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McKerchar H, Dyer JM, Gerrard JA, Maes E, Clerens S, Dobson RC. Characterizing lysinoalanine crosslinks in food systems: Discovery of a diagnostic ion in model peptides using MALDI mass spectrometry. Food Chem X 2023; 19:100800. [PMID: 37780262 PMCID: PMC10534164 DOI: 10.1016/j.fochx.2023.100800] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2023] [Revised: 07/03/2023] [Accepted: 07/14/2023] [Indexed: 10/03/2023] Open
Abstract
Formation of lysinoalanine protein-protein crosslinks during food processing adversely impacts nutritional value. However, mapping lysinoalanine directly in food is challenging. We characterized the fragmentation pattern of lysinoalanine crosslinks in synthetic peptide models over a range of pH and time treatments using mass spectrometry. A putative diagnostic ion resulting from the cleavage of the α-carbon and β-carbon of lysinoalanine is identified in MALDI MS/MS spectra. This represents the first step in mapping lysinoalanine in real food samples with higher precision than currently identifiable through standard or customized software. We then determined a correlated trend in the reduction of disulfide bonds and formation of lysinoalanine with increasing pH and time. Mapping lysinoalanine formation is critical to enhance our understanding of molecular processes impacting the nutritional value of foods, including notably in the development of protein alternatives that use alkaline treatment to extract protein isolates.
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Affiliation(s)
- Hannah McKerchar
- Biomolecular Interaction Centre, School of Biological Sciences, University of Canterbury, Christchurch 8140, New Zealand
- Riddet Institute, Based Massey University, Palmerston North 4442, New Zealand
- Proteins and Metabolites Team, AgResearch Lincoln Research Centre, Lincoln 7608, New Zealand
| | - Jolon M. Dyer
- Biomolecular Interaction Centre, School of Biological Sciences, University of Canterbury, Christchurch 8140, New Zealand
- The New Zealand Institute for Plant and Food Research, Lincoln Research Centre, Lincoln 7608, New Zealand
- Department of Wine, Food and Molecular Biosciences, Lincoln University, Lincoln 7647, New Zealand
| | - Juliet A. Gerrard
- Biomolecular Interaction Centre, School of Biological Sciences, University of Canterbury, Christchurch 8140, New Zealand
- Riddet Institute, Based Massey University, Palmerston North 4442, New Zealand
- School of Biological Sciences and School of Chemical Sciences, University of Auckland, Auckland, New Zealand
| | - Evelyne Maes
- Biomolecular Interaction Centre, School of Biological Sciences, University of Canterbury, Christchurch 8140, New Zealand
- Riddet Institute, Based Massey University, Palmerston North 4442, New Zealand
- Proteins and Metabolites Team, AgResearch Lincoln Research Centre, Lincoln 7608, New Zealand
| | - Stefan Clerens
- Biomolecular Interaction Centre, School of Biological Sciences, University of Canterbury, Christchurch 8140, New Zealand
- Riddet Institute, Based Massey University, Palmerston North 4442, New Zealand
- Proteins and Metabolites Team, AgResearch Lincoln Research Centre, Lincoln 7608, New Zealand
| | - Renwick C.J. Dobson
- Biomolecular Interaction Centre, School of Biological Sciences, University of Canterbury, Christchurch 8140, New Zealand
- Riddet Institute, Based Massey University, Palmerston North 4442, New Zealand
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Victoria 3010, Australia
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2
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Zhang W, Forester NT, Chettri P, Heilijgers M, Mace WJ, Maes E, Morozova Y, Applegate ER, Johnson RD, Johnson LJ. Characterization of the Biosynthetic Gene Cluster for the Ribosomally Synthesized Cyclic Peptide Epichloëcyclins in Epichloë festucae. J Agric Food Chem 2023; 71:13965-13978. [PMID: 37704203 PMCID: PMC10540207 DOI: 10.1021/acs.jafc.3c03073] [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] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 08/14/2023] [Accepted: 08/16/2023] [Indexed: 09/15/2023]
Abstract
The various grass-induced epichloëcyclins of the Epichloë spp. are ribosomally synthesized and post-translationally modified peptides (RiPPs), produced as small, secreted cyclopeptides from a single gene, gigA. Here, four clustered and coregulated genes (gigA, gigB, gigC, and kexB) with predicted roles in epichloëcyclin production in Epichloë festucae were evaluated through gene disruption. Subsequent chemical analysis indicates that GigB is a DUF3328 domain-containing protein associated with cyclization of epichloëcyclins; GigC is a methyltransferase enzyme responsible for N-methylation of desmethylepichloëcyclins; and KexB is a subtilisin-like enzyme, partly responsible for the propeptide cleavage of epichloëcyclin intermediates. Symbiotic effects on the host phenotype were not observed for gigA, gigC, or kexB mutants, although ΔgigB infection correlated with increased host tiller height and biomass, while only ΔkexB exhibited an effect on endophyte morphology. Disrupting epichloëcyclin biosynthesis showed negligible influence on the biosynthesis of E. festucae-associated alkaloids. Epichloëcyclins may perform other secondary metabolism functions in Epichloë and other fungi.
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Affiliation(s)
- Wei Zhang
- Grasslands
Research Centre, AgResearch Limited, Palmerston North 4442, New Zealand
| | - Natasha T. Forester
- Grasslands
Research Centre, AgResearch Limited, Palmerston North 4442, New Zealand
| | - Pranav Chettri
- Grasslands
Research Centre, AgResearch Limited, Palmerston North 4442, New Zealand
| | - Maurice Heilijgers
- Grasslands
Research Centre, AgResearch Limited, Palmerston North 4442, New Zealand
| | - Wade J. Mace
- Grasslands
Research Centre, AgResearch Limited, Palmerston North 4442, New Zealand
| | - Evelyne Maes
- Lincoln
Research Centre, AgResearch Limited, Lincoln 7608, New Zealand
| | - Yulia Morozova
- Grasslands
Research Centre, AgResearch Limited, Palmerston North 4442, New Zealand
| | - Emma R. Applegate
- Grasslands
Research Centre, AgResearch Limited, Palmerston North 4442, New Zealand
| | - Richard D. Johnson
- Grasslands
Research Centre, AgResearch Limited, Palmerston North 4442, New Zealand
| | - Linda J. Johnson
- Grasslands
Research Centre, AgResearch Limited, Palmerston North 4442, New Zealand
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3
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Leite JAS, Montoya CA, Maes E, Hefer C, Cruz RAPA, Roy NC, McNabb WC. Effect of Heat Treatment on Protein Self-Digestion in Ruminants' Milk. Foods 2023; 12:3511. [PMID: 37761220 PMCID: PMC10529618 DOI: 10.3390/foods12183511] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 09/19/2023] [Accepted: 09/20/2023] [Indexed: 09/29/2023] Open
Abstract
This study investigated whether heat treatments (raw, 63 °C for 30 min, and 85 °C for 5 min) affect protein hydrolysis by endogenous enzymes in the milk of ruminants (bovine, ovine, and caprine) using a self-digestion model. Self-digestion consisted of the incubation for six hours at 37 °C of the ruminants' milk. Free amino group concentration was measured by the o-phthaldialdehyde method, and peptide sequences were identified by chromatography-mass spectrometry. Results showed that heat treatments prior to self-digestion decreased the free NH2 by 59% in bovine milk heated at 85 °C/5 min, and by 44 and 53% in caprine milk heated at 63 °C/30 min and 85 °C/5 min, respectively. However, after self-digestion, only new free amino groups were observed for the raw and heated at 63 °C/30 min milk. β-Casein was the most cleaved protein in the raw and heated at 63 °C/30 min bovine milk. A similar trend was observed in raw ovine and caprine milk. Self-digestion increased 6.8-fold the potential antithrombin peptides in the bovine milk heated at 63 °C/30 min. Enhancing bioactive peptide abundance through self-digestion has potential applications in the industry for functional products. Overall, heat treatments affected the free amino groups according to the species and heat treatment applied, which was reflected in the varying degrees of cleaved peptide bonds and peptides released during self-digestion.
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Affiliation(s)
- Juliana A. S. Leite
- Riddet Institute, Te Ohu Rangahau Kai Facility, Massey University, Palmerston North 4474, New Zealand; (J.A.S.L.); (C.A.M.); (E.M.); (N.C.R.)
| | - Carlos A. Montoya
- Riddet Institute, Te Ohu Rangahau Kai Facility, Massey University, Palmerston North 4474, New Zealand; (J.A.S.L.); (C.A.M.); (E.M.); (N.C.R.)
- Smart Foods & Bioproducts Innovation Centre of Excellence, AgResearch Limited, Palmerston North 4474, New Zealand
| | - Evelyne Maes
- Riddet Institute, Te Ohu Rangahau Kai Facility, Massey University, Palmerston North 4474, New Zealand; (J.A.S.L.); (C.A.M.); (E.M.); (N.C.R.)
- Proteins & Metabolites Team, AgResearch Lincoln Research Centre, Lincoln 7608, New Zealand
| | - Charles Hefer
- Data Science South Team, AgResearch Lincoln Research Centre, Lincoln 7608, New Zealand;
| | - Raul A. P. A. Cruz
- School of Food & Advanced Technology, Massey University, Palmerston North 4442, New Zealand;
| | - Nicole C. Roy
- Riddet Institute, Te Ohu Rangahau Kai Facility, Massey University, Palmerston North 4474, New Zealand; (J.A.S.L.); (C.A.M.); (E.M.); (N.C.R.)
- High-Value Nutrition National Science Challenge, Auckland 1010, New Zealand
- Department of Nutrition, University of Otago, Dunedin 9016, New Zealand
| | - Warren C. McNabb
- Riddet Institute, Te Ohu Rangahau Kai Facility, Massey University, Palmerston North 4474, New Zealand; (J.A.S.L.); (C.A.M.); (E.M.); (N.C.R.)
- High-Value Nutrition National Science Challenge, Auckland 1010, New Zealand
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4
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Ta HP, Clarisse C, Maes E, Yamakawa N, Guérardel Y, Krzewinski F, Zarzycka W, Touboul D, Girardeau A, Fonseca F, Kermarrec A, Viau M, Riaublanc A, Ropers MH. Membrane lipid composition of Carnobacterium maltaromaticum CNCM I-3298, a highly cryoresistant lactic bacterium. Chem Phys Lipids 2023; 255:105326. [PMID: 37414116 DOI: 10.1016/j.chemphyslip.2023.105326] [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] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 06/30/2023] [Accepted: 07/03/2023] [Indexed: 07/08/2023]
Abstract
The growing consumption of fermented products has led to an increasing demand for lactic acid bacteria (LAB), especially for LAB tolerant to freezing/thawing conditions. Carnobacterium maltaromaticum is a psychrotrophic and freeze-thawing resistant lactic acid bacterium. The membrane is the primary site of damage during the cryo-preservation process and requires modulation to improve cryoresistance. However, knowledge about the membrane structure of this LAB genus is limited. We presented here the first study of the membrane lipid composition of C. maltaromaticum CNCM I-3298 including the polar heads and the fatty acid compositions of each lipid family (neutral lipids, glycolipids, phospholipids). The strain CNCM I-3298 is principally composed of glycolipids (32%) and phospholipids (55%). About 95% of glycolipids are dihexaosyldiglycerides while less than 5% are monohexaosyldiglycerides. The disaccharide chain of dihexaosyldiglycerides is composed of α-Gal(1-2)-α-Glc chain, evidenced for the first time in a LAB strain other than Lactobacillus strains. Phosphatidylglycerol is the main phospholipid (94%). All polar lipids are exceptionally rich in C18:1 (from 70% to 80%). Regarding the fatty acid composition, C. maltaromaticum CNCM I-3298 is an atypical bacterium within the genus Carnobacterium due to its high C18:1 proportion but resemble the other Carnobacterium strains as they mostly do not contain cyclic fatty acids.
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Affiliation(s)
- H P Ta
- INRAE, BIA, F-44316 Nantes, France.
| | - C Clarisse
- Univ. Lille, CNRS, INSERM, CHU Lille, Institut Pasteur de Lille, US 41-UAR 2014-PLBS, F-59000 Lille, France
| | - E Maes
- Univ. Lille, CNRS, INSERM, CHU Lille, Institut Pasteur de Lille, US 41-UAR 2014-PLBS, F-59000 Lille, France
| | - N Yamakawa
- Univ. Lille, CNRS, INSERM, CHU Lille, Institut Pasteur de Lille, US 41-UAR 2014-PLBS, F-59000 Lille, France
| | - Y Guérardel
- Univ. Lille, CNRS, UMR 8576 - UGSF - Unité de Glycobiologie Structurale et Fonctionnelle, F-59000 Lille, France; Institute for Glyco-core Research (iGCORE), Gifu University, Gifu, Japan
| | - F Krzewinski
- Univ. Lille, CNRS, UMR 8576 - UGSF - Unité de Glycobiologie Structurale et Fonctionnelle, F-59000 Lille, France
| | - W Zarzycka
- Université Paris-Saclay, CNRS, Institut de Chimie des Substances Naturelles, UPR 2301, 91198, Gif-sur-Yvette, France
| | - D Touboul
- Université Paris-Saclay, CNRS, Institut de Chimie des Substances Naturelles, UPR 2301, 91198, Gif-sur-Yvette, France
| | - A Girardeau
- Université Paris-Saclay, INRAE, AgroParisTech, UMR SayFood, F-91120 Palaiseau, France
| | - F Fonseca
- Université Paris-Saclay, INRAE, AgroParisTech, UMR SayFood, F-91120 Palaiseau, France
| | | | - M Viau
- INRAE, BIA, F-44316 Nantes, France
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5
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Gathercole J, Maes E, Thomas A, Wieliczko R, Grosvenor A, Haines S, Clerens S, Deb-Choudhury S. Unlocking the bioactivity of meat proteins: Comparison of meat and meat hydrolysate via simulated gastrointestinal digestion. J Proteomics 2023; 273:104806. [PMID: 36587727 DOI: 10.1016/j.jprot.2022.104806] [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] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 12/22/2022] [Accepted: 12/27/2022] [Indexed: 12/31/2022]
Abstract
Understanding the functional attributes of meat proteins is crucial for determining their nutritional benefits. Depending on the form in which meat proteins are available, the digestive process can release peptides which are valuable for nutrition and may also possess bioactive properties, affecting physiology. Liquid chromatography - mass spectrometry (LC-MS) was used to quantitatively compare the molecular peptide features (representing non-redundant peptides), during the different stages of a simulated gastrointestinal digestion process of a minimally processed powdered meat and its enzymatically produced hydrolysate. Results from a principal component analysis (PCA) indicated that the hydrolysate did not undergo extensive additional digestion whereas the powdered meat was digested both at the gastric and in the intestinal phases. Bioactive peptide sequence prediction identified the meat hydrolysate but not the meat powder as the only source of exact and partial bioactive matches in the angiotensin-I converting enzyme and dipeptidyl peptidase IV inhibition categories. Also, a higher source of cryptides (encrypted bioactive peptides), indicated that meat hydrolysates are potentially a better substrate for the release of these enzyme inhibitory peptides. These observations thus suggest that pre-digestion of a complex food matrix such as meat, may enhance its bioavailability following oral consumption early in the digestion process. SIGNIFICANCE: This work highlights enzymatic hydrolysis of meat proteins prior to ingestion allows for potentially higher bioavailability of bioactive peptides that inhibit angiotensin-I converting enzyme and dipeptidyl peptidase IV, thus possibly aiding high blood pressure and type 2 diabetes management.
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Affiliation(s)
| | - Evelyne Maes
- Smart Foods & Bioproducts, AgResearch Lincoln, New Zealand
| | - Ancy Thomas
- Smart Foods & Bioproducts, AgResearch Lincoln, New Zealand
| | | | | | - Stephen Haines
- Smart Foods & Bioproducts, AgResearch Lincoln, New Zealand
| | - Stefan Clerens
- Smart Foods & Bioproducts, AgResearch Lincoln, New Zealand; Biomolecular Interaction Centre, University of Canterbury, Christchurch, New Zealand; Riddet Institute, Massey University, Palmerston North, New Zealand
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6
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Ahmad R, Dalziel JE, Nguyen HT, Rounce J, Day L, Maes E. Investigation of free amino acids in lactic acid bacteria fermented milk and their ability to activate the calcium sensing receptor. Int Dairy J 2022. [DOI: 10.1016/j.idairyj.2022.105568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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7
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Ross AB, Maes E, Lee EJ, Homewood I, Marsh JM, Davis SL, Willicut RJ. UV and visible light exposure to hair leads to widespread changes in the hair lipidome. Int J Cosmet Sci 2022; 44:672-684. [PMID: 35924329 PMCID: PMC9804959 DOI: 10.1111/ics.12810] [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: 03/31/2022] [Revised: 07/15/2022] [Accepted: 08/02/2022] [Indexed: 01/09/2023]
Abstract
OBJECTIVE Scalp hair is among the most exposed parts of the human body, yet the impact of visible and UV light on hair lipids, an important structural component of hair, is poorly researched. We have used lipidomics, a broad-based approach to measure lipids in samples, which has hitherto not been applied to UV-exposed hair in the published literature, and could allow for a wider understanding of how UV light impacts on specific hair lipids. METHODS Mixed blonde Caucasian hair switches were divided into two groups of five, with half of the hair switches exposed to UV and visible light mimicking normal daytime exposure and half left unexposed. LC-MS lipidomics was used to profile the lipids in the hair samples. RESULTS A total of 791 lipids and 32 lipid classes with tentative identifications were detected in the hair samples. Nineteen lipid classes and 397 lipids differed between UV-treated and non-treated hair. The main lipid classes that differed were vitamin A fatty acid esters, sterol esters, several ceramides, mono-, di- and triglycerides, phosphatidylethanolamines (all decreased in UV-exposed hair) and bismonoacylglycerolphosphates, acylcarnitines and acylglycines (all increased in UV-exposed hair). Most detected lipids were decreased in UV-exposed hair, supporting earlier work that has found that UV exposure causes oxidation of lipids which would result in a decrease in most lipid classes. CONCLUSION Light exposure to hair has a widespread impact on the hair lipidome. This study also adds to the emerging literature on the hair lipidome, broadening the range of lipid classes reported in hair.
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Affiliation(s)
| | - Evelyne Maes
- Proteins and Metabolites, AgResearchLincolnNew Zealand,Riddet Institute based at Massey UniversityPalmerston NorthNew Zealand,Biomolecular Interaction CentreUniversity of CanterburyChristchurchNew Zealand
| | - Erin J. Lee
- Proteins and Metabolites, AgResearchLincolnNew Zealand
| | - Ines Homewood
- Proteins and Metabolites, AgResearchLincolnNew Zealand
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8
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Feijen M, Beles M, Than YZ, Cordon A, Dupont M, Treskes RW, Caputo M, Mullens W, Van Bokstal K, Auricchio A, Egorova AD, Maes E, Beeres SLMA, Heggermont WA. Activation of the HeartLogic algorithm on top of heart failure care: a multicenter propensity-matched cohort analysis. Eur Heart J 2022. [DOI: 10.1093/eurheartj/ehac544.2800] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Abstract
Background
Hospitalization for decompensated heart failure may be prevented by early detection of fluid retention. The multisensory HeartLogic™ algorithm, incorporated in a cardiac implantable electronic device (CIED) aims to detect impending fluid retention and thereby enables timely adjustment of medical therapy. However, it is to be investigated whether HeartLogic™ provides clinical benefit compared to heart failure care with conventional telemonitoring. This analysis investigates the effects of activating HeartLogic™ on top of heart failure care with telemonitoring on the number of episodes with fluid retention and heart failure related hospitalizations.
Methods
Heart failure patients with a CIED were recruited from the outpatient clinics of four European cardiology departments. All patients were included from January 2017 until December 2020, and followed-up for 365 days. Patients with a CIED and an activated HeartLogic™ algorithm were compared to a 1:1 propensity score-based matched control group consisting of patients with CIED on routine telemonitoring. Data of all episodes of (impending) fluid retention with ≥2 signs and symptoms of congestion were included for analyses.
Results
Data of 127 patients with an activated HeartLogic™ algorithm were adequately matched with 127 heart failure patients with a CIED on routine telemonitoring. Median age was 68 [59–75], majority of patients were male (80%), 46% had an ischemic etiology of heart failure. Total follow-up consisted of 254 patient years. During follow up, 77 (61%) individual patients with HeartLogic™ experienced an episode of fluid retention, compared to 85 (67%) induvial patients on routine telemonitoring. Patients with an activated HeartLogic™ algorithm had 1.62±1.78 events of fluid retention per patient year (PPY) compared to 2.61±3.71 events PPY in patients on routine telemonitoring, p<0.01 (Figure 1). Hospitalization for fluid retention occurred in 7 (6%) HeartLogic™ patients (0.06±0.27 hospitalizations PPY) compared to 13 (10%) patients on routine telemonitoring (0.15±0.45 PPY), p=0.07 (Figure 2A). Mean length of hospitalization in days PPY was 0.29±1.46 in patients with HeartLogic™ and 1.59±6.30 in patients on routine telemonitoring, p=0.02 (Figure 2B).
Conclusion
In a real-world multicenter heart failure population, activation of the HeartLogic™ algorithm was associated with a lower number of episodes of fluid retention per patient and a shorter duration of hospitalization for congestive heart failure.
Funding Acknowledgement
Type of funding sources: None.
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Affiliation(s)
- M Feijen
- Leiden University Medical Center , Leiden , The Netherlands
| | - M Beles
- Cardiovascular Research Center Aalst , Aalst , Belgium
| | - Y Z Than
- Deloitte HEOR (Health-Economics and Outcome Research) , Zaventem , Belgium
| | - A Cordon
- Deloitte HEOR (Health-Economics and Outcome Research) , Zaventem , Belgium
| | - M Dupont
- Hospital Oost-Limburg (ZOL) , Genk , Belgium
| | - R W Treskes
- Leiden University Medical Center , Leiden , The Netherlands
| | - M Caputo
- Cardiocentro Ticino Foundation , Lugano , Switzerland
| | - W Mullens
- Hospital Oost-Limburg (ZOL) , Genk , Belgium
| | - K Van Bokstal
- Cardiovascular Research Center Aalst , Aalst , Belgium
| | - A Auricchio
- Cardiocentro Ticino Foundation , Lugano , Switzerland
| | - A D Egorova
- Leiden University Medical Center , Leiden , The Netherlands
| | - E Maes
- Cardiovascular Research Center Aalst , Aalst , Belgium
| | - S L M A Beeres
- Leiden University Medical Center , Leiden , The Netherlands
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Ye Y, Maes E, Deb-Choudhury S, Hefer CA, Schreurs NM, Realini CE. Proteomic Profile of M. Longissimus Thoracis from Commercial Lambs Reared in Different Forage Systems. Foods 2022; 11:foods11101419. [PMID: 35626989 PMCID: PMC9141604 DOI: 10.3390/foods11101419] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2022] [Revised: 05/05/2022] [Accepted: 05/11/2022] [Indexed: 02/01/2023] Open
Abstract
This study compared the protein composition of M. longissimus thoracis of lambs from six commercial forage production systems in New Zealand. A total of 286 proteins were identified based on liquid chromatography-tandem mass spectrometry. First, a binomial model showed that different production groups could be distinguished based on abundances of 16 proteins. Second, pair-wise comparisons were performed to search for protein abundance differences in meat due to animal sex (ewe vs. wether), diet (perennial ryegrass vs. chicory), and age (4 vs. 6–8 months old). Greater abundance of some myofibrillar and sarcoplasmic proteins were observed in lamb loins from ewes compared to wethers. Chicory diet and older age at slaughter were associated with meat with lower abundance of some myofibrillar proteins, possibly due to a greater proportion of muscle glycolytic fibres. The proteins that showed significant differences in their abundances due to production factors could be further investigated to understand their influence on meat quality.
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Affiliation(s)
- Yangfan Ye
- AgResearch Limited, Te Ohu Rangahau Kai, Massey University Campus, Grasslands, Tennent Drive, Palmerston North 4474, New Zealand; (Y.Y.); (C.E.R.)
- Animal Science, School of Agriculture and Environment, Massey University, Private Bag 11222, Palmerston North 4442, New Zealand;
| | - Evelyne Maes
- AgResearch Limited, Lincoln Research Centre, 1365 Springs Road, Lincoln 7674, New Zealand; (E.M.); (C.A.H.)
- Riddet Institute, Based at Massey University, Palmerston North 4474, New Zealand
| | - Santanu Deb-Choudhury
- AgResearch Limited, Lincoln Research Centre, 1365 Springs Road, Lincoln 7674, New Zealand; (E.M.); (C.A.H.)
- Correspondence:
| | - Charles A. Hefer
- AgResearch Limited, Lincoln Research Centre, 1365 Springs Road, Lincoln 7674, New Zealand; (E.M.); (C.A.H.)
| | - Nicola M. Schreurs
- Animal Science, School of Agriculture and Environment, Massey University, Private Bag 11222, Palmerston North 4442, New Zealand;
| | - Carolina E. Realini
- AgResearch Limited, Te Ohu Rangahau Kai, Massey University Campus, Grasslands, Tennent Drive, Palmerston North 4474, New Zealand; (Y.Y.); (C.E.R.)
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10
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Maes E, Deb-Choudhury S, Clerens S, Davis SL, Davis MG, Marsh JM, Willicut RJ, Dyer JM. Redox proteomics analysis of hair shaft proteins upon hydrothermal and alkaline insult. Int J Cosmet Sci 2021; 44:82-90. [PMID: 34860415 DOI: 10.1111/ics.12756] [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: 09/20/2021] [Revised: 11/23/2021] [Accepted: 12/01/2021] [Indexed: 11/28/2022]
Abstract
OBJECTIVE Human hair is regularly subjected to chemical and physical insults, such as heat, UV-irradiation and alkaline hair care products. These insults result in molecular modifications at the hair protein level that underpin mechanical and sensory property changes in the fibres. These changes can manifest itself in reduced hair quality and performance attributes observable to the consumer. In this work, changes in protein modification as a result of heat and alkaline treatments are determined. METHODS Redox proteomic profiling using high-resolution mass spectrometry was applied to map and evaluate amino acid residue modifications in human hair exposed to a combination of thermal treatments and alkali exposure with the aim to understand the underlying chemical processes. RESULTS Our results show that an increase in redox-related modifications is associated with exposure to higher levels of hydrothermal and alkaline insult. Post-translational modification profiling at the protein primary structural level delivered some further insights into the site-specificity of these modifications, with a clear increase in the number of cysteic acid modifications noticed in samples subjected to more extreme insults. CONCLUSION Pinpointing modification sides within proteins and the hair shaft proteome can be used as a basis for employing mitigation or repair strategies of hair protein damage caused by environmental or hair treatment-related insults.
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Affiliation(s)
- Evelyne Maes
- Beyond Food Centre of Excellence, AgResearch Ltd, Christchurch, New Zealand.,Riddet Institute, based at Massey University, Palmerston North, New Zealand.,Biomolecular Interaction Centre, University of Canterbury, Christchurch, New Zealand
| | | | - Stefan Clerens
- Beyond Food Centre of Excellence, AgResearch Ltd, Christchurch, New Zealand.,Riddet Institute, based at Massey University, Palmerston North, New Zealand.,Biomolecular Interaction Centre, University of Canterbury, Christchurch, New Zealand
| | | | | | | | | | - Jolon M Dyer
- Beyond Food Centre of Excellence, AgResearch Ltd, Christchurch, New Zealand.,Riddet Institute, based at Massey University, Palmerston North, New Zealand.,Biomolecular Interaction Centre, University of Canterbury, Christchurch, New Zealand
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11
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Murphy F, Gathercole J, Lee E, Homewood I, Ross AB, Clerens S, Maes E. Discrimination of milk fermented with different starter cultures by MALDI-TOF MS and REIMS fingerprinting. Int Dairy J 2021. [DOI: 10.1016/j.idairyj.2021.105143] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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12
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Aranciaga N, Morton JD, Maes E, Gathercole JL, Berg DK. Proteomic determinants of uterine receptivity for pregnancy in early and mid-postpartum dairy cows†. Biol Reprod 2021; 105:1458-1473. [PMID: 34647570 DOI: 10.1093/biolre/ioab190] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Revised: 08/03/2021] [Accepted: 10/13/2021] [Indexed: 11/14/2022] Open
Abstract
Dairy cow subfertility is a worldwide issue arising from multiple factors. It manifests in >30% early pregnancy losses in seasonal pasture-grazed herds, especially when cows are inseminated in the early post-partum period. Most losses occur before implantation, when embryo growth depends on factors present in maternal tract fluids. Here we examined the proteomic composition of early and mid-postpartum uterine luminal fluid in crossbred lactating dairy cows to identify molecular determinants of fertility. We also explored changes in uterine luminal fluid from first to third estrus cycles postpartum in individual cows, linking those changes with divergent embryo development. For this, we flushed uteri of 87 cows at day 7 of pregnancy at first and third estrus postpartum, recovering and grading their embryos. Out of 1563 proteins detected, 472 had not been previously reported in this fluid, and 408 were predicted to be actively secreted by bioinformatic analysis. The abundance of 18 proteins with roles in immune regulation and metabolic function (e.g. cystatin B, pyruvate kinase M2) was associated with contrasting embryo quality. Matched-paired pathway analysis indicated that, from first to third estrus postpartum, upregulation of metabolic (e.g. creatine and carbohydrate) and immune (e.g. complement regulation, antiviral defense) processes were related to poorer quality embryos in the third estrus cycle postpartum. Conversely, upregulated signal transduction and protein trafficking appeared related to improved embryo quality in third estrus. These results advance the characterization of the molecular environment of bovine uterine luminal fluid and may aid understanding fertility issues in other mammals, including humans.
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Affiliation(s)
- Nicolas Aranciaga
- Proteins and Metabolites Team, Agresearch, Christchurch, New Zealand.,Faculty of Agriculture and Life Sciences, Lincoln University, Christchurch, New Zealand.,Animal Biotechnology Team, Agresearch, Hamilton, New Zealand
| | - James D Morton
- Faculty of Agriculture and Life Sciences, Lincoln University, Christchurch, New Zealand
| | - Evelyne Maes
- Proteins and Metabolites Team, Agresearch, Christchurch, New Zealand
| | | | - Debra K Berg
- Animal Biotechnology Team, Agresearch, Hamilton, New Zealand
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13
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Maes E, Bell F, Hefer C, Thomas A, Harland D, Noble A, Plowman J, Clerens S, Grosvenor A. Insights in Human Hair Curvature by Proteome Analysis of Two Distinct Hair Shapes. J Cosmet Sci 2021; 72:249-267. [PMID: 35361314] [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] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Scalp hair is a universal human characteristic, and a wide range of hair shape and color variations exists. Although differences in human scalp hair shape are visually apparent, the underpinning molecular insights are yet to be fully explored. This work reports the determination of differences at the protein level between two distinct groups of hair shape: very straight samples versus very curly hair samples. An in-depth highresolution liquid-chromatography mass spectrometry proteome analysis study was performed on hair samples from 50 individuals (pooled in 10 × 5 samples) with very curly hair and 50 subjects with very straight hair (pooled in 10 × 5 samples) to decipher differences between the two experimental groups at the protein level. Our results demonstrate that a distinction between the two experimental groups (very straight vs. very curly) can be made based on their overall protein profiles in a multivariate analysis approach. Further investigation of the protein expression levels between these two groups pinpointed 13 unique proteins which were found to be significantly different between the two groups, with an adjusted p-value < 0.05 and a fold change of more than two. Although differences between the very curly and the very straight hair sample groups could be identified, linkage between population differences and curl phenotype is currently unknown and requires further investigation.
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Affiliation(s)
- Evelyne Maes
- Beyond Food, AgResearch Ltd., Lincoln 7674, New Zealand (E.M., A.T., D.H., J.P., S.C., A.G.), Unilever R&D, Port Sunlight, Bebington, Wirral CH63 3JW (F.B.), United Kingdom, Knowledge and Analytics, AgResearch Ltd., Lincoln 7674, New Zealand (C.H., A.N.), Biomolecular Interaction Centre, University of Canterbury, Christchurch 8041, New Zealand (S.C.), Riddet Institute, Massey University, Palmerston North 4474, New Zealand (S.C.)
| | - Fraser Bell
- Beyond Food, AgResearch Ltd., Lincoln 7674, New Zealand (E.M., A.T., D.H., J.P., S.C., A.G.), Unilever R&D, Port Sunlight, Bebington, Wirral CH63 3JW (F.B.), United Kingdom, Knowledge and Analytics, AgResearch Ltd., Lincoln 7674, New Zealand (C.H., A.N.), Biomolecular Interaction Centre, University of Canterbury, Christchurch 8041, New Zealand (S.C.), Riddet Institute, Massey University, Palmerston North 4474, New Zealand (S.C.)
| | - Charles Hefer
- Beyond Food, AgResearch Ltd., Lincoln 7674, New Zealand (E.M., A.T., D.H., J.P., S.C., A.G.), Unilever R&D, Port Sunlight, Bebington, Wirral CH63 3JW (F.B.), United Kingdom, Knowledge and Analytics, AgResearch Ltd., Lincoln 7674, New Zealand (C.H., A.N.), Biomolecular Interaction Centre, University of Canterbury, Christchurch 8041, New Zealand (S.C.), Riddet Institute, Massey University, Palmerston North 4474, New Zealand (S.C.)
| | - Ancy Thomas
- Beyond Food, AgResearch Ltd., Lincoln 7674, New Zealand (E.M., A.T., D.H., J.P., S.C., A.G.), Unilever R&D, Port Sunlight, Bebington, Wirral CH63 3JW (F.B.), United Kingdom, Knowledge and Analytics, AgResearch Ltd., Lincoln 7674, New Zealand (C.H., A.N.), Biomolecular Interaction Centre, University of Canterbury, Christchurch 8041, New Zealand (S.C.), Riddet Institute, Massey University, Palmerston North 4474, New Zealand (S.C.)
| | - Duane Harland
- Beyond Food, AgResearch Ltd., Lincoln 7674, New Zealand (E.M., A.T., D.H., J.P., S.C., A.G.), Unilever R&D, Port Sunlight, Bebington, Wirral CH63 3JW (F.B.), United Kingdom, Knowledge and Analytics, AgResearch Ltd., Lincoln 7674, New Zealand (C.H., A.N.), Biomolecular Interaction Centre, University of Canterbury, Christchurch 8041, New Zealand (S.C.), Riddet Institute, Massey University, Palmerston North 4474, New Zealand (S.C.)
| | - Alasdair Noble
- Beyond Food, AgResearch Ltd., Lincoln 7674, New Zealand (E.M., A.T., D.H., J.P., S.C., A.G.), Unilever R&D, Port Sunlight, Bebington, Wirral CH63 3JW (F.B.), United Kingdom, Knowledge and Analytics, AgResearch Ltd., Lincoln 7674, New Zealand (C.H., A.N.), Biomolecular Interaction Centre, University of Canterbury, Christchurch 8041, New Zealand (S.C.), Riddet Institute, Massey University, Palmerston North 4474, New Zealand (S.C.)
| | - Jeffrey Plowman
- Beyond Food, AgResearch Ltd., Lincoln 7674, New Zealand (E.M., A.T., D.H., J.P., S.C., A.G.), Unilever R&D, Port Sunlight, Bebington, Wirral CH63 3JW (F.B.), United Kingdom, Knowledge and Analytics, AgResearch Ltd., Lincoln 7674, New Zealand (C.H., A.N.), Biomolecular Interaction Centre, University of Canterbury, Christchurch 8041, New Zealand (S.C.), Riddet Institute, Massey University, Palmerston North 4474, New Zealand (S.C.)
| | - Stefan Clerens
- Beyond Food, AgResearch Ltd., Lincoln 7674, New Zealand (E.M., A.T., D.H., J.P., S.C., A.G.), Unilever R&D, Port Sunlight, Bebington, Wirral CH63 3JW (F.B.), United Kingdom, Knowledge and Analytics, AgResearch Ltd., Lincoln 7674, New Zealand (C.H., A.N.), Biomolecular Interaction Centre, University of Canterbury, Christchurch 8041, New Zealand (S.C.), Riddet Institute, Massey University, Palmerston North 4474, New Zealand (S.C.)
| | - Anita Grosvenor
- Beyond Food, AgResearch Ltd., Lincoln 7674, New Zealand (E.M., A.T., D.H., J.P., S.C., A.G.), Unilever R&D, Port Sunlight, Bebington, Wirral CH63 3JW (F.B.), United Kingdom, Knowledge and Analytics, AgResearch Ltd., Lincoln 7674, New Zealand (C.H., A.N.), Biomolecular Interaction Centre, University of Canterbury, Christchurch 8041, New Zealand (S.C.), Riddet Institute, Massey University, Palmerston North 4474, New Zealand (S.C.)
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14
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Leite JAS, Montoya CA, Loveday SM, Maes E, Mullaney JA, McNabb WC, Roy NC. Heat-Treatments Affect Protease Activities and Peptide Profiles of Ruminants' Milk. Front Nutr 2021; 8:626475. [PMID: 33777990 PMCID: PMC7987661 DOI: 10.3389/fnut.2021.626475] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [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] [Received: 11/05/2020] [Accepted: 02/08/2021] [Indexed: 01/30/2023] Open
Abstract
Proteases present in milk are heat-sensitive, and their activities increase or decrease depending on the intensity of the thermal treatment applied. The thermal effects on the protease activity are well-known for bovine milk but poorly understood for ovine and caprine milk. This study aimed to determine the non-specific and specific protease activities in casein and whey fractions isolated from raw bovine, ovine, and caprine milk collected in early lactation, and to determine the effects of low-temperature, long-time (63°C for 30 min) and high-temperature, short-time (85°C for 5 min) treatments on protease activities within each milk fraction. The non-specific protease activities in raw and heat-treated milk samples were determined using the substrate azocasein. Plasmin (the main protease in milk) and plasminogen-derived activities were determined using the chromogenic substrate S-2251 (D-Val-Leu-Lys-pNA dihydrochloride). Peptides were characterized using high-resolution liquid chromatography coupled with tandem mass spectrometry. The activity of all native proteases, shown as non-specific proteases, was similar between raw bovine and caprine milk samples, but lower (P < 0.05) than raw ovine milk in the whey fraction. There was no difference (P > 0.05) between the non-specific protease activity of the casein fraction of raw bovine and caprine milk samples; both had higher activity than ovine milk. After 63°C/30 min, the non-specific protease activity decreased (44%; P > 0.05) for the bovine casein fraction only. In contrast, the protease activity of the milk heated at 85°C/5 min changed depending on the species and fraction. For instance, the activity decreased by 49% for ovine whey fraction, but it increased by 68% for ovine casein fraction. Plasmin and plasminogen were in general inactivated (P > 0.05) when all milk fractions were heated at 85°C/5 min. Most of the peptides present in heat-treated milk were derived from β-casein and αS1-casein, and they matched the hydrolysis profile of cathepsin D and plasmin. Identified peptides in ruminant milk samples had purported immunomodulatory and inhibitory functions. These findings indicate that the non-specific protease activity in whey and casein fractions differed between ruminant milk species, and specific thermal treatments could be used to retain better protease activity for all ruminant milk species.
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Affiliation(s)
| | - Carlos A. Montoya
- Riddet Institute, Massey University, Palmerston North, New Zealand
- Smart Foods Innovation Centre of Excellence, AgResearch Limited, Palmerston North, New Zealand
| | - Simon M. Loveday
- Riddet Institute, Massey University, Palmerston North, New Zealand
- Smart Foods Innovation Centre of Excellence, AgResearch Limited, Palmerston North, New Zealand
| | - Evelyne Maes
- Beyond Foods Innovation Centre of Excellence, AgResearch Limited, Lincoln, New Zealand
| | - Jane A. Mullaney
- Riddet Institute, Massey University, Palmerston North, New Zealand
- Smart Foods Innovation Centre of Excellence, AgResearch Limited, Palmerston North, New Zealand
- High-Value Nutrition National Science Challenge, Auckland, New Zealand
| | - Warren C. McNabb
- Riddet Institute, Massey University, Palmerston North, New Zealand
- High-Value Nutrition National Science Challenge, Auckland, New Zealand
| | - Nicole C. Roy
- Riddet Institute, Massey University, Palmerston North, New Zealand
- High-Value Nutrition National Science Challenge, Auckland, New Zealand
- Liggins Institute, The University of Auckland, Auckland, New Zealand
- Department of Nutrition, University of Otago, Dunedin, New Zealand
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15
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Maes E, Cools N, Willems H, Baggerman G. FACS-Based Proteomics Enables Profiling of Proteins in Rare Cell Populations. Int J Mol Sci 2020; 21:ijms21186557. [PMID: 32911660 PMCID: PMC7554798 DOI: 10.3390/ijms21186557] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 08/31/2020] [Accepted: 09/04/2020] [Indexed: 12/22/2022] Open
Abstract
Understanding disease pathology often does not require an overall proteomic analysis of clinical samples but rather the analysis of different, often rare, subpopulations of cells in a heterogeneous mixture of cell types. For the isolation of pre-specified cellular subtypes, fluorescence activated cell sorting (FACS) is commonly used for its ability to isolate the required cell populations with high purity, even of scarce cell types. The proteomic analysis of a limited number of FACS-sorted cells, however, is very challenging as both sample preparation inefficiencies and limits in terms of instrument sensitivity are present. In this study, we used CD14+CD15+ immune cells sorted out of peripheral blood mononuclear cells isolated from whole blood to improve and evaluate FACS-based proteomics. To optimize both the protein extraction protocol and the mass spectrometry (MS) data acquisition method, PBMCs as well as commercialized HeLa digest were used. To reflect the limited number of sorted cells in some clinical samples, different numbers of sorted cells (1000, 5000, 10,000, or 50,000) were used. This allowed comparing protein profiles across samples with limited protein material and provided further insights in the benefits and limitations of using a very limited numbers of cells.
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Affiliation(s)
- Evelyne Maes
- Food & Bio-Based Products, AgResearch Ltd., Lincoln 7674, New Zealand;
| | - Nathalie Cools
- Laboratory of Experimental Hematology, Faculty of Medicine and Health Sciences, Vaccine and Infectious Disease Institute (VaxInfectio), Antwerp University Hospital (UZA), University of Antwerp, 2020 Antwerpen, Belgium;
- Center for Cell Therapy and Regenerative Medicine, Antwerp University Hospital, 2650 Edegem, Belgium
| | - Hanny Willems
- Centre for Proteomics, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerpen, Belgium;
- Health Unit, Vlaamse Instelling voor Technologisch Onderzoek (VITO), Boeretang 200, 2400 Mol, Belgium
| | - Geert Baggerman
- Centre for Proteomics, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerpen, Belgium;
- Health Unit, Vlaamse Instelling voor Technologisch Onderzoek (VITO), Boeretang 200, 2400 Mol, Belgium
- Correspondence: ; Tel.: +32-476472918
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16
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Berghmans E, Jacobs J, Deben C, Hermans C, Broeckx G, Smits E, Maes E, Raskin J, Pauwels P, Baggerman G. Mass Spectrometry Imaging Reveals Neutrophil Defensins as Additional Biomarkers for Anti-PD-(L)1 Immunotherapy Response in NSCLC Patients. Cancers (Basel) 2020; 12:E863. [PMID: 32252405 PMCID: PMC7225984 DOI: 10.3390/cancers12040863] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [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: 03/05/2020] [Revised: 03/30/2020] [Accepted: 04/01/2020] [Indexed: 12/17/2022] Open
Abstract
(1) Background: Therapeutic blocking of the interaction between programmed death-1 (PD-1) with its ligand PD-L1, an immune checkpoint, is a promising approach to restore the antitumor immune response. Improved clinical outcomes have been shown in different human cancers, including non-small cell lung cancer (NSCLC). Unfortunately, still a high number of NSCLC patients are treated with immunotherapy without obtaining any clinical benefit, due to the limitations of PD-L1 protein expression as the currently sole predictive biomarker for clinical use; (2) Methods: In this study, we applied mass spectrometry imaging (MSI) to discover new protein biomarkers, and to assess the possible correlation between candidate biomarkers and a positive immunotherapy response by matrix-assisted laser desorption/ionization (MALDI) MSI in 25 formalin-fixed paraffin-embedded (FFPE) pretreatment tumor biopsies (Biobank@UZA); (3) Results: Using MALDI MSI, we revealed that the addition of neutrophil defensin 1, 2 and 3 as pretreatment biomarkers may more accurately predict the outcome of immunotherapy treatment in NSCLC. These results were verified and confirmed with immunohistochemical analyses. In addition, we provide in-vitro evidence of the immune stimulatory effect of neutrophil defensins towards cancer cells; and (4) Conclusions: With proteomic approaches, we have discovered neutrophil defensins as additional prospective biomarkers for an anti-PD-(L)1 immunotherapy response. Thereby, we also demonstrated that the neutrophil defensins contribute in the activation of the immune response towards cancer cells, which could provide a new lead towards an anticancer therapy.
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Affiliation(s)
- Eline Berghmans
- Centre for Proteomics, University of Antwerp, 2020 Antwerpen, Belgium;
- Health Unit, VITO, 2400 Mol, Belgium
| | - Julie Jacobs
- Center for Oncological Research, University of Antwerp, 2610 Wilrijk, Belgium; (J.J.); (C.D.); (C.H.); (G.B.); (E.S.); (P.P.)
- Pathology Department, Antwerp University Hospital, 2650 Edegem, Belgium
| | - Christophe Deben
- Center for Oncological Research, University of Antwerp, 2610 Wilrijk, Belgium; (J.J.); (C.D.); (C.H.); (G.B.); (E.S.); (P.P.)
- Pathology Department, Antwerp University Hospital, 2650 Edegem, Belgium
| | - Christophe Hermans
- Center for Oncological Research, University of Antwerp, 2610 Wilrijk, Belgium; (J.J.); (C.D.); (C.H.); (G.B.); (E.S.); (P.P.)
- Pathology Department, Antwerp University Hospital, 2650 Edegem, Belgium
| | - Glenn Broeckx
- Center for Oncological Research, University of Antwerp, 2610 Wilrijk, Belgium; (J.J.); (C.D.); (C.H.); (G.B.); (E.S.); (P.P.)
- Pathology Department, Antwerp University Hospital, 2650 Edegem, Belgium
| | - Evelien Smits
- Center for Oncological Research, University of Antwerp, 2610 Wilrijk, Belgium; (J.J.); (C.D.); (C.H.); (G.B.); (E.S.); (P.P.)
- Center for Cell Therapy and Regenerative Medicine, Antwerp University Hospital, 2650 Edegem, Belgium
| | - Evelyne Maes
- Food & Bio-Based Products, AgResearch Ltd., Lincoln 7674, New Zealand;
| | - Jo Raskin
- Thoracic Oncology Department, Antwerp University Hospital, 2650 Edegem, Belgium;
| | - Patrick Pauwels
- Center for Oncological Research, University of Antwerp, 2610 Wilrijk, Belgium; (J.J.); (C.D.); (C.H.); (G.B.); (E.S.); (P.P.)
- Pathology Department, Antwerp University Hospital, 2650 Edegem, Belgium
| | - Geert Baggerman
- Centre for Proteomics, University of Antwerp, 2020 Antwerpen, Belgium;
- Health Unit, VITO, 2400 Mol, Belgium
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17
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Budamgunta H, Maes E, Willems H, Menschaert G, Schildermans K, Kumar AA, Boonen K, Baggerman G. Multiple solvent elution, a method to counter the effects of coelution and ion suppression in LC-MS analysis in bottom up proteomics. J Chromatogr B Analyt Technol Biomed Life Sci 2019; 1124:256-264. [PMID: 31238262 DOI: 10.1016/j.jchromb.2019.06.017] [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: 03/01/2019] [Revised: 06/10/2019] [Accepted: 06/13/2019] [Indexed: 10/26/2022]
Abstract
On average a human cell type expresses around 10,000 different protein coding genes synthesizing all the different molecular forms of the protein product (proteoforms) found in a cell. In a typical shotgun bottom up proteomic approach, the proteins are enzymatically cleaved, producing several 100,000 s of different peptides that are analyzed with liquid chromatography-tandem mass spectrometry (LC-MSMS). One of the major consequences of this high sample complexity is that coelution of peptides cannot be avoided. Moreover, low abundant peptides are difficult to identify as they have a lower chance of being selected for fragmentation due to ion-suppression effects and the semi-stochastic nature of the precursor selection in data-dependent shotgun proteomic analysis where peptides are selected for fragmentation analysis one-by-one as they elute from the column. In the current study we explore a simple novel approach that has the potential to counter some of the effect of coelution of peptides and improves the number of peptide identifications in a bottom-up proteomic analysis. In this method, peptides from a HeLa cell digest were eluted from the reverse phase column using three different elution solvents (acetonitrile, methanol and acetone) in three replicate reversed phase LC-MS/MS shotgun proteomic analysis. Results were compared with three technical replicates using the same solvent, which is common practice in proteomic analysis. In total, we see an increase of up to 10% in unique protein and up to 30% in unique peptide identifications from the combined analysis using different elution solvents when compared to the combined identifications from the three replicates of the same solvent. In addition, the overlap of unique peptide identifications common in all three LC-MS analyses in our approach is only 23% compared to 50% in the replicates using the same solvent. The method presented here thus provides an easy to implement method to significantly reduce the effects of coelution and ion suppression of peptides and improve protein coverage in shotgun proteomics. Data are available via ProteomeXchange with identifier PXD011908.
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Affiliation(s)
| | - Evelyne Maes
- Food & Bio-Based Products, AgResearch Ltd., 1365 Springs Road, Lincoln 7674, New Zealand
| | - Hanny Willems
- Unit Environmental Risk & Health, VITO, Mol, Belgium
| | - Gerben Menschaert
- BioBix Lab, Department of Mathematical Modelling, Statistics and Bio-informatics, Ghent University, Ghent, Belgium
| | | | | | - Kurt Boonen
- Centre for Proteomics, UAntwerp, Antwerp, Belgium; Unit Environmental Risk & Health, VITO, Mol, Belgium
| | - Geert Baggerman
- Centre for Proteomics, UAntwerp, Antwerp, Belgium; Unit Environmental Risk & Health, VITO, Mol, Belgium.
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18
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Berghmans E, Van Raemdonck G, Schildermans K, Willems H, Boonen K, Maes E, Mertens I, Pauwels P, Baggerman G. MALDI Mass Spectrometry Imaging Linked with Top-Down Proteomics as a Tool to Study the Non-Small-Cell Lung Cancer Tumor Microenvironment. Methods Protoc 2019; 2:mps2020044. [PMID: 31164623 PMCID: PMC6632162 DOI: 10.3390/mps2020044] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [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: 03/29/2019] [Revised: 05/10/2019] [Accepted: 05/22/2019] [Indexed: 02/06/2023] Open
Abstract
Advanced non-small-cell lung cancer (NSCLC) is generally linked with a poor prognosis and is one of the leading causes of cancer-related deaths worldwide. Since only a minority of the patients respond well to chemotherapy and/or targeted therapies, immunotherapy might be a valid alternative in the lung cancer treatment field, as immunotherapy attempts to strengthen the body’s own immune response to recognize and eliminate malignant tumor cells. However, positive response patterns to immunotherapy remain unclear. In this study, we demonstrate how immune-related factors could be visualized from single NSCLC tissue sections (Biobank@UZA) while retaining their spatial information by using matrix assisted laser desorption/ionization (MALDI) mass spectrometry imaging (MSI), in order to unravel the molecular profile of NSCLC patients. In this way, different regions in lung cancerous tissues could be discriminated based on the molecular composition. In addition, we linked visualization (MALDI MSI) and identification (based on liquid chromatography higher resolution mass spectrometry) of the molecules of interest for the correct biological interpretation of the observed molecular differences within the area in which these molecules are detected. This is of major importance to fully understand the underlying molecular profile of the NSCLC tumor microenvironment.
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Affiliation(s)
- Eline Berghmans
- Centre for Proteomics, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerpen, Belgium.
- Health Unit, VITO, Boeretang 200, 2400 Mol, Belgium.
| | - Geert Van Raemdonck
- Centre for Proteomics, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerpen, Belgium.
| | - Karin Schildermans
- Centre for Proteomics, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerpen, Belgium.
- Health Unit, VITO, Boeretang 200, 2400 Mol, Belgium.
| | - Hanny Willems
- Centre for Proteomics, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerpen, Belgium.
- Health Unit, VITO, Boeretang 200, 2400 Mol, Belgium.
| | - Kurt Boonen
- Centre for Proteomics, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerpen, Belgium.
- Health Unit, VITO, Boeretang 200, 2400 Mol, Belgium.
| | - Evelyne Maes
- Food & Bio-Based Products, AgResearch Ltd., 8140 Christchurch, New Zealand.
| | - Inge Mertens
- Centre for Proteomics, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerpen, Belgium.
- Health Unit, VITO, Boeretang 200, 2400 Mol, Belgium.
| | - Patrick Pauwels
- Department of Pathology, Antwerp University Hospital, Wilrijkstraat 10, 2650 Edegem, Belgium.
| | - Geert Baggerman
- Centre for Proteomics, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerpen, Belgium.
- Health Unit, VITO, Boeretang 200, 2400 Mol, Belgium.
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19
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Maes E, Oeyen E, Boonen K, Schildermans K, Mertens I, Pauwels P, Valkenborg D, Baggerman G. The challenges of peptidomics in complementing proteomics in a clinical context. Mass Spectrom Rev 2019; 38:253-264. [PMID: 30372792 DOI: 10.1002/mas.21581] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Accepted: 10/01/2018] [Indexed: 06/08/2023]
Abstract
Naturally occurring peptides, including growth factors, hormones, and neurotransmitters, represent an important class of biomolecules and have crucial roles in human physiology. The study of these peptides in clinical samples is therefore as relevant as ever. Compared to more routine proteomics applications in clinical research, peptidomics research questions are more challenging and have special requirements with regard to sample handling, experimental design, and bioinformatics. In this review, we describe the issues that confront peptidomics in a clinical context. After these hurdles are (partially) overcome, peptidomics will be ready for a successful translation into medical practice.
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Affiliation(s)
- Evelyne Maes
- Flemish Institute for Technological Research (VITO), Mol, Belgium
- Centre for Proteomics, University of Antwerp, Antwerp, Belgium
- Food and Bio-Based Products, AgResearch Ltd., Lincoln, New Zealand
| | - Eline Oeyen
- Flemish Institute for Technological Research (VITO), Mol, Belgium
- Centre for Proteomics, University of Antwerp, Antwerp, Belgium
| | - Kurt Boonen
- Flemish Institute for Technological Research (VITO), Mol, Belgium
- Centre for Proteomics, University of Antwerp, Antwerp, Belgium
| | - Karin Schildermans
- Flemish Institute for Technological Research (VITO), Mol, Belgium
- Centre for Proteomics, University of Antwerp, Antwerp, Belgium
| | - Inge Mertens
- Flemish Institute for Technological Research (VITO), Mol, Belgium
- Centre for Proteomics, University of Antwerp, Antwerp, Belgium
| | - Patrick Pauwels
- Molecular Pathology Unit, Department of Pathology, Antwerp University Hospital, Edegem, Belgium
| | - Dirk Valkenborg
- Flemish Institute for Technological Research (VITO), Mol, Belgium
- Centre for Proteomics, University of Antwerp, Antwerp, Belgium
- Center for Statistics, Hasselt University, Diepenbeek, Belgium
| | - Geert Baggerman
- Flemish Institute for Technological Research (VITO), Mol, Belgium
- Centre for Proteomics, University of Antwerp, Antwerp, Belgium
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McKerchar HJ, Clerens S, Dobson RC, Dyer JM, Maes E, Gerrard JA. Protein-protein crosslinking in food: Proteomic characterisation methods, consequences and applications. Trends Food Sci Technol 2019. [DOI: 10.1016/j.tifs.2019.02.005] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Maes E, Clerens S, Dyer JM, Deb-Choudhury S. Improved Detection and Fragmentation of Disulphide-Linked Peptides. Methods Protoc 2018; 1:mps1030033. [PMID: 31164574 PMCID: PMC6481087 DOI: 10.3390/mps1030033] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Revised: 08/24/2018] [Accepted: 08/28/2018] [Indexed: 12/04/2022] Open
Abstract
Characterisation of peptides containing intact disulphide bonds (DSBs) via mass spectrometry is challenging. Our study demonstrates that the addition of aniline to alpha-cyano-4-hydroxycinnamic acid improves detection and fragmentation of complex DSB peptides by matrix-assisted laser desorption/ionization, tandem time-of-flight mass spectrometry (MALDI-TOF-TOF MS). This improved assignment will be a significant new tool when a simple screening to confirm the DSB existence is required.
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Affiliation(s)
- Evelyne Maes
- Food & Bio-Based Products, AgResearch Ltd., 1365 Springs Road, Lincoln 7674, New Zealand.
| | - Stefan Clerens
- Food & Bio-Based Products, AgResearch Ltd., 1365 Springs Road, Lincoln 7674, New Zealand.
- Biomolecular Interaction Centre, University of Canterbury, Christchurch 8140, New Zealand.
| | - Jolon M Dyer
- Food & Bio-Based Products, AgResearch Ltd., 1365 Springs Road, Lincoln 7674, New Zealand.
- Biomolecular Interaction Centre, University of Canterbury, Christchurch 8140, New Zealand.
- Riddet Institute, Massey University, Palmerston North 4442, New Zealand.
- Wine, Food & Molecular Biosciences, Lincoln University, Lincoln 7674, New Zealand.
| | - Santanu Deb-Choudhury
- Food & Bio-Based Products, AgResearch Ltd., 1365 Springs Road, Lincoln 7674, New Zealand.
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22
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Jensen AHB, Maes E, Gillet C, Legrand-Monsieur A. Reliability of Amidolytic Assays for Progressive Antithrombin and Heparin Cofactor Activities on Capillary Blood. Thromb Haemost 2018. [DOI: 10.1055/s-0038-1650027] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
SummaryAmidolytic assay of antithrombin III on capillary blood can validly substitute for similar assays performed on venous blood, as an excellent correlation exists (r = 0.95).For the amidolytic assays of heparin cofactor activity, a much less satisfactory correlation is found (r = 0.81). Results are far more dispersed and a decrease is observed in late capillary samples.Using a low heparin concentration to assay heparin cofactor activity leads to surprisingly high activities for capillary blood. The same type of discrepancy is observed during the earliest stages of clotting of venous blood.
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Affiliation(s)
- A Hurlet-Birk Jensen
- The Haemostasis and Thrombosis Research Unit, University of Louvain, Brussels, Belgium
| | - E Maes
- The Haemostasis and Thrombosis Research Unit, University of Louvain, Brussels, Belgium
| | - C Gillet
- The Haemostasis and Thrombosis Research Unit, University of Louvain, Brussels, Belgium
| | - A Legrand-Monsieur
- The Haemostasis and Thrombosis Research Unit, University of Louvain, Brussels, Belgium
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23
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Budamgunta H, Olexiouk V, Luyten W, Schildermans K, Maes E, Boonen K, Menschaert G, Baggerman G. Comprehensive Peptide Analysis of Mouse Brain Striatum Identifies Novel sORF-Encoded Polypeptides. Proteomics 2018; 18:e1700218. [DOI: 10.1002/pmic.201700218] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Revised: 03/30/2018] [Indexed: 11/10/2022]
Affiliation(s)
| | - Volodimir Olexiouk
- BioBix; Lab for Bioinformatics and Computational Genomics; Department of Mathematical Modelling; Statistics and Bio-informatics; Ghent University; Ghent Belgium
| | - Walter Luyten
- Animal Physiology and Neurobiology; KULeuven; Leuven Belgium
| | | | - Evelyne Maes
- Centre for Proteomics; UAntwerp; Antwerp Belgium
- Proteins and Biomaterials; AgResearch; Christchurch New Zealand
| | - Kurt Boonen
- Centre for Proteomics; UAntwerp; Antwerp Belgium
- Unit Environmental Risk and Health; VITO; Mol Belgium
| | - Gerben Menschaert
- BioBix; Lab for Bioinformatics and Computational Genomics; Department of Mathematical Modelling; Statistics and Bio-informatics; Ghent University; Ghent Belgium
| | - Geert Baggerman
- Centre for Proteomics; UAntwerp; Antwerp Belgium
- Unit Environmental Risk and Health; VITO; Mol Belgium
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24
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Maes E, Dyer JM, McKerchar HJ, Deb-Choudhury S, Clerens S. Protein-protein cross-linking and human health: the challenge of elucidating with mass spectrometry. Expert Rev Proteomics 2017; 14:917-929. [PMID: 28759730 DOI: 10.1080/14789450.2017.1362336] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [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: 01/22/2023]
Abstract
INTRODUCTION In several biomedical research fields, the cross-linking of peptides and proteins has an important impact on health and wellbeing. It is therefore of crucial importance to study this class of post-translational modifications in detail. The huge potential of mass spectrometric technologies in the mapping of these protein-protein cross-links is however overshadowed by the challenges that the field has to overcome. Areas covered: In this review, we summarize the different pitfalls and challenges that the protein-protein cross-linking field is confronted with when using mass spectrometry approaches. We additionally focus on native disulfide bridges as an example and provide some examples of cross-links that are important in the biomedical field. Expert commentary: The current flow of methodological improvements, mainly from the chemical cross-linking field, has delivered a significant contribution to deciphering native and insult-induced cross-links. Although an automated data analysis of proteome-wide peptide cross-linking is currently only possible in chemical cross-linking experiments, the field is well on the way towards a more automated analysis of native and insult-induced cross-links in raw mass spectrometry data that will boost its potential in biomedical applications.
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Affiliation(s)
- Evelyne Maes
- a Food & Bio-Based Products, AgResearch Ltd ., Lincoln , New Zealand
| | - Jolon M Dyer
- a Food & Bio-Based Products, AgResearch Ltd ., Lincoln , New Zealand.,b Biomolecular Interaction Centre , University of Canterbury , Christchurch , New Zealand.,c Riddet Institute, Massey University , Palmerston North , New Zealand.,d Wine, Food & Molecular Biosciences , Lincoln University , Lincoln , New Zealand
| | - Hannah J McKerchar
- a Food & Bio-Based Products, AgResearch Ltd ., Lincoln , New Zealand.,b Biomolecular Interaction Centre , University of Canterbury , Christchurch , New Zealand
| | | | - Stefan Clerens
- a Food & Bio-Based Products, AgResearch Ltd ., Lincoln , New Zealand.,b Biomolecular Interaction Centre , University of Canterbury , Christchurch , New Zealand
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Vanopdenbosch LJ, Maes E, Oliver DJ. European Academy of Neurology/European Association for Palliative Care Taskforce on Neurology Consensus recommendations on palliative care for patients with chronic and progressive neurological disease - acceptability for Belgian neurologists. Eur J Neurol 2017; 24:995-998. [DOI: 10.1111/ene.13325] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Accepted: 04/13/2017] [Indexed: 12/12/2022]
Affiliation(s)
| | - E. Maes
- Department of Psychology; AZ Sint-Jan Brugge Oostende; Brugge Belgium
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26
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Akpo E, Jansen I, Maes E, Simoens S. Lipegfilgrastim highly cost-effective in reducing chemotherapy-induced neutropenia in breast cancer patients. Eur J Cancer 2017. [DOI: 10.1016/s0959-8049(17)30223-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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27
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Broeckx V, Boonen K, Pringels L, Sagaert X, Prenen H, Landuyt B, Schoofs L, Maes E. Comparison of multiple protein extraction buffers for GeLC-MS/MS proteomic analysis of liver and colon formalin-fixed, paraffin-embedded tissues. Mol Biosyst 2016; 12:553-65. [PMID: 26676081 DOI: 10.1039/c5mb00670h] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Formalin-fixed paraffin-embedded (FFPE) tissue specimens represent a potential valuable source of samples for clinical research. Since these specimens are banked in hospital archives, large cohorts of samples can be collected in short periods of time which can all be linked with a patients' clinical history. Therefore, the use of FFPE tissue in protein biomarker discovery studies gains interest. However, despite the growing number of FFPE proteome studies in the literature, there is a lack of a FFPE proteomics standard operating procedure (SOP). One of the challenging steps in the development of such a SOP is the ability to obtain an efficient and repeatable extraction of full length FFPE proteins. In this study, the protein extraction efficiency of eight protein extraction buffers is critically compared with GeLC-MS/MS (1D gel electrophoresis followed by in-gel digestion and LC-MS/MS). The data variation caused by using these extraction buffers was investigated since the variation is a very important aspect when using FFPE tissue as a source for biomarker detection. In addition, a qualitative comparison was made between the protein extraction efficiency and repeatability for FFPE tissue and fresh frozen tissue.
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Affiliation(s)
- Valérie Broeckx
- Research Group of Functional Genomics and Proteomics, Department of Biology, University of Leuven, Zoological Institute, Naamsestraat 59, 3000 Leuven, Belgium.
| | - Kurt Boonen
- Research Group of Functional Genomics and Proteomics, Department of Biology, University of Leuven, Zoological Institute, Naamsestraat 59, 3000 Leuven, Belgium.
| | - Lentel Pringels
- Research Group of Functional Genomics and Proteomics, Department of Biology, University of Leuven, Zoological Institute, Naamsestraat 59, 3000 Leuven, Belgium.
| | - Xavier Sagaert
- Centre for Translational Cell and Tissue Research, University Hospital of Leuven, Herestraat 49, 3000 Leuven, Belgium
| | - Hans Prenen
- Department of Gastro-Enterology, Digestive Oncology Unit, University Hospital of Leuven, Herestraat 49, 3000 Leuven, Belgium
| | - Bart Landuyt
- Research Group of Functional Genomics and Proteomics, Department of Biology, University of Leuven, Zoological Institute, Naamsestraat 59, 3000 Leuven, Belgium.
| | - Liliane Schoofs
- Research Group of Functional Genomics and Proteomics, Department of Biology, University of Leuven, Zoological Institute, Naamsestraat 59, 3000 Leuven, Belgium.
| | - Evelyne Maes
- Flemish Institute for Technological Research (VITO), Boeretang 200, 2400 Mol, Belgium and Centre for Proteomics, University of Antwerp/Flemish Institute for Technological Research (VITO), Groenenborgerlaan 171, 2020 Antwerp, Belgium
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28
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Maes E, Hadiwikarta WW, Mertens I, Baggerman G, Hooyberghs J, Valkenborg D. CONSTANd : A Normalization Method for Isobaric Labeled Spectra by Constrained Optimization. Mol Cell Proteomics 2016; 15:2779-90. [PMID: 27302888 DOI: 10.1074/mcp.m115.056911] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2015] [Indexed: 01/05/2023] Open
Abstract
In quantitative proteomics applications, the use of isobaric labels is a very popular concept as they allow for multiplexing, such that peptides from multiple biological samples are quantified simultaneously in one mass spectrometry experiment. Although this multiplexing allows that peptide intensities are affected by the same amount of instrument variability, systematic effects during sample preparation can also introduce a bias in the quantitation measurements. Therefore, normalization methods are required to remove this systematic error. At present, a few dedicated normalization methods for isobaric labeled data are at hand. Most of these normalization methods include a framework for statistical data analysis and rely on ANOVA or linear mixed models. However, for swift quality control of the samples or data visualization a simple normalization technique is sufficient. To this aim, we present a new and easy-to-use data-driven normalization method, named CONSTANd. The CONSTANd method employs constrained optimization and prior information about the labeling strategy to normalize the peptide intensities. Further, it allows maintaining the connection to any biological effect while reducing the systematic and technical errors. As a result, peptides can not only be compared directly within a multiplexed experiment, but are also comparable between other isobaric labeled datasets from multiple experimental designs that are normalized by the CONSTANd method, without the need to include a reference sample in every experimental setup. The latter property is especially useful when more than six, eight or ten (TMT/iTRAQ) biological samples are required to detect differential peptides with sufficient statistical power and to optimally make use of the multiplexing capacity of isobaric labels.
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Affiliation(s)
- Evelyne Maes
- From the: ‡Applied Bio & molecular Systems, VITO, Boeretang 200, 2400 Mol, Belgium; §Center for Proteomics, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp, Belgium
| | | | - Inge Mertens
- From the: ‡Applied Bio & molecular Systems, VITO, Boeretang 200, 2400 Mol, Belgium; §Center for Proteomics, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp, Belgium
| | - Geert Baggerman
- From the: ‡Applied Bio & molecular Systems, VITO, Boeretang 200, 2400 Mol, Belgium; §Center for Proteomics, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp, Belgium
| | - Jef Hooyberghs
- From the: ‡Applied Bio & molecular Systems, VITO, Boeretang 200, 2400 Mol, Belgium; ¶Theoretical Physics, Hasselt University, Agoralaan 1, 3590 Diepenbeek, Belgium
| | - Dirk Valkenborg
- From the: ‡Applied Bio & molecular Systems, VITO, Boeretang 200, 2400 Mol, Belgium; §Center for Proteomics, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp, Belgium; ‖Center for Statistics, Hasselt University, Agoralaan 1, 3590 Diepenbeek, Belgium
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Maes E, Tirez K, Baggerman G, Valkenborg D, Schoofs L, Encinar JR, Mertens I. The use of elemental mass spectrometry in phosphoproteomic applications. Mass Spectrom Rev 2016; 35:350-360. [PMID: 25139451 DOI: 10.1002/mas.21440] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2013] [Revised: 05/14/2014] [Accepted: 05/14/2014] [Indexed: 06/03/2023]
Abstract
Reversible phosphorylation is one of the most important post-translational modifications in mammalian cells. Because this molecular switch is an important mechanism that diversifies and regulates proteins in cellular processes, knowledge about the extent and quantity of phosphorylation is very important to understand the complex cellular interplay. Although phosphoproteomics strategies are applied worldwide, they mainly include only molecular mass spectrometry (like MALDI or ESI)-based experiments. Although identification and relative quantification of phosphopeptides is straightforward with these techniques, absolute quantification is more complex and usually requires for specific isotopically phosphopeptide standards. However, the use of elemental mass spectrometry, and in particular inductively coupled plasma mass spectrometry (ICP-MS), in phosphoproteomics-based experiments, allow one to absolutely quantify phosphopeptides. Here, these phosphoproteomic applications with ICP-MS as elemental detector are reviewed. Pioneering work and recent developments in the field are both described. Additionally, the advantage of the parallel use of molecular and elemental mass spectrometry is stressed.
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Affiliation(s)
- Evelyne Maes
- Flemish Institute for Technological Research (VITO), Mol, Belgium
- KU Leuven, Research Group of Functional Genomics and Proteomics, Leuven, Belgium
| | - Kristof Tirez
- Flemish Institute for Technological Research (VITO), Mol, Belgium
| | - Geert Baggerman
- Flemish Institute for Technological Research (VITO), Mol, Belgium
- CFP-CeProMa, University of Antwerp, Antwerp, Belgium
| | - Dirk Valkenborg
- Flemish Institute for Technological Research (VITO), Mol, Belgium
- CFP-CeProMa, University of Antwerp, Antwerp, Belgium
- Interuniversity Institute for Biostatistics and Statistical Bioinformatics, Hasselt University, Diepenbeek, Belgium
| | - Liliane Schoofs
- KU Leuven, Research Group of Functional Genomics and Proteomics, Leuven, Belgium
| | - Jorge Ruiz Encinar
- Department of Physical and Analytical Chemistry, University of Oviedo, Oviedo, Spain
| | - Inge Mertens
- Flemish Institute for Technological Research (VITO), Mol, Belgium
- CFP-CeProMa, University of Antwerp, Antwerp, Belgium
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Maes E, Kelchtermans P, Bittremieux W, De Grave K, Degroeve S, Hooyberghs J, Mertens I, Baggerman G, Ramon J, Laukens K, Martens L, Valkenborg D. Designing biomedical proteomics experiments: state-of-the-art and future perspectives. Expert Rev Proteomics 2016; 13:495-511. [PMID: 27031651 DOI: 10.1586/14789450.2016.1172967] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
With the current expanded technical capabilities to perform mass spectrometry-based biomedical proteomics experiments, an improved focus on the design of experiments is crucial. As it is clear that ignoring the importance of a good design leads to an unprecedented rate of false discoveries which would poison our results, more and more tools are developed to help researchers designing proteomic experiments. In this review, we apply statistical thinking to go through the entire proteomics workflow for biomarker discovery and validation and relate the considerations that should be made at the level of hypothesis building, technology selection, experimental design and the optimization of the experimental parameters.
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Affiliation(s)
- Evelyne Maes
- a Applied Bio & molecular systems , VITO , Mol , Belgium.,b CFP , University of Antwerp , Antwerp , Belgium
| | - Pieter Kelchtermans
- b CFP , University of Antwerp , Antwerp , Belgium.,c Medical Biotechnology Center , VIB , Ghent , Belgium.,d Department of Biochemistry , Ghent University , Ghent , Belgium.,e Bioinformatics Institute Ghent , Ghent University , Ghent , Belgium
| | - Wout Bittremieux
- f Department of Mathematics and Computer Science , University of Antwerp , Antwerp , Belgium.,g Biomedical Informatics Research Center Antwerp (biomina) , University of Antwerp/Antwerp University Hospital , Antwerp , Belgium
| | - Kurt De Grave
- h Department of Computer Science , KU Leuven , Leuven , Belgium
| | - Sven Degroeve
- c Medical Biotechnology Center , VIB , Ghent , Belgium.,d Department of Biochemistry , Ghent University , Ghent , Belgium.,e Bioinformatics Institute Ghent , Ghent University , Ghent , Belgium
| | - Jef Hooyberghs
- a Applied Bio & molecular systems , VITO , Mol , Belgium
| | - Inge Mertens
- a Applied Bio & molecular systems , VITO , Mol , Belgium.,b CFP , University of Antwerp , Antwerp , Belgium
| | - Geert Baggerman
- a Applied Bio & molecular systems , VITO , Mol , Belgium.,b CFP , University of Antwerp , Antwerp , Belgium
| | - Jan Ramon
- h Department of Computer Science , KU Leuven , Leuven , Belgium.,i INRIA , Lille , France
| | - Kris Laukens
- f Department of Mathematics and Computer Science , University of Antwerp , Antwerp , Belgium.,g Biomedical Informatics Research Center Antwerp (biomina) , University of Antwerp/Antwerp University Hospital , Antwerp , Belgium
| | - Lennart Martens
- c Medical Biotechnology Center , VIB , Ghent , Belgium.,d Department of Biochemistry , Ghent University , Ghent , Belgium.,e Bioinformatics Institute Ghent , Ghent University , Ghent , Belgium
| | - Dirk Valkenborg
- a Applied Bio & molecular systems , VITO , Mol , Belgium.,b CFP , University of Antwerp , Antwerp , Belgium.,j Interuniversity Institute for Biostatistics and statistical Bioinformatics , Hasselt University , Hasselt , Belgium
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31
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Maes E, Wenes M, Valkenborg D, Mertens I, Prenen H, Mazzone M, Baggerman G. Abstract B46: The use of quantitative proteomics to increase the knowledge about metabolic symbiosis in a tumor microenvironment. Mol Cancer Res 2016. [DOI: 10.1158/1557-3125.metca15-b46] [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] [Indexed: 11/16/2022]
Abstract
Abstract
For more than a century, it is known that in a solid tumor, malignant cancer cells co-reside with stromal cells including fibroblasts and immune cells. In addition, changes in metabolic requirements of malignant cells are necessary to cover their high proliferative rate. Although it has been demonstrated that complementary metabolic functions of tumor cells and their supporting local stroma (e.g. cancer-associated fibroblasts, adipocytes) contribute to the progression of cancer, less is known about the metabolic needs of immune cells in this local tumor microenvironment. However, in the context of cancer, immune cells, including tumor-associated macrophages (TAMs) are of high interest since it is known that these cells are able to influence tumor progression by allowing the establishment of an attractive environment for tumor growth and metastasis. Studying the expression profiles of proteins involved in metabolic processes of these cells might be a good strategy to elucidate this question.
In this study, we applied quantitative proteomics to study the differences in protein expression of TAMs vs. control macrophages (both bone marrow-derived and peritoneal macrophages) isolated from an in vivo murine model for non-small cell lung adenocarcinoma. In our peptide-centric two dimensional liquid chromatography (LC)- tandem mass spectrometry (MS/MS) setup where Tandem Mass Tag (TMT) labeling is applied, we were able to identify 1250 unique proteins, of which 1178 proteins were quantified with all six TMT reporter ions. Interestingly, analysis of the differentially expressed proteins indicate that several Gene Ontology terms regarding metabolic pathways including glutathione metabolic processes (p= 3.47 e-14) and pentose phosphate shunt (p= 2.29 e-8) were enriched. These data suggest that TAMs can reprogram their metabolism in order to survive to the oxidative stress existing in this kind of microenvironment.
In conclusion, our results illustrate that proteome analysis is a good strategy to obtain insights in the biology of tumor-associated macrophages.
Citation Format: Evelyne Maes, Mathias Wenes, Dirk Valkenborg, Inge Mertens, Hans Prenen, Massimiliano Mazzone, Geert Baggerman. The use of quantitative proteomics to increase the knowledge about metabolic symbiosis in a tumor microenvironment. [abstract]. In: Proceedings of the AACR Special Conference: Metabolism and Cancer; Jun 7-10, 2015; Bellevue, WA. Philadelphia (PA): AACR; Mol Cancer Res 2016;14(1_Suppl):Abstract nr B46.
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Affiliation(s)
- Evelyne Maes
- 1Flemish Institute for Technological Research (VITO), Mol, Belgium,
| | | | - Dirk Valkenborg
- 1Flemish Institute for Technological Research (VITO), Mol, Belgium,
| | - Inge Mertens
- 1Flemish Institute for Technological Research (VITO), Mol, Belgium,
| | - Hans Prenen
- 3University Hospital Gasthuisberg, Leuven, Belgium
| | | | - Geert Baggerman
- 1Flemish Institute for Technological Research (VITO), Mol, Belgium,
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Maes E, Mertens I, Valkenborg D, Pauwels P, Rolfo C, Baggerman G. Proteomics in cancer research: Are we ready for clinical practice? Crit Rev Oncol Hematol 2015; 96:437-48. [PMID: 26277237 DOI: 10.1016/j.critrevonc.2015.07.006] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2015] [Revised: 05/20/2015] [Accepted: 07/14/2015] [Indexed: 12/13/2022] Open
Abstract
Although genomics has delivered major advances in cancer prognostics, treatment and diagnostics, it still only provides a static image of the situation. To study more dynamic molecular entities, proteomics has been introduced into the cancer research field more than a decade ago. Currently, however, the impact of clinical proteomics on patient management and clinical decision-making is low and the implementations of scientific results in the clinic appear to be scarce. The search for cancer-related biomarkers with proteomics however, has major potential to improve risk assessment, early detection, diagnosis, prognosis, treatment selection and monitoring. In this review, we provide an overview of the transition of oncoproteomics towards translational oncology. We describe which lessons are learned from currently approved protein biomarkers and previous proteomic studies, what the pitfalls and challenges are in clinical proteomics applications, and how proteomic research can be successfully translated into medical practice.
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Affiliation(s)
- Evelyne Maes
- Flemish Institute for Technological Research (VITO), Mol, Belgium; CFP-CeProMa, University of Antwerp, Antwerp, Belgium
| | - Inge Mertens
- Flemish Institute for Technological Research (VITO), Mol, Belgium; CFP-CeProMa, University of Antwerp, Antwerp, Belgium
| | - Dirk Valkenborg
- Flemish Institute for Technological Research (VITO), Mol, Belgium; CFP-CeProMa, University of Antwerp, Antwerp, Belgium
| | - Patrick Pauwels
- Molecular Pathology Unit, Pathology Department, Antwerp University Hospital, Edegem, Belgium
| | - Christian Rolfo
- Phase I - Early Clinical Trials Unit, Oncology Department, Antwerp University Hospital & Center for Oncological Research (CORE), Antwerp University, Edegem, Belgium.
| | - Geert Baggerman
- Flemish Institute for Technological Research (VITO), Mol, Belgium; CFP-CeProMa, University of Antwerp, Antwerp, Belgium
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Abstract
Mass spectrometry-based clinical proteomics approaches were introduced into the biomedical field more than two decades ago. Despite recent developments both in the field of mass spectrometry and bioinformatics, the gap between proteomics results and their translation into clinical practice still needs to be closed, as implementation of proteomics results in the clinic appears to be scarce. An extra focus on the importance of the experimental design is therefore of crucial importance.
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Affiliation(s)
- Evelyne Maes
- Center for Proteomics, University of Antwerp/Flemish Institute for Technological Research (VITO), Groenenborgerlaan 171, 2020 Antwerp, Belgium
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Broeckx V, Peeters L, Maes E, Pringels L, Verjans ET, Landuyt B. Formalin-fixed paraffin-embedded tissue: The holy grail of clinical proteomics. Proteomics Clin Appl 2015; 8:735-6. [PMID: 25231873 DOI: 10.1002/prca.201400132] [Citation(s) in RCA: 3] [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: 09/09/2014] [Accepted: 09/10/2014] [Indexed: 11/10/2022]
Abstract
Tissue is the most relevant biological material to gather insight in disease mechanisms by means of omics technologies. However, fresh frozen tissue, which is generally regarded as the best imaginable source for such studies, is often not available. In case it is available, the different ways of storage (e.g. -20°C, -80°C, liquid nitrogen, etc.) hamper the conduction of reproducible multicenter studies because of different protein degradation rates. Formalin-fixed paraffin-embedded (FFPE) tissue on the contrary is considered as a valuable alternative for fresh frozen tissue, because only a few standard operation procedures are applied worldwide for the preparation of these tissues and because they are all stored in the same way. However, a study on the impact of the different preparation protocols for FFPE tissue was still lacking. Therefore, Bronsert et al. in this issue [Bronsert, P., Weißer, J., Biniossek, M. L., Kuehs, M. et al., Proteomics Clin. Appl. 2014, 8 786-804] conducted such a study that provides proof that there is no significant effect between these sample preparations procedures, and thereby they further open the gate for FFPE tissues to enter the field of clinical proteomics.
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Affiliation(s)
- Valérie Broeckx
- Functional Genomics and Proteomics Unit, KU Leuven, Leuven, Belgium
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Maes E, Brusten W, Beutels F, Baggerman G, Mertens I, Valkenborg D, Landuyt B, Schoofs L, Tirez K. The benefits and limitations of reaction cell and sector field inductively coupled plasma mass spectrometry in the detection and quantification of phosphopeptides. Rapid Commun Mass Spectrom 2015; 29:35-44. [PMID: 25462361 DOI: 10.1002/rcm.7079] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2014] [Revised: 10/16/2014] [Accepted: 10/16/2014] [Indexed: 06/04/2023]
Abstract
RATIONALE The phosphorylation of proteins is one of the most important post-translational modifications in nature. Knowledge of the quantity or degree of protein phosphorylation in biological samples is extremely important. A combination of liquid chromatography (LC) and inductively coupled plasma mass spectrometry (ICP-MS) allows the absolute and relative quantification of the phosphorus signal. METHODS A comparison between dynamic reaction cell quadrupole ICP-MS (DRC-Q-ICP-MS) and high-resolution sector field ICP-MS (SF-ICP-MS) in detecting signals of phosphorus-containing species using identical capillary LC (reversed-phase technology) and nebulizer settings was performed. RESULTS A method to diminish the reversed-phase gradient-related signal instability in phosphorus detection with LC/ICP-MS applications was developed. Bis(4-nitrophenyl)phosphate (BNPP) was used as a standard to compare signal-to-noise ratios and limits of detection (LODs) between the two instrumental setups. The LOD reaches a value of 0.8 µg L(-1) when applying the DRC technology in Q-ICP-MS and an LOD of 0.09 µg L(-1) was found with the SF-ICP-MS setup. This BNPP standard was further used to compare the absolute quantification possibilities of phosphopeptides in these two setups. CONCLUSIONS This one-to-one comparison of two interference-reducing ICP-MS instruments demonstrates that absolute quantification of individual LC-separated phosphopeptides is possible. However, based on the LOD values, SF-ICP-MS has a higher sensitivity in detecting phosphorus signals and thus is preferred in phosphopeptide analysis.
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Affiliation(s)
- Evelyne Maes
- Flemish Institute for Technological Research (VITO), Mol, Belgium; CFP-CeProMa, University of Antwerp, Antwerp, Belgium; KU Leuven, Research Group of Functional Genomics and Proteomics, Leuven, Belgium
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Stoop D, Maes E, Polyzos NP, Verheyen G, Tournaye H, Nekkebroeck J. Does oocyte banking for anticipated gamete exhaustion influence future relational and reproductive choices? A follow-up of bankers and non-bankers. Hum Reprod 2014; 30:338-44. [DOI: 10.1093/humrep/deu317] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Vu TN, Mrzic A, Valkenborg D, Maes E, Lemière F, Goethals B, Laukens K. Unravelling associations between unassigned mass spectrometry peaks with frequent itemset mining techniques. Proteome Sci 2014; 12:54. [PMID: 25429250 PMCID: PMC4243190 DOI: 10.1186/s12953-014-0054-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [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: 05/08/2014] [Accepted: 10/23/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Mass spectrometry-based proteomics experiments generate spectra that are rich in information. Often only a fraction of this information is used for peptide/protein identification, whereas a significant proportion of the peaks in a spectrum remain unexplained. In this paper we explore how a specific class of data mining techniques termed "frequent itemset mining" can be employed to discover patterns in the unassigned data, and how such patterns can help us interpret the origin of the unexpected/unexplained peaks. RESULTS First a model is proposed that describes the origin of the observed peaks in a mass spectrum. For this purpose we use the classical correlative database search algorithm. Peaks that support a positive identification of the spectrum are termed explained peaks. Next, frequent itemset mining techniques are introduced to infer which unexplained peaks are associated in a spectrum. The method is validated on two types of experimental proteomic data. First, peptide mass fingerprint data is analyzed to explain the unassigned peaks in a full scan mass spectrum. Interestingly, a large numbers of experimental spectra reveals several highly frequent unexplained masses, and pattern mining on these frequent masses demonstrates that subsets of these peaks frequently co-occur. Further evaluation shows that several of these co-occurring peaks indeed have a known common origin, and other patterns are promising hypothesis generators for further analysis. Second, the proposed methodology is validated on tandem mass spectrometral data using a public spectral library, where associations within the mass differences of unassigned peaks and peptide modifications are explored. The investigation of the found patterns illustrates that meaningful patterns can be discovered that can be explained by features of the employed technology and found modifications. CONCLUSIONS This simple approach offers opportunities to monitor accumulating unexplained mass spectrometry data for emerging new patterns, with possible applications for the development of mass exclusion lists, for the refinement of quality control strategies and for a further interpretation of unexplained spectral peaks in mass spectrometry and tandem mass spectrometry.
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Affiliation(s)
- Trung Nghia Vu
- Department of Mathematics and Computer Science, University of Antwerp, Antwerp, Belgium ; Biomedical Informatics Research Center Antwerp (biomina), University of Antwerp / Antwerp University Hospital, Edegem, Belgium
| | - Aida Mrzic
- Department of Mathematics and Computer Science, University of Antwerp, Antwerp, Belgium ; Biomedical Informatics Research Center Antwerp (biomina), University of Antwerp / Antwerp University Hospital, Edegem, Belgium
| | - Dirk Valkenborg
- Applied Bio & molecular Systems, VITO, Mol, Belgium ; Center for Proteomics, Antwerp, Belgium ; Interuniversity Institute for Biostatistics and Statistical Bioinformatics, Hasselt University, Hasselt, Belgium
| | - Evelyne Maes
- Applied Bio & molecular Systems, VITO, Mol, Belgium ; Center for Proteomics, Antwerp, Belgium ; KU Leuven, Functional Genomics and Proteomics lab, Leuven, Belgium
| | - Filip Lemière
- Department of Chemistry, University of Antwerp, Antwerp, Belgium
| | - Bart Goethals
- Department of Mathematics and Computer Science, University of Antwerp, Antwerp, Belgium
| | - Kris Laukens
- Department of Mathematics and Computer Science, University of Antwerp, Antwerp, Belgium ; Biomedical Informatics Research Center Antwerp (biomina), University of Antwerp / Antwerp University Hospital, Edegem, Belgium
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Reumer A, Maes E, Mertens I, Cho WCS, Landuyt B, Valkenborg D, Schoofs L, Baggerman G. Colorectal cancer biomarker discovery and validation using LC-MS/MS-based proteomics in blood: truth or dare? Expert Rev Proteomics 2014; 11:449-463. [PMID: 24702250 DOI: 10.1586/14789450.2014.905743] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
Globally, colorectal cancer (CRC) is the third most common malignant neoplasm. However, highly sensitive, specific, noninvasive tests that allow CRC diagnosis at an early stage are still needed. As circulatory blood reflects the physiological status of an individual and/or the disease status for several disorders, efforts have been undertaken to identify candidate diagnostic CRC markers in plasma and serum. In this review, the challenges, bottlenecks and promising properties of mass spectrometry (MS)-based proteomics in blood are discussed. More specifically, important aspects in clinical design, sample retrieval, sample preparation, and MS analysis are presented. The recent developments in targeted MS approaches in plasma or serum are highlighted as well.
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Affiliation(s)
- Ank Reumer
- KU Leuven, Animal Physiology and Neurobiology Section, Naamsestraat 59, BE-3000 Leuven, Belgium
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Maes E, Valkenborg D, Mertens I, Broeckx V, Baggerman G, Sagaert X, Landuyt B, Prenen H, Schoofs L. Proteomic analysis of formalin-fixed paraffin-embedded colorectal cancer tissue using tandem mass tag protein labeling. Mol Biosyst 2014; 9:2686-95. [PMID: 23986405 DOI: 10.1039/c3mb70177h] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
In clinical research, repositories of biological samples form a rich source of clinical material for biomarker studies. Banked material, however, is often not stored in optimal conditions regarding the technology used for biomarker research. A case in point is formalin-fixed paraffin-embedded (FFPE) tissue that could be used to obtain large cohorts of samples over a short period of time, as these tissues are routinely prepared for pathological analysis. However, in the context of mass spectrometry based peptide-centric proteomics, protein extraction and identification can be hampered by formalin-induced crosslinking. Furthermore, the molecular formalin crosslinks might be entangled differently across various samples, making it more difficult to reproducibly extract the same proteins from different samples. In this study, we establish the crosslink variability using Tandem Mass Tag (TMT) protein labeling followed by digestion, separation, identification and quantification of proteins extracted from FFPE colorectal cancer and paired healthy tissues. Moreover, by applying de novo interpretation of tandem mass spectra and subsequent analysis by Peaks PTM, unspecified modifications could be elucidated, leading to increased protein and proteome coverage. This approach might be useful for future FFPE proteomics studies.
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Affiliation(s)
- Evelyne Maes
- Flemish Institute for Technological Research (VITO), Mol, Belgium
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Roness H, Kalich-Philosoph L, Carmely A, Fishel-Bartal M, Ligumsky H, Paglin S, Wolf I, Kanety H, Sredni B, Meirow D, Stoop D, Maes E, Polyzos NP, Verheyen G, Tournaye H, Nekkebroeck J, Parmegiani L, Cognigni GE, Bernardi S, Troilo E, Arnone A, Maccarini AM, Lanzilotti S, Rastellini A, Filicori M, Di Emidio G, Vitti M, Tatone C, Abir R, Lerer-Serfaty G, Samara N, Ben-Haroush A, Shachar M, Kossover O, Fisch B, Winkler K, Nederegger V, Ayuandari S, Salama M, Rosenfellner D, Murach KF, Zervomanolakis I, Hofer S, Wildt L, Ziehr SC, Stein A, Hadar S, Kaisler E, Fisch B, Pinkas H. Session 30: Fertility preservation for medical and non-medical indications. Hum Reprod 2013. [DOI: 10.1093/humrep/det163] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Lashkarashvili M, Galdavadze K, Tevzadze L, Geleishvili M, Rush T, Maes E. Salmonella hindmarsh outbreak in Sachkhere, Georgia, 2011. Int J Infect Dis 2012. [DOI: 10.1016/j.ijid.2012.05.426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022] Open
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Nikolaishvili M, Tushishvili T, Sidamonidze K, Geleishvili M, Maes E, Rush T. Rabies in Georgia, 2011 (Georgia, Gardabani region, Village of Nazarlo) August 2011 – December 14. Int J Infect Dis 2012. [DOI: 10.1016/j.ijid.2012.05.658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022] Open
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Rivière C, Goossens L, Guerardel Y, Maes E, Garénaux E, Pommery J, Pommery N, Désiré O, Lemoine A, Telliez A, Delelis A, Hénichart J. Chemotaxonomic interest of iridoids isolated from a Malagasy species: Perichlaena richardii. BIOCHEM SYST ECOL 2011. [DOI: 10.1016/j.bse.2011.07.016] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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Haenen S, Vanoirbeek JAJ, De Vooght V, Maes E, Schoofs L, Nemery B, Hoet PHM, Clynen E. Proteome analysis of multiple compartments in a mouse model of chemical-induced asthma. J Proteome Res 2010; 9:5868-76. [PMID: 20860378 DOI: 10.1021/pr100638m] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Occupational asthma is the principal cause of work-related respiratory disease in the industrial world. Toluene-2,4-diisocyanate (TDI) is one of the most common respiratory sensitizers leading to occupational asthma. Using a mouse model of chemical-induced asthma, we explored proteome changes in multiple compartments of mice sensitized and challenged with TDI or acetone-olive oil (AOO; vehicle). Airway reactivity to methacholine and a bronchoalveolar lavage (BAL) cell count was assessed in treated and control mice, 1 day after challenge. Subsequently, two-dimensional differential gel electrophoresis (2D-DIGE) was performed on auricular lymph nodes, BAL, and serum comparing TDI-treated and vehicle-treated control mice. The differentially expressed proteins were identified by mass spectrometry and pathway analysis was performed. TDI-treated mice exhibit increased airway reactivity (2.6-fold increase) and a neutrophilic inflammation in the BAL fluid, compared to control mice. 2D-DIGE showed 53, 210, and 40 differentially expressed proteins in the auricular lymph nodes, BAL, and serum of TDI-treated versus vehicle-treated mice, respectively. Several of the identified proteins could be linked with inflammation, neutrophil chemotaxis, and/or oxidative stress. Physiologic and immunologic readouts of the asthmatic phenotype, such as inflammation, were confirmed in three compartments by several of the differentially expressed proteins via 2D-DIGE and computerized pathway analysis.
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Affiliation(s)
- Steven Haenen
- Katholieke Universiteit Leuven, Research Unit Lung Toxicology, 3000 Leuven, Belgium
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Mebonia N, Eloshvili M, Malakmadze N, Chlikadze R, Maes E. Unexpected non-seasonal increase of bacterial meningitis cases in Georgia in 2009. Georgian Med News 2010:44-50. [PMID: 20834075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
In summer of 2009, During the period of 20-June - 31-August in total 32 patients with the clinical diagnosis of bacterial meningitis were hospitalized in two hospitals of Tbilisi (Center for Infectious Pathologies and Iashvili Child Clinic). Within a week's time (13 July-19 July) 9 persons with suspected cases of bacterial meningitis were hospitalized in both clinic. Our attention was attracted by the increased number of hospitalized patients within non-seasonal period. Goal of investigation was to establish the extent of the outbreak, to detect possible exposures, and to establish recommendations for prevention activities of disease. For laboratory confirmation cerebral spinal fluid biochemical and bacteriological (culturing) testing was used, but no single causative agent was isolated. To detect risk factors patients' were interviewed. 78.5% (25) of the hospitalized persons were under 14 years of age, and among them--70% (22) preschool children. The most common exposure identified through the interviews with patients included active or passive exposure to tobacco smoking (38%), an existence of the recent upper respiratory infection (31%), and attending crowded places (23%). Since causative agents were not isolated, we were not able to establish whether the increasing number of disease was caused from different etiologic pathogens or from single agent. We were not able to establish the presence of an outbreak since no single causative agent was isolated. Previous use of antibiotics remains the only likely reason for low detection of the pathogen. Detected risk-factors for distribution of disease were smoking, existence of the recent upper respiratory infection, and attending crowded places. In order to control increasing number of bacterial meningitis, improving basic laboratory diagnosis by implementing advanced methods that are not affected by the prior use of antibiotics, such as serological testing might be crucial, as well as increasing awareness of population about risk factors of bacterial meningitis and importance of early seeking medical care.
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Kozukeev TB, Ajeilat S, Maes E, Favorov M. Risk factors for brucellosis--Leylek and Kadamjay districts, Batken Oblast, Kyrgyzstan, January-November, 2003. MMWR Suppl 2006; 55:31-4. [PMID: 16645580] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/08/2023] Open
Abstract
INTRODUCTION Brucellosis is a zoonotic disease that is associated with chronic serious sequelae in humans. During 1997-2002, the reported incidence of human brucellosis in Kyrgyzstan increased nearly twofold, from 20 to 36 per 100,000 population. In 2002, the highest incidence of brucellosis was reported in two rural districts of Batkan Oblast: Leylek (106 per 100,000 population) and Kadamjay (80 per 100,000 population). During January-November 2003, trainees from the Applied Epidemiology Training program in Central Asia conducted a matched, hospital-based, case-control study to identify risk factors for brucellosis and describe the epidemiology of disease in these two districts. METHODS Brucellosis cases were defined on the basis of epidemiologic, clinical, and laboratory criteria. During January-November 2003, a total of 100 persons with confirmed brucellosis were identified in the infectious disease wards of the two district hospitals; these persons were matched by age and date of admission to 100 controls who were admitted to other hospital wards for unrelated conditions. Data on socioeconomic and occupational factors and history of exposure to animals and animal products were collected by using a structured questionnaire. Conditional logistic regression was used to study the association between exposure variables and brucellosis. RESULTS Among the 100 persons with confirmed brucellosis during the study period, 86 (86%) owned farm animals, and 45 (45%) became ill during April-May, the birthing season for farm animals. Multivariate analysis indicated that brucellosis was associated with exposure to aborted farm animals in the household (odds ratio [OR] = 29.8; 95% confidence interval [CI] = 4.4-203.4) and consumption of home-made milk products obtained from bazaars or neighbors (OR = 11.4; CI = 1.6-83.9). Knowledge of the mode of brucellosis transmission appeared to be protective against disease transmission (OR = 0.2; CI = 0.03-0.8). DISCUSSION Exposure to aborted home-owned animals and consumption of home-made milk products obtained from bazaars or neighbors were identified as probable sources of human brucellosis infections in the study districts. This finding suggests that brucellosis spreads among farm animals in the area and that home-made milk products are not adequately pasteurized. CONCLUSION To reduce the burden of brucellosis in Batken Oblast, veterinary services should be improved, and health education programs should be increased. Implementing these measures should minimize exposure to farm animals and reduce the risk for infection from locally produced milk products.
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Affiliation(s)
- Turatbek B Kozukeev
- Applied Epidemiology Training Program, Central Asia Regional Program, CDC, USA
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Capon C, Maes E, Michalski JC, Leffler H, Kim YS. Sd(a)-antigen-like structures carried on core 3 are prominent features of glycans from the mucin of normal human descending colon. Biochem J 2001; 358:657-64. [PMID: 11577689 PMCID: PMC1222115 DOI: 10.1042/bj3580657] [Citation(s) in RCA: 61] [Impact Index Per Article: 2.7] [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] [Indexed: 11/17/2022]
Abstract
This paper describes structural characterization by NMR, MS and degradative studies of mucin glycans from normal human descending colon obtained freshly at autopsy. The saccharides were mainly based on core 3 (GlcNAcbeta1-3GalNAc). Among the terminal saccharide determinants Sd(a)/Cad-antigen-like structures were prominent, and Lewis x, sialyl Lewis x and sulphated Lewis x were found as minor components, whereas blood group H and A antigenic determinants were absent. The saccharides were markedly different from those of mucins from colon cancers or colon cancer cell lines analysed so far, in which cores 1 and 2 are prominent features, and in which various other terminal determinants have been found, but not Sd(a)/Cad.
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Affiliation(s)
- C Capon
- Laboratoire de Glycobiologie structurale et fonctionnelle, Unité Mixte du Centre National de la Recherche Scientifique, Université des Sciences et Technologies de Lille, Villeneuve d'Ascq Cedex, France
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Guérardel Y, Balanzino L, Maes E, Leroy Y, Coddeville B, Oriol R, Strecker G. The nematode Caenorhabditis elegans synthesizes unusual O-linked glycans: identification of glucose-substituted mucin-type O-glycans and short chondroitin-like oligosaccharides. Biochem J 2001; 357:167-82. [PMID: 11415447 PMCID: PMC1221939 DOI: 10.1042/0264-6021:3570167] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The free-living nematode Caenorhabditis elegans is a relevant model for studies on the role of glycoconjugates during development of multicellular organisms. Several genes coding for glycosyltransferases involved in the synthesis of N- and O-linked glycans have already been isolated, but, apart from repetitive dimers of glycosaminoglycans, no detailed structure of either type of component has been published so far. This study aimed to establish the structures of the major O-glycans synthesized by C. elegans to give an insight into the endogenous glycosyltransferase activities expressed in this organism. By the use of NMR and MS, we have resolved the sequence of seven of these components that present very unusual features. Most of them were characterized by the type-1 core substituted on Gal and/or GalNAc by (beta1-4)Glc and (beta1-6)Glc residues. Another compound exhibited the GalNAc(beta1-4)N-acetylglucosaminitol sequence in the terminal position, to which was attached a tetramer of beta-Gal substituted by both Fuc and 2-O-methyl-fucose residues. Our experimental procedure led also to the isolation of glycosaminoglycan-like components and oligomannosyl-type N-glycans. In particular, the data confirmed that C. elegans synthesizes the ubiquitous linker sequence GlcA(beta1-3)Gal(beta1-3)Gal(beta1-4)Xyl.
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Affiliation(s)
- Y Guérardel
- Laboratoire de Chimie Biologique et Unité Mixte de Recherche du CNRS 8576, Université des Sciences et Technologies de Lille, F-59655 Villeneuve d'Ascq, France.
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Cebo C, Dambrouck T, Maes E, Laden C, Strecker G, Michalski JC, Zanetta JP. Recombinant human interleukins IL-1alpha, IL-1beta, IL-4, IL-6, and IL-7 show different and specific calcium-independent carbohydrate-binding properties. J Biol Chem 2001; 276:5685-91. [PMID: 11050099 DOI: 10.1074/jbc.m008662200] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
A method was developed for the determination of putative lectin activities of cytokines. It involved the immunoblotting measurement of the quantity of these cytokines unbound to a series of different immobilized glycoconjugates and displacement of the bound cytokines with oligosaccharides of known structures. This method allows demonstrating that the following interleukins specifically recognize different oligosaccharide structures in a calcium-independent mechanism: interleukin-1alpha binds to the biantennary disialylated N-glycan completed with two Neu5Acalpha2-3 residues; interleukin-1beta to a GM4 sialylated glycolipid Neu5Acalpha2-3Galbeta1-Cer having very long and unusual long-chain bases; interleukin-4 to the 1,7 intramolecular lactone of N-acetyl-neuraminic acid; interleukin-6 to compounds having N-linked and O-linked HNK-1-like epitopes; and interleukin-7 to the sialyl-Tn antigen. Because the glycan ligands are rare structures in human circulating cells, it is suggested that such activities could be essential for providing specific signaling systems to cells having both the receptors and the oligosaccharide ligands of the interleukin at their cell surface.
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Affiliation(s)
- C Cebo
- Laboratoire de Chimie Biologique Université des Sciences et Technologies de Lille, CNRS Unité Mixte de Recherche 8576 Glycobiologie Structurale et Fonctionnelle, 59655 Villeneuve d'Ascq cedex, France
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Guerardel Y, Kol O, Maes E, Lefebvre T, Boilly B, Davril M, Strecker G. O-glycan variability of egg-jelly mucins from Xenopus laevis: characterization of four phenotypes that differ by the terminal glycosylation of their mucins. Biochem J 2000; 352 Pt 2:449-63. [PMID: 11085939 PMCID: PMC1221477] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/18/2023]
Abstract
Eggs from Xenopus laevis are surrounded by several layers of jelly that are needed for proper fertilization. Jelly coat is composed of high-molecular-mass glycoconjugates to which are bound many globular proteins. O-glycans released from the jelly coat of X. laevis have been partially described in previous studies. In this study, we compared the glycosylation pattern of the egg jelly coat isolated from six specimens of X. laevis. The O-glycans were released from jelly coats by alkali/borohydride treatment. Structural characterization was performed through a combination of one- and two-dimensional (1)H-NMR and methylation analysis. This allowed the description of a new family of sulphated O-glycans present in jelly coats of all X. laevis. However, the jelly O-glycans showed a low extent of polymorphism between specimens. This intra-specific variability was restricted to the terminal substitution of O-linked oligosaccharides. The differential expression of two glycosyltransferase [an alpha-(1-->4) galactosyltransferase and an alpha-(1-->3) fucosyltransferase] activities resulted in the characterization of four phenotypes of X. laevis. Furthermore, electrophoretic analysis suggested that the high-molecular-mass fraction of jelly coat was mostly composed of mucin-type glycoproteins. Blot analysis with lectins confirmed that the glycan variability was borne by these mucin-type components. However, fertilization assays suggested that the glycan polymorphism had no repercussion on egg fertilizability.
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Affiliation(s)
- Y Guerardel
- Laboratoire de Chimie Biologique et Unité Mixte de Recherche du CNRS 8576, Université des Sciences et Technologies de Lille, F-59655 Villeneuve d'Ascq, France
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