Identification of biomarkers for ovarian cancer using strong anion-exchange ProteinChips: Potential use in diagnosis and prognosis

Kozak, Katherine R.; Amneus, M.; Pusey, Suzanne M.; Su, Feng; Luong, Mui; Luong, Sam A.; Reddy, Srinivasa T.; Farias‐Eisner, Robin

doi:10.1073/pnas.2033602100

Cited by 245 publications

(159 citation statements)

References 41 publications

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“…Multivariate analysis can then be used to determine whether the intensities of the peaks in the SELDI spectra of different patient groups possess discriminatory ability. Studies have suggested the possible utility of SELDI analysis in diagnosing ovarian (Petricoin et al, 2002;Kozak et al, 2003), prostate Qu et al, 2002;Banez et al, 2003), breast (Li et al, 2002), bladder (Vlahou et al, 2001), hepatic (Poon et al, 2003;Ward et al, 2006) and pancreatic cancer using serum. Concerns with several aspects of this approach have been raised, including potential bias in sample collection protocols, accuracy/ resolution of the PBS IIc mass spectrometer employed in SELDI analysis, alignment of the detected peaks and over fitting of the data (Ransohoff, 2004).…”

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confidence: 99%

Identification of serum biomarkers for colon cancer by proteomic analysis

et al. 2006

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Colorectal cancer (CRC) is often diagnosed at a late stage with concomitant poor prognosis. Early detection greatly improves prognosis; however, the invasive, unpleasant and inconvenient nature of current diagnostic procedures limits their applicability. No serum-based test is currently of sufficient sensitivity or specificity for widespread use. In the best currently available blood test, carcinoembryonic antigen exhibits low sensitivity and specificity particularly in the setting of early disease. Hence, there is great need for new biomarkers for early detection of CRC. We have used surface-enhanced laser desorbtion/ionisation (SELDI) to investigate the serum proteome of 62 CRC patients and 31 noncancer subjects. We have identified proteins (complement C3a des-arg, a1-antitrypsin and transferrin) with diagnostic potential. Artificial neural networks trained using only the intensities of the SELDI peaks corresponding to identified proteins were able to classify the patients used in this study with 95% sensitivity and 91% specificity.

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confidence: 99%

Identification of serum biomarkers for colon cancer by proteomic analysis

et al. 2006

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“…One such approach is proteomic profiling (Adam et al, 2002;Li et al, 2002;Kozak et al, 2003;Poon et al, 2003;Chen et al, 2004;Paradis et al, 2005;Schwegler et al, 2005;Yang et al, 2005;Ward et al, 2006a -c). We and other groups have suggested that patients with HCC may express a characteristic protein 'signature' even in the case of small tumours (Poon et al, 2003;Paradis et al, 2005;Schwegler et al, 2005;Ward et al, 2006a -c).…”

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confidence: 99%

“…These signatures are customarily detected using Surface-Enhanced Laser Desorption/ Ionisation (SELDI) technology, which permits the mass spectrum of a specific subset of serum proteins to be compared between cancer and non-cancer patients using various pattern recognition programmes. While there has been considerable controversy about the robustness of this approach, particularly with regard to its reproducibility and the techniques used to validate results (Diamandis, 2004;Petricoin et al, 2004;Ransohoff, 2004), a large body of evidence does suggest that such signatures are detectable (Adam et al, 2002;Li et al, 2002;Kozak et al, 2003;Poon et al, 2003;Chen et al, 2004;Paradis et al, 2005;Schwegler et al, 2005;Yang et al, 2005;Ward et al, 2006a -c), even if clinical utility remains to be convincingly shown.…”

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confidence: 99%

Preclinical and post-treatment changes in the HCC-associated serum proteome

et al. 2006

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SELDI-based proteomic profiling of body fluids is currently in widespread use for cancer biomarker discovery. We have successfully used this technology for the diagnosis of hepatocellular carcinoma (HCC) in hepatitis C patients and now report its application to serial serum samples from 37 hepatitis C patients before development of HCC, with HCC and following radiofrequency ablation of the tumour. As with alpha-fetoprotein, an accepted biomarker for HCC, we hypothesised that HCC-associated proteomic features would 'return to normal' following successful treatment and the primary aim of our study was to test this hypothesis. Several SELDI peaks that changed significantly during HCC development were detected but they did not reverse following treatment. These data may be interpreted to suggest that the characteristic SELDI profile is not linearly related to tumour burden but may result from the progression of underlying liver disease or from the emergence of precancerous lesions. b2-Microglobulin, a protein previously reported to be markedly elevated in patients with HCV related HCC, was also the most significantly HCC associated proteomic feature (m/z 11720) in this study.

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“…[9][10][11][12][13][15][16][17][18][19][20][21]25 The most interesting discovery of the study was the finding that a SELDI-derived peak (m/z 4,462) was as effective at discriminating cancer from benign serum as the tumor markers CEA or CA19.9, while combining these three serum markers marginally improved classification. Classification could be further improved with data generated from a panel of peaks, suggesting analysis of proteomic profiles, rather than individual proteins, may yield improved diagnostic ability.…”

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confidence: 99%

“…Proteomic profiling of serum has been used with a number of other malignancies to discover potential biomarkers. 7,8 In particular, affinity-based arrays-such as the protein chips analyzed via surface-enhanced laser desorption/ionization time-offlight mass spectrometry (SELDI-TOF MS) used in this study-have been used to successfully identify malignant patterns in serum from ovarian, [9][10][11] pancreatic, [12][13][14] head and neck, 15,16 prostate, 17 transitional cell, 18 renal cell, 19,20 and breast 21 cancers. TOF-MS separates ions derived from proteins or protein fragments that are differentially detected according to their mass-to-charge ratio.…”

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confidence: 99%

Proteomic profiling of cholangiocarcinoma: Diagnostic potential of SELDI-TOF MS in malignant bile duct stricture

et al. 2006

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Proteomic techniques promise to improve the diagnosis of cholangiocarcinoma (CC) in both tissue and serum as histological diagnosis and existing serum markers exhibit poor sensitivities. We explored the use of surface-enhanced laser desorption/ionization time-of-flight mass spectrometry (SELDI-TOF MS) to identify potential protein biomarkers of CC. Twenty-two resected CC samples were compared with adjacent noninvolved bile duct tissue. Serum from patients with CC (n ‫؍‬ 20) was compared with patients with benign disease (n ‫؍‬ 20), and healthy volunteers (n ‫؍‬ 25). Samples were analyzed on hydrophobic protein chips via SELDI-TOF MS, and classification models were developed using logistic regression and cross-validation analysis. Univariate analysis revealed 14 individual peaks differentially expressed between CC and bile duct tissue, 4 peaks between CC and benign disease, and 12 peaks between CC and sera of healthy volunteers. The 4,462 mass-to-charge serum peak had superior discriminatory ability to carbohydrate antigen 19.9 (CA19.9) and carcinoembryonic antigen ( C holangiocarcinoma (CC) is a rare but devastating neoplasm that accounts for 3% of all gastrointestinal cancers and 15% of all primary liver cancers worldwide. 1 Five thousand new cases are diagnosed on average per year in the United States, and the incidence is rising. 2 Northeast Thailand sees the highest incidence, with 96 cases per 100,000. 1 Surgical resection is the only current chance of cure, with no proven adjunctive therapy; however, this approach has a mortality rate of 5% to 10%. 3 Even with margin-free resection, 5-year survival figures only reach 20% to 40%. 3,4 Unresectable disease is usually fatal within 6 months to 1 year, and over one third of patients present at a stage too late for resection. 3 This confirms the need for earlier and more accurate diagnostic processes.At present, diagnosis of CC relies on imaging of the biliary tree with computed tomography or ultrasonography in the presence of high clinical suspicion. Tissue diagnostic confirmation is possible for intrahepatic tumors but is very difficult in more distal and more common (2/3 of cases) extrahepatic cases. These frequently present as a stricture of the common bile duct, which can be further characterized by means of endoscopic retrograde cholangio-pancreatography. 5

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Identification of biomarkers for ovarian cancer using strong anion-exchange ProteinChips: Potential use in diagnosis and prognosis

Cited by 245 publications

References 41 publications

Identification of serum biomarkers for colon cancer by proteomic analysis

Identification of serum biomarkers for colon cancer by proteomic analysis

Preclinical and post-treatment changes in the HCC-associated serum proteome

Proteomic profiling of cholangiocarcinoma: Diagnostic potential of SELDI-TOF MS in malignant bile duct stricture

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