Preanalytic Influence of Sample Handling on SELDI-TOF Serum Protein Profiles

Timms, John F.; Arslan-Low, Elif; Gentry‐Maharaj, Aleksandra; Luo, Zhiyuan; T'Jampens, Davy; Podust, Vladimir N.; Ford, Jane B.; Fung, Eric T.; Gammerman, Alexander; Jacobs, Ian; Menon, Usha

doi:10.1373/clinchem.2006.080101

Cited by 130 publications

(113 citation statements)

References 36 publications

(34 reference statements)

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“…the median time to progression was 7 months and overall survival was 11 months, which is comparable to other studies of anthracycline, cisplatin and 5-fluorouracil chemotherapeutic combination regimens in patients with advanced gastric cancer (20). the study was conducted according to a strict protocol regarding serum collection, handling and storage at -30˚C to minimize pre-analytic influence of serum sampling on the SELDI-TOF protein profiles (21). the selected patients had advanced gastric adenocarcinoma and underwent standard first-line chemotherapy.…”

Section: Discussionsupporting

confidence: 73%

Serum proteomics and disease-specific biomarkers of patients with advanced gastric cancer

Helgason

Engwegen²,

Zapatka³

et al. 2010

Oncology Letters

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Abstract. gastric cancer is a commonly diagnosed solid tumor which is associated with a dismal prognosis making early diagnosis essential. thus, this study aimed to identify novel biomarkers in gastric cancer. serum of patients with advanced gastric cancer was collected according to a predefined schedule: prior to first-line chemotherapy with epirubicin (50 mg/m 2 , day 1), cisplatin (60 mg/m 2 , day 1) and capecitabine (1,000 mg/m 2 , twice daily on days 1-14). the serum was collected serially before the treatment cycles and then analyzed by selDI-toF Ms. normal control subjects were matched according to age, gender and serum collection. serum proteomic mass spectrometry data of all subjects were processed using the tbimass r-package and compared. We analyzed i) whether proteomic profile changes were associated with a response to chemotherapy and survival, and ii) whether changes in proteomic profiles occurring during the time period of chemotherapy were associated with tumor response. In total, 82 patients with adenocarcinoma of the stomach (mean age 57 years, males 69.5%) were treated with a mean number of five chemotherapy cycles. The overall tumor response rate, complete and partial remission combined, was 37%, median time to progression was 7 months (95% cI, 6-8) and median overall survival 11 months (95% cI, 9.5-12). By comparing 77 serum samples of patients with normal matched controls, we identified 32 proteins which discriminated the two groups. By selecting the most differentiating proteins, we built a classification model that correctly categorized 81% of the gastric cancer patients and 90% of the normal controls.Furthermore, we found a statistically significant correlation between the pre-treatment intensity of serum amyloid-α (sAA) and overall survival in gastric cancer patients, whereby a low intensity of sAA predicted a longer patient survival. A classification model, based on the 32 most discriminating proteins differentiating gastric cancer from normal controls, correctly classified subjects with relatively high sensitivity and specificity.

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Section: Discussionsupporting

confidence: 73%

Serum proteomics and disease-specific biomarkers of patients with advanced gastric cancer

Helgason

Engwegen²,

Zapatka³

et al. 2010

Oncology Letters

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“…In cases where multiple identifications were made from the same gel spots, all protein groups are reported. Identification of differential SELDI‐TOF peaks was carried out essentially as described 17. Briefly, proteins were fractionated by LC and ultrafiltration and identified either by direct MS/MS sequencing (<5 kDa) or purified by SDS‐PAGE prior to staining, excision, tryptic digestion, and MS/MS (>5 kDa).…”

Section: Methodsmentioning

confidence: 99%

“…Despite this, proteomic coverage is still limited and few if any robust cancer biomarkers have been identified using classical proteomic profiling methods. The need for identical handling of clinical samples is also of paramount importance in order to avoid largely proteolysis‐driven changes unrelated to biological variation and has been highlighted by numerous studies 12, 13, 14, 15, 16, 17. Finally, issues related to reproducibility and the robustness of class‐discriminating algorithms used for proteomic biomarker discovery have also been raised 18, 19.…”

Section: Introductionmentioning

confidence: 99%

Discovery of serum biomarkers of ovarian cancer using complementary proteomic profiling strategies

Timms

Arslan-Low

Kabir

et al. 2014

Proteomics Clinical Apps

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PurposeOvarian cancer is a devastating disease and biomarkers for its early diagnosis are urgently required. Serum may be a valuable source of biomarkers that may be revealed by proteomic profiling. Herein, complementary serum protein profiling strategies were employed for discovery of biomarkers that could discriminate cases of malignant and benign ovarian cancer.Experimental designIdentically collected and processed serum samples from 22 cases of invasive epithelial ovarian cancer, 45 benign ovarian neoplasms, and 64 healthy volunteers were subjected to immunodepletion and protein equalization coupled to 2D‐DIGE/MS and multidimensional fractionation coupled to SELDI‐TOF profiling with MS/MS for protein identification. Selected candidates were verified by ELISA in samples from malignant (n = 70) and benign (n = 89) cases and combined marker panels tested against serum CA125.ResultsBoth profiling platforms were complementary in identifying biomarker candidates, four of which (A1AT, SLPI, APOA4, VDBP) significantly discriminated malignant from benign cases. However, no combination of markers was as good as CA125 for diagnostic accuracy. SLPI was further tested as an early marker using prediagnosis serum samples. While it rose in cases toward diagnosis, it did not discriminate prediagnosis cases from controls.Conclusions and clinical relevanceThe candidate biomarkers warrant further validation in independent sample sets.

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“…on analytical outcome, particularly for protein and proteomic studies (3,(8)(9)(10)(11). A recent perspective on the subject has been put forward with specific focus on proteome analyses of blood (12).…”

Section: Introductionmentioning

confidence: 99%

Thrombin induces broad spectrum proteolysis in human serum samples

O'Mullan¹,

Craft²,

Yi³

et al. 2009

Clinical Chemistry and Laboratory Medicine

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Background: During clotting, a thrombin cleaves fibrinogen releasing fibrinopeptide A (FPA). FPA is easily identified in serum using matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry (MS). Using MALDI-TOF MS, we observed multiple, progressively shorter fragments of serum FPA. Following ambient incubation of serum, variations in the content of FPA fragments occur over time. Denaturation of a thrombin by heating the serum sample appears to minimize this variation. These observations suggest that intrinsic proteolytic and peptidolytic activity is elevated in serum and perhaps originates from the coagulation cascade enzymes themselves, especially a thrombin. Methods: Extrinsic addition of a thrombin to a subset (3-30 kDa) of plasma proteins was carried out to induce proteolysis and to examine the resultant peptides to reveal a thrombin susceptible parent proteins. One of these identified proteins, hemopexin, was directly digested by a thrombin and the peptides examined to confirm the observations from the initial plasma protein digestion. Results: Extrinsic addition of a thrombin to a subset (3-30 kDa) of plasma proteins results in wide-spread digestion of proteins unrelated to coagulation, revealing a substrate range encompassing more than fibrinogen. Direct digestion of one of these proteins, hemopexin, by a thrombin confirms these observations. Conclusions: The resulting peptides indicate broad tolerance beyond the consensus R-G cleavage site of fibrinogen; in fact, there appears to be no bias for the amino acid following the R/K residue. These data support our hypothesis that the enzymatic activities inherent to coagulation, or at least to thrombin, contribute to destabilization of the protein and peptide content of serum. Clin Chem Lab Med 2009;47:685-93.

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Preanalytic Influence of Sample Handling on SELDI-TOF Serum Protein Profiles

Cited by 130 publications

References 36 publications

Serum proteomics and disease-specific biomarkers of patients with advanced gastric cancer

Serum proteomics and disease-specific biomarkers of patients with advanced gastric cancer

Discovery of serum biomarkers of ovarian cancer using complementary proteomic profiling strategies

Thrombin induces broad spectrum proteolysis in human serum samples

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