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Vellan CJ, Jayapalan JJ, Yoong BK, Abdul-Aziz A, Mat-Junit S, Subramanian P. Application of Proteomics in Pancreatic Ductal Adenocarcinoma Biomarker Investigations: A Review. Int J Mol Sci 2022; 23:2093. [PMID: 35216204 PMCID: PMC8879036 DOI: 10.3390/ijms23042093] [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: 12/16/2021] [Revised: 01/07/2022] [Accepted: 01/09/2022] [Indexed: 12/12/2022] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC), a highly aggressive malignancy with a poor prognosis is usually detected at the advanced stage of the disease. The only US Food and Drug Administration-approved biomarker that is available for PDAC, CA 19-9, is most useful in monitoring treatment response among PDAC patients rather than for early detection. Moreover, when CA 19-9 is solely used for diagnostic purposes, it has only a recorded sensitivity of 79% and specificity of 82% in symptomatic individuals. Therefore, there is an urgent need to identify reliable biomarkers for diagnosis (specifically for the early diagnosis), ascertain prognosis as well as to monitor treatment response and tumour recurrence of PDAC. In recent years, proteomic technologies are growing exponentially at an accelerated rate for a wide range of applications in cancer research. In this review, we discussed the current status of biomarker research for PDAC using various proteomic technologies. This review will explore the potential perspective for understanding and identifying the unique alterations in protein expressions that could prove beneficial in discovering new robust biomarkers to detect PDAC at an early stage, ascertain prognosis of patients with the disease in addition to monitoring treatment response and tumour recurrence of patients.
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Affiliation(s)
- Christina Jane Vellan
- Department of Molecular Medicine, Faculty of Medicine, Universiti Malaya, Kuala Lumpur 50603, Malaysia; (C.J.V.); (A.A.-A.); (S.M.-J.)
| | - Jaime Jacqueline Jayapalan
- Department of Molecular Medicine, Faculty of Medicine, Universiti Malaya, Kuala Lumpur 50603, Malaysia; (C.J.V.); (A.A.-A.); (S.M.-J.)
- University of Malaya Centre for Proteomics Research (UMCPR), Universiti Malaya, Kuala Lumpur 50603, Malaysia
| | - Boon-Koon Yoong
- Department of Surgery, Faculty of Medicine, Universiti Malaya, Kuala Lumpur 50603, Malaysia;
| | - Azlina Abdul-Aziz
- Department of Molecular Medicine, Faculty of Medicine, Universiti Malaya, Kuala Lumpur 50603, Malaysia; (C.J.V.); (A.A.-A.); (S.M.-J.)
| | - Sarni Mat-Junit
- Department of Molecular Medicine, Faculty of Medicine, Universiti Malaya, Kuala Lumpur 50603, Malaysia; (C.J.V.); (A.A.-A.); (S.M.-J.)
| | - Perumal Subramanian
- Department of Biochemistry and Biotechnology, Annamalai University, Chidambaram 608002, Tamil Nadu, India;
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Suzuki SR, Kuno A, Ozaki H. Cell-to-cell interaction analysis of prognostic ligand-receptor pairs in human pancreatic ductal adenocarcinoma. Biochem Biophys Rep 2021; 28:101126. [PMID: 34522794 PMCID: PMC8426203 DOI: 10.1016/j.bbrep.2021.101126] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 08/25/2021] [Accepted: 08/31/2021] [Indexed: 12/12/2022] Open
Abstract
Cell-to-cell interactions (CCIs) through ligand-receptor (LR) pairs in the tumor microenvironment underlie the poor prognosis of pancreatic ductal adenocarcinoma (PDAC). However, there is scant knowledge of the association of CCIs with PDAC prognosis, which is critical to the identification of potential therapeutic candidates. Here, we sought to identify the LR pairs associated with PDAC patient prognosis by integrating survival analysis and single-cell CCI prediction. Via survival analysis using gene expression from cancer cohorts, we found 199 prognostic LR pairs. CCI prediction based on single-cell RNA-seq data revealed the enriched LR pairs associated with poor prognosis. Notably, the CCIs involved epithelial tumor cells, cancer-associated fibroblasts, and tumor-associated macrophages through integrin-related and ANXA1-FPR pairs. Finally, we determined that CCIs involving 33 poor-prognostic LR pairs were associated with tumor grade. Although the clinical implication of the set of LR pairs must be determined, our results may provide potential therapeutic targets in PDAC.
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Affiliation(s)
- Sayaka R. Suzuki
- Program in Human Biology, School of Integrative and Global Majors, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8575, Japan
- Bioinformatics Laboratory, Faculty of Medicine, University of Tsukuba, Tsukuba 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8577, Japan
| | - Akihiro Kuno
- Program in Human Biology, School of Integrative and Global Majors, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8575, Japan
- Department of Anatomy and Embryology, Faculty of Medicine, University of Tsukuba, Tsukuba 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8577, Japan
| | - Haruka Ozaki
- Bioinformatics Laboratory, Faculty of Medicine, University of Tsukuba, Tsukuba 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8577, Japan
- Center for Artificial Intelligence Research, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8577, Japan
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Nweke EE, Naicker P, Aron S, Stoychev S, Devar J, Tabb DL, Omoshoro-Jones J, Smith M, Candy G. SWATH-MS based proteomic profiling of pancreatic ductal adenocarcinoma tumours reveals the interplay between the extracellular matrix and related intracellular pathways. PLoS One 2020; 15:e0240453. [PMID: 33048956 PMCID: PMC7553299 DOI: 10.1371/journal.pone.0240453] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 09/27/2020] [Indexed: 02/06/2023] Open
Abstract
Pancreatic cancer accounts for 2.8% of new cancer cases worldwide and is projected to become the second leading cause of cancer-related deaths by 2030. Patients of African ancestry appear to be at an increased risk for pancreatic ductal adenocarcinoma (PDAC), with more severe disease and outcomes. The purpose of this study was to map the proteomic and genomic landscape of a cohort of PDAC patients of African ancestry. Thirty tissues (15 tumours and 15 normal adjacent tissues) were obtained from consenting South African PDAC patients. Optimisation of the sample preparation method allowed for the simultaneous extraction of high-purity protein and DNA for SWATH-MS and OncoArray SNV analyses. We quantified 3402 proteins with 49 upregulated and 35 downregulated proteins at a minimum 2.1 fold change and FDR adjusted p-value (q-value) ≤ 0.01 when comparing tumour to normal adjacent tissue. Many of the upregulated proteins in the tumour samples are involved in extracellular matrix formation (ECM) and related intracellular pathways. In addition, proteins such as EMIL1, KBTB2, and ZCCHV involved in the regulation of ECM proteins were observed to be dysregulated in pancreatic tumours. Downregulation of pathways involved in oxygen and carbon dioxide transport were observed. Genotype data showed missense mutations in some upregulated proteins, such as MYPN, ESTY2 and SERPINB8. Approximately 11% of the dysregulated proteins, including ISLR, BP1, PTK7 and OLFL3, were predicted to be secretory proteins. These findings help in further elucidating the biology of PDAC and may aid in identifying future plausible markers for the disease.
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Affiliation(s)
- Ekene Emmanuel Nweke
- Department of Surgery, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- * E-mail:
| | - Previn Naicker
- Department of Biosciences, Council for Scientific and Industrial Research, Pretoria, South Africa
| | - Shaun Aron
- Sydney Brenner Institute for Molecular Bioscience, University of the Witwatersrand, Johannesburg, South Africa
| | - Stoyan Stoychev
- Department of Biosciences, Council for Scientific and Industrial Research, Pretoria, South Africa
| | - John Devar
- Department of Surgery, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - David L. Tabb
- Bioinformatics Unit, South African Tuberculosis Bioinformatics Initiative, Division of Molecular Biology and Human Genetics, Department of Biomedical Sciences, Stellenbosch University, Cape Town, South Africa
| | - Jones Omoshoro-Jones
- Department of Surgery, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Martin Smith
- Department of Surgery, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Geoffrey Candy
- Department of Surgery, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
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Carrick E, Vanmassenhove J, Glorieux G, Metzger J, Dakna M, Pejchinovski M, Jankowski V, Mansoorian B, Husi H, Mullen W, Mischak H, Vanholder R, Van Biesen W. Development of a MALDI MS-based platform for early detection of acute kidney injury. Proteomics Clin Appl 2016; 10:732-42. [PMID: 27119821 PMCID: PMC4950042 DOI: 10.1002/prca.201500117] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2015] [Revised: 03/21/2016] [Accepted: 04/11/2016] [Indexed: 12/24/2022]
Abstract
PURPOSE Septic acute kidney injury (AKI) is associated with poor outcome. This can partly be attributed to delayed diagnosis and incomplete understanding of the underlying pathophysiology. Our aim was to develop an early predictive test for AKI based on the analysis of urinary peptide biomarkers by MALDI-MS. EXPERIMENTAL DESIGN Urine samples from 95 patients with sepsis were analyzed by MALDI-MS. Marker search and multimarker model establishment were performed using the peptide profiles from 17 patients with existing or within the next 5 days developing AKI and 17 with no change in renal function. Replicates of urine sample pools from the AKI and non-AKI patient groups and normal controls were also included to select the analytically most robust AKI markers. RESULTS Thirty-nine urinary peptides were selected by cross-validated variable selection to generate a support vector machine multidimensional AKI classifier. Prognostic performance of the AKI classifier on an independent validation set including the remaining 61 patients of the study population (17 controls and 44 cases) was good with an area under the receiver operating characteristics curve of 0.82 and a sensitivity and specificity of 86% and 76%, respectively. CONCLUSION AND CLINICAL RELEVANCE A urinary peptide marker model detects onset of AKI with acceptable accuracy in septic patients. Such a platform can eventually be transferred to the clinic as fast MALDI-MS test format.
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Affiliation(s)
- Emma Carrick
- Institute of Cardiovascular and Medical Sciences, Glasgow, UK
| | | | | | | | | | - Martin Pejchinovski
- Mosaiques Diagnostics GmbH, Hannover, Germany.,Charite-Universitätsmedizin Berlin, Berlin, Germany
| | - Vera Jankowski
- RWTH Aachen, Institute of Molecular Cardiovascular Research, Aachen, Germany
| | | | - Holger Husi
- Institute of Cardiovascular and Medical Sciences, Glasgow, UK
| | - William Mullen
- Institute of Cardiovascular and Medical Sciences, Glasgow, UK
| | - Harald Mischak
- Institute of Cardiovascular and Medical Sciences, Glasgow, UK.,Mosaiques Diagnostics GmbH, Hannover, Germany
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