Proteomic profiling identifies afamin as a potential biomarker for ovarian cancer

PURPOSE

To discover and validate serum glycoprotein biomarkers in ovarian cancer using proteomic-based approaches.

EXPERIMENTAL DESIGN

Serum samples from a "discovery set" of 20 patients with ovarian cancer or benign ovarian cysts or healthy volunteers were compared by fluorescence two-dimensional differential in-gel electrophoresis and parallel lectin-based two-dimensional profiling. Validation of a candidate biomarker was carried out with Western blotting and immunoassay (n = 424).

RESULTS

Twenty-six proteins that changed significantly were identified by mass spectrometric sequencing. One of these, confirmed by Western blotting, was afamin, a vitamin E binding protein, with two isoforms decreasing in patients with ovarian cancer. Validation using cross-sectional samples from 303 individuals (healthy controls and patients with benign, borderline, or malignant ovarian conditions and other cancers) assayed by ELISA showed significantly decreased total afamin concentrations in patients with ovarian cancer compared with healthy controls (P = 0.002) and patients with benign disease (P = 0.046). However, the receiver operating characteristic areas for total afamin for the comparison of ovarian cancer with healthy controls or benign controls were only 0.67 and 0.60, respectively, with comparable figures for CA-125 being 0.92 and 0.88 although corresponding figures for a subgroup of samples analyzed by isoelectric focusing for afamin isoform 2 were 0.85 and 0.79. Analysis of a further 121 samples collected prospectively from 9 patients pretreatment through to relapse indicated complementarity of afamin with CA-125, including two cases in whom CA-125 was noninformative.

CONCLUSIONS

Afamin shows potential complementarity with CA-125 in longitudinal monitoring of patients with ovarian cancer, justifying prospective larger-scale investigation. Changes in specific isoforms may provide further information.

Prostatic tissue protein alterations due to delayed time to freezing

Clinical studies often produce fresh tissue samples, which ideally should be immediately snap frozen for storage and subsequent analysis. However, this is often not practically possible, and there is inevitably a time period during which the sample is stored on ice. The delay in freezing may allow endogenous degradation of proteins to occur, affecting 2-D gel protein profiles. This study aims to investigate the type and extent of this degradation by examining how the time-to-freezing delay alters prostatic tissue protein profile. The prostate carcinoma-3 cell line (PC-3), prostate cancer xenografts and canine prostate were used with fluorescence 2-D DIGE to assess protein degradation. It was found that 30-min processing time had minimal effects on the protein profile. Longer delays had little visible effect, but subtle alterations in protein profile began to accumulate as time increased. These data support the practice of completing tissue processing as rapidly as possible, and indicate that short processing times do not notably perturb the 2-D gel spot pattern from prostatic tissue.

Statistical models of shape for the analysis of protein spots in two-dimensional electrophoresis gel images

In image analysis of two-dimensional electrophoresis gels, individual spots need to be identified and quantified. Two classes of algorithms are commonly applied to this task. Parametric methods rely on a model, making strong assumptions about spot appearance, but are often insufficiently flexible to adequately represent all spots that may be present in a gel. Nonparametric methods make no assumptions about spot appearance and consequently impose few constraints on spot detection, allowing more flexibility but reducing robustness when image data is complex. We describe a parametric representation of spot shape that is both general enough to represent unusual spots, and specific enough to introduce constraints on the interpretation of complex images. Our method uses a model of shape based on the statistics of an annotated training set. The model allows new spot shapes, belonging to the same statistical distribution as the training set, to be generated. To represent spot appearance we use the statistically derived shape convolved with a Gaussian kernel, simulating the diffusion process in spot formation. We show that the statistical model of spot appearance and shape is able to fit to image data more closely than the commonly used spot parameterizations based solely on Gaussian and diffusion models. We show that improvements in model fitting are gained without degrading the specificity of the representation.

Using statistical image models for objective evaluation of spot detection in two-dimensional gels

Protein spot detection is central to the analysis of two-dimensional electrophoresis gel images. There are many commercially available packages, each implementing a protein spot detection algorithm. Despite this, there have been relatively few studies comparing the performance characteristics of the different packages. This is in part due to the fact that different packages employ different sets of user-adjustable parameters. It is also partly due to the fact that the images are complex. To carry out an evaluation, "ground truth" data specifying spot position, shape and intensities needs to be defined subjectively on selected test images. We address this problem by proposing a method of evaluation using synthetic images with unambiguous interpretation. The characteristics of the spots in the synthetic images are determined from statistical models of the shape, intensity, size, spread and location of real spot data. The distribution of parameters is described using a Gaussian mixture model obtained from training images. The synthetic images allow us to investigate the effects of individual image properties, such as signal-to-noise ratios and degree of spot overlap, by measuring quantifiable outcomes, e.g. accuracy of spot position, false positive and false negative detection. We illustrate the approach by carrying out quantitative evaluations of spot detection on a number of widely used analysis packages.

Cell culture model for acetaminophen-induced hepatocyte death in vivo

Overdose of the popular, and relatively safe, analgesic acetaminophen (N-acetyl-p-aminophenol, APAP, paracetamol) can produce a fatal centrilobular liver injury. APAP-induced cell death was investigated in a differentiated, transforming growth factor alpha (TGFalpha)-overexpressing, hepatocyte cell line and found to occur at concentrations, and over time frames, relevant to clinical overdose situations. Coordinated multiorganellar collapse was evident during APAP-induced cytotoxicity with widespread, yet selective, protein degradation events in vitro. Cellular proteasomal activity was inhibited with APAP treatment but not with the comparatively nonhepatotoxic APAP regioisomer, N-acetyl-m-aminophenol (AMAP). Low concentrations of the proteasome-directed inhibitor MG132 (N-carbobenzoxyl-Leu-Leu-Leucinal) increased chromatin condensation and cellular stress responses preferentially in AMAP-treated cultures, suggesting a contribution of the proteasome in APAP- but not AMAP-mediated cell death. APAP-specific alterations to mitochondria were observed morphologically with evidence of mitochondrial proliferation in vitro. Biochemical alterations to cellular proteolytic events were also found in vivo, including APAP- or AMAP-mediated inhibition of caspase-3 processing. These results indicate that, although retaining some attributes of apoptosis, both APAP- and AMAP-mediated cell death have additional distinctive features consistent with longer term necrosis.

Genomics and proteomics analysis of acetaminophen toxicity in mouse liver

Overdose of acetaminophen (APAP) causes severe centrilobular hepatic necrosis in humans and experimental animals. Here, to explore its mechanism, we administered APAP at subtoxic (150 mg/kg ip) and toxic (500 mg/kg ip) doses to overnight fasted mice. Animals were sacrificed at different time points from 15 min to 4 h postinjection. We assessed liver toxicity by plasma ALT activity and by electron microscopy. Using nylon filter arrays and RTQPCR, we performed genomics analysis in liver. We ran proteomics on liver mitochondrial subfractions using the newly developed quantitative fluorescent 2D-DIGE method (Amersham Pharmacia Biotech UK Limited). As soon as 15 min postinjection, centrilobular hepatocyte mitochondria were already slightly enlarged and GSH total content dropped by a third at top dose. GM-CSF mRNA, which is a granulocyte specific gene likely coming from resident Kupffer cells, was also induced to its maximum of 3-fold at both doses. Chaperone proteins Hsp10 and Hsp60 were readily decreased by half in mitochondria at both doses, most likely by leaking into cytoplasm. Although APAP is known as an apoptotic trigger, no apoptosis was observed at any time point. Most of the protein changes in mitochondria were present at 15 min postinjection, thus preceding most of the gene regulations. The decrease of ATP synthase subunits and beta-oxidation pathway proteins indicated a loss of energy production. As the morphology of mitochondria was also affected very early at top dose, we concluded that APAP toxicity was a direct action of its known reactive metabolite NAPQI, rather than a consequence of gene regulation. However, the latter will either worsen the toxicity or lead toward cell recovery depending on the cellular damage level.

Enhanced acetaminophen hepatotoxicity in transgenic mice overexpressing BCL-2

Mitochondria play an important role in the cell death induced by many drugs, including hepatotoxicity from overdose of the popular analgesic, acetaminophen (APAP). To investigate mitochondrial alterations associated with APAP-induced hepatotoxicity, the subcellular distribution of proapoptotic BAX was determined. Based on the antiapoptotic characteristics of BCL-2, we further hypothesized that if a BAX component was evident then BCL-2 overexpression may be hepatoprotective. Mice, either with a human bcl-2 transgene (-/+) or wild-type mice (WT; -/-), were dosed with 500 or 600 mg/kg (i.p.) APAP or a nonhepatotoxic isomer, N-acetyl-m-aminophenol (AMAP). Immunoblot analyses indicated increased mitochondrial BAX-beta content very early after APAP or AMAP treatment. This was paralleled by disappearance of BAX-alpha from the cytosol of APAP treated animals and, to a lesser extent, with AMAP treatment. Early pathological evidence of APAP-induced zone 3 necrosis was seen in bcl-2 (-/+) mice, which progressed to massive panlobular necrosis with hemorrhage by 24 h. In contrast, WT mice dosed with APAP showed a more typical, and less severe, centrilobular necrosis. AMAP-treated bcl-2 (-/+) mice displayed only early microvesicular steatosis without progression to extensive necrosis. Decreased complex III activity, evident as early as 6 h after treatment, correlated well with plasma enzyme activities at 24 h (AST r(2) = 0.89, ALT r(2) = 0.87) thereby confirming a role for mitochondria in APAP-mediated hepatotoxicity. In conclusion, these data suggest for the first time that BAX may be an early determinant of APAP-mediated hepatotoxicity and that BCL-2 overexpression unexpectedly enhances APAP hepatotoxicity.

Role of CYP1A2 in the hepatotoxicity of acetaminophen: investigations using Cyp1a2 null mice

Acetaminophen (APAP) is known to cause centrilobular hepatic necrosis under overdose conditions. This is thought to be mediated via the P450-generated reactive intermediate N-acetyl-p-benzoquinone imine (NAPQI). Initially, NAPQI is detoxified by conjugation with glutathione (GSH), but once GSH is depleted, NAPQI reacts more extensively with hepatic proteins leading to hepatocellular damage. The P450 isoforms thought to be responsible for APAP hepatotoxicity in humans are CYP2E1, CYP1A2, and CYP3A4, and thus, we have investigated the effect of murine Cyp1a2 on APAP hepatotoxicity using Cyp1a2 knockout mice (Liang et al., Proc. Natl. Acad. Sci. USA 93, 1671-1676, 1996). Doses of 250 mg/kg were markedly hepatotoxic in these mice, and surprisingly, deaths only occurred in the knock-out and heterozygote mice over a 24-h period after dosing. Furthermore, there were no significant differences among survivors of any genotype in serum ALT concentrations, a well correlated indicator of APAP hepatotoxicity in mice. Finally, no differences were observed in the urinary metabolites excreted ove the 24-h period, including those derived from GSH conjugation of the major reactive metabolite NAPQI. Consistent with the effects on hepatotoxicity and metabolism, 2 h after hepatotoxic doses (500 mg/kg, i.p.) of APAP no significant differences were observed in total whole liver homogenate nonprotein thiol concentrations among the three genotypes even though hepatic thiols were decreased compared to control animals (> 90%). In addition, when the liver cytosol and microsome samples were examined by immunoblotting for the presence of APAP-protein adducts using a specific antiserum, there were no observable differences in either the intensity of staining or in the spectrum of adducts formed between APAP-dosed mice of any genotype. The cumulative data suggest that Cyp1a2 doses not play a significant role in APAP hepatotoxicity in these mice.