Hasmik Grigoryan

Profiling Cys34 Adducts of Human Serum Albumin by Fixed-Step Selected Reaction Monitoring

A method is described for profiling putative adducts (or other unknown covalent modifications) at the Cys34 locus of human serum albumin (HSA), which represents the preferred reaction site for small electrophilic species in human serum. By comparing profiles of putative HSA-Cys34 adducts across populations of interest it is theoretically possible to explore environmental causes of degenerative diseases and cancer caused by both exogenous and endogenous chemicals. We report a novel application of selected-reaction-monitoring (SRM) mass spectrometry, termed fixed-step SRM (FS-SRM), that allows detection of essentially all HSA-Cys34 modifications over a specified range of mass increases (added masses). After tryptic digestion, HSA-Cys34 adducts are contained in the third largest peptide (T3), which contains 21 amino acids and an average mass of 2433.87 Da. The FS-SRM method does not require that exact masses of T3 adducts be known in advance but rather uses a theoretical list of T3-adduct m/z values separated by a fixed increment of 1.5. In terms of added masses, each triply charged parent ion represents a bin of ±2.3 Da between 9.1 Da and 351.1 Da. Synthetic T3 adducts were used to optimize FS-SRM and to establish screening rules based upon selected b- and y-series fragment ions. An isotopically labeled T3 adduct is added to protein digests to facilitate quantification of putative adducts. We used FS-SRM to generate putative adduct profiles from six archived specimens of HSA that had been pooled by gender, race, and smoking status. An average of 66 putative adduct hits (out of a possible 77) were detected in these samples. Putative adducts covered a wide range of concentrations, were most abundant in the mass range below 100 Da, and were more abundant in smokers than in nonsmokers. With minor modifications, the FS-SRM methodology can be applied to other nucleophilic sites and proteins.

Cys34 adducts of reactive oxygen species in human serum albumin.

Long-term exposures to reactive oxygen species (ROS) have been linked to scores of chronic diseases. This has motivated interest in oxidation products of the only free cysteine residue (Cys34) of human serum albumin (HSA) as possible biomarkers of ROS exposure. However, Cys34 oxidation products have not been detected in human serum or plasma. Using liquid chromatography-high resolution tandem mass spectrometry, we report accurate masses and molecular compositions of Cys34 oxidation products in the 2432 Da peptide resulting from tryptic digestion of HSA. Peptides containing the expected sulfinic (Cys-SO(2)H) and sulfonic (Cys-SO(3)H) acids, as well as an adduct representing addition of one oxygen atom and loss of two hydrogen atoms, were detected in four archived samples of human plasma and one fresh sample of human serum. We speculate that this latter adduct is a sulfinamide formed by intramolecular reaction between either the Cys34 sulfenic acid (Cys-SOH) or sulfinic acid (Cys-SO(2)H) and the adjacent glutamine residue (Gln33). All three Cys34 adducts were measured in the five human samples with levels decreasing in the order sulfinic acid > (proposed) sulfinamide > sulfonic acid. Parallel measurements of a negative control detected only small amounts of the Cys34 sulfonic acid and the (proposed) sulfinamide and did not detect the sulfinic acid.

Antibody enrichment and mass spectrometry of albumin-Cys34 adducts.

Untargeted analyses of tryptic peptides of human serum albumin (HSA) have been used to investigate unknown exposures to reactive electrophiles (adductomics). To reduce the complexity of the analytical matrix and thereby enhance identification of adducts by liquid chromatography-high-resolution mass spectrometry (LC-HRMS), a polyclonal anti-T3 antibody was designed to capture Cys34 adducts in tryptic digests of HSA (T3 is the third largest tryptic peptide). Epitopes were selected from sequences at both C- and N-termini based on the three-dimensional structure of the T3 peptide to minimize the influence of modified Cys34 residues. The assay was simplified by attaching magnetic beads to the anti-T3 antibody. When applied to commercial HSA and to plasma samples from healthy humans and analyzed by LC-HRMS, antibody treatment greatly reduced the background of non-T3 peptides in the sample matrix. Although other lipophilic HSA peptides were still present, presumably due to nonspecific binding to the antibody-magnetic-bead surfaces, their concentrations in antibody-treated samples were reduced about 6-fold compared to the same samples that had not been treated with the antibody. Analysis of antibody-enriched HSA digests from human plasma samples revealed 10 modified T3 peptides of which 8 were identified from accurate masses. Identified peptides included Cys34 oxidation and cysteinylation products and modifications representing losses of water and Lys and transpeptidation of Arg.

Adductomic signatures of benzene exposure provide insights into cancer induction

Although benzene has long been recognized as a cause of human leukemia, the mechanism by which this simple molecule causes cancer has been problematic. A complicating factor is benzene metabolism, which produces many reactive intermediates, some specific to benzene and others derived from redox processes. Using archived serum from 20 nonsmoking Chinese workers, 10 with and 10 without occupational exposure to benzene (exposed: 3.2-88.9 ppm, controls: 0.002-0.020 ppm), we employed an adductomic pipeline to characterize protein modifications at Cys34 of human serum albumin, a nucleophilic hotspot in extracellular fluids. Of the 47 measured human serum albumin modifications, 39 were present at higher concentrations in benzene-exposed workers than in controls and many of the exposed-control differences were statistically significant. Correlation analysis identified three prominent clusters of adducts, namely putative modifications by benzene oxide and a benzene diolepoxide that grouped with other measures of benzene exposure, adducts of reactive oxygen and carbonyl species, and Cys34 disulfides of small thiols that are formed following oxidation of Cys34. Benzene diolepoxides are potent mutagens and carcinogens that have received little attention as potential causes of human leukemia. Reactive oxygen and carbonyl species-generated by redox processes involving polyphenolic benzene metabolites and by Cyp2E1 regulation following benzene exposure-can modify DNA and proteins in ways that contribute to cancer. The fact that these diverse human serum albumin modifications differed between benzene-exposed and control workers suggests that benzene can increase leukemia risks via multiple pathways involving a constellation of reactive molecules.

Using lysine adducts of human serum albumin to investigate the disposition of exogenous formaldehyde in human blood

Formaldehyde is a human carcinogen that readily binds to nucleophiles, including proteins and DNA. To investigate whether exogenous formaldehyde produces adducts in extracellular fluids, we characterized modifications to human serum albumin (HSA) following incubation of whole blood, plasma, and saliva with formaldehyde at concentrations of 1, 10 and 100μM. The only HSA locus that showed the presence of formaldehyde modifications was Lys199. A N(6)-Lys adduct with added mass of 12Da, representing a putative intramolecular crosslink, was detected in biological fluids that had been incubated with formaldehyde but not in control fluids. An adduct representing N(6)-Lys formylation was detected in all fluids, but levels did not increase above control values over the tested range of formaldehyde concentrations. An adduct representing N(6)-Lys199 acetylation was also measured in all samples. We then applied the assay to repeated samples of human plasma from 6 nonsmoking volunteer subjects (from Berkeley, CA), and single samples of serum from 15 workers exposed to airborne formaldehyde at about 1.5ppm in a production facility and 15 control workers from Tianjin, China. Although all human plasma/serum samples contained basal levels of the products of N(6)-Lys formylation and acetylation, the putative crosslink product was not detected. Since the putative crosslink was observed in plasma incubated with formaldehyde at 1μM, this suggests that the endogenous concentration of formaldehyde in serum was much lower than reported in the literature. Furthermore, concentrations of the formyl adduct were not higher in workers exposed to formaldehyde at about 1.5ppm than in controls. Follow-up in vitro experiments with gaseous formaldehyde at 1.4ppm detected the putative crosslink in plasma but not whole blood. This combination of results suggests that N(6) formylation occurs within cells with subsequent release of adducted HSA to the systemic circulation. Comparing across human samples, levels of N(6)-Lys199 formyl adducts were present at similar concentrations in subjects from California and China (about 1mmol/mol HSA), but N(6)-Lys199 acetyl adducts were present at higher concentrations in Chinese subjects (0.34 vs. 0.13mmol/mol HSA).

Evaluating Ultra-long Chain Fatty Acids as Biomarkers of Colorectal Cancer Risk

Background: Cross-sectional studies reported a novel set of hydroxylated ultra-long-chain fatty acids (ULCFA) that were present at significantly lower levels in colorectal cancer cases than controls. Follow-up studies suggested that these molecules were potential biomarkers of protective exposure for colorectal cancer. To test the hypothesis that ULCFAs reflect causal pathways, we measured their levels in prediagnostic serum from incident colorectal cancer cases and controls. Methods: Serum from 95 colorectal cancer patients and 95 matched controls was obtained from the Italian arm of the European Prospective Investigation into Cancer and Nutrition cohort and analyzed by liquid chromatography–high-resolution mass spectrometry. Levels of 8 ULCFAs were compared between cases and controls with paired t tests and a linear model that used time to diagnosis (TTD) to determine whether case–control differences were influenced by disease progression. Results: Although paired t tests detected significantly lower levels of four ULCFAs in colorectal cancer cases, confirming earlier reports, the case–control differences diminished significantly with increasing TTD (7 days–14 years). Conclusion: Levels of several ULCFAs were lower in incident colorectal cancer cases than controls. However, because case–control differences decreased with increasing TTD, we conclude that these molecules were likely consumed by processes related to cancer progression rather than causal pathways. Impact: ULCFA levels are unlikely to represent exposures that protect individuals from colorectal cancer. Future research should focus on the diagnostic potential and origins of these molecules. Our use of TTD as a covariate in a linear model provides an efficient method for distinguishing causal and reactive biomarkers in biospecimens from prospective cohorts. Cancer Epidemiol Biomarkers Prev; 25(8); 1216–23. ©2016 AACR.

Cys34 Adductomes Differ between Patients with Chronic Lung or Heart Disease and Healthy Controls in Central London

Oxidative stress generates reactive species that modify proteins, deplete antioxidant defenses, and contribute to chronic obstructive pulmonary disease (COPD) and ischemic heart disease (IHD). To determine whether protein modifications differ between COPD or IHD patients and healthy subjects, we performed untargeted analysis of adducts at the Cys34 locus of human serum albumin (HSA). Biospecimens were obtained from nonsmoking participants from London, U.K., including healthy subjects (n = 20) and patients with COPD (n = 20) or IHD (n = 10). Serum samples were digested with trypsin and analyzed by liquid chromatography-high resolution mass spectrometry. Effects of air pollution on adduct levels were also investigated based on estimated residential exposures to PM2.5, O3 and NO2. For the 39 adducts with sufficient data, levels were essentially identical in blood samples collected from the same subjects on two consecutive days, consistent with the 28 day residence time of HSA. Multivariate linear regression revealed 21 significant associations, mainly with the underlying diseases but also with air-pollution exposures (p-value < 0.05). Interestingly, most of the associations indicated that adduct levels decreased with the presence of disease or increased pollutant concentrations. Negative associations of COPD and IHD with the Cys34 disulfide of glutathione and two Cys34 sulfoxidations, were consistent with previous results from smoking and nonsmoking volunteers and nonsmoking women exposed to indoor combustion of coal and wood.

Untargeted lipidomic features associated with colorectal cancer in a prospective cohort

BackgroundEpidemiologists are beginning to employ metabolomics and lipidomics with archived blood from incident cases and controls to discover causes of cancer. Although several such studies have focused on colorectal cancer (CRC), they all followed targeted or semi-targeted designs that limited their ability to find discriminating molecules and pathways related to the causes of CRC.MethodsUsing an untargeted design, we measured lipophilic metabolites in prediagnostic serum from 66 CRC patients and 66 matched controls from the European Prospective Investigation into Cancer and Nutrition (Turin, Italy). Samples were analyzed by liquid chromatography-high-resolution mass spectrometry (LC-MS), resulting in 8690 features for statistical analysis.ResultsRather than the usual multiple-hypothesis-testing approach, we based variable selection on an ensemble of regression methods, which found nine features to be associated with case-control status. We then regressed each selected feature on time-to-diagnosis to determine whether the feature was likely to be either a potentially causal biomarker or a reactive product of disease progression (reverse causality).ConclusionsOf the nine selected LC-MS features, four appear to be involved in CRC etiology and merit further investigation in prospective studies of CRC. Four other features appear to be related to progression of the disease (reverse causality), and may represent biomarkers of value for early detection of CRC.