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It is a challenging task to verify and quantify potential biomarkers expressed at elevated levels in sera from cancer patients. An immunoaffinity-mass spectrometry-based approach has been developed using antibodies to enrich proteins of interest from sera followed by mass spectrometry-based quantification. Antibodies specific to the protein of interest were immobilized to hydrazide resin via the carbohydrate moiety on the Fc region of the antibody. Captured proteins were eluted, reduced, alkylated, and digested with trypsin. Peptides were analyzed by LC coupled with multiple reaction monitoring approach, and quantification was achieved by the addition of stable isotope-labeled (heavy) standard peptides. Using this methodology, we were able to achieve a linear response from 15 to 250 ng/ml for carcinoembryonic antigen (CEA), a known tumor biomarker. Moreover we observed elevated levels of CEA in sera samples from lung cancer patients that to our knowledge is the first time that circulating CEA has been detected by mass spectrometry-based analysis. This approach was further applied to potential protein biomarkers discovered from tumor cell lines and tumor tissues. A linear response was obtained from a multiplex spiking experiment in normal human sera for secretory leukocyte peptidase inhibitor (4-500 ng/ml), tissue factor pathway inhibitor (TFPI) (42-1000 ng/ml), tissue factor pathway inhibitor 2 (TFPI2) (2-250 ng/ml), and metalloproteinase inhibitor 1 (TIMP1) (430-1000 ng/ml). A replicate experiment for a single concentration value yielded a relative coefficient of variation better than 11% for TFPI, secretory leukocyte peptidase inhibitor, and TFPI2. The expression level of the proteins in lung cancer patient sera was assayed by an immunoaffinity-multiple reaction monitoring method, and the results were comparable with those obtained from ELISA. This immunoaffinity-mass spectrometry-based quantification approach thus provides a specific and accurate assay for verifying the expression of potential biomarkers in patient serum samples especially for those proteins for which the necessary reagents for ELISA development are unavailable.

Background: Support for early detection of lung cancer has emerged from the National Lung Screening Trial (NLST), in which low-dose computed tomography (LDCT) screening reduced lung cancer mortality by 20 % relative to chest x-ray. The US Preventive Services Task Force (USPSTF) recently recommended annual screening for the high-risk population, concluding that the benefits (life years gained) outweighed harms (false positive findings, abortive biopsy/surgery, radiation exposure). In making their recommendation, the USPSTF noted that the moderate net benefit of screening was dependent on the resolution of most false-positive results without invasive procedures. Circulating biomarkers may serve as a valuable adjunctive tool to imaging. Results: We developed a broad-based proteomics discovery program, integrating liquid chromatography/mass spectrometry (LC/MS) analyses of freshly resected lung tumor specimens (n = 13), lung cancer cell lines (n = 17), and conditioned media collected from tumor cell lines (n = 7). To enrich for biomarkers likely to be found at elevated levels in the peripheral circulation of lung cancer patients, proteins were prioritized based on predicted subcellular localization (secreted, cell-membrane associated) and differential expression in disease samples. 179 candidate biomarkers were identified. Several markers selected for further validation showed elevated levels in serum collected from subjects with stage I NSCLC (n = 94), relative to healthy smoker controls (n = 189). An 8-marker model was developed (TFPI, MDK, OPN, MMP2, TIMP1, CEA, CYFRA 21-1, SCC) which accurately distinguished subjects with lung cancer (n = 50) from high risk smokers (n = 50) in an independent validation study (AUC = 0.775). Conclusions: Integrating biomarker discovery from multiple sample types (fresh tissue, cell lines and conditioned medium) has resulted in a diverse repertoire of candidate biomarkers. This unique collection of biomarkers may have clinical utility in lung cancer detection and diagnoses. [ABSTRACT FROM AUTHOR]

Obesity is a major risk factor for a number of disorders ranging from type II diabetes to cardiovascular disease, however, the molecular basis for these associations has not been be fully clarified. A number of adipokines, cytokines expressed exclusively or at an elevated level in adipose tissue, have been identified that play key roles in regulating energy homeostasis by affecting insulin sensitivity, glucose and lipid metabolism and satiety. Dysregulated expression of adipokines may link obesity with its related metabolic disorders. We have developed a proteomics platform that enables the direct identification and functional characterization of adipokines from cells derived from human subcutaneous and visceral adipose depots. Adipocytes isolated from different fat depots (subcutaneous and visceral) from subjects with a spectrum of BMI (19-42) and diabetic progression, were subjected to Mass Spectrometric (MS) analyses. Preadipocytes isolated from adipose tissue were differentiated for 2 weeks, before being incubated in conditioned medium. Secreted and shed proteins released into the medium were labeled with ICAT and digested with trypsin. The cysteine-containing peptides were subjected to Liquid Chromatography (LC) / MS analysis. Peptide maps representing different adipocyte populations were compared and candidates that were differentially expressed were selected. Sequence-composition was resolved through tandem MS and database search. The functionality of a number of these adipokines was evaluated in a series of RNAi-based assays, established in human adipocytes, to determine the possible involvement of these secreted proteins in key metabolic transitions including: lipolysis and glucose uptake. Our systematic proteomic analysis has resulted in the identification of > 20 adipokines. A number of previously characterized secreted proteins, including visfatin and complement C1r were identified. In addition, a number of novel candidates that included: a protease inhibitor, a hydrolase and a molecule involved in cell-adhesion, were also resolved. Interestingly, subsequent comparison of the MS maps within the adipocyte samples revealed significant differences in expression of secreted / shed proteins isolated from: (i) subcutaneous and visceral depots, (ii) lean and obese subjects and (iii) normal and diabetic patients. [ABSTRACT FROM AUTHOR]