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Bertok T, Pinkeova A, Lorencova L, Datkova A, Hires M, Jane E, Tkac J. Glycoproteomics of Gastrointestinal Cancers and Its Use in Clinical Diagnostics. J Proteome Res 2025. [PMID: 40368336 DOI: 10.1021/acs.jproteome.5c00095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2025]
Abstract
Cancer is a leading cause of death worldwide, resulting in substantial economic costs. Because cancer is a complex, heterogeneous group of diseases affecting a variety of cells, its detection may sometimes be difficult. Herein we review a large group of the gastrointestinal cancers (oral, esophageal, stomach, pancreatic, liver, and bowel cancers) and the possibility of using glycans conjugated to protein backbones for less-invasive diagnoses than the commonly used endoscopic approaches. The reality of bacterial N-glycosylation and the effect of epithelial mucosa on gut microbiota are discussed. Current advantages, barriers, and advantages in the prospective use of selected glycomic approaches in clinical practice are also detailed.
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Affiliation(s)
- Tomas Bertok
- Institute of Chemistry, Slovak Academy of Sciences, Dubravska cesta 9, 845 38 Bratislava, Slovak Republic
| | - Andrea Pinkeova
- Institute of Chemistry, Slovak Academy of Sciences, Dubravska cesta 9, 845 38 Bratislava, Slovak Republic
- Glycanostics, Kudlakova 7, 841 01 Bratislava, Slovak Republic
| | - Lenka Lorencova
- Institute of Chemistry, Slovak Academy of Sciences, Dubravska cesta 9, 845 38 Bratislava, Slovak Republic
| | - Anna Datkova
- Institute of Chemistry, Slovak Academy of Sciences, Dubravska cesta 9, 845 38 Bratislava, Slovak Republic
| | - Michal Hires
- Institute of Chemistry, Slovak Academy of Sciences, Dubravska cesta 9, 845 38 Bratislava, Slovak Republic
| | - Eduard Jane
- Institute of Chemistry, Slovak Academy of Sciences, Dubravska cesta 9, 845 38 Bratislava, Slovak Republic
- Glycanostics, Kudlakova 7, 841 01 Bratislava, Slovak Republic
| | - Jan Tkac
- Institute of Chemistry, Slovak Academy of Sciences, Dubravska cesta 9, 845 38 Bratislava, Slovak Republic
- Glycanostics, Kudlakova 7, 841 01 Bratislava, Slovak Republic
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Peduzzi G, Archibugi L, Farinella R, de Leon Pisani RP, Vodickova L, Vodicka P, Kraja B, Sainz J, Bars-Cortina D, Daniel N, Silvestri R, Uysal-Onganer P, Landi S, Dulińska-Litewka J, Comandatore A, Campa D, Hughes DJ, Rizzato C. The exposome and pancreatic cancer, lifestyle and environmental risk factors for PDAC. Semin Cancer Biol 2025; 113:100-129. [PMID: 40368260 DOI: 10.1016/j.semcancer.2025.05.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2025] [Revised: 04/08/2025] [Accepted: 05/04/2025] [Indexed: 05/16/2025]
Abstract
Pancreatic cancer (PC), particularly pancreatic ductal adenocarcinoma (PDAC), is a significant global health issue with high mortality rates. PDAC, though only 3 % of cancer diagnoses, causes 7 % of cancer deaths due to its severity and asymptomatic early stages. Risk factors include lifestyle choices, environmental exposures, and genetic predispositions. Conditions like new-onset type 2 diabetes and chronic pancreatitis also contribute significantly. Modifiable risk factors include smoking, alcohol consumption, non-alcoholic fatty pancreatic disease (NAFPD), and obesity. Smoking and heavy alcohol consumption increase PC risk, while NAFPD and obesity, particularly central adiposity, contribute through chronic inflammation and insulin resistance. Refined sugar and sugar-sweetened beverages (SSBs) are also linked to increased PC risk, especially among younger individuals. Hormonal treatments and medications like statins, aspirin, and metformin have mixed results on PC risk, with some showing protective effects. The gut microbiome influences PC through the gut-pancreas axis, with disruptions leading to inflammation and carcinogenesis. Exposure to toxic substances, including heavy metals and chemicals, is associated with increased PC risk. Glycome changes, such as abnormal glycosylation patterns, are significant in PDAC development and offer potential for early diagnosis. Interactions between environmental and genetic factors are crucial in PDAC susceptibility. Genome-wide association studies (GWAS) have identified several single nucleotide polymorphisms (SNPs) linked to PDAC, but gene-environment interactions remain largely unexplored. Future research should focus on polygenic risk scores (PRS) and large-scale studies to better understand these interactions and their impact on PDAC risk.
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Affiliation(s)
| | - Livia Archibugi
- Pancreato-Biliary Endoscopy and Endosonography Division, Pancreas Translational and Clinical Research Center, IRCCS Ospedale San Raffaele, Milan, Italy
| | | | - Ruggero Ponz de Leon Pisani
- Pancreato-Biliary Endoscopy and Endosonography Division, Pancreas Translational and Clinical Research Center, IRCCS Ospedale San Raffaele, Milan, Italy
| | - Ludmila Vodickova
- Biomedical Center Martin, Bioinformatic Center, Comenius University in Bratislava, Jessenius Faculty of Medicine in Martin, Slovakia; Faculty of Medicine and Biomedical Center in Pilsen, Charles University, Pilsen, Czech Republic
| | - Pavel Vodicka
- Biomedical Center Martin, Bioinformatic Center, Comenius University in Bratislava, Jessenius Faculty of Medicine in Martin, Slovakia; Faculty of Medicine and Biomedical Center in Pilsen, Charles University, Pilsen, Czech Republic
| | - Bledar Kraja
- University Clinic of Gastrohepatology, University Hospital Center Mother Teresa, Tirana, Albania
| | - Juan Sainz
- Department of Biochemistry and Molecular Biology, University of Granada, Granada, Spain; Centro de Investigación Biomédica en Red de Epidemiología y Salud Pública (CIBERESP), Madrid 28029, Spain; GENYO. Centre for Genomics and Oncological Research. Genomic Oncology department, Granada, Spain; Instituto de Investigación Biosanitaria Ibs.Granada, Granada, Spain
| | - David Bars-Cortina
- Institut Català d'Oncologia (ICO) IDIBELL, Unit of Biomarkers and Susceptibility (UBS), Oncology Data Analytics Program (ODAP), Catalan Institute of Oncology (ICO), L'Hospitalet del Llobregat, Barcelona, Spain; Institut Català d'Oncologia (ICO) IDIBELL, ONCOBELL Program, Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain
| | - Neil Daniel
- Molecular Epidemiology of Cancer Group, UCD Conway Institute, School of Biomolecular and Biomedical Science, University College Dublin, Dublin, Ireland
| | | | - Pinar Uysal-Onganer
- Cancer Mechanisms and Biomarkers Research Group, School of Life Sciences, University of Westminster, London, UK
| | - Stefano Landi
- Department of Biology, University of Pisa, Pisa, Italy
| | | | - Annalisa Comandatore
- General Surgery Unit, Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Italy
| | - Daniele Campa
- Department of Biology, University of Pisa, Pisa, Italy
| | - David J Hughes
- Molecular Epidemiology of Cancer Group, UCD Conway Institute, School of Biomolecular and Biomedical Science, University College Dublin, Dublin, Ireland
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Harvey DJ. Analysis of carbohydrates and glycoconjugates by matrix-assisted laser desorption/ionization mass spectrometry: An update for 2021-2022. MASS SPECTROMETRY REVIEWS 2025; 44:213-453. [PMID: 38925550 PMCID: PMC11976392 DOI: 10.1002/mas.21873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 02/05/2024] [Accepted: 02/12/2024] [Indexed: 06/28/2024]
Abstract
The use of matrix-assisted laser desorption/ionization (MALDI) mass spectrometry for the analysis of carbohydrates and glycoconjugates is a well-established technique and this review is the 12th update of the original article published in 1999 and brings coverage of the literature to the end of 2022. As with previous review, this review also includes a few papers that describe methods appropriate to analysis by MALDI, such as sample preparation, even though the ionization method is not MALDI. The review follows the same format as previous reviews. It is divided into three sections: (1) general aspects such as theory of the MALDI process, matrices, derivatization, MALDI imaging, fragmentation, quantification and the use of computer software for structural identification. (2) Applications to various structural types such as oligo- and polysaccharides, glycoproteins, glycolipids, glycosides and biopharmaceuticals, and (3) other general areas such as medicine, industrial processes, natural products and glycan synthesis where MALDI is extensively used. Much of the material relating to applications is presented in tabular form. MALDI is still an ideal technique for carbohydrate analysis, particularly in its ability to produce single ions from each analyte and advancements in the technique and range of applications show little sign of diminishing.
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Klatte DCF, Meziani J, Cahen DL, van Diepen M, Bruno MJ, van Leerdam ME. Pancreatic cancer surveillance: Risk stratification of individuals with a germline CDKN2A pathogenic variant. United European Gastroenterol J 2024; 12:1399-1403. [PMID: 39508364 PMCID: PMC11652335 DOI: 10.1002/ueg2.12662] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/15/2024] [Accepted: 08/19/2024] [Indexed: 11/15/2024] Open
Abstract
BACKGROUND Individuals carrying a germline CDKN2A pathogenic variant (PV) are at a high risk of developing pancreatic ductal adenocarcinoma. Risk stratification could allow tailored surveillance. OBJECTIVE To develop a Fine-Gray prediction model for the risk of PDAC in carriers of a CDKN2A PV. METHODS Data from two large Dutch pancreatic cancer surveillance programs were used. A limited set of predictor variables were selected bsased on previous literature and the clinical expertise of the study group. RESULTS A total of 506 CDKN2A PV carriers were included, among whom we showed a substantial lifetime risk of PDAC (23%). The model identifies having a first-degree relative with PDAC (B = 0.7256) and a history of smoking (B = 0.4776) as significant risk factors. However, the model shows limited discrimination (c-statistic 0.64) and calibration. CONCLUSION Our study highlights the high lifetime risk of PDAC in carriers of a CDKN2A PV. While identifying significant risk factors such as family history of PDAC and smoking, our prediction model shows limited precision, highlighting the need for additional factors such as biomarkers to improve its clinical utility for tailored surveillance of high-risk individuals.
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Affiliation(s)
- Derk C. F. Klatte
- Department of Gastroenterology and HepatologyLeiden University Medical CenterLeidenThe Netherlands
| | - Jihane Meziani
- Department of Gastroenterology and HepatologyErasmus Medical CenterRotterdamThe Netherlands
| | - Djuna L. Cahen
- Department of Gastroenterology and HepatologyErasmus Medical CenterRotterdamThe Netherlands
| | - Merel van Diepen
- Department of Clinical EpidemiologyLeiden University Medical CenterLeidenThe Netherlands
| | - Marco J. Bruno
- Department of Gastroenterology and HepatologyErasmus Medical CenterRotterdamThe Netherlands
| | - Monique E. van Leerdam
- Department of Gastroenterology and HepatologyLeiden University Medical CenterLeidenThe Netherlands
- Department of Gastrointestinal OncologyNetherlands Cancer InstituteAmsterdamThe Netherlands
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Maurer E, Lehman B, Matthäi E, Denzer U, Figiel J, Jesinghaus M, Slater EP, Stefenelli U, Gress TM, Bartsch DK. Pancreatic cancer screening is effective in individuals at risk with predisposing germline gene variants, but not in gene variant-negative familial pancreatic cancer families. United European Gastroenterol J 2024; 12:1211-1221. [PMID: 39031472 PMCID: PMC11578844 DOI: 10.1002/ueg2.12631] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/17/2024] [Accepted: 06/20/2024] [Indexed: 07/22/2024] Open
Abstract
OBJECTIVE To evaluate the diagnostic yield of pancreatic cancer screening in individuals at risk (IAR) from familial pancreatic cancer (FPC) families with respect to the presence or absence of pathogenic germline variants predisposing to pancreatic adenocarcinoma (PDAC). DESIGN In a 20 years period, IAR from FPC families were enrolled in a prospective screening program of the national case collection for FPC of Germany, including magnet resonance imaging (MRI) and endoscopic ultrasound (EUS). The diagnostic yield was analyzed regarding significant pancreatic lesions such as PDAC, high-grade pancreatic-intraepithelial-neoplasia (PanIN3) and intraductal-papillary-mucinous-neoplasia (IPMN) with high-grade dysplasia. Screening results were compared between carriers of pathogenic variants and variant-negative IAR. RESULTS 337 IAR, including 74 (22%) variant-carriers and 263 IAR of variant-negative FPC families (mean age 49; standard deviation [SD] + 8.9) were followed 64 (SD + 55) months. IAR underwent 5.1 (SD + 3.9) screening visits with 1733 MRI (5.1,SD + 3.9 per IAR) and 728 EUS (2.2,SD + 1.7 per IAR). In 12 (4%) cases, significant pancreatic lesions were detected, including 4 PDAC, 3 PanIN3 and 5 high-grade IPMN. Three of 4 IAR with PDAC died after a mean of 27 months postoperatively, and one IAR is alive without evidence of disease after 31 months. The diagnostic yield for significant lesions was 13.5% (10/74) for variant carriers compared to 0.8% (2/263) for IAR of variant-negative FPC families (p < 0.001). Logistic regression analysis revealed that a negative variant status was almost always accompanied by the absence of a significant lesion over time with a negative predictive value of 99.2% (95% CI 97.3%-99.9%). CONCLUSION The diagnostic yield seems to justify PDAC screening in IAR of FPC-families with pathogenic germline variants in PDAC predisposing genes, not in IAR of variant-negative families.
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Affiliation(s)
- Elisabeth Maurer
- Department of Visceral‐Thoracic‐ and Vascular SurgeryPhilipps University MarburgMarburgGermany
| | - Bettina Lehman
- Department of Visceral‐Thoracic‐ and Vascular SurgeryPhilipps University MarburgMarburgGermany
| | - Elvira Matthäi
- Department of Visceral‐Thoracic‐ and Vascular SurgeryPhilipps University MarburgMarburgGermany
| | - Ulrike Denzer
- Department of GastroenterologyEndocrinologyMetabolism and InfectiologyPhilipps University MarburgMarburgGermany
| | - Jens Figiel
- Department of Diagnostic and Interventional RadiologyPhilipps University MarburgMarburgGermany
| | | | - Emily P. Slater
- Department of Visceral‐Thoracic‐ and Vascular SurgeryPhilipps University MarburgMarburgGermany
| | | | - Thomas M. Gress
- Department of GastroenterologyEndocrinologyMetabolism and InfectiologyPhilipps University MarburgMarburgGermany
| | - Detlef K. Bartsch
- Department of Visceral‐Thoracic‐ and Vascular SurgeryPhilipps University MarburgMarburgGermany
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Bogdanski AM, van Hooft JE, Boekestijn B, Bonsing BA, Wasser MNJM, Klatte DCF, van Leerdam ME. Aspects and outcomes of surveillance for individuals at high-risk of pancreatic cancer. Fam Cancer 2024; 23:323-339. [PMID: 38619782 PMCID: PMC11255004 DOI: 10.1007/s10689-024-00368-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Accepted: 02/24/2024] [Indexed: 04/16/2024]
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is a leading cause of cancer-related deaths and is associated with a poor prognosis. The majority of these cancers are detected at a late stage, contributing to the bad prognosis. This underscores the need for novel, enhanced early detection strategies to improve the outcomes. While population-based screening is not recommended due to the relatively low incidence of PDAC, surveillance is recommended for individuals at high risk for PDAC due to their increased incidence of the disease. However, the outcomes of pancreatic cancer surveillance in high-risk individuals are not sorted out yet. In this review, we will address the identification of individuals at high risk for PDAC, discuss the objectives and targets of surveillance, outline how surveillance programs are organized, summarize the outcomes of high-risk individuals undergoing pancreatic cancer surveillance, and conclude with a future perspective on pancreatic cancer surveillance and novel developments.
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Affiliation(s)
- Aleksander M Bogdanski
- Department of Gastroenterology and Hepatology, Leiden University Medical Center, Albinusdreef 2, 2333 ZA, Leiden, The Netherlands.
| | - Jeanin E van Hooft
- Department of Gastroenterology and Hepatology, Leiden University Medical Center, Albinusdreef 2, 2333 ZA, Leiden, The Netherlands
| | - Bas Boekestijn
- Department of Radiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Bert A Bonsing
- Department of Surgery, Leiden University Medical Center, Leiden, The Netherlands
| | - Martin N J M Wasser
- Department of Radiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Derk C F Klatte
- Department of Gastroenterology and Hepatology, Leiden University Medical Center, Albinusdreef 2, 2333 ZA, Leiden, The Netherlands
| | - Monique E van Leerdam
- Department of Gastroenterology and Hepatology, Leiden University Medical Center, Albinusdreef 2, 2333 ZA, Leiden, The Netherlands
- Department of Gastrointestinal Oncology, Netherlands Cancer Institute, Amsterdam, The Netherlands
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Pongracz T, Mayboroda OA, Wuhrer M. The Human Blood N-Glycome: Unraveling Disease Glycosylation Patterns. JACS AU 2024; 4:1696-1708. [PMID: 38818049 PMCID: PMC11134357 DOI: 10.1021/jacsau.4c00043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Revised: 03/28/2024] [Accepted: 04/01/2024] [Indexed: 06/01/2024]
Abstract
Most of the proteins in the circulation are N-glycosylated, shaping together the total blood N-glycome (TBNG). Glycosylation is known to affect protein function, stability, and clearance. The TBNG is influenced by genetic, environmental, and metabolic factors, in part epigenetically imprinted, and responds to a variety of bioactive signals including cytokines and hormones. Accordingly, physiological and pathological events are reflected in distinct TBNG signatures. Here, we assess the specificity of the emerging disease-associated TBNG signatures with respect to a number of key glycosylation motifs including antennarity, linkage-specific sialylation, fucosylation, as well as expression of complex, hybrid-type and oligomannosidic N-glycans, and show perplexing complexity of the glycomic dimension of the studied diseases. Perspectives are given regarding the protein- and site-specific analysis of N-glycosylation, and the dissection of underlying regulatory layers and functional roles of blood protein N-glycosylation.
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Affiliation(s)
- Tamas Pongracz
- Center for Proteomics and Metabolomics, Leiden University Medical Center, 2333ZA Leiden, The Netherlands
| | - Oleg A. Mayboroda
- Center for Proteomics and Metabolomics, Leiden University Medical Center, 2333ZA Leiden, The Netherlands
| | - Manfred Wuhrer
- Center for Proteomics and Metabolomics, Leiden University Medical Center, 2333ZA Leiden, The Netherlands
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van der Burgt Y, Wuhrer M. The role of clinical glyco(proteo)mics in precision medicine. Mol Cell Proteomics 2023:100565. [PMID: 37169080 DOI: 10.1016/j.mcpro.2023.100565] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 04/12/2023] [Accepted: 05/02/2023] [Indexed: 05/13/2023] Open
Abstract
Glycoproteomics reveals site-specific O- and N-glycosylation that may influence protein properties including binding, activity and half-life. The increasingly mature toolbox with glycomic- and glycoproteomic strategies is applied for the development of biopharmaceuticals and discovery and clinical evaluation of glycobiomarkers in various disease fields. Notwithstanding the contributions of glycoscience in identifying new drug targets, the current report is focused on the biomarker modality that is of interest for diagnostic and monitoring purposes. To this end it is noted that the identification of biomarkers has received more attention than corresponding quantification. Most analytical methods are very efficient in detecting large numbers of analytes but developments to accurately quantify these have so far been limited. In this perspective a parallel is made with earlier proposed tiers for protein quantification using mass spectrometry. Moreover, the foreseen reporting of multimarker readouts is discussed to describe an individual's health or disease state and their role in clinical decision-making. The potential of longitudinal sampling and monitoring of glycomic features for diagnosis and treatment monitoring is emphasized. Finally, different strategies that address quantification of a multimarker panel will be discussed.
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Affiliation(s)
- Yuri van der Burgt
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands.
| | - Manfred Wuhrer
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
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