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Reijnders E, van der Laarse A, Ruhaak LR, Cobbaert CM. Closing the gaps in patient management of dyslipidemia: stepping into cardiovascular precision diagnostics with apolipoprotein profiling. Clin Proteomics 2024; 21:19. [PMID: 38429638 PMCID: PMC10908091 DOI: 10.1186/s12014-024-09465-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Accepted: 02/14/2024] [Indexed: 03/03/2024] Open
Abstract
In persons with dyslipidemia, a high residual risk of cardiovascular disease remains despite lipid lowering therapy. Current cardiovascular risk prediction mainly focuses on low-density lipoprotein cholesterol (LDL-c) levels, neglecting other contributing risk factors. Moreover, the efficacy of LDL-c lowering by statins resulting in reduced cardiovascular risk is only partially effective. Secondly, from a metrological viewpoint LDL-c falls short as a reliable measurand. Both direct and calculated LDL-c tests produce inaccurate test results at the low end under aggressive lipid lowering therapy. As LDL-c tests underperform both clinically and metrologically, there is an urging need for molecularly defined biomarkers. Over the years, apolipoproteins have emerged as promising biomarkers in the context of cardiovascular disease as they are the functional workhorses in lipid metabolism. Among these, apolipoprotein B (ApoB), present on all atherogenic lipoprotein particles, has demonstrated to clinically outperform LDL-c. Other apolipoproteins, such as Apo(a) - the characteristic apolipoprotein of the emerging risk factor lipoprotein(a) -, and ApoC-III - an inhibitor of triglyceride-rich lipoprotein clearance -, have attracted attention as well. To support personalized medicine, we need to move to molecularly defined risk markers, like the apolipoproteins. Molecularly defined diagnosis and molecularly targeted therapy require molecularly measured biomarkers. This review provides a summary of the scientific validity and (patho)physiological role of nine serum apolipoproteins, Apo(a), ApoB, ApoC-I, ApoC-II, ApoC-III, ApoE and its phenotypes, ApoA-I, ApoA-II, and ApoA-IV, in lipid metabolism, their association with cardiovascular disease, and their potential as cardiovascular risk markers when measured in a multiplex apolipoprotein panel.
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Affiliation(s)
- Esther Reijnders
- Department of Clinical Chemistry and Laboratory Medicine, Leiden University Medical Center, Leiden, the Netherlands.
| | - Arnoud van der Laarse
- Department of Clinical Chemistry and Laboratory Medicine, Leiden University Medical Center, Leiden, the Netherlands
| | - L Renee Ruhaak
- Department of Clinical Chemistry and Laboratory Medicine, Leiden University Medical Center, Leiden, the Netherlands
| | - Christa M Cobbaert
- Department of Clinical Chemistry and Laboratory Medicine, Leiden University Medical Center, Leiden, the Netherlands
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Diederiks NM, Ruhaak LR, Romijn FPHTM, Pieterse MM, Smit NPM, Cobbaert CM. An LC-MS-based designated comparison method with similar performance to the Lp(a) reference measurement procedure to guide molar Lp(a) standardization. Clin Proteomics 2024; 21:5. [PMID: 38267848 PMCID: PMC10809433 DOI: 10.1186/s12014-023-09446-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Accepted: 12/07/2023] [Indexed: 01/26/2024] Open
Abstract
BACKGROUND The 2022 consensus statement of the European Atherosclerosis Society (EAS) on lipoprotein(a) (Lp(a)) recognizes the role of Lp(a) as a relevant genetically determined risk factor and recommends its measurement at least once in an individual's lifetime. It also strongly urges that Lp(a) test results are expressed as apolipoprotein (a) (apo(a)) amount of substance in molar units and no longer in confounded Lp(a) mass units (mg/dL or mg/L). Therefore, IVD manufacturers should transition to molar units. A prerequisite for this transition is the availability of an Lp(a) Reference Measurement Procedure (RMP) that allows unequivocal molecular detection and quantification of apo(a) in Lp(a). To that end an ISO 17511:2020 compliant LC-MS based and IFCC-endorsed RMP has been established that targets proteotypic peptides of apolipoprotein(a) (apo(a)) in Lp(a). The RMP is laborious and requires highly skilled operators. To guide IVD-manufacturers of immunoassay-based Lp(a) test kits in the transition from mass to molar units, a Designated Comparison Method (DCM) has been developed and evaluated. METHODS To assess whether the DCM provides equivalent results compared to the RMP, the procedural designs were compared and the analytical performance of DCM and RMP were first evaluated in a head-to-head comparison. Subsequently, apo(a) was quantified in 153 human clinical serum samples. Both DCM and RMP were calibrated using external native calibrators that produce results traceable to SRM2B. Measurement uncertainty (MU) was checked against predefined allowable MU. RESULTS The major difference in the design of the DCM for apo(a) is the use of only one enzymatic digestion step. The analytical performance of the DCM and RMP for apo(a) is highly similar. In a direct method comparison, equivalent results were obtained with a median regression slope 0.997 of and a median bias of - 0.2 nmol/L (- 0.2%); the intermediate imprecision of the test results was within total allowable error (TEa) (CVa of 10.2% at 90 nmol/L). CONCLUSIONS The semi-automated, higher throughput, LC-MS-based method for Lp(a) meets the predefined analytical performance specifications and allowable MU and is hence applicable as a higher order Designated Comparison Method, which is ideally suited to guide IVD manufacturers in the transition from Lp(a) mass to molar units.
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Affiliation(s)
- Nina M Diederiks
- Department of Clinical Chemistry and Laboratory Medicine, Leiden University Medical Center, Postzone E2-P, Albinusdreef 2, 2333 ZA, Leiden, The Netherlands
| | - L Renee Ruhaak
- Department of Clinical Chemistry and Laboratory Medicine, Leiden University Medical Center, Postzone E2-P, Albinusdreef 2, 2333 ZA, Leiden, The Netherlands
| | - Fred P H T M Romijn
- Department of Clinical Chemistry and Laboratory Medicine, Leiden University Medical Center, Postzone E2-P, Albinusdreef 2, 2333 ZA, Leiden, The Netherlands
| | - Mervin M Pieterse
- Department of Clinical Chemistry and Laboratory Medicine, Leiden University Medical Center, Postzone E2-P, Albinusdreef 2, 2333 ZA, Leiden, The Netherlands
| | - Nico P M Smit
- Department of Clinical Chemistry and Laboratory Medicine, Leiden University Medical Center, Postzone E2-P, Albinusdreef 2, 2333 ZA, Leiden, The Netherlands
| | - Christa M Cobbaert
- Department of Clinical Chemistry and Laboratory Medicine, Leiden University Medical Center, Postzone E2-P, Albinusdreef 2, 2333 ZA, Leiden, The Netherlands.
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Szarek M, Reijnders E, Jukema JW, Bhatt DL, Bittner VA, Diaz R, Fazio S, Garon G, Goodman SG, Harrington RA, Ruhaak LR, Schwertfeger M, Tsimikas S, White HD, Steg PG, Cobbaert C, Schwartz GG. Relating Lipoprotein(a) Concentrations to Cardiovascular Event Risk After Acute Coronary Syndrome: A Comparison of 3 Tests. Circulation 2024; 149:192-203. [PMID: 37632469 PMCID: PMC10782942 DOI: 10.1161/circulationaha.123.066398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Accepted: 08/23/2023] [Indexed: 08/28/2023]
Abstract
BACKGROUND Lipoprotein(a) is a risk factor for cardiovascular events and modifies the benefit of PCSK9 (proprotein convertase subtilisin/kexin type 9) inhibitors. Lipoprotein(a) concentration can be measured with immunoassays reporting mass or molar concentration or a reference measurement system using mass spectrometry. Whether the relationships between lipoprotein(a) concentrations and cardiovascular events in a high-risk cohort differ across lipoprotein(a) methods is unknown. We compared the prognostic and predictive value of these types of lipoprotein(a) tests for major adverse cardiovascular events (MACE). METHODS The ODYSSEY OUTCOMES trial (Evaluation of Cardiovascular Outcomes After an Acute Coronary Syndrome During Treatment With Alirocumab) compared the PCSK9 inhibitor alirocumab with placebo in patients with recent acute coronary syndrome. We compared risk of a MACE in the placebo group and MACE risk reduction with alirocumab according to baseline lipoprotein(a) concentration measured by Siemens N-latex nephelometric immunoassay (IA-mass; mg/dL), Roche Tina-Quant turbidimetric immunoassay (IA-molar; nmol/L), and a noncommercial mass spectrometry-based test (MS; nmol/L). Lipoprotein(a) values were transformed into percentiles for comparative modeling. Natural cubic splines estimated continuous relationships between baseline lipoprotein(a) and outcomes in each treatment group. Event rates were also determined across baseline lipoprotein(a) quartiles defined by each assay. RESULTS Among 11 970 trial participants with results from all 3 tests, baseline median (Q1, Q3) lipoprotein(a) concentrations were 21.8 (6.9, 60.0) mg/dL, 45.0 (13.2, 153.8) nmol/L, and 42.2 (14.3, 143.1) nmol/L for IA-mass, IA-molar, and MS, respectively. The strongest correlation was between IA-molar and MS (r=0.990), with nominally weaker correlations between IA-mass and MS (r=0.967) and IA-mass and IA-molar (r=0.972). Relationships of lipoprotein(a) with MACE risk in the placebo group were nearly identical with each test, with estimated cumulative incidences differing by ≤0.4% across lipoprotein(a) percentiles, and all were incrementally prognostic after accounting for low-density lipoprotein cholesterol levels (all spline P≤0.0003). Predicted alirocumab treatment effects were also nearly identical for each of the 3 tests, with estimated treatment hazard ratios differing by ≤0.07 between tests across percentiles and nominally less relative risk reduction by alirocumab at lower percentiles for all 3 tests. Absolute risk reduction with alirocumab increased with increasing lipoprotein(a) measured by each test, with significant linear trends across quartiles. CONCLUSIONS In patients with recent acute coronary syndrome, 3 lipoprotein(a) tests were similarly prognostic for MACE in the placebo group and predictive of MACE reductions with alirocumab at the cohort level. REGISTRATION URL: https://www.clinicaltrials.gov; Unique identifier: NCT01663402.
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Affiliation(s)
- Michael Szarek
- Division of Cardiology, University of Colorado School of Medicine, Aurora (M. Szarek, G.G.S.)
- CPC Clinical Research, Aurora, CO (M. Szarek)
- State University of New York, Downstate Health Sciences University, Brooklyn (M. Szarek)
| | - Esther Reijnders
- Departments of Clinical Chemistry and Laboratory Medicine (E.R., L.R.R., C.C.), Leiden University Medical Center, the Netherlands
| | - J. Wouter Jukema
- Cardiology (J.W.J.), Leiden University Medical Center, the Netherlands
- Netherlands Heart Institute, Utrecht (J.W.J.)
| | - Deepak L. Bhatt
- Mount Sinai Heart, Icahn School of Medicine at Mount Sinai Health System, New York, NY (D.L.B.)
| | - Vera A. Bittner
- Division of Cardiovascular Disease, University of Alabama at Birmingham (V.A.B.)
| | - Rafael Diaz
- Estudios Cardiológicos Latino América, Instituto Cardiovascular de Rosario, Argentina (R.D.)
| | - Sergio Fazio
- Regeneron Pharmaceuticals Inc, Tarrytown, NY (S.F.)
| | | | - Shaun G. Goodman
- Canadian VIGOUR Centre, University of Alberta, Edmonton, Canada (S.G.G.)
- St Michael’s Hospital, University of Toronto, Ontario, Canada (S.G.G.)
| | - Robert A. Harrington
- Stanford Center for Clinical Research, Department of Medicine, Stanford University, CA (R.A.H.)
| | - L. Renee Ruhaak
- Departments of Clinical Chemistry and Laboratory Medicine (E.R., L.R.R., C.C.), Leiden University Medical Center, the Netherlands
| | | | - Sotirios Tsimikas
- Sulpizio Cardiovascular Center, Division of Cardiovascular Medicine, University of California San Diego, La Jolla (S.T.)
| | - Harvey D. White
- Green Lane Cardiovascular Research Unit, Te Whatu Ora–Health New Zealand, Te Toka Tumai, and University of Auckland, New Zealand (H.D.W.)
| | - P. Gabriel Steg
- Université Paris-Cité, INSERM-UMR1148, Assistance Publique-Hôpitaux de Paris, Hôpital Bichat, FACT (French Alliance for Cardiovascular Trials), and Institut Universitaire de France, Paris (P.G.S.)
| | - Christa Cobbaert
- Departments of Clinical Chemistry and Laboratory Medicine (E.R., L.R.R., C.C.), Leiden University Medical Center, the Netherlands
| | - Gregory G. Schwartz
- Division of Cardiology, University of Colorado School of Medicine, Aurora (M. Szarek, G.G.S.)
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Diederiks NM, van der Burgt YEM, Ruhaak LR, Cobbaert CM. Developing an SI-traceable Lp(a) reference measurement system: a pilgrimage to selective and accurate apo(a) quantification. Crit Rev Clin Lab Sci 2023; 60:483-501. [PMID: 37128734 DOI: 10.1080/10408363.2023.2199353] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Revised: 03/14/2023] [Accepted: 04/01/2023] [Indexed: 05/03/2023]
Abstract
In the past decade a remarkable rebirth of serum/plasma lipoprotein(a) (Lp(a)) as an independent risk factor of cardiovascular disease (CVD) occurred. Updated evidence for a causal continuous association in different ethnic groups between Lp(a) concentrations and cardiovascular outcomes has been published in the latest European Atherosclerosis Society (EAS) Lp(a) consensus statement. Interest in measuring Lp(a) at least once in a person's lifetime moreover originates from the development of promising new Lp(a) lowering drugs. Accurate and clinically effective Lp(a) tests are of key importance for the timely detection of high-risk individuals and for future evaluation of the therapeutic effects of Lp(a) lowering medication. To this end, it is necessary to improve the performance and standardization of existing Lp(a) tests, as is also noted in the Lp(a) consensus statement. Consequently, a state-of-the-art internationally endorsed reference measurement system (RMS) must be in place that allows for performance evaluation of Lp(a) field tests in order to certify their validity and accuracy. An ELISA-based RMS from Northwest Lipid Research Laboratory (University of Washington, Seattle, USA) has been available since the 1990s. A next-generation apo(a)/Lp(a) RMS is now being developed by a working group from the International Federation of Clinical Chemistry and Laboratory Medicine (IFCC). The envisioned apo(a) RMS is based on the direct measurement of selected proteotypic fragments generated after proteolytic digestion using quantitative protein mass spectrometry (MS). The choice for an MS-based RMS enables selective measurement of the proteotypic peptides and is by design apo(a) isoform insensitive. Clearly, the equimolar conversion of apo(a) into the surrogate peptide measurands is required to obtain accurate Lp(a) results. The completeness of proteolysis under reaction conditions from the candidate reference measurement procedure (RMP) has been demonstrated for the quantifying apo(a) peptides. Currently, the candidate apo(a) RMP is endorsed by the IFCC and recommendations for suitable secondary reference materials have been made in a recent commutability study paper. Ongoing efforts toward a complete apo(a) RMS that is listed by the Joint Committee on Traceability in Laboratory Medicine (JCTLM) are focused on the peptide-based calibration and the establishment of a network of calibration laboratories running the apo(a) RMS in a harmonized way. Once completed, it will be the holy grail for evaluation and certification of Lp(a) field methods.
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Affiliation(s)
- Nina M Diederiks
- Department of Clinical Chemistry and Laboratory Medicine, Leiden University Medical Center, Leiden, ZA, The Netherlands
| | - Yuri E M van der Burgt
- Department of Clinical Chemistry and Laboratory Medicine, Leiden University Medical Center, Leiden, ZA, The Netherlands
| | - L Renee Ruhaak
- Department of Clinical Chemistry and Laboratory Medicine, Leiden University Medical Center, Leiden, ZA, The Netherlands
| | - Christa M Cobbaert
- Department of Clinical Chemistry and Laboratory Medicine, Leiden University Medical Center, Leiden, ZA, The Netherlands
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van Duijl TT, de Rooij ENM, Treep MM, Koelemaij ME, Romijn FPHTM, Hoogeveen EK, Ruhaak LR, le Cessie S, de Fijter JW, Cobbaert CM. Urinary Kidney Injury Biomarkers Are Associated with Ischemia-Reperfusion Injury Severity in Kidney Allograft Recipients. Clin Chem 2023:hvad086. [PMID: 37477911 DOI: 10.1093/clinchem/hvad086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Accepted: 05/10/2023] [Indexed: 07/22/2023]
Abstract
BACKGROUND We explored the potential of emerging and conventional urinary kidney injury biomarkers in recipients of living donor (LD) or donation after circulatory death (DCD) kidney transplantation, patients with chronic kidney disease (CKD), and individuals from the general population. METHODS Urine samples from kidney allograft recipients with mild (LD; n = 199) or severe (DCD; n = 71) ischemia-reperfusion injury (IRI) were analyzed for neutrophil gelatinase-associated lipocalin (NGAL), insulin-like growth factor-binding protein 7 (IGFBP7), tissue inhibitor of metalloproteinases 2 (TIMP2), kidney injury molecule-1 (KIM-1), chemokine C-X-C motif (CXCL9), solute carrier family 22 member 2 (SLC22A2), nephrin, and uromodulin (UMOD) by quantitative multiplex LC-MS/MS analysis. The fold-change in biomarker levels was determined in mild and severe IRI and in patients with CKD stage 1-2 (n = 127) or stage ≥3 (n = 132) in comparison to the general population (n = 1438). Relationships between the biomarkers and total protein, β2-microglobulin (B2M), creatinine, and osmolality were assessed. RESULTS NGAL, IGFBP7, TIMP2, KIM-1, CXCL9, and UMOD were quantifiable, whereas nephrin and SLC22A2 were below the limit of detection. Kidney injury biomarkers were increased up to 6.2-fold in allograft recipients with mild IRI and 8.3-fold in recipients with severe IRI, compared to the reference population, with the strongest response observed for NGAL and B2M. In CKD stage 1-2, B2M, NGAL, IGFBP7, TIMP2, KIM-1, UMOD, and CXCL9 were not altered, but in individuals with CKD stage ≥3, B2M, NGAL, and KIM-1 were increased up to 1.3-fold. IGFBP7, TIMP2, NGAL, and CXCL9 were strongly correlated (all r ≥ 0.8); correlations with B2M and TP were smaller (all r ≤ 0.6). CONCLUSIONS IRI, but not stable CKD, was associated with increased urinary levels of kidney injury biomarkers determined by LC-MS/MS. Absolute and multiplexed protein quantitation by LC-MS/MS is an effective strategy for biomarker panel evaluation for translation toward the clinical laboratory.
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Affiliation(s)
- Tirsa T van Duijl
- Department of Clinical Chemistry and Laboratory Medicine, Leiden University Medical Center, Leiden, the Netherlands
| | - Esther N M de Rooij
- Department of Nephrology, Leiden University Medical Center, Leiden, the Netherlands
- Department of Clinical Epidemiology, Leiden University Medical Center, Leiden, the Netherlands
| | - Maxim M Treep
- Department of Clinical Chemistry and Laboratory Medicine, Leiden University Medical Center, Leiden, the Netherlands
| | - Marte E Koelemaij
- Department of Clinical Chemistry and Laboratory Medicine, Leiden University Medical Center, Leiden, the Netherlands
| | - Fred P H T M Romijn
- Department of Clinical Chemistry and Laboratory Medicine, Leiden University Medical Center, Leiden, the Netherlands
| | - Ellen K Hoogeveen
- Department of Nephrology, Leiden University Medical Center, Leiden, the Netherlands
- Department of Clinical Epidemiology, Leiden University Medical Center, Leiden, the Netherlands
- Department of Nephrology, Jeroen Bosch Ziekenhuis, 's-Hertogenbosch, the Netherlands
| | - L Renee Ruhaak
- Department of Clinical Chemistry and Laboratory Medicine, Leiden University Medical Center, Leiden, the Netherlands
| | - Saskia le Cessie
- Department of Clinical Epidemiology, Leiden University Medical Center, Leiden, the Netherlands
- Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden, the Netherlands
| | - Johan W de Fijter
- Department of Nephrology, Leiden University Medical Center, Leiden, the Netherlands
- Department of Nephrology and Hypertension, Antwerp University Hospital, Edegem, Belgium
| | - Christa M Cobbaert
- Department of Clinical Chemistry and Laboratory Medicine, Leiden University Medical Center, Leiden, the Netherlands
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Lentjes EGWM, Bui HN, Ruhaak LR, Kema IP, Coene KLM, van den Ouweland JMW. LC-MS/MS in Clinical Chemistry: did it live up to its promise?: Consideration from the Dutch EQAS organisation. Clin Chim Acta 2023; 546:117391. [PMID: 37196897 DOI: 10.1016/j.cca.2023.117391] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 05/09/2023] [Accepted: 05/10/2023] [Indexed: 05/19/2023]
Abstract
BACKGROUND Over the past decade the use of LC-MS/MS has increased significantly in the hospital laboratories. Clinical laboratories have switched from immunoassays to LC-MS/MS methods due to the promise of improvements in sensitivity and specificity, better standardization with often non-commutable international standards, and better between-laboratory comparison. However, it remains unclear whether routine performance of the LC-MS/MS methods have met these expectations. METHOD This study examined the EQAS results, from the Dutch SKML, of serum cortisol, testosterone, 25OH-vitaminD and cortisol in urine and saliva over 9 surveys (2020 to first half of 2021). RESULTS The study found a significant increase in the number of compounds and in the number of results measured in the different matrices, with LC-MS/MS over a period of eleven years. In 2021, approximately 4000 LC-MS/MS results were submitted (serum: urine: saliva = 58:31:11%) compared to only 34 in 2010. When compared to the individual immunoassays, the LC-MS/MS based methods for serum cortisol, testosterone and 25OH-vitaminD showed comparable but also higher between-laboratory CVs in different samples of the surveys. For cortisol, testosterone and 25OH-vitaminD the median CV was 6.8%, 6.1% and 4.7% respectively for the LC-MS/MS compared to 3.9-8.0%,4.5-6.7%, and 7.5-18.3% for immunoassays. However, the bias and imprecision of the LC-MS/MS was better than that of the immunoassays. CONCLUSION Despite the expectation that LC-MS/MS methods would result in smaller between-laboratory differences, as they are relatively matrix independent and better to standardize, the results of the SKML round robins do not reflect this for some analytes and may be in part explained by the fact that in most cases laboratory developed tests were used.
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Affiliation(s)
- E G W M Lentjes
- Central Diagnostic Laboratory, University Medical Center Utrecht, The Netherlands.
| | - H N Bui
- Clinical Chemistry , Reinier de Graaf Groep Diagnostisch Centrum SSDZ, The Netherlands
| | - L R Ruhaak
- Department of Clinical Chemistry and Laboratory Medicine, Leiden University Medical Center, The Netherlands
| | - I P Kema
- Department of Laboratory Medicine, University Medical Center Groningen, the Netherlands
| | - K L M Coene
- Laboratory of Clinical Chemistry & Hematology, Elisabeth TweeSteden Hospital, Tilburg, the Netherlands
| | - J M W van den Ouweland
- Department of Clinical Chemistry, Canisius-Wilhelmina Hospital, Nijmegen, The Netherlands
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Ruhaak LR, Romijn FPHTM, Begcevic Brkovic I, Kuklenyik Z, Dittrich J, Ceglarek U, Hoofnagle AN, Althaus H, Angles-Cano E, Coassin S, Delatour V, Deprez L, Dikaios I, Kostner GM, Kronenberg F, Lyle A, Prinzing U, Vesper HW, Cobbaert CM. Development of an LC-MRM-MS-Based Candidate Reference Measurement Procedure for Standardization of Serum Apolipoprotein (a) Tests. Clin Chem 2023; 69:251-261. [PMID: 36644914 DOI: 10.1093/clinchem/hvac204] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 11/02/2022] [Indexed: 01/17/2023]
Abstract
BACKGROUND Medical results generated by European CE Marking for In Vitro Diagnostic or in-house tests should be traceable to higher order reference measurement systems (RMS), such as International Federation of Clinical Chemistry and Laboratory Medicine (IFCC)-endorsed reference measurement procedures (RMPs) and reference materials. Currently, serum apolipoprotein (a) [apo(a)] is recognized as a novel risk factor for cardiovascular risk assessment and patient management. The former RMS for serum apo(a) is no longer available; consequently, an International System of Units (SI)-traceable, ideally multiplexed, and sustainable RMS for apo(a) is needed. METHODS A mass spectrometry (MS)-based candidate RMP (cRMP) for apo(a) was developed using quantitative bottom-up proteomics targeting 3 proteotypic peptides. The method was provisionally validated according to ISO 15193 using a single human serum based calibrator traceable to the former WHO-IFCC RMS. RESULTS The quantitation of serum apo(a) was by design independent of its size polymorphism, was linear from 3.8 to 456 nmol/L, and had a lower limit of quantitation for apo(a) of 3.8 nmol/L using peptide LFLEPTQADIALLK. Interpeptide agreement showed Pearson Rs of 0.987 and 0.984 for peptides GISSTVTGR and TPENYPNAGLTR, and method comparison indicated good correspondence (slopes 0.977, 1.033, and 1.085 for LFLEPTQADIALLK, GISSTVTGR, and TPENYPNAGLTR). Average within-laboratory imprecision of the cRMP was 8.9%, 11.9%, and 12.8% for the 3 peptides. CONCLUSIONS A robust, antibody-independent, MS-based cRMP was developed as higher order RMP and an essential part of the apo(a) traceability chain and future RMS. The cRMP fulfils predefined analytical performance specifications, making it a promising RMP candidate in an SI-traceable MS-based RMS for apo(a).
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Affiliation(s)
- L Renee Ruhaak
- Department of Clinical Chemistry and Laboratory Medicine, Leiden University Medical Center, Leiden, The Netherlands
| | - Fred P H T M Romijn
- Department of Clinical Chemistry and Laboratory Medicine, Leiden University Medical Center, Leiden, The Netherlands
| | - Ilijana Begcevic Brkovic
- Institute of Laboratory Medicine, Clinical Chemistry and Molecular Diagnostics, University Hospital Leipzig, Leipzig, Germany
| | - Zsusanna Kuklenyik
- Division of Laboratory Sciences, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Julia Dittrich
- Institute of Laboratory Medicine, Clinical Chemistry and Molecular Diagnostics, University Hospital Leipzig, Leipzig, Germany
| | - Uta Ceglarek
- Institute of Laboratory Medicine, Clinical Chemistry and Molecular Diagnostics, University Hospital Leipzig, Leipzig, Germany
- Division Clinical Mass Spectrometry of the German Society of Clinical Chemistry and Laboratory Medicine (DGKL), Berlin, Germany
| | - Andrew N Hoofnagle
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Harald Althaus
- Siemens Healthcare Diagnostics Products GmbH, Marburg, Germany
| | - Eduardo Angles-Cano
- French Institute of Health and Medical Research (Inserm), Université Paris Descartes, Paris, France
| | - Stefan Coassin
- Department of Genetics and Pharmacology, Institute of Genetic Epidemiology, Medical University of Innsbruck, Innsbruck, Austria
| | | | - Liesbet Deprez
- European Commission, Joint Research Centre, Geel, Belgium
| | | | - Gerhard M Kostner
- Division of Molecular Biology and Biochemistry, Gottfried Schatz Research Center (for Cell Signaling, Metabolism and Aging), Medical University of Graz, Graz, Austria
| | - Florian Kronenberg
- Department of Genetics and Pharmacology, Institute of Genetic Epidemiology, Medical University of Innsbruck, Innsbruck, Austria
| | - Alicia Lyle
- Division of Laboratory Sciences, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | | | - Hubert W Vesper
- Division of Laboratory Sciences, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Christa M Cobbaert
- Department of Clinical Chemistry and Laboratory Medicine, Leiden University Medical Center, Leiden, The Netherlands
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Dikaios I, Althaus H, Angles-Cano E, Ceglarek U, Coassin S, Cobbaert CM, Delatour V, Dieplinger B, Grimmler M, Hoofnagle AN, Kostner GM, Kronenberg F, Kuklenyik Z, Lyle AN, Prinzing U, Ruhaak LR, Scharnagl H, Vesper HW, Deprez L. Commutability Assessment of Candidate Reference Materials for Lipoprotein(a) by Comparison of a MS-based Candidate Reference Measurement Procedure with Immunoassays. Clin Chem 2023; 69:262-272. [PMID: 36644921 DOI: 10.1093/clinchem/hvac203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 11/02/2022] [Indexed: 01/17/2023]
Abstract
BACKGROUND Elevated concentrations of lipoprotein(a) [Lp(a)] are directly related to an increased risk of cardiovascular diseases, making it a relevant biomarker for clinical risk assessment. However, the lack of global standardization of current Lp(a) measurement procedures (MPs) leads to inconsistent patient care. The International Federation for Clinical Chemistry and Laboratory Medicine working group on quantitating apolipoproteins by mass spectrometry (MS) aims to develop a next-generation SI (International system of units)-traceable reference measurement system consisting of a MS-based, peptide-calibrated reference measurement procedure (RMP) and secondary serum-based reference materials (RMs) certified for their apolipoprotein(a) [apo(a)] content. To reach measurement standardization through this new measurement system, 2 essential requirements need to be fulfilled: a sufficient correlation among the MPs and appropriate commutability of future serum-based RMs. METHODS The correlation among the candidate RMP (cRMP) and immunoassay-based MPs was assessed by measuring a panel of 39 clinical samples (CS). In addition, the commutability of 14 different candidate RMs was investigated. RESULTS Results of the immunoassay-based MPs and the cRMPs demonstrated good linear correlations for the CS but some significant sample-specific differences were also observed. The results of the commutability study show that RMs based on unspiked human serum pools can be commutable with CS, whereas human pools spiked with recombinant apo(a) show different behavior compared to CS. CONCLUSIONS The results of this study show that unspiked human serum pools are the preferred candidate secondary RMs in the future SI-traceable Lp(a) Reference Measurement System.
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Affiliation(s)
- Ioannis Dikaios
- European Commission, Joint Research Centre (JRC), Geel, Belgium
| | - Harald Althaus
- Siemens Healthcare Diagnostics Products GmbH, Marburg, Germany
| | - Eduardo Angles-Cano
- French Institute of Health and Medical Research (INSERM) Université Paris Cité, Paris, France
| | - Uta Ceglarek
- Institute of Laboratory Medicine, Clinical Chemistry and Molecular Diagnostics, University Hospital Leipzig, Leipzig, Germany
- LIFE-Leipzig Research Center for Civilization Diseases, University of Leipzig, Leipzig, Germany
- Division Clinical Mass Spectrometry of the German Society of Clinical Chemistry and Laboratory Medicine (DGKL), Berlin, Germany
| | - Stefan Coassin
- Institute of Genetic Epidemiology, Medical University of Innsbruck, Innsbruck, Austria
| | - Christa M Cobbaert
- Department of Clinical Chemistry and Laboratory Medicine, Leiden University Medical Center, Leiden, The Netherlands
| | | | - Benjamin Dieplinger
- Department of Laboratory Medicine, Konventhospital Barmherzige Brueder Linz and Ordensklinikum Linz Barmherzige Schwestern, Linz, Austria
| | | | - Andrew N Hoofnagle
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, USA
| | - Gerhard M Kostner
- Division of Molecular Biology and Biochemistry, Medical University of Graz, Graz, Austria
| | - Florian Kronenberg
- Institute of Genetic Epidemiology, Medical University of Innsbruck, Innsbruck, Austria
| | - Zsusanna Kuklenyik
- Division of Laboratory Sciences, Centers for Disease Control and Prevention (CDC), Atlanta, USA
| | - Alicia N Lyle
- Division of Laboratory Sciences, Centers for Disease Control and Prevention (CDC), Atlanta, USA
| | | | - L Renee Ruhaak
- Department of Clinical Chemistry and Laboratory Medicine, Leiden University Medical Center, Leiden, The Netherlands
| | - Hubert Scharnagl
- Division of Molecular Biology and Biochemistry, Medical University of Graz, Graz, Austria
| | - Hubert W Vesper
- Division of Laboratory Sciences, Centers for Disease Control and Prevention (CDC), Atlanta, USA
| | - Liesbet Deprez
- European Commission, Joint Research Centre (JRC), Geel, Belgium
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9
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Kruijt M, Treep MM, Cobbaert CM, Ruhaak LR. Antithrombin diagnostics by mass spectrometry: Development and analytical validation of a next-generation test. Res Pract Thromb Haemost 2023; 7:100079. [PMID: 36949768 PMCID: PMC10025100 DOI: 10.1016/j.rpth.2023.100079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 01/06/2023] [Accepted: 01/25/2023] [Indexed: 02/11/2023] Open
Abstract
Background Antithrombin deficiency is a rare but severe disorder leading to high risk of thrombosis. The current clinical care pathway relies on activity tests, which only provide overall functional information on the in vitro activity of antithrombin. However, antithrombin exists in many different forms, also known as proteoforms, with varying clinical phenotypes. Precision diagnostics, facilitated by mass spectrometry, provides a strategy to improve patient diagnostics by molecular characterization. Objectives To develop and analytically validate a mass spectrometry-based test for molecular characterization of antithrombin. Methods The test was analytically validated based on predefined analytical performance specifications. The validation covered imprecision, carryover, linearity, stability, analytical specificity, a provisional reference interval, and an explorative method comparison. Results The test passed the predefined analytical performance specifications with a mean within-laboratory imprecision of 5.9%, linearity between 0.08 and 2.58 μmol/L, and a provisional reference interval of 1.07 to 1.49 μmol/L. When measuring samples with a suspected quantitative deficiency, the test showed a good correlation with a commercial activity test (Pearson r = 0.88). Conclusion The test passed the validation, and we now envision the use of the test for exploration of the clinical relevance of specific antithrombin proteoforms. Puzzling cases of antithrombin deficiency, for instance, due to ambiguous activity results or an atypical clinical presentation, can be investigated by the LC-MRM mass spectrometry test serving as an add-on to the activity test and providing a molecular diagnosis. Clinical studies are planned to investigate the potential of the test to improve antithrombin diagnostics. Furthermore, the molecular information gained using the test may aid in establishing better risk stratification and a basis for personalized medicine.
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Affiliation(s)
- Mirjam Kruijt
- Correspondence Mirjam Kruijt, Leiden University Medical Center, Department of Clinical Chemistry and Laboratory Medicine, Albinusdreef 2, 2333 ZA, Leiden, the Netherlands.
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10
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Smit NPM, Romijn FPHTM, van Ham VJJ, Reijnders E, Cobbaert CM, Ruhaak LR. Quantitative protein mass-spectrometry requires a standardized pre-analytical phase. Clin Chem Lab Med 2023; 61:55-66. [PMID: 36069790 DOI: 10.1515/cclm-2022-0735] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 08/21/2022] [Indexed: 12/15/2022]
Abstract
OBJECTIVES Quantitative protein mass-spectrometry (QPMS) in blood depends on tryptic digestion of proteins and subsequent measurement of representing peptides. Whether serum and plasma can be used interchangeably and whether in-vitro anticoagulants affect the recovery is unknown. In our laboratory serum samples are the preferred matrix for QPMS measurement of multiple apolipoproteins. In this study, we investigated the effect of different matrices on apolipoprotein quantification by mass spectrometry. METHODS Blood samples were collected from 44 healthy donors in Beckton Dickinson blood tubes simultaneously for serum (with/without gel) and plasma (heparin, citrate or EDTA). Nine apolipoproteins were quantified according to standard operating procedure using value-assigned native serum calibrators for quantitation. Tryptic digestion kinetics were investigated in the different matrices by following formation of peptides for each apolipoprotein in time, up to 22 h. RESULTS In citrate plasma recovery of apolipoproteins showed an overall reduction with a bias of -14.6%. For heparin plasma only -0.3% bias was found compared to serum, whereas for EDTA-plasma reduction was more pronounced (-5.3% bias) and variable with >14% reduction for peptides of apoA-I, A-II and C-III. Digestion kinetics revealed that especially slow forming peptides showed reduced formation in EDTA-plasma. CONCLUSIONS Plasma anticoagulants affect QPMS test results. Heparin plasma showed comparable results to serum. Reduced concentrations in citrate plasma can be explained by dilution, whereas reduced recovery in EDTA-plasma is dependent on altered proteolytic digestion efficiency. The results highlight the importance of a standardized pre-analytical phase for accurate QPMS applications in clinical chemistry.
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Affiliation(s)
- Nico P M Smit
- Department of Clinical Chemistry and Laboratory Medicine, Leiden University Medical Center, Leiden, The Netherlands
| | - Fred P H T M Romijn
- Department of Clinical Chemistry and Laboratory Medicine, Leiden University Medical Center, Leiden, The Netherlands
| | | | - Esther Reijnders
- Department of Clinical Chemistry and Laboratory Medicine, Leiden University Medical Center, Leiden, The Netherlands
| | - Christa M Cobbaert
- Department of Clinical Chemistry and Laboratory Medicine, Leiden University Medical Center, Leiden, The Netherlands
| | - L Renee Ruhaak
- Department of Clinical Chemistry and Laboratory Medicine, Leiden University Medical Center, Leiden, The Netherlands
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11
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Diederiks N, Ravensbergen CJ, Treep M, van Wezel M, Kuruc M, Renee Ruhaak L, Tollenaar RA, Cobbaert CM, van der Burgt YE, Mesker WE. Development of Tier 2 LC-MRM-MS protein quantification methods for liquid biopsies. J Mass Spectrom Adv Clin Lab 2022; 27:49-55. [PMID: 36619217 PMCID: PMC9811211 DOI: 10.1016/j.jmsacl.2022.12.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 12/13/2022] [Accepted: 12/15/2022] [Indexed: 12/24/2022] Open
Abstract
In the pursuit of personalized diagnostics and tailored treatments, quantitative protein tests contribute to a more precise definition of health and disease. The development of new quantitative protein tests should be driven by an unmet clinical need and performed in a collaborative effort that involves all stakeholders. With regard to the analytical part, mass spectrometry (MS)-based platforms are an excellent tool for quantification of specific proteins in body fluids, for example focused on cancer. The obtained readouts have great potential in determining tumor aggressiveness to facilitate treatment decisions, and can furthermore be used to monitor patient response. Internationally standardized TNM classifications of malignant tumors are beneficial for diagnosis, however treatment outcome and survival of cancer patients is poorly predicted. To this end, the importance of the tumor microenvironment has endorsed the introduction of the tumor-stroma ratio as a prognostic parameter in solid primary tumor types. Currently, the stromal content of tumor tissues is determined via routine diagnostic pathology slides. With the development of liquid chromatography (LC)-MS methods we aim at quantification of tumor-stroma specific proteins in body fluids. In this mini-review the analytical aspect of this developmental trajectory is further detailed.
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Affiliation(s)
- Nina Diederiks
- Department of Clinical Chemistry and Laboratory Medicine, Leiden University Medical Center, Albinusdreef 2, 2333 ZA Leiden, the Netherlands
| | - Cor J. Ravensbergen
- Department of Surgery, Leiden University Medical Center, Albinusdreef 2, 2333 ZA Leiden, the Netherlands
| | - Maxim Treep
- Department of Clinical Chemistry and Laboratory Medicine, Leiden University Medical Center, Albinusdreef 2, 2333 ZA Leiden, the Netherlands
| | - Madelein van Wezel
- Department of Clinical Chemistry and Laboratory Medicine, Leiden University Medical Center, Albinusdreef 2, 2333 ZA Leiden, the Netherlands
| | - Matt Kuruc
- Biotech Support Group LLC, 1 Deer Park Drive, Suite M, Monmouth Junction, NJ 08852, USA
| | - L. Renee Ruhaak
- Department of Clinical Chemistry and Laboratory Medicine, Leiden University Medical Center, Albinusdreef 2, 2333 ZA Leiden, the Netherlands
| | - Rob A.E.M. Tollenaar
- Department of Surgery, Leiden University Medical Center, Albinusdreef 2, 2333 ZA Leiden, the Netherlands
| | - Christa M. Cobbaert
- Department of Clinical Chemistry and Laboratory Medicine, Leiden University Medical Center, Albinusdreef 2, 2333 ZA Leiden, the Netherlands
| | - Yuri E.M. van der Burgt
- Department of Clinical Chemistry and Laboratory Medicine, Leiden University Medical Center, Albinusdreef 2, 2333 ZA Leiden, the Netherlands,Corresponding author.
| | - Wilma E. Mesker
- Department of Surgery, Leiden University Medical Center, Albinusdreef 2, 2333 ZA Leiden, the Netherlands
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12
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Maverakis E, Liakos W, Park D, Patel F, Siddiqui F, Kailemia MJ, Ruhaak LR, Marusina AI, Luxardi G, Gudjonsson JE, Le ST, Armstrong AW, Liao W, Merleev AA, Lebrilla CB. The Psoriasis Glycome: Differential Expression of Cholesterol Particle Glycans and IgA Glycans Linked to Disease Severity. J Invest Dermatol 2022; 142:2817-2820.e7. [PMID: 35469905 DOI: 10.1016/j.jid.2022.03.030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 02/21/2022] [Accepted: 03/15/2022] [Indexed: 11/26/2022]
Affiliation(s)
- Emanual Maverakis
- Department of Dermatology, University of California, Davis, Sacramento, California, USA.
| | - William Liakos
- Department of Dermatology, University of California, Davis, Sacramento, California, USA
| | - Dayoung Park
- Department of Chemistry, University of California Davis, Davis, California, USA; Department of Surgery, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, USA
| | - Forum Patel
- Department of Dermatology, University of California, Davis, Sacramento, California, USA
| | - Fariha Siddiqui
- Department of Dermatology, University of California, Davis, Sacramento, California, USA
| | - Muchena J Kailemia
- Department of Chemistry, University of California Davis, Davis, California, USA
| | - L Renee Ruhaak
- Department of Clinical Chemistry and Laboratory Medicine, Leiden University Medical Center, Leiden, The Netherlands
| | - Alina I Marusina
- Department of Dermatology, University of California, Davis, Sacramento, California, USA
| | - Guillaume Luxardi
- Department of Dermatology, University of California, Davis, Sacramento, California, USA
| | | | - Stephanie T Le
- Department of Dermatology, University of California, Davis, Sacramento, California, USA
| | - April W Armstrong
- Department of Dermatology, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - Wilson Liao
- Department of Dermatology, University of California San Francisco, San Francisco, California, USA
| | - Alexander A Merleev
- Department of Dermatology, University of California, Davis, Sacramento, California, USA
| | - Carlito B Lebrilla
- Department of Chemistry, University of California Davis, Davis, California, USA
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13
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Kruijt M, van der Pol LM, Eikenboom J, Verburg HJ, Cobbaert CM, Ruhaak LR. Unraveling a borderline antithrombin deficiency case with quantitative mass spectrometry. J Thromb Haemost 2022; 20:145-148. [PMID: 34653293 PMCID: PMC9298056 DOI: 10.1111/jth.15553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 10/08/2021] [Accepted: 10/11/2021] [Indexed: 11/27/2022]
Abstract
Antithrombin deficiency diagnostics by first-line activity tests suffer from a lack of sensitivity sometimes resulting in diagnostic uncertainty. We here present a case of a woman with recurrent pregnancy loss who was screened for inherited thrombophilia. Antithrombin activity was borderline low, resulting in uncertainty about the correct diagnosis. Using a mass spectrometry-based test, the antithrombin protein of the patient was characterized at the molecular level and a heterozygous p.Pro73Leu mutation was identified. The mutation, also known as antithrombin "Basel," increases the risk of venous thromboembolism and obstetric complications. This case is illustrative of current antithrombin deficiency screening, in which diagnoses may be missed by traditional diagnostics. Next-generation protein diagnostics by mass spectrometry provides molecular insight into the proteoforms present in vivo. This information is essential for laboratory specialists and clinicians to unambiguously diagnose patients and will aid in evolving healthcare from traditional to precision diagnostics.
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Affiliation(s)
- Mirjam Kruijt
- Department of Clinical Chemistry and Laboratory MedicineLeiden University Medical CenterLeidenThe Netherlands
| | - Liselotte M. van der Pol
- Department of Internal MedicineDivision of Thrombosis and HemostasisLeiden University Medical CenterLeidenThe Netherlands
| | - Jeroen Eikenboom
- Department of Internal MedicineDivision of Thrombosis and HemostasisLeiden University Medical CenterLeidenThe Netherlands
| | - Harjo J. Verburg
- Department of Gynecology and FertilityLeiden University Medical CenterLeidenThe Netherlands
| | - Christa M. Cobbaert
- Department of Clinical Chemistry and Laboratory MedicineLeiden University Medical CenterLeidenThe Netherlands
| | - L. Renee Ruhaak
- Department of Clinical Chemistry and Laboratory MedicineLeiden University Medical CenterLeidenThe Netherlands
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14
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van Duijl TT, Ruhaak LR, Smit NPM, Pieterse MM, Romijn FPHTM, Dolezal N, Drijfhout JW, de Fijter JW, Cobbaert CM. Development and Provisional Validation of a Multiplex LC-MRM-MS Test for Timely Kidney Injury Detection in Urine. J Proteome Res 2021; 20:5304-5314. [PMID: 34735145 PMCID: PMC8650098 DOI: 10.1021/acs.jproteome.1c00532] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
![]()
Kidney injury is
a complication frequently encountered in hospitalized
patients. Early detection of kidney injury prior to loss of renal
function is an unmet clinical need that should be targeted by a protein-based
biomarker panel. In this study, we aim to quantitate urinary kidney
injury biomarkers at the picomolar to nanomolar level by liquid chromatography
coupled to tandem mass spectrometry in multiple reaction monitoring
mode (LC-MRM-MS). Proteins were immunocaptured from urinary samples,
denatured, reduced, alkylated, and digested into peptides before LC-MRM-MS
analysis. Stable-isotope-labeled peptides functioned as internal standards,
and biomarker concentrations were attained by an external calibration
strategy. The method was evaluated for selectivity, carryover, matrix
effects, linearity, and imprecision. The LC-MRM-MS method enabled
the quantitation of KIM-1, NGAL, TIMP2, IGFBP7, CXCL9, nephrin, and
SLC22A2 and the detection of TGF-β1, cubilin, and uromodulin.
Two to three peptides were included per protein, and three transitions
were monitored per peptide for analytical selectivity. The analytical
carryover was <1%, and minimal urine matrix effects were observed
by combining immunocapture and targeted LC-MRM-MS analysis. The average
total CV of all quantifier peptides was 26%. The linear measurement
range was determined per measurand and found to be 0.05–30
nmol/L. The targeted MS-based method enables the multiplex quantitation
of low-abundance urinary kidney injury biomarkers for future clinical
evaluation.
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Affiliation(s)
- Tirsa T van Duijl
- Department of Clinical Chemistry and Laboratory Medicine, Leiden University Medical Center, Albinusdreef 2, 2333 ZA Leiden, The Netherlands
| | - L Renee Ruhaak
- Department of Clinical Chemistry and Laboratory Medicine, Leiden University Medical Center, Albinusdreef 2, 2333 ZA Leiden, The Netherlands
| | - Nico P M Smit
- Department of Clinical Chemistry and Laboratory Medicine, Leiden University Medical Center, Albinusdreef 2, 2333 ZA Leiden, The Netherlands
| | - Mervin M Pieterse
- Department of Clinical Chemistry and Laboratory Medicine, Leiden University Medical Center, Albinusdreef 2, 2333 ZA Leiden, The Netherlands
| | - Fred P H T M Romijn
- Department of Clinical Chemistry and Laboratory Medicine, Leiden University Medical Center, Albinusdreef 2, 2333 ZA Leiden, The Netherlands
| | - Natasja Dolezal
- Department of Immunology, Leiden University Medical Center, Albinusdreef 2, 2333 ZA Leiden, The Netherlands
| | - Jan Wouter Drijfhout
- Department of Immunology, Leiden University Medical Center, Albinusdreef 2, 2333 ZA Leiden, The Netherlands
| | - Johan W de Fijter
- Department of Nephrology, Leiden University Medical Center, Albinusdreef 2, 2333 ZA, Leiden, The Netherlands
| | - Christa M Cobbaert
- Department of Clinical Chemistry and Laboratory Medicine, Leiden University Medical Center, Albinusdreef 2, 2333 ZA Leiden, The Netherlands
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15
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Maverakis E, Merleev AA, Park D, Kailemia MJ, Xu G, Ruhaak LR, Kim K, Hong Q, Li Q, Leung P, Liakos W, Wan YJY, Bowlus CL, Marusina AI, Lal NN, Xie Y, Luxardi G, Lebrilla CB. Glycan biomarkers of autoimmunity and bile acid-associated alterations of the human glycome: Primary biliary cirrhosis and primary sclerosing cholangitis-specific glycans. Clin Immunol 2021; 230:108825. [PMID: 34403816 DOI: 10.1016/j.clim.2021.108825] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 08/10/2021] [Accepted: 08/11/2021] [Indexed: 12/13/2022]
Abstract
We have recently introduced multiple reaction monitoring (MRM) mass spectrometry as a novel tool for glycan biomarker research and discovery. Herein, we employ this technique to characterize the site-specific glycan alterations associated with primary biliary cirrhosis (PBC) and primary sclerosing cholangitis (PSC). Glycopeptides associated with disease severity were also identified. Multinomial regression modelling was employed to construct and validate multi-analyte diagnostic models capable of accurately distinguishing PBC, PSC, and healthy controls from one another (AUC = 0.93 ± 0.03). Finally, to investigate how disease-relevant environmental factors can influence glycosylation, we characterized the ability of bile acids known to be differentially expressed in PBC to alter glycosylation. We hypothesize that this could be a mechanism by which altered self-antigens are generated and become targets for immune attack. This work demonstrates the utility of the MRM method to identify diagnostic site-specific glycan classifiers capable of distinguishing even related autoimmune diseases from one another.
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Affiliation(s)
- Emanual Maverakis
- Department of Dermatology, University of California Davis School of Medicine, Sacramento, CA, USA.
| | - Alexander A Merleev
- Department of Dermatology, University of California Davis School of Medicine, Sacramento, CA, USA
| | - Dayoung Park
- Department of Chemistry, University of California Davis, Davis, CA, USA; Department of Surgery, Center for Drug Discovery and Translational Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA; Wyss Institute of Biologically Inspired Engineering, Harvard University, Boston, MA, USA
| | | | - Gege Xu
- Department of Chemistry, University of California Davis, Davis, CA, USA
| | - L Renee Ruhaak
- Department of Chemistry, University of California Davis, Davis, CA, USA; Department of Clinical Chemistry and Laboratory Medicine, Leiden University Medical Center, ZA, Leiden, the Netherlands
| | - Kyoungmi Kim
- Division of Biostatistics, Department of Public Health Sciences, University of California Davis, Davis, CA, USA
| | - Qiuting Hong
- Department of Chemistry, University of California Davis, Davis, CA, USA
| | - Qiongyu Li
- Department of Chemistry, University of California Davis, Davis, CA, USA
| | - Patrick Leung
- Department of Internal Medicine, Division of Rheumatology, Allergy and Clinical Immunology, University of California Davis School of Medicine, Davis, CA, USA
| | - William Liakos
- Department of Dermatology, University of California Davis School of Medicine, Sacramento, CA, USA
| | - Yu-Jui Yvonne Wan
- Department of Medical Pathology and Laboratory Medicine, University of California Davis School of Medicine, Sacramento, CA, USA
| | - Christopher L Bowlus
- Division of Gastroenterology and Hepatology, UC Davis School of Medicine, CA, USA
| | - Alina I Marusina
- Department of Dermatology, University of California Davis School of Medicine, Sacramento, CA, USA
| | - Nelvish N Lal
- Department of Dermatology, University of California Davis School of Medicine, Sacramento, CA, USA
| | - Yixuan Xie
- Department of Chemistry, University of California Davis, Davis, CA, USA
| | - Guillaume Luxardi
- Department of Dermatology, University of California Davis School of Medicine, Sacramento, CA, USA
| | - Carlito B Lebrilla
- Department of Chemistry, University of California Davis, Davis, CA, USA; Department of Biochemistry and Molecular Medicine, University of California Davis, Davis, CA, USA; Foods for Health Institute, University of California Davis, Davis, CA, USA
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16
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Smit NPM, Ruhaak LR, Romijn FPHTM, Pieterse MM, van der Burgt YEM, Cobbaert CM. The Time Has Come for Quantitative Protein Mass Spectrometry Tests That Target Unmet Clinical Needs. J Am Soc Mass Spectrom 2021; 32:636-647. [PMID: 33522792 PMCID: PMC7944566 DOI: 10.1021/jasms.0c00379] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 12/22/2020] [Accepted: 01/19/2021] [Indexed: 05/04/2023]
Abstract
Protein mass spectrometry (MS) is an enabling technology that is ideally suited for precision diagnostics. In contrast to immunoassays with indirect readouts, MS quantifications are multiplexed and include identification of proteoforms in a direct manner. Although widely used for routine measurements of drugs and metabolites, the number of clinical MS-based protein applications is limited. In this paper, we share our experience and aim to take away the concerns that have kept laboratory medicine from implementing quantitative protein MS. To ensure added value of new medical tests and guarantee accurate test results, five key elements of test evaluation have been established by a working group within the European Federation for Clinical Chemistry and Laboratory Medicine. Moreover, it is emphasized to identify clinical gaps in the contemporary clinical pathways before test development is started. We demonstrate that quantitative protein MS tests that provide an additional layer of clinical information have robust performance and meet long-term desirable analytical performance specifications as exemplified by our own experience. Yet, the adoption of quantitative protein MS tests into medical laboratories is seriously hampered due to its complexity, lack of robotization and high initial investment costs. Successful and widespread implementation in medical laboratories requires uptake and automation of this next generation protein technology by the In-Vitro Diagnostics industry. Also, training curricula of lab workers and lab specialists should include education on enabling technologies for transitioning to precision medicine by quantitative protein MS tests.
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Affiliation(s)
- Nico P. M. Smit
- Department of Clinical Chemistry and
Laboratory Medicine, Leiden University Medical
Center, Albinusdreef 2, 2333 ZA Leiden, The Netherlands
| | - L. Renee Ruhaak
- Department of Clinical Chemistry and
Laboratory Medicine, Leiden University Medical
Center, Albinusdreef 2, 2333 ZA Leiden, The Netherlands
| | - Fred P. H. T. M. Romijn
- Department of Clinical Chemistry and
Laboratory Medicine, Leiden University Medical
Center, Albinusdreef 2, 2333 ZA Leiden, The Netherlands
| | - Mervin M. Pieterse
- Department of Clinical Chemistry and
Laboratory Medicine, Leiden University Medical
Center, Albinusdreef 2, 2333 ZA Leiden, The Netherlands
| | - Yuri E. M. van der Burgt
- Department of Clinical Chemistry and
Laboratory Medicine, Leiden University Medical
Center, Albinusdreef 2, 2333 ZA Leiden, The Netherlands
| | - Christa M. Cobbaert
- Department of Clinical Chemistry and
Laboratory Medicine, Leiden University Medical
Center, Albinusdreef 2, 2333 ZA Leiden, The Netherlands
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17
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Cobbaert CM, Althaus H, Begcevic Brkovic I, Ceglarek U, Coassin S, Delatour V, Deprez L, Dikaios I, Dittrich J, Hoofnagle AN, Kostner GM, Kronenberg F, Kuklenyik Z, Prinzing U, Vesper HW, Zegers I, Ruhaak LR. Towards an SI-Traceable Reference Measurement System for Seven Serum Apolipoproteins Using Bottom-Up Quantitative Proteomics: Conceptual Approach Enabled by Cross-Disciplinary/Cross-Sector Collaboration. Clin Chem 2021; 67:478-489. [PMID: 33331636 DOI: 10.1093/clinchem/hvaa239] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 09/15/2020] [Indexed: 12/15/2022]
Abstract
Current dyslipidemia management in patients with atherosclerotic cardiovascular disease (ASCVD) is based on traditional serum lipids. Yet, there is some indication from basic research that serum apolipoproteins A-I, (a), B, C-I, C-II, C-III, and E may give better pathophysiological insight into the root causes of dyslipidemia. To facilitate the future adoption of clinical serum apolipoprotein (apo) profiling for precision medicine, strategies for accurate testing should be developed in advance. Recent discoveries in basic science and translational medicine set the stage for the IFCC Working Group on Apolipoproteins by Mass Spectrometry. Main drivers were the convergence of unmet clinical needs in cardiovascular disease (CVD) patients with enabling technology and metrology. First, the residual cardiovascular risk after accounting for established risk factors demonstrates that the current lipid panel is too limited to capture the full complexity of lipid metabolism in patients. Second, there is a need for accurate test results in highly polymorphic and atherogenic apolipoproteins such as apo(a). Third, sufficient robustness of mass spectrometry technology allows reproducible protein quantification at the molecular level. Fourth, several calibration hierarchies in the revised ISO 17511:2020 guideline facilitate metrological traceability of test results, the highest achievable standard being traceability to SI. This article outlines the conceptual approach aimed at achieving a novel, multiplexed Reference Measurement System (RMS) for seven apolipoproteins based on isotope dilution mass spectrometry and peptide-based calibration. This RMS should enable standardization of existing and emerging apolipoprotein assays to SI, within allowable limits of measurement uncertainty, through a sustainable network of Reference Laboratories.
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Affiliation(s)
- Christa M Cobbaert
- Department of Clinical Chemistry and Laboratory Medicine, Leiden University Medical Center, Leiden, The Netherlands
| | - Harald Althaus
- Siemens Healthcare Diagnostics Products GmbH, Marburg, Germany
| | - Ilijana Begcevic Brkovic
- Institute of Laboratory Medicine, Clinical Chemistry and Molecular Diagnostics, University Hospital Leipzig, Leipzig,Germany.,LIFE-Leipzig Research Center for Civilization Diseases, University of Leipzig, Leipzig, Germany
| | - Uta Ceglarek
- Institute of Laboratory Medicine, Clinical Chemistry and Molecular Diagnostics, University Hospital Leipzig, Leipzig,Germany.,LIFE-Leipzig Research Center for Civilization Diseases, University of Leipzig, Leipzig, Germany
| | - Stefan Coassin
- Institute of Genetic Epidemiology, Department of Genetics and Pharmacology, Medical University of Innsbruck, Innsbruck, Austria
| | | | - Liesbet Deprez
- European Commission, Joint Research Centre (JRC), Geel, Belgium
| | - Ioannis Dikaios
- European Commission, Joint Research Centre (JRC), Geel, Belgium
| | - Julia Dittrich
- Institute of Laboratory Medicine, Clinical Chemistry and Molecular Diagnostics, University Hospital Leipzig, Leipzig,Germany.,LIFE-Leipzig Research Center for Civilization Diseases, University of Leipzig, Leipzig, Germany
| | - Andrew N Hoofnagle
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA
| | - Gerhard M Kostner
- Gottfried Schatz Research Center (for Cell Signaling, Metabolism and Aging), Division of Molecular Biology and Biochemistry, Medical University of Graz, Graz, Austria
| | - Florian Kronenberg
- Institute of Genetic Epidemiology, Department of Genetics and Pharmacology, Medical University of Innsbruck, Innsbruck, Austria
| | - Zsusanna Kuklenyik
- Division of Laboratory Sciences, Centers for Disease Control and Prevention, Atlanta, GA
| | | | - Hubert W Vesper
- Division of Laboratory Sciences, Centers for Disease Control and Prevention, Atlanta, GA
| | - Ingrid Zegers
- Laboratoire National de Métrologie et d'Essais, Paris, France
| | - L Renee Ruhaak
- Department of Clinical Chemistry and Laboratory Medicine, Leiden University Medical Center, Leiden, The Netherlands
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18
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van Duijl TT, Soonawala D, de Fijter JW, Ruhaak LR, Cobbaert CM. Rational selection of a biomarker panel targeting unmet clinical needs in kidney injury. Clin Proteomics 2021; 18:10. [PMID: 33618665 PMCID: PMC7898424 DOI: 10.1186/s12014-021-09315-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Accepted: 01/30/2021] [Indexed: 12/01/2022] Open
Abstract
The pipeline of biomarker translation from bench to bedside is challenging and limited biomarkers have been adopted to routine clinical care. Ideally, biomarker research and development should be driven by unmet clinical needs in health care. To guide researchers, clinical chemists and clinicians in their biomarker research, the European Federation of Clinical Chemistry and Laboratory Medicine (EFLM) has developed a structured questionnaire in which the clinical gaps in current clinical pathways are identified and desirable performance specifications are predefined. In kidney injury, the high prevalence of the syndrome acute kidney injury (AKI) in the hospital setting has a significant impact on morbidity, patient survival and health care costs, but the use of biomarkers indicating early kidney injury in daily patient care remains limited. Routinely, medical labs measure serum creatinine, which is a functional biomarker, insensitive for detecting early kidney damage and cannot distinguish between renal and prerenal AKI. The perceived unmet clinical needs in kidney injury were identified through the EFLM questionnaire. Nephrologists within our tertiary care hospital emphasized that biomarkers are needed for (1) early diagnosis of in-hospital AKI after a medical insult and in critically ill patients, (2) risk stratification for kidney injury prior to a scheduled (elective) intervention, (3) kidney injury monitoring in patients scheduled to receive nephrotoxic medication and after kidney transplantation and (4) differentiation between prerenal AKI and structural kidney damage. The biomarker search and selection strategy resulted in a rational selection of an eleven-protein urinary panel for kidney injury that target these clinical needs. To assess the clinical utility of the proposed biomarker panel in kidney injury, a multiplexed LC-MS test is now in development for the intended translational research.
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Affiliation(s)
- T T van Duijl
- Department of Clinical Chemistry and Laboratory Medicine, Leiden University Medical Center, Postzone E2-P, Albinusdreef 2, 2333 ZA, Leiden, The Netherlands.
| | - D Soonawala
- Department of Nephrology, Leiden University Medical Center, Leiden, The Netherlands
- Department of Internal Medicine, Haga Teaching Hospital, The Hague, The Netherlands
| | - J W de Fijter
- Department of Nephrology, Leiden University Medical Center, Leiden, The Netherlands
| | - L R Ruhaak
- Department of Clinical Chemistry and Laboratory Medicine, Leiden University Medical Center, Postzone E2-P, Albinusdreef 2, 2333 ZA, Leiden, The Netherlands
| | - C M Cobbaert
- Department of Clinical Chemistry and Laboratory Medicine, Leiden University Medical Center, Postzone E2-P, Albinusdreef 2, 2333 ZA, Leiden, The Netherlands
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19
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Merleev AA, Park D, Xie Y, Kailemia MJ, Xu G, Ruhaak LR, Kim K, Hong Q, Li Q, Patel F, Wan YJY, Marusina AI, Adamopoulos IE, Lal NN, Mitra A, Le ST, Shimoda M, Luxardi G, Lebrilla CB, Maverakis E. A site-specific map of the human plasma glycome and its age and gender-associated alterations. Sci Rep 2020; 10:17505. [PMID: 33060657 PMCID: PMC7567094 DOI: 10.1038/s41598-020-73588-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Accepted: 09/10/2020] [Indexed: 01/08/2023] Open
Abstract
Alterations in the human glycome have been associated with cancer and autoimmunity. Thus, constructing a site-specific map of the human glycome for biomarker research and discovery has been a highly sought-after objective. However, due to analytical barriers, comprehensive site-specific glycoprofiling is difficult to perform. To develop a platform to detect easily quantifiable, site-specific, disease-associated glycan alterations for clinical applications, we have adapted the multiple reaction monitoring mass spectrometry method for use in glycan biomarker research. The adaptations allow for highly precise site-specific glycan monitoring with minimum sample prep. Using this technique, we successfully mapped out the relative abundances of the most common 159 glycopeptides in the plasma of 97 healthy volunteers. This plasma glycome map revealed 796 significant (FDR < 0.05) site-specific inter-protein and intra-protein glycan associations, of which the vast majority were previously unknown. Since age and gender are relevant covariants in biomarker research, these variables were also characterized. 13 glycopeptides were found to be associated with gender and 41 to be associated with age. Using just five age-associated glycopeptides, a highly accurate age prediction model was constructed and validated (r2 = 0.62 ± 0.12). The human plasma site-specific glycan map described herein has utility in applications ranging from glycan biomarker research and discovery to the development of novel glycan-altering interventions.
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Affiliation(s)
- Alexander A Merleev
- Department of Dermatology, University of California Davis School of Medicine, 3301 C Street Suite 1400, Sacramento, CA, 95816, USA
| | - Dayoung Park
- Department of Surgery, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
- Department of Chemistry, University of California Davis, One Shields Ave, 2465 Chemistry Annex, Davis, CA, 95616, USA
| | - Yixuan Xie
- Department of Chemistry, University of California Davis, One Shields Ave, 2465 Chemistry Annex, Davis, CA, 95616, USA
| | - Muchena J Kailemia
- Department of Chemistry, University of California Davis, One Shields Ave, 2465 Chemistry Annex, Davis, CA, 95616, USA
| | - Gege Xu
- Department of Chemistry, University of California Davis, One Shields Ave, 2465 Chemistry Annex, Davis, CA, 95616, USA
| | - L Renee Ruhaak
- Department of Chemistry, University of California Davis, One Shields Ave, 2465 Chemistry Annex, Davis, CA, 95616, USA
- Department of Clinical Chemistry and Laboratory Medicine, Leiden University Medical Center, ZA, Leiden, The Netherlands
| | - Kyoungmi Kim
- Division of Biostatistics, Department of Public Health Sciences, University of California Davis, Davis, CA, USA
| | - Qiuting Hong
- Department of Chemistry, University of California Davis, One Shields Ave, 2465 Chemistry Annex, Davis, CA, 95616, USA
| | - Qiongyu Li
- Department of Chemistry, University of California Davis, One Shields Ave, 2465 Chemistry Annex, Davis, CA, 95616, USA
| | - Forum Patel
- Department of Dermatology, University of California Davis School of Medicine, 3301 C Street Suite 1400, Sacramento, CA, 95816, USA
| | - Yu-Jui Yvonne Wan
- Department of Medical Pathology and Laboratory Medicine, University of California Davis School of Medicine, Sacramento, CA, USA
| | - Alina I Marusina
- Department of Dermatology, University of California Davis School of Medicine, 3301 C Street Suite 1400, Sacramento, CA, 95816, USA
| | - Iannis E Adamopoulos
- Department of Internal Medicine, Division of Rheumatology, Allergy and Clinical Immunology, University of California Davis School of Medicine, Davis, CA, USA
- Institute for Pediatric Regenerative Medicine, Shriners Hospitals for Children Northern California, Sacramento, CA, USA
| | - Nelvish N Lal
- Department of Dermatology, University of California Davis School of Medicine, 3301 C Street Suite 1400, Sacramento, CA, 95816, USA
| | - Anupum Mitra
- Division of Biostatistics, Department of Public Health Sciences, University of California Davis, Davis, CA, USA
| | - Stephanie T Le
- Department of Dermatology, University of California Davis School of Medicine, 3301 C Street Suite 1400, Sacramento, CA, 95816, USA
| | - Michiko Shimoda
- Department of Dermatology, University of California Davis School of Medicine, 3301 C Street Suite 1400, Sacramento, CA, 95816, USA
| | - Guillaume Luxardi
- Department of Dermatology, University of California Davis School of Medicine, 3301 C Street Suite 1400, Sacramento, CA, 95816, USA
| | - Carlito B Lebrilla
- Department of Chemistry, University of California Davis, One Shields Ave, 2465 Chemistry Annex, Davis, CA, 95616, USA.
- Department of Biochemistry and Molecular Medicine, University of California Davis, Davis, CA, USA.
- Foods for Health Institute, University of California Davis, Davis, CA, USA.
| | - Emanual Maverakis
- Department of Dermatology, University of California Davis School of Medicine, 3301 C Street Suite 1400, Sacramento, CA, 95816, USA.
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20
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Benedetti E, Gerstner N, Pučić-Baković M, Keser T, Reiding KR, Ruhaak LR, Štambuk T, Selman MH, Rudan I, Polašek O, Hayward C, Beekman M, Slagboom E, Wuhrer M, Dunlop MG, Lauc G, Krumsiek J. Systematic Evaluation of Normalization Methods for Glycomics Data Based on Performance of Network Inference. Metabolites 2020; 10:E271. [PMID: 32630764 PMCID: PMC7408386 DOI: 10.3390/metabo10070271] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 05/29/2020] [Accepted: 06/04/2020] [Indexed: 01/15/2023] Open
Abstract
Glycomics measurements, like all other high-throughput technologies, are subject to technical variation due to fluctuations in the experimental conditions. The removal of this non-biological signal from the data is referred to as normalization. Contrary to other omics data types, a systematic evaluation of normalization options for glycomics data has not been published so far. In this paper, we assess the quality of different normalization strategies for glycomics data with an innovative approach. It has been shown previously that Gaussian Graphical Models (GGMs) inferred from glycomics data are able to identify enzymatic steps in the glycan synthesis pathways in a data-driven fashion. Based on this finding, here, we quantify the quality of a given normalization method according to how well a GGM inferred from the respective normalized data reconstructs known synthesis reactions in the glycosylation pathway. The method therefore exploits a biological measure of goodness. We analyzed 23 different normalization combinations applied to six large-scale glycomics cohorts across three experimental platforms: Liquid Chromatography - ElectroSpray Ionization - Mass Spectrometry (LC-ESI-MS), Ultra High Performance Liquid Chromatography with Fluorescence Detection (UHPLC-FLD), and Matrix Assisted Laser Desorption Ionization - Furier Transform Ion Cyclotron Resonance - Mass Spectrometry (MALDI-FTICR-MS). Based on our results, we recommend normalizing glycan data using the 'Probabilistic Quotient' method followed by log-transformation, irrespective of the measurement platform. This recommendation is further supported by an additional analysis, where we ranked normalization methods based on their statistical associations with age, a factor known to associate with glycomics measurements.
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Affiliation(s)
- Elisa Benedetti
- Department of Physiology and Biophysics, Institute for Computational Biomedicine, Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY 10022, USA;
- Institute of Computational Biology, Helmholtz Zentrum München—German Research Center for Environmental Health, 85764 Neuherberg, Germany;
| | - Nathalie Gerstner
- Institute of Computational Biology, Helmholtz Zentrum München—German Research Center for Environmental Health, 85764 Neuherberg, Germany;
- Max Planck Institute for Psychiatry, 80804 Munich, Germany
| | - Maja Pučić-Baković
- Genos Glycoscience Research Laboratory, 10000 Zagreb, Croatia; (M.P.-B.); (G.L.)
| | - Toma Keser
- Faculty of Pharmacy and Biochemistry, University of Zagreb, 10000 Zagreb, Croatia; (T.K.); (T.Š.)
| | - Karli R. Reiding
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, 3584 CH Utrecht, The Netherlands; (K.R.R.); (M.H.J.S.)
- Center for Proteomics and Metabolomics, Leiden University Medical Center, 2333 ZC Leiden, The Netherlands; (L.R.R.); (M.W.)
| | - L. Renee Ruhaak
- Center for Proteomics and Metabolomics, Leiden University Medical Center, 2333 ZC Leiden, The Netherlands; (L.R.R.); (M.W.)
- Department of Clinical Chemistry and Laboratory Medicine, Leiden University Medical Center, 2333 ZC Leiden, The Netherlands
| | - Tamara Štambuk
- Faculty of Pharmacy and Biochemistry, University of Zagreb, 10000 Zagreb, Croatia; (T.K.); (T.Š.)
| | - Maurice H.J. Selman
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, 3584 CH Utrecht, The Netherlands; (K.R.R.); (M.H.J.S.)
| | - Igor Rudan
- Usher Institute of Population Health Sciences and Informatics, University of Edinburgh, Edinburgh EH8 9AG, UK;
| | - Ozren Polašek
- Medical School, University of Split, 21000 Split, Croatia;
- Gen-Info Ltd., 10000 Zagreb, Croatia
| | - Caroline Hayward
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK;
| | - Marian Beekman
- Section of Molecular Epidemiology, Leiden University Medical Center, 2333 ZC Leiden, The Netherlands; (M.B.); (E.S.)
| | - Eline Slagboom
- Section of Molecular Epidemiology, Leiden University Medical Center, 2333 ZC Leiden, The Netherlands; (M.B.); (E.S.)
| | - Manfred Wuhrer
- Center for Proteomics and Metabolomics, Leiden University Medical Center, 2333 ZC Leiden, The Netherlands; (L.R.R.); (M.W.)
| | - Malcolm G. Dunlop
- Colon Cancer Genetics Group, Institute of Genetics and Molecular Medicine, University of Edinburgh and Medical Research Council Human Genetics Unit, Edinburgh EH8 9YL, UK;
| | - Gordan Lauc
- Genos Glycoscience Research Laboratory, 10000 Zagreb, Croatia; (M.P.-B.); (G.L.)
- Faculty of Pharmacy and Biochemistry, University of Zagreb, 10000 Zagreb, Croatia; (T.K.); (T.Š.)
| | - Jan Krumsiek
- Department of Physiology and Biophysics, Institute for Computational Biomedicine, Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY 10022, USA;
- Institute of Computational Biology, Helmholtz Zentrum München—German Research Center for Environmental Health, 85764 Neuherberg, Germany;
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21
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van der Burgt YEM, Siliakus KM, Cobbaert CM, Ruhaak LR. HILIC-MRM-MS for Linkage-Specific Separation of Sialylated Glycopeptides to Quantify Prostate-Specific Antigen Proteoforms. J Proteome Res 2020; 19:2708-2716. [PMID: 32142289 PMCID: PMC8280738 DOI: 10.1021/acs.jproteome.0c00050] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
![]()
Elevated serum prostate-specific
antigen (PSA) levels in body fluids
may indicate prostate cancer (PCa), but it is noted that the clinical
performance is rather poor. Specificity and sensitivity values of
20 and 94% at a cutoff value of 4.1 ng/mL, respectively, result in
overdiagnosis and unnecessary interventions. Previous exploratory
studies have indicated that the glycosylation of PSA potentially leads
to improved PCa diagnosis based on qualitative analyses. However,
the applied methods are not suited for a quantitative evaluation or
implementation in a medical laboratory. Therefore, in this proof-of-principle
study, we have evaluated the use of hydrophilic interaction liquid
chromatography (HILIC) in combination with targeted quantitative mass
spectrometry for the sialic acid linkage-specific analysis of PSA
glyco-proteoforms based on either trypsin or ArgC peptides. The efficiency
of PSA proteolysis was optimized as well as the glycopeptide separation
conditions (buffer type, strength, and pH). The HILIC-based analysis
of PSA glyco-proteoforms presented here has the potential for the
clinical validation of patient cohorts. The method shows the feasibility
of the use of a HILIC stationary phase for the separation of isomeric
glycopeptides to detect specific glyco-proteoforms. This is the first
step toward the development and evaluation of PSA glyco-proteoforms
for use in a clinical chemistry setting aiming for improved PCa diagnosis
or screening.
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Affiliation(s)
- Yuri E M van der Burgt
- Department of Clinical Chemistry and Laboratory Medicine, Leiden University Medical Center, Albinusdreef 2, 2333 ZA Leiden, The Netherlands
| | - Kasper M Siliakus
- Department of Clinical Chemistry and Laboratory Medicine, Leiden University Medical Center, Albinusdreef 2, 2333 ZA Leiden, The Netherlands
| | - Christa M Cobbaert
- Department of Clinical Chemistry and Laboratory Medicine, Leiden University Medical Center, Albinusdreef 2, 2333 ZA Leiden, The Netherlands
| | - L Renee Ruhaak
- Department of Clinical Chemistry and Laboratory Medicine, Leiden University Medical Center, Albinusdreef 2, 2333 ZA Leiden, The Netherlands
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22
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Ruhaak LR, Smit NPM, Suchiman HED, Pieterse MM, Romijn FPHTM, Beekman M, Cobbaert CM. MS-based proteomics: a metrological sound and robust alternative for apolipoprotein E phenotyping in a multiplexed test. Clin Chem Lab Med 2019; 57:e102-e104. [PMID: 30240356 DOI: 10.1515/cclm-2018-0782] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Accepted: 08/27/2018] [Indexed: 12/11/2022]
Affiliation(s)
- L Renee Ruhaak
- Department of Clinical Chemistry and Laboratory Medicine, Leiden University Medical Center, Leiden, TheNetherlands
| | - Nico P M Smit
- Department of Clinical Chemistry and Laboratory Medicine, Leiden University Medical Center, Leiden, TheNetherlands
| | - H Eka D Suchiman
- Section of Molecular Epidemiology, Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden, TheNetherlands
| | - Mervin M Pieterse
- Department of Clinical Chemistry and Laboratory Medicine, Leiden University Medical Center, Leiden, TheNetherlands
| | - Fred P H T M Romijn
- Department of Clinical Chemistry and Laboratory Medicine, Leiden University Medical Center, Leiden, TheNetherlands
| | - Marian Beekman
- Section of Molecular Epidemiology, Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden, TheNetherlands
| | - Christa M Cobbaert
- Department of Clinical Chemistry and Laboratory Medicine, Leiden University Medical Center, Leiden, TheNetherlands
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23
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Orsi FA, Lijfering WM, Van der Laarse A, Ruhaak LR, Rosendaal FR, Cannegieter SC, Cobbaert C. Association of apolipoproteins C-I, C-II, C-III and E with coagulation markers and venous thromboembolism risk. Clin Epidemiol 2019; 11:625-633. [PMID: 31413640 PMCID: PMC6659780 DOI: 10.2147/clep.s196266] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Accepted: 05/23/2019] [Indexed: 12/12/2022] Open
Abstract
Purpose Apolipoproteins C-I, C-II, C-III and E have been associated with risk of arterial thrombotic diseases. We investigated whether these apolipoproteins have prothrombotic properties and are associated with risk of venous thromboembolism (VTE). Patients and methods A total of 127 VTE patients and 299 controls were randomly selected from the Multiple Environmental and Genetic Assessment of Risk Factors for Venous Thrombosis study (1999–2004), in the Netherlands. The apolipoproteins were quantified using mass spectrometry (LC/MS/MS), and their levels were analyzed as continuous variable (per SD increase). Results In controls, increases in levels of apolipoproteins were associated with increases in levels of vitamin K-dependent factors, factor XI, antithrombin and clot lysis time. Additionally, increasing apolipoproteins C-III and E levels were associated with higher factor VIII and von Willebrand factor levels. Levels of C-reactive protein were not associated with any apolipoprotein. The age- and sex-adjusted odds ratios of apolipoproteins E, C-III, CII and CI to the risk of venous thrombosis were 1.21 (95% CI, 0.98–1.49), 1.19 (95% CI, 0.99–1.44), 1.24 (95% CI, 0.95–1.61) and 1.06 (95% CI, 0.87–1.30) per SD increase, respectively. These odds ratios did not attenuate after adjustments for statin use, estrogen use, BMI, alcohol use, and self-reported diabetes. Conclusions Levels of apolipoproteins C-I, C-II, C-III and E are associated with those of several coagulation factors. However, whether these apolipoproteins are also associated with an increased risk of VTE remains to be established.
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Affiliation(s)
- Fernanda A Orsi
- Department of Clinical Pathology, School of Medical Sciences, University of Campinas (UNICAMP), Campinas, Brazil.,Department of Clinical Epidemiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Willem M Lijfering
- Department of Clinical Epidemiology, Leiden University Medical Center, Leiden, The Netherlands.,Einthoven Laboratory for Experimental Vascular Medicine, Leiden University Medical Center, Leiden, The Netherlands
| | - Arnoud Van der Laarse
- Department of Clinical Chemistry and Laboratory Medicine, Leiden University Medical Center, Leiden, The Netherlands.,Department of Cardiology, Leiden University Medical Center, Leiden, The Netherlands
| | - L Renee Ruhaak
- Department of Clinical Chemistry and Laboratory Medicine, Leiden University Medical Center, Leiden, The Netherlands
| | - Frits R Rosendaal
- Department of Clinical Epidemiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Suzanne C Cannegieter
- Department of Clinical Epidemiology, Leiden University Medical Center, Leiden, The Netherlands.,Einthoven Laboratory for Experimental Vascular Medicine, Leiden University Medical Center, Leiden, The Netherlands.,Department of Internal Medicine, Section of Thrombosis and Hemostasis, Leiden University Medical Center, Leiden, The Netherlands
| | - Christa Cobbaert
- Department of Clinical Chemistry and Laboratory Medicine, Leiden University Medical Center, Leiden, The Netherlands
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24
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Ruhaak LR, Romijn FPHTM, Smit NPM, van der Laarse A, Pieterse MM, de Maat MPM, Haas FJLM, Kluft C, Amiral J, Meijer P, Cobbaert CM. Detecting molecular forms of antithrombin by LC-MRM-MS: defining the measurands. Clin Chem Lab Med 2019; 56:1704-1714. [PMID: 29708875 DOI: 10.1515/cclm-2017-1111] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Accepted: 03/16/2018] [Indexed: 12/20/2022]
Affiliation(s)
- L Renee Ruhaak
- Department of Clinical Chemistry and Laboratory Medicine, Leiden University Medical Center, Postzone E2-P, Albinusdreef 2, 2333 ZA Leiden, The Netherlands, Phone: +31-71526-6397
| | - Fred P H T M Romijn
- Department of Clinical Chemistry and Laboratory Medicine, Leiden University Medical Center, Leiden, The Netherlands
| | - Nico P M Smit
- Department of Clinical Chemistry and Laboratory Medicine, Leiden University Medical Center, Leiden, The Netherlands
| | - Arnoud van der Laarse
- Department of Clinical Chemistry and Laboratory Medicine, Leiden University Medical Center, Leiden, The Netherlands
| | - Mervin M Pieterse
- Department of Clinical Chemistry and Laboratory Medicine, Leiden University Medical Center, Leiden, The Netherlands
| | | | | | | | | | - Piet Meijer
- ECAT Foundation, Voorschoten, The Netherlands
| | - Christa M Cobbaert
- Department of Clinical Chemistry and Laboratory Medicine, Leiden University Medical Center, Leiden, The Netherlands
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25
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Abstract
An elevated low-density lipoprotein cholesterol concentration is a classical risk factor for cardiovascular disease. This has led to pharmacotherapy in patients with atherosclerotic heart disease or high heart disease risk with statins to reduce serum low-density lipoprotein cholesterol. Even in patients in whom the target levels of low-density lipoprotein cholesterol are reached, there remains a significant residual cardiovascular risk; this is due, in part, to a focus on low-density lipoprotein cholesterol alone and neglect of other important aspects of lipoprotein metabolism. A more refined lipoprotein analysis will provide additional information on the accumulation of very low-density lipoproteins, intermediate density lipoproteins, chylomicrons, chylomicron-remnants and Lp(a) concentrations. Instead of measuring the cholesterol and triglyceride content of the lipoproteins, measurement of their apolipoproteins (apos) is more informative. Apos are either specific for a particular lipoprotein or for a group of lipoproteins. In particular measurement of apos in atherogenic particles is more biologically meaningful than the measurement of the cholesterol concentration contained in these particles. Applying apo profiling will not only improve characterization of the lipoprotein abnormality, but will also improve definition of therapeutic targets. Apo profiling aligns with the concept of precision medicine by which an individual patient is not treated as 'average' patient by the average (dose of) therapy. This concept of precision medicine fits the unmet clinical need for stratified cardiovascular medicine. The requirements for clinical application of proteomics, including apo profiling, can now be met using robust mass spectrometry technology which offers desirable analytical performance and standardization.
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Affiliation(s)
- L Renee Ruhaak
- 1 Department of Clinical Chemistry and Laboratory Medicine, Leiden University Medical Center, Leiden, The Netherlands
| | - Arnoud van der Laarse
- 1 Department of Clinical Chemistry and Laboratory Medicine, Leiden University Medical Center, Leiden, The Netherlands.,2 Department of Cardiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Christa M Cobbaert
- 1 Department of Clinical Chemistry and Laboratory Medicine, Leiden University Medical Center, Leiden, The Netherlands
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26
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Bodde MC, Hermans MPJ, Jukema JW, Schalij MJ, Lijfering WM, Rosendaal FR, Romijn FPHTM, Ruhaak LR, van der Laarse A, Cobbaert CM. Apolipoproteins A1, B, and apoB/apoA1 ratio are associated with first ST-segment elevation myocardial infarction but not with recurrent events during long-term follow-up. Clin Res Cardiol 2018; 108:520-538. [PMID: 30298424 PMCID: PMC6484771 DOI: 10.1007/s00392-018-1381-5] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Accepted: 09/27/2018] [Indexed: 12/31/2022]
Abstract
INTRODUCTION The current way to assess the risk of cardiovascular disease (CVD) is to measure conventional lipid and lipoprotein cholesterol fractions. Despite the success of statin treatment, residual cardiovascular risk remains high. Therefore, the value of extensive serum apolipoprotein (apo) profiling to assess the risk of ST-segment elevation myocardial infarction (STEMI) and of major adverse cardiac events (MACE) in patients with STEMI was investigated in a case-control design. METHODS AND RESULTS Serum apo levels were measured using liquid chromatography and mass spectrometry in 299 healthy individuals and 220 patients with STEMI. First, the association of apo profiles in baseline samples with risk of STEMI was examined, and second, the association of apo profiles at baseline with risk of recurrent MACE in patients with STEMI in a longitudinal study design was studied. High baseline (> 1.25 g/L) apoA1 levels were associated with a decreased risk of STEMI [odds ratio (OR) 0.17; 95% CI 0.11-0.26], whereas high apoB (> 1.00 g/L) levels (OR 2.17; 95% CI 1.40-3.36) and apoB/apoA1 ratio (OR per 1 SD (OR/SD): 2.16; 95% CI 1.76-2.65) were associated with an increased risk. Very-low-density-lipoprotein (VLDL)-associated apos gave conflicting results. Neither conventional lipid levels nor apo levels were associated with MACE in the STEMI group. CONCLUSION In conclusion, apoA1, apoB, and apoB/apoA1 were strongly associated with risk of STEMI. No clear relation between VLDL-associated apos and the risk of STEMI was found. Neither baseline serum apos nor lipids predicted MACE in statin-treated patients during long-term follow-up after a first STEMI.
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Affiliation(s)
- Mathijs C Bodde
- Department of Cardiology, C5-P, Leiden University Medical Center, P.O. Box 9600, 2300 RC, Leiden, The Netherlands.
| | - Maaike P J Hermans
- Department of Cardiology, C5-P, Leiden University Medical Center, P.O. Box 9600, 2300 RC, Leiden, The Netherlands
| | - J Wouter Jukema
- Department of Cardiology, C5-P, Leiden University Medical Center, P.O. Box 9600, 2300 RC, Leiden, The Netherlands
| | - Martin J Schalij
- Department of Cardiology, C5-P, Leiden University Medical Center, P.O. Box 9600, 2300 RC, Leiden, The Netherlands
| | - Willem M Lijfering
- Department of Cardiology, C5-P, Leiden University Medical Center, P.O. Box 9600, 2300 RC, Leiden, The Netherlands
| | - Frits R Rosendaal
- Department of Epidemiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Fred P H T M Romijn
- Department of Clinical Chemistry and Laboratory Medicine, Leiden University Medical Center, Leiden, The Netherlands
| | - L Renee Ruhaak
- Department of Clinical Chemistry and Laboratory Medicine, Leiden University Medical Center, Leiden, The Netherlands
| | - Arnoud van der Laarse
- Department of Clinical Chemistry and Laboratory Medicine, Leiden University Medical Center, Leiden, The Netherlands
| | - Christa M Cobbaert
- Department of Clinical Chemistry and Laboratory Medicine, Leiden University Medical Center, Leiden, The Netherlands
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27
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Abstract
Glycomic and glycoproteomic analyses involve the characterization of oligosaccharides (glycans) conjugated to proteins. Glycans are produced through a complicated nontemplate driven process involving the competition of enzymes that extend the nascent chain. The large diversity of structures, the variations in polarity of the individual saccharide residues, and the poor ionization efficiencies of glycans all conspire to make the analysis arguably much more difficult than any other biopolymer. Furthermore, the large number of glycoforms associated with a specific protein site makes it more difficult to characterize than any post-translational modification. Nonetheless, there have been significant progress, and advanced separation and mass spectrometry methods have been at its center and the main reason for the progress. While glycomic and glycoproteomic analyses are still typically available only through highly specialized laboratories, new software and workflow is making it more accessible. This review focuses on the role of mass spectrometry and separation methods in advancing glycomic and glycoproteomic analyses. It describes the current state of the field and progress toward making it more available to the larger scientific community.
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Affiliation(s)
- L Renee Ruhaak
- Department of Clinical Chemistry and Laboratory Medicine , Leiden University Medical Center , 2333 ZA Leiden , The Netherlands
| | - Gege Xu
- Department of Chemistry , University of California, Davis , One Shields Avenue , Davis , California 95616 , United States
| | - Qiongyu Li
- Department of Chemistry , University of California, Davis , One Shields Avenue , Davis , California 95616 , United States
| | - Elisha Goonatilleke
- Department of Chemistry , University of California, Davis , One Shields Avenue , Davis , California 95616 , United States
| | - Carlito B Lebrilla
- Department of Chemistry , University of California, Davis , One Shields Avenue , Davis , California 95616 , United States.,Department of Biochemistry and Molecular Medicine , University of California, Davis , Davis , California 95616 , United States.,Foods for Health Institute , University of California, Davis , Davis , California 95616 , United States
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28
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Dittrich J, Adam M, Maas H, Hecht M, Reinicke M, Ruhaak LR, Cobbaert C, Engel C, Wirkner K, Löffler M, Thiery J, Ceglarek U. Targeted On-line SPE-LC-MS/MS Assay for the Quantitation of 12 Apolipoproteins from Human Blood. Proteomics 2018; 18. [PMID: 29280342 DOI: 10.1002/pmic.201700279] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Revised: 12/01/2017] [Indexed: 12/22/2022]
Abstract
Laborious sample pretreatment of biological samples represents the most limiting factor for the translation of targeted proteomics assays from research to clinical routine. An optimized method for the simultaneous quantitation of 12 major apolipoproteins (apos) combining on-line SPE and fast LC-MS/MS analysis in 6.5 min total run time was developed, reducing the manual sample pretreatment time of 3 μL serum or plasma by 60%. Within-run and between-day imprecisions below 10 and 15% (n = 10) and high recovery rates (94-131%) were obtained applying the high-throughput setup. High-quality porcine trypsin was used, which outperformed cost-effective bovine trypsin regarding digestion efficiency. Comparisons with immunoassays and another LC-MS/MS assay demonstrated good correlation (Pearson's R: 0.81-0.98). Further, requirements on sample quality concerning sampling, processing, and long-term storage up to 1 year were investigated revealing significant influences of the applied sampling material and coagulant on quantitation results. Apo profiles of 1339 subjects of the LIFE-Adult-Study were associated with lifestyle and physiological parameters as well as establish parameters of lipid metabolism (e.g., triglycerides, cholesterol). Besides gender effects, most significant impact was seen regarding lipid-lowering medication. In conclusion, this novel highly standardized, high-throughput targeted proteomics assay utilizes a fast, simultaneous analysis of 12 apos from least sample amounts.
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Affiliation(s)
- Julia Dittrich
- Institute of Laboratory Medicine, Clinical Chemistry and Molecular Diagnostics, University Hospital Leipzig, Leipzig, Germany.,LIFE, Leipzig Research Center for Civilization Diseases, Leipzig University, Leipzig, Germany
| | - Melanie Adam
- Institute of Laboratory Medicine, Clinical Chemistry and Molecular Diagnostics, University Hospital Leipzig, Leipzig, Germany
| | - Hilke Maas
- Institute of Laboratory Medicine, Clinical Chemistry and Molecular Diagnostics, University Hospital Leipzig, Leipzig, Germany
| | - Max Hecht
- Institute of Laboratory Medicine, Clinical Chemistry and Molecular Diagnostics, University Hospital Leipzig, Leipzig, Germany
| | - Madlen Reinicke
- Institute of Laboratory Medicine, Clinical Chemistry and Molecular Diagnostics, University Hospital Leipzig, Leipzig, Germany
| | - L Renee Ruhaak
- Department of Clinical Chemistry and Laboratory Medicine, Leiden University Medical Center, Leiden, The Netherlands
| | - Christa Cobbaert
- Department of Clinical Chemistry and Laboratory Medicine, Leiden University Medical Center, Leiden, The Netherlands
| | - Christoph Engel
- LIFE, Leipzig Research Center for Civilization Diseases, Leipzig University, Leipzig, Germany.,Institute for Medical Informatics, Statistics and Epidemiology, Leipzig University, Leipzig, Germany
| | - Kerstin Wirkner
- LIFE, Leipzig Research Center for Civilization Diseases, Leipzig University, Leipzig, Germany
| | - Markus Löffler
- LIFE, Leipzig Research Center for Civilization Diseases, Leipzig University, Leipzig, Germany.,Institute for Medical Informatics, Statistics and Epidemiology, Leipzig University, Leipzig, Germany
| | - Joachim Thiery
- Institute of Laboratory Medicine, Clinical Chemistry and Molecular Diagnostics, University Hospital Leipzig, Leipzig, Germany.,LIFE, Leipzig Research Center for Civilization Diseases, Leipzig University, Leipzig, Germany
| | - Uta Ceglarek
- Institute of Laboratory Medicine, Clinical Chemistry and Molecular Diagnostics, University Hospital Leipzig, Leipzig, Germany.,LIFE, Leipzig Research Center for Civilization Diseases, Leipzig University, Leipzig, Germany
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29
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Song T, Chen P, Stroble C, Ruhaak LR, Wang H, Li Z, He W, Lebrilla CB. Serum glycosylation characterization of osteonecrosis of the femoral head by mass spectrometry. Eur J Mass Spectrom (Chichester) 2018; 24:178-187. [PMID: 29224385 PMCID: PMC6201689 DOI: 10.1177/1469066717740010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Osteonecrosis of the femoral head is a recalcitrant and paralyzing disease often discovered in the end stage at the time of diagnosis, which is often performed by physical examination and diagnostic imaging. Osteonecrosis of the femoral head is typically caused by trauma or long-term steroid use. There are over 30 million patients in the US taking steroids, and roughly 40% will develop osteonecrosis of the femoral head. However, the exact pathophysiological process is not well understood. This study aims to examine the alteration in serum glycosylation of osteonecrosis of the femoral head using the state-of-the-art analytical tools to provide more chemical data for pathophysiology research and possibly biomarker discovery. A training set containing 27 serum samples from steroid-induced osteonecrosis of the femoral head patients and 25 from gender- and age-matched controls was collected and analyzed. Glycosylation of whole serum and site-specific glycosylation of immunoglobulins are characterized using electrospray ionization-Q-time of flight and electrospray ionization-Triple-Quadruple via multiple reaction monitoring, respectively. The whole serum glycosylation analysis yielded 14 N-glycan compositions and multiple reaction monitoring yielded eight glycopeptides that were altered between cases and controls with statistical significance. The increase of nonsialylated, nonfucosylated N-glycans and decrease of fucosylated N-glycans are associated with the development of osteonecrosis of the femoral head. Glycosylation is a posttranslational protein modification and is apparently affected by osteonecrosis of the femoral head. Future studies with a larger cohort and patients from earlier stage will be performed to assess these potential markers' value in disease onset.
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Affiliation(s)
- Ting Song
- Department of Chemistry, University of California Davis, Davis, California, 95616, United States
| | - Peng Chen
- First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, 510405, China
- Cancer Center, University of California Davis, Sacramento, California, 95817, United States
| | - Carol Stroble
- Department of Chemistry, University of California Davis, Davis, California, 95616, United States
| | - L. Renee Ruhaak
- Department of Chemistry, University of California Davis, Davis, California, 95616, United States
| | - Haibin Wang
- First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, 510405, China
| | - Ziqi Li
- First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, 510405, China
| | - Wei He
- First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, 510405, China
| | - Carlito B. Lebrilla
- Department of Chemistry, University of California Davis, Davis, California, 95616, United States
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30
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Ruhaak LR, Smit NPM, Romijn FPHTM, Pieterse MM, van der Laarse A, van der Burgt YEM, Cobbaert CM. Robust and Accurate 2-Year Performance of a Quantitative Mass Spectrometry-Based Apolipoprotein Test in a Clinical Chemistry Laboratory. Clin Chem 2018; 64:747-749. [PMID: 29378689 DOI: 10.1373/clinchem.2017.285098] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- L Renee Ruhaak
- Department of Clinical Chemistry and Laboratory Medicine Leiden University Medical Center Leiden, the Netherlands
| | - Nico P M Smit
- Department of Clinical Chemistry and Laboratory Medicine Leiden University Medical Center Leiden, the Netherlands
| | - Fred P H T M Romijn
- Department of Clinical Chemistry and Laboratory Medicine Leiden University Medical Center Leiden, the Netherlands
| | - Mervin M Pieterse
- Department of Clinical Chemistry and Laboratory Medicine Leiden University Medical Center Leiden, the Netherlands
| | - Arnoud van der Laarse
- Department of Clinical Chemistry and Laboratory Medicine Leiden University Medical Center Leiden, the Netherlands
| | - Yuri E M van der Burgt
- Department of Clinical Chemistry and Laboratory Medicine Leiden University Medical Center Leiden, the Netherlands
| | - Christa M Cobbaert
- Department of Clinical Chemistry and Laboratory Medicine Leiden University Medical Center Leiden, the Netherlands
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31
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Miyamoto S, Stroble CD, Taylor S, Hong Q, Lebrilla CB, Leiserowitz GS, Kim K, Ruhaak LR. Multiple Reaction Monitoring for the Quantitation of Serum Protein Glycosylation Profiles: Application to Ovarian Cancer. J Proteome Res 2017; 17:222-233. [PMID: 29207246 DOI: 10.1021/acs.jproteome.7b00541] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Protein glycosylation fingerprints are widely recognized as potential markers for disease states, and indeed differential glycosylation has been identified in multiple types of autoimmune diseases and several types of cancer. However, releasing the glycans leave the glycoproteins unknown; therefore, there exists a need for high-throughput methods that allow quantification of site- and protein-specific glycosylation patterns from complex biological mixtures. In this study, a targeted multiple reaction monitoring (MRM)-based method for the protein- and site-specific quantitation involving serum proteins immunoglobulins A, G and M, alpha-1-antitrypsin, transferrin, alpha-2-macroglobulin, haptoglobin, alpha-1-acid glycoprotein and complement C3 was developed. The method is based on tryptic digestion of serum glycoproteins, followed by immediate reverse phase UPLC-QQQ-MS analysis of glycopeptides. To quantitate protein glycosylation independent of the protein serum concentration, a nonglycosylated peptide was also monitored. Using this strategy, 178 glycopeptides and 18 peptides from serum glycoproteins are analyzed with good repeatability (interday CVs of 3.65-21-92%) in a single 17 min run. To assess the potential of the method, protein glycosylation was analyzed in serum samples from ovarian cancer patients and controls. A training set consisting of 40 cases and 40 controls was analyzed, and differential analyses were performed to identify aberrant glycopeptide levels. All findings were validated in an independent test set (n = 44 cases and n = 44 controls). In addition to the differential glycosylation on the immunoglobulins, which was reported previously, aberrant glycosylation was also observed on each of the glycoproteins, which could be corroborated in the test set. This report shows the development of a method for targeted protein- and site-specific glycosylation analysis and the potential of such methods in biomarker development.
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Affiliation(s)
- Suzanne Miyamoto
- UC Davis Cancer Center , Sacramento, California 95817, United States
| | - Carol D Stroble
- UC Davis Cancer Center , Sacramento, California 95817, United States.,Department of Chemistry, University of California , Davis, California 95616, United States
| | - Sandra Taylor
- Division of Biostatistics, Department of Public Health Sciences, University of California , Davis, California 95616, United States
| | - Qiuting Hong
- Department of Chemistry, University of California , Davis, California 95616, United States
| | - Carlito B Lebrilla
- Department of Chemistry, University of California , Davis, California 95616, United States
| | - Gary S Leiserowitz
- Division of Gynecologic Oncology, UC Davis Medical Center , Sacramento, California 95817, United States
| | - Kyoungmi Kim
- Division of Biostatistics, Department of Public Health Sciences, University of California , Davis, California 95616, United States
| | - L Renee Ruhaak
- Department of Chemistry, University of California , Davis, California 95616, United States.,Department of Clinical Chemistry and Laboratory Medicine, Leiden University Medical Center , 2333 ZA Leiden, The Netherlands
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32
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Taylor SL, Ruhaak LR, Kelly K, Weiss RH, Kim K. Effects of imputation on correlation: implications for analysis of mass spectrometry data from multiple biological matrices. Brief Bioinform 2017; 18:312-320. [PMID: 26896791 DOI: 10.1093/bib/bbw010] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2015] [Indexed: 11/14/2022] Open
Abstract
With expanded access to, and decreased costs of, mass spectrometry, investigators are collecting and analyzing multiple biological matrices from the same subject such as serum, plasma, tissue and urine to enhance biomarker discoveries, understanding of disease processes and identification of therapeutic targets. Commonly, each biological matrix is analyzed separately, but multivariate methods such as MANOVAs that combine information from multiple biological matrices are potentially more powerful. However, mass spectrometric data typically contain large amounts of missing values, and imputation is often used to create complete data sets for analysis. The effects of imputation on multiple biological matrix analyses have not been studied. We investigated the effects of seven imputation methods (half minimum substitution, mean substitution, k-nearest neighbors, local least squares regression, Bayesian principal components analysis, singular value decomposition and random forest), on the within-subject correlation of compounds between biological matrices and its consequences on MANOVA results. Through analysis of three real omics data sets and simulation studies, we found the amount of missing data and imputation method to substantially change the between-matrix correlation structure. The magnitude of the correlations was generally reduced in imputed data sets, and this effect increased with the amount of missing data. Significant results from MANOVA testing also were substantially affected. In particular, the number of false positives increased with the level of missing data for all imputation methods. No one imputation method was universally the best, but the simple substitution methods (Half Minimum and Mean) consistently performed poorly.
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Affiliation(s)
- Sandra L Taylor
- Division of Biostatistics, Department of Public Health Sciences, University of California School of Medicine, CA, USA
| | - L Renee Ruhaak
- Department of Chemistry, University of California, CA, USA
| | - Karen Kelly
- Division of Hematology and Oncology, University of California Davis Comprehensive Cancer Center , Sacramento, California, USA
| | - Robert H Weiss
- Division of Nephrology, Department of Internal Medicine, University of California, CA, USA
| | - Kyoungmi Kim
- Division of Biostatistics, Department of Public Health Sciences, University of California , California, USA
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33
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Abstract
In recent years, high-throughput glycomics approaches have been developed and applied to either complete biofluids, cell lysates or tissues, or proteins isolated thereof. However, during such analyses the N-glycan are released from the protein backbone and therefore site- and protein-specific information is lost. There exists a need for high-throughput methods that allow quantification of site- and protein-specific glycosylation patterns from complex biological mixtures. We here describe the use of a multiple reaction monitoring mass spectrometry based method for the generation of glycopeptide profiles of the nine high abundance glycoproteins IgG, IgA, IgM, haptoglobin, alpha-1-antitrypsin, alpha-2-macroglobulin, alpha-1-acid glycoprotein, transferrin, and complement C3. We show that the sample preparation can be performed at the 96-well level, and using a 17-min gradient on a RP-UPLC-QQQ instrument, 96 samples can be analyzed within 3 days.
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Affiliation(s)
- L Renee Ruhaak
- Department of Translational Molecular Pathology, UT MD Anderson Cancer Center, 6767 Bertner Avenue, Houston, TX, 77030, USA.
- Department of Chemistry, UC Davis, One Shields Avenue, Davis, CA, 95616, USA.
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Abstract
Human milk oligosaccharides (HMOs) are a highly abundant constituent in human milk, and its protective and prebiotic properties have attracted considerable attention. HMOs have been shown to directly and indirectly benefit the overall health of the infant due to a number of functions including serving as a beneficial food for gut bacteria, block to pathogens, and aiding in brain development. Researchers are currently exploring whether these structures may act as possible disease and nutrition biomarkers. Because of this, rapid-throughput methods are desired to investigate biological activity in large patient sets. We have optimized a rapid-throughput protocol to analyze human milk oligosaccharides using micro-volumes of human breast milk for nutritional biomarkers. This method may additionally be applied to other biological fluid substrates such as plasma, urine, and feces. The protocol involves lipid separation via centrifugation, protein precipitation using ethanol, alditol reduction with sodium borohydride, and a final solid-phase extraction purification step using graphitized carbon cartridges. Samples are analyzed using HPLC-Chip/TOF-MS and data filtered on Agilent MassHunter using an in-house library. Individual structural identification is matched against a previously developed HMO library using accurate mass and retention time. Using this method will allow in-depth characterization and profiling of HMOs in large patient sets, and will ease the process of discovering significant nutritional biomarkers in human milk.
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Affiliation(s)
- Lauren D Wu
- Department of Chemistry, University of California, Davis, CA, 95616, USA
| | - L Renee Ruhaak
- Department of Translational Molecular Pathology, UT MD Anderson Cancer Center, 6767 Bertner Avenue, Houston, TX, 77030, USA
- Department of Chemistry, UC Davis, One Shields Avenue, Davis, CA, 95616, USA
| | - Carlito B Lebrilla
- Department of Chemistry, University of California, Davis, CA, 95616, USA.
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35
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Reiding KR, Ruhaak LR, Uh HW, El Bouhaddani S, van den Akker EB, Plomp R, McDonnell LA, Houwing-Duistermaat JJ, Slagboom PE, Beekman M, Wuhrer M. Human Plasma N-glycosylation as Analyzed by Matrix-Assisted Laser Desorption/Ionization-Fourier Transform Ion Cyclotron Resonance-MS Associates with Markers of Inflammation and Metabolic Health. Mol Cell Proteomics 2016; 16:228-242. [PMID: 27932526 DOI: 10.1074/mcp.m116.065250] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Revised: 12/01/2016] [Indexed: 12/22/2022] Open
Abstract
Glycosylation is an abundant co- and post-translational protein modification of importance to protein processing and activity. Although not template-defined, glycosylation does reflect the biological state of an organism and is a high-potential biomarker for disease and patient stratification. However, to interpret a complex but informative sample like the total plasma N-glycome, it is important to establish its baseline association with plasma protein levels and systemic processes. Thus far, large-scale studies (n >200) of the total plasma N-glycome have been performed with methods of chromatographic and electrophoretic separation, which, although being informative, are limited in resolving the structural complexity of plasma N-glycans. MS has the opportunity to contribute additional information on, among others, antennarity, sialylation, and the identity of high-mannose type species.Here, we have used matrix-assisted laser desorption/ionization (MALDI)-Fourier transform ion cyclotron resonance (FTICR)-MS to study the total plasma N-glycome of 2144 healthy middle-aged individuals from the Leiden Longevity Study, to allow association analysis with markers of metabolic health and inflammation. To achieve this, N-glycans were enzymatically released from their protein backbones, labeled at the reducing end with 2-aminobenzoic acid, and following purification analyzed by negative ion mode intermediate pressure MALDI-FTICR-MS. In doing so, we achieved the relative quantification of 61 glycan compositions, ranging from Hex4HexNAc2 to Hex7HexNAc6dHex1Neu5Ac4, as well as that of 39 glycosylation traits derived thereof. Next to confirming known associations of glycosylation with age and sex by MALDI-FTICR-MS, we report novel associations with C-reactive protein (CRP), interleukin 6 (IL-6), body mass index (BMI), leptin, adiponectin, HDL cholesterol, triglycerides (TG), insulin, gamma-glutamyl transferase (GGT), alanine aminotransferase (ALT), and smoking. Overall, the bisection, galactosylation, and sialylation of diantennary species, the sialylation of tetraantennary species, and the size of high-mannose species proved to be important plasma characteristics associated with inflammation and metabolic health.
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Affiliation(s)
- Karli R Reiding
- From the ‡Center for Proteomics and Metabolomics, Leiden University Medical Center, 2300 RC Leiden, The Netherlands
| | - L Renee Ruhaak
- §Department of Clinical Chemistry and Laboratory Medicine, Leiden University Medical Center, 2300 RC Leiden, The Netherlands
| | - Hae-Won Uh
- ¶Department of Medical Statistics and Bioinformatics, Leiden University Medical Center, 2300 RC Leiden, The Netherlands
| | - Said El Bouhaddani
- ¶Department of Medical Statistics and Bioinformatics, Leiden University Medical Center, 2300 RC Leiden, The Netherlands
| | - Erik B van den Akker
- ¶Department of Medical Statistics and Bioinformatics, Leiden University Medical Center, 2300 RC Leiden, The Netherlands.,**Pattern Recognition & Bioinformatics, Delft University of Technology, 2600 GA Delft, The Netherlands
| | - Rosina Plomp
- From the ‡Center for Proteomics and Metabolomics, Leiden University Medical Center, 2300 RC Leiden, The Netherlands
| | - Liam A McDonnell
- From the ‡Center for Proteomics and Metabolomics, Leiden University Medical Center, 2300 RC Leiden, The Netherlands
| | - Jeanine J Houwing-Duistermaat
- ¶Department of Medical Statistics and Bioinformatics, Leiden University Medical Center, 2300 RC Leiden, The Netherlands.,‡‡Department of Statistics, University of Leeds, LS2 9JT Leeds, United Kingdom
| | - P Eline Slagboom
- ‖Department of Molecular Epidemiology, Leiden University Medical Center, 2300 RC Leiden, The Netherlands
| | - Marian Beekman
- ‖Department of Molecular Epidemiology, Leiden University Medical Center, 2300 RC Leiden, The Netherlands
| | - Manfred Wuhrer
- From the ‡Center for Proteomics and Metabolomics, Leiden University Medical Center, 2300 RC Leiden, The Netherlands;
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36
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Ruhaak LR, van der Burgt YE, Cobbaert CM. Prospective applications of ultrahigh resolution proteomics in clinical mass spectrometry. Expert Rev Proteomics 2016; 13:1063-1071. [DOI: 10.1080/14789450.2016.1253477] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- L. Renee Ruhaak
- Department of Clinical Chemistry and Laboratory Medicine, Leiden University Medical Center, Leiden, the Netherlands
| | - Yuri E.M. van der Burgt
- Department of Clinical Chemistry and Laboratory Medicine, Leiden University Medical Center, Leiden, the Netherlands
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, the Netherlands
| | - Christa M. Cobbaert
- Department of Clinical Chemistry and Laboratory Medicine, Leiden University Medical Center, Leiden, the Netherlands
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Beekman M, Uh HW, van Heemst D, Wuhrer M, Ruhaak LR, Gonzalez-Covarrubias V, Hankemeier T, Houwing-Duistermaat JJ, Slagboom PE. Classification for Longevity Potential: The Use of Novel Biomarkers. Front Public Health 2016; 4:233. [PMID: 27840811 PMCID: PMC5083840 DOI: 10.3389/fpubh.2016.00233] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Accepted: 10/06/2016] [Indexed: 11/29/2022] Open
Abstract
Background In older people, chronological age may not be the best predictor of residual lifespan and mortality, because with age the heterogeneity in health is increasing. Biomarkers for biological age and residual lifespan are being developed to predict disease and mortality better at an individual level than chronological age. In the current paper, we aim to classify a group of older people into those with longevity potential or controls. Methods In the Leiden Longevity Study participated 1671 offspring of nonagenarian siblings, as the group with longevity potential, and 744 similarly aged controls. Using known risk factors for cardiovascular disease, previously reported markers for human longevity and other physiological measures as predictors, classification models for longevity potential were constructed with multiple logistic regression of the offspring-control status. Results The Framingham Risk Score (FRS) is predictive for longevity potential [area under the receiver operating characteristic curve (AUC) = 64.7]. Physiological parameters involved in immune responses and glucose, lipid and energy metabolism further improve the prediction performance for longevity potential (AUCmale = 71.4, AUCfemale = 68.7). Conclusion Using the FRS, the classification of older people in groups with longevity potential and controls is moderate, but can be improved to a reasonably good classification in combination with markers of immune response, glucose, lipid, and energy metabolism. We show that individual classification of older people for longevity potential may be feasible using biomarkers from a wide variety of different biological processes.
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Affiliation(s)
- Marian Beekman
- Molecular Epidemiology, Leiden University Medical Center , Leiden , Netherlands
| | - Hae-Won Uh
- Medical Statistics and Bioinformatics, Leiden University Medical Center , Leiden , Netherlands
| | - Diana van Heemst
- Gerontology and Geriatrics, Leiden University Medical Center , Leiden , Netherlands
| | - Manfred Wuhrer
- Center for Proteomics and Metabolomics, Leiden University Medical Center , Leiden , Netherlands
| | - L Renee Ruhaak
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, Netherlands; Department of Translational Molecular Pathology, MD Anderson Cancer Center, Houston, TX, USA
| | - Vanessa Gonzalez-Covarrubias
- Analytical Biosciences, Leiden Academic Centre for Drug Research, Leiden, Netherlands; Instituto Nacional de Medicina Genomica (INMEGEN), Mexico City, Mexico
| | - Thomas Hankemeier
- Analytical Biosciences, Leiden Academic Centre for Drug Research, Leiden, Netherlands; Netherlands Metabolomics Centre, Leiden, Netherlands
| | | | - P Eline Slagboom
- Molecular Epidemiology, Leiden University Medical Center , Leiden , Netherlands
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Taylor SL, Ruhaak LR, Weiss RH, Kelly K, Kim K. Multivariate two-part statistics for analysis of correlated mass spectrometry data from multiple biological specimens. Bioinformatics 2016; 33:17-25. [PMID: 27592710 DOI: 10.1093/bioinformatics/btw578] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Revised: 08/30/2016] [Accepted: 08/31/2016] [Indexed: 11/14/2022] Open
Abstract
MOTIVATION High through-put mass spectrometry (MS) is now being used to profile small molecular compounds across multiple biological sample types from the same subjects with the goal of leveraging information across biospecimens. Multivariate statistical methods that combine information from all biospecimens could be more powerful than the usual univariate analyses. However, missing values are common in MS data and imputation can impact between-biospecimen correlation and multivariate analysis results. RESULTS We propose two multivariate two-part statistics that accommodate missing values and combine data from all biospecimens to identify differentially regulated compounds. Statistical significance is determined using a multivariate permutation null distribution. Relative to univariate tests, the multivariate procedures detected more significant compounds in three biological datasets. In a simulation study, we showed that multi-biospecimen testing procedures were more powerful than single-biospecimen methods when compounds are differentially regulated in multiple biospecimens but univariate methods can be more powerful if compounds are differentially regulated in only one biospecimen. AVAILABILITY AND IMPLEMENTATION We provide R functions to implement and illustrate our method as supplementary information CONTACT: sltaylor@ucdavis.eduSupplementary information: Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Sandra L Taylor
- Division of Biostatistics, Department of Public Health Sciences, University of California Davis, CA, 95616, USA
| | - L Renee Ruhaak
- Department of Clinical Chemistry and Laboratory Medicine, Leiden University Medical Center, Leiden, The Netherlands
| | | | - Karen Kelly
- Division of Hematology and Oncology, Department of Internal Medicine School of Medicine, University of California, Davis, CA 95616, USA
| | - Kyoungmi Kim
- Division of Biostatistics, Department of Public Health Sciences, University of California Davis, CA, 95616, USA
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Miyamoto S, Ruhaak LR, Stroble C, Salemi MR, Phinney B, Lebrilla CB, Leiserowitz GS. Glycoproteomic Analysis of Malignant Ovarian Cancer Ascites Fluid Identifies Unusual Glycopeptides. J Proteome Res 2016; 15:3358-76. [PMID: 27500424 DOI: 10.1021/acs.jproteome.6b00548] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Ovarian cancer is a major cause of cancer mortality among women, largely due to late diagnosis of advanced metastatic disease. More extensive molecular analysis of metastatic ovarian cancer is needed to identify post-translational modifications of proteins, especially glycosylation that is particularly associated with metastatic disease to better understand the metastatic process and identify potential therapeutic targets. Glycoproteins in ascites fluid were enriched by affinity binding to lectins (ConA or WGA) and other affinity matrices. Separate glycomic, proteomic, and glycopeptide analyses were performed. Relative abundances of different N-glycan groups and proteins were identified from ascites fluids and a serum control. Levels of biomarkers CA125, MUC1, and fibronectin were also monitored in OC ascites samples by Western blot analysis. N-Glycan analysis of ascites fluids showed the presence of large, highly fucosylated and sialylated complex and hybrid glycans, some of which were not observed in normal serum. OC ascites glycoproteins, haptoglobin, fibronectin, lumican, fibulin, hemopexin, ceruloplasmin, alpha-1-antitrypsin, and alpha-1-antichymotrypsin were more abundant in OC ascites or not present in serum control samples. Further glycopeptide analysis of OC ascites identified N- and O-glycans in clusterin, hemopexin, and fibulin glycopeptides, some of which are unusual and may be important in OC metastasis.
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Affiliation(s)
- Suzanne Miyamoto
- Division of Hematology and Oncology, Department of Internal Medicine, UC Davis School of Medicine , Sacramento, California 95817, United States
| | - L Renee Ruhaak
- Department of Chemistry, UC Davis , Davis, California 95616, United States
| | - Carol Stroble
- Division of Hematology and Oncology, Department of Internal Medicine, UC Davis School of Medicine , Sacramento, California 95817, United States
| | - Michelle R Salemi
- Proteomic Core, Genome Center, UC Davis , Davis, California 95616, United States
| | - Brett Phinney
- Proteomic Core, Genome Center, UC Davis , Davis, California 95616, United States
| | - Carlito B Lebrilla
- Department of Chemistry, UC Davis , Davis, California 95616, United States
| | - Gary S Leiserowitz
- Division of Gynecologic Oncology, UC Davis Medical Center , Sacramento, California 95817, United States
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40
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Ruhaak LR, Kim K, Stroble C, Taylor SL, Hong Q, Miyamoto S, Lebrilla CB, Leiserowitz G. Protein-Specific Differential Glycosylation of Immunoglobulins in Serum of Ovarian Cancer Patients. J Proteome Res 2016; 15:1002-10. [PMID: 26813784 DOI: 10.1021/acs.jproteome.5b01071] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Previous studies indicated that glycans in serum may serve as biomarkers for diagnosis of ovarian cancer; however, it was unclear to which proteins these glycans belong. We hypothesize that protein-specific glycosylation profiles of the glycans may be more informative of ovarian cancer and can provide insight into biological mechanisms underlying glycan aberration in serum of diseased individuals. Serum samples from women diagnosed with epithelial ovarian cancer (EOC, n = 84) and matched healthy controls (n = 84) were obtained from the Gynecologic Oncology Group. Immunoglobulin (IgG, IgA, and IgM) concentrations and glycosylation profiles were quantified using multiple reaction monitoring mass spectrometry. Differential and classification analyses were performed to identify aberrant protein-specific glycopeptides using a training set. All findings were validated in an independent test set. Multiple glycopeptides from immunoglubins IgA, IgG, and IgM were found to be differentially expressed in serum of EOC patients compared with controls. The protein-specific glycosylation profiles showed their potential in the diagnosis of EOC. In particular, IgG-specific glycosylation profiles are the most powerful in discriminating between EOC case and controls. Additional studies of protein- and site-specific glycosylation profiles of immunoglobulins and other proteins will allow further elaboration on the characteristics of biological functionality and causality of the differential glycosylation in ovarian cancer and thus ultimately lead to increased sensitivity and specificity of diagnosis.
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Affiliation(s)
- L Renee Ruhaak
- Department of Chemistry, University of California , Davis, California 95616, United States
| | - Kyoungmi Kim
- Division of Biostatistics, Department of Public Health Sciences, University of California , Davis, California 95616, United States
| | - Carol Stroble
- Department of Chemistry, University of California , Davis, California 95616, United States.,University of California Davis Medical Center , Sacramento, California 95817, United States
| | - Sandra L Taylor
- Division of Biostatistics, Department of Public Health Sciences, University of California , Davis, California 95616, United States
| | - Qiuting Hong
- Department of Chemistry, University of California , Davis, California 95616, United States
| | - Suzanne Miyamoto
- University of California Davis Medical Center , Sacramento, California 95817, United States
| | - Carlito B Lebrilla
- Department of Chemistry, University of California , Davis, California 95616, United States
| | - Gary Leiserowitz
- University of California Davis Medical Center , Sacramento, California 95817, United States.,Division of Gynecologic Oncology, University of California Davis Medical Center , Sacramento, California 98517, United States
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Ruhaak LR, Stroble C, Dai J, Barnett M, Taguchi A, Goodman GE, Miyamoto S, Gandara D, Feng Z, Lebrilla CB, Hanash S. Serum Glycans as Risk Markers for Non-Small Cell Lung Cancer. Cancer Prev Res (Phila) 2016; 9:317-23. [PMID: 26813970 DOI: 10.1158/1940-6207.capr-15-0033] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2015] [Accepted: 01/18/2016] [Indexed: 11/16/2022]
Abstract
Previous studies have suggested occurrence of altered serum glycan profiles in patients with lung cancer. Here, we aimed to determine the predictive value of serum glycans to distinguish non-small cell lung cancer (NSCLC) cases from controls in prediagnostic samples using a previously validated predictive protein marker pro-SFTPB, as anchor. Blinded prediagnostic serum samples were obtained from the Carotene and Retinol Efficacy Trial (CARET), and included a discovery set of 100 NSCLC cases and 199 healthy controls. A second test set consisted of 108 cases and 216 controls. Cases and controls were matched for age at baseline (5-year groups), sex, smoking status (current vs. former), study enrollment cohort, and date of blood draw. Serum glycan profiles were determined by mass spectrometry. Twelve glycan variables were identified to have significant discriminatory power between cases and controls in the discovery set (AUC > 0.6). Of these, four were confirmed in the independent validation set. A combination marker yielded AUCs of 0.74 and 0.64 in the discovery and test set, respectively. Four glycan variables exhibited significant incremental value when combined with pro-SFTPB compared with pro-SFTPB alone with AUCs of 0.73, 0.72, 0.72, and 0.72 in the test set, indicating that serum glycan signatures have relevance to risk assessment for NSCLC.
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Affiliation(s)
- L Renee Ruhaak
- Department of Chemistry, University of California Davis, Davis, California. Department of Translational Molecular Pathology, University of Texas MD Anderson Cancer Center, Houston, Texas.
| | - Carol Stroble
- Department of Chemistry, University of California Davis, Davis, California. Division of Hematology and Oncology, University of California Davis Comprehensive Cancer Center, Sacramento, California
| | - Jianliang Dai
- Department of Biostatistics, University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Matt Barnett
- Division of Public Health Sciences, Fred Hutchison Cancer Research Center, Seattle, Washington
| | - Ayumu Taguchi
- Department of Translational Molecular Pathology, University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Gary E Goodman
- Division of Public Health Sciences, Fred Hutchison Cancer Research Center, Seattle, Washington
| | - Suzanne Miyamoto
- Division of Hematology and Oncology, University of California Davis Comprehensive Cancer Center, Sacramento, California
| | - David Gandara
- Division of Hematology and Oncology, University of California Davis Comprehensive Cancer Center, Sacramento, California
| | - Ziding Feng
- Department of Biostatistics, University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Carlito B Lebrilla
- Department of Chemistry, University of California Davis, Davis, California
| | - Samir Hanash
- Department of Clinical Cancer Prevention - Research, Clinical Cancer Prevention, University of Texas MD Anderson Cancer Center, Houston, Texas
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Hong Q, Ruhaak LR, Stroble C, Parker E, Huang J, Maverakis E, Lebrilla CB. A Method for Comprehensive Glycosite-Mapping and Direct Quantitation of Serum Glycoproteins. J Proteome Res 2015; 14:5179-92. [PMID: 26510530 DOI: 10.1021/acs.jproteome.5b00756] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
A comprehensive glycan map was constructed for the top eight abundant glycoproteins in plasma using both specific and nonspecific enzyme digestions followed by nano liquid chromatography (LC)-chip/quadrupole time-of-flight mass spectrometry (MS) analysis. Glycopeptides were identified using an in-house software tool, GPFinder. A sensitive and reproducible multiple reaction monitoring (MRM) technique on a triple quadrupole MS was developed and applied to quantify immunoglobulins G, A, M, and their site-specific glycans simultaneously and directly from human serum/plasma without protein enrichments. A total of 64 glycopeptides and 15 peptides were monitored for IgG, IgA, and IgM in a 20 min ultra high performance (UP)LC gradient. The absolute protein contents were quantified using peptide calibration curves. The glycopeptide ion abundances were normalized to the respective protein abundances to separate protein glycosylation from protein expression. This technique yields higher method reproducibility and less sample loss when compared with the quantitation method that involves protein enrichments. The absolute protein quantitation has a wide linear range (3-4 orders of magnitude) and low limit of quantitation (femtomole level). This rapid and robust quantitation technique, which provides quantitative information for both proteins and glycosylation, will further facilitate disease biomarker discoveries.
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Affiliation(s)
- Qiuting Hong
- Department of Chemistry and ‡Department of Dermatology, School of Medicine, University of California , Davis, California 95616, United States
| | - L Renee Ruhaak
- Department of Chemistry and ‡Department of Dermatology, School of Medicine, University of California , Davis, California 95616, United States
| | - Carol Stroble
- Department of Chemistry and ‡Department of Dermatology, School of Medicine, University of California , Davis, California 95616, United States
| | - Evan Parker
- Department of Chemistry and ‡Department of Dermatology, School of Medicine, University of California , Davis, California 95616, United States
| | - Jincui Huang
- Department of Chemistry and ‡Department of Dermatology, School of Medicine, University of California , Davis, California 95616, United States
| | - Emanual Maverakis
- Department of Chemistry and ‡Department of Dermatology, School of Medicine, University of California , Davis, California 95616, United States
| | - Carlito B Lebrilla
- Department of Chemistry and ‡Department of Dermatology, School of Medicine, University of California , Davis, California 95616, United States
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43
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Ruhaak LR, Taylor SL, Stroble C, Nguyen UT, Parker EA, Song T, Lebrilla CB, Rom WN, Pass H, Kim K, Kelly K, Miyamoto S. Differential N-Glycosylation Patterns in Lung Adenocarcinoma Tissue. J Proteome Res 2015; 14:4538-49. [PMID: 26322380 DOI: 10.1021/acs.jproteome.5b00255] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
To decrease the mortality of lung cancer, better screening and diagnostic tools as well as treatment options are needed. Protein glycosylation is one of the major post-translational modifications that is altered in cancer, but it is not exactly clear which glycan structures are affected. A better understanding of the glycan structures that are differentially regulated in lung tumor tissue is highly desirable and will allow us to gain greater insight into the underlying biological mechanisms of aberrant glycosylation in lung cancer. Here, we assess differential glycosylation patterns of lung tumor tissue and nonmalignant tissue at the level of individual glycan structures using nLC-chip-TOF-MS. Using tissue samples from 42 lung adenocarcinoma patients, 29 differentially expressed (FDR < 0.05) glycan structures were identified. The levels of several oligomannose type glycans were upregulated in tumor tissue. Furthermore, levels of fully galactosylated glycans, some of which were of the hybrid type and mostly without fucose, were decreased in cancerous tissue, whereas levels of non- or low-galactosylated glycans mostly with fucose were increased. To further assess the regulation of the altered glycosylation, the glycomics data was compared to publicly available gene expression data from lung adenocarcinoma tissue compared to nonmalignant lung tissue. The results are consistent with the possibility that the observed N-glycan changes have their origin in differentially expressed glycosyltransferases. These results will be used as a starting point for the further development of clinical glycan applications in the fields of imaging, drug targeting, and biomarkers for lung cancer.
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Affiliation(s)
| | | | - Carol Stroble
- Division of Hematology and Oncology, University of California Davis Comprehensive Cancer Center , Sacramento, California 95817, United States
| | | | | | | | | | - William N Rom
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, New York University School of Medicine , New York, New York 10016, United States
| | - Harvey Pass
- Department of Cardiothoracic Surgery, NYU Langone Medical Center , New York, New York 10016, United States
| | | | - Karen Kelly
- Division of Hematology and Oncology, University of California Davis Comprehensive Cancer Center , Sacramento, California 95817, United States
| | - Suzanne Miyamoto
- Division of Hematology and Oncology, University of California Davis Comprehensive Cancer Center , Sacramento, California 95817, United States
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Ruhaak LR, Barkauskas DA, Torres J, Cooke CL, Wu LD, Stroble C, Ozcan S, Williams CC, Camorlinga M, Rocke DM, Lebrilla CB, Solnick JV. The Serum Immunoglobulin G Glycosylation Signature of Gastric Cancer. EuPA Open Proteom 2015; 6:1-9. [PMID: 25685702 DOI: 10.1016/j.euprot.2014.11.002] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Biomarkers may facilitate detection of gastric cancer at an earlier stage and reduce mortality. Here we sought to determine if the glycosylation profile of serum immunoglobulin G (IgG) could distinguish patients with non-atrophic gastritis (NAG), duodenal ulcer (DU) and gastric cancer (GC). Serum IgG was released and analyzed using nano-LC-TOF mass spectrometry. Statistically significant false discovery rate (FDR)-adjusted p-values were observed for 18 glycans, eight that differed significantly between NAG and GC, three that distinguished NAG from DU, and eight that differed between DU and GC. The IgG glycosylation signature may be useful as a predictive marker for gastric cancer.
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Affiliation(s)
- L Renee Ruhaak
- Department of Chemistry, University of California, Davis, CA, 95616
| | - Donald A Barkauskas
- Department of Preventive Medicine, University of Southern California, Los Angeles, CA, 90089
| | - Javier Torres
- Infectious Diseases Research Unit, Instituto Mexicano del Seguro Social, Mexico
| | - Cara L Cooke
- Departments of Medicine and Microbiology & Immunology; Center for Comparative Medicine, University of California, Davis School of Medicine, Davis, CA, 95616
| | - Lauren D Wu
- Department of Chemistry, University of California, Davis, CA, 95616
| | - Carol Stroble
- Department of Chemistry, University of California, Davis, CA, 95616
| | - Sureyya Ozcan
- Department of Chemistry, University of California, Davis, CA, 95616
| | | | | | - David M Rocke
- Department of Biomedical Engineering, University of California, Davis, CA, 95616 ; Division of Biostatistics, Department of Public Health Sciences, University of California, Davis, CA, 95616
| | - Carlito B Lebrilla
- Department of Chemistry, University of California, Davis, CA, 95616 ; Department of Biochemistry and Molecular Medicine, University of California, Davis, CA 95616
| | - Jay V Solnick
- Departments of Medicine and Microbiology & Immunology; Center for Comparative Medicine, University of California, Davis School of Medicine, Davis, CA, 95616
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45
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Maverakis E, Kim K, Shimoda M, Gershwin ME, Patel F, Wilken R, Raychaudhuri S, Ruhaak LR, Lebrilla CB. Glycans in the immune system and The Altered Glycan Theory of Autoimmunity: a critical review. J Autoimmun 2015; 57:1-13. [PMID: 25578468 DOI: 10.1016/j.jaut.2014.12.002] [Citation(s) in RCA: 293] [Impact Index Per Article: 32.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2014] [Accepted: 12/03/2014] [Indexed: 12/24/2022]
Abstract
Herein we will review the role of glycans in the immune system. Specific topics covered include: the glycosylation sites of IgE, IgM, IgD, IgE, IgA, and IgG; how glycans can encode "self" identity by functioning as either danger associated molecular patterns (DAMPs) or self-associated molecular patterns (SAMPs); the role of glycans as markers of protein integrity and age; how the glycocalyx can dictate the migration pattern of immune cells; and how the combination of Fc N-glycans and Ig isotype dictate the effector function of immunoglobulins. We speculate that the latter may be responsible for the well-documented association between alterations of the serum glycome and autoimmunity. Due to technological limitations, the extent of these autoimmune-associated glycan alterations and their role in disease pathophysiology has not been fully elucidated. Thus, we also review the current technologies available for glycan analysis, placing an emphasis on Multiple Reaction Monitoring (MRM), a rapid high-throughput technology that has great potential for glycan biomarker research. Finally, we put forth The Altered Glycan Theory of Autoimmunity, which states that each autoimmune disease will have a unique glycan signature characterized by the site-specific relative abundances of individual glycan structures on immune cells and extracellular proteins, especially the site-specific glycosylation patterns of the different immunoglobulin(Ig) classes and subclasses.
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Affiliation(s)
- Emanual Maverakis
- Department of Dermatology, University of California, Davis School of Medicine, 3301 C Street, Suite 1400, Sacramento, CA 95816, USA.
| | - Kyoungmi Kim
- Department of Public Health Sciences, Division of Biostatistics, University of California, Davis Medical Center, Sacramento, CA 95816, USA
| | - Michiko Shimoda
- Department of Dermatology, University of California, Davis School of Medicine, 3301 C Street, Suite 1400, Sacramento, CA 95816, USA
| | - M Eric Gershwin
- Department of Internal Medicine, Division of Rheumatology, University of California, Davis School of Medicine, Sacramento, CA 95817, USA
| | - Forum Patel
- Department of Dermatology, University of California, Davis School of Medicine, 3301 C Street, Suite 1400, Sacramento, CA 95816, USA
| | - Reason Wilken
- Department of Dermatology, University of California, Davis School of Medicine, 3301 C Street, Suite 1400, Sacramento, CA 95816, USA
| | - Siba Raychaudhuri
- Department of Internal Medicine, Division of Rheumatology, University of California, Davis School of Medicine, Sacramento, CA 95817, USA
| | - L Renee Ruhaak
- Department of Public Health Sciences, Division of Biostatistics, University of California, Davis Medical Center, Sacramento, CA 95816, USA
| | - Carlito B Lebrilla
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, CA 95616, USA
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Abstract
Multiple reaction monitoring or MRM is widely acknowledged for its accuracy of quantitation. The applications have mostly been in the analysis of small molecules and proteins, but its utility is expanding. Protein glycosylation was recently identified as a new paradigm in biomarker discovery for health and disease. A number of recent studies have now identified differential glycosylation patterns associated with health and disease states, including aging, pregnancy, rheumatoid arthritis and different types of cancer. While the use of MRM in clinical glycomics is still in its infancy, it can likely play a role in the quantitation of protein glycosylation in the clinical setting. Here, we aim to review the current advances in the nascent application of MRM in the field of glycomics.
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Affiliation(s)
- L Renee Ruhaak
- Department of Chemistry, University of California Davis. One Shields Avenue, Davis, CA, USA
| | - Carlito B Lebrilla
- Department of Chemistry, University of California Davis. One Shields Avenue, Davis, CA, USA
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Totten SM, Wu LD, Parker EA, Davis JCC, Hua S, Stroble C, Ruhaak LR, Smilowitz JT, German JB, Lebrilla CB. Rapid-throughput glycomics applied to human milk oligosaccharide profiling for large human studies. Anal Bioanal Chem 2014; 406:7925-35. [PMID: 25358913 DOI: 10.1007/s00216-014-8261-2] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2014] [Revised: 10/02/2014] [Accepted: 10/08/2014] [Indexed: 12/25/2022]
Abstract
Glycomic analysis is the comprehensive determination of glycan (oligosaccharide) structures with quantitative information in a biological sample. Rapid-throughput glycomics is complicated due to the lack of a template, which has greatly facilitated analysis in the field of proteomics. Furthermore, the large similarities in structures make fragmentation spectra (as obtained in electron impact ionization and tandem mass spectrometry) less definitive for identification as it has been in metabolomics. In this study, we develop a concept of rapid-throughput glycomics on human milk oligosaccharides, which have proven to be an important bioactive component of breast milk, providing the infant with protection against pathogenic infection and supporting the establishment of a healthy microbiota. To better understand the relationship between diverse oligosaccharides structures and their biological function as anti-pathogenic and prebiotic compounds, large human studies are needed, which necessitate rapid- to high-throughput analytical platforms. Herein, a complete glycomics methodology is presented, evaluating the most effective human milk oligosaccharide (HMO) extraction protocols, the linearity and reproducibility of the nano-liquid chromatography chip time-of-flight mass spectrometry (nano-LC chip-TOF MS) method, and the efficacy of newly developed, in-house software for chromatographic peak alignment that allows for rapid data analysis. High instrument stability and retention time reproducibility, together with the successful automated alignment of hundreds of features in hundreds of milk samples, allow for the use of an HMO library for rapid assignment of fully annotated structures.
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Affiliation(s)
- Sarah M Totten
- Department of Chemistry, University of California, Davis, CA, 95616, USA
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Ruhaak LR, Stroble C, Underwood MA, Lebrilla CB. Detection of milk oligosaccharides in plasma of infants. Anal Bioanal Chem 2014; 406:5775-84. [PMID: 25059723 DOI: 10.1007/s00216-014-8025-z] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2014] [Revised: 07/02/2014] [Accepted: 07/08/2014] [Indexed: 01/09/2023]
Abstract
Human milk oligosaccharides (HMO) are one of the major components of human milk. HMO are non-digestible by the human gut, where they are known to play important functions as prebiotics and decoys for binding pathogens. Moreover, it has been proposed that HMO may provide sialic acids to the infant that are important in brain development, however this would require absorption of HMO into the bloodstream. HMO have consistently been found in the urine of humans and other mammals, suggesting systemic absorption. Here, we present a procedure for the profiling of milk oligosaccharides (MO) in plasma samples obtained from 13 term infants hospitalized for surgery for congenital heart disease. The method comprises protein denaturation, oligosaccharide reduction, and porous graphitized carbon solid phase extraction for purification followed by analysis using nHPLC-PGC-chip-TOF-MS. Approximately 15 free MO were typically observed in the plasma of human infants, including LNT, LDFP, LNFT, 3'SL, 6'SL, 3'SLN, and 6'SLN, of which the presence was confirmed using fragmentation studies. A novel third isomer of SLN, not found in human or bovine milk was also consistently detected. Differences in the free MO profiles were observed between infants that were totally formula-fed and infants that received at least some part breast milk. Our results indicate that free MO similar in structure to those found in human milk and urine are present in the blood of infants. The method and results presented here will facilitate further research toward the possible roles of free MO in the development of the infant.
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Affiliation(s)
- L Renee Ruhaak
- Department of Chemistry, University of California Davis, One Shields Avenue, Davis, CA, 95616, USA,
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Affiliation(s)
- L. Renee Ruhaak
- Center
for Proteomics and Metabolomics, Leiden University Medical Center, Leiden 2333 ZA, The Netherlands
- Department
of Chemistry, University of California Davis, Davis, California 95616, United States
| | - Hae-Won Uh
- Department
of Medical Statistics and Bioinformatics, Section of Medical Statistics, Leiden University Medical Center, Leiden 2333 ZA, The Netherlands
| | - André M. Deelder
- Center
for Proteomics and Metabolomics, Leiden University Medical Center, Leiden 2333 ZA, The Netherlands
| | - Radboud E. J. M. Dolhain
- Department
of Rheumatology, Erasmus MC University Medical Center, Rotterdam 3015 CE, The Netherlands
| | - M. Wuhrer
- Center
for Proteomics and Metabolomics, Leiden University Medical Center, Leiden 2333 ZA, The Netherlands
- Division
of BioAnalytical Chemistry, VU University Amsterdam, Amsterdam 1081 HV, The Netherlands
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Hong Q, Ruhaak LR, Totten SM, Smilowitz JT, German JB, Lebrilla CB. Label-free absolute quantitation of oligosaccharides using multiple reaction monitoring. Anal Chem 2014; 86:2640-7. [PMID: 24502421 PMCID: PMC3983013 DOI: 10.1021/ac404006z] [Citation(s) in RCA: 75] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
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An absolute quantitation method for
measuring free human milk oligosaccharides
(HMOs) in milk samples was developed using multiple reaction monitoring
(MRM). To obtain the best sensitivity, the instrument conditions were
optimized to reduce the source and postsource fragmentation prior
to the quadrupole transmission. Fragmentation spectra of HMOs using
collision-induced dissociation were studied to obtain the best characteristic
fragments. At least two MRM transitions were used to quantify and
identify each structure in the same run. The fragment ions corresponded
to the production of singly charged mono-, di-, and trisaccharide
fragments. The sensitivity and accuracy of the quantitation using
MRM were determined, with the detection limit in the femtomole level
and the calibration range spanning over 5 orders of magnitude. Seven
commercial HMO standards were used to create calibration curves and
were used to determine a universal response for all HMOs. The universal
response factor was used to estimate absolute amounts of other structures
and the total oligosaccharide content in milk. The quantitation method
was applied to 20 human milk samples to determine the variations in
HMO concentrations from women classified as secretors and nonsecretors,
a phenotype that can be identified by the concentration of 2′-fucosylation
in their milk.
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Affiliation(s)
- Qiuting Hong
- Department of Chemistry, University of California , One Shields Avenue, Davis, California 95616, United States
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