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Byeon S, McKay MJ, Molloy MP, Gill AJ, Samra JS, Mittal A, Sahni S. Novel serum protein biomarker panel for early diagnosis of pancreatic cancer. Int J Cancer 2024; 155:365-371. [PMID: 38519999 DOI: 10.1002/ijc.34928] [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: 10/27/2023] [Revised: 01/29/2024] [Accepted: 03/05/2024] [Indexed: 03/25/2024]
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is one of the deadliest cancers. Late presentation of disease at the time of diagnosis is one of the major reasons for dismal prognostic outcomes for PDAC patients. Currently, there is a lack of clinical biomarkers, which can be used to diagnose PDAC patients at an early resectable stage. This study performed proteomic mass spectrometry to identify novel blood-based biomarkers for early diagnosis of PDAC. Serum specimens from 88 PDAC patients and 88 healthy controls (60 discovery cohort and 28 validation cohort) were analyzed using data independent acquisition high resolution mass spectrometry to identify candidate biomarker proteins. A total of 249 proteins were identified and quantified by the mass spectrometric analysis. Six proteins were markedly (>1.5 fold) and significantly (p < .05; q < 0.1) increased in PDAC patients compared to healthy controls in discovery cohort. Notably, four of these six proteins were significantly upregulated in an independent validation cohort. The top three upregulated proteins (i.e., Polymeric Immunoglobulin Receptor [PIGR], von Willebrand Factor [vWF], and Fibrinogen) were validated using enzyme linked immunosorbent assay, which led to selection of PIGR and vWF as a diagnostic biomarker panel for PDAC. The panel showed high ability to diagnose early stage (stage I and II) PDAC patients (area under the curve [AUC]: 0.8926), which was further improved after the addition of clinically used prognostic biomarker (Ca 19-9) to the panel (AUC: 0.9798). In conclusion, a novel serum protein biomarker panel for early diagnosis of PDAC was identified.
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Affiliation(s)
- Sooin Byeon
- Faculty of Medicine and Health, Northern Clinical School, University of Sydney, Sydney, New South Wales, Australia
- Kolling Institute of Medical Research, University of Sydney, Sydney, New South Wales, Australia
| | - Matthew J McKay
- Kolling Institute of Medical Research, University of Sydney, Sydney, New South Wales, Australia
- Bowel Cancer and Biomarker Laboratory, School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, Sydney, New South Wales, Australia
| | - Mark P Molloy
- Kolling Institute of Medical Research, University of Sydney, Sydney, New South Wales, Australia
- Bowel Cancer and Biomarker Laboratory, School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, Sydney, New South Wales, Australia
| | - Anthony J Gill
- Faculty of Medicine and Health, Northern Clinical School, University of Sydney, Sydney, New South Wales, Australia
- Kolling Institute of Medical Research, University of Sydney, Sydney, New South Wales, Australia
- NSW Health Pathology, Department of Anatomical Pathology, Royal North Shore Hospital, Sydney, New South Wales, Australia
| | - Jaswinder S Samra
- Australian Pancreatic Centre, St Leonards, Sydney, New South Wales, Australia
- Upper GI Surgical Unit, Royal North Shore Hospital and North Shore Private Hospital, St Leonards, New South Wales, Australia
| | - Anubhav Mittal
- Faculty of Medicine and Health, Northern Clinical School, University of Sydney, Sydney, New South Wales, Australia
- Australian Pancreatic Centre, St Leonards, Sydney, New South Wales, Australia
- Upper GI Surgical Unit, Royal North Shore Hospital and North Shore Private Hospital, St Leonards, New South Wales, Australia
- Department of Surgery, The University of Notre Dame Australia, Sydney, New South Wales, Australia
| | - Sumit Sahni
- Faculty of Medicine and Health, Northern Clinical School, University of Sydney, Sydney, New South Wales, Australia
- Kolling Institute of Medical Research, University of Sydney, Sydney, New South Wales, Australia
- Australian Pancreatic Centre, St Leonards, Sydney, New South Wales, Australia
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2
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Stillger MN, Kurowski K, Bronsert P, Brombacher E, Kreutz C, Werner M, Tang L, Timme-Bronsert S, Schilling O. Neoadjuvant chemo- or chemo-radiation-therapy of pancreatic ductal adenocarcinoma differentially shift ECM composition, complement activation, energy metabolism and ribosomal proteins of the residual tumor mass. Int J Cancer 2024; 154:2162-2175. [PMID: 38353498 DOI: 10.1002/ijc.34867] [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: 08/21/2023] [Revised: 11/08/2023] [Accepted: 12/20/2023] [Indexed: 04/14/2024]
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is a highly lethal cancer, often diagnosed at stages that dis-qualify for surgical resection. Neoadjuvant therapies offer potential tumor regression and improved resectability. Although features of the tumor biology (e.g., molecular markers) may guide adjuvant therapy, biological alterations after neoadjuvant therapy remain largely unexplored. We performed mass spectrometry to characterize the proteomes of 67 PDAC resection specimens of patients who received either neoadjuvant chemo (NCT) or chemo-radiation (NCRT) therapy. We employed data-independent acquisition (DIA), yielding a proteome coverage in excess of 3500 proteins. Moreover, we successfully integrated two publicly available proteome datasets of treatment-naïve PDAC to unravel proteome alterations in response to neoadjuvant therapy, highlighting the feasibility of this approach. We found highly distinguishable proteome profiles. Treatment-naïve PDAC was characterized by enrichment of immunoglobulins, complement and extracellular matrix (ECM) proteins. Post-NCT and post-NCRT PDAC presented high abundance of ribosomal and metabolic proteins as compared to treatment-naïve PDAC. Further analyses on patient survival and protein expression identified treatment-specific prognostic candidates. We present the first proteomic characterization of the residual PDAC mass after NCT and NCRT, and potential protein candidate markers associated with overall survival. We conclude that residual PDAC exhibits fundamentally different proteome profiles as compared to treatment-naïve PDAC, influenced by the type of neoadjuvant treatment. These findings may impact adjuvant or targeted therapy options.
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Affiliation(s)
- Maren N Stillger
- Faculty of Medicine, Institute for Surgical Pathology, Medical Center-University of Freiburg, University of Freiburg, Freiburg, Germany
- Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Konrad Kurowski
- Faculty of Medicine, Institute for Surgical Pathology, Medical Center-University of Freiburg, University of Freiburg, Freiburg, Germany
- Faculty of Medicine, Core Facility for Histopathology and Digital Pathology, Medical Center-University of Freiburg, Freiburg, Germany
| | - Peter Bronsert
- Faculty of Medicine, Institute for Surgical Pathology, Medical Center-University of Freiburg, University of Freiburg, Freiburg, Germany
- Faculty of Medicine, Core Facility for Histopathology and Digital Pathology, Medical Center-University of Freiburg, Freiburg, Germany
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Eva Brombacher
- Faculty of Biology, University of Freiburg, Freiburg, Germany
- Faculty of Medicine and Medical Center, Institute of Medical Biometry and Statistics, University of Freiburg, Freiburg, Germany
- Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, Freiburg, Germany
- Centre for Integrative Biological Signaling Studies (CIBSS), University of Freiburg, Freiburg, Germany
| | - Clemens Kreutz
- Faculty of Medicine and Medical Center, Institute of Medical Biometry and Statistics, University of Freiburg, Freiburg, Germany
| | - Martin Werner
- Faculty of Medicine, Institute for Surgical Pathology, Medical Center-University of Freiburg, University of Freiburg, Freiburg, Germany
- Faculty of Medicine, Core Facility for Histopathology and Digital Pathology, Medical Center-University of Freiburg, Freiburg, Germany
| | - Laura Tang
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Sylvia Timme-Bronsert
- Faculty of Medicine, Institute for Surgical Pathology, Medical Center-University of Freiburg, University of Freiburg, Freiburg, Germany
| | - Oliver Schilling
- Faculty of Medicine, Institute for Surgical Pathology, Medical Center-University of Freiburg, University of Freiburg, Freiburg, Germany
- Faculty of Medicine, Core Facility for Histopathology and Digital Pathology, Medical Center-University of Freiburg, Freiburg, Germany
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3
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O'Rourke MB, Hansbro PP, Molloy MP. Reusing Peptide Spectral Reference Libraries to Discover Putative Plasma Biomarkers of Response to Cancer Chemotherapy. Methods Mol Biol 2024; 2823:241-251. [PMID: 39052224 DOI: 10.1007/978-1-0716-3922-1_15] [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: 07/27/2024]
Abstract
Biofluids such as blood plasma are rich reservoirs of potential biomarkers for disease diagnosis, prognosis, and prediction of treatment response. However, mass spectrometry analysis of circulating plasma proteins remains challenging. The introduction of data-independent acquisition mass spectrometry (DIA-MS) is an important step toward addressing detection of less abundant plasma proteins. Numerous plasma peptide MS/MS spectral library datasets produced from extensive plasma fractionation are accessible from public archives, and these can be repurposed as spectral reference libraries to increase the depth of proteomic analysis when DIA-MS is used. Here we describe the workflow that relies on reusing the existing spectral reference libraries by populating them with locally obtained peptide MS/MS data acquired by DIA-MS. This approach was demonstrated effectively to identify putative plasma biomarkers of response to neoadjuvant chemotherapy in the setting of pancreatic ductal adenocarcinoma (PDAC) (O'Rourke et al., J Proteomics 231:103998, 2021).
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Affiliation(s)
- Matthew B O'Rourke
- Bowel Cancer & Biomarker Laboratory, School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, St Leonards, NSW, Australia
- Centre for Inflammation, Centenary Institute, Camperdown, NSW, Australia
- School of Life Sciences, Faculty of Science, University of Technology Sydney, Ultimo, NSW, Australia
| | - Philip P Hansbro
- Centre for Inflammation, Centenary Institute, Camperdown, NSW, Australia
- School of Life Sciences, Faculty of Science, University of Technology Sydney, Ultimo, NSW, Australia
| | - Mark P Molloy
- Bowel Cancer & Biomarker Laboratory, School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, St Leonards, NSW, Australia.
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Ramalhete L, Vigia E, Araújo R, Marques HP. Proteomics-Driven Biomarkers in Pancreatic Cancer. Proteomes 2023; 11:24. [PMID: 37606420 PMCID: PMC10443269 DOI: 10.3390/proteomes11030024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 07/28/2023] [Accepted: 08/03/2023] [Indexed: 08/23/2023] Open
Abstract
Pancreatic cancer is a devastating disease that has a grim prognosis, highlighting the need for improved screening, diagnosis, and treatment strategies. Currently, the sole biomarker for pancreatic ductal adenocarcinoma (PDAC) authorized by the U.S. Food and Drug Administration is CA 19-9, which proves to be the most beneficial in tracking treatment response rather than in early detection. In recent years, proteomics has emerged as a powerful tool for advancing our understanding of pancreatic cancer biology and identifying potential biomarkers and therapeutic targets. This review aims to offer a comprehensive survey of proteomics' current status in pancreatic cancer research, specifically accentuating its applications and its potential to drastically enhance screening, diagnosis, and treatment response. With respect to screening and diagnostic precision, proteomics carries the capacity to augment the sensitivity and specificity of extant screening and diagnostic methodologies. Nonetheless, more research is imperative for validating potential biomarkers and establishing standard procedures for sample preparation and data analysis. Furthermore, proteomics presents opportunities for unveiling new biomarkers and therapeutic targets, as well as fostering the development of personalized treatment strategies based on protein expression patterns associated with treatment response. In conclusion, proteomics holds great promise for advancing our understanding of pancreatic cancer biology and improving patient outcomes. It is essential to maintain momentum in investment and innovation in this arena to unearth more groundbreaking discoveries and transmute them into practical diagnostic and therapeutic strategies in the clinical context.
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Affiliation(s)
- Luís Ramalhete
- Blood and Transplantation Center of Lisbon—Instituto Português do Sangue e da Transplantação, Alameda das Linhas de Torres, n° 117, 1769-001 Lisbon, Portugal
- Nova Medical School, Faculdade de Ciências Médicas, Universidade NOVA de Lisboa, 1169-056 Lisbon, Portugal
- iNOVA4Health—Advancing Precision Medicine, RG11: Reno-Vascular Diseases Group, NOVA Medical School, Faculdade de Ciências Médicas, Universidade NOVA de Lisboa, 1169-056 Lisbon, Portugal
| | - Emanuel Vigia
- Nova Medical School, Faculdade de Ciências Médicas, Universidade NOVA de Lisboa, 1169-056 Lisbon, Portugal
- Centro Hospitalar de Lisboa Central, Department of Hepatobiliopancreatic and Transplantation, 1050-099 Lisbon, Portugal
| | - Rúben Araújo
- Nova Medical School, Faculdade de Ciências Médicas, Universidade NOVA de Lisboa, 1169-056 Lisbon, Portugal
- CHRC—Comprehensive Health Research Centre, NOVA Medical School, 1150-199 Lisbon, Portugal
| | - Hugo Pinto Marques
- Nova Medical School, Faculdade de Ciências Médicas, Universidade NOVA de Lisboa, 1169-056 Lisbon, Portugal
- Centro Hospitalar de Lisboa Central, Department of Hepatobiliopancreatic and Transplantation, 1050-099 Lisbon, Portugal
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5
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O'Rourke MB, Januszewski AS, Sullivan DR, Lengyel I, Stewart AJ, Arya S, Ma RC, Galande S, Hardikar AA, Joglekar MV, Keech AC, Jenkins AJ, Molloy MP. Optimised plasma sample preparation and LC-MS analysis to support large-scale proteomic analysis of clinical trial specimens: Application to the Fenofibrate Intervention and Event Lowering in Diabetes (FIELD) trial. Proteomics Clin Appl 2023; 17:e2200106. [PMID: 36891577 PMCID: PMC10909541 DOI: 10.1002/prca.202200106] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Revised: 02/10/2023] [Accepted: 02/28/2023] [Indexed: 03/10/2023]
Abstract
PURPOSE Robust, affordable plasma proteomic biomarker workflows are needed for large-scale clinical studies. We evaluated aspects of sample preparation to allow liquid chromatography-mass spectrometry (LC-MS) analysis of more than 1500 samples from the Fenofibrate Intervention and Event Lowering in Diabetes (FIELD) trial of adults with type 2 diabetes. METHODS Using LC-MS with data-independent acquisition we evaluated four variables: plasma protein depletion, EDTA or citrated anti-coagulant blood collection tubes, plasma lipid depletion strategies and plasma freeze-thaw cycles. Optimised methods were applied in a pilot study of FIELD participants. RESULTS LC-MS of undepleted plasma conducted over a 45 min gradient yielded 172 proteins after excluding immunoglobulin isoforms. Cibachrome-blue-based depletion yielded additional proteins but with cost and time expenses, while immunodepleting albumin and IgG provided few additional identifications. Only minor variations were associated with blood collection tube type, delipidation methods and freeze-thaw cycles. From 65 batches involving over 1500 injections, the median intra-batch quantitative differences in the top 100 proteins of the plasma external standard were less than 2%. Fenofibrate altered seven plasma proteins. CONCLUSIONS AND CLINICAL RELEVANCE A robust plasma handling and LC-MS proteomics workflow for abundant plasma proteins has been developed for large-scale biomarker studies that balance proteomic depth with time and resource costs.
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Affiliation(s)
- Matthew B. O'Rourke
- Bowel Cancer & Biomarker LabSchool of Medical SciencesFaculty of Medicine and HealthThe University of SydneySydneyAustralia
- Centre for InflammationCentenary InstituteSydneyAustralia
- School of Life SciencesFaculty of ScienceUniversity of Technology SydneySydneyAustralia
| | - Andrzej S. Januszewski
- NHMRC Clinical Trials CentreFaculty of Medicine and HealthThe University of SydneySydneyAustralia
| | - David R. Sullivan
- NHMRC Clinical Trials CentreFaculty of Medicine and HealthThe University of SydneySydneyAustralia
- Department of Chemical PathologyRoyal Prince Alfred HospitalNSW Health PathologyAustralia
| | - Imre Lengyel
- Wellcome‐Wolfson Institute for Experimental MedicineSchool of MedicineDentistry and Biomedical ScienceQueen's University BelfastBelfastBelfastUK
| | | | - Swati Arya
- School of MedicineUniversity of St AndrewsSt AndrewsFifeUK
| | - Ronald C. Ma
- Department of Medicine and TherapeuticsThe Chinese University of Hong KongHong KongChina
| | | | - Anandwardhan A. Hardikar
- NHMRC Clinical Trials CentreFaculty of Medicine and HealthThe University of SydneySydneyAustralia
- Present address:
Diabetes and Islet Biology groupSchool of MedicineWestern Sydney UniversityCampbelltownAustralia
| | - Mugdha V. Joglekar
- NHMRC Clinical Trials CentreFaculty of Medicine and HealthThe University of SydneySydneyAustralia
- Present address:
Diabetes and Islet Biology groupSchool of MedicineWestern Sydney UniversityCampbelltownAustralia
| | - Anthony C. Keech
- NHMRC Clinical Trials CentreFaculty of Medicine and HealthThe University of SydneySydneyAustralia
| | - Alicia J. Jenkins
- NHMRC Clinical Trials CentreFaculty of Medicine and HealthThe University of SydneySydneyAustralia
- Baker Heart and Diabetes InstituteMelbourneAustralia
| | - Mark P. Molloy
- Bowel Cancer & Biomarker LabSchool of Medical SciencesFaculty of Medicine and HealthThe University of SydneySydneyAustralia
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6
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Chen H, Aneman I, Nikolic V, Karadzov Orlic N, Mikovic Z, Stefanovic M, Cakic Z, Jovanovic H, Town SEL, Padula MP, McClements L. Maternal plasma proteome profiling of biomarkers and pathogenic mechanisms of early-onset and late-onset preeclampsia. Sci Rep 2022; 12:19099. [PMID: 36351970 PMCID: PMC9646706 DOI: 10.1038/s41598-022-20658-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 09/16/2022] [Indexed: 11/10/2022] Open
Abstract
Preeclampsia is still the leading cause of morbidity and mortality in pregnancy without a cure. There are two phenotypes of preeclampsia, early-onset (EOPE) and late-onset (LOPE) with poorly defined pathogenic differences. This study aimed to facilitate better understanding of the mechanisms of pathophysiology of EOPE and LOPE, and identify specific biomarkers or therapeutic targets. In this study, we conducted an untargeted, label-free quantitative proteomic analyses of plasma samples from pregnant women with EOPE (n = 17) and LOPE (n = 11), and age, BMI-matched normotensive controls (n = 18). Targeted proteomics approach was also employed to validate a subset of proteins (n = 17). In total, there were 26 and 20 differentially abundant proteins between EOPE or LOPE, and normotensive controls, respectively. A series of angiogenic and inflammatory proteins, including insulin-like growth factor-binding protein 4 (IGFBP4; EOPE: FDR = 0.0030 and LOPE: FDR = 0.00396) and inter-alpha-trypsin inhibitor heavy chain H2-4 (ITIH2-4), were significantly altered in abundance in both phenotypes. Through validation we confirmed that ITIH2 was perturbed only in LOPE (p = 0.005) whereas ITIH3 and ITIH4 were perturbed in both phenotypes (p < 0.05). Overall, lipid metabolism/transport proteins associated with atherosclerosis were highly abundant in LOPE, however, ECM proteins had a more pronounced role in EOPE. The complement cascade and binding and uptake of ligands by scavenger receptors, pathways, were associated with both EOPE and LOPE.
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Affiliation(s)
- Hao Chen
- grid.117476.20000 0004 1936 7611School of Life Sciences, Faculty of Science, University of Technology Sydney, Ultimo, NSW Australia
| | - Ingrid Aneman
- grid.117476.20000 0004 1936 7611School of Life Sciences, Faculty of Science, University of Technology Sydney, Ultimo, NSW Australia
| | - Valentina Nikolic
- grid.11374.300000 0001 0942 1176Department of Pharmacology and Toxicology, Faculty of Medicine, University of Nis, Nis, Serbia
| | - Natasa Karadzov Orlic
- Department of Gynaecology and Obstetrics, Narodni Front, Belgrade, Serbia ,grid.7149.b0000 0001 2166 9385Faculty of Medicine, University of Belgrade, Belgrade, Serbia
| | - Zeljko Mikovic
- Department of Gynaecology and Obstetrics, Narodni Front, Belgrade, Serbia ,grid.7149.b0000 0001 2166 9385Faculty of Medicine, University of Belgrade, Belgrade, Serbia
| | - Milan Stefanovic
- grid.11374.300000 0001 0942 1176Department of Gynaecology and Obstetrics, Faculty of Medicine, University of Nis, Nis, Serbia ,grid.418653.d0000 0004 0517 2741Gynaecology and Obstetrics Clinic, Clinical Centre Nis, Nis, Serbia
| | - Zoran Cakic
- Department of Gynaecology and Obstetrics, General Hospital of Leskovac, Leskovac, Serbia
| | - Hristina Jovanovic
- grid.11374.300000 0001 0942 1176Department of Pharmacology and Toxicology, Faculty of Medicine, University of Nis, Nis, Serbia
| | - Stephanie E. L. Town
- grid.117476.20000 0004 1936 7611School of Life Sciences, Faculty of Science, University of Technology Sydney, Ultimo, NSW Australia
| | - Matthew P. Padula
- grid.117476.20000 0004 1936 7611School of Life Sciences, Faculty of Science, University of Technology Sydney, Ultimo, NSW Australia
| | - Lana McClements
- grid.117476.20000 0004 1936 7611School of Life Sciences, Faculty of Science, University of Technology Sydney, Ultimo, NSW Australia ,grid.117476.20000 0004 1936 7611Institute for Biomedical Materials and Devices, Faculty of Science, University of Technology Sydney, Ultimo, NSW Australia
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7
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Systemic Biomarkers and Unique Pathways in Different Phenotypes of Heart Failure with Preserved Ejection Fraction. Biomolecules 2022; 12:biom12101419. [PMID: 36291628 PMCID: PMC9599828 DOI: 10.3390/biom12101419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 09/28/2022] [Accepted: 09/29/2022] [Indexed: 11/16/2022] Open
Abstract
Heart failure with preserved ejection fraction (HFpEF) accounts for around 50% of all heart failure cases. It is a heterogeneous condition with poorly understood pathogenesis. Here, we aimed to identify unique pathogenic mechanisms in acute and chronic HFpEF and hypertrophic cardiomyopathy (HCM). We performed unbiased, comprehensive proteomic analyses of plasma samples from gender- and BMI-matched patients with acute HFpEF (n = 8), chronic HFpEF (n = 9) and HCM (n = 14) using liquid chromatography–mass spectrometry. Distinct molecular signatures were observed in different HFpEF forms. Clusters of biomarkers differentially abundant between HFpEF forms were predominantly associated with microvascular inflammation. New candidate protein markers were also identified, including leucine-rich alpha-2-glycoprotein 1 (LRG1), serum amyloid A1 (SAA1) and inter-alpha-trypsin inhibitor heavy chain 3 (ITIH3). Our study is the first to apply systematic, quantitative proteomic screening of plasma samples from patients with different subtypes of HFpEF and identify candidate biomarkers for improved management of acute and chronic HFpEF and HCM.
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8
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Boys EL, Liu J, Robinson PJ, Reddel RR. Clinical applications of mass spectrometry-based proteomics in cancer: where are we? Proteomics 2022; 23:e2200238. [PMID: 35968695 DOI: 10.1002/pmic.202200238] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 08/07/2022] [Accepted: 08/09/2022] [Indexed: 11/12/2022]
Abstract
Tumor tissue processing methodologies in combination with data-independent acquisition mass spectrometry (DIA-MS) have emerged that can comprehensively analyze the proteome of multiple tumor samples accurately and reproducibly. Increasing recognition and adoption of these technologies has resulted in a tranche of studies providing novel insights into cancer classification systems, functional tumor biology, cancer biomarkers, treatment response and drug targets. Despite this, with some limited exceptions, MS-based proteomics has not yet been implemented in routine cancer clinical practice. Here, we summarize the use of DIA-MS in studies that may pave the way for future clinical cancer applications, and highlight the role of alternative MS technologies and multi-omic strategies. We discuss limitations and challenges of studies in this field to date and propose steps for integrating proteomic data into the cancer clinic. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Emma L Boys
- ProCan®, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, NSW, Australia
| | - Jia Liu
- ProCan®, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, NSW, Australia.,The Kinghorn Cancer Centre, St Vincent's Hospital, Darlinghurst, NSW, Australia.,School of Clinical Medicine, St Vincent's Campus, University of New South Wales, Sydney, NSW, Australia
| | - Phillip J Robinson
- ProCan®, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, NSW, Australia
| | - Roger R Reddel
- ProCan®, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, NSW, Australia
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Hortle E, Tran VL, Wright K, Fontaine AR, Pinello N, O'Rourke MB, Wong JJL, Hansbro PM, Britton WJ, Oehlers SH. OXSR1 inhibits inflammasome activation by limiting potassium efflux during mycobacterial infection. Life Sci Alliance 2022; 5:5/9/e202201476. [PMID: 35545295 PMCID: PMC9107790 DOI: 10.26508/lsa.202201476] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 04/15/2022] [Accepted: 04/19/2022] [Indexed: 12/13/2022] Open
Abstract
Mycobacteria up-regulate host kinase OXSR1 preventing potassium efflux and inflammasome activation. Depletion or inhibition of OXSR1 potentiates inflammasome activation and decreases bacterial burden. Pathogenic mycobacteria inhibit inflammasome activation to establish infection. Although it is known that potassium efflux is a trigger for inflammasome activation, the interaction between mycobacterial infection, potassium efflux, and inflammasome activation has not been investigated. Here, we use Mycobacterium marinum infection of zebrafish embryos and Mycobacterium tuberculosis infection of THP-1 cells to demonstrate that pathogenic mycobacteria up-regulate the host WNK signalling pathway kinases SPAK and OXSR1 which control intracellular potassium balance. We show that genetic depletion or inhibition of OXSR1 decreases bacterial burden and intracellular potassium levels. The protective effects of OXSR1 depletion are at least partially mediated by NLRP3 inflammasome activation, caspase-mediated release of IL-1β, and downstream activation of protective TNF-α. The elucidation of this druggable pathway to potentiate inflammasome activation provides a new avenue for the development of host-directed therapies against intracellular infections.
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Affiliation(s)
- Elinor Hortle
- Tuberculosis Research Program Centenary Institute, The University of Sydney, Camperdown, Australia .,The University of Sydney, Discipline of Infectious Diseases and Immunology and Sydney Institute for Infectious Diseases, Camperdown, Australia.,Centre for Inflammation and University of Technology Sydney, Faculty of Science, School of Life Sciences, Sydney, Australia
| | - Vi Lt Tran
- Tuberculosis Research Program Centenary Institute, The University of Sydney, Camperdown, Australia
| | - Kathryn Wright
- Tuberculosis Research Program Centenary Institute, The University of Sydney, Camperdown, Australia
| | - Angela Rm Fontaine
- Centenary Imaging and Sydney Cytometry at the Centenary Institute, The University of Sydney, Camperdown, Australia
| | - Natalia Pinello
- Epigenetics and RNA Biology Program Centenary Institute, The University of Sydney, Camperdown, Australia.,The University of Sydney, Faculty of Medicine and Health, Camperdown, Australia
| | - Matthew B O'Rourke
- Centre for Inflammation and University of Technology Sydney, Faculty of Science, School of Life Sciences, Sydney, Australia
| | - Justin J-L Wong
- Epigenetics and RNA Biology Program Centenary Institute, The University of Sydney, Camperdown, Australia.,The University of Sydney, Faculty of Medicine and Health, Camperdown, Australia
| | - Philip M Hansbro
- Centre for Inflammation and University of Technology Sydney, Faculty of Science, School of Life Sciences, Sydney, Australia
| | - Warwick J Britton
- Tuberculosis Research Program Centenary Institute, The University of Sydney, Camperdown, Australia.,Department of Clinical Immunology, Royal Prince Alfred Hospital, Camperdown, Australia
| | - Stefan H Oehlers
- Tuberculosis Research Program Centenary Institute, The University of Sydney, Camperdown, Australia .,The University of Sydney, Discipline of Infectious Diseases and Immunology and Sydney Institute for Infectious Diseases, Camperdown, Australia.,A*STAR Infectious Diseases Labs (A*STAR ID Labs), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
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10
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Molloy MP, Hill C, O'Rourke MB, Chandra J, Steffen P, McKay MJ, Pascovici D, Herbert BR. Proteomic Analysis of Whole Blood Using Volumetric Absorptive Microsampling for Precision Medicine Biomarker Studies. J Proteome Res 2022; 21:1196-1203. [PMID: 35166117 DOI: 10.1021/acs.jproteome.1c00971] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Microsampling of patient blood promises several benefits over conventional phlebotomy practices to facilitate precision medicine studies. These include at-home patient blood collection, supporting telehealth monitoring, minimal postcollection processing, and compatibility with nonrefrigerated transport and storage. However, for proteomic biomarker studies, mass spectrometry of whole blood has generally been avoided in favor of using plasma or serum obtained from venepuncture. We evaluated the use of a volumetric absorptive microsampling (VAMS) device as a sample preparation matrix to enable LC-MS proteomic analyses of dried whole blood. We demonstrated the detection and robust quantitation of up to 1600 proteins from single-shot shotgun-LC-MS analysis of dried whole blood, greatly enhancing proteome depth compared with conventional single-shot LC-MS analyses of undepleted plasma. Some proteins not previously reported in blood were detected using this approach. Various washing reagents were used to demonstrate that proteins can be preferentially removed from VAMS devices prior to downstream analyses. We provide a demonstration that archival frozen blood cell pellets housed under long-term storage (exceeding 5 years) are compatible with VAMS to enable quantitation of potential biomarker proteins from biobank repositories. These demonstrations are important steps in establishing viable analysis workflows to underpin large-scale precision medicine studies. Data are available via ProteomeXchange with the identifier PXD028605.
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Affiliation(s)
- Mark P Molloy
- Bowel Cancer and Biomarker Research Laboratory, School of Medical Sciences, The University of Sydney, Sydney 2065, Australia
| | | | - Matthew B O'Rourke
- Bowel Cancer and Biomarker Research Laboratory, School of Medical Sciences, The University of Sydney, Sydney 2065, Australia
| | - Jason Chandra
- Bowel Cancer and Biomarker Research Laboratory, School of Medical Sciences, The University of Sydney, Sydney 2065, Australia
| | - Pascal Steffen
- Bowel Cancer and Biomarker Research Laboratory, School of Medical Sciences, The University of Sydney, Sydney 2065, Australia
| | - Matthew J McKay
- Bowel Cancer and Biomarker Research Laboratory, School of Medical Sciences, The University of Sydney, Sydney 2065, Australia
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Abstract
Cancer accounted for 16% of all death worldwide in 2018. Significant progress has been made in understanding tumor occurrence, progression, diagnosis, treatment, and prognosis at the molecular level. However, genomics changes cannot truly reflect the state of protein activity in the body due to the poor correlation between genes and proteins. Quantitative proteomics, capable of quantifying the relatively different protein abundance in cancer patients, has been increasingly adopted in cancer research. Quantitative proteomics has great application potentials, including cancer diagnosis, personalized therapeutic drug selection, real-time therapeutic effects and toxicity evaluation, prognosis and drug resistance evaluation, and new therapeutic target discovery. In this review, the development, testing samples, and detection methods of quantitative proteomics are introduced. The biomarkers identified by quantitative proteomics for clinical diagnosis, prognosis, and drug resistance are reviewed. The challenges and prospects of quantitative proteomics for personalized medicine are also discussed.
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