The pancreatic cancer proteome - recent advances and future promise

Of the common cancers, pancreatic ductal adenocarcinoma is one of the most lethal. The cancer's aggressive biology, leading to rapid dissemination, combined with a lack of clearly recognisable symptoms means that for many patients, the disease is at an advanced stage when diagnosed. The prognosis is consequently very poor, with as few as 3-5% of patients surviving 5?years. Recently, proteomic technologies have been employed in an effort to identify protein biomarkers, therapeutic targets and disease response markers for pancreatic cancer. Research has primarily relied upon pancreatic tissue samples, and body fluids such as pancreatic juice and blood serum. In this article, we will highlight the current proteomic techniques, qualitative and quantitative, employed in the field of pancreatic cancer research. We will review both the progress made and the challenges ahead, in elaborating the biology of pancreatic cancer and identifying novel biomarkers.     

Searching for potential biomarkers of cisplatin resistance in human ovarian cancer using a label-free LC/MS-based protein quantification method

Platinum-based chemotherapy, such as cisplatin, is the primary treatment for ovarian cancer. However, drug resistance has become a major impediment to the successful treatment of ovarian cancer. To date, the molecular mechanisms of resistance to platinum-based chemotherapy remain unclear. In this study, we applied an LC/MS-based protein quantification method to examine the global protein expression of two pairs of ovarian cancer cell lines, A2780/A2780-CP (cisplatin-sensitive/cisplatin-resistant) and 2008/2008-C13*5.25 (cisplatin-sensitive/cisplatin-resistant). We identified and quantified over 2000 proteins from these cell lines and 760 proteins showed significant expression changes with a false discovery rate of less than 5% between paired groups. Based on the results we obtained, we suggest several potential pathways that may be involved in cisplatin resistance in human ovarian cancer. This study provides not only a new proteomic platform for large-scale quantitative protein analysis, but also important information for discovery of potential biomarkers of cisplatin resistance in ovarian cancer. Furthermore, these results may be clinically relevant for diagnostics, prognostics, and therapeutic improvement for ovarian cancer treatment.     

Utilizing endoscopic technology to reveal real-time proteomic alterations in response to chemoprevention

Cancer chemoprevention approaches use either pharmacological or dietary agents to impede, arrest or reverse the carcinogenic process. Although several agents have shown effectiveness against colon cancer, present intervention strategies provide only partial reduction. In this study, we utilized high-resolution endoscopy to obtain colon tumor biopsy specimens from Apc mutant mice before and after 2-wk sulindac intervention. To acquire information beyond genomics, proteome analysis using the ProteomeLab PF2D platform was implemented to generate 2-D protein expression maps from biopsies. Chromatograms produced common signature profiles between sulindac and nonsulindac treated samples, and contrasting profiles termed "fingerprints". We selected a double peak that appeared in tumor biopsies from sulindac-treated mice. Further analyses using MS sequencing identified this protein as histone H2B. The location of H2B in the 1(st) dimension strongly suggested PTM, consistent with identification of two oxidized methionines. While further studies on sulindac proteomic fingerprints are underway, this study demonstrates the feasibility and advantages of "real-time" proteomic analysis for obtaining information on biomarker discovery and drug activity that would not be revealed by a genetic assay. This approach should be broadly applicable for assessing lesion responsiveness in a wide range of translational and human clinical studies.     

Analysis of the HLA class I associated peptide repertoire in a hepatocellular carcinoma cell line reveals tumor-specific peptides as putative targets for immunotherapy

HLA class I molecules present peptides on the cell surface to CD8(+) T cells. The repertoire of peptides that associate to class I molecules represents the cellular proteome. Therefore, cells expressing different proteomes could generate different class I-associated peptide repertoires. A large number of peptides have been sequenced from HLA class I alleles, mostly from lymphoid cells. On the other hand, T cell immunotherapy is a goal in the fight against cancer, but the identification of T cell epitopes is a laborious task. Proteomic techniques allow the definition of putative T cell epitopes by the identification of HLA natural ligands in tumor cells. In this study, we have compared the HLA class I-associated peptide repertoire from the hepatocellular carcinoma (HCC) cell line SK-Hep-1 with that previously described from lymphoid cells. The analysis of the peptide pool confirmed that, as expected, the peptides from SK-Hep-1 derive from proteins localized in the same compartments as in lymphoid cells. Within this pool, we have identified 12 HLA class I peptides derived from HCC-related proteins. This confirms that tumor cell lines could be a good source of tumor associated antigens to be used, together with MS, to define putative epitopes for cytotoxic T cells from cancer patients.     

Detection of colorectal adenoma and cancer based on transthyretin and C3a-desArg serum levels

Colorectal cancer is the second leading cause of cancer death, and it develops from benign colorectal adenomas in over 95% of patients. Early detection of these cancer precursors by screening tests and their removal can potentially eradicate more than 95% of colorectal cancers before they develop. To discover sensitive and specific biomarkers for improvement of pre‐clinical diagnosis of colorectal adenoma and cancer, we analysed in two independent studies (n = 87 and n = 83 patients) serum samples from colorectal cancer (stage III), colorectal adenoma and control patients using SELDI‐TOF‐MS. Extensive statistical analysis was performed to establish homogeneous patient groups based on their clinical data. Two biomarkers that were each able to distinguish control patients from either colorectal adenoma or colorectal cancer patients (p<0.001) were identified as transthyretin (pre‐albumin) and C3a‐desArg by MS/MS and were further validated by antibody‐based assays (radial immunodiffusion, ELISA). A combination of both proteins clearly indicated the presence of colorectal adenoma or carcinoma. Using a cut‐off of <0.225 g/L for transthyretin and >1974 ng/mL for C3a‐desArg, we found a sensitivity and specificity for colorectal adenoma of 96% and 70%, respectively.     

Subacute proteome changes following traumatic injury of the developing brain: Implications for a dysregulation of neuronal migration and neurite arborization

Traumatic brain injury (TBI) is a major cause of morbidity and mortality among children and adolescents. To gain insight into developmental events influenced by TBI, we analyzed subacute mouse brain proteome changes in a percussion head trauma model at P7 ipsi- and contralateral to the site of injury. The comparison of brain proteomes of trauma mice and controls revealed reproducible changes in the intensity of 28 proteins (30 protein spots) in response to trauma. The changes detected suggest that TBI leads to apoptosis, inflammation, and oxidative stress. These changes were consistent with our results of histological and biochemical evaluation of the brains which revealed widespread apoptotic neurodegeneration, microglia activation, and increased levels of protein carbonyls. Furthermore, we detected changes in proteins involved in neuronal migration as well as axonal and dendritic growth and guidance, suggesting interference of trauma with these developmental events.     

Scanning electron microscopic observations on micro-organisms in the root nodules of Tribulus terrestris L. (Zygophyllaceae)

Scanning electron microscopic observations were made on the micro-organisms of root nodules of Tribulus terrestris L. The results showed that nodules of T. terrestris contained dual infection consisting of Rhizobium sp. and Newmania karachiensis. Based on these observations, T. terrestris should be grouped with nonlegume Parasponia-type bacterial nodules.     

Prospective memory failures as an unexplored threat to patient safety: results from a pilot study using patient simulators to investigate the missed execution of intentions

This study investigated failures of prospective memory (PM) as a relevant but neglected error type in medicine. A patient simulator was used to investigate PM failures. The influence of subjective importance (high, low) and type of intention (educational, internal, external) on the (missed) execution of intention was investigated in a 2 x 2 design. The effects on missed executions by importance (high < low) and type of intention (educational < external < internal) were hypothesized. Of 73 valid intentions in 40 prepared simulator scenarios 19 (26%) were missed overall. A total of 64% of unimportant and 80% of important intentions were executed 79% of educational 67% of external and 72% of internal intentions were executed. Neither difference was statistically significant using chi(2) tests. Interaction was significant for missed executions (p = 0.025; n = 19; df = 2; chi(2) = 7.41) and for executions (p = 0.002; n = 54; df = 2; chi(2) = 12.50). Despite low statistical support and some methodological limitations, it was possible to show that PM failures are relevant to patient safety and that patient simulators are a suitable but so far unused tool for their investigation.