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Schuster-Little N, Sokolovsky AD, Gentry A, Saraf A, Etzel MR, Patankar MS, Whelan RJ. Immunoaffinity-free chromatographic purification of ovarian cancer biomarker CA125 (MUC16) from blood serum enables mass spectrometry characterization. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2024. [PMID: 39177265 DOI: 10.1039/d4ay01172d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/24/2024]
Abstract
The enrichment of trace proteins from human fluid samples is of great importance in diverse clinical and industrial applications. In clinical diagnostics, such enrichment may enable detection of trace proteins that serve as biomarkers of disease. Affinity-based approaches, such as immunoaffinity pulldown, are widely used to enrich trace proteins, but this strategy relies on the availability and performance of antibodies that act on all proteoforms in an unbiased manner. Our prior work to characterize MUC16 (the mucin protein that carries the ovarian cancer biomarker CA125) by mass spectrometry successfully overcame the reliance on affinity-based enrichment and was used to enrich this biomarker from ascites of individual ovarian cancer patients, however, this strategy was not demonstrated on clinically relevant volumes of serum, a biofluid that is more accessible than ascites. The present work developed a non-affinity-based chromatographic method to enrich MUC16 from serum. The enriched MUC16 sample was further processed using a Midi Top 14 abundant protein depletion column. Peptides identified using bottom-up proteomics yielded 1-8% coverage of MUC16. Additionally, MUC16 was detected in samples containing less than the clinical cut-off level of CA125 (35 U mL-1), suggesting that this strategy of enrichment and bottom-up proteomics can enable analysis of CA125 from the serum of individuals with early-stage ovarian cancer and those whose tumors express CA125 (MUC16) at low levels.
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Affiliation(s)
- Naviya Schuster-Little
- Department of Chemistry, University of Kansas, Lawrence, KS, USA.
- Ralph N. Adams Institute for Bioanalytical Chemistry, University of Kansas, Lawrence, KS, USA
| | - Andrew D Sokolovsky
- Department of Chemistry, University of Kansas, Lawrence, KS, USA.
- Ralph N. Adams Institute for Bioanalytical Chemistry, University of Kansas, Lawrence, KS, USA
| | - Ashten Gentry
- Department of Chemistry, University of Kansas, Lawrence, KS, USA.
- Ralph N. Adams Institute for Bioanalytical Chemistry, University of Kansas, Lawrence, KS, USA
| | - Anita Saraf
- Mass Spectrometry and Analytical Proteomics Laboratory, University of Kansas, Lawrence, KS, USA
| | - Mark R Etzel
- Department of Food Science, University of Wisconsin-Madison, Madison, WI, USA
| | - Manish S Patankar
- Department of Obstetrics and Gynecology, University of Wisconsin-Madison, Madison, WI, USA
| | - Rebecca J Whelan
- Department of Chemistry, University of Kansas, Lawrence, KS, USA.
- Ralph N. Adams Institute for Bioanalytical Chemistry, University of Kansas, Lawrence, KS, USA
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Chen ZZ, Dufresne J, Bowden P, Miao M, Marshall JG. Extraction of naturally occurring peptides versus the tryptic digestion of proteins from fetal versus adult bovine serum for LC-ESI-MS/MS. Anal Biochem 2024; 689:115497. [PMID: 38461948 DOI: 10.1016/j.ab.2024.115497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 02/23/2024] [Accepted: 02/25/2024] [Indexed: 03/12/2024]
Abstract
The naturally occurring peptides and digested proteins of fetal versus adult bovine serum were compared by LC-ESI-MS/MS after correction against noise from blank injections and random MS/MS spectra as statistical controls. Serum peptides were extracted by differential precipitation with mixtures of acetonitrile and water. Serum proteins were separated by partition chromatography over quaternary amine resin followed by tryptic digestion. The rigorous X!TANDEM goodness of fit algorithm that has a low error rate as demonstrated by low FDR q-values (q ≤ 0.01) showed qualitative and quantitative agreement with the SEQUEST cross correlation algorithm on 12,052 protein gene symbols. Tryptic digestion provided a quantitative identification of the serum proteins where observation frequency reflected known high abundance. In contrast, the naturally occurring peptides reflected the cleavage of common serum proteins such as C4A, C3, FGB, HPX, A2M but also proteins in lower concentration such as F13A1, IK, collagens and protocadherins. Proteins associated with cellular growth and development such as actins (ACT), ribosomal proteins like Ribosomal protein S6 (RPS6), synthetic enzymes and extracellular matrix factors were enriched in fetal calf serum. In contrast to the large literature from cord blood, IgG light chains were absent from fetal serum as observed by LC-ESI-MS/MS and confirmed by ELISA.
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Affiliation(s)
- Zhuo Zhen Chen
- Research Analytical Biochemistry Laboratory (RABL), Department of Chemistry and Biology, Toronto Metropolitan University, Canada.
| | - Jaimie Dufresne
- Research Analytical Biochemistry Laboratory (RABL), Department of Chemistry and Biology, Toronto Metropolitan University, Canada.
| | - Peter Bowden
- Research Analytical Biochemistry Laboratory (RABL), Department of Chemistry and Biology, Toronto Metropolitan University, Canada.
| | - Ming Miao
- Research Analytical Biochemistry Laboratory (RABL), Department of Chemistry and Biology, Toronto Metropolitan University, Canada.
| | - John G Marshall
- Research Analytical Biochemistry Laboratory (RABL), Department of Chemistry and Biology, Toronto Metropolitan University, Canada.
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Chen ZZ, Johnson L, Trahtemberg U, Baker A, Huq S, Dufresne J, Bowden P, Miao M, Ho JA, Hsu CC, Dos Santos CC, Marshall JG. Mitochondria and cytochrome components released into the plasma of severe COVID-19 and ICU acute respiratory distress syndrome patients. Clin Proteomics 2023; 20:17. [PMID: 37031181 PMCID: PMC10082440 DOI: 10.1186/s12014-023-09394-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Accepted: 01/20/2023] [Indexed: 04/10/2023] Open
Abstract
INTRODUCTION Proteomic analysis of human plasma by LC-ESI-MS/MS has discovered a limited number of new cellular protein biomarkers that may be confirmed by independent biochemical methods. Analysis of COVID-19 plasma has indicated the re-purposing of known biomarkers that might be used as prognostic markers of COVID-19 infection. However, multiple molecular approaches have previously indicated that the SARS-COV2 infection cycle is linked to the biology of mitochondria and that the response to infections may involve the action of heme containing oxidative enzymes. METHODS Human plasma from COVID-19 and ICU-ARDS was analyzed by classical analytical biochemistry techniques and classical frequency-based statistical approaches to look for prognostic markers of severe COVID-19 lung damage. Plasma proteins from COVID-19 and ICU-ARDS were identified and enumerated versus the controls of normal human plasma (NHP) by LC-ESI-MS/MS. The observation frequency of proteins detected in COVID-19 and ICU-ARDS patients were compared to normal human plasma, alongside random and noise MS/MS spectra controls, using the Chi Square (χ2) distribution. RESULTS PCR showed the presence of MT-ND1 DNA in the plasma of COVID-19, ICU-ARDS, as well as normal human plasma. Mitochondrial proteins such as MRPL, L2HGDH, ATP, CYB, CYTB, CYP, NDUF and others, were increased in COVID-19 and ICU-ARDS plasma. The apparent activity of the cytochrome components were tested alongside NHP by dot blotting on PVDF against a purified cytochrome c standard preparation for H2O2 dependent reaction with luminol as measured by enhanced chemiluminescence (ECL) that showed increased activity in COVID-19 and ICU-ARDS patients. DISCUSSION The results from PCR, LC-ESI-MS/MS of tryptic peptides, and cytochrome ECL assays confirmed that mitochondrial components were present in the plasma, in agreement with the established central role of the mitochondria in SARS-COV-2 biology. The cytochrome activity assay showed that there was the equivalent of at least nanogram amounts of cytochrome(s) in the plasma sample that should be clearly detectable by LC-ESI-MS/MS. The release of the luminol oxidase activity from cells into plasma forms the basis of a simple and rapid test for the severity of cell damage and lung injury in COVID-19 infection and ICU-ARDS.
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Affiliation(s)
- Zhuo Zhen Chen
- Department of Chemistry and Biology, Faculty of Science, Toronto Metropolitan, University, 350 Victoria Street, Toronto, ON, Canada
| | - Lloyd Johnson
- Department of Chemistry and Biology, Faculty of Science, Toronto Metropolitan, University, 350 Victoria Street, Toronto, ON, Canada
| | - Uriel Trahtemberg
- St. Michael's Hospital, Keenan Research Centre for Biomedical Science, Toronto, Canada
| | - Andrew Baker
- St. Michael's Hospital, Keenan Research Centre for Biomedical Science, Toronto, Canada
| | - Saaimatul Huq
- Department of Chemistry and Biology, Faculty of Science, Toronto Metropolitan, University, 350 Victoria Street, Toronto, ON, Canada
| | | | | | | | - Ja-An Ho
- Department of Chemistry, National Taiwan University, Taipei, Taiwan
| | - Cheng-Chih Hsu
- Department of Chemistry, National Taiwan University, Taipei, Taiwan
| | - Claudia C Dos Santos
- St. Michael's Hospital, Keenan Research Centre for Biomedical Science, Toronto, Canada.
| | - John G Marshall
- Department of Chemistry and Biology, Faculty of Science, Toronto Metropolitan, University, 350 Victoria Street, Toronto, ON, Canada.
- Integrated BioBank of Luxembourg, Luxembourg Institute of Health, 6 R. Nicolas-Ernest Barblé, Luxembourg, Luxembourg.
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Chen ZZ, Bowden P, Dufresne J, Miao M, Marshall JG. LEDGF is a new growth factor in fetal serum. Anal Biochem 2022; 655:114845. [PMID: 35970411 DOI: 10.1016/j.ab.2022.114845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Revised: 06/23/2022] [Accepted: 08/01/2022] [Indexed: 11/26/2022]
Abstract
Fetal serum supports the immortal growth of mammalian cell lines in culture while adult serum leads to the terminal differentiation and death of cells in culture. Many of the proteins in fetal serum that support the indefinite division and growth of cancerous cell lines remain obscure. The peptides and proteins of fetal versus adult serum were analyzed by liquid chromatography, nano electrospray ionization and tandem mass spectrometry (LC-ESI-MS/MS). Three batches of fetal serum contained the Alpha Fetoprotein marker while adult serum batches did not. Insulin (INS), and insulin-like growth factor (ILGF), fibroblast growth factor (FGF), epidermal growth factor (EGF) and platelet derived growth factor (PDGF) were increased in fetal serum. New fetal growth factors including MEGF, HDGFRP and PSIP1 and soluble growth receptors such as TNFR, EGFR, NTRK2 and THRA were discovered. Addition of insulin or the homeotic transcription factor PSIP1, also referred to as Lens Epithelium Derived Growth Factor (LEDGF), partially restored the rounded phenotype of rapidly dividing cells but was not as effective as fetal serum. Thus, a new growth factor in fetal serum, LEDGF/PSIP1, was directly observed by tandem mass spectrometry and confirmed by add back experiments to cell culture media alongside insulin.
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Affiliation(s)
- Zhuo Zhen Chen
- Research Analytical Biochemistry Laboratory (RABL), Department of Chemistry and Biology, Toronto Metropolitan University, Canada.
| | - Peter Bowden
- Research Analytical Biochemistry Laboratory (RABL), Department of Chemistry and Biology, Toronto Metropolitan University, Canada.
| | - Jaimie Dufresne
- Research Analytical Biochemistry Laboratory (RABL), Department of Chemistry and Biology, Toronto Metropolitan University, Canada.
| | - Ming Miao
- Research Analytical Biochemistry Laboratory (RABL), Department of Chemistry and Biology, Toronto Metropolitan University, Canada.
| | - John G Marshall
- Research Analytical Biochemistry Laboratory (RABL), Department of Chemistry and Biology, Toronto Metropolitan University, Canada.
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Florentinus-Mefailoski A, Bowden P, Scheltens P, Killestein J, Teunissen C, Marshall JG. The plasma peptides of Alzheimer's disease. Clin Proteomics 2021; 18:17. [PMID: 34182925 PMCID: PMC8240224 DOI: 10.1186/s12014-021-09320-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 04/20/2021] [Indexed: 02/06/2023] Open
Abstract
Background A practical strategy to discover proteins specific to Alzheimer’s dementia (AD) may be to compare the plasma peptides and proteins from patients with dementia to normal controls and patients with neurological conditions like multiple sclerosis or other diseases. The aim was a proof of principle for a method to discover proteins and/or peptides of plasma that show greater observation frequency and/or precursor intensity in AD. The endogenous tryptic peptides of Alzheimer’s were compared to normals, multiple sclerosis, ovarian cancer, breast cancer, female normal, sepsis, ICU Control, heart attack, along with their institution-matched controls, and normal samples collected directly onto ice. Methods Endogenous tryptic peptides were extracted from blinded, individual AD and control EDTA plasma samples in a step gradient of acetonitrile for random and independent sampling by LC–ESI–MS/MS with a set of robust and sensitive linear quadrupole ion traps. The MS/MS spectra were fit to fully tryptic peptides within proteins identified using the X!TANDEM algorithm. Observation frequency of the identified proteins was counted using SEQUEST algorithm. The proteins with apparently increased observation frequency in AD versus AD Control were revealed graphically and subsequently tested by Chi Square analysis. The proteins specific to AD plasma by Chi Square with FDR correction were analyzed by the STRING algorithm. The average protein or peptide log10 precursor intensity was compared across disease and control treatments by ANOVA in the R statistical system. Results Peptides and/or phosphopeptides of common plasma proteins such as complement C2, C7, and C1QBP among others showed increased observation frequency by Chi Square and/or precursor intensity in AD. Cellular gene symbols with large Chi Square values (χ2 ≥ 25, p ≤ 0.001) from tryptic peptides included KIF12, DISC1, OR8B12, ZC3H12A, TNF, TBC1D8B, GALNT3, EME2, CD1B, BAG1, CPSF2, MMP15, DNAJC2, PHACTR4, OR8B3, GCK, EXOSC7, HMGA1 and NT5C3A among others. Similarly, increased frequency of tryptic phosphopeptides were observed from MOK, SMIM19, NXNL1, SLC24A2, Nbla10317, AHRR, C10orf90, MAEA, SRSF8, TBATA, TNIK, UBE2G1, PDE4C, PCGF2, KIR3DP1, TJP2, CPNE8, and NGF amongst others. STRING analysis showed an increase in cytoplasmic proteins and proteins associated with alternate splicing, exocytosis of luminal proteins, and proteins involved in the regulation of the cell cycle, mitochondrial functions or metabolism and apoptosis. Increases in mean precursor intensity of peptides from common plasma proteins such as DISC1, EXOSC5, UBE2G1, SMIM19, NXNL1, PANO, EIF4G1, KIR3DP1, MED25, MGRN1, OR8B3, MGC24039, POLR1A, SYTL4, RNF111, IREB2, ANKMY2, SGKL, SLC25A5, CHMP3 among others were associated with AD. Tryptic peptides from the highly conserved C-terminus of DISC1 within the sequence MPGGGPQGAPAAAGGGGVSHRAGSRDCLPPAACFR and ARQCGLDSR showed a higher frequency and highest intensity in AD compared to all other disease and controls. Conclusion Proteins apparently expressed in the brain that were directly related to Alzheimer’s including Nerve Growth Factor (NFG), Sphingomyelin Phosphodiesterase, Disrupted in Schizophrenia 1 (DISC1), the cell death regulator retinitis pigmentosa (NXNl1) that governs the loss of nerve cells in the retina and the cell death regulator ZC3H12A showed much higher observation frequency in AD plasma vs the matched control. There was a striking agreement between the proteins known to be mutated or dis-regulated in the brains of AD patients with the proteins observed in the plasma of AD patients from endogenous peptides including NBN, BAG1, NOX1, PDCD5, SGK3, UBE2G1, SMPD3 neuronal proteins associated with synapse function such as KSYTL4, VTI1B and brain specific proteins such as TBATA. Supplementary Information The online version contains supplementary material available at 10.1186/s12014-021-09320-2.
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Affiliation(s)
- Angelique Florentinus-Mefailoski
- Ryerson Analytical Biochemistry Laboratory (RABL), Department of Chemistry and Biology, Faculty of Science, Ryerson University, 350 Victoria St., Toronto, ON, Canada
| | - Peter Bowden
- Ryerson Analytical Biochemistry Laboratory (RABL), Department of Chemistry and Biology, Faculty of Science, Ryerson University, 350 Victoria St., Toronto, ON, Canada
| | - Philip Scheltens
- Alzheimer Center, Dept of Neurology, Amsterdam University Medical Centers, Vrije Universiteit, Amsterdam Neuroscience, Amsterdam, The Netherlands
| | - Joep Killestein
- MS Center, Dept of Neurology, Amsterdam University Medical Centers, Vrije Universiteit, Amsterdam Neuroscience, Amsterdam, The Netherlands
| | - Charlotte Teunissen
- Neurochemistry Lab and Biobank, Dept of Clinical Chemistry, Amsterdam University Medical Centers, Vrije Universiteit, Amsterdam Neuroscience, Amsterdam, The Netherlands
| | - John G Marshall
- Ryerson Analytical Biochemistry Laboratory (RABL), Department of Chemistry and Biology, Faculty of Science, Ryerson University, 350 Victoria St., Toronto, ON, Canada. .,International Biobank of Luxembourg (IBBL), Luxembourg Institute of Health (Formerly CRP Sante Luxembourg), Strassen, Luxembourg.
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Thavarajah T, Dos Santos CC, Slutsky AS, Marshall JC, Bowden P, Romaschin A, Marshall JG. The plasma peptides of sepsis. Clin Proteomics 2020; 17:26. [PMID: 32636717 PMCID: PMC7331219 DOI: 10.1186/s12014-020-09288-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Accepted: 06/15/2020] [Indexed: 12/28/2022] Open
Abstract
Background A practical strategy to discover sepsis specific proteins may be to compare the plasma peptides and proteins from patients in the intensive care unit with and without sepsis. The aim was to discover proteins and/or peptides that show greater observation frequency and/or precursor intensity in sepsis. The endogenous tryptic peptides of ICU-Sepsis were compared to ICU Control, ovarian cancer, breast cancer, female normal, sepsis, heart attack, Alzheimer’s and multiple sclerosis along with their institution-matched controls, female normals and normal samples collected directly onto ice. Methods Endogenous tryptic peptides were extracted from individual sepsis and control EDTA plasma samples in a step gradient of acetonitrile for random and independent sampling by LC–ESI–MS/MS with a set of robust and sensitive linear quadrupole ion traps. The MS/MS spectra were fit to fully tryptic peptides within proteins using the X!TANDEM algorithm. The protein observation frequency was counted using the SEQUEST algorithm after selecting the single best charge state and peptide sequence for each MS/MS spectra. The protein observation frequency of ICU-sepsis versus ICU Control was subsequently tested by Chi square analysis. The average protein or peptide log10 precursor intensity was compared across disease and control treatments by ANOVA in the R statistical system. Results Peptides and/or phosphopeptides of common plasma proteins such as ITIH3, SAA2, SAA1, and FN1 showed increased observation frequency by Chi square (χ2 > 9, p < 0.003) and/or precursor intensity in sepsis. Cellular gene symbols with large Chi square values from tryptic peptides included POTEB, CTNNA1, U2SURP, KIF24, NLGN2, KSR1, GTF2H1, KIT, RPS6KL1, VAV2, HSPA7, SMC2, TCEB3B, ZNF300, SUPV3L1, ADAMTS20, LAMB4, MCCC1, SUPT6H, SCN9A, SBNO1, EPHA1, ABLIM2, cB5E3.2, EPHA10, GRIN2B, HIVEP2, CCL16, TKT, LRP2 and TMF1 amongst others showed increased observation frequency. Similarly, increased frequency of tryptic phosphopeptides were observed from POM121C, SCN8A, TMED8, NSUN7, SLX4, MADD, DNLZ, PDE3B, UTY, DEPDC7, MTX1, MYO1E, RXRB, SYDE1, FN1, PUS7L, FYCO1, USP26, ACAP2, AHI1, KSR2, LMAN1, ZNF280D and SLC8A2 amongst others. Increases in mean precursor intensity in peptides from common plasma proteins such as ITIH3, SAA2, SAA1, and FN1 as well as cellular proteins such as COL24A1, POTEB, KANK1, SDCBP2, DNAH11, ADAMTS7, MLLT1, TTC21A, TSHR, SLX4, MTCH1, and PUS7L among others were associated with sepsis. The processing of SAA1 included the cleavage of the terminal peptide D/PNHFRPAGLPEKY from the most hydrophilic point of SAA1 on the COOH side of the cystatin C binding that was most apparent in ICU-Sepsis patients compared to all other diseases and controls. Additional cleavage of SAA1 on the NH2 terminus side of the cystatin binding site were observed in ICU-Sepsis. Thus there was disease associated variation in the processing of SAA1 in ICU-Sepsis versus ICU controls or other diseases and controls. Conclusion Specific proteins and peptides that vary between diseases might be discovered by the random and independent sampling of multiple disease and control plasma from different hospital and clinics by LC–ESI–MS/MS for storage in a relational SQL Server database and analysis with the R statistical system that will be a powerful tool for clinical research. The processing of SAA1 may play an unappreciated role in the inflammatory response to Sepsis.
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Affiliation(s)
- Thanusi Thavarajah
- Ryerson Analytical Biochemistry Laboratory (RABL), Department of Chemistry and Biology, Faculty of Science, Ryerson University, 350 Victoria St., Toronto, ON Canada
| | - Claudia C Dos Santos
- St. Michael's Hospital, Keenan Research Centre for Biomedical Science, Toronto, Canada
| | - Arthur S Slutsky
- St. Michael's Hospital, Keenan Chair in Medicine, University of Toronto, Toronto, Canada
| | - John C Marshall
- International Biobank of Luxembourg (IBBL), Institute of Health (formerly CRP Sante Luxembourg), Dudelange, Luxembourg
| | - Pete Bowden
- Ryerson Analytical Biochemistry Laboratory (RABL), Department of Chemistry and Biology, Faculty of Science, Ryerson University, 350 Victoria St., Toronto, ON Canada
| | - Alexander Romaschin
- St. Michael's Hospital, Keenan Research Centre for Biomedical Science, Toronto, Canada
| | - John G Marshall
- Ryerson Analytical Biochemistry Laboratory (RABL), Department of Chemistry and Biology, Faculty of Science, Ryerson University, 350 Victoria St., Toronto, ON Canada.,International Biobank of Luxembourg (IBBL), Institute of Health (formerly CRP Sante Luxembourg), Dudelange, Luxembourg
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