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Kumarasamy G, Mohd Salim NH, Mohd Afandi NS, Hazlami Habib MA, Mat Amin ND, Ismail MN, Musa M. Glycoproteomics-based liquid biopsy: translational outlook for colorectal cancer clinical management in Southeast Asia. Future Oncol 2023; 19:2313-2332. [PMID: 37937446 DOI: 10.2217/fon-2023-0704] [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] [Indexed: 11/09/2023] Open
Abstract
Colorectal cancer (CRC) signifies a significant healthcare challenge in Southeast Asia. Despite advancements in screening approaches and treatment modalities, significant medical gaps remain, ranging from prevention and early diagnosis to determining targeted therapy and establishing personalized approaches to managing CRC. There is a need to expand more validated biomarkers in clinical practice. An advanced technique incorporating high-throughput mass spectrometry as a liquid biopsy to unravel a repertoire of glycoproteins and glycans would potentially drive the development of clinical tools for CRC screening, diagnosis and monitoring, and it can be further adapted to the existing standard-of-care procedure. Therefore this review offers a perspective on glycoproteomics-driven liquid biopsy and its potential integration into the clinical care of CRC in the southeast Asia region.
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Affiliation(s)
- Gaayathri Kumarasamy
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, Pulau Pinang, 11800, Malaysia
| | - Nurul Hakimah Mohd Salim
- Department of Pathology, School of Medical Sciences, Universiti Sains Malaysia, Kubang Kerian, Kelantan, 16150, Malaysia
| | - Nur Syafiqah Mohd Afandi
- Analytical Biochemistry Research Centre, Universiti Sains Malaysia, Bayan Lepas, Pulau Pinang, 11900, Malaysia
| | - Mohd Afiq Hazlami Habib
- Analytical Biochemistry Research Centre, Universiti Sains Malaysia, Bayan Lepas, Pulau Pinang, 11900, Malaysia
| | - Nor Datiakma Mat Amin
- Analytical Biochemistry Research Centre, Universiti Sains Malaysia, Bayan Lepas, Pulau Pinang, 11900, Malaysia
- Nature Products Division, Forest Research Institute Malaysia, Kepong, Selangor, 52109, Malaysia
| | - Mohd Nazri Ismail
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, Pulau Pinang, 11800, Malaysia
- Analytical Biochemistry Research Centre, Universiti Sains Malaysia, Bayan Lepas, Pulau Pinang, 11900, Malaysia
| | - Marahaini Musa
- Human Genome Centre, School of Medical Sciences, Universiti Sains Malaysia, Kubang Kerian, Kelantan, 16150, Malaysia
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2
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Resnik N, Višnjar T, Smrkolj T, Kreft ME, Romih R, Zupančič D. Selective targeting of lectins and their macropinocytosis in urothelial tumours: translation from in vitro to ex vivo. Histochem Cell Biol 2023; 160:435-452. [PMID: 37535087 PMCID: PMC10624759 DOI: 10.1007/s00418-023-02224-2] [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] [Accepted: 07/11/2023] [Indexed: 08/04/2023]
Abstract
Urinary bladder cancer can be treated by intravesical application of therapeutic agents, but the specific targeting of cancer urothelial cells and the endocytotic pathways of the agents are not known. During carcinogenesis, the superficial urothelial cells exhibit changes in sugar residues on the apical plasma membranes. This can be exploited for selective targeting from the luminal side of the bladder. Here we show that the plant lectins Jacalin (from Artocarpus integrifolia), ACA (from Amaranthus caudatus) and DSA (from Datura stramonium) selectively bind to the apical plasma membrane of low- (RT4) and high-grade (T24) cancer urothelial cells in vitro and urothelial tumours ex vivo. The amount of lectin binding was significantly different between RT4 and T24 cells. Endocytosis of lectins was observed only in cancer urothelial cells and not in normal urothelial cells. Transmission electron microscopy analysis showed macropinosomes, endosome-like vesicles and multivesicular bodies filled with lectins in RT4 and T24 cells and also in cells of urothelial tumours ex vivo. Endocytosis of Jacalin and ACA in cancer cells was decreased in vitro after addition of inhibitor of macropinocytosis 5-(N-ethyl-N-isopropyl) amiloride (EIPA) and increased after stimulation of macropinocytosis with epidermal growth factor (EGF). Clathrin, caveolin and flotillin did not colocalise with lectins. These results confirm that the predominant mechanism of lectin endocytosis in cancer urothelial cells is macropinocytosis. Therefore, we propose that lectins in combination with conjugated therapeutic agents are promising tools for improved intravesical therapy by targeting cancer cells.
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Affiliation(s)
- Nataša Resnik
- Institute of Cell Biology, Faculty of Medicine, University of Ljubljana, Vrazov Trg 2, 1000, Ljubljana, Slovenia
| | - Tanja Višnjar
- Clinical Institute of Genomic Medicine, University Medical Centre Ljubljana, Ljubljana, Slovenia
| | - Tomaž Smrkolj
- Department of Urology, University Medical Centre Ljubljana, Ljubljana, Slovenia
- Department of Surgery, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Mateja Erdani Kreft
- Institute of Cell Biology, Faculty of Medicine, University of Ljubljana, Vrazov Trg 2, 1000, Ljubljana, Slovenia
| | - Rok Romih
- Institute of Cell Biology, Faculty of Medicine, University of Ljubljana, Vrazov Trg 2, 1000, Ljubljana, Slovenia
| | - Daša Zupančič
- Institute of Cell Biology, Faculty of Medicine, University of Ljubljana, Vrazov Trg 2, 1000, Ljubljana, Slovenia.
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3
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Tian J, Ma J. The Value of Microbes in Cancer Neoantigen Immunotherapy. Pharmaceutics 2023; 15:2138. [PMID: 37631352 PMCID: PMC10459105 DOI: 10.3390/pharmaceutics15082138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 08/06/2023] [Accepted: 08/11/2023] [Indexed: 08/27/2023] Open
Abstract
Tumor neoantigens are widely used in cancer immunotherapy, and a growing body of research suggests that microbes play an important role in these neoantigen-based immunotherapeutic processes. The human body and its surrounding environment are filled with a large number of microbes that are in long-term interaction with the organism. The microbiota can modulate our immune system, help activate neoantigen-reactive T cells, and play a great role in the process of targeting tumor neoantigens for therapy. Recent studies have revealed the interconnection between microbes and neoantigens, which can cross-react with each other through molecular mimicry, providing theoretical guidance for more relevant studies. The current applications of microbes in immunotherapy against tumor neoantigens are mainly focused on cancer vaccine development and immunotherapy with immune checkpoint inhibitors. This article summarizes the related fields and suggests the importance of microbes in immunotherapy against neoantigens.
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Affiliation(s)
- Junrui Tian
- NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha 410013, China;
- Cancer Research Institute and School of Basic Medical Science, Central South University, Changsha 410078, China
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Hunan Key Laboratory of Nonresolving Inflammation and Cancer, Changsha 410078, China
| | - Jian Ma
- NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha 410013, China;
- Cancer Research Institute and School of Basic Medical Science, Central South University, Changsha 410078, China
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Hunan Key Laboratory of Nonresolving Inflammation and Cancer, Changsha 410078, China
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4
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Koutros S, Kiemeney LA, Pal Choudhury P, Milne RL, Lopez de Maturana E, Ye Y, Joseph V, Florez-Vargas O, Dyrskjøt L, Figueroa J, Dutta D, Giles GG, Hildebrandt MAT, Offit K, Kogevinas M, Weiderpass E, McCullough ML, Freedman ND, Albanes D, Kooperberg C, Cortessis VK, Karagas MR, Johnson A, Schwenn MR, Baris D, Furberg H, Bajorin DF, Cussenot O, Cancel-Tassin G, Benhamou S, Kraft P, Porru S, Carta A, Bishop T, Southey MC, Matullo G, Fletcher T, Kumar R, Taylor JA, Lamy P, Prip F, Kalisz M, Weinstein SJ, Hengstler JG, Selinski S, Harland M, Teo M, Kiltie AE, Tardón A, Serra C, Carrato A, García-Closas R, Lloreta J, Schned A, Lenz P, Riboli E, Brennan P, Tjønneland A, Otto T, Ovsiannikov D, Volkert F, Vermeulen SH, Aben KK, Galesloot TE, Turman C, De Vivo I, Giovannucci E, Hunter DJ, Hohensee C, Hunt R, Patel AV, Huang WY, Thorleifsson G, Gago-Dominguez M, Amiano P, Golka K, Stern MC, Yan W, Liu J, Li SA, Katta S, Hutchinson A, Hicks B, Wheeler WA, Purdue MP, McGlynn KA, Kitahara CM, Haiman CA, Greene MH, Rafnar T, Chatterjee N, Chanock SJ, Wu X, Real FX, Silverman DT, Garcia-Closas M, Stefansson K, Prokunina-Olsson L, Malats N, Rothman N. Genome-wide Association Study of Bladder Cancer Reveals New Biological and Translational Insights. Eur Urol 2023; 84:127-137. [PMID: 37210288 PMCID: PMC10330197 DOI: 10.1016/j.eururo.2023.04.020] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 03/16/2023] [Accepted: 04/19/2023] [Indexed: 05/22/2023]
Abstract
BACKGROUND Genomic regions identified by genome-wide association studies (GWAS) for bladder cancer risk provide new insights into etiology. OBJECTIVE To identify new susceptibility variants for bladder cancer in a meta-analysis of new and existing genome-wide genotype data. DESIGN, SETTING, AND PARTICIPANTS Data from 32 studies that includes 13,790 bladder cancer cases and 343,502 controls of European ancestry were used for meta-analysis. OUTCOME MEASUREMENTS AND STATISTICAL ANALYSES Log-additive associations of genetic variants were assessed using logistic regression models. A fixed-effects model was used for meta-analysis of the results. Stratified analyses were conducted to evaluate effect modification by sex and smoking status. A polygenic risk score (PRS) was generated on the basis of known and novel susceptibility variants and tested for interaction with smoking. RESULTS AND LIMITATIONS Multiple novel bladder cancer susceptibility loci (6p.22.3, 7q36.3, 8q21.13, 9p21.3, 10q22.1, 19q13.33) as well as improved signals in three known regions (4p16.3, 5p15.33, 11p15.5) were identified, bringing the number of independent markers at genome-wide significance (p < 5 × 10-8) to 24. The 4p16.3 (FGFR3/TACC3) locus was associated with a stronger risk for women than for men (p-interaction = 0.002). Bladder cancer risk was increased by interactions between smoking status and genetic variants at 8p22 (NAT2; multiplicative p value for interaction [pM-I] = 0.004), 8q21.13 (PAG1; pM-I = 0.01), and 9p21.3 (LOC107987026/MTAP/CDKN2A; pM-I = 0.02). The PRS based on the 24 independent GWAS markers (odds ratio per standard deviation increase 1.49, 95% confidence interval 1.44-1.53), which also showed comparable results in two prospective cohorts (UK Biobank, PLCO trial), revealed an approximately fourfold difference in the lifetime risk of bladder cancer according to the PRS (e.g., 1st vs 10th decile) for both smokers and nonsmokers. CONCLUSIONS We report novel loci associated with risk of bladder cancer that provide clues to its biological underpinnings. Using 24 independent markers, we constructed a PRS to stratify lifetime risk. The PRS combined with smoking history, and other established risk factors, has the potential to inform future screening efforts for bladder cancer. PATIENT SUMMARY We identified new genetic markers that provide biological insights into the genetic causes of bladder cancer. These genetic risk factors combined with lifestyle risk factors, such as smoking, may inform future preventive and screening strategies for bladder cancer.
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Affiliation(s)
- Stella Koutros
- Occupational and Environmental Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA.
| | - Lambertus A Kiemeney
- Department for Health Evidence, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Parichoy Pal Choudhury
- Trans-Divisional Research Program, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA; American Cancer Society, Atlanta, GA, USA
| | - Roger L Milne
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, Australia; Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Australia; Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, Australia
| | - Evangelina Lopez de Maturana
- Genetic and Molecular Epidemiology Group, Spanish National Cancer Research Centre (CNIO) and CIBERONC, Madrid, Spain
| | | | - Vijai Joseph
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Oscar Florez-Vargas
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Lars Dyrskjøt
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Jonine Figueroa
- Usher Institute, University of Edinburgh, Edinburgh, UK; Integrative Tumor Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Diptavo Dutta
- Integrative Tumor Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Graham G Giles
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, Australia; Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Australia; Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, Australia
| | | | - Kenneth Offit
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | | | | | - Neal D Freedman
- Metabolic Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Demetrius Albanes
- Metabolic Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Charles Kooperberg
- Division of Public Health Sciences, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Victoria K Cortessis
- Department of Population and Public Health Sciences, Epidemiology and Genetics, University of Southern California, Los Angeles, CA, USA
| | - Margaret R Karagas
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Hanover, NH, USA
| | | | | | - Dalsu Baris
- Occupational and Environmental Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Helena Furberg
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Dean F Bajorin
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Olivier Cussenot
- Centre de Recherche sur les Pathologies Prostatiques et Urologiques, Paris, France
| | - Geraldine Cancel-Tassin
- Centre de Recherche sur les Pathologies Prostatiques et Urologiques, Paris, France; GRC 5 Predictive Onco-Urology, Sorbonne University, Paris, France
| | - Simone Benhamou
- INSERM U1018, Research Centre on Epidemiology and Population Health, Villejuif, France
| | - Peter Kraft
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Stefano Porru
- Department of Diagnostics and Public Health, Section of Occupational Medicine, University of Verona, Verona, Italy
| | - Angela Carta
- Department of Diagnostics and Public Health, Section of Occupational Medicine, University of Verona, Verona, Italy
| | - Timothy Bishop
- Section of Epidemiology and Biostatistics, Leeds Institute of Cancer and Pathology, University of Leeds, Leeds, UK
| | - Melissa C Southey
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, Australia; Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, Australia; Department of Clinical Pathology, The University of Melbourne, Parkville, Australia
| | - Giuseppe Matullo
- Department of Medical Sciences, University of Turin, Turin, Italy
| | - Tony Fletcher
- London School of Hygiene and Tropical Medicine, London, UK
| | - Rajiv Kumar
- Division of Functional Genome Analysis, German Cancer Research Center, Heidelberg, Germany
| | - Jack A Taylor
- Epidemiology Branch and Epigenetic and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, USA
| | - Philippe Lamy
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Frederik Prip
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Mark Kalisz
- Epithelial Carcinogenesis Group, Spanish National Cancer Research Centre (CNIO) and CIBERONC, Madrid, Spain
| | - Stephanie J Weinstein
- Metabolic Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Jan G Hengstler
- Leibniz Research Centre for Working Environment and Human Factors at TU Dortmund (IfADo), Dortmund, Germany
| | - Silvia Selinski
- Leibniz Research Centre for Working Environment and Human Factors at TU Dortmund (IfADo), Dortmund, Germany
| | - Mark Harland
- Section of Epidemiology and Biostatistics, Leeds Institute of Cancer and Pathology, University of Leeds, Leeds, UK
| | - Mark Teo
- Section of Epidemiology and Biostatistics, Leeds Institute of Cancer and Pathology, University of Leeds, Leeds, UK
| | - Anne E Kiltie
- Rowett Institute, School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Aberdeen, UK
| | - Adonina Tardón
- Department of Preventive Medicine, Universidad de Oviedo, ISPA and CIBERESP, Spain
| | - Consol Serra
- Center for Research in Occupational Health, Universitat Pompeu Fabra, Hospital del Mar Medical Research Institut, CIBERESP, Barcelona, Spain
| | - Alfredo Carrato
- Department of Medicine, Alcalá University, IRYCIS, CIBERONC, Madrid, Spain
| | | | - Josep Lloreta
- Hospital del Mar, Universitat Pompeu Fabra, Barcelona, Spain
| | - Alan Schned
- Department of Pathology, Dartmouth Medical School, Hanover, NH, USA
| | - Petra Lenz
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Elio Riboli
- School of Public Health, Imperial College London, London, UK
| | - Paul Brennan
- International Agency for Research on Cancer, Lyon, France
| | | | - Thomas Otto
- Department of Urology, Rheinland Klinikum, Lukaskrankenhaus, Neuss, Germany
| | | | - Frank Volkert
- Department of Urology, Evangelic Hospital, Paul Gerhardt Foundation, Lutherstadt Wittenberg, Germany
| | - Sita H Vermeulen
- Department for Health Evidence, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Katja K Aben
- Department for Health Evidence, Radboud University Medical Center, Nijmegen, The Netherlands; Netherlands Comprehensive Cancer Organisation, Utrecht, The Netherlands
| | - Tessel E Galesloot
- Department for Health Evidence, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Constance Turman
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Immaculata De Vivo
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA; Department of Medicine, Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Edward Giovannucci
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - David J Hunter
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA; Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Chancellor Hohensee
- Division of Public Health Sciences, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Rebecca Hunt
- Division of Public Health Sciences, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Alpa V Patel
- Population Science, American Cancer Society, Atlanta, GA, USA
| | - Wen-Yi Huang
- Metabolic Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | | | - Manuela Gago-Dominguez
- Fundación Pública Galega de Medicina Xenómica, Servicio Galego de Saude, Health Research Institute of Santiago de Compostela, Santiago de Compostela, Spain
| | - Pilar Amiano
- Ministry of Health of the Basque Government, Sub Directorate for Public Health and Addictions of Gipuzkoa, San Sebastian, Spain; Biodonostia Health Research Institute, Epidemiology of Chronic and Communicable Diseases Group, San Sebastian, Spain; Spanish Consortium for Research on Epidemiology and Public Health (CIBERESP), Instituto de Salud Carlos III, Madrid, Spain
| | - Klaus Golka
- Leibniz Research Centre for Working Environment and Human Factors at TU Dortmund (IfADo), Dortmund, Germany
| | - Mariana C Stern
- Department of Population and Public Health Sciences, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Wusheng Yan
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Jia Liu
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Shengchao Alfred Li
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Shilpa Katta
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Amy Hutchinson
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Belynda Hicks
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | | | - Mark P Purdue
- Occupational and Environmental Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Katherine A McGlynn
- Metabolic Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Cari M Kitahara
- Radiation Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Christopher A Haiman
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Mark H Greene
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | | | | | - Stephen J Chanock
- Office of the Director, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Xifeng Wu
- Zhejiang University, Hangzhou, China
| | - Francisco X Real
- Epithelial Carcinogenesis Group, Spanish National Cancer Research Centre (CNIO) and CIBERONC, Madrid, Spain; Departament de Medicina i Ciències de la Vida, Universitat Pompeu Fabra, Barcelona, Spain
| | - Debra T Silverman
- Occupational and Environmental Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Montserrat Garcia-Closas
- Trans-Divisional Research Program, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | | | - Ludmila Prokunina-Olsson
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Núria Malats
- Genetic and Molecular Epidemiology Group, Spanish National Cancer Research Centre (CNIO) and CIBERONC, Madrid, Spain
| | - Nathaniel Rothman
- Occupational and Environmental Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
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5
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Szydlak R, Øvreeide IH, Luty M, Zieliński T, Prot VE, Zemła J, Stokke BT, Lekka M. Bladder Cancer Cells Interaction with Lectin-Coated Surfaces under Static and Flow Conditions. Int J Mol Sci 2023; 24:ijms24098213. [PMID: 37175920 PMCID: PMC10179195 DOI: 10.3390/ijms24098213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 04/21/2023] [Accepted: 04/29/2023] [Indexed: 05/15/2023] Open
Abstract
Aberrant expression of glycans, i.e., oligosaccharide moiety covalently attached to proteins or lipids, is characteristic of various cancers, including urothelial ones. The binding of lectins to glycans is classified as molecular recognition, which makes lectins a strong tool for understanding their role in developing diseases. Here, we present a quantitative approach to tracing glycan-lectin interactions in cells, from the initial to the steady phase of adhesion. The cell adhesion was measured between urothelial cell lines (non-malignant HCV29 and carcinoma HT1376 and T24 cells) and lectin-coated surfaces. Depending on the timescale, single-cell force spectroscopy, and adhesion assays conducted in static and flow conditions were applied. The obtained results reveal that the adhesion of urothelial cells to two specific lectins, i.e., phytohemagglutinin-L and wheat germ agglutinin, was specific and selective. Thus, these lectins can be applied to selectively capture, identify, and differentiate between cancer types in a label-free manner. These results open up the possibility of designing lectin-based biosensors for diagnostic or prognostic purposes and developing strategies for drug delivery that could target cancer-associated glycans.
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Affiliation(s)
- Renata Szydlak
- Department of Biophysical Microstructures, Institute of Nuclear Physics, Polish Academy of Sciences, PL-31342 Kraków, Poland
| | - Ingrid H Øvreeide
- Biophysics and Medical Technology, Department of Physics, The Norwegian University of Science and Technology (NTNU), NO-7491 Trondheim, Norway
| | - Marcin Luty
- Department of Biophysical Microstructures, Institute of Nuclear Physics, Polish Academy of Sciences, PL-31342 Kraków, Poland
| | - Tomasz Zieliński
- Department of Biophysical Microstructures, Institute of Nuclear Physics, Polish Academy of Sciences, PL-31342 Kraków, Poland
| | - Victorien E Prot
- Biomechanics, Department of Structural Engineering, The Norwegian University of Science and Technology (NTNU), NO-7491 Trondheim, Norway
| | - Joanna Zemła
- Department of Biophysical Microstructures, Institute of Nuclear Physics, Polish Academy of Sciences, PL-31342 Kraków, Poland
| | - Bjørn T Stokke
- Biophysics and Medical Technology, Department of Physics, The Norwegian University of Science and Technology (NTNU), NO-7491 Trondheim, Norway
| | - Małgorzata Lekka
- Department of Biophysical Microstructures, Institute of Nuclear Physics, Polish Academy of Sciences, PL-31342 Kraków, Poland
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6
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Freitas R, Peixoto A, Ferreira E, Miranda A, Santos LL, Ferreira JA. Immunomodulatory glycomedicine: Introducing next generation cancer glycovaccines. Biotechnol Adv 2023; 65:108144. [PMID: 37028466 DOI: 10.1016/j.biotechadv.2023.108144] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 03/17/2023] [Accepted: 03/30/2023] [Indexed: 04/09/2023]
Abstract
Cancer remains a leading cause of death worldwide due to the lack of safer and more effective therapies. Cancer vaccines developed from neoantigens are an emerging strategy to promote protective and therapeutic anti-cancer immune responses. Advances in glycomics and glycoproteomics have unveiled several cancer-specific glycosignatures, holding tremendous potential to foster effective cancer glycovaccines. However, the immunosuppressive nature of tumours poses a major obstacle to vaccine-based immunotherapy. Chemical modification of tumour associated glycans, conjugation with immunogenic carriers and administration in combination with potent immune adjuvants constitute emerging strategies to address this bottleneck. Moreover, novel vaccine vehicles have been optimized to enhance immune responses against otherwise poorly immunogenic cancer epitopes. Nanovehicles have shown increased affinity for antigen presenting cells (APCs) in lymph nodes and tumours, while reducing treatment toxicity. Designs exploiting glycans recognized by APCs have further enhanced the delivery of antigenic payloads, improving glycovaccine's capacity to elicit innate and acquired immune responses. These solutions show potential to reduce tumour burden, while generating immunological memory. Building on this rationale, we provide a comprehensive overview on emerging cancer glycovaccines, emphasizing the potential of nanotechnology in this context. A roadmap towards clinical implementation is also delivered foreseeing advances in glycan-based immunomodulatory cancer medicine.
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Affiliation(s)
- Rui Freitas
- Experimental Pathology and Therapeutics Group, IPO Porto Research Center (CI-IPOP), RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute (IPO Porto), 4200-072 Porto, Portugal; Institute for Research and Innovation in Health (i3S), University of Porto, 4200-135 Porto, Portugal; Porto Comprehensive Cancer Center (P.ccc), 4200-072 Porto, Portugal; Abel Salazar Biomedical Sciences Institute - University of Porto (ICBAS), 4050-313 Porto, Portugal
| | - Andreia Peixoto
- Experimental Pathology and Therapeutics Group, IPO Porto Research Center (CI-IPOP), RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute (IPO Porto), 4200-072 Porto, Portugal; Institute for Research and Innovation in Health (i3S), University of Porto, 4200-135 Porto, Portugal; Porto Comprehensive Cancer Center (P.ccc), 4200-072 Porto, Portugal
| | - Eduardo Ferreira
- Experimental Pathology and Therapeutics Group, IPO Porto Research Center (CI-IPOP), RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute (IPO Porto), 4200-072 Porto, Portugal
| | - Andreia Miranda
- Experimental Pathology and Therapeutics Group, IPO Porto Research Center (CI-IPOP), RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute (IPO Porto), 4200-072 Porto, Portugal; Abel Salazar Biomedical Sciences Institute - University of Porto (ICBAS), 4050-313 Porto, Portugal
| | - Lúcio Lara Santos
- Experimental Pathology and Therapeutics Group, IPO Porto Research Center (CI-IPOP), RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute (IPO Porto), 4200-072 Porto, Portugal; Porto Comprehensive Cancer Center (P.ccc), 4200-072 Porto, Portugal; Abel Salazar Biomedical Sciences Institute - University of Porto (ICBAS), 4050-313 Porto, Portugal; Health School of University Fernando Pessoa, 4249-004 Porto, Portugal; GlycoMatters Biotech, 4500-162 Espinho, Portugal; Department of Surgical Oncology, Portuguese Oncology Institute (IPO Porto), 4200-072 Porto, Portugal
| | - José Alexandre Ferreira
- Experimental Pathology and Therapeutics Group, IPO Porto Research Center (CI-IPOP), RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute (IPO Porto), 4200-072 Porto, Portugal; Porto Comprehensive Cancer Center (P.ccc), 4200-072 Porto, Portugal; GlycoMatters Biotech, 4500-162 Espinho, Portugal.
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7
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A roadmap for translational cancer glycoimmunology at single cell resolution. J Exp Clin Cancer Res 2022; 41:143. [PMID: 35428302 PMCID: PMC9013178 DOI: 10.1186/s13046-022-02335-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Accepted: 03/17/2022] [Indexed: 11/11/2022] Open
Abstract
Cancer cells can evade immune responses by exploiting inhibitory immune checkpoints. Immune checkpoint inhibitor (ICI) therapies based on anti-CTLA-4 and anti-PD-1/PD-L1 antibodies have been extensively explored over the recent years to unleash otherwise compromised anti-cancer immune responses. However, it is also well established that immune suppression is a multifactorial process involving an intricate crosstalk between cancer cells and the immune systems. The cancer glycome is emerging as a relevant source of immune checkpoints governing immunosuppressive behaviour in immune cells, paving an avenue for novel immunotherapeutic options. This review addresses the current state-of-the-art concerning the role played by glycans controlling innate and adaptive immune responses, while shedding light on available experimental models for glycoimmunology. We also emphasize the tremendous progress observed in the development of humanized models for immunology, the paramount contribution of advances in high-throughput single-cell analysis in this context, and the importance of including predictive machine learning algorithms in translational research. This may constitute an important roadmap for glycoimmunology, supporting careful adoption of models foreseeing clinical translation of fundamental glycobiology knowledge towards next generation immunotherapies.
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8
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De Masi R, Orlando S. GANAB and N-Glycans Substrates Are Relevant in Human Physiology, Polycystic Pathology and Multiple Sclerosis: A Review. Int J Mol Sci 2022; 23:7373. [PMID: 35806376 PMCID: PMC9266668 DOI: 10.3390/ijms23137373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 06/22/2022] [Accepted: 06/28/2022] [Indexed: 11/29/2022] Open
Abstract
Glycans are one of the four fundamental macromolecular components of living matter, and they are highly regulated in the cell. Their functions are metabolic, structural and modulatory. In particular, ER resident N-glycans participate with the Glc3Man9GlcNAc2 highly conserved sequence, in protein folding process, where the physiological balance between glycosylation/deglycosylation on the innermost glucose residue takes place, according GANAB/UGGT concentration ratio. However, under abnormal conditions, the cell adapts to the glucose availability by adopting an aerobic or anaerobic regimen of glycolysis, or to external stimuli through internal or external recognition patterns, so it responds to pathogenic noxa with unfolded protein response (UPR). UPR can affect Multiple Sclerosis (MS) and several neurological and metabolic diseases via the BiP stress sensor, resulting in ATF6, PERK and IRE1 activation. Furthermore, the abnormal GANAB expression has been observed in MS, systemic lupus erythematous, male germinal epithelium and predisposed highly replicating cells of the kidney tubules and bile ducts. The latter is the case of Polycystic Liver Disease (PCLD) and Polycystic Kidney Disease (PCKD), where genetically induced GANAB loss affects polycystin-1 (PC1) and polycystin-2 (PC2), resulting in altered protein quality control and cyst formation phenomenon. Our topics resume the role of glycans in cell physiology, highlighting the N-glycans one, as a substrate of GANAB, which is an emerging key molecule in MS and other human pathologies.
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Affiliation(s)
- Roberto De Masi
- Complex Operative Unit of Neurology, “F. Ferrari” Hospital, Casarano, 73042 Lecce, Italy;
- Laboratory of Neuroproteomics, Multiple Sclerosis Centre, “F. Ferrari” Hospital, Casarano, 73042 Lecce, Italy
| | - Stefania Orlando
- Laboratory of Neuroproteomics, Multiple Sclerosis Centre, “F. Ferrari” Hospital, Casarano, 73042 Lecce, Italy
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9
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Crocetto F, Cimmino A, Ferro M, Terracciano D. Circulating tumor cells in bladder cancer: a new horizon of liquid biopsy for precision medicine. J Basic Clin Physiol Pharmacol 2021; 33:525-527. [PMID: 34563104 DOI: 10.1515/jbcpp-2021-0233] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Affiliation(s)
- Felice Crocetto
- Department of Neurosciences, Sciences of Reproduction and Odontostomatology, University of Naples Federico II, Naples, Italy
| | - Amelia Cimmino
- Institute of Genetics and Biophysics, National Research Council, Naples, Italy
| | - Matteo Ferro
- Department of Urology of European Institute of Oncology (IEO), IRCCS, Milan, Italy
| | - Daniela Terracciano
- Department of Translational Medical Sciences, University of Naples "Federico II", Naples, Italy
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10
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Siglec-6 as a New Potential Immune Checkpoint for Bladder Cancer Patients. Eur Urol Focus 2021; 8:748-751. [PMID: 34147404 DOI: 10.1016/j.euf.2021.06.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 05/06/2021] [Accepted: 06/04/2021] [Indexed: 01/03/2023]
Abstract
Among the growing family of inhibitory receptors regulating immunity, sialic acid-binding immunoglobulin domain-containing lectins (Siglecs) have recently emerged as immunoregulatory receptors recognizing sialylated ligands on tumor cell surface. However, their role in the immunoregulation of bladder cancer (BCa) remains unknown. Here, we determined the presence of eight Siglec ligands (SLs) on bladder nontumor and tumor cell lines. S2L, S3L, and S6L were not expressed, and few bladder tumor cell lines expressed S5L and S14L. In contrast, S7L and S10L were upregulated on all bladder tumor cell lines. We found a discrepency in S9L expression by nontumor cell lines, which is however highly expressed by bladder tumor cell lines. Notably, expression of S5L, S6L, and S14L was increased upon bacillus Calmette-Guérin (BCG) infection. Furthermore, we analyzed the expression of Siglecs on T cells from healthy donors and BCa patients. Circulating T cells only expressed Siglec-6, which is upregulated in non-muscle-invasive BCa patients. In addition, BCG therapy induced the overexpression of Siglec-6 by urinary CD8+ T cells. In vitro functional assays suggested that Siglecs may decrease cytotoxic functions of effector CD8+ T cells. Finally, analyses from two BCa datasets (The Cancer Genome Atlas and UROMOL cohorts) showed that Siglec-6 is associated with tumor progression and poor survival. Our findings indicate that Siglec-6 might be a new target for BCa treatments. PATIENT SUMMARY: We investigated the expression of Siglecs, a family of immunoregulatory receptors, in bladder cancer patients. We observed that the expression of Siglec-6 is increased on circulating and urinary T cells of non-muscle-invasive bladder cancer patients. We also showed that Siglec-6 is associated with lower survival in bladder cancer patients and might contribute to bladder cancer recurrence.
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11
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Peixoto A, Ferreira D, Azevedo R, Freitas R, Fernandes E, Relvas-Santos M, Gaiteiro C, Soares J, Cotton S, Teixeira B, Paulo P, Lima L, Palmeira C, Martins G, Oliveira MJ, Silva AMN, Santos LL, Ferreira JA. Glycoproteomics identifies HOMER3 as a potentially targetable biomarker triggered by hypoxia and glucose deprivation in bladder cancer. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2021; 40:191. [PMID: 34108014 PMCID: PMC8188679 DOI: 10.1186/s13046-021-01988-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Accepted: 05/17/2021] [Indexed: 01/11/2023]
Abstract
BACKGROUND Muscle invasive bladder cancer (MIBC) remains amongst the deadliest genitourinary malignancies due to treatment failure and extensive molecular heterogeneity, delaying effective targeted therapeutics. Hypoxia and nutrient deprivation, oversialylation and O-glycans shortening are salient features of aggressive tumours, creating cell surface glycoproteome fingerprints with theranostics potential. METHODS A glycomics guided glycoproteomics workflow was employed to identify potentially targetable biomarkers using invasive bladder cancer cell models. The 5637 and T24 cells O-glycome was characterized by mass spectrometry (MS), and the obtained information was used to guide glycoproteomics experiments, combining sialidase, lectin affinity and bottom-up protein identification by nanoLC-ESI-MS/MS. Data was curated by a bioinformatics approach developed in-house, sorting clinically relevant molecular signatures based on Human Protein Atlas insights. Top-ranked targets and glycoforms were validated in cell models, bladder tumours and metastases by MS and immunoassays. Cells grown under hypoxia and glucose deprivation disclosed the contribution of tumour microenvironment to the expression of relevant biomarkers. Cancer-specificity was validated in healthy tissues by immunohistochemistry and MS in 20 types of tissues/cells of different individuals. RESULTS Sialylated T (ST) antigens were found to be the most abundant glycans in cell lines and over 900 glycoproteins were identified potentially carrying these glycans. HOMER3, typically a cytosolic protein, emerged as a top-ranked targetable glycoprotein at the cell surface carrying short-chain O-glycans. Plasma membrane HOMER3 was observed in more aggressive primary tumours and distant metastases, being an independent predictor of worst prognosis. This phenotype was triggered by nutrient deprivation and concomitant to increased cellular invasion. T24 HOMER3 knockdown significantly decreased proliferation and, to some extent, invasion in normoxia and hypoxia; whereas HOMER3 knock-in increased its membrane expression, which was more pronounced under glucose deprivation. HOMER3 overexpression was associated with increased cell proliferation in normoxia and potentiated invasion under hypoxia. Finally, the mapping of HOMER3-glycosites by EThcD-MS/MS in bladder tumours revealed potentially targetable domains not detected in healthy tissues. CONCLUSION HOMER3-glycoforms allow the identification of patients' subsets facing worst prognosis, holding potential to address more aggressive hypoxic cells with limited off-target effects. The molecular rationale for identifying novel bladder cancer molecular targets has been established.
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Affiliation(s)
- Andreia Peixoto
- Experimental Pathology and Therapeutics Group, Research Center (CI-IPOP), Portuguese Institute of Oncology, 4200-072, Porto, Portugal.,Institute of Biomedical Sciences Abel Salazar (ICBAS), University of Porto, 4050-313, Porto, Portugal.,Institute for Research and Innovation in Health (i3S), University of Porto, 4200-135, Porto, Portugal.,Institute for Biomedical Engineering (INEB), University of Porto, 4200-135, Porto, Portugal
| | - Dylan Ferreira
- Experimental Pathology and Therapeutics Group, Research Center (CI-IPOP), Portuguese Institute of Oncology, 4200-072, Porto, Portugal.,Institute for Research and Innovation in Health (i3S), University of Porto, 4200-135, Porto, Portugal.,Institute for Biomedical Engineering (INEB), University of Porto, 4200-135, Porto, Portugal
| | - Rita Azevedo
- Experimental Pathology and Therapeutics Group, Research Center (CI-IPOP), Portuguese Institute of Oncology, 4200-072, Porto, Portugal
| | - Rui Freitas
- Experimental Pathology and Therapeutics Group, Research Center (CI-IPOP), Portuguese Institute of Oncology, 4200-072, Porto, Portugal
| | - Elisabete Fernandes
- Experimental Pathology and Therapeutics Group, Research Center (CI-IPOP), Portuguese Institute of Oncology, 4200-072, Porto, Portugal.,Institute for Research and Innovation in Health (i3S), University of Porto, 4200-135, Porto, Portugal.,Institute for Biomedical Engineering (INEB), University of Porto, 4200-135, Porto, Portugal
| | - Marta Relvas-Santos
- Experimental Pathology and Therapeutics Group, Research Center (CI-IPOP), Portuguese Institute of Oncology, 4200-072, Porto, Portugal.,Institute of Biomedical Sciences Abel Salazar (ICBAS), University of Porto, 4050-313, Porto, Portugal.,Institute for Research and Innovation in Health (i3S), University of Porto, 4200-135, Porto, Portugal.,Institute for Biomedical Engineering (INEB), University of Porto, 4200-135, Porto, Portugal.,REQUIMTE-LAQV, Department of Chemistry and Biochemistry, Faculty of Sciences of the University of Porto, 4169-007, Porto, Portugal
| | - Cristiana Gaiteiro
- Experimental Pathology and Therapeutics Group, Research Center (CI-IPOP), Portuguese Institute of Oncology, 4200-072, Porto, Portugal.,Institute of Biomedical Sciences Abel Salazar (ICBAS), University of Porto, 4050-313, Porto, Portugal
| | - Janine Soares
- Experimental Pathology and Therapeutics Group, Research Center (CI-IPOP), Portuguese Institute of Oncology, 4200-072, Porto, Portugal.,Institute of Biomedical Sciences Abel Salazar (ICBAS), University of Porto, 4050-313, Porto, Portugal
| | - Sofia Cotton
- Experimental Pathology and Therapeutics Group, Research Center (CI-IPOP), Portuguese Institute of Oncology, 4200-072, Porto, Portugal.,Institute of Biomedical Sciences Abel Salazar (ICBAS), University of Porto, 4050-313, Porto, Portugal
| | - Beatriz Teixeira
- Experimental Pathology and Therapeutics Group, Research Center (CI-IPOP), Portuguese Institute of Oncology, 4200-072, Porto, Portugal
| | - Paula Paulo
- Cancer Genetics Group, Research Center (CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto), 4200-072, Porto, Portugal
| | - Luís Lima
- Experimental Pathology and Therapeutics Group, Research Center (CI-IPOP), Portuguese Institute of Oncology, 4200-072, Porto, Portugal
| | - Carlos Palmeira
- Experimental Pathology and Therapeutics Group, Research Center (CI-IPOP), Portuguese Institute of Oncology, 4200-072, Porto, Portugal.,Immunology Department, Portuguese Institute of Oncology of Porto, 4200-072, Porto, Portugal.,Health School of University Fernando Pessoa, 4249-004, Porto, Portugal
| | - Gabriela Martins
- Immunology Department, Portuguese Institute of Oncology of Porto, 4200-072, Porto, Portugal
| | - Maria José Oliveira
- Institute for Research and Innovation in Health (i3S), University of Porto, 4200-135, Porto, Portugal.,Institute for Biomedical Engineering (INEB), University of Porto, 4200-135, Porto, Portugal
| | - André M N Silva
- REQUIMTE-LAQV, Department of Chemistry and Biochemistry, Faculty of Sciences of the University of Porto, 4169-007, Porto, Portugal
| | - Lúcio Lara Santos
- Experimental Pathology and Therapeutics Group, Research Center (CI-IPOP), Portuguese Institute of Oncology, 4200-072, Porto, Portugal.,Institute of Biomedical Sciences Abel Salazar (ICBAS), University of Porto, 4050-313, Porto, Portugal.,Health School of University Fernando Pessoa, 4249-004, Porto, Portugal.,Department of Surgical Oncology, Portuguese Institute of Oncology, 4200-072, Porto, Portugal.,Porto Comprehensive Cancer Center (P.ccc), 4200-072, Porto, Portugal
| | - José Alexandre Ferreira
- Experimental Pathology and Therapeutics Group, Research Center (CI-IPOP), Portuguese Institute of Oncology, 4200-072, Porto, Portugal. .,Institute of Biomedical Sciences Abel Salazar (ICBAS), University of Porto, 4050-313, Porto, Portugal. .,Porto Comprehensive Cancer Center (P.ccc), 4200-072, Porto, Portugal.
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12
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Ferreira JA, Relvas-Santos M, Peixoto A, M N Silva A, Lara Santos L. Glycoproteogenomics: Setting the Course for Next-generation Cancer Neoantigen Discovery for Cancer Vaccines. GENOMICS, PROTEOMICS & BIOINFORMATICS 2021; 19:25-43. [PMID: 34118464 PMCID: PMC8498922 DOI: 10.1016/j.gpb.2021.03.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 01/25/2021] [Accepted: 03/01/2021] [Indexed: 12/24/2022]
Abstract
Molecular-assisted precision oncology gained tremendous ground with high-throughput next-generation sequencing (NGS), supported by robust bioinformatics. The quest for genomics-based cancer medicine set the foundations for improved patient stratification, while unveiling a wide array of neoantigens for immunotherapy. Upfront pre-clinical and clinical studies have successfully used tumor-specific peptides in vaccines with minimal off-target effects. However, the low mutational burden presented by many lesions challenges the generalization of these solutions, requiring the diversification of neoantigen sources. Oncoproteogenomics utilizing customized databases for protein annotation by mass spectrometry (MS) is a powerful tool toward this end. Expanding the concept toward exploring proteoforms originated from post-translational modifications (PTMs) will be decisive to improve molecular subtyping and provide potentially targetable functional nodes with increased cancer specificity. Walking through the path of systems biology, we highlight that alterations in protein glycosylation at the cell surface not only have functional impact on cancer progression and dissemination but also originate unique molecular fingerprints for targeted therapeutics. Moreover, we discuss the outstanding challenges required to accommodate glycoproteomics in oncoproteogenomics platforms. We envisage that such rationale may flag a rather neglected research field, generating novel paradigms for precision oncology and immunotherapy.
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Affiliation(s)
- José Alexandre Ferreira
- Experimental Pathology and Therapeutics Group, Portuguese Institute of Oncology, Porto 4200-072, Portugal; Institute of Biomedical Sciences Abel Salazar, University of Porto, Porto 4050-313, Portugal; Porto Comprehensive Cancer Center (P.ccc), Porto 4200-072, Portugal.
| | - Marta Relvas-Santos
- Experimental Pathology and Therapeutics Group, Portuguese Institute of Oncology, Porto 4200-072, Portugal; Institute of Biomedical Sciences Abel Salazar, University of Porto, Porto 4050-313, Portugal; REQUIMTE-LAQV, Department of Chemistry and Biochemistry, Faculty of Sciences of the University of Porto, Porto 4169-007, Portugal
| | - Andreia Peixoto
- Experimental Pathology and Therapeutics Group, Portuguese Institute of Oncology, Porto 4200-072, Portugal; Institute of Biomedical Sciences Abel Salazar, University of Porto, Porto 4050-313, Portugal
| | - André M N Silva
- REQUIMTE-LAQV, Department of Chemistry and Biochemistry, Faculty of Sciences of the University of Porto, Porto 4169-007, Portugal
| | - Lúcio Lara Santos
- Experimental Pathology and Therapeutics Group, Portuguese Institute of Oncology, Porto 4200-072, Portugal; Institute of Biomedical Sciences Abel Salazar, University of Porto, Porto 4050-313, Portugal; Porto Comprehensive Cancer Center (P.ccc), Porto 4200-072, Portugal
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13
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Peixoto A, Cotton S, Santos LL, Ferreira JA. The Tumour Microenvironment and Circulating Tumour Cells: A Partnership Driving Metastasis and Glycan-Based Opportunities for Cancer Control. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 1329:1-33. [PMID: 34664231 DOI: 10.1007/978-3-030-73119-9_1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Circulating tumour cells (CTC) are rare cells that actively detach or are shed from primary tumours into the lymph and blood. Some CTC subpopulations gain the capacity to survive, home and colonize distant locations, forming metastasis. This results from a multifactorial process in which cancer cells optimize motility, invasion, immune escape and cooperative relationships with microenvironmental cues. Here we present evidences of a self-fuelling molecular crosstalk between cancer cells and the tumour stroma supporting the main milestones leading to metastasis. We discuss how the tumour microenvironment supports pre-metastatic niches and CTC development and ultimately dictates CTC fate in targeted organs. Finally, we highlight the key role played by protein glycosylation in metastasis development, its prompt response to microenvironmental stimuli and the tremendous potential of glycan-based molecular signatures for liquid biopsies and targeted therapeutics.
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Affiliation(s)
- Andreia Peixoto
- Experimental Pathology and Therapeutics Group, Portuguese Institute of Oncology, Porto, Portugal. .,Institute of Biomedical Sciences Abel Salazar (ICBAS), University of Porto, Porto, Portugal. .,Institute for Research and Innovation in Health (i3s), University of Porto, Porto, Portugal. .,Institute for Biomedical Engineering (INEB), Porto, Portugal. .,Porto Comprehensive Cancer Centre (P.ccc), Porto, Portugal.
| | - Sofia Cotton
- Experimental Pathology and Therapeutics Group, Portuguese Institute of Oncology, Porto, Portugal.,Institute of Biomedical Sciences Abel Salazar (ICBAS), University of Porto, Porto, Portugal.,Institute for Research and Innovation in Health (i3s), University of Porto, Porto, Portugal.,Institute for Biomedical Engineering (INEB), Porto, Portugal.,Porto Comprehensive Cancer Centre (P.ccc), Porto, Portugal
| | - Lúcio Lara Santos
- Experimental Pathology and Therapeutics Group, Portuguese Institute of Oncology, Porto, Portugal.,Institute of Biomedical Sciences Abel Salazar (ICBAS), University of Porto, Porto, Portugal.,Porto Comprehensive Cancer Centre (P.ccc), Porto, Portugal.,Department of Surgical Oncology, Portuguese Institute of Oncology of Porto, Porto, Portugal
| | - José Alexandre Ferreira
- Experimental Pathology and Therapeutics Group, Portuguese Institute of Oncology, Porto, Portugal.,Institute of Biomedical Sciences Abel Salazar (ICBAS), University of Porto, Porto, Portugal.,Porto Comprehensive Cancer Centre (P.ccc), Porto, Portugal
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14
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Abstract
Glycobiology is a glycan-based field of study that focuses on the structure, function, and biology of carbohydrates, and glycomics is a sub-study of the field of glycobiology that aims to define structure/function of glycans in living organisms. With the popularity of the glycobiology and glycomics, application of computational modeling expanded in the scientific area of glycobiology over the last decades. The recent availability of progressive Wet-Lab methods in the field of glycobiology and glycomics is promising for the impact of systems biology on the research area of the glycome, an emerging field that is termed “systems glycobiology.” This chapter will summarize the up-to-date leading edge in the use of bioinformatics tools in the field of glycobiology. The chapter provides basic knowledge both for glycobiologists interested in the application of bioinformatics tools and scientists of computational biology interested in studying the glycome.
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15
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Insights into Bioinformatic Applications for Glycosylation: Instigating an Awakening towards Applying Glycoinformatic Resources for Cancer Diagnosis and Therapy. Int J Mol Sci 2020; 21:ijms21249336. [PMID: 33302373 PMCID: PMC7762546 DOI: 10.3390/ijms21249336] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 11/26/2020] [Accepted: 12/01/2020] [Indexed: 01/10/2023] Open
Abstract
Glycosylation plays a crucial role in various diseases and their etiology. This has led to a clear understanding on the functions of carbohydrates in cell communication, which eventually will result in novel therapeutic approaches for treatment of various disease. Glycomics has now become one among the top ten technologies that will change the future. The direct implication of glycosylation as a hallmark of cancer and for cancer therapy is well established. As in proteomics, where bioinformatics tools have led to revolutionary achievements, bioinformatics resources for glycosylation have improved its practical implication. Bioinformatics tools, algorithms and databases are a mandatory requirement to manage and successfully analyze large amount of glycobiological data generated from glycosylation studies. This review consolidates all the available tools and their applications in glycosylation research. The achievements made through the use of bioinformatics into glycosylation studies are also presented. The importance of glycosylation in cancer diagnosis and therapy is discussed and the gap in the application of widely available glyco-informatic tools for cancer research is highlighted. This review is expected to bring an awakening amongst glyco-informaticians as well as cancer biologists to bridge this gap, to exploit the available glyco-informatic tools for cancer.
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16
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Carvalho S, Abreu CM, Ferreira D, Lima L, Ferreira JA, Santos LL, Ribeiro R, Grenha V, Martínez-Fernández M, Duenas M, Suárez-Cabrera C, Paramio JM, Diéguez L, Freitas PP, Oliveira MI. Phenotypic Analysis of Urothelial Exfoliated Cells in Bladder Cancer via Microfluidic Immunoassays: Sialyl-Tn as a Novel Biomarker in Liquid Biopsies. Front Oncol 2020; 10:1774. [PMID: 33042825 PMCID: PMC7526084 DOI: 10.3389/fonc.2020.01774] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Accepted: 08/10/2020] [Indexed: 12/29/2022] Open
Abstract
Bladder cancer is the most common malignancy of the urinary tract, having one of the highest recurrence rates and progression from non-muscle to muscle invasive bladder cancer that commonly leads to metastasis. Cystoscopy and urine cytology are the standard procedures for its detection but have limited clinical sensitivity and specificity. Herein, a microfluidic device, the UriChip, was developed for the enrichment of urothelial exfoliated cells from fresh and frozen urine, based on deformability and size, and the cancer-associated glycan Sialyl-Tn explored as a putative bladder cancer urinary biomarker. Spiking experiments with bladder cancer cell lines showed an isolation efficiency of 53%, while clinical sample analyses revealed retention of cells with various morphologies and sizes. in situ immunoassays demonstrated significantly higher number of Sialyl-Tn-positive cells in fresh and frozen voided urine from bladder cancer patients, compared to healthy individuals. Of note, urothelial exfoliated cells from cryopreserved urine sediments were also successfully isolated by the UriChip, and found to express significantly high levels of Sialyl-Tn. Remarkably, Sialyl-Tn expression is correlated with tumor stage and grade. Overall, our findings demonstrate the potential of UriChip and Sialyl-Tn to detect urothelial bladder cancer cells in follow-up and long-term retrospective studies.
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Affiliation(s)
- Sandra Carvalho
- International Iberian Nanotechnology Laboratory, Department of Life Sciences, Braga, Portugal
| | - Catarina M. Abreu
- International Iberian Nanotechnology Laboratory, Department of Life Sciences, Braga, Portugal
| | - Dylan Ferreira
- Experimental Pathology and Therapeutics Group, Research Center of the Portuguese Institute of Oncology (CI-IPOP), Porto, Portugal
- Porto Comprehensive Cancer Center (P.ccc), Porto, Portugal
| | - Luís Lima
- Experimental Pathology and Therapeutics Group, Research Center of the Portuguese Institute of Oncology (CI-IPOP), Porto, Portugal
- Porto Comprehensive Cancer Center (P.ccc), Porto, Portugal
- School of Health, Polytechnic Institute of Porto, Porto, Portugal
| | - José A. Ferreira
- Experimental Pathology and Therapeutics Group, Research Center of the Portuguese Institute of Oncology (CI-IPOP), Porto, Portugal
- Porto Comprehensive Cancer Center (P.ccc), Porto, Portugal
| | - Lúcio L. Santos
- Experimental Pathology and Therapeutics Group, Research Center of the Portuguese Institute of Oncology (CI-IPOP), Porto, Portugal
- Porto Comprehensive Cancer Center (P.ccc), Porto, Portugal
| | - Ricardo Ribeiro
- Tumor & Microenvironment Group, i3S/INEB, Instituto de Investigação e Inovação em Saúde/Instituto de Engenharia Biomédica, University of Porto, Porto, Portugal
- Faculty of Medicine, Environmental Health Institute, University of Lisbon, Lisbon, Portugal
- Departament of Clinical Pathology, Centro Hospitalar e Universitário de Coimbra, Coimbra, Portugal
| | - Vânia Grenha
- Department of Urology, Centro Hospitalar Do Alto Ave, Guimarães, Portugal
| | - Mónica Martínez-Fernández
- Genomes and Disease Lab., Research Center of Molecular Medicine and Chronic Diseases (CIMUS), University of Santiago de Compostela, Santiago de Compostela, Spain
| | - Marta Duenas
- Molecular Oncology Unit, CIEMAT, Madrid, Spain
- CIBERONC, Institute of Biomedical Research, University Hospital “12 de Octubre”, Madrid, Spain
| | - Cristian Suárez-Cabrera
- Molecular Oncology Unit, CIEMAT, Madrid, Spain
- CIBERONC, Institute of Biomedical Research, University Hospital “12 de Octubre”, Madrid, Spain
| | - Jesus M. Paramio
- Molecular Oncology Unit, CIEMAT, Madrid, Spain
- CIBERONC, Institute of Biomedical Research, University Hospital “12 de Octubre”, Madrid, Spain
| | - Lorena Diéguez
- International Iberian Nanotechnology Laboratory, Department of Life Sciences, Braga, Portugal
| | - Paulo P. Freitas
- International Iberian Nanotechnology Laboratory, Department of Nanoelectronics Engineering, Braga, Portugal
| | - Marta I. Oliveira
- International Iberian Nanotechnology Laboratory, Department of Life Sciences, Braga, Portugal
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17
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Lokeshwar VB, Morera DS, Hasanali SL, Yates TJ, Hupe MC, Knapp J, Lokeshwar SD, Wang J, Hennig MJP, Baskar R, Escudero DO, Racine RR, Dhir N, Jordan AR, Hoye K, Azih I, Manoharan M, Klaassen Z, Kavuri S, Lopez LE, Ghosh S, Lokeshwar BL. A Novel Splice Variant of HYAL-4 Drives Malignant Transformation and Predicts Outcome in Patients with Bladder Cancer. Clin Cancer Res 2020; 26:3455-3467. [PMID: 32094233 PMCID: PMC7334064 DOI: 10.1158/1078-0432.ccr-19-2912] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Revised: 01/13/2020] [Accepted: 02/19/2020] [Indexed: 11/16/2022]
Abstract
PURPOSE Poor prognosis of patients with muscle-invasive bladder cancer that often metastasizes drives the need for discovery of molecular determinants of bladder cancer progression. Chondroitin sulfate proteoglycans, including CD44, regulate cancer progression; however, the identity of a chondroitinase (Chase) that cleaves chondroitin sulfate from proteoglycans is unknown. HYAL-4 is an understudied gene suspected to encode a Chase, with no known biological function. We evaluated HYAL-4 expression and its role in bladder cancer. EXPERIMENTAL DESIGN In clinical specimens, HYAL-4 wild-type (Wt) and V1 expression was evaluated by RT-qPCR, IHC, and/or immunoblotting; a novel assay measured Chase activity. Wt and V1 were stably expressed or silenced in normal urothelial and three bladder cancer cell lines. Transfectants were analyzed for stem cell phenotype, invasive signature and tumorigenesis, and metastasis in four xenograft models, including orthotopic bladder. RESULTS HYAL-4 expression, specifically a novel splice variant (V1), was elevated in bladder tumors; Wt expression was barely detectable. V1 encoded a truncated 349 amino acid protein that was secreted. In bladder cancer tissues, V1 levels associated with metastasis and cancer-specific survival with high efficacy and encoded Chase activity. V1 cleaved chondroitin-6-sulfate from CD44, increasing CD44 secretion. V1 induced stem cell phenotype, motility/invasion, and an invasive signature. CD44 knockdown abrogated these phenotypes. V1-expressing urothelial cells developed angiogenic, muscle-invasive tumors. V1-expressing bladder cancer cells formed tumors at low density and formed metastatic bladder tumors when implanted orthotopically. CONCLUSIONS Our study discovered the first naturally-occurring eukaryotic/human Chase and connected it to disease pathology, specifically cancer. V1-Chase is a driver of malignant bladder cancer and potential predictor of outcome in patients with bladder cancer.
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Affiliation(s)
- Vinata B Lokeshwar
- Department of Biochemistry and Molecular Biology, Medical College of Georgia, Augusta University, Augusta, Georgia.
| | - Daley S Morera
- Department of Biochemistry and Molecular Biology, Medical College of Georgia, Augusta University, Augusta, Georgia
| | - Sarrah L Hasanali
- Department of Biochemistry and Molecular Biology, Medical College of Georgia, Augusta University, Augusta, Georgia
| | - Travis J Yates
- Sheila and David Fuente Graduate Program in Cancer Biology, University of Miami-Miller School of Medicine, Miami, Florida
| | - Marie C Hupe
- Department of Urology, University-Hospital Schleswig-Holstein, Campus Luebeck, Luebeck, Germany
| | - Judith Knapp
- Department of Urology, University-Hospital Schleswig-Holstein, Campus Luebeck, Luebeck, Germany
| | - Soum D Lokeshwar
- Honors Program in Medical Education, University of Miami-Miller School of Medicine, Miami, Florida
| | - Jiaojiao Wang
- Department of Biochemistry and Molecular Biology, Medical College of Georgia, Augusta University, Augusta, Georgia
| | - Martin J P Hennig
- Department of Urology, University-Hospital Schleswig-Holstein, Campus Luebeck, Luebeck, Germany
| | - Rohitha Baskar
- Department of Biochemistry and Molecular Biology, Medical College of Georgia, Augusta University, Augusta, Georgia
| | - Diogo O Escudero
- Molecular Cell and Developmental Biology Graduate Program, University of Miami-Miller School of Medicine, Miami, Florida
| | - Ronny R Racine
- Department of Urology, University of Miami-Miller School of Medicine, Miami, Florida
| | - Neetika Dhir
- Department of Urology, University of Miami-Miller School of Medicine, Miami, Florida
| | - Andre R Jordan
- Department of Biochemistry and Molecular Biology, Medical College of Georgia, Augusta University, Augusta, Georgia
- Sheila and David Fuente Graduate Program in Cancer Biology, University of Miami-Miller School of Medicine, Miami, Florida
| | - Kelly Hoye
- Sheila and David Fuente Graduate Program in Cancer Biology, University of Miami-Miller School of Medicine, Miami, Florida
| | - Ijeoma Azih
- Clinical Trials Office, Medical College of Georgia, Augusta University, Augusta, Georgia
| | - Murugesan Manoharan
- Division of Urologic Oncology Surgery, Miami Cancer Institute, Baptist Health South Florida, Miami, Florida
| | - Zachary Klaassen
- Division of Urology, Department of Surgery, Medical College of Georgia, Augusta University, Augusta, Georgia
| | - Sravan Kavuri
- Department of Pathology, Medical College of Georgia, Augusta University, Augusta, Georgia
| | - Luis E Lopez
- Department of Biochemistry and Molecular Biology, Medical College of Georgia, Augusta University, Augusta, Georgia
| | - Santu Ghosh
- Department of Population Health Sciences, Medical College of Georgia, Augusta University, Augusta, Georgia
| | - Bal L Lokeshwar
- Georgia Cancer Center, Medical College of Georgia, Augusta University, Augusta, Georgia
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18
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Pereira PMR, Parada B, Ribeiro-Rodrigues TM, Fontes-Ribeiro CA, Girão H, Tomé JPC, Fernandes R. Caveolin-1 Modulation Increases Efficacy of a Galacto-Conjugated Phthalocyanine in Bladder Cancer Cells Resistant to Photodynamic Therapy. Mol Pharm 2020; 17:2145-2154. [DOI: 10.1021/acs.molpharmaceut.0c00298] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Patrícia M. R. Pereira
- QOPNA, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal
- Coimbra Institute for Clinical and Biomedical Research (iCBR), Faculty of Medicine, University of Coimbra, 3000-548 Coimbra, Portugal
| | - Belmiro Parada
- Coimbra Institute for Clinical and Biomedical Research (iCBR), Faculty of Medicine, University of Coimbra, 3000-548 Coimbra, Portugal
- Urology and Renal Transplantation Department, Coimbra University Hospital Centre (CHUC), 3004-561 Coimbra, Portugal
| | - Teresa M. Ribeiro-Rodrigues
- Coimbra Institute for Clinical and Biomedical Research (iCBR), Faculty of Medicine, University of Coimbra, 3000-548 Coimbra, Portugal
- Center for Innovative Biomedicine and Biotechnology (CIBB), University of Coimbra, 3004-531 Coimbra, Portugal
| | - Carlos A. Fontes-Ribeiro
- Coimbra Institute for Clinical and Biomedical Research (iCBR), Faculty of Medicine, University of Coimbra, 3000-548 Coimbra, Portugal
- Center for Innovative Biomedicine and Biotechnology (CIBB), University of Coimbra, 3004-531 Coimbra, Portugal
| | - Henrique Girão
- Coimbra Institute for Clinical and Biomedical Research (iCBR), Faculty of Medicine, University of Coimbra, 3000-548 Coimbra, Portugal
- Center for Innovative Biomedicine and Biotechnology (CIBB), University of Coimbra, 3004-531 Coimbra, Portugal
| | - João P. C. Tomé
- QOPNA, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal
- CQE & Departamento de Engenharia Química, Instituto Superior Técnico, Universidade de Lisboa, 1649-004 Lisboa, Portugal
| | - Rosa Fernandes
- Coimbra Institute for Clinical and Biomedical Research (iCBR), Faculty of Medicine, University of Coimbra, 3000-548 Coimbra, Portugal
- Center for Innovative Biomedicine and Biotechnology (CIBB), University of Coimbra, 3004-531 Coimbra, Portugal
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19
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Fernandes E, Freitas R, Ferreira D, Soares J, Azevedo R, Gaiteiro C, Peixoto A, Oliveira S, Cotton S, Relvas-Santos M, Afonso LP, Palmeira C, Oliveira MJ, Ferreira R, Silva AMN, Lara Santos L, Ferreira JA. Nucleolin-Sle A Glycoforms as E-Selectin Ligands and Potentially Targetable Biomarkers at the Cell Surface of Gastric Cancer Cells. Cancers (Basel) 2020; 12:cancers12040861. [PMID: 32252346 PMCID: PMC7226152 DOI: 10.3390/cancers12040861] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Revised: 03/24/2020] [Accepted: 03/28/2020] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Gastric cancer (GC) is a major health burden worldwide, with half of patients developing metastases within 5 years after treatment, urging novel biomarkers for diagnosis and efficient therapeutic targeting. Sialyl-Lewis A (SLeA), a terminal glycoepitope of glycoproteins and glycolipids, offers tremendous potential towards this objective. It is rarely expressed in healthy tissues and blood cells, while it is present in highly metastatic cell lines and metastases. SLeA is also involved in E-selectin mediated metastasis, making it an ideal target to control disease dissemination. METHODS AND RESULTS To improve cancer specificity, we have explored the SLeA-glycoproteome of six GC cell models, with emphasis on glycoproteins showing affinity for E-selectin. A novel bioinformatics-assisted algorithm identified nucleolin (NCL), a nuclear protein, as a potential targetable biomarker potentially involved in metastasis. Several immunoassays, including Western blot and in situ proximity ligation reinforced the existence of cell surface NCL-SLeA glycoforms in GC. The NCL-SLeA glycophenotype was associated with decreased survival and was not reflected in relevant healthy tissues. CONCLUSIONS NCL-SLeA is a biomarker of poor prognosis in GC holding potential for precise cancer targeting. This is the first report describing SLeA in preferentially nuclear protein, setting a new paradigm for cancer biomarkers discovery and targeted therapies.
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Affiliation(s)
- Elisabete Fernandes
- Experimental Pathology and Therapeutics Group, Portuguese Institute of Oncology, 4200-162 Porto, Portugal; (E.F.); (R.F.); (D.F.); (J.S.); (R.A.); (C.G.); (A.P.); (S.O.); (S.C.); (M.R.-S.); (L.P.A.); (C.P.); (L.L.S.)
- Institute of Biomedical Sciences Abel Salazar (ICBAS), University of Porto, 4050-013 Porto, Portugal
- Institute for Research and Innovation in Health (i3S), University of Porto, 4200-135 Porto, Portugal;
- Institute for Biomedical Engineering (INEB), Porto, Portugal, 4200-135 Porto, Portugal
- Digestive Cancer Research Group, 1495-161 Algés, Portugal
| | - Rui Freitas
- Experimental Pathology and Therapeutics Group, Portuguese Institute of Oncology, 4200-162 Porto, Portugal; (E.F.); (R.F.); (D.F.); (J.S.); (R.A.); (C.G.); (A.P.); (S.O.); (S.C.); (M.R.-S.); (L.P.A.); (C.P.); (L.L.S.)
| | - Dylan Ferreira
- Experimental Pathology and Therapeutics Group, Portuguese Institute of Oncology, 4200-162 Porto, Portugal; (E.F.); (R.F.); (D.F.); (J.S.); (R.A.); (C.G.); (A.P.); (S.O.); (S.C.); (M.R.-S.); (L.P.A.); (C.P.); (L.L.S.)
- Institute for Research and Innovation in Health (i3S), University of Porto, 4200-135 Porto, Portugal;
- Institute for Biomedical Engineering (INEB), Porto, Portugal, 4200-135 Porto, Portugal
- Digestive Cancer Research Group, 1495-161 Algés, Portugal
| | - Janine Soares
- Experimental Pathology and Therapeutics Group, Portuguese Institute of Oncology, 4200-162 Porto, Portugal; (E.F.); (R.F.); (D.F.); (J.S.); (R.A.); (C.G.); (A.P.); (S.O.); (S.C.); (M.R.-S.); (L.P.A.); (C.P.); (L.L.S.)
- Institute of Biomedical Sciences Abel Salazar (ICBAS), University of Porto, 4050-013 Porto, Portugal
- REQUIMTE-LAQV, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal;
| | - Rita Azevedo
- Experimental Pathology and Therapeutics Group, Portuguese Institute of Oncology, 4200-162 Porto, Portugal; (E.F.); (R.F.); (D.F.); (J.S.); (R.A.); (C.G.); (A.P.); (S.O.); (S.C.); (M.R.-S.); (L.P.A.); (C.P.); (L.L.S.)
| | - Cristiana Gaiteiro
- Experimental Pathology and Therapeutics Group, Portuguese Institute of Oncology, 4200-162 Porto, Portugal; (E.F.); (R.F.); (D.F.); (J.S.); (R.A.); (C.G.); (A.P.); (S.O.); (S.C.); (M.R.-S.); (L.P.A.); (C.P.); (L.L.S.)
- Institute of Biomedical Sciences Abel Salazar (ICBAS), University of Porto, 4050-013 Porto, Portugal
| | - Andreia Peixoto
- Experimental Pathology and Therapeutics Group, Portuguese Institute of Oncology, 4200-162 Porto, Portugal; (E.F.); (R.F.); (D.F.); (J.S.); (R.A.); (C.G.); (A.P.); (S.O.); (S.C.); (M.R.-S.); (L.P.A.); (C.P.); (L.L.S.)
- Institute of Biomedical Sciences Abel Salazar (ICBAS), University of Porto, 4050-013 Porto, Portugal
- Institute for Research and Innovation in Health (i3S), University of Porto, 4200-135 Porto, Portugal;
- Institute for Biomedical Engineering (INEB), Porto, Portugal, 4200-135 Porto, Portugal
| | - Sara Oliveira
- Experimental Pathology and Therapeutics Group, Portuguese Institute of Oncology, 4200-162 Porto, Portugal; (E.F.); (R.F.); (D.F.); (J.S.); (R.A.); (C.G.); (A.P.); (S.O.); (S.C.); (M.R.-S.); (L.P.A.); (C.P.); (L.L.S.)
| | - Sofia Cotton
- Experimental Pathology and Therapeutics Group, Portuguese Institute of Oncology, 4200-162 Porto, Portugal; (E.F.); (R.F.); (D.F.); (J.S.); (R.A.); (C.G.); (A.P.); (S.O.); (S.C.); (M.R.-S.); (L.P.A.); (C.P.); (L.L.S.)
- Institute of Biomedical Sciences Abel Salazar (ICBAS), University of Porto, 4050-013 Porto, Portugal
| | - Marta Relvas-Santos
- Experimental Pathology and Therapeutics Group, Portuguese Institute of Oncology, 4200-162 Porto, Portugal; (E.F.); (R.F.); (D.F.); (J.S.); (R.A.); (C.G.); (A.P.); (S.O.); (S.C.); (M.R.-S.); (L.P.A.); (C.P.); (L.L.S.)
- Institute for Biomedical Engineering (INEB), Porto, Portugal, 4200-135 Porto, Portugal
- REQUIMTE-LAQV, Department of Chemistry and Biochemistry, Faculty of Sciences of the University of Porto, 4169-007 Porto, Portugal;
| | - Luis Pedro Afonso
- Experimental Pathology and Therapeutics Group, Portuguese Institute of Oncology, 4200-162 Porto, Portugal; (E.F.); (R.F.); (D.F.); (J.S.); (R.A.); (C.G.); (A.P.); (S.O.); (S.C.); (M.R.-S.); (L.P.A.); (C.P.); (L.L.S.)
- Pathology Department, Portuguese Institute of Oncology of Porto, 4200-162 Porto, Portugal
| | - Carlos Palmeira
- Experimental Pathology and Therapeutics Group, Portuguese Institute of Oncology, 4200-162 Porto, Portugal; (E.F.); (R.F.); (D.F.); (J.S.); (R.A.); (C.G.); (A.P.); (S.O.); (S.C.); (M.R.-S.); (L.P.A.); (C.P.); (L.L.S.)
- Immunology Department, Portuguese Institute of Oncology of Porto, 4200-162 Porto, Portugal
- Health Science Faculty, University of Fernando Pessoa, 4249-004 Porto, Portugal
| | - Maria José Oliveira
- Institute for Research and Innovation in Health (i3S), University of Porto, 4200-135 Porto, Portugal;
- Institute for Biomedical Engineering (INEB), Porto, Portugal, 4200-135 Porto, Portugal
| | - Rita Ferreira
- REQUIMTE-LAQV, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal;
| | - André M. N. Silva
- REQUIMTE-LAQV, Department of Chemistry and Biochemistry, Faculty of Sciences of the University of Porto, 4169-007 Porto, Portugal;
| | - Lúcio Lara Santos
- Experimental Pathology and Therapeutics Group, Portuguese Institute of Oncology, 4200-162 Porto, Portugal; (E.F.); (R.F.); (D.F.); (J.S.); (R.A.); (C.G.); (A.P.); (S.O.); (S.C.); (M.R.-S.); (L.P.A.); (C.P.); (L.L.S.)
- Institute of Biomedical Sciences Abel Salazar (ICBAS), University of Porto, 4050-013 Porto, Portugal
- Digestive Cancer Research Group, 1495-161 Algés, Portugal
- Health Science Faculty, University of Fernando Pessoa, 4249-004 Porto, Portugal
- Department of Surgical Oncology, Portuguese Institute of Oncology of Porto, 4200-162 Porto, Portugal
- Department, Porto Comprehensive Cancer Centre (P.ccc), 4200-162 Porto, Portugal
| | - José Alexandre Ferreira
- Experimental Pathology and Therapeutics Group, Portuguese Institute of Oncology, 4200-162 Porto, Portugal; (E.F.); (R.F.); (D.F.); (J.S.); (R.A.); (C.G.); (A.P.); (S.O.); (S.C.); (M.R.-S.); (L.P.A.); (C.P.); (L.L.S.)
- Institute of Biomedical Sciences Abel Salazar (ICBAS), University of Porto, 4050-013 Porto, Portugal
- Department, Porto Comprehensive Cancer Centre (P.ccc), 4200-162 Porto, Portugal
- Correspondence: ; Tel.: +351-225084000 (ext. 5111)
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20
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Fernandes E, Sores J, Cotton S, Peixoto A, Ferreira D, Freitas R, Reis CA, Santos LL, Ferreira JA. Esophageal, gastric and colorectal cancers: Looking beyond classical serological biomarkers towards glycoproteomics-assisted precision oncology. Am J Cancer Res 2020; 10:4903-4928. [PMID: 32308758 PMCID: PMC7163443 DOI: 10.7150/thno.42480] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Accepted: 01/16/2020] [Indexed: 12/24/2022] Open
Abstract
Esophageal (OC), gastric (GC) and colorectal (CRC) cancers are amongst the digestive track tumors with higher incidence and mortality due to significant molecular heterogeneity. This constitutes a major challenge for patients' management at different levels, including non-invasive detection of the disease, prognostication, therapy selection, patient's follow-up and the introduction of improved and safer therapeutics. Nevertheless, important milestones have been accomplished pursuing the goal of molecular-based precision oncology. Over the past five years, high-throughput technologies have been used to interrogate tumors of distinct clinicopathological natures, generating large-scale biological datasets (e.g. genomics, transcriptomics, and proteomics). As a result, GC and CRC molecular subtypes have been established to assist patient stratification in the clinical settings. However, such molecular panels still require refinement and are yet to provide targetable biomarkers. In parallel, outstanding advances have been made regarding targeted therapeutics and immunotherapy, paving the way for improved patient care; nevertheless, important milestones towards treatment personalization and reduced off-target effects are also to be accomplished. Exploiting the cancer glycoproteome for unique molecular fingerprints generated by dramatic alterations in protein glycosylation may provide the necessary molecular rationale towards this end. Therefore, this review presents functional and clinical evidences supporting a reinvestigation of classical serological glycan biomarkers such as sialyl-Tn (STn) and sialyl-Lewis A (SLeA) antigens from a tumor glycoproteomics perspective. We anticipate that these glycobiomarkers that have so far been employed in non-invasive cancer prognostication may hold unexplored value for patients' management in precision oncology settings.
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21
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Song W, Zhou X, Benktander JD, Gaunitz S, Zou G, Wang Z, Novotny MV, Jacobson SC. In-Depth Compositional and Structural Characterization of N-Glycans Derived from Human Urinary Exosomes. Anal Chem 2019; 91:13528-13537. [PMID: 31539226 PMCID: PMC6834888 DOI: 10.1021/acs.analchem.9b02620] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The study of exosomes has become increasingly popular due to their potentially important biological roles. Urine can be used as an effective source of exosomes for noninvasive investigations into the pathophysiological states of the urinary system, but first, detailed characterization of exosomal components in healthy individuals is essential. Here, we significantly extend the number of N-glycan compositions, including sulfated species, identified from urinary exosomes and determine the sialic acid linkages for many of those compositions. Capillary electrophoresis-mass spectrometry (CE-MS), matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS), and capillary liquid chromatography-tandem mass spectrometry (LC-MS/MS) were used to identify N-glycan and sulfated N-glycan compositions. Second, because the alteration of sialylation patterns has been previously implicated in various disease states, ion-exchange chromatography, microfluidic capillary electrophoresis (CE), and MALDI-MS were adopted to resolve positional isomers of sialic acids. Structures of the sialyl-linkage isomers were assigned indirectly through α2-3 sialidase treatment and sialic acid linkage-specific alkylamidation (SALSA). In total, we have identified 219 N-glycan structures that include 175 compositions, 64 sialic acid linkage isomers, 26 structural isomers, and 27 sulfated glycans.
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Affiliation(s)
- Woran Song
- Department of Chemistry , Indiana University , Bloomington , Indiana 47405-7102 , United States
| | - Xiaomei Zhou
- Department of Chemistry , Indiana University , Bloomington , Indiana 47405-7102 , United States
| | - John D Benktander
- Department of Chemistry , Indiana University , Bloomington , Indiana 47405-7102 , United States
| | - Stefan Gaunitz
- Department of Chemistry , Indiana University , Bloomington , Indiana 47405-7102 , United States
| | - Guozhang Zou
- Department of Chemistry , Indiana University , Bloomington , Indiana 47405-7102 , United States
| | - Ziyu Wang
- Department of Chemistry , Indiana University , Bloomington , Indiana 47405-7102 , United States
| | - Milos V Novotny
- Department of Chemistry , Indiana University , Bloomington , Indiana 47405-7102 , United States
| | - Stephen C Jacobson
- Department of Chemistry , Indiana University , Bloomington , Indiana 47405-7102 , United States
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22
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Kunej T. Rise of Systems Glycobiology and Personalized Glycomedicine: Why and How to Integrate Glycomics with Multiomics Science? OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2019; 23:615-622. [PMID: 31651212 DOI: 10.1089/omi.2019.0149] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Glycomics is a rapidly emerging subspecialty of system sciences that evaluates the structures and functions of glycans in biological systems. Moreover, glycomics informs allied scholarships such as systems glycobiology and personalized glycomedicine that collectively aim to explain the role of glycans in person-to-person and between-population variations in disease susceptibility and response to health interventions such as drugs, nutrition, and vaccines. For glycomics to make greater, systems-scale, contributions to biology and medical research, it is facing a new developmental challenge: transition from single omics to multiomics integrative technology platforms. A comprehensive map of all possible connections between glycomics and other omics types has not yet been developed. Glycomics aims to discover a complex interplay of molecular interactions; however, little is known about the regulatory networks controlling these complex processes. In addition, the glycomics knowledgebase is presently scattered across various publications and databases, and therefore does not enable a holistic or systems view of this study field. Therefore, researchers are not always aware, for example, that a given analyzed genetic locus is linked with glycans, and that there are also glycomics determinants of complex phenotypes in health and biology. This review presents several published examples of glycomics science in association with other omics levels, such as genomics, transcriptomics, proteomics, metabolomics, epigenomics, ncRNomics, lipidomics, and interactomics. I also highlight the salient knowledge gaps and suggest future research directions. Understanding the interconnections of glycomics with other omics technologies will facilitate multiomics science and knowledge integration, enhance development of systems glycobiology and personalized glycomedicine.
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Affiliation(s)
- Tanja Kunej
- University of Ljubljana, Biotechnical Faculty, Department of Animal Science, Domzale, Slovenia
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23
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Fernandes E, Ferreira D, Peixoto A, Freitas R, Relvas-Santos M, Palmeira C, Martins G, Barros A, Santos LL, Sarmento B, Ferreira JA. Glycoengineered nanoparticles enhance the delivery of 5-fluoroucil and paclitaxel to gastric cancer cells of high metastatic potential. Int J Pharm 2019; 570:118646. [PMID: 31465836 DOI: 10.1016/j.ijpharm.2019.118646] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Revised: 07/26/2019] [Accepted: 08/24/2019] [Indexed: 01/08/2023]
Abstract
Gastric cancer is the third leading cause of cancer-related death worldwide, with half of patients developing metastasis within 5 years after curative treatment. Moreover, many patients cannot tolerate or complete systemic treatment due severe side-effects, reducing their effectiveness. Thus, targeted therapeutics are warranted to improve treatment outcomes and reduce toxicity. Herein, poly(lactic-co-glycolic acid) (PLGA) nanoparticles loaded with 5-fluorouracil (5-FU) and paclitaxel were surface-functionalized with a monoclonal antibody targeting sialyl-Lewis A (sLeA), a known glycan mediating hematogenous metastasis. Nanoparticles, ranging from 137 to 330 nm, enabled the controlled release of cytotoxic drugs at neutral and acid pH, supporting potential for intravenous and oral administration. Nanoencapsulation also reduced the initial toxicity of the drugs against gastric cells, suggesting it may constitute a safer administration vehicle. Furthermore, nanoparticle functionalization significantly enhanced targeting to sLeA cells in vitro and ex vivo (over 40% in comparison to non-targeted nanoparticles). In summary, a glycoengineered nano-vehicle was successfully developed to deliver 5-FU and paclitaxel therapeutic agents to metastatic gastric cancer cells. We anticipate that this may constitute an important milestone to establish improved targeted therapeutics against gastric cancer. Given the pancarcinomic nature of the sLeA antigen, the translation of this solution to other models may be also envisaged.
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Affiliation(s)
- Elisabete Fernandes
- Experimental Pathology and Therapeutics Group, Portuguese Institute of Oncology, 4200-162 Porto, Portugal; Institute of Biomedical Sciences Abel Salazar (ICBAS), University of Porto, 4050-013 Porto, Portugal; Institute for Research and Innovation in Health (i3s), University of Porto, 4200-135 Porto, Portugal; Institute for Biomedical Engineering (INEB), 4200-135 Porto, Portugal; Digestive Cancer Research Group, 1495-161 Algés, Portugal
| | - Dylan Ferreira
- Experimental Pathology and Therapeutics Group, Portuguese Institute of Oncology, 4200-162 Porto, Portugal; Digestive Cancer Research Group, 1495-161 Algés, Portugal
| | - Andreia Peixoto
- Experimental Pathology and Therapeutics Group, Portuguese Institute of Oncology, 4200-162 Porto, Portugal; Institute of Biomedical Sciences Abel Salazar (ICBAS), University of Porto, 4050-013 Porto, Portugal; Institute for Research and Innovation in Health (i3s), University of Porto, 4200-135 Porto, Portugal; Institute for Biomedical Engineering (INEB), 4200-135 Porto, Portugal
| | - Rui Freitas
- Experimental Pathology and Therapeutics Group, Portuguese Institute of Oncology, 4200-162 Porto, Portugal; QOPNA, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Marta Relvas-Santos
- Experimental Pathology and Therapeutics Group, Portuguese Institute of Oncology, 4200-162 Porto, Portugal; Digestive Cancer Research Group, 1495-161 Algés, Portugal
| | - Carlos Palmeira
- Experimental Pathology and Therapeutics Group, Portuguese Institute of Oncology, 4200-162 Porto, Portugal; Immunology Department, Portuguese Institute of Oncology of Porto, 4200-162 Porto, Portugal; Health Science Faculty, University of Fernando Pessoa, 4249-004 Porto, Portugal
| | - Gabriela Martins
- Immunology Department, Portuguese Institute of Oncology of Porto, 4200-162 Porto, Portugal
| | - Anabela Barros
- Digestive Cancer Research Group, 1495-161 Algés, Portugal; Department of Medical Oncology, Coimbra Hospital and University Centre, 3075-075 Coimbra, Portugal
| | - Lúcio Lara Santos
- Experimental Pathology and Therapeutics Group, Portuguese Institute of Oncology, 4200-162 Porto, Portugal; Institute of Biomedical Sciences Abel Salazar (ICBAS), University of Porto, 4050-013 Porto, Portugal; Digestive Cancer Research Group, 1495-161 Algés, Portugal; Department of Surgical Oncology, Portuguese Institute of Oncology of Porto, 4200-162 Porto, Portugal; Porto Comprehensive Cancer Centre (P.ccc), 4200-162 Porto, Portugal
| | - Bruno Sarmento
- Institute for Research and Innovation in Health (i3s), University of Porto, 4200-135 Porto, Portugal; Institute for Biomedical Engineering (INEB), 4200-135 Porto, Portugal; Institute of Research and Advanced Training in Health Sciences and Technologies (CESPU), 4585-116 Gandra PRD, Portugal
| | - José Alexandre Ferreira
- Experimental Pathology and Therapeutics Group, Portuguese Institute of Oncology, 4200-162 Porto, Portugal; Institute of Biomedical Sciences Abel Salazar (ICBAS), University of Porto, 4050-013 Porto, Portugal; Porto Comprehensive Cancer Centre (P.ccc), 4200-162 Porto, Portugal.
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Deb B, Patel K, Sathe G, Kumar P. N-Glycoproteomic Profiling Reveals Alteration In Extracellular Matrix Organization In Non-Type Bladder Carcinoma. J Clin Med 2019; 8:jcm8091303. [PMID: 31450586 PMCID: PMC6780497 DOI: 10.3390/jcm8091303] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Revised: 08/01/2019] [Accepted: 08/11/2019] [Indexed: 01/03/2023] Open
Abstract
Treatment of advanced and metastatic bladder carcinoma is often ineffective and displays variable clinical outcomes. Studying this aggressive molecular subtype of bladder carcinoma will lead to better understanding of the pathogenesis which may lead to the identification of new therapeutic strategies. The non-type bladder subtype is phenotypically mesenchymal and has mesenchymal features with a high metastatic ability. Post-translational addition of oligosaccharide residues is an important modification that influences cellular functions and contributes to disease pathology. Here, we report the comparative analysis of N-linked glycosylation across bladder cancer subtypes. To analyze the glycosite-containing peptides, we carried out LC-MS/MS-based quantitative proteomic and glycoproteomic profiling. We identified 1299 unique N-linked glycopeptides corresponding to 460 proteins. Additionally, we identified 118 unique N-linked glycopeptides corresponding to 84 proteins to be differentially glycosylated only in non-type subtypes as compared to luminal/basal subtypes. Most of the altered glycoproteins were also observed with changes in their global protein expression levels. However, alterations in 55 differentially expressed glycoproteins showed no significant change at the protein abundance level, representing that the glycosylation site occupancy was changed between the non-type subtype and luminal/basal subtypes. Importantly, the extracellular matrix organization pathway was dysregulated in the non-type subtype of bladder carcinoma. N-glycosylation modifications in the extracellular matrix organization proteins may be a contributing factor for the mesenchymal aggressive phenotype in non-type subtype. These aberrant protein glycosylation would provide additional avenues to employ glycan-based therapies and may lead to the identification of novel therapeutic targets.
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Affiliation(s)
- Barnali Deb
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, India
- Manipal Academy of Higher Education (MAHE), Manipal 576104, Karnataka, India
| | - Krishna Patel
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, India
- School of Biotechnology, Amrita Vishwa Vidyapeetham, Kollam 690525, India
| | - Gajanan Sathe
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, India.
- Manipal Academy of Higher Education (MAHE), Manipal 576104, Karnataka, India.
| | - Prashant Kumar
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, India.
- Manipal Academy of Higher Education (MAHE), Manipal 576104, Karnataka, India.
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25
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Peixoto A, Relvas-Santos M, Azevedo R, Santos LL, Ferreira JA. Protein Glycosylation and Tumor Microenvironment Alterations Driving Cancer Hallmarks. Front Oncol 2019; 9:380. [PMID: 31157165 PMCID: PMC6530332 DOI: 10.3389/fonc.2019.00380] [Citation(s) in RCA: 190] [Impact Index Per Article: 38.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Accepted: 04/23/2019] [Indexed: 12/12/2022] Open
Abstract
Decades of research have disclosed a plethora of alterations in protein glycosylation that decisively impact in all stages of disease and ultimately contribute to more aggressive cell phenotypes. The biosynthesis of cancer-associated glycans and its reflection in the glycoproteome is driven by microenvironmental cues and these events act synergistically toward disease evolution. Such intricate crosstalk provides the molecular foundations for the activation of relevant oncogenic pathways and leads to functional alterations driving invasion and disease dissemination. However, it also provides an important source of relevant glyco(neo)epitopes holding tremendous potential for clinical intervention. Therefore, we highlight the transversal nature of glycans throughout the currently accepted cancer hallmarks, with emphasis on the crosstalk between glycans and the tumor microenvironment stromal components. Focus is also set on the pressing need to include glycans and glycoconjugates in comprehensive panomics models envisaging molecular-based precision medicine capable of improving patient care. We foresee that this may provide the necessary rationale for more comprehensive studies and molecular-based intervention.
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Affiliation(s)
- Andreia Peixoto
- Experimental Pathology and Therapeutics Group, Portuguese Institute of Oncology, Porto, Portugal.,Institute of Biomedical Sciences Abel Salazar, University of Porto, Porto, Portugal.,Tumour and Microenvironment Interactions Group, INEB-Institute for Biomedical Engineering, Porto, Portugal.,Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
| | - Marta Relvas-Santos
- Experimental Pathology and Therapeutics Group, Portuguese Institute of Oncology, Porto, Portugal
| | - Rita Azevedo
- Experimental Pathology and Therapeutics Group, Portuguese Institute of Oncology, Porto, Portugal.,Institute of Biomedical Sciences Abel Salazar, University of Porto, Porto, Portugal
| | - Lúcio Lara Santos
- Experimental Pathology and Therapeutics Group, Portuguese Institute of Oncology, Porto, Portugal.,Department of Surgical Oncology, Portuguese Institute of Oncology, Porto, Portugal
| | - José Alexandre Ferreira
- Experimental Pathology and Therapeutics Group, Portuguese Institute of Oncology, Porto, Portugal.,Institute of Biomedical Sciences Abel Salazar, University of Porto, Porto, Portugal.,Porto Comprehensive Cancer Center, Porto, Portugal
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26
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Neves M, Azevedo R, Lima L, Oliveira MI, Peixoto A, Ferreira D, Soares J, Fernandes E, Gaiteiro C, Palmeira C, Cotton S, Mereiter S, Campos D, Afonso LP, Ribeiro R, Fraga A, Tavares A, Mansinho H, Monteiro E, Videira PA, Freitas PP, Reis CA, Santos LL, Dieguez L, Ferreira JA. Exploring sialyl-Tn expression in microfluidic-isolated circulating tumour cells: A novel biomarker and an analytical tool for precision oncology applications. N Biotechnol 2018; 49:77-87. [PMID: 30273682 DOI: 10.1016/j.nbt.2018.09.004] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2018] [Revised: 09/14/2018] [Accepted: 09/25/2018] [Indexed: 12/17/2022]
Abstract
Circulating tumour cells (CTCs) originating from a primary tumour, lymph nodes and distant metastases hold great potential for liquid biopsies by providing a molecular fingerprint for disease dissemination and its temporal evolution through the course of disease management. CTC enumeration, classically defined on the basis of surface expression of Epithelial Cell Adhesion Molecule (EpCAM) and absence of the pan-leukocyte marker CD45, has been shown to correlate with clinical outcome. However, existing approaches introduce bias into the subsets of captured CTCs, which may exclude biologically and clinically relevant subpopulations. Here we explore the overexpression of the membrane protein O-glycan sialyl-Tn (STn) antigen in advanced bladder and colorectal tumours, but not in blood cells, to propose a novel CTC isolation technology. Using a size-based microfluidic device, we show that the majority (>90%) of CTCs isolated from the blood of patients with metastatic bladder and colorectal cancers express the STn antigen, supporting a link with metastasis. STn+ CTC counts were significantly higher than EpCAM-based detection in colorectal cancer, providing a more efficient cell-surface biomarker for CTC isolation. Exploring this concept, we constructed a glycan affinity-based microfluidic device for selective isolation of STn+ CTCs and propose an enzyme-based strategy for the recovery of viable cancer cells for downstream investigations. Finally, clinically relevant cancer biomarkers (transcripts and mutations) in bladder and colorectal tumours, were identified in cells isolated by microfluidics, confirming their malignant origin and highlighting the potential of this technology in the context of precision oncology.
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Affiliation(s)
- Manuel Neves
- Portuguese Institute of Oncology, Porto, Portugal; Institute of Biomedical Sciences Abel Salazar, University of Porto, Portugal; International Iberian Nanotechnology Laboratory (INL), Braga, Portugal
| | - Rita Azevedo
- Portuguese Institute of Oncology, Porto, Portugal; Institute of Biomedical Sciences Abel Salazar, University of Porto, Portugal
| | - Luís Lima
- Portuguese Institute of Oncology, Porto, Portugal; Glycobiology in Cancer, Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Portugal; Instituto de Investigação e Inovação em Saúde (I3S), University of Porto, Portugal
| | - Marta I Oliveira
- International Iberian Nanotechnology Laboratory (INL), Braga, Portugal
| | - Andreia Peixoto
- Portuguese Institute of Oncology, Porto, Portugal; Institute of Biomedical Sciences Abel Salazar, University of Porto, Portugal; Instituto de Investigação e Inovação em Saúde (I3S), University of Porto, Portugal; INEB-Institute for Biomedical Engineering of Porto, Portugal
| | | | - Janine Soares
- Portuguese Institute of Oncology, Porto, Portugal; Institute of Biomedical Sciences Abel Salazar, University of Porto, Portugal
| | - Elisabete Fernandes
- Portuguese Institute of Oncology, Porto, Portugal; Institute of Biomedical Sciences Abel Salazar, University of Porto, Portugal; Instituto de Investigação e Inovação em Saúde (I3S), University of Porto, Portugal; INEB-Institute for Biomedical Engineering of Porto, Portugal
| | - Cristiana Gaiteiro
- Portuguese Institute of Oncology, Porto, Portugal; Institute of Biomedical Sciences Abel Salazar, University of Porto, Portugal
| | | | - Sofia Cotton
- Portuguese Institute of Oncology, Porto, Portugal; Institute of Biomedical Sciences Abel Salazar, University of Porto, Portugal
| | - Stefan Mereiter
- Glycobiology in Cancer, Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Portugal; Instituto de Investigação e Inovação em Saúde (I3S), University of Porto, Portugal
| | - Diana Campos
- Glycobiology in Cancer, Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Portugal; Instituto de Investigação e Inovação em Saúde (I3S), University of Porto, Portugal
| | | | - Ricardo Ribeiro
- Instituto de Investigação e Inovação em Saúde (I3S), University of Porto, Portugal; INEB-Institute for Biomedical Engineering of Porto, Portugal
| | - Avelino Fraga
- Hospital Centre- Hospital of Santo António of Porto, Portugal
| | - Ana Tavares
- Portuguese Institute of Oncology, Porto, Portugal
| | - Hélder Mansinho
- Hemato-Oncology Clinic, Hospital Garcia de Orta, EPE, Almada, Portugal; Gupo de Investigação do Cancro Digestivo-GICD, Portugal
| | | | - Paula A Videira
- Glycoimmunology Group, UCIBIO, Departamento Ciências da Vida, Faculdade de Ciência e Tecnologia, Universidade NOVA de Lisboa, Caparica, Portugal
| | - Paulo P Freitas
- International Iberian Nanotechnology Laboratory (INL), Braga, Portugal; INESC - Microsistemas e Nanotecnologias, Lisboa, Lisbon, Portugal
| | - Celso A Reis
- Institute of Biomedical Sciences Abel Salazar, University of Porto, Portugal; Glycobiology in Cancer, Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Portugal; Instituto de Investigação e Inovação em Saúde (I3S), University of Porto, Portugal; Faculty of Medicine, University of Porto, Portugal
| | - Lúcio Lara Santos
- Portuguese Institute of Oncology, Porto, Portugal; Institute of Biomedical Sciences Abel Salazar, University of Porto, Portugal; UFP: School of Health Sciences, Fernando Pessoa University of Porto, Portugal; Porto Comprehensive Cancer Center (P.ccc), Porto, Portugal
| | - Lorena Dieguez
- International Iberian Nanotechnology Laboratory (INL), Braga, Portugal
| | - José Alexandre Ferreira
- Portuguese Institute of Oncology, Porto, Portugal; Institute of Biomedical Sciences Abel Salazar, University of Porto, Portugal; International Iberian Nanotechnology Laboratory (INL), Braga, Portugal; Glycobiology in Cancer, Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Portugal; Instituto de Investigação e Inovação em Saúde (I3S), University of Porto, Portugal.
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27
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Drabik A. Glycopeptides as a Tool for Early Detection of Cancer. Proteomics Clin Appl 2018; 12:e1800108. [PMID: 30094950 DOI: 10.1002/prca.201800108] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Indexed: 12/17/2022]
Abstract
Protein glycosylation, as one of the most common and complex posttranslational modifications, plays an important role in many biological processes. Along with the intensive progress in MS techniques and development of glycan search tools and databases, glycoproteomics has become a popular subject of studies. The possibility of simultaneous identification of amino acid sequence, glycosylation sites, and glycan composition enabled the monitoring of changes in glycosylation patterns in various pathological states. In this issue, Saraswat et al. describe MS-based investigations of glycopeptide changes in oral cavity squamous cell carcinoma (OSCC). Their findings indicate glycopeptides with changed expression levels and the presence of altered glycan forms observed in four proteins derived from OSCC patients' sera. Proteins carrying this distinctive pattern are in the group of the most abundant components of serum, IgG1, IgG4, HPT, and TRFE, which makes their identification more accessible. Described changes, characteristic for cancer serum samples, may be considered as potential diagnostic indicators of OSCC; however, there is still a need to establish a universal glycopeptide-based biomarkers database, where all glycoproteomic data can be collected from all types of cancer studies and evaluated using meta-analyses. Only then, early diagnosis of patients using MS-based approach will make sense, as those investigations are very convoluted, and all efforts made during sample preparation and analysis will pay off when comprehensive anticancer prevention will be achieved during single measurement.
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Affiliation(s)
- Anna Drabik
- Department of Biochemistry and Neurobiology, AGH University of Science and Technology, Krakow, Poland
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28
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Ferdosi S, Ho TH, Castle EP, Stanton ML, Borges CR. Behavior of blood plasma glycan features in bladder cancer. PLoS One 2018; 13:e0201208. [PMID: 30040854 PMCID: PMC6057681 DOI: 10.1371/journal.pone.0201208] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Accepted: 07/10/2018] [Indexed: 01/01/2023] Open
Abstract
Despite systemic therapy and cystectomy, bladder cancer is characterized by a high recurrence rate. Serum glycomics represents a promising source of prognostic markers for monitoring patients. Our approach, which we refer to as "glycan node analysis", constitutes the first example of molecularly "bottom-up" glycomics. It is based on a global glycan methylation analysis procedure that is applied to whole blood plasma/serum. The approach detects and quantifies partially methylated alditol acetates arising from unique glycan features such as α2-6 sialylation, β1-4 branching, and core fucosylation that have been pooled together from across all intact glycans within a sample into a single GC-MS chromatographic peak. We applied this method to 122 plasma samples from former and current bladder cancer patients (n = 72 former cancer patients with currently no evidence of disease (NED); n = 38 non-muscle invasive bladder cancer (NMIBC) patients; and n = 12 muscle invasive bladder cancer (MIBC) patients) along with plasma from 30 certifiably healthy living kidney donors. Markers for α2-6 sialylation, β1-4 branching, β1-6 branching, and outer-arm fucosylation were able to separate current and former (NED) cases from certifiably healthy controls (ROC curve c-statistics ~ 0.80); but NED, NMIBC, and MIBC were not distinguished from one another. Based on the unexpectedly high levels of these glycan nodes in the NED patients, we hypothesized that recurrence of this disease could be predicted by some of the elevated glycan features. Indeed, α2-6 sialylation and β1-6 branching were able to predict recurrence from the NED state using a Cox proportional hazards regression model adjusted for age, gender, and time from cancer. The levels of these two glycan features were correlated to C-reactive protein concentration, an inflammation marker and known prognostic indicator for bladder cancer, further strengthening the link between inflammation and abnormal plasma protein glycosylation.
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Affiliation(s)
- Shadi Ferdosi
- School of Molecular Sciences, Arizona State University, Tempe, AZ, United States of America
- Virginia G. Piper Center for Personalized Diagnostics, The Biodesign Institute at Arizona State University, Tempe, AZ, United States of America
| | - Thai H. Ho
- Division of Hematology and Medical Oncology, Mayo Clinic, Phoenix, AZ, United States of America
| | - Erik P. Castle
- Department of Urology, Mayo Clinic, Phoenix, AZ, United States of America
| | - Melissa L. Stanton
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Phoenix, AZ, United States of America
| | - Chad R. Borges
- School of Molecular Sciences, Arizona State University, Tempe, AZ, United States of America
- Virginia G. Piper Center for Personalized Diagnostics, The Biodesign Institute at Arizona State University, Tempe, AZ, United States of America
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29
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Glycan affinity magnetic nanoplatforms for urinary glycobiomarkers discovery in bladder cancer. Talanta 2018; 184:347-355. [DOI: 10.1016/j.talanta.2018.03.028] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2017] [Revised: 03/07/2018] [Accepted: 03/11/2018] [Indexed: 01/26/2023]
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30
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Azevedo R, Soares J, Peixoto A, Cotton S, Lima L, Santos LL, Ferreira JA. Circulating tumor cells in bladder cancer: Emerging technologies and clinical implications foreseeing precision oncology. Urol Oncol 2018. [PMID: 29530466 DOI: 10.1016/j.urolonc.2018.02.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
CONTEXT Circulating tumor cells (CTC) in peripheral blood of cancer patients provide an opportunity for real-time liquid biopsies capable of aiding early intervention, therapeutic decision, response to therapy, and prognostication. Nevertheless, the rare and potentially heterogeneous molecular nature of CTC has delayed the standardization of robust high-throughput capture/enrichment and characterization technologies. OBJECTIVE This review aims to systematize emerging solutions for CTC analysis in bladder cancer (BC), their opportunities and limitations, while providing key insights on specific technologic aspects that may ultimately guide molecular studies and clinical implementation. EVIDENCE ACQUISITION State-of-the-art screening for CTC technologies and clinical applications in BC was conducted in MEDLINE through PubMed. EVIDENCE SYNTHESIS From 200 records identified by the search query, 25 original studies and 1 meta-analysis met the full criteria for selection. A significant myriad of CTC technological platforms, including immunoaffinity, biophysical, and direct CTC detection by molecular methods have been presented. Despite their preliminary nature and irrespective of the applied technology, most studies concluded that CTC counts in peripheral blood correlated with metastasis. Associations with advanced tumor stage and grade and worst prognosis have been suggested. However, the unspecific nature, low sensitivity, and the lack of standardization of current methods still constitutes a major drawback. Moreover, few comprehensive molecular studies have been conducted on these poorly known class of malignant cells. CONCLUSION The current rationale supports the importance of moving the CTC field beyond proof of concept studies toward molecular-based solutions capable of improving disease management. The road has been paved for identification of highly specific CTC biomarkers and novel targeted approaches, foreseeing successful clinical applications.
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Affiliation(s)
- Rita Azevedo
- Experimental Pathology and Therapeutics Group, Research Centre, Portuguese Oncology Institute of Porto (IPO-Porto), R. Dr. António Bernardino de Almeida 62, 4200-162 Porto, Portugal; Institute of Biomedical Sciences Abel Salazar, University of Porto, R. Jorge de Viterbo Ferreira 228, 4050-013 Porto, Portugal
| | - Janine Soares
- Experimental Pathology and Therapeutics Group, Research Centre, Portuguese Oncology Institute of Porto (IPO-Porto), R. Dr. António Bernardino de Almeida 62, 4200-162 Porto, Portugal
| | - Andreia Peixoto
- Experimental Pathology and Therapeutics Group, Research Centre, Portuguese Oncology Institute of Porto (IPO-Porto), R. Dr. António Bernardino de Almeida 62, 4200-162 Porto, Portugal; Institute of Biomedical Sciences Abel Salazar, University of Porto, R. Jorge de Viterbo Ferreira 228, 4050-013 Porto, Portugal; Institute for Research and Innovation in Health (i3S), University of Porto, R. Alfredo Allen, 4200-135 Porto, Portugal
| | - Sofia Cotton
- Experimental Pathology and Therapeutics Group, Research Centre, Portuguese Oncology Institute of Porto (IPO-Porto), R. Dr. António Bernardino de Almeida 62, 4200-162 Porto, Portugal
| | - Luís Lima
- Experimental Pathology and Therapeutics Group, Research Centre, Portuguese Oncology Institute of Porto (IPO-Porto), R. Dr. António Bernardino de Almeida 62, 4200-162 Porto, Portugal; Institute for Research and Innovation in Health (i3S), University of Porto, R. Alfredo Allen, 4200-135 Porto, Portugal; Glycobiology in Cancer, Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), R. Júlio Amaral de Carvalho 45, 4200-135 Porto, Portugal; Porto Comprehensive Cancer Centre (P.ccc), R. Dr. António Bernardino de Almeida 62, 4200-162 Porto, Portugal
| | - Lúcio Lara Santos
- Experimental Pathology and Therapeutics Group, Research Centre, Portuguese Oncology Institute of Porto (IPO-Porto), R. Dr. António Bernardino de Almeida 62, 4200-162 Porto, Portugal; Institute of Biomedical Sciences Abel Salazar, University of Porto, R. Jorge de Viterbo Ferreira 228, 4050-013 Porto, Portugal; Health School of University Fernando Pessoa, Praça de 9 de Abril 349, 4249-004 Porto, Portugal; Department of Surgical Oncology, Portuguese Institute of Oncology (IPO-Porto), R. Dr. António Bernardino de Almeida 62, 4200-162 Porto, Portugal
| | - José Alexandre Ferreira
- Experimental Pathology and Therapeutics Group, Research Centre, Portuguese Oncology Institute of Porto (IPO-Porto), R. Dr. António Bernardino de Almeida 62, 4200-162 Porto, Portugal; Institute of Biomedical Sciences Abel Salazar, University of Porto, R. Jorge de Viterbo Ferreira 228, 4050-013 Porto, Portugal; Institute for Research and Innovation in Health (i3S), University of Porto, R. Alfredo Allen, 4200-135 Porto, Portugal; Glycobiology in Cancer, Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), R. Júlio Amaral de Carvalho 45, 4200-135 Porto, Portugal; Porto Comprehensive Cancer Centre (P.ccc), R. Dr. António Bernardino de Almeida 62, 4200-162 Porto, Portugal; International Iberian Nanotechnology Laboratory (INL), Avda. Mestre José Veiga, 4715 Braga, Portugal.
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