Proteomic methodologies and their application in colorectal cancer research

A review of the zone broadening contributions in free-flow electrophoresis

The broadening of analyte streams, as they migrate through a free-flow electrophoresis (FFE) channel, often limits the resolving power of FFE separations. Under laminar flow conditions, such zonal spreading occurs due to analyte diffusion perpendicular to the direction of streamflow and variations in the lateral distance electrokinetically migrated by the analyte molecules. Although some of the factors that give rise to these contributions are inherent to the FFE method, others originate from non-idealities in the system, such as Joule heating, pressure-driven crossflows, and a difference between the electrical conductivities of the sample stream and background electrolyte. The injection process can further increase the stream width in FFE separations but normally influencing all analyte zones to an equal extent. Recently, several experimental and theoretical works have been reported that thoroughly investigate the various contributions to stream variance in an FFE device for better understanding, and potentially minimizing their magnitudes. In this review article, we carefully examine the findings from these studies and discuss areas in which more work is needed to advance our comprehension of the zone broadening contributions in FFE assays.

Mining the fecal proteome: from biomarkers to personalised medicine

INTRODUCTION

Fecal proteomics has gained increased prominence in recent years. It can provide insights into the diagnosis and surveillance of many bowel diseases by both identifying potential biomarkers in stool samples and helping identify disease-related pathways. Fecal proteomics has already shown its potential for the discovery and validation of biomarkers for colorectal cancer screening, and the analysis of fecal microbiota by MALDI-MS for the diagnosis of a range of bowel diseases is gaining clinical acceptance. Areas covered: Based on a comprehensive analysis of the current literature, we introduce the range of sensitive and specific proteomics methods which comprise the current 'Proteomics Toolbox', explain how the integration of fecal proteomics with data processing/bioinformatics has been used for the identification of potential biomarkers for both CRC and other gut-related pathologies and analysis of the fecal microbiome, outline some of the current fecal assays in current clinical practice and introduce the concept of personalised medicine which these technologies will help inform. Expert commentary: Integration of fecal proteomics with other proteomics and genomics strategies as well as bioinformatics is paving the way towards personalised medicine, which will bring with it improved global healthcare.

Antibody-based proteomics and biomarker research - current status and limitations

Antibody-based proteomics play a very important role in biomarker discovery and validation, facilitating the high-throughput evaluation of candidate markers. Most proteomics-driven discovery is nowadays based on the use of MS. MS has many advantages, including its suitability for hypothesis-free biomarker discovery, since information on protein content of a sample is not required prior to analysis. However, MS presents one main caveat which is the limited sensitivity in complex samples, especially for body fluids, where protein expression covers a huge dynamic range. Antibody-based technologies remain the main solution to address this challenge since they reach higher sensitivity. In this article, we review the benefits and limitations of antibody-based proteomics in preclinical and clinical biomarker research for discovery and validation in body fluids and tissue. The combination of antibodies and MS, utilizing the best of both worlds, opens new avenues in biomarker research.

Proteomics, genomics and transcriptomics: their emerging roles in the discovery and validation of colorectal cancer biomarkers

Colorectal cancer (CRC) is the second most common cancer in females and the third in males. Since CRC is often diagnosed at an advanced stage when prognosis is poor, identification of biomarkers for early diagnosis is urgently required. Recent advances in proteomics, genomics and transcriptomics have facilitated high-throughput profiling of data generated from CRC-related genes and proteins, providing a window of information for biomarker discovery and validation. However, transfer of candidate biomarkers from bench to bedside remains a dilemma. In this review, we will discuss emerging proteomic technologies and highlight various sample types utilized for proteomics-based identification of CRC biomarkers. Moreover, recent breakthroughs in genomics and transcriptomics for the identification of CRC biomarkers, with particular emphasis on the merits of emerging methylomic and miRNAomic strategies, will be discussed. Integration of proteomics, genomics and transcriptomics will facilitate the discovery and validation of CRC biomarkers leading to the emergence of personalized medicine.

Differential proteomics identifies PDIA3 as a novel chemoprevention target in human colon cancer cells

Chemoprevention offers a promising strategy to prevent or delay the development of various cancers. Critical to this approach is the identification of molecular targets that may track with chemopreventive efficacy. To address this issue, we screened a panel of chemoprevention agents, including resveratrol, epigallocatechin-3-gallate, ursodeoxycholic acid, and sulindac sulfide for their effects on human colon cancer cell viability. Resveratrol elicited the most potent effect in HCT116 cells and was selected for further study. Proteomic PF 2D maps were generated from HCT116 cells treated with resveratrol versus vehicle alone. Analysis of proteomic maps using tandem mass spectrometry (MS) identified a panel of differentially modified proteins. Two proteins, actin and Hsp60, were previously shown in other cell culture systems to be affected by resveratrol, validating our approach. PDIA3, RPL19, histone H2B and TCP1β were uniquely identified by our proteomic discovery platform. PDIA3 was of particular interest given its potential role in regulating chemosensitivity of cancer cells. Total levels of PDIA3 in HCT116 cells were unchanged following 24 h of resveratrol treatment, confirmed by Western blot analysis. Immunoprecipitation of PDIA3 revealed a new set of client proteins following resveratrol treatment, including α, β, and δ-catenins, and cellular fractionation identified decreased nuclear localization of α-catenin by resveratrol. These data establish differential proteomic mapping as a powerful tool for identifying novel molecular targets of chemopreventive agents.

Serum peptidome patterns of colorectal cancer based on magnetic bead separation and MALDI-TOF mass spectrometry analysis

Background. Colorectal cancer (CRC) is one of the most common cancers in the world, identification of biomarkers for early detection of CRC represents a relevant target. The present study aims to determine serum peptidome patterns for CRC diagnosis. Methods. The present work focused on serum proteomic analysis of 32 health volunteers and 38 CRC by ClinProt Kit combined with mass spectrometry. This approach allowed the construction of a peptide patterns able to differentiate the studied populations. An independent group of serum (including 33 health volunteers, 34 CRC, 16 colorectal adenoma, 36 esophageal carcinoma, and 31 gastric carcinoma samples) was used to verify the diagnostic and differential diagnostic capability of the peptidome patterns blindly. An immunoassay method was used to determine serum CEA of CRC and controls. Results. A quick classifier algorithm was used to construct the peptidome patterns for identification of CRC from controls. Two of the identified peaks at m/z 741 and 7772 were used to construct peptidome patterns, achieving an accuracy close to 100% (>CEA, P < 0.05). Furthermore, the peptidome patterns could differentiate validation group with high accuracy. Conclusions. These results suggest that the ClinProt Kit combined with mass spectrometry yields significantly higher accuracy for the diagnosis and differential diagnosis of CRC.

Diagnosis of colorectal cancer by MALDI-TOF-MS combined with WCX magnetic beads

AIM: To explore the difference in serum proteomic spectra between patients with colorectal cancer and healthy individuals, and to identify the specific protein biomarkers.

METHODS: Serum samples collected from 67 colorectal cancer patients and 66 healthy individuals were randomized into model construction group and validation group. Magnetic beads-based weak cation exchange (MB-WCX) kit and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) were used to profile serum proteome. Flex analysis software was used to analyze protein peaks for significant difference. A diagnostic model was then built using ClinproTools2.2software and evaluated blindly for reliability.

RESULTS: Thirty-three differentially expressed proteins in serum were screened between colorectal cancer patients and healthy individuals, including 25 up-regulated proteins and 8 down-regulated ones. Five proteins (759, 3316, 4645, 4248, and 2645 Dr) were used for building a ClinProt model which was able to classify colorectal cancer patients and healthy individuals with a sensitivity of 94.12% (32/34) and a specificity of 96.97% (32/33). A double blind validation test showed that the ClinProt model yielded a sensitivity of 93.94 (31/33) and a specificity of 96.97% (32/33).

CONCLUSION: Combination of MALDI-TOF-MS with WCX kit allows to directly screen proteins differentially expressed in the serum of patients with colorectal cancer, and these proteins can be used to diagnose early-stage colorectal cancer.

Identification of key players for colorectal cancer metastasis by iTRAQ quantitative proteomics profiling of isogenic SW480 and SW620 cell lines

This study compared the whole cell proteome profiles of two isogenic colorectal cancer (CRC) cell lines (primary SW480 cell line and its lymph node metastatic variant SW620), as an in vitro metastatic model, to gain an insight into the molecular events of CRC metastasis. Using iTRAQ (isobaric tags for relative and absolute quantitation) based shotgun proteomics approach, we identified 1140 unique proteins, out of which 147 were found to be significantly altered in the metastatic cell. Ingenuity pathway analysis with those significantly altered proteins, revealed cellular organization and assembly as the top-ranked altered biological function. Differential expression pattern of 6 candidate proteins were validated by Western blot. Among these, the low expression level of β-catenin combined with the up-regulation of CacyBP (Calcyclin binding Protein), a β-catenin degrading protein, in the metastatic cell provided a rational guide for the downstream functional assays. The relative expression pattern of these two proteins was further validated in three other CRC cells by Western blot and quantitative immunofluorescence studies. Overexpression of CacyBP in three different primary CRC cell lines showed significant reduction in adhesion characteristics as well as cellular β-catenin level as confirmed by our experiments, indicating the possible involvement of CacyBP in CRC metastasis. In short, this study demonstrates successful application of a quantitative proteomics approach to identify novel key players for CRC metastasis, which may serve as biomarkers and/or drug targets to improve CRC therapy.

Janice Drew’s work on diet and cancer

Obesity and associated reduced consumption of plant derived foods are linked to increased risk of colon cancer as well as a number of other organ specific cancers. Inflammatory processes are a contributing factor but the precise mechanisms remain elusive. Obesity and cancer incidence are increasing worldwide, presenting bleak prospects for reducing, or preventing, obesity related cancers. The incidence of these preventable cancers can be achieved with greater understanding of the molecular mechanisms linking diet and carcinogenesis. Janice Drew has developed a research program over recent years to investigate molecular mechanisms related to consumption of anti-inflammatory metabolites generated from consumption of plant based diets, the impact of high fat diets and associated altered metabolism and obesity on regulation of colon inflammatory responses and processes regulating the colon epithelium. Comprehensive strategies have been developed incorporating transcriptomics, including the novel gene expression technology, the GenomeLab System and proteomics, together with biochemical analyses of plasma and tissue samples to assess correlated changes in oxidative stress, inflammation and pathology. The approaches developed have achieved success in establishing antioxidant and anti-inflammatory activity of dietary antioxidants and associated genes and pathways that interact to modulate redox status in the colon. Cellular processes and genes altered in response to obesity and high fat diets have provided evidence of molecular mechanisms that are implicated in obesity related cancer.

Significance of alanine aminopeptidase N (APN) in bile in the diagnosis of acute cellular rejection after liver transplantation

BACKGROUND

Allograft dysfunction after liver transplantation requires histopathologic examination for confirmation of the diagnosis, however, the procedure is invasive and its interpretation is not always accurate. The aim of this study was to find novel protein markers in bile for the diagnosis of acute cellular rejection (ACR) after liver transplantation.

MATERIALS AND METHODS

Quantitative proteomic analysis using the (18)O labeling method was used to search for bile proteins of interest. Nine recipients were selected who had liver dysfunction, diagnosed by liver biopsy, either with ACR (ACR group, n = 5) or without (LD group, n = 4). Donor bile samples were obtained from nine independent live liver donors. Enzyme activity in bile samples was assayed and liver biopsy specimens were immunostained for candidate protein of ACR.

RESULTS

The analysis identified 78 proteins, among which alanine aminopeptidase N (APN/CD13) was considered a candidate marker of ACR. Comparative analysis of the ACR and LD groups showed high APN enzyme activity in three (60%) of five cases of the ACR group, while it was as low as donor level in all patients of the LD group. APN enzyme activity in bile samples of liver dysfunction liver transplantation (LDLT) recipients of the ACR group collected within 3 d before biopsy-confirmed ACR (n = 10) was significantly higher (584 ± 434 U/g protein) than in those of recipients free of ACR (n = 96, 301 ± 271 U/g protein) (P = 0.004). APN overexpression along bile canaliculi was observed during ACR in all five cases of the ACR group.

CONCLUSION

APN in bile seems to be a useful and noninvasive biomarker of ACR after liver transplantation.

Cell surface markers in colorectal cancer prognosis

The classification of colorectal cancers (CRC) is currently based largely on histologically determined tumour characteristics, such as differentiation status and tumour stage, i.e., depth of tumour invasion, involvement of regional lymph nodes and the occurrence of metastatic spread to other organs. These are the conventional prognostic factors for patient survival and often determine the requirement for adjuvant therapy after surgical resection of the primary tumour. However, patients with the same CRC stage can have very different disease-related outcomes. For some, surgical removal of early-stage tumours leads to full recovery, while for others, disease recurrence and metastasis may occur regardless of adjuvant therapy. It is therefore important to understand the molecular processes that lead to disease progression and metastasis and to find more reliable prognostic markers and novel targets for therapy. This review focuses on cell surface proteins that correlate with tumour progression, metastasis and patient outcome, and discusses some of the challenges in finding prognostic protein markers in CRC.

The discovery and validation of colorectal cancer biomarkers

Colorectal cancer is currently the third most common malignancy in the world. Patients have excellent prognosis following surgical resection if their tumour is still localized at diagnosis. By contrast, once the tumour has started to metastasize, prognosis is much poorer. Accurate early detection can therefore significantly reduce the mortality from this disease. However, current tests either lack the required sensitivity and selectivity or are costly and invasive. Improved biomarkers, or panels of biomarkers, are therefore urgently required. We have addressed current screening strategies and potential protein biomarkers that have been proposed. The role of both discovery and hypothesis-driven proteomics approaches for biomarker discovery and validation is discussed. Using such approaches we show how multiple reaction monitoring (MRM) can be successfully developed and used for quantitative multiplexed analysis of potential faecal biomarkers.

Proteomic serum biomarkers and their potential application in cancer screening programs

Early diagnosis of cancer is of pivotal importance to reduce disease-related mortality. There is great need for non-invasive screening methods, yet current screening protocols have limited sensitivity and specificity. The use of serum biomarkers to discriminate cancer patients from healthy persons might be a tool to improve screening programs. Mass spectrometry based proteomics is widely applied as a technology for mapping and identifying peptides and proteins in body fluids. One commonly used approach in proteomics is peptide and protein profiling. Here, we present an overview of profiling methods that have the potential for implementation in a clinical setting and in national screening programs.

SELDI-TOF serum proteomics and colorectal cancer: a current overview

Surface enhanced laser desorption/ionization time-of-flight mass spectrometry (SELDI-TOF-MS) is a widely used technology platform for diagnostic biomarker discovery in tissue, plasma and serum. High-throughput and simplicity of experimental procedures have allowed this technology to become an important research tool for biomarker discovery during the last years. This review provides an overview of SELDI-TOF functionality, its advantages and drawbacks and gives a current literature overview of colorectal cancer based serum biomarker detection. Further improvements in instrumentation sensitivity and labelling chemistries will enable detection of novel, tissue-leakage biomarkers in serum. However, major emphasis should be given on subsequent identification of differentially observed protein peaks detected by SELDI-TOF. Clinical validation in large patient cohorts will then allow transferring novel biomarkers into clinical use.