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Mikami M, Tanabe K, Imanishi T, Ikeda M, Hirasawa T, Yasaka M, Machida H, Yoshida H, Hasegawa M, Shimada M, Kato T, Kitamura S, Kato H, Fujii T, Kobayashi Y, Suzuki N, Tanaka K, Murakami I, Katahira T, Hayashi C, Matsuo K. Comprehensive serum glycopeptide spectra analysis to identify early-stage epithelial ovarian cancer. Sci Rep 2024; 14:20000. [PMID: 39198565 PMCID: PMC11358426 DOI: 10.1038/s41598-024-70228-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2024] [Accepted: 08/14/2024] [Indexed: 09/01/2024] Open
Abstract
Epithelial ovarian cancer (EOC) is widely recognized as the most lethal gynecological malignancy; however, its early-stage detection remains a considerable clinical challenge. To address this, we have introduced a new method, named Comprehensive Serum Glycopeptide Spectral Analysis (CSGSA), which detects early-stage cancer by combining glycan alterations in serum glycoproteins with tumor markers. We detected 1712 glycopeptides using liquid chromatography-mass spectrometry from the sera obtained from 564 patients with EOC and 1149 controls across 13 institutions. Furthermore, we used a convolutional neural network to analyze the expression patterns of the glycopeptides and tumor markers. Using this approach, we successfully differentiated early-stage EOC (Stage I) from non-EOC, with an area under the curve (AUC) of 0.924 in receiver operating characteristic (ROC) analysis. This method markedly outperforms conventional tumor markers, including cancer antigen 125 (CA125, 0.842) and human epididymis protein 4 (HE4, 0.717). Notably, our method exhibited remarkable efficacy in differentiating early-stage ovarian clear cell carcinoma from endometrioma, achieving a ROC-AUC of 0.808, outperforming CA125 (0.538) and HE4 (0.557). Our study presents a promising breakthrough in the early detection of EOC through the innovative CSGSA method. The integration of glycan alterations with cancer-related tumor markers has demonstrated exceptional diagnostic potential.
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Affiliation(s)
- Mikio Mikami
- Department of Obstetrics and Gynecology, Tokai University School of Medicine, Isehara, Kanagawa, Japan.
| | - Kazuhiro Tanabe
- Medical Solution Promotion Department, Medical Solution Segment, LSI Medience Corporation, Itabashi-ku, Tokyo, Japan.
| | - Tadashi Imanishi
- Genome Diversity Research Center, Graduate School of Medicine, Tokai University, Isehara, Kanagawa, Japan
- Department of Molecular Life Science, Tokai University School of Medicine, Isehara, Kanagawa, Japan
- Institute of Medical Sciences, Tokai University, Isehara, Kanagawa, Japan
| | - Masae Ikeda
- Department of Obstetrics and Gynecology, Tokai University School of Medicine, Isehara, Kanagawa, Japan
| | - Takeshi Hirasawa
- Department of Obstetrics and Gynecology, Tokai University School of Medicine, Isehara, Kanagawa, Japan
| | - Miwa Yasaka
- Department of Obstetrics and Gynecology, Tokai University School of Medicine, Isehara, Kanagawa, Japan
| | - Hiroko Machida
- Department of Obstetrics and Gynecology, Tokai University School of Medicine, Isehara, Kanagawa, Japan
| | - Hiroshi Yoshida
- Department of Obstetrics and Gynecology, Tokai University School of Medicine, Isehara, Kanagawa, Japan
| | - Masanori Hasegawa
- Department of Urology, Tokai University School of Medicine, Isehara, Kanagawa, Japan
| | - Muneaki Shimada
- Department of Obstetrics and Gynecology, Tohoku University School of Medicine, Sendai, Miyagi, Japan
| | - Tomoyasu Kato
- Department of Gynecology, National Cancer Center Hospital, Chuo-ku, Tokyo, Japan
| | - Shoichi Kitamura
- Department of Gynecology, National Cancer Center Hospital, Chuo-ku, Tokyo, Japan
| | - Hisamori Kato
- Department of Gynecologic Oncology, Kanagawa Cancer Center, Yokohama, Kanagawa, Japan
| | - Takuma Fujii
- Department of Obstetrics and Gynecology, Fujita Health University School of Medicine, Toyoake, Aichi, Japan
| | - Yoichi Kobayashi
- Department of Obstetrics and Gynecology, Faculty of Medicine, Kyorin University, Mitaka, Tokyo, Japan
| | - Nao Suzuki
- Department of Obstetrics and Gynecology, St. Marianna University School of Medicine, Kawasaki, Kanagawa, Japan
| | - Kyoko Tanaka
- Department of Obstetrics and Gynecology, Toho University Ohashi Medical Center, Meguro-ku, Tokyo, Japan
| | - Isao Murakami
- Department of Obstetrics and Gynecology, Toho University Ohashi Medical Center, Meguro-ku, Tokyo, Japan
| | - Tomoko Katahira
- Medical Solution Promotion Department, Medical Solution Segment, LSI Medience Corporation, Itabashi-ku, Tokyo, Japan
| | - Chihiro Hayashi
- Medical Solution Promotion Department, Medical Solution Segment, LSI Medience Corporation, Itabashi-ku, Tokyo, Japan
| | - Koji Matsuo
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, University of Southern California, Los Angeles, CA, USA
- Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, USA
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2
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Zertuche-Martínez C, Velázquez-Enríquez JM, González-García K, Santos-Álvarez JC, Romero-Tlalolini MDLÁ, Pina-Canseco S, Pérez-Campos Mayoral L, Muriel P, Villa-Treviño S, Baltiérrez-Hoyos R, Arellanes-Robledo J, Vásquez-Garzón VR. Discovery of candidate biomarkers from plasma-derived extracellular vesicles of patients with cirrhosis and hepatocellular carcinoma: an exploratory proteomic study. Mol Omics 2024; 20:483-495. [PMID: 39011654 DOI: 10.1039/d4mo00043a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/17/2024]
Abstract
Extracellular vesicles (EVs) represent an attractive source of biomarkers due to their biomolecular cargo. The aim of this study was to identify candidate protein biomarkers from plasma-derived EVs of patients with liver cirrhosis (LC) and hepatocellular carcinoma (HCC). Plasma-derived EVs from healthy participants (HP), LC, and HCC patients (eight samples each) were subjected to label-free quantitative proteomic analysis using LC-MS/MS. A total of 248 proteins were identified, and differentially expressed proteins (DEPs) were obtained after pairwise comparison. We found that DEPs mainly involve complement cascade activation, coagulation pathways, cholesterol metabolism, and extracellular matrix components. By choosing a panel of up- and down-regulated proteins involved in cirrhotic and carcinogenesis processes, TGFBI, LGALS3BP, C7, SERPIND1, and APOC3 were found to be relevant for LC patients, while LRG1, TUBA1C, TUBB2B, ACTG1, C9, HP, FGA, FGG, FN1, PLG, APOB and ITIH2 were associated with HCC patients, which could discriminate both diseases. In addition, we identified the top shared proteins in both diseases, which included LCAT, SERPINF2, A2M, CRP, and VWF. Thus, our exploratory proteomic study revealed that these proteins might play an important role in the disease progression and represent a panel of candidate biomarkers for the prognosis and diagnosis of LC and HCC.
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Affiliation(s)
- Cecilia Zertuche-Martínez
- Laboratorio de Fibrosis y cáncer, Facultad de Medicina y Cirugía, Universidad Autónoma Benito Juárez de Oaxaca, Oaxaca de Juárez 68120, Oaxaca, Mexico
| | - Juan Manuel Velázquez-Enríquez
- Laboratorio de Fibrosis y cáncer, Facultad de Medicina y Cirugía, Universidad Autónoma Benito Juárez de Oaxaca, Oaxaca de Juárez 68120, Oaxaca, Mexico
| | - Karina González-García
- Laboratorio de Fibrosis y cáncer, Facultad de Medicina y Cirugía, Universidad Autónoma Benito Juárez de Oaxaca, Oaxaca de Juárez 68120, Oaxaca, Mexico
| | - Jovito Cesar Santos-Álvarez
- Laboratorio de Fibrosis y cáncer, Facultad de Medicina y Cirugía, Universidad Autónoma Benito Juárez de Oaxaca, Oaxaca de Juárez 68120, Oaxaca, Mexico
| | | | - Socorro Pina-Canseco
- Centro de Investigación Facultad de Medicina UNAM UABJO, Facultad de Medicina y Cirugía, Universidad Autónoma Benito Juárez de Oaxaca, Oaxaca de Juárez 68120, Oaxaca, Mexico
| | - Laura Pérez-Campos Mayoral
- Centro de Investigación Facultad de Medicina UNAM UABJO, Facultad de Medicina y Cirugía, Universidad Autónoma Benito Juárez de Oaxaca, Oaxaca de Juárez 68120, Oaxaca, Mexico
| | - Pablo Muriel
- Laboratorio de Hepatología Experimental, Departamento de Farmacología, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Ciudad de México 07000, Mexico
| | - Saúl Villa-Treviño
- Departamento de Biología Celular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Ciudad de México 07360, Mexico
| | - Rafael Baltiérrez-Hoyos
- CONAHCYT-Facultad de Medicina y Cirugía, Universidad Autónoma Benito Juárez de Oaxaca, Oaxaca de Juárez 68120, Oaxaca, Mexico.
| | | | - Verónica Rocío Vásquez-Garzón
- CONAHCYT-Facultad de Medicina y Cirugía, Universidad Autónoma Benito Juárez de Oaxaca, Oaxaca de Juárez 68120, Oaxaca, Mexico.
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3
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Urbiola-Salvador V, Jabłońska A, Miroszewska D, Kamysz W, Duzowska K, Drężek-Chyła K, Baber R, Thieme R, Gockel I, Zdrenka M, Śrutek E, Szylberg Ł, Jankowski M, Bała D, Zegarski W, Nowikiewicz T, Makarewicz W, Adamczyk A, Ambicka A, Przewoźnik M, Harazin-Lechowska A, Ryś J, Macur K, Czaplewska P, Filipowicz N, Piotrowski A, Dumanski JP, Chen Z. Mass Spectrometry Proteomics Characterization of Plasma Biomarkers for Colorectal Cancer Associated With Inflammation. Biomark Insights 2024; 19:11772719241257739. [PMID: 38911905 PMCID: PMC11191626 DOI: 10.1177/11772719241257739] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Accepted: 05/07/2024] [Indexed: 06/25/2024] Open
Abstract
Background Colorectal cancer (CRC) prognosis is determined by the disease stage with low survival rates for advanced stages. Current CRC screening programs are mainly using colonoscopy, limited by its invasiveness and high cost. Therefore, non-invasive, cost-effective, and accurate alternatives are urgently needed. Objective and design This retrospective multi-center plasma proteomics study was performed to identify potential blood-based biomarkers in 36 CRC patients and 26 healthy volunteers by high-resolution mass spectrometry proteomics followed by the validation in an independent CRC cohort (60 CRC patients and 44 healthy subjects) of identified selected biomarkers. Results Among the 322 identified plasma proteins, 37 were changed between CRC patients and healthy volunteers and were associated with the complement cascade, cholesterol metabolism, and SERPIN family members. Increased levels in CRC patients of the complement proteins C1QB, C4B, and C5 as well as pro-inflammatory proteins, lipopolysaccharide-binding protein (LBP) and serum amyloid A4, constitutive (SAA4) were revealed for first time. Importantly, increased level of C5 was verified in an independent validation CRC cohort. Increased C4B and C8A levels were correlated with cancer-associated inflammation and CRC progression, while cancer-associated inflammation was linked to the acute-phase reactant leucine-rich alpha-2-glycoprotein 1 (LRG1) and ceruloplasmin. Moreover, a 4-protein signature including C4B, C8A, apolipoprotein C2 (APO) C2, and immunoglobulin heavy constant gamma 2 was changed between early and late CRC stages. Conclusion Our results suggest that C5 could be a potential biomarker for CRC diagnosis. Further validation studies will aid the application of these new potential biomarkers to improve CRC diagnosis and patient care.
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Affiliation(s)
- Víctor Urbiola-Salvador
- Intercollegiate Faculty of Biotechnology of University of Gdańsk and Medical University of Gdańsk, University of Gdańsk, Gdańsk, Pomeranian, Poland
| | - Agnieszka Jabłońska
- Intercollegiate Faculty of Biotechnology of University of Gdańsk and Medical University of Gdańsk, University of Gdańsk, Gdańsk, Pomeranian, Poland
| | - Dominika Miroszewska
- Intercollegiate Faculty of Biotechnology of University of Gdańsk and Medical University of Gdańsk, University of Gdańsk, Gdańsk, Pomeranian, Poland
| | - Weronika Kamysz
- Intercollegiate Faculty of Biotechnology of University of Gdańsk and Medical University of Gdańsk, University of Gdańsk, Gdańsk, Pomeranian, Poland
| | - Katarzyna Duzowska
- 3P-Medicine Laboratory, Medical University of Gdańsk, Gdańsk, Pomeranian, Poland
| | - Kinga Drężek-Chyła
- 3P-Medicine Laboratory, Medical University of Gdańsk, Gdańsk, Pomeranian, Poland
| | - Ronny Baber
- Institute of Laboratory Medicine, Clinical Chemistry and Molecular Diagnostics, Universitätsklinikum Leipzig, Leipzig University, Leipzig, Saxony, Germany
- Leipzig Medical Biobank, Leipzig University, Leipzig, Saxony, Germany
| | - René Thieme
- Department of Visceral, Transplant, Thoracic and Vascular Surgery, University Hospital Leipzig, Leipzig, Saxony, Germany
| | - Ines Gockel
- Department of Visceral, Transplant, Thoracic and Vascular Surgery, University Hospital Leipzig, Leipzig, Saxony, Germany
| | - Marek Zdrenka
- Department of Tumor Pathology and Pathomorphology, Oncology Center‒Prof. Franciszek Łukaszczyk Memorial Hospital, Bydgoszcz, Kuyavian-Pomeranian, Poland
| | - Ewa Śrutek
- Department of Tumor Pathology and Pathomorphology, Oncology Center‒Prof. Franciszek Łukaszczyk Memorial Hospital, Bydgoszcz, Kuyavian-Pomeranian, Poland
| | - Łukasz Szylberg
- Department of Tumor Pathology and Pathomorphology, Oncology Center‒Prof. Franciszek Łukaszczyk Memorial Hospital, Bydgoszcz, Kuyavian-Pomeranian, Poland
- Department of Obstetrics, Gynaecology and Oncology, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Torun, Bydgoszcz, Kuyavian-Pomeranian, Poland
| | - Michał Jankowski
- Surgical Oncology, Ludwik Rydygier’s Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Torun, Bydgoszcz, Kuyavian-Pomeranian, Poland
- Department of Surgical Oncology, Oncology Center‒Prof. Franciszek Łukaszczyk Memorial Hospital, Bydgoszcz, Kuyavian-Pomeranian, Poland
| | - Dariusz Bała
- Surgical Oncology, Ludwik Rydygier’s Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Torun, Bydgoszcz, Kuyavian-Pomeranian, Poland
- Department of Surgical Oncology, Oncology Center‒Prof. Franciszek Łukaszczyk Memorial Hospital, Bydgoszcz, Kuyavian-Pomeranian, Poland
| | - Wojciech Zegarski
- Surgical Oncology, Ludwik Rydygier’s Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Torun, Bydgoszcz, Kuyavian-Pomeranian, Poland
- Department of Surgical Oncology, Oncology Center‒Prof. Franciszek Łukaszczyk Memorial Hospital, Bydgoszcz, Kuyavian-Pomeranian, Poland
| | - Tomasz Nowikiewicz
- Surgical Oncology, Ludwik Rydygier’s Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Torun, Bydgoszcz, Kuyavian-Pomeranian, Poland
- Department of Breast Cancer and Reconstructive Surgery, Oncology Center‒Prof. Franciszek Łukaszczyk Memorial Hospital, Bydgoszcz, Kuyavian-Pomeranian, Poland
| | - Wojciech Makarewicz
- Clinic of General and Oncological Surgery, Specialist Hospital of Kościerzyna, Kościerzyna, Pomeranian, Poland
| | - Agnieszka Adamczyk
- Department of Tumor Pathology, Maria Skłodowska-Curie National Research Institute of Oncology, Kraków, Lesser Poland, Poland
| | - Aleksandra Ambicka
- Department of Tumor Pathology, Maria Skłodowska-Curie National Research Institute of Oncology, Kraków, Lesser Poland, Poland
| | - Marcin Przewoźnik
- Department of Tumor Pathology, Maria Skłodowska-Curie National Research Institute of Oncology, Kraków, Lesser Poland, Poland
| | - Agnieszka Harazin-Lechowska
- Department of Tumor Pathology, Maria Skłodowska-Curie National Research Institute of Oncology, Kraków, Lesser Poland, Poland
| | - Janusz Ryś
- Department of Tumor Pathology, Maria Skłodowska-Curie National Research Institute of Oncology, Kraków, Lesser Poland, Poland
| | - Katarzyna Macur
- Laboratory of Mass Spectrometry-Core Facility Laboratories, Intercollegiate Faculty of Biotechnology University of Gdańsk and Medical University of Gdańsk, University of Gdańsk, Gdańsk, Pomeranian, Poland
| | - Paulina Czaplewska
- Laboratory of Mass Spectrometry-Core Facility Laboratories, Intercollegiate Faculty of Biotechnology University of Gdańsk and Medical University of Gdańsk, University of Gdańsk, Gdańsk, Pomeranian, Poland
| | - Natalia Filipowicz
- 3P-Medicine Laboratory, Medical University of Gdańsk, Gdańsk, Pomeranian, Poland
| | - Arkadiusz Piotrowski
- 3P-Medicine Laboratory, Medical University of Gdańsk, Gdańsk, Pomeranian, Poland
| | - Jan P Dumanski
- 3P-Medicine Laboratory, Medical University of Gdańsk, Gdańsk, Pomeranian, Poland
- Department of Immunology, Genetics and Pathology and Science for Life Laboratory, Uppsala University, Uppsala, Uppland, Sweden
- Department of Biology and Pharmaceutical Botany, Medical University of Gdańsk, Gdańsk, Pomeranian, Poland
| | - Zhi Chen
- Intercollegiate Faculty of Biotechnology of University of Gdańsk and Medical University of Gdańsk, University of Gdańsk, Gdańsk, Pomeranian, Poland
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, North Ostrobothnia, Finland
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4
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Soares J, Eiras M, Ferreira D, Santos DAR, Relvas-Santos M, Santos B, Gonçalves M, Ferreira E, Vieira R, Afonso LP, Santos LL, Dinis-Ribeiro M, Lima L, Ferreira JA. Stool Glycoproteomics Signatures of Pre-Cancerous Lesions and Colorectal Cancer. Int J Mol Sci 2024; 25:3722. [PMID: 38612533 PMCID: PMC11012158 DOI: 10.3390/ijms25073722] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Revised: 03/22/2024] [Accepted: 03/25/2024] [Indexed: 04/14/2024] Open
Abstract
Colorectal cancer (CRC) screening relies primarily on stool analysis to identify occult blood. However, its sensitivity for detecting precancerous lesions is limited, requiring the development of new tools to improve CRC screening. Carcinogenesis involves significant alterations in mucosal epithelium glycocalyx that decisively contribute to disease progression. Building on this knowledge, we examined patient series comprehending premalignant lesions, colorectal tumors, and healthy controls for the T-antigen-a short-chain O-glycosylation of proteins considered a surrogate marker of malignancy in multiple solid cancers. We found the T-antigen in the secretions of dysplastic lesions as well as in cancer. In CRC, T-antigen expression was associated with the presence of distant metastases. In parallel, we analyzed a broad number of stools from individuals who underwent colonoscopy, which showed high T expressions in high-grade dysplasia and carcinomas. Employing mass spectrometry-based lectin-affinity enrichment, we identified a total of 262 proteins, 67% of which potentially exhibited altered glycosylation patterns associated with cancer and advanced pre-cancerous lesions. Also, we found that the stool (glyco)proteome of pre-cancerous lesions is enriched for protein species involved in key biological processes linked to humoral and innate immune responses. This study offers a thorough analysis of the stool glycoproteome, laying the groundwork for harnessing glycosylation alterations to improve non-invasive cancer detection.
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Affiliation(s)
- Janine Soares
- Experimental Pathology and Therapeutics Group, Research Center of IPO Porto (CI-IPOP), RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto), Porto Comprehensive Cancer Center Raquel Seruca (Porto.CCC Raquel Seruca), 4200-072 Porto, Portugal; (J.S.); (M.E.); (D.F.); (D.A.R.S.); (M.R.-S.); (B.S.); (M.G.); (E.F.); (L.P.A.); (L.L.S.)
- Institute of Biomedical Sciences Abel Salazar (ICBAS), University of Porto, 4050-313 Porto, Portugal
- REQUIMTE-LAQV, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Mariana Eiras
- Experimental Pathology and Therapeutics Group, Research Center of IPO Porto (CI-IPOP), RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto), Porto Comprehensive Cancer Center Raquel Seruca (Porto.CCC Raquel Seruca), 4200-072 Porto, Portugal; (J.S.); (M.E.); (D.F.); (D.A.R.S.); (M.R.-S.); (B.S.); (M.G.); (E.F.); (L.P.A.); (L.L.S.)
| | - Dylan Ferreira
- Experimental Pathology and Therapeutics Group, Research Center of IPO Porto (CI-IPOP), RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto), Porto Comprehensive Cancer Center Raquel Seruca (Porto.CCC Raquel Seruca), 4200-072 Porto, Portugal; (J.S.); (M.E.); (D.F.); (D.A.R.S.); (M.R.-S.); (B.S.); (M.G.); (E.F.); (L.P.A.); (L.L.S.)
- Institute of Biomedical Sciences Abel Salazar (ICBAS), University of Porto, 4050-313 Porto, Portugal
- Center for Applied Medical Research, University of Navarra, 31008 Pamplona, Spain
- i3S—Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal
- INEB-Instituto Nacional de Engenharia Biomédica, Universidade do Porto, 4200-135 Porto, Portugal
| | - Daniela A. R. Santos
- Experimental Pathology and Therapeutics Group, Research Center of IPO Porto (CI-IPOP), RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto), Porto Comprehensive Cancer Center Raquel Seruca (Porto.CCC Raquel Seruca), 4200-072 Porto, Portugal; (J.S.); (M.E.); (D.F.); (D.A.R.S.); (M.R.-S.); (B.S.); (M.G.); (E.F.); (L.P.A.); (L.L.S.)
- Institute of Biomedical Sciences Abel Salazar (ICBAS), University of Porto, 4050-313 Porto, Portugal
- Faculty of Medicine (FMUP), University of Porto, 4200-072 Porto, Portugal;
| | - Marta Relvas-Santos
- Experimental Pathology and Therapeutics Group, Research Center of IPO Porto (CI-IPOP), RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto), Porto Comprehensive Cancer Center Raquel Seruca (Porto.CCC Raquel Seruca), 4200-072 Porto, Portugal; (J.S.); (M.E.); (D.F.); (D.A.R.S.); (M.R.-S.); (B.S.); (M.G.); (E.F.); (L.P.A.); (L.L.S.)
- Institute of Biomedical Sciences Abel Salazar (ICBAS), University of Porto, 4050-313 Porto, Portugal
- i3S—Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal
- INEB-Instituto Nacional de Engenharia Biomédica, Universidade do Porto, 4200-135 Porto, Portugal
- REQUIMTE-LAQV, Department of Chemistry and Biochemistry, Faculty of Sciences, University of Porto, 4169-007 Porto, Portugal
| | - Beatriz Santos
- Experimental Pathology and Therapeutics Group, Research Center of IPO Porto (CI-IPOP), RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto), Porto Comprehensive Cancer Center Raquel Seruca (Porto.CCC Raquel Seruca), 4200-072 Porto, Portugal; (J.S.); (M.E.); (D.F.); (D.A.R.S.); (M.R.-S.); (B.S.); (M.G.); (E.F.); (L.P.A.); (L.L.S.)
| | - Martina Gonçalves
- Experimental Pathology and Therapeutics Group, Research Center of IPO Porto (CI-IPOP), RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto), Porto Comprehensive Cancer Center Raquel Seruca (Porto.CCC Raquel Seruca), 4200-072 Porto, Portugal; (J.S.); (M.E.); (D.F.); (D.A.R.S.); (M.R.-S.); (B.S.); (M.G.); (E.F.); (L.P.A.); (L.L.S.)
| | - Eduardo Ferreira
- Experimental Pathology and Therapeutics Group, Research Center of IPO Porto (CI-IPOP), RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto), Porto Comprehensive Cancer Center Raquel Seruca (Porto.CCC Raquel Seruca), 4200-072 Porto, Portugal; (J.S.); (M.E.); (D.F.); (D.A.R.S.); (M.R.-S.); (B.S.); (M.G.); (E.F.); (L.P.A.); (L.L.S.)
| | - Renata Vieira
- Department of Pathology, Portuguese Oncology Institute of Porto, 4200-072 Porto, Portugal;
| | - Luís Pedro Afonso
- Experimental Pathology and Therapeutics Group, Research Center of IPO Porto (CI-IPOP), RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto), Porto Comprehensive Cancer Center Raquel Seruca (Porto.CCC Raquel Seruca), 4200-072 Porto, Portugal; (J.S.); (M.E.); (D.F.); (D.A.R.S.); (M.R.-S.); (B.S.); (M.G.); (E.F.); (L.P.A.); (L.L.S.)
- Department of Pathology, Portuguese Oncology Institute of Porto, 4200-072 Porto, Portugal;
| | - Lúcio Lara Santos
- Experimental Pathology and Therapeutics Group, Research Center of IPO Porto (CI-IPOP), RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto), Porto Comprehensive Cancer Center Raquel Seruca (Porto.CCC Raquel Seruca), 4200-072 Porto, Portugal; (J.S.); (M.E.); (D.F.); (D.A.R.S.); (M.R.-S.); (B.S.); (M.G.); (E.F.); (L.P.A.); (L.L.S.)
- Institute of Biomedical Sciences Abel Salazar (ICBAS), University of Porto, 4050-313 Porto, Portugal
- FF-I3ID, University Fernando Pessoa, 4249-004 Porto, Portugal
- GlycoMatters Biotech, 4500-162 Espinho, Portugal
- Department of Surgical Oncology, Portuguese Oncology Institute of Porto (IPO-Porto), 4200-072 Porto, Portugal
| | - Mário Dinis-Ribeiro
- Faculty of Medicine (FMUP), University of Porto, 4200-072 Porto, Portugal;
- Precancerous Lesions and Early Cancer Management Group, Research Center of IPO Porto (CI-IPOP), Rise@CI-IPOP (Health Research Group), Portuguese Institute of Oncology of Porto (IPO Porto), Porto Comprehensive Cancer Center Raquel Seruca (Porto.CCC Raquel Seruca), 4200-072 Porto, Portugal
- Department of Gastroenterology, Portuguese Oncology Institute of Porto, 4200-072 Porto, Portugal
| | - Luís Lima
- Experimental Pathology and Therapeutics Group, Research Center of IPO Porto (CI-IPOP), RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto), Porto Comprehensive Cancer Center Raquel Seruca (Porto.CCC Raquel Seruca), 4200-072 Porto, Portugal; (J.S.); (M.E.); (D.F.); (D.A.R.S.); (M.R.-S.); (B.S.); (M.G.); (E.F.); (L.P.A.); (L.L.S.)
| | - José Alexandre Ferreira
- Experimental Pathology and Therapeutics Group, Research Center of IPO Porto (CI-IPOP), RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto), Porto Comprehensive Cancer Center Raquel Seruca (Porto.CCC Raquel Seruca), 4200-072 Porto, Portugal; (J.S.); (M.E.); (D.F.); (D.A.R.S.); (M.R.-S.); (B.S.); (M.G.); (E.F.); (L.P.A.); (L.L.S.)
- Institute of Biomedical Sciences Abel Salazar (ICBAS), University of Porto, 4050-313 Porto, Portugal
- GlycoMatters Biotech, 4500-162 Espinho, Portugal
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5
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Hua H, Wang T, Pan L, Du X, Xia T, Fa Z, Gu L, Gao F, Yu C, Gao F, Liao L, Shen Z. A proteomic classifier panel for early screening of colorectal cancer: a case control study. J Transl Med 2024; 22:188. [PMID: 38383428 PMCID: PMC10880210 DOI: 10.1186/s12967-024-04983-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Accepted: 02/12/2024] [Indexed: 02/23/2024] Open
Abstract
BACKGROUND Diagnosis of colorectal cancer (CRC) during early stages can greatly improve patient outcome. Although technical advances in the field of genomics and proteomics have identified a number of candidate biomarkers for non-invasive screening and diagnosis, developing more sensitive and specific methods with improved cost-effectiveness and patient compliance has tremendous potential to help combat the disease. METHODS We enrolled three cohorts of 479 subjects, including 226 CRC cases, 197 healthy controls, and 56 advanced precancerous lesions (APC). In the discovery cohort, we used quantitative mass spectrometry to measure the expression profile of plasma proteins and applied machine-learning to select candidate proteins. We then developed a targeted mass spectrometry assay to measure plasma concentrations of seven proteins and a logistic regression classifier to distinguish CRC from healthy subjects. The classifier was further validated using two independent cohorts. RESULTS The seven-protein panel consisted of leucine rich alpha-2-glycoprotein 1 (LRG1), complement C9 (C9), insulin-like growth factor binding protein 2 (IGFBP2), carnosine dipeptidase 1 (CNDP1), inter-alpha-trypsin inhibitor heavy chain 3 (ITIH3), serpin family A member 1 (SERPINA1), and alpha-1-acid glycoprotein 1 (ORM1). The panel classified CRC and healthy subjects with high accuracy, since the area under curve (AUC) of the training and testing cohort reached 0.954 and 0.958. The AUC of the two independent validation cohorts was 0.905 and 0.909. In one validation cohort, the panel had an overall sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) of 89.9%, 81.8%, 89.2%, and 82.9%, respectively. In another blinded validation cohort, the panel classified CRC from healthy subjects with a sensitivity of 81.5%, specificity of 97.9%, and overall accuracy of 92.0%. Finally, the panel was able to detect APC with a sensitivity of 49%. CONCLUSIONS This seven-protein classifier is a clear improvement compared to previously published blood-based protein biomarkers for detecting early-stage CRC, and is of translational potential to develop into a clinically useful assay.
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Affiliation(s)
- Hanju Hua
- Department of Colorectal Surgery (H.H), and Department of Gastroenterology (C.Y. and Z.S.), College of Medicine, The First Affiliated Hospital, Zhejiang University, Hangzhou, 310006, Zhejiang, China
| | - Tingting Wang
- Durbrain Medical Laboratory, Hangzhou, 310000, Zhejiang, China
| | - Liangxuan Pan
- Durbrain Medical Laboratory, Hangzhou, 310000, Zhejiang, China
| | - Xiaoyao Du
- Durbrain Medical Laboratory, Hangzhou, 310000, Zhejiang, China
| | - Tianxue Xia
- Department of Colorectal Surgery (H.H), and Department of Gastroenterology (C.Y. and Z.S.), College of Medicine, The First Affiliated Hospital, Zhejiang University, Hangzhou, 310006, Zhejiang, China
| | - Zhenzhong Fa
- Changzhou Wujin People's Hospital, Changzhou, 213000, Jiangsu, China
| | - Lei Gu
- Department of General Surgery, School of Medicine, Shanghai Tenth People's Hospital, Tongji University, Shanghai, 200072, China
| | - Fei Gao
- Durbrain Medical Laboratory, Hangzhou, 310000, Zhejiang, China
| | - Chaohui Yu
- Department of Colorectal Surgery (H.H), and Department of Gastroenterology (C.Y. and Z.S.), College of Medicine, The First Affiliated Hospital, Zhejiang University, Hangzhou, 310006, Zhejiang, China.
| | - Feng Gao
- Changzhou Wujin People's Hospital, Changzhou, 213000, Jiangsu, China.
| | - Lujian Liao
- Durbrain Medical Laboratory, Hangzhou, 310000, Zhejiang, China.
- Shanghai Key Laboratory of Regulatory Biology, School of Life Sciences, East China Normal University, Shanghai, 200241, China.
| | - Zhe Shen
- Department of Colorectal Surgery (H.H), and Department of Gastroenterology (C.Y. and Z.S.), College of Medicine, The First Affiliated Hospital, Zhejiang University, Hangzhou, 310006, Zhejiang, China.
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6
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Luo B, Que Z, Lu X, Qi D, Qiao Z, Yang Y, Qian F, Jiang Y, Li Y, Ke R, Shen X, Xiao H, Li H, Wu E, Tian J. Identification of exosome protein panels as predictive biomarkers for non-small cell lung cancer. Biol Proced Online 2023; 25:29. [PMID: 37953280 PMCID: PMC10641949 DOI: 10.1186/s12575-023-00223-0] [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: 08/28/2023] [Accepted: 10/20/2023] [Indexed: 11/14/2023] Open
Abstract
BACKGROUND Non-small cell lung cancer (NSCLC) remains a leading cause of cancer-related deaths worldwide, primarily due to its propensity for metastasis. Patients diagnosed with localized primary cancer have higher survival rates than those with metastasis. Thus, it is imperative to discover biomarkers for the early detection of NSCLC and the timely prediction of tumor metastasis to improve patient outcomes. METHODS Here, we utilized an integrated approach to isolate and characterize plasma exosomes from NSCLC patients as well as healthy individuals. We then conducted proteomics analysis and parallel reaction monitoring to identify and validate the top-ranked proteins of plasma exosomes. RESULTS Our study revealed that the proteome in exosomes from NSCLC patients with metastasis was distinctly different from that from healthy individuals. The former had larger diameters and lower concentrations of exosomes than the latter. Furthermore, among the 1220 identified exosomal proteins, we identified two distinct panels of biomarkers. The first panel of biomarkers (FGB, FGG, and VWF) showed potential for early NSCLC diagnosis and demonstrated a direct correlation with the survival duration of NSCLC patients. The second panel of biomarkers (CFHR5, C9, and MBL2) emerged as potential biomarkers for assessing NSCLC metastasis, of which CFHR5 alone was significantly associated with the overall survival of NSCLC patients. CONCLUSIONS These findings underscore the potential of plasma exosomal biomarkers for early NSCLC diagnosis and metastasis prediction. Notably, CFHR5 stands out as a promising prognostic indicator for NSCLC patients. The clinical utility of exosomal biomarkers offers the potential to enhance the management of NSCLC.
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Affiliation(s)
- Bin Luo
- Clinical Oncology Center, Shanghai Municipal Hospital of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, 200071, China
- Department of Oncology, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, 200032, China
| | - Zujun Que
- Institute of Oncology, Shanghai Municipal Hospital of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, 200071, China
| | - Xinyi Lu
- Clinical Oncology Center, Shanghai Municipal Hospital of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, 200071, China
| | - Dan Qi
- Department of Neurosurgery and Neuroscience Institute, Baylor Scott & White Health, Temple, TX, 76502, USA
- Department of Neurosurgery, Baylor College of Medicine, Temple, TX, 76508, USA
| | - Zhi Qiao
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Yun Yang
- Clinical Oncology Center, Shanghai Municipal Hospital of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, 200071, China
| | - Fangfang Qian
- Department of Oncology, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, 200032, China
| | - Yi Jiang
- Department of Oncology, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, 200032, China
| | - Yan Li
- Clinical Oncology Center, Shanghai Municipal Hospital of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, 200071, China
| | - Ronghu Ke
- Department of Neurosurgery and Neuroscience Institute, Baylor Scott & White Health, Temple, TX, 76502, USA
| | - Xiaoyun Shen
- Prism Genomic Medicine, Sugar Land, TX, 77478, USA
| | - Hua Xiao
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China.
| | - Hegen Li
- Department of Oncology, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, 200032, China.
| | - Erxi Wu
- Department of Neurosurgery and Neuroscience Institute, Baylor Scott & White Health, Temple, TX, 76502, USA.
- Department of Neurosurgery, Baylor College of Medicine, Temple, TX, 76508, USA.
- School of Medicine, Texas A&M University, College Station, TX, 77843, USA.
- Irma Lerma Rangel School of Pharmacy, Texas A&M University, College Station, TX, 77843, USA.
- LIVESTRONG Cancer Institutes and Department of Oncology, Dell Medical School, The University of Texas at Austin, Austin, TX, 78712, USA.
| | - Jianhui Tian
- Clinical Oncology Center, Shanghai Municipal Hospital of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, 200071, China.
- Department of Oncology, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, 200032, China.
- Institute of Oncology, Shanghai Municipal Hospital of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, 200071, China.
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7
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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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8
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Tornyi I, Lazar J, Pettko-Szandtner A, Hunyadi-Gulyas E, Takacs L. Epitomics: Analysis of Plasma C9 Epitope Heterogeneity in the Plasma of Lung Cancer Patients and Control Subjects. Int J Mol Sci 2023; 24:14359. [PMID: 37762663 PMCID: PMC10531758 DOI: 10.3390/ijms241814359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2023] [Revised: 09/15/2023] [Accepted: 09/16/2023] [Indexed: 09/29/2023] Open
Abstract
The human proteome is more complex than the genetic code predicts it to be. Epitomics, or protein epitome profiling, is a tool for understanding sub-protein level variation. With the ultimate goal to explore C9 proteoforms and their relevance to lung cancer, here we report plasma C9 epitope-associated molecular heterogeneity in plasma samples of lung cancer patients and control subjects. We show three C9 epitopes (BSI0449, BSI0581, BSI0639) with markedly different association with lung cancer ("unaltered", "upregulated" and "downregulated"). In order to exclude confounding effects, we show first that the three epitope-defining mAbs recognize C9 in purified form and in the natural context, in the human plasma. Then, we present data demonstrating the lack of major epitope interdependence or overlap. The next experiments represent a quest toward the understanding of the molecular basis of apparent disparate association with lung cancer. Using immunochemistry, SDS PAGE and LC-MS/MS technologies, we demonstrate that epitope-specific immunoprecipitates of plasma C9 seem identical regarding peptide sequence. However, we found epitope-specific posttranslational modification and coprecipitated protein composition differences with respect to control and lung cancer plasma. Epitope profiling enabled the classification of hypothetical C9 proteoforms through differential association with lung cancer.
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Affiliation(s)
- Ilona Tornyi
- Department of Human Genetics, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary;
- Department of Pulmonology, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary
- Doctoral School of Molecular Cell and Immune Biology, University of Debrecen, 4032 Debrecen, Hungary
- Biosystems Immunolab Zrt., 4025 Debrecen, Hungary;
| | - Jozsef Lazar
- Biosystems Immunolab Zrt., 4025 Debrecen, Hungary;
- Biosystems International Kft., 4025 Debrecen, Hungary
| | - Aladar Pettko-Szandtner
- Proteomics Laboratory, Biological Research Center, 6726 Szeged, Hungary; (A.P.-S.); (E.H.-G.)
| | - Eva Hunyadi-Gulyas
- Proteomics Laboratory, Biological Research Center, 6726 Szeged, Hungary; (A.P.-S.); (E.H.-G.)
| | - Laszlo Takacs
- Department of Human Genetics, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary;
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9
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Dutt M, Hartel G, Richards RS, Shah AK, Mohamed A, Apostolidou S, Gentry‐Maharaj A, Hooper JD, Perrin LC, Menon U, Hill MM. Discovery and validation of serum glycoprotein biomarkers for high grade serous ovarian cancer. Proteomics Clin Appl 2023; 17:e2200114. [PMID: 37147936 PMCID: PMC7615076 DOI: 10.1002/prca.202200114] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 04/06/2023] [Accepted: 04/27/2023] [Indexed: 05/07/2023]
Abstract
PURPOSE This study aimed to identify serum glycoprotein biomarkers for early detection of high-grade serous ovarian cancer (HGSOC), the most common and aggressive histotype of ovarian cancer. EXPERIMENTAL DESIGN The glycoproteomics pipeline lectin magnetic bead array (LeMBA)-mass spectrometry (MS) was used in age-matched case-control serum samples. Clinical samples collected at diagnosis were divided into discovery (n = 30) and validation (n = 98) sets. We also analysed a set of preclinical sera (n = 30) collected prior to HGSOC diagnosis in the UK Collaborative Trial of Ovarian Cancer Screening. RESULTS A 7-lectin LeMBA-MS/MS discovery screen shortlisted 59 candidate proteins and three lectins. Validation analysis using 3-lectin LeMBA-multiple reaction monitoring (MRM) confirmed elevated A1AT, AACT, CO9, HPT and ITIH3 and reduced A2MG, ALS, IBP3 and PON1 glycoforms in HGSOC. The best performing multimarker signature had 87.7% area under the receiver operating curve, 90.7% specificity and 70.4% sensitivity for distinguishing HGSOC from benign and healthy groups. In the preclinical set, CO9, ITIH3 and A2MG glycoforms were altered in samples collected 11.1 ± 5.1 months prior to HGSOC diagnosis, suggesting potential for early detection. CONCLUSIONS AND CLINICAL RELEVANCE Our findings provide evidence of candidate early HGSOC serum glycoprotein biomarkers, laying the foundation for further study in larger cohorts.
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Affiliation(s)
- Mriga Dutt
- QIMR Berghofer Medical Research InstituteBrisbaneQLDAustralia
| | - Gunter Hartel
- QIMR Berghofer Medical Research InstituteBrisbaneQLDAustralia
| | | | - Alok K. Shah
- QIMR Berghofer Medical Research InstituteBrisbaneQLDAustralia
| | - Ahmed Mohamed
- QIMR Berghofer Medical Research InstituteBrisbaneQLDAustralia
| | - Sophia Apostolidou
- MRC Clinical Trials UnitInstitute of Clinical Trials and Methodology, University College LondonLondonUK
| | - Aleksandra Gentry‐Maharaj
- MRC Clinical Trials UnitInstitute of Clinical Trials and Methodology, University College LondonLondonUK
| | | | - John D. Hooper
- Mater Research Institute – The University of QueenslandTranslational Research InstituteWoolloongabbaQLDAustralia
| | - Lewis C. Perrin
- Mater Research Institute – The University of QueenslandTranslational Research InstituteWoolloongabbaQLDAustralia
- Mater Adult HospitalSouth BrisbaneQLDAustralia
| | - Usha Menon
- MRC Clinical Trials UnitInstitute of Clinical Trials and Methodology, University College LondonLondonUK
| | - Michelle M. Hill
- QIMR Berghofer Medical Research InstituteBrisbaneQLDAustralia
- UQ Centre for Clinical ResearchFaculty of MedicineThe University of QueenslandBrisbaneAustralia
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10
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Starodubtseva NL, Tokareva AO, Rodionov VV, Brzhozovskiy AG, Bugrova AE, Chagovets VV, Kometova VV, Kukaev EN, Soares NC, Kovalev GI, Kononikhin AS, Frankevich VE, Nikolaev EN, Sukhikh GT. Integrating Proteomics and Lipidomics for Evaluating the Risk of Breast Cancer Progression: A Pilot Study. Biomedicines 2023; 11:1786. [PMID: 37509426 PMCID: PMC10376786 DOI: 10.3390/biomedicines11071786] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 06/16/2023] [Accepted: 06/19/2023] [Indexed: 07/30/2023] Open
Abstract
Metastasis is a serious and often life-threatening condition, representing the leading cause of death among women with breast cancer (BC). Although the current clinical classification of BC is well-established, the addition of minimally invasive laboratory tests based on peripheral blood biomarkers that reflect pathological changes in the body is of utmost importance. In the current study, the serum proteome and lipidome profiles for 50 BC patients with (25) and without (25) metastasis were studied. Targeted proteomic analysis for concertation measurements of 125 proteins in the serum was performed via liquid chromatography-multiple reaction monitoring mass spectrometry (LC-MRM MS) using the BAK 125 kit (MRM Proteomics Inc., Victoria, BC, Canada). Untargeted label-free lipidomic analysis was performed using liquid chromatography coupled to tandem mass-spectrometry (LC-MS/MS), in both positive and negative ion modes. Finally, 87 serum proteins and 295 lipids were quantified and showed a moderate correlation with tumor grade, histological and biological subtypes, and the number of lymph node metastases. Two highly accurate classifiers that enabled distinguishing between metastatic and non-metastatic BC were developed based on proteomic (accuracy 90%) and lipidomic (accuracy 80%) features. The best classifier (91% sensitivity, 89% specificity, AUC = 0.92) for BC metastasis diagnostics was based on logistic regression and the serum levels of 11 proteins: alpha-2-macroglobulin, coagulation factor XII, adiponectin, leucine-rich alpha-2-glycoprotein, alpha-2-HS-glycoprotein, Ig mu chain C region, apolipoprotein C-IV, carbonic anhydrase 1, apolipoprotein A-II, apolipoprotein C-II and alpha-1-acid glycoprotein 1.
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Affiliation(s)
- Natalia L Starodubtseva
- V.I. Kulakov National Medical Research Center of Obstetrics, Gynecology, and Perinatology, Ministry of Health of Russia, 117997 Moscow, Russia
- Department of Chemical Physics, Moscow Institute of Physics and Technology, 141700 Moscow, Russia
| | - Alisa O Tokareva
- V.I. Kulakov National Medical Research Center of Obstetrics, Gynecology, and Perinatology, Ministry of Health of Russia, 117997 Moscow, Russia
| | - Valeriy V Rodionov
- V.I. Kulakov National Medical Research Center of Obstetrics, Gynecology, and Perinatology, Ministry of Health of Russia, 117997 Moscow, Russia
| | - Alexander G Brzhozovskiy
- V.I. Kulakov National Medical Research Center of Obstetrics, Gynecology, and Perinatology, Ministry of Health of Russia, 117997 Moscow, Russia
- Laboratory of Omics Technologies and Big Data for Personalized Medicine and Health, Skolkovo Institute of Science and Technology, 121205 Moscow, Russia
| | - Anna E Bugrova
- V.I. Kulakov National Medical Research Center of Obstetrics, Gynecology, and Perinatology, Ministry of Health of Russia, 117997 Moscow, Russia
- Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, 119334 Moscow, Russia
| | - Vitaliy V Chagovets
- V.I. Kulakov National Medical Research Center of Obstetrics, Gynecology, and Perinatology, Ministry of Health of Russia, 117997 Moscow, Russia
| | - Vlada V Kometova
- V.I. Kulakov National Medical Research Center of Obstetrics, Gynecology, and Perinatology, Ministry of Health of Russia, 117997 Moscow, Russia
| | - Evgenii N Kukaev
- V.I. Kulakov National Medical Research Center of Obstetrics, Gynecology, and Perinatology, Ministry of Health of Russia, 117997 Moscow, Russia
- V.L. Talrose Institute for Energy Problems of Chemical Physics, N.N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, 119334 Moscow, Russia
| | - Nelson C Soares
- Department of Medicinal Chemistry, College of Pharmacy, University of Sharjah, Sharjah 27272, United Arab Emirates
| | - Grigoriy I Kovalev
- Laboratory of Omics Technologies and Big Data for Personalized Medicine and Health, Skolkovo Institute of Science and Technology, 121205 Moscow, Russia
| | - Alexey S Kononikhin
- V.I. Kulakov National Medical Research Center of Obstetrics, Gynecology, and Perinatology, Ministry of Health of Russia, 117997 Moscow, Russia
- Laboratory of Omics Technologies and Big Data for Personalized Medicine and Health, Skolkovo Institute of Science and Technology, 121205 Moscow, Russia
| | - Vladimir E Frankevich
- V.I. Kulakov National Medical Research Center of Obstetrics, Gynecology, and Perinatology, Ministry of Health of Russia, 117997 Moscow, Russia
- Laboratory of Translational Medicine, Siberian State Medical University, 634050 Tomsk, Russia
| | - Evgeny N Nikolaev
- Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, 121205 Moscow, Russia
| | - Gennady T Sukhikh
- V.I. Kulakov National Medical Research Center of Obstetrics, Gynecology, and Perinatology, Ministry of Health of Russia, 117997 Moscow, Russia
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11
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Verathamjamras C, Chantaraamporn J, Sornprachum T, Mutapat P, Chokchaichamnankit D, Mingkwan K, Luevisadpibul V, Srisomsap C, Chutipongtanate S, Svasti J, Champattanachai V. Label-free quantitative proteomics reveals aberrant expression levels of LRG, C9, FN, A1AT and AGP1 in the plasma of patients with colorectal cancer. Clin Proteomics 2023; 20:15. [PMID: 37024778 PMCID: PMC10077704 DOI: 10.1186/s12014-023-09407-y] [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: 10/25/2022] [Accepted: 03/28/2023] [Indexed: 04/08/2023] Open
Abstract
BACKGROUND Colorectal cancer (CRC) is one of the major causes of cancer-related death worldwide. Although commercial biomarkers of CRC are currently available, they are still lacking in terms of sensitivity and specificity; thus, searching for reliable blood-based biomarkers are important for the primary screening of CRC. METHODS Plasma samples of patients with non-metastatic (NM) and metastatic (M) CRC and healthy controls were fractionated using MARS-14 immunoaffinity chromatography. The flow-through and elute fractions representing low- and high-abundant proteins, respectively, were analyzed by label-free quantitative proteomics mass spectrometry. The functional analysis of the proteins with greater than 1.5-fold differential expression level between the CRC and the healthy control groups were analyzed for their biological processes and molecular functions. In addition, the levels of plasma proteins showing large alterations in CRC patients were confirmed by immunoblotting using two independent cohorts. Moreover, receiver operating characteristic (ROC) curve analysis was performed for individual and combinations of biomarker candidates so as to evaluate the diagnostic performance of biomarker candidates. RESULTS From 163 refined identifications, five proteins were up-regulated and two proteins were down-regulated in NM-CRC while eight proteins were up-regulated and three proteins were down-regulated in M-CRC, respectively. Altered plasma proteins in NM-CRC were mainly involved in complement activation, while those in M-CRC were clustered in acute-phase response, complement activation, and inflammatory response. Results from the study- and validation-cohorts indicate that the levels of leucine-rich alpha-2-glycoprotein-1(LRG), complement component C9 (C9), alpha-1-acid glycoprotein 1 (AGP1), and alpha-1-antitrypsin (A1AT) were statistically increased, while fibronectin (FN) level was statistically decreased in CRC patients compared to healthy controls, with most alterations found in a metastatic stage-dependent manner. ROC analysis revealed that FN exhibited the best diagnostic performance to discriminate CRC patients and healthy controls while AGP1 showed the best discrimination between the disease stages in both cohorts. The combined biomarker candidates, FN + A1AT + AGP1, exhibited perfect discriminatory power to discriminate between the CRC population and healthy controls whereas LRG + A1AT + AGP1 was likely to be the best panel to discriminate the metastatic stages in both cohorts. CONCLUSIONS This study identified and quantified distinct plasma proteome profiles of CRC patients. Selected CRC biomarker candidates including FN, LRG, C9, A1AT, and AGP1 may be further applied for screening larger cohorts including disease groups from other types of cancer or other diseases.
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Affiliation(s)
| | | | | | - Photsathorn Mutapat
- Laboratory of Biochemistry, Chulabhorn Research Institute, Bangkok, Thailand
| | | | - Kanokwan Mingkwan
- Division of Surgery, Sapphasitthiprasong Hospital, Ubon Ratchathani, Thailand
| | - Virat Luevisadpibul
- Division of Information and Technology, Ubonrak Thonburi Hospital, Ubon Ratchathani, Thailand
| | | | - Somchai Chutipongtanate
- Pediatric Translational Research Unit, Department of Pediatrics, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
- Department of Environmental and Public Health Sciences, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Jisnuson Svasti
- Laboratory of Biochemistry, Chulabhorn Research Institute, Bangkok, Thailand
- Applied Biological Science Program, Chulabhorn Graduate Institute, Chulabhorn Royal Academy, Bangkok, Thailand
| | - Voraratt Champattanachai
- Laboratory of Biochemistry, Chulabhorn Research Institute, Bangkok, Thailand.
- Applied Biological Science Program, Chulabhorn Graduate Institute, Chulabhorn Royal Academy, Bangkok, Thailand.
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12
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Kasahara K, Narumi R, Nagayama S, Masuda K, Esaki T, Obama K, Tomonaga T, Sakai Y, Shimizu Y, Adachi J. A large-scale targeted proteomics of plasma extracellular vesicles shows utility for prognosis prediction subtyping in colorectal cancer. Cancer Med 2022; 12:7616-7626. [PMID: 36394150 PMCID: PMC10067095 DOI: 10.1002/cam4.5442] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 08/03/2022] [Accepted: 11/02/2022] [Indexed: 11/18/2022] Open
Abstract
PURPOSE The pathogenesis of cancers depends on the molecular background of each individual patient. Therefore, verifying as many biomarkers as possible and clarifying their relationships with each disease status would be very valuable. We performed a large-scale targeted proteomics analysis of plasma extracellular vesicles (EVs) that may affect tumor progression and/or therapeutic resistance. EXPERIMENTAL DESIGN Plasma EVs from 59 were collected patients with colorectal cancer (CRC) and 59 healthy controls (HC) in cohort 1, and 150 patients with CRC in cohort 2 for the large-scale targeted proteomics analysis of 457 proteins as candidate CRC markers. The Mann-Whitney-Wilcoxon test and random forest model were applied in cohort 1 to select promising markers. Consensus clustering was applied to classify patients with CRC in cohort 2. The Kaplan-Meier method and Cox regression analysis were performed to identify potential molecular factors contributing to the overall survival (OS) of patients. RESULTS In the analysis of cohort 1, 99 proteins were associated with CRC. The analysis of cohort 2 revealed two clusters showing significant differences in OS (p = 0.017). Twelve proteins, including alpha-1-acid glycoprotein 1 (ORM1), were suggested to be associated with the identified CRC subtypes, and ORM1 was shown to significantly contribute to OS, suggesting that ORM1 might be one of the factors closely related to the OS. CONCLUSIONS The study identified two novel subtypes of CRC, which exhibit differences in OS, as well as important biomarker proteins that are closely related to the identified subtypes. Liquid biopsy assessment with targeted proteomics analysis was proposed to be crucial for predicting the CRC prognosis.
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Affiliation(s)
- Keiko Kasahara
- Department of SurgeryKyoto University Graduate School of MedicineKyotoJapan
- Laboratory of Proteome ResearchNational Institutes of Biomedical Innovation, Health and NutritionOsakaJapan
- Laboratory of Proteomics for Drug DiscoveryCenter for Drug Design Research, National Institute of Biomedical Innovation, Health and NutritionOsakaJapan
| | - Ryohei Narumi
- Laboratory of Proteome ResearchNational Institutes of Biomedical Innovation, Health and NutritionOsakaJapan
- Laboratory of Proteomics for Drug DiscoveryCenter for Drug Design Research, National Institute of Biomedical Innovation, Health and NutritionOsakaJapan
- Laboratory of Clinical and Analytical ChemistryCollaborative Research Center for Health and Medicine, National Institute of Biomedical Innovation, Health and NutritionOsakaJapan
| | - Satoshi Nagayama
- Department of Gastroenterological SurgeryGastroenterological Center, Cancer Institute Hospital, Japanese Foundation for Cancer ResearchTokyoJapan
- Department of SurgeryUji‐Tokusyukai Medical CenterKyotoJapan
| | - Keiko Masuda
- Laboratory for Cell‐Free Protein SynthesisRIKEN Center for Biosystems Dynamics ResearchOsakaJapan
| | - Tsuyoshi Esaki
- The Center for Data Science Education and ResearchShiga UniversityShigaJapan
| | - Kazutaka Obama
- Department of SurgeryKyoto University Graduate School of MedicineKyotoJapan
| | - Takeshi Tomonaga
- Laboratory of Proteome ResearchNational Institutes of Biomedical Innovation, Health and NutritionOsakaJapan
- Laboratory of Proteomics for Drug DiscoveryCenter for Drug Design Research, National Institute of Biomedical Innovation, Health and NutritionOsakaJapan
| | | | - Yoshihiro Shimizu
- Laboratory for Cell‐Free Protein SynthesisRIKEN Center for Biosystems Dynamics ResearchOsakaJapan
| | - Jun Adachi
- Laboratory of Proteome ResearchNational Institutes of Biomedical Innovation, Health and NutritionOsakaJapan
- Laboratory of Proteomics for Drug DiscoveryCenter for Drug Design Research, National Institute of Biomedical Innovation, Health and NutritionOsakaJapan
- Laboratory of Clinical and Analytical ChemistryCollaborative Research Center for Health and Medicine, National Institute of Biomedical Innovation, Health and NutritionOsakaJapan
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13
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Multi-Omics Approaches in Colorectal Cancer Screening and Diagnosis, Recent Updates and Future Perspectives. Cancers (Basel) 2022; 14:cancers14225545. [PMID: 36428637 PMCID: PMC9688479 DOI: 10.3390/cancers14225545] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Revised: 11/07/2022] [Accepted: 11/09/2022] [Indexed: 11/15/2022] Open
Abstract
Colorectal cancer (CRC) is common Cancer as well as the third leading cause of mortality around the world; its exact molecular mechanism remains elusive. Although CRC risk is significantly correlated with genetic factors, the pathophysiology of CRC is also influenced by external and internal exposures and their interactions with genetic factors. The field of CRC research has recently benefited from significant advances through Omics technologies for screening biomarkers, including genes, transcripts, proteins, metabolites, microbiome, and lipidome unbiasedly. A promising application of omics technologies could enable new biomarkers to be found for the screening and diagnosis of CRC. Single-omics technologies cannot fully understand the molecular mechanisms of CRC. Therefore, this review article aims to summarize the multi-omics studies of Colorectal cancer, including genomics, transcriptomics, proteomics, microbiomics, metabolomics, and lipidomics that may shed new light on the discovery of novel biomarkers. It can contribute to identifying and validating new CRC biomarkers and better understanding colorectal carcinogenesis. Discovering biomarkers through multi-omics technologies could be difficult but valuable for disease genotyping and phenotyping. That can provide a better knowledge of CRC prognosis, diagnosis, and treatments.
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14
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Li W, Li M, Zhang X, Yue S, Xu Y, Jian W, Qin Y, Lin L, Liu W. Improved profiling of low molecular weight serum proteome for gastric carcinoma by data-independent acquisition. Anal Bioanal Chem 2022; 414:6403-6417. [PMID: 35773495 DOI: 10.1007/s00216-022-04196-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 06/06/2022] [Accepted: 06/22/2022] [Indexed: 11/27/2022]
Abstract
Low molecular weight proteins (LMWPs) in the bloodstream participate in various biological processes and are closely associated with disease status, whereas identification of serous LMWPs remains a great technical challenge due to the wide dynamic range of protein components. In this study, we constructed an integrated LMWP library by combining the LMWPs obtained by three enrichment methods (50% ACN, 20% ACN + 20 mM ABC, and 30 kDa) and their fractions identified by the data-dependent acquisition method. With this newly constructed library, we comprehensively profiled LMWPs in serum using data-independent acquisition and reliably achieved quantitative results for 75% serous LMWPs. When applying this strategy to quantify LMWPs in human serum samples, we could identify 405 proteins on average per sample, of which 136 proteins were with a MW less than 30 kDa and 293 proteins were with a MW less than 65 kDa. Of note, pre- and post-operative gastric carcinoma (GC) patients showed differentially expressed serous LWMPs, which was also different from the pattern of LWMP expression in healthy controls. In conclusion, our results showed that LMWPs could efficiently distinguish GC patients from healthy controls as well as between pre- and post-operative statuses, and more importantly, our newly developed LMWP profiling platform could be used to discover candidate LMWP biomarkers for disease diagnosis and status monitoring.
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Affiliation(s)
- Weifeng Li
- The Central Laboratory, Shenzhen Second People's Hospital/the First Affiliated Hospital of Shenzhen University, Shenzhen, 518035, China
| | - Mengna Li
- The Central Laboratory, Shenzhen Second People's Hospital/the First Affiliated Hospital of Shenzhen University, Shenzhen, 518035, China
| | - Xiaoli Zhang
- The Central Laboratory, Shenzhen Second People's Hospital/the First Affiliated Hospital of Shenzhen University, Shenzhen, 518035, China
| | - Siqin Yue
- The Central Laboratory, Shenzhen Second People's Hospital/the First Affiliated Hospital of Shenzhen University, Shenzhen, 518035, China
| | - Yun Xu
- The Central Laboratory, Shenzhen Second People's Hospital/the First Affiliated Hospital of Shenzhen University, Shenzhen, 518035, China
| | - Wenjing Jian
- The Central Laboratory, Shenzhen Second People's Hospital/the First Affiliated Hospital of Shenzhen University, Shenzhen, 518035, China
| | - Yin Qin
- Department of Gastrointestinal Surgery, Shenzhen Second People's Hospital/the First Affiliated Hospital of Shenzhen University, Shenzhen, 518035, China.
| | - Lin Lin
- Sustech Core Research Facilities, Southern University of Science and Technology, Shenzhen, 518055, China.
| | - Wenlan Liu
- The Central Laboratory, Shenzhen Second People's Hospital/the First Affiliated Hospital of Shenzhen University, Shenzhen, 518035, China.
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15
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Zhu G, Jin L, Sun W, Wang S, Liu N. Proteomics of post-translational modifications in colorectal cancer: Discovery of new biomarkers. Biochim Biophys Acta Rev Cancer 2022; 1877:188735. [PMID: 35577141 DOI: 10.1016/j.bbcan.2022.188735] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2021] [Revised: 05/08/2022] [Accepted: 05/09/2022] [Indexed: 02/07/2023]
Abstract
Colorectal cancer (CRC) is one of the costliest health problems and ranks second in cancer-related mortality in developed countries. With the aid of proteomics, many protein biomarkers for the diagnosis, prognosis, and precise management of CRC have been identified. Furthermore, some protein biomarkers exhibit structural diversity after modifications. Post-translational modifications (PTMs), most of which are catalyzed by a variety of enzymes, extensively increase protein diversity and are involved in many complex and dynamic cellular processes through the regulation of protein function. Accumulating evidence suggests that abnormal PTM events are associated with a variety of human diseases, such as CRC, thus highlighting the need for studying PTMs to discover both the molecular mechanisms and therapeutic targets of CRC. In this review, we begin with a brief overview of the importance of protein PTMs, discuss the general strategies for proteomic profiling of several key PTMs (including phosphorylation, acetylation, glycosylation, ubiquitination, methylation, and citrullination), shift the emphasis to describing the specific methods used for delineating the global landscapes of each of these PTMs, and summarize the recent applications of these methods to explore the potential roles of the PTMs in CRC. Finally, we discuss the current status of PTM research on CRC and provide future perspectives on how PTM regulation can play an essential role in translational medicine for early diagnosis, prognosis stratification, and therapeutic intervention in CRC.
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Affiliation(s)
- Gengjun Zhu
- Department Oncology and Hematology, The Second Hospital of Jilin University, Changchun, China
| | - Lifang Jin
- Department Oncology and Hematology, The Second Hospital of Jilin University, Changchun, China
| | - Wanchun Sun
- Key Laboratory of Zoonosis Research, Ministry of Education, Jilin University, Changchun, China
| | - Shuang Wang
- Dermatological department, The Second Hospital of Jilin University, Changchun, China.
| | - Ning Liu
- Key Laboratory of Zoonosis Research, Ministry of Education, Jilin University, Changchun, China; Central Laboratory, The Second Hospital of Jilin University, Changchun, China.
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16
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Kolka CM, Webster J, Lepletier A, Winterford C, Brown I, Richards RS, Zelek WM, Cao Y, Khamis R, Shanmugasundaram KB, Wuethrich A, Trau M, Brosda S, Barbour A, Shah AK, Eslick GD, Clemons NJ, Morgan BP, Hill MM. C5b-9 Membrane Attack Complex Formation and Extracellular Vesicle Shedding in Barrett's Esophagus and Esophageal Adenocarcinoma. Front Immunol 2022; 13:842023. [PMID: 35345676 PMCID: PMC8957096 DOI: 10.3389/fimmu.2022.842023] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Accepted: 02/10/2022] [Indexed: 02/05/2023] Open
Abstract
The early complement components have emerged as mediators of pro-oncogenic inflammation, classically inferred to cause terminal complement activation, but there are limited data on the activity of terminal complement in cancer. We previously reported elevated serum and tissue C9, the terminal complement component, in esophageal adenocarcinoma (EAC) compared to the precursor condition Barrett’s Esophagus (BE) and healthy controls. Here, we investigate the level and cellular fates of the terminal complement complex C5b-9, also known as the membrane attack complex. Punctate C5b-9 staining and diffuse C9 staining was detected in BE and EAC by multiplex immunohistofluorescence without corresponding increase of C9 mRNA transcript. Increased C9 and C5b-9 staining were observed in the sequence normal squamous epithelium, BE, low- and high-grade dysplasia, EAC. C5b-9 positive esophageal cells were morphologically intact, indicative of sublytic or complement-evasion mechanisms. To investigate this at a cellular level, we exposed non-dysplastic BE (BAR-T and CP-A), high-grade dysplastic BE (CP-B and CP-D) and EAC (FLO-1 and OE-33) cell lines to the same sublytic dose of immunopurified human C9 (3 µg/ml) in the presence of C9-depleted human serum. Cellular C5b-9 was visualized by immunofluorescence confocal microscopy. Shed C5b-9 in the form of extracellular vesicles (EV) was measured in collected conditioned medium using recently described microfluidic immunoassay with capture by a mixture of three tetraspanin antibodies (CD9/CD63/CD81) and detection by surface-enhanced Raman scattering (SERS) after EV labelling with C5b-9 or C9 antibody conjugated SERS nanotags. Following C9 exposure, all examined cell lines formed C5b-9, internalized C5b-9, and shed C5b-9+ and C9+ EVs, albeit at varying levels despite receiving the same C9 dose. In conclusion, these results confirm increased esophageal C5b-9 formation during EAC development and demonstrate capability and heterogeneity in C5b-9 formation and shedding in BE and EAC cell lines following sublytic C9 exposure. Future work may explore the molecular mechanisms and pathogenic implications of the shed C5b-9+ EV.
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Affiliation(s)
- Cathryn M Kolka
- QIMR Berghofer Medical Research Institute, Herston, QLD, Australia
| | - Julie Webster
- QIMR Berghofer Medical Research Institute, Herston, QLD, Australia
| | - Ailin Lepletier
- QIMR Berghofer Medical Research Institute, Herston, QLD, Australia
| | - Clay Winterford
- QIMR Berghofer Medical Research Institute, Herston, QLD, Australia
| | - Ian Brown
- Envoi Pathology, Herston, QLD, Australia
| | - Renee S Richards
- QIMR Berghofer Medical Research Institute, Herston, QLD, Australia
| | - Wioleta M Zelek
- Division of Infection & Immunity, School of Medicine, Cardiff University, Cardiff, United Kingdom
| | - Yilang Cao
- QIMR Berghofer Medical Research Institute, Herston, QLD, Australia
| | - Ramlah Khamis
- Centre for Personalised Nanomedicine, Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, St Lucia, QLD, Australia
| | - Karthik B Shanmugasundaram
- Centre for Personalised Nanomedicine, Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, St Lucia, QLD, Australia
| | - Alain Wuethrich
- Centre for Personalised Nanomedicine, Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, St Lucia, QLD, Australia
| | - Matt Trau
- Centre for Personalised Nanomedicine, Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, St Lucia, QLD, Australia.,School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD, Australia
| | - Sandra Brosda
- University of Queensland Diamantina Institute, Faculty of Medicine, The University of Queensland, St Lucia, QLD, Australia
| | - Andrew Barbour
- University of Queensland Diamantina Institute, Faculty of Medicine, The University of Queensland, St Lucia, QLD, Australia
| | - Alok K Shah
- QIMR Berghofer Medical Research Institute, Herston, QLD, Australia
| | - Guy D Eslick
- National Health and Medical Research Council (NHMRC) Centre of Research Excellence in Digestive Health, Hunter Medical Research Institute, The University of Newcastle, Newcastle, NSW, Australia
| | - Nicholas J Clemons
- Cancer Research Division, Peter MaCallum Cancer Centre, Melbourne VIC, Australia.,Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, VIC, Australia
| | - B Paul Morgan
- Division of Infection & Immunity, School of Medicine, Cardiff University, Cardiff, United Kingdom
| | - Michelle M Hill
- QIMR Berghofer Medical Research Institute, Herston, QLD, Australia.,University of Queensland Diamantina Institute, Faculty of Medicine, The University of Queensland, St Lucia, QLD, Australia
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17
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Islam Khan MZ, Tam SY, Law HKW. Advances in High Throughput Proteomics Profiling in Establishing Potential Biomarkers for Gastrointestinal Cancer. Cells 2022; 11:973. [PMID: 35326424 PMCID: PMC8946849 DOI: 10.3390/cells11060973] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Revised: 03/05/2022] [Accepted: 03/08/2022] [Indexed: 12/24/2022] Open
Abstract
Gastrointestinal cancers (GICs) remain the most diagnosed cancers and accounted for the highest cancer-related death globally. The prognosis and treatment outcomes of many GICs are poor because most of the cases are diagnosed in advanced metastatic stages. This is primarily attributed to the deficiency of effective and reliable early diagnostic biomarkers. The existing biomarkers for GICs diagnosis exhibited inadequate specificity and sensitivity. To improve the early diagnosis of GICs, biomarkers with higher specificity and sensitivity are warranted. Proteomics study and its functional analysis focus on elucidating physiological and biological functions of unknown or annotated proteins and deciphering cellular mechanisms at molecular levels. In addition, quantitative analysis of translational proteomics is a promising approach in enhancing the early identification and proper management of GICs. In this review, we focus on the advances in mass spectrometry along with the quantitative and functional analysis of proteomics data that contributes to the establishment of biomarkers for GICs including, colorectal, gastric, hepatocellular, pancreatic, and esophageal cancer. We also discuss the future challenges in the validation of proteomics-based biomarkers for their translation into clinics.
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Affiliation(s)
| | | | - Helen Ka Wai Law
- Department of Health Technology and Informatics, Faculty of Health and Social Sciences, The Hong Kong Polytechnic University, Hung Hom, Hong Kong, China; (M.Z.I.K.); (S.Y.T.)
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18
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Ahn SB, Kamath KS, Mohamedali A, Noor Z, Wu JX, Pascovici D, Adhikari S, Cheruku HR, Guillemin GJ, McKay MJ, Nice EC, Baker MS. Use of a Recombinant Biomarker Protein DDA Library Increases DIA Coverage of Low Abundance Plasma Proteins. J Proteome Res 2021; 20:2374-2389. [PMID: 33752330 DOI: 10.1021/acs.jproteome.0c00898] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Credible detection and quantification of low abundance proteins from human blood plasma is a major challenge in precision medicine biomarker discovery when using mass spectrometry (MS). In this proof-of-concept study, we employed a mixture of selected recombinant proteins in DDA libraries to subsequently identify (not quantify) cancer-associated low abundance plasma proteins using SWATH/DIA. The exemplar DDA recombinant protein spectral library (rPSL) was derived from tryptic digestion of 36 recombinant human proteins that had been previously implicated as possible cancer biomarkers from both our own and other studies. The rPSL was then used to identify proteins from nondepleted colorectal cancer (CRC) EDTA plasmas by SWATH-MS. Most (32/36) of the proteins used in the rPSL were reliably identified from CRC plasma samples, including 8 proteins (i.e., BTC, CXCL10, IL1B, IL6, ITGB6, TGFα, TNF, TP53) not previously detected using high-stringency protein inference MS according to PeptideAtlas. The rPSL SWATH-MS protocol was compared to DDA-MS using MARS-depleted and postdigestion peptide fractionated plasmas (here referred to as a human plasma DDA library). Of the 32 proteins identified using rPSL SWATH, only 12 could be identified using DDA-MS. The 20 additional proteins exclusively identified using the rPSL SWATH approach were almost exclusively lower abundance (i.e., <10 ng/mL) proteins. To mitigate justified FDR concerns, and to replicate a more typical library creation approach, the DDA rPSL library was merged with a human plasma DDA library and SWATH identification repeated using such a merged library. The majority (33/36) of the low abundance plasma proteins added from the rPSL were still able to be identified using such a merged library when high-stringency HPP Guidelines v3.0 protein inference criteria were applied to our data set. The MS data set has been deposited to ProteomeXchange Consortium via the PRIDE partner repository (PXD022361).
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Affiliation(s)
- Seong Beom Ahn
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, Macquarie Park, NSW 2109, Australia
| | - Karthik S Kamath
- Australian Proteome Analysis Facility (APAF), Department of Molecular Sciences, Faculty of Science and Engineering, Macquarie University, Macquarie Park, NSW 2109, Australia
| | - Abidali Mohamedali
- Department of Molecular Sciences, Faculty of Science and Engineering, Macquarie University, Macquarie Park, NSW 2109, Australia
| | - Zainab Noor
- ProCan, Children's Medical Research Institute, The University of Sydney, Westmead, Newtown, NSW 2042, Australia
| | - Jemma X Wu
- Australian Proteome Analysis Facility (APAF), Department of Molecular Sciences, Faculty of Science and Engineering, Macquarie University, Macquarie Park, NSW 2109, Australia
| | - Dana Pascovici
- Australian Proteome Analysis Facility (APAF), Department of Molecular Sciences, Faculty of Science and Engineering, Macquarie University, Macquarie Park, NSW 2109, Australia
| | - Subash Adhikari
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, Macquarie Park, NSW 2109, Australia
| | - Harish R Cheruku
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, Macquarie Park, NSW 2109, Australia
| | - Gilles J Guillemin
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, Macquarie Park, NSW 2109, Australia
| | - Matthew J McKay
- Australian Proteome Analysis Facility (APAF), Department of Molecular Sciences, Faculty of Science and Engineering, Macquarie University, Macquarie Park, NSW 2109, Australia
| | - Edouard C Nice
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, VIC 3800, Australia
| | - Mark S Baker
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, Macquarie Park, NSW 2109, Australia
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