Beruflich Dokumente
Kultur Dokumente
Received 20 August 2010, Accepted 23 August 2010 Published online in Wiley Online Library: 6 November 2010
Introduction
Unfortunately colorectal cancer (CRC) is very common in the Western world and is a signicant cause of morbidity and mortality. A 6% lifetime risk of developing CRC (Davies et al., 2005) translates into it being the third most common malignancy in the world (Parkin et al., 2001). In Australia, it is the second most commonly diagnosed malignancy in both males and females, as well as the second highest cause of cancer-related death (Young, 2009). However, CRC is potentially curable if detected early. Patients treated by surgical resection of their tumour when the tumour is still localized to the colon or rectum (Dukes Stage A) have a 5 year survival rate of >90% (White and Miller, 2007). By stark contrast, patients with Dukes Stage D cancer at presentation, where the tumour has metastasized to other organs, have a 5 year survival rate of <10% (Altekruse et al., 2009; Etzioni et al., 2003; Jemal et al., 2008; Ramsoekh et al., 2007; Fig. 1). It is known that the pathogenesis of CRC is a progressive accumulation of mutations including genes such as the APC, KRAS, SMAD2/ SMAD4 and p53 (Fearon and Vogelstein, 1990). This typically results in a 510 latency period and oers a window of opportunity for eective screening (Davies et al., 2005; Jimenez et al., 2010). Despite this, there has been little change in the rate of survival in CRC over the last two decades, with more than 50% of patients having regional or distant metastasis at the time of presentation (Etzioni et al., 2003).
However, it is costly, requires highly trained sta, is invasive and requires uncomfortable bowel preparation. There is also a small but nite risk of morbidity and mortality attached to the procedure (Davies et al., 2005). Unfortunately, in countries where national colonoscopy screening is available, compliance has often been low (Hundt et al., 2007; Tonus et al., 2006). This has been reported to be due to the unpleasant nature of the bowel preparation, discomfort of the procedure, the need for sedation and patients embarrassment. Flexible sigmoidoscopy (Terdiman, 2005) is often used as an alternative to colonoscopy since it is a rapid proceedure, requires no sedation or overnight hospital stay and has a very low complication rate (Hassan et al., 2008). However, it only allows screening of the distal colon (Fig. 2) and hence misses tumours located in the transverse and ascending colon and the caecum. It has a reported sensitivity of 69% and specicity of 95% in determining the presence or absence of disease (Goodbrand, 2008).
* Correspondence to: E. C. Nice, Head, Clinical Biomarker Discovery and Validation, Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia. E-mail: ed.nice@med.monash.edu.au
a
Ludwig Institute for Cancer Research, Melbourne Tumour Biology Branch, Melbourne, Australia The University of Melbourne, Melbourne, Australia Monash University, Department of Biochemistry, Melbourne, Australia Department of Primary Industries, Biosciences Research Division, Victorian AgriBiosciences Centre, Bundoora, Australia Abbreviations used: CRC, colorectal cancer; CCAP, colorectal cancer associated protein; CEA, carcinoembryonic antigen; CT, computed tomography; FOBT, faecal occult blood test; FS, exible sigmoidoscopy; IMAC, immobilized metal anity chromatography; MALDI, matrix-assisted laser desorption/ionization; MRM, multiple reaction monitoring; SELDI, surface enhanced laser desorption and ionization time-of-ight mass spectrometry; QQQ, triple quadrupole; SEC, size exclusion chromatography
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The discovery and validation of colorectal cancer biomarkers CRC do not bleed continuously but rather intermittently with variable blood loss (Levin et al., 2003). Also, the accuracy of gFOBT is often aected by high levels of dietary haeme found in red meat and peroxidases present in fruit and vegetables (Ouyang et al., 2005), an eect that has been shown to last for up to 3 days (Feinberg et al., 1990). Antioxidants such as Vitamin C can interfere with the assay, resulting in false negatives while gastro-intestinal bleeding, which can be caused by medications such as aspirin, can result in a false-positive result (Greenwald, 2005). The antibody-based iFOBT is more specic for human blood and has a reported sensitivity of 52.6% and a specicity of 87.2% (Nakazato et al., 2006). It is also more likely to be specic for blood originating from the colorectum as blood from the gut degrades as it travels down the digestive tract (Potack and Itzkowitz, 2010). Hence, upper gastro-intestinal bleeding (due to, for example, gastritis, gastric ulcer, duodenal ulcer) is less likely to skew results. Since all positive FOBTs should be followed up with colonoscopy, the poor selectivity and sensitivity of the test puts an excessive burden on current colonoscopy services and subjects a large number of patients to unnecessary colonoscopy. There is therefore an urgent need to develop more sensitive, reliable and specic screening tests for early stage colon cancer when therapy is most likely to be eective.
Figure 1. Colorectal cancer 5 year survival rate based on the tumour location at diagnosis (SEER annual report 19982006 (Altekruse et al., 2009).
The use of computed tomographic (CT) colonography has been suggested as an alternative to endoscopy for the detection of colorectal cancer (Pickhardt et al., 2003). This method uses radiation-based imaging and various methods of image manipulation (multiplanar reconstructions, three-dimensional constructions) to visualize the endolumen of the colon for polyps. Detection of large polyps (>10 mm) in populations with a higher prevalence of polyps has been reported to have a sensitivity of 90% and a specicity of 94%. In contrast, it has also been shown that, for CT colonography used in populations with average risk of development CRC and low-prevalence of polyps (i.e. the general population), sensitivity ranged from 55 to 94% at a specicity of ~95%. Furthermore, it is recognized that CT colongraphy has diculty in detecting at or depressed polyps (van Gelder et al., 2005). The procedure still requires prior bowel preparation and there are risks associated with the use of the ionizing radiation doses required to produce the images. Patients have also reported discomfort associated with the ination of the colon; these patients were not provided with bowel relaxants. Whilst patient compliance for CT colongraphy is better than for exible sigmoidoscopy (FS) or FOBT, attendance rates are still low at 28.4% (Edwards et al., 2004). The FOBT is currently the most widely prescribed primary screening tool. This test screens for the presence of blood or blood products in stool samples, is cheap and non-invasive, but has a high rate of both false-positive and false-negative results (Davies et al., 2005). The FOBT exists in two alternative assay forms, guaiac-based (gFOBT, e.g. Hemoccult II and Hemoccult II SENSA). which is dependent on the peroxidase-like activity of haem in the stool, and immunochemical-based tests (iFOBT, e.g. HemeSelect and InSure), which use human heamoglobin-specic antibodies. Four large randomized controlled trials have consistently shown that biennial screening with FOBT reduces CRC mortality (Kewenter et al., 1994; Kronborg et al., 2004; Scholeeld et al., 2002). A meta-analysis of these studies showed a 16% reduction in CRC mortality, or a 25% reduction when adjusted for non-compliance (Hewitson et al., 2007). However, a number of factors inuence the eectiveness of FOBT with many studies reporting low predictive values (Hewitson et al., 2007). Firstly,
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Figure 2. testing.
Regions of the colorectum screened by dierent CRC diagnostic tests: FOBT, DNA stool testing, colonoscopy, CT, FS and proteomic stool
number of a small number of highly abundant housekeeping proteins, means only the most abundant tumour-derived proteins will be detected without signicant sample workup. Urine, which is readily available, has been primarily used for metabolomic studies (Cai et al., 2006; Qiu et al., 2010). Low-molecular weight proteins (less than 40 kDa) readily pass through the glomerular ltration barrier and are reabsorbed. Because of their low plasma concentrations, only small amounts of these proteins are seen in the urine. Stool testing provides important advantages over other screening methods. It is noninvasive, requires no unpleasant bowel preparations, can be performed at home and thus does not require time away to visit health care practitioners (Osborn and Ahlquist, 2005). One is not sample limited and importantly the stool eectively monitors the entire colon during transit down the gastro-intestinal tract (Osborn and Ahlquist, 2005). On the downside, there is reluctance by many people to handle faeces, leading to low compliance. Additionally, the gut microora can potentially play a major role in proteolysis in the human colon, leading to protein degredation (Gibson et al., 1989; Macfarlane et al., 1986). Lastly there is signicant variation in sample size and composition. Thus, as in urine where normalization based upon creatinine and other parameters is frequently used (Warrack et al., 2009), there is a need to nd a suitable control faecal marker to compensate for this. Faecal DNA testing is an alternative noninvasive CRC screening tool which relies on quantitatively assaying mutant DNA from stool samples (Ahlquist, 2009). Unlike occult blood, human DNA is shed continuously into the gut lumen but represents only 0.01% of total stool DNA (Potack and Itzkowitz, 2010). Initial studies have been able to identify presence of mutated KRAS and p53 genes in stool, both known to be associated with the pathogenesis of CRC (Ahlquist, 2009; Fearon and Vogelstein, 1990). Since then, second-generation DNA stool tests have combined a number of mutant DNA markers in a single test and have demonstrated better sensitivity over FOBT (Ahlquist, 2009; Imperiale et al., 2004). One study looking at 15 dierent markers on a single
panel showed a sensitivity of 92% for CRC and 82% for large adenomas, at a specicity of 93% (Ahlquist, 2009). However, despite promising initial results, DNA stool testing has been reported to have a number of problems including poor discriminative ability of the markers, lack of eective quantitative assaying techniques and bacterial degradation of the DNA during sample transportation (Ahlquist et al., 2008). Development of better genetic markers, DNA stabilizing buers and improved sample extraction techniques is underway and promises to increase the accuracy of future tests (Ahlquist, 2009). However, there are several signicant limitations restricting the use of DNA stool testing as a routine population-based screening tool. Firstly, the use of multi-marker panels makes the test very expensive and time-consuming to process (Davies et al., 2005). Pricing of single tests has been quoted at US$400800 (Davies et al., 2005; Levin et al., 2003) and lack of automation in processing samples makes DNA stool testing inappropriate on a population-level. Also, the test currently requires the entire bowel moment and the collection kit is large, revealing issues of patient acceptability and sample transport and storage (Levin et al., 2003).
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The discovery and validation of colorectal cancer biomarkers However, these markers have been found to be poor markers of CRC due to their low sensitivity and specicity when used individually. Secreted proteins potentially oer a much better source of potential biomarkers for screening as they can be analysed by relatively non-invasive techniques (Ouyang et al., 2005). For example mucus is normally secreted into the colorectum to lubricate and facilitate faecal movement through the digestive tract (Osborn and Ahlquist, 2005). The mucins, which are large (generally >200 kDa) proteins with predominantly O-linked oligosaccharide side chains (Kim et al., 1996), found within mucus have been shown to be dysregulated in neoplasia (Boland et al., 1982). Abnormal mucins have been hypothesized to be potential biomarkers for CRC (Byrd and Bresalier, 2004; Kim et al., 1996; Taylor et al., 2009). Other markers have been evaluated for potential use as biomarkers. Carcinoembryonic antigen (CEA), a serum protein marker used in monitoring of CRC, has recently been studied in faeces. One study showed faecal CEA to have better sensitivity for CRC than FOBT at 86% with a specicity of >90% (Kim et al., 2003). Levels of faecal CEA, measured using an automated immunoassay system, were 44.1 70.1 ng/mg stool in cancer patients and 3.7 3.5 ng/mg stool in controls. Minichromosomal maintenance protein (MCM2) and decay-accelerating factor (CAF) are two other faecal proteins that have been proposed for use as a screening tool. However, data to date have shown suboptimal sensitivities (Davies et al., 2002). Faecal tumour M2 pyruvate kinase (M2-PK) has also been suggested as a potential CRC biomarker (Tonus et al., 2006). This study measured samples from 33 patients with CRC, 21 patients with rectal carcinoma and 42 controls using a commercially available sandwich ELISA which specically detects the dimeric, cancer-related, form of the protein. The overall sensitivity for CRC was 78% at 93% selectivity. Levels correlated well with tumour stage. A more recent study by Karl et al. (2008) investigated six dierent faecal markers. The best individual diagnostic performance was for S100A12 followed by TIMP-1, haemoglobinhaptoglobin, haemoglobin, calprotectin and carcinoembryogenic antigen. Using a combination of markers, they showed a specicity and sensitivity of 98 and 79%, respectively, using the combination of haemoglobin haptoglobin and S100A12. The specicity and sensitivity were increased to 98 and 82% when TIMP-1 was added to the panel. Based on the clinical samples screened (186 CRC, 113 advanced adenoma and 252 control patients), this biomarker panel was found to detect CRC at a signicantly higher rate than iFOBT alone. The sensitivity for early stage cancer was 74%. RNA editing (Keegan et al., 2001; Maniatis and Tasic, 2002) and proteolytic processing (Ehrmann and Clausen, 2004). Moreover protein subspecies can be greatly increased through posttranslational modications such as phosphorylation, glycosylation, methylation and ubiquitination to name a few (Reviewed by Walsh et al. (Walsh et al., 2005)). Thus, while it is now generally accepted that the human genome only contains around 2025,000 proteins (IHGSC, 2004), the human proteome is predicted to be considerably higher (>150,000 individual proteins) (Hoehenwarter et al., 2010). It therefore represents a signicant analytical problem.
The Need for Sample Pre-fractionation to Mine Deeper into the Proteome
The critical factor for a successful mass spectrometry-based biomarker discovery study is the identication and quantication of all the proteins of interest. There is currently, however, no perfect or universal method for identifying the entire proteome or any instrument that is capable of identifying and quantifying the components of a complex protein sample in a simple onestep procedure (Nice et al., 2007). For example, in a large-scale identication of proteins using 2D-PAGE gel electrophoresis, geLCMS and 2D-LCMS, a total of 1218 proteins were identied by the three methods in exponentially growing Bacillus subtilis cells, but only 140 proteins were consistently identied in all three analyses (Wol et al., 2006). This study clearly demonstrated the need for orthogonal purication strategies that utilize the specic selectivities associated with each method. A large variety of alternative strategies for analysing the complexity of the proteome have been investigated. They can be broadly grouped into three main types: gel based techniques [e.g. 2D PAGE (Gorg et al., 2000; OFarrell, 1975), geLCMS (Li et al., 2003), chromatographic fractionation of proteins/peptides including multidimensional/ orthogonal liquid fractionation (Nice et al., 2007; Wang et al., 2002)], removal of abundant proteins or selective enrichment of proteins/peptides [e.g. abundant protein depletion (Gong et al., 2006), IMAC columns (Andersson and Porath, 1986), ICAT (Gygi et al., 1999), glycoprotein enrichment (Taylor et al., 2009; Yang and Hancock, 2004)] and advances in instrumentation [e.g. LTQ Orbitraps (Olsen et al., 2009), application of electron transfer dissociation (Syka et al., 2004) etc.]. Our own data (Ang et al., 2009; Nice et al., 2007) has also shown that alternative separation protocols can reveal the presence of dierent proteins in the same sample (see below). However, for such techniques to be ultimately suitable for routine clinical analysis they need to be capable of simple automation. In particular the use of magnetic-bead based supports appears to have signicant potential for this purpose (Safarik and Safarikova, 2004): they can be used with very crude, particulate, samples (unlike chromatographic supports or membranes), multiple washings can eliminate non-specic binding and, importantly, analysis can be readily automated using simple robotics (Nice et al., 2007; Rothacker et al., 2007; Safarik and Safarikova, 2004). Using a magnetic bead-based protocol we have been able to isolate exfoliated cancer cells, and measure the associated telomerase levels using luminescence-based detection, from the urine of bladder cancer patients and exfoliated colonocytes isolated from faecal samples from colorectal cancer patients postcolonoscopy and prior to resection (Rothacker et al., 2007). The potential of magnetic-bead based purication using supports with chromatographic functionality has recently been shown for
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CS. Ang et al. expression proling and biomarker discovery using samples from patients with head and neck cancer pre- and post-treatment (Freed et al., 2008). Bruker Daltronics have released a range of magnetic-bead based supports (www.bdal.com, ClinProt) with various selectivities including reversed-phase, ion exchange, IMAC and lectin anity. More recently automated SPE using robotic control of chromatographic supports loaded into pipette tip-like columns (Phynexus, Atoll) has also been reported (www. tecan.com, application notes 396241, 395627, 395450). These include, for example, the identication of dierentially expressed proteins in serum (Engwegen et al., 2008; Liu et al., 2006a, b; Ward et al., 2006), the use of cancer cell lines (Zhao et al., 2007), comparison of the secretome of colorectal cancer cell lines (Mathivanan et al., 2010; Wu et al., 2008), comparison of urine samples (Ward et al., 2008) or comparison of paired tumouradjacent normal colorectal tissues (Friedman et al., 2004; Ma et al., 2009; Roessler et al., 2006). Proling of blood, tissues and the secretome from cell lines will be reviewed in the following sections. It cannot be overstated that for all proteomics studies where comparative studies are to be made, standard operating procedures must to be generated, validated and strictly adhered to (Apweiler et al., 2009). The HUPO Plasma Proteome Project has addressed these issues for plasma proteome samples (Rai et al., 2005). Several recent editorials have discussed the issue of bias in clinical biomarker studies on sample selection, choice of technology and appropriate quality control, and the need for collaborative interdisciplinary eorts involving clinicians and scientists (Diamandis, 2007; Hortin, 2005).
Blood Proling
Owing to the sample complexity, a number of blood-based proling studies for colorectal cancer biomarker discovery have been based on the surface enhanced laser desorption and ionization time-of-ight mass spectrometry (SELDI) approach. This technique involves incubating the protein mixture on a protein chip array with dened chemical or biochemical functionality (e.g. reversed phase, ion-exchange, IMAC, antibody anity). Proteins that have anity to these surfaces will be enriched and retained and can be subsequently characterized by TOF mass spectrometry (Hutchens and Yip, 1993). In a study by Ward et al. (2006), a total of 62 CRC and 31 non-cancer serums were screened by SELDI and the results subjected to articial neural network analysis based on the altered intensities of a number of characteristic peaks. This resulted in a reported assay sensitivity and specicity for CRC of 95 and 91%, respectively. Three of the dierentially regulated peaks were subsequently identied to be complement C3a des-arg, a1-antitrypsin and transferrin (Ward et al., 2006). A similar SELDI approach was used to analyse serum from74 CRC patients and 48 age- and sex-matched healthy subjects to identify a diagnostic pattern for the identication of CRC samples (Liu et al., 2006b). Using the dierential proteomic patterns, sensitivity and specicity of 95% was achieved in an independent set of masked serum samples from 60 CRC patients and 39 healthy subjects, although the identity of the representative peaks was not determined. A third study using the SELDI approach used a training set of 63 patients with CRC, 20 with benign colorectal diseases and 26 healthy volunteers (Zheng et al., 2006). Using a four-peak model, they were able to achieve a sensitivity and specicity of 87.5 and 93.8% respectively in discriminating cancer from non-cancer samples. However, as in the Liu et al. (2006b) study, the identity of the four discriminating peaks was not reported. Much of the early SELDI data has attracted signicant criticism with valid questions being raised as to experimental design, lack of reproducibility, statistical processing of the data, the low resolution of the mass spectrometer and the biological relevance of the generated data (Baggerly et al., 2004; Ivanov et al., 2006; Lambert et al., 2005; Paweletz et al., 2006; Weston and Hood, 2004). In many cases, including some of the examples cited above, peak patterns have been used as diagnostic ngerprints
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The discovery and validation of colorectal cancer biomarkers without characterization of the individual proteins. In some studies, when the putative biomarkers were fully characterized they were found to not be directly associated with tumour biochemistry, but instead correspond to ubiquitous proteins, such as the family of acute-phase response proteins (Villar-Garea et al., 2007; Engwegen et al., 2006). Without some form of additional sample pre-fractionation and concentration trace components are unlikely to be detected. Although the technique was originally reported to be compatible with the analysis of high molecular weight compounds (up to 200 kDa), it appears to work optimally in the 1.520 kDa range (Seibert et al., 2005). Despite this, it is worth mentioning that in September 2009 the FDA approved the rst diagnostic tool (OVA1) based on biomarkers discovered and validated using the SELDI approach. This test uses a ve-biomarker panel: transthyretin (TT or prealbumin), apolipoprotein A-1 (Apo A-1), beta2-microglobulin (Beta2M), transferrin (Tfr) and cancer antigen 125 (CA 125 II) to determine the likelihood of ovarian cancer in women with pelvic mass for whom surgery is planned.
Tissue Proling
Comparison of the proteome changes between tumour and neighbouring normal colorectal mucosa is a common methodology employed to identify proteins that have altered abundance associated with tumourigenesis. These protein tumour markers could potentially escape from the tumour and be detected in blood or faeces and hence form the basis for detection of the disease. One of the earlier studies in colorectal marker discovery by Friedman and colleagues using 2D PAGE based analysis (Friedman et al., 2004) identied a total of 52 unique proteins that had altered expression between the tumour and adjacent normal mucosa. A similar study carried out by Ma et al. (2009) identied 42 proteins that also had dierential expression; interestingly several proteins such as nucleoside diphosphate kinase, desmin, tropomyosin, myosin, transgelin and annexin were common to both studies. In particular, desmin, an intermediate lament protein identiable in the serum of CRC patients was shown to correlate with both severity of CRC and also as a prognostic marker based on screening of 92 CRC patients, 25 patients with benign bowel disease and 45 healthy controls (Ma et al., 2009). Roessler et al. (2006) used a 2D PAGE approach to compare the protein prole of colon tumour tissue, adjacent normal tissue and adjacent stripped mucosa from 16 patients. A tumour-associated antiapoptotic factor PSME3 (Nikaido et al., 1989) was detected in seven of the 10 tumour tissues but not in adjacent normal tissues (Roessler et al., 2006). Interestingly, dierential expression was not obvious on the observed spot pattern on 2D-SDS PAGE. The PSME3-containing spot on tumour gels showed no visible dierence to the corresponding spot on matched control gels. Subsequently MS analysis revealed the presence of two proteins, PSME3 and annexin 4 (ANXA4) in the same spot on tumour gels, whereas the matched spot on control gels contained only ANXA4. Screening of PSME3 was subsequently undertaken on 109 CRC and 317 healthy control samples and compared with the equivalent data for CEA. Receiver-operating characteristic curves were derived by plotting the relationship between the specicity and the sensitivity at various cuto levels. The area under the curve was 0.76 for CEA and 0.77 for PSME3.
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Figure 3. Schematic of protein biomarker identication and quantitation by MRM (left panel). Shotgun proteomics is based on tryptic digestion of the protein followed by prefractionation of the peptides on nano-reversed phase liquid chromatography. The characteristic mass of the individual peptides is then determined by ESI-MS. The peptides are fragmented (MS/MS) and the resultant fragment mass and fragmentation pattern used to search a sequence database to match the peptide sequence. (Right panel) Multiple reaction monitoring (MRM) works by selecting a known precursor mass and the signature fragmentation ions characteristic of a known peptide. In the example shown, at the rst quadrupole (Q1) only peptides with the mass of 769.9 were allowed through to the collision cell (Q2). After fragmentation of the peptide, fragment ions with mass of 958.5 (characteristic of the y9 ion) are allowed through to be specically detected. Multiple MRM cycles targeting several fragmentation ions of the parent peptide increase the condence of identication.
studies using proteomics and protein arrays (Haab and Zhou, 2004; MacBeath, 2002; Smolec et al., 2005) have demonstrated that antibody specicity is often lacking, and considerable care must be taken in validation of the signals observed (Ackermann and Berna, 2007; Carney et al., 2003; Michaud et al., 2003; Nice et al., 2007; Nishizuka et al., 2003; Smolec et al., 2005). The number of inconsistent, and sometimes contradictory, publications in this area provides ample evidence of this problem. In one publication (Michaud et al., 2003) a polyclonal antibody was found to cross react with over 1500 dierent proteins. A comparison of the EGFR levels in clinical samples using two dierent antibody-based assays (Baron et al., 2001) gave over a 1000-fold dierence in recorded levels, with no direct correlation between the two assay sets, clearly indicating a major problem with one (or both) of the assays. Additionally, homogeneous protein standards need to be carefully generated, validated and quantied for antibody-based assays (Barker, 2003; Smolec et al., 2005). The expense (estimated at US$1,000,000) (Stahl-Zeng et al., 2007) and time (13 years; Fortin et al., 2009)) of developing a validated ELISA coupled with recent advances in MS technology is further stimulating the development of quantitative MS technologies for protein and peptide biomarker analysis (Ackermann and Berna, 2007). The limited specicity of many ELISAs, and in many cases limited antibody availability, coupled with recent advances in MS
technology, is stimulating the development of quantitative MS technologies for protein and peptide analysis (Anderson and Hunter, 2006; Kuhn et al., 2004; Wolf-Yadlin et al., 2007). Indeed MS of small molecules is already routinely used for clinical assays including multiple analyte screening for inborn errors of metabolism (Dooley, 2003; Kuhara, 2007) and drug analysis (Streit et al., 2002). For proteins, multiple reaction monitoring (MRM, also known as selective reaction monitoring, SRM), in which a triple quadrupole mass spectrometer (QQQ) is used to monitor both the intact peptide mass and one or more specic fragment ions of that peptide over the course of an LC-MS experiment, is rapidly becoming the method of choice (Fig. 3) (Ackermann and Berna, 2007; Stahl-Zeng et al., 2007; Wolf-Yadlin et al., 2007). The relative advantages and disadvantages of antibody and MS-based techniques for quantitative analysis are shown in Table 1. Triple Quad-based MRM Quantitation The principals of this technology are shown in Fig. 3. Triplequadrupole mass spectrometers can be programmed to scan specic preset mass-charge (m/z) ratios thus oering a high duty cycle facilitating identication and quantication of low-level components in complex biological samples such as plasma, urine or faeces. Importantly, the use of MRM can reveal trace peptides present in complex biological samples (Fig. 4). The combination
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Table 1. Advantages and disadvantages of antibody and MS-based quantitative analysis Antibody based assays Disadvantages Development is slow and expensive (Stahl-Zeng et al., 2007) Antibodies need to be available Many antibodies lack specicity Epitopes needs to be preserved in the sample Multiplexing requires individual reagents to be developed for each target MS based assays Advantages Generic method Lends itself to multiplexing Multiple peptide signatures Specic epitope not required In established clinical use for small molecules (e.g. drugs of abuse, inborn errors of metabolism; Rashed et al., 1997) Medium throughput Low cost per sample Disadvantages Less sensitive than ELISA (ng/mL becoming routine; pg/mL requires additional fractionation) Sophisticated instrumentation required
Advantages
Once developed, can be applied to a large number of samples Sensitive (pg to ng/mL) Simple instrumentation Established technology High throughput Used for routine clinical analysis
Figure 4. The specicity of MRM for identifying specic proteins in a complex sample. Faecal proteins were rst prefractionated using RP-HPLC and an individual fraction selected for futher analysis. Following tryptic digestion, the generated peptides were monitored on a mass spectrometer using both full scan (total ion chromatogram, TIC) and MRM mode. In the MRM mode, haemoglobin, haptoglobin and CEA were specically monitored, allowing them to be readily identied in the complex mixture (collaboration with Dr Alun Jones, University of Queensland, Australia).
of retention time, peptide mass and fragment mass practically eliminates ambiguities in peptide assignments and extends the quantication range to 45 orders of magnitude with sensitivity for direct analysis of 50100 ng/mL which can be extended to the picogram/mL range by the use of simple chromatographic enrichment techniques (Ackermann and Berna, 2007; Stahl-Zeng et al., 2007). Dozens of targets can be analysed simultaneously:
scheduled MRM, in which selected transitions are coupled to chromatographic windows (Stahl-Zeng et al., 2007), has facilitated analysis of more than 1000 precursor-product ion pairs (Martin et al., 2008). Absolute quantitation can be achieved using appropriate isotope labelled synthetic standards generated either by peptide synthesis (Stemmann et al., 2001) or by recombinant expression of articial genes encoding a concatenation of
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(A)
(B)
Pre-fractionation SEC
18 fractions
RP HPLC
13 fractions
SDS PAGE
Selection of CCAP from literature And excising from gel based on l l weight i ht molecular Identication of protein using MRM
appropriate tryptic peptides (Pratt et al., 2006). Recently, the availability of low-cost libraries of crude, unpuried synthetic peptides (JPT Peptide Technologies) as reference for validation of peptide identity have enabled high-throughput optimization, validation and development of MRM assays (Picotti et al., 2009a). Examples of the successful use of MRM for the detection of serum proteins include analysis of PSA (Barnidge et al., 2004; Keshishian et al., 2007), C-reactive protein (Kuhn et al., 2004), the multiplexed analysis of 53 medium abundance proteins including L-selectin in a single run (Anderson and Hunter, 2006) and quantitative analysis of a number of N-glycosites including megakaryocyte stimulating factor (Stahl-Zeng et al., 2007). A further advantage of proteomics/MRM analysis is the potential to identify and quantitate protein isoforms (Jenkins et al., 2006). Such isoforms may be linked to abnormal expression at tumour sites (Bourdon, 2007). However all isoforms may not be readily detectable using currently available antibodies (Bourdon, 2007; Lehmann et al., 2008). Proteomics/MRM-based analysis can circumvent this problem by targeting specic peptide sequences
of the dierent isoforms: a recent study (Lehmann et al., 2008) demonstrated the feasibility of simultaneously measuring four isoforms of the sucrose phosphate synthase enzyme that could not be dierentiated by antibodies.
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The discovery and validation of colorectal cancer biomarkers viable biomarkers with adequate sensitivity and selectivity either individually or as a panel (Zolg and Langen, 2004). The rst step in the discovery based biomarker approach is therefore to obtain a library of proteins identied in the biological sample of interest. Data generated in-house, obtained from the literature or derived in silico can be used to generate this library. The most reliable data will clearly come from analyses performed on the biological extract under study (in our case faecal samples) since they will be subjected to the same sample workup (sample preparation, chromatographic separation etc.) and most importantly the eect of ion suppression due to the presence of highlevel contaminant proteins, which will be dierent for dierent biological matrixes, will be accounted for. For the development of MRM-based assays, the identity of appropriate peptides and their characteristic peptide fragments is required before they can be programmed for specic targetting on the QQQ mass spectrometer. These MS/MS fragmentation data together with their precursor peptide mass are then used to set up and validate MRM transitions (using synthetic peptides) which can be trialled on a small set of additional clinical samples |(with relative quantitation) to conrm their ecacy for detecting multiple biomarkers of interest prior to investing in expensive assay standards for their absolute quantitation. protein prole as the mice mature and display the disease phenotype thus provide a good starting point for future targeted proteomic/immunological approaches for the detection/ quantitation of proteins involved in the initiation and progression of CRC. The work ow began with sample collection whereby individual murine stools were recovered manually using forceps (the animal will typically defecate when picked up), which avoids contamination of the faecal sample by urine or bedding materials The samples were stored at -70C until use. Following manual disruption of the faeces in 0.15%TFA, aliquots were taken for 1D SDS-PAGE. The gels were then Coomassie stained and sectioned into 1 mm strips which were reduced, alkylated and digested with trypsin prior to protein identication using nanoHPLC coupled to an ion trap mass spectrometry. In total 336 proteins were identied with 115 being of murine origin, 201 from gut bacteria and 18 food related (Ang et al., 2009). Although not a strict comparative experiment, murine homologues of colorectal cancer-associated proteins (CCAP) such as haemoglobin, haptoglobin, haemopexin, alpha-2 macroglobulin and cadherin-17 were identied in the faeces of aged C57BL/ApcMin+ mice, demonstrating the potential of faecal proteomics for detecting potential biomarkers and paving the way for subsequent MS/MS-based biomarker studies on similar human samples.
The Use of Faecal Proteomics for the Discovery and Validation of CRC Biomarkers
Our hypothesis for developing faecal proteomics was that samples from patients with asymptomatic advanced adenomas or colorectal cancer would contain signature proteins and/or peptides relating to the presence of the adenoma or tumour that are not present in stools from healthy people. These proteins/ peptides should be relatively more abundant in faeces than in blood, thereby facilitating their detection (Kim et al., 2003). Stools therefore prove an ideal non-invasive biological sample for the identication of potential CRC biomarkers. Once potential biomarkers have been identied, MRM can be used for the validation of potential biomarker panels for the detection and monitoring of adenomas and CRC, staging of the disease, response to treatment or recurrance. It is now generally accepted that individual biomarkers are unlikely to have the required sensitivity and specicity and that panels of biomarkers will be required for accurate diagnosis (Duy et al., 2003; Leach et al., 2005; MacBeath, 2002).
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CS. Ang et al. colonoscopy and prior to surgical resection, or from volunteers who had recently undergone colonoscopy and had no evidence of disease. Samples were collected under the appropriate human ethics approval using a simple standard operating procedure (SOP). Patients or volunteers were given a sample collection kit when they had consented. They were instructed to empty their bladder, and then ush the toilet prior to sample collection. A cellulose biodegradable sample collection sheet was then placed in the toilet bowl to retain the stool sample. Once the stool had been collected, an aliquot was recovered using a plastic spatula and placed into a sample collection tube which was dispatched immediately to the laboratory. Samples were only used for subsequent analysis if received within 2 h of defecation. They were stored immediately at -70C prior to proteomic analysis. Samples (typically 50100 mg) were homogenized in 0.15% TFA, using the protocol we had developed for the murine faecal proteomics (Ang and Nice, 2010) and then processed using the protocol shown in Fig. 5(A). acterized: no human proteins were identied. It was proposed that this was due to low similarity to proteins in the available databases (Klaassens et al., 2007). By contrast, in a recent study using shotgun proteomics of human faecal samples obtained from 37-year-old female healthy monozygotic twins, 2214 nonredundant proteins were identied (Verberkmoes et al., 2009). Although in this study the sample preparation (dierential centrifugation) was specically designed for the recovery of bacterial proteins, almost 30% of the proteins identied were of human origin due to contamination of the bacterial fraction with highly abundant human proteins in the samples with a large number of spectral counts (Verberkmoes et al., 2009).
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Table 2. Subset of CCAP identied in human faeces Function Inamation Stromal markers/inammation Leakage/inammation Cell shedding Brush border enzymes Angiogenesis Protein binding Proteins identied Defensin 1, Defensin 3, Lipocalin, IgGFcBP S100A8, S100A9, S100A12, S100P Haemoglobin, haptoglobin, a1-antitrypsin, lactoferrin A33, CEA, M2PK, MMP9, TIMP1, cadherin-17, DPP1, DPPIV, maltose glucoamylase, CA1, CA2 IGFBP2 Selenium BP, galectin 3BP
Figure 6. Identication and validation of peptides using MRM. (A) Extracted ion chromatogram (EIC) of the an endogenous proteotypic peptide VGAHAGEYGAEALLER (haemoglobin alpha) from the faecal extract of a CRC patient. (B) EIC of the corresponding synthetic peptide VGAHAGEYGAEALLER showing equivalent HPLC retention time and MSMS fragmentation pattern. (C) The y-series transition ions used for the MRM assay. (D) Using the most intense fragment ion (y4), screening of eight CRC patients and seven normal volunteers was carried out. No signal was observed in any of the normal samples.
would help overcome potential problems of the resulting protein fragments having dierent physiochemical properties (e.g dierent molecular weights, pI, hydrophobicity) resulting in assay bias, which is not desirable in a clinical assay. Once good signal-tonoise had been established with the absence of any interfering signals, the corresponding synthetic peptides were then purchased (JBT Peptide Technologies) to conrm the peptide identities. The combination of equivalent chromatographic retention time, peptide mass, fragment mass and fragmentation pattern
for the endogenous and synthetic peptides (e.g. Fig. 6A,B) eliminates ambiguities in peptide identication (Ang and Nice, 2010; Gupta et al., 2009). Optimizations of the peptide collision energies were then carried out using PeptideOptimizer (Agilent). As mentioned above, to be useful as a clinical diagnostic assay, sample manipulation should be kept to a minimum in order to maintain the samples integrity, reduce losses and assay variability and keep costs to a minimum. Sample manipulation steps such as immuno-depletion or prefractionation are generally not
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CS. Ang et al. encouraged as they add a level of bias. We have employed an approach whereby screening was carried out on the unfractionated samples through direct nanoLC-MRM following sample extraction, digestion and sample cleanup to minimize the amount of manipulation following sample collection, similar to that of a clinical laboratory setting. Following screening of individual samples from the eight CRC patients and seven normal volunteers, we have currently identied nine proteins that are only found in the faeces of CRC patients and are in the process of validating the eectiveness of these nine proteins for CRC detection in a larger sample size (manuscript submitted). One of the proteins only identied in the unfractionated faeces from CRC patients is alpha-1 antitrypsin. Alpha-1 antitrypsin, a protein used as a measure of protein leakage into the intestinal track, has been proposed as a good alternative blood-borne marker for CRC since an increase in enteric protein loss from colorectal cancers may also relate to increased epithelial turnover and leakage (Moran et al., 1993; Waldmann, 1985; Ward et al., 2006). Haemoglobin, which forms the basis of the FOBT test, was only found in the faeces of the CRC patients tested (Fig. 6). Haemoglobin was identied from eight transition ions and was further veried using an equivalent synthetic peptide which displayed equivalent HPLC retention time and MSMS fragmentation patterns. Isotopically labelled peptides for absolute quantitation [labelled at the C-terminus with the heavy stable isotope lysine or arginine (13C15N)] were purchased from JPT Peptide Technologies in a 96-well plate format. Once cleaved from the plate with trypsin they were puried by micropreparative HPLC and quantied by amino acid analysis. Known amounts of the labelled peptides were spiked into faecal extracts from eight CRC patients and seven normal volunteers (manuscript submitted). Quantitation using MRM revealed levels of haemoglobin ranges from 6 to 13470 ng peptides/mg stool (2864500 ng protein/mg stool) in CRC patients. There was no detectable level in the normal samples. These data are consistent with the clinical pathologies. denced by their detection in lower molecular weight regions of the gel. Karl et al. (2008) in their study on faecal biomarkers for CRC diagnosis had also shown stability of a number of faecal proteins including CEA, calprotectin and TIMP-1 (Karl et al., 2008). CCAPs such as protocadherin 24, carcinoembryonic antigen 6, S100 calcium binding proteins (S100A6, A8 and A9), prolin-1, L-plastin and selenium binding protein were detected. Identied proteins were validated with their respective synthetic peptides based on equivalent HPLC retention time and MSMS fragmentation patterns (Fig. 6). A relative comparison of the 16 stable proteins was carried out using samples from ve CRC patients and ve normal volunteers. These studies showed that in this sample set haemoglobin, myeloperoxidase, S100A9, lamin A and L-plastin were only present in the faeces of CRC patients. Data for haemoblobin is showed in Fig. 6. Validation of this panel of ve proteins in a larger cohort of patients/normal volunteers will reveal the diagnostic nature of these proteins. This directed process could easily be applied to other biological uids such as serum, urine or semen,or other disease states. This hypothesis-driven approach could also be adapted for other biological studies including pathway analysis, quantication of immuno-anity-enriched proteins, degredomics or analysis of protein complexes. This approach should signicantly reduce the time taken for clinical assay development, with the added advantage that many proteins targeted will have been validated previously using in vitro and/or in vivo studies.
Conclusions
The early years of clinical proteomics saw much discussion as to the success and cost ecacy of such studies (Huber, 2003; Zolg and Langen, 2004). In the eld of biomarker research it was noted that, in spite of the large amount of eort being put into such studies, few proposed biomarkers were achieving FDA approval (Carr and Anderson, 2008; Ludwig and Weinstein, 2005) and that there was a long and uncertain path to clinical utility (Rifai et al., 2006), due largely to problems with clinical validation (Carr and Anderson, 2008). As we enter a new decade it is interesting to see a renewed optimism emerging (Abu-Farha et al., 2009; Pan et al., 2009; Parker et al., 2010). This is being driven largely by the development of novel, sensitive, cost-eective, quantitative MS-based techniques (e.g. MRM; Abu-Farha et al., 2009). These techniques provide a generic platform technology that can be used to address numerous disease situations without the requirement of generating specic reagents. Once MRM assays have been established, they readily lend themselves to multiplex analysis (Picotti et al., 2009b; Schiess et al., 2009). By multiplexing tens to hundreds of potential biomarkers and comparing them across a large number of clinical samples, it will be possible to rapidly screen and assess their suitability. The generation of comprehensive MRM libraries for dierent biological matrices will facilitate a directed, hypothesis driven approach (Ang and Nice, 2010; Schiess et al., 2009; Yang and Lazar, 2009). Importantly, these techniques appear to be highly reproducible within, and across, laboratories (Addona et al., 2009).
Acknowledgements
C.S.A. and E.C.N. were supported, in part, by research grant 433620 from the Cancer Council of Victoria and a grant from the Department of Innovation, Industry and Regional Development, Australia.
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