell proliferation and in the extracellular matrix formation/organisation, which plays a role in tumour progression and chemo-resistance
Summary
Pancreatic ductal adenocarcinoma (PDAC) accounts for 85% of all pancreatic cancers. Worldwide, the incidence and mortality rates of PDAC are rising compared to other cancers [1]. The survival rate is dismal, with a five-year survival rate of 8% [2]. These poor statistics are due to late detection, allowing for invasion and metastasis of cancer, and therapeutic resistance. In multiracial countries such as the United States of America, African Americans have increased incidence and poorer survival rates compared to other ethnicities. This has been largely attributed to social factors such as smoking, alcohol consumption, obesity and diabetes mellitus, current studies have determined genetics as an underlying factor [3,4,5]
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