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Savva KV, Kawka M, Vadhwana B, Penumaka R, Patton I, Khan K, Perrott C, Das S, Giot M, Mavroveli S, Hanna GB, Ni MZ, Peters CJ. The Biomarker Toolkit - an evidence-based guideline to predict cancer biomarker success and guide development. BMC Med 2023; 21:383. [PMID: 37794461 PMCID: PMC10552368 DOI: 10.1186/s12916-023-03075-3] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 09/08/2023] [Indexed: 10/06/2023] Open
Abstract
BACKGROUND An increased number of resources are allocated on cancer biomarker discovery, but very few of these biomarkers are clinically adopted. To bridge the gap between Biomarker discovery and clinical use, we aim to generate the Biomarker Toolkit, a tool designed to identify clinically promising biomarkers and promote successful biomarker translation. METHODS All features associated with a clinically useful biomarker were identified using mixed-methodology, including systematic literature search, semi-structured interviews, and an online two-stage Delphi-Survey. Validation of the checklist was achieved by independent systematic literature searches using keywords/subheadings related to clinically and non-clinically utilised breast and colorectal cancer biomarkers. Composite aggregated scores were generated for each selected publication based on the presence/absence of an attribute listed in the Biomarker Toolkit checklist. RESULTS Systematic literature search identified 129 attributes associated with a clinically useful biomarker. These were grouped in four main categories including: rationale, clinical utility, analytical validity, and clinical validity. This checklist was subsequently developed using semi-structured interviews with biomarker experts (n=34); and 88.23% agreement was achieved regarding the identified attributes, via the Delphi survey (consensus level:75%, n=51). Quantitative validation was completed using clinically and non-clinically implemented breast and colorectal cancer biomarkers. Cox-regression analysis suggested that total score is a significant driver of biomarker success in both cancer types (BC: p>0.0001, 95.0% CI: 0.869-0.935, CRC: p>0.0001, 95.0% CI: 0.918-0.954). CONCLUSIONS This novel study generated a validated checklist with literature-reported attributes linked with successful biomarker implementation. Ultimately, the application of this toolkit can be used to detect biomarkers with the highest clinical potential and shape how biomarker studies are designed/performed.
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Affiliation(s)
- Katerina-Vanessa Savva
- Division of Surgery, Department of Surgery and Cancer, Imperial College London, London, UK.
| | - Michal Kawka
- Division of Surgery, Department of Surgery and Cancer, Imperial College London, London, UK
| | - Bhamini Vadhwana
- Division of Surgery, Department of Surgery and Cancer, Imperial College London, London, UK
| | - Rahul Penumaka
- Division of Surgery, Department of Surgery and Cancer, Imperial College London, London, UK
| | - Imogen Patton
- Division of Surgery, Department of Surgery and Cancer, Imperial College London, London, UK
| | - Komal Khan
- Division of Surgery, Department of Surgery and Cancer, Imperial College London, London, UK
| | - Claire Perrott
- Division of Surgery, Department of Surgery and Cancer, Imperial College London, London, UK
| | - Saranya Das
- Division of Surgery, Department of Surgery and Cancer, Imperial College London, London, UK
| | - Maxime Giot
- Division of Surgery, Department of Surgery and Cancer, Imperial College London, London, UK
| | - Stella Mavroveli
- Division of Surgery, Department of Surgery and Cancer, Imperial College London, London, UK
| | - George B Hanna
- Division of Surgery, Department of Surgery and Cancer, Imperial College London, London, UK
| | - Melody Zhifang Ni
- Division of Surgery, Department of Surgery and Cancer, Imperial College London, London, UK
| | - Christopher J Peters
- Division of Surgery, Department of Surgery and Cancer, Imperial College London, London, UK
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2
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Savva KV, Das B, Antonowicz S, Hanna GB, Peters CJ. Progress with Metabolomic Blood Tests for Gastrointestinal Cancer Diagnosis-An Assessment of Biomarker Translation. Cancer Epidemiol Biomarkers Prev 2022; 31:2095-2105. [PMID: 36215181 DOI: 10.1158/1055-9965.epi-22-0307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 06/27/2022] [Accepted: 09/30/2022] [Indexed: 12/30/2022] Open
Abstract
There is an urgent need for cost-effective, non-invasive tools to detect early stages of gastrointestinal cancer (colorectal, gastric, and esophageal cancers). Despite many publications suggesting circulating metabolites acting as accurate cancer biomarkers, few have reached the clinic. In upper gastrointestinal cancer this is critically important, as there is no test to complement gold-standard endoscopic evaluation in patients with mild symptoms that do not meet referral criteria. Therefore, this study aimed to describe and solve this translational gap. Studies reporting diagnostic accuracy of metabolomic blood-based gastrointestinal cancer biomarkers from 2007 to 2020 were systematically reviewed and progress of each biomarker along the discovery-validation-adoption pathway was mapped. Successful biomarker translation was defined as a composite endpoint, including patent protection/FDA approval/recommendation in national guidelines. The review found 77 biomarker panels of gastrointestinal cancer, including 25 with an AUROC >0.9. All but one was stalled at the discovery phase, 9.09% were patented and none were clinically approved, confirming the extent of biomarker translational gap. In addition, there were numerous "re-discoveries," including histidine, discovered in 7 colorectal studies. Finally, this study quantitatively supports the presence of a translational gap between discovery and clinical adoption, despite clear evidence of highly performing biomarkers with significant potential clinical value.
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Affiliation(s)
- Katerina-Vanessa Savva
- Department of Surgery and Cancer, Imperial College London, St. Mary's Hospital, London, United Kingdom
| | - Bibek Das
- Department of Surgery and Cancer, Imperial College London, St. Mary's Hospital, London, United Kingdom
| | - Stefan Antonowicz
- Department of Surgery and Cancer, Imperial College London, St. Mary's Hospital, London, United Kingdom
| | - George B Hanna
- Department of Surgery and Cancer, Imperial College London, St. Mary's Hospital, London, United Kingdom
| | - Christopher J Peters
- Department of Surgery and Cancer, Imperial College London, St. Mary's Hospital, London, United Kingdom
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3
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Fernández-Metzler C, Ackermann B, Garofolo F, Arnold ME, DeSilva B, Gu H, Laterza O, Mao Y, Rose M, Vazvaei-Smith F, Steenwyk R. Biomarker Assay Validation by Mass Spectrometry. AAPS J 2022; 24:66. [PMID: 35534647 DOI: 10.1208/s12248-022-00707-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Accepted: 03/31/2022] [Indexed: 11/30/2022] Open
Abstract
Decades of discussion and publication have gone into the guidance from the scientific community and the regulatory agencies on the use and validation of pharmacokinetic and toxicokinetic assays by chromatographic and ligand binding assays for the measurement of drugs and metabolites. These assay validations are well described in the FDA Guidance on Bioanalytical Methods Validation (BMV, 2018). While the BMV included biomarker assay validation, the focus was on understanding the challenges posed in validating biomarker assays and the importance of having reliable biomarker assays when used for regulatory submissions, rather than definition of the appropriate experiments to be performed. Different from PK bioanalysis, analysis of biomarkers can be challenging due to the presence of target analyte(s) in the control matrices used for calibrator and quality control sample preparation, and greater difficulty in procuring appropriate reference standards representative of the endogenous molecule. Several papers have been published offering recommendations for biomarker assay validation. The situational nature of biomarker applications necessitates fit-for-purpose (FFP) assay validation. A unifying theme for FFP analysis is that method validation requirements be consistent with the proposed context of use (COU) for any given biomarker. This communication provides specific recommendations for biomarker assay validation (BAV) by LC-MS, for both small and large molecule biomarkers. The consensus recommendations include creation of a validation plan that contains definition of the COU of the assay, use of the PK assay validation elements that support the COU, and definition of assay validation elements adapted to fit biomarker assays and the acceptance criteria for both.
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Affiliation(s)
| | - Brad Ackermann
- Eli Lilly & Company, Lilly Corporate Center, Indianapolis, IN, 46285, USA
| | - Fabio Garofolo
- BRI - a Frontage Company, 8898 Heather St, Vancouver, British Columbia, V6P 3S8, Canada
| | - Mark E Arnold
- Labcorp Drug Development, 221 Tulip Tree Drive, Westampton, NJ, 08060-5511, USA
| | - Binodh DeSilva
- Bristol-Myers Squibb Co., Route 206 & Province Line Road, Princeton, NJ, 08543, USA
| | - Huidong Gu
- Bristol-Myers Squibb Co., Route 206 & Province Line Road, Princeton, NJ, 08543, USA
| | - Omar Laterza
- Merck and Co Inc., 90 E Scott Ave, Rahway, NJ, 07065, USA
| | - Yan Mao
- Boehringer-Ingelheim Pharmaceuticals, 900 Ridgebury Road, Ridgefield, CT, 06877, USA
| | - Mark Rose
- Gossamer Bio Inc., 3013 Science Park Road, Suite 200, San Diego, CA, 92121, USA
| | | | - Rick Steenwyk
- Pfizer-Retired, 8739 N Homestead Circle, Irons, MI, 49644, USA
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4
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Kaur G, Poljak A, Ali SA, Zhong L, Raftery MJ, Sachdev P. Extending the Depth of Human Plasma Proteome Coverage Using Simple Fractionation Techniques. J Proteome Res 2021; 20:1261-1279. [PMID: 33471535 DOI: 10.1021/acs.jproteome.0c00670] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Human plasma is one of the most widely used tissues in clinical analysis, and plasma-based biomarkers are used for monitoring patient health status and/or response to medical treatment to avoid unnecessary invasive biopsy. Data-driven plasma proteomics has suffered from a lack of throughput and detection sensitivity, largely due to the complexity of the plasma proteome and in particular the enormous quantitative dynamic range, estimated to be between 9 and 13 orders of magnitude between the lowest and the highest abundance protein. A major challenge is to identify workflows that can achieve depth of plasma proteome coverage while minimizing the complexity of the sample workup and maximizing the sample throughput. In this study, we have performed intensive depletion of high-abundant plasma proteins or enrichment of low-abundant proteins using the Agilent multiple affinity removal liquid chromatography (LC) column-Human 6 (Hu6), the Agilent multiple affinity removal LC column-Human 14 (Hu14), and ProteoMiner followed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS PAGE) and C18 prefractionation techniques. We compared the performance of each of these fractionation approaches to identify the method that satisfies requirements for analysis of clinical samples and to include good plasma proteome coverage in combination with reasonable sample output. In this study, we report that one-dimensional (1D) gel-based prefractionation allows parallel sample processing and no loss of proteome coverage, compared with serial chromatographic separation, and significantly accelerates analysis time, particularly important for large clinical projects. Furthermore, we show that a variety of methodologies can achieve similarly high plasma proteome coverage, allowing flexibility in method selection based on project-specific needs. These considerations are important in the effort to accelerate plasma proteomics research so as to provide efficient, reliable, and accurate diagnoses, population-based health screening, clinical research studies, and other clinical work.
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Affiliation(s)
- Gurjeet Kaur
- Centre for Healthy Brain Ageing, School of Psychiatry, University of New South Wales, Sydney, NSW 2052, Australia.,Bioanalytical Mass Spectrometry Facility, Mark Wainwright Analytical Centre, University of New South Wales, Wallace Wurth Building (C27), Sydney, NSW 2052, Australia
| | - Anne Poljak
- Centre for Healthy Brain Ageing, School of Psychiatry, University of New South Wales, Sydney, NSW 2052, Australia.,Bioanalytical Mass Spectrometry Facility, Mark Wainwright Analytical Centre, University of New South Wales, Wallace Wurth Building (C27), Sydney, NSW 2052, Australia
| | - Syed Azmal Ali
- Cell Biology and Proteomics Lab, National Dairy Research Institute, Karnal, Haryana 132001, India
| | - Ling Zhong
- Bioanalytical Mass Spectrometry Facility, Mark Wainwright Analytical Centre, University of New South Wales, Wallace Wurth Building (C27), Sydney, NSW 2052, Australia
| | - Mark J Raftery
- Bioanalytical Mass Spectrometry Facility, Mark Wainwright Analytical Centre, University of New South Wales, Wallace Wurth Building (C27), Sydney, NSW 2052, Australia
| | - Perminder Sachdev
- Centre for Healthy Brain Ageing, School of Psychiatry, University of New South Wales, Sydney, NSW 2052, Australia.,Neuropsychiatric Institute, Euroa Centre, Prince of Wales Hospital, Sydney, NSW 2052, Australia
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5
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Faraldi M, Gomarasca M, Perego S, Sansoni V, Banfi G, Lombardi G. Effect of collection matrix, platelet depletion, and storage conditions on plasma extracellular vesicles and extracellular vesicle-associated miRNAs measurements. Clin Chem Lab Med 2020; 59:893-903. [PMID: 33555147 DOI: 10.1515/cclm-2020-1296] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 11/17/2020] [Indexed: 12/20/2022]
Abstract
OBJECTIVES The interest around circulating extracellular vesicles and their cargo in diagnostics has greatly increased; however, several pre-analytical variables affect their determination. In this study, we investigated the effects of sample matrix, processing, and plasma storage delay and temperature on extracellular vesicles and their miRNA content. METHODS Blood was collected from 10 male volunteers in dipotassium ethylendiaminotetraacetate-coated tubes (K2EDTA), either with plasma-preparation tube (PPT) or without (K2E) gel separator. A stepwise centrifugation was applied to K2E aliquots to obtain platelet-poor plasma (PPP). K2E, PPP and PPT plasma, stored under different conditions, were assayed for extracellular vesicles concentration and size distribution, through dynamic laser light scattering, and microRNAs content, by qPCR. RESULTS PPP samples were characterized by the lowest extracellular vesicles count and miRNA detectability. Although having no effects on extracellular vesicles total concentration, storage conditions influenced microRNAs detectability, mainly in PPP and PPT samples. Extracellular vesicles-associated miRNAs levels in K2E were, in general, higher than in PPP and to a very limited extent to PPT. Storage temperature and delay did not affect their profile in K2E samples. CONCLUSIONS Extracellular vesicles count and extracellular vesicles miRNA profile changed under the analyzed pre-analytical variables, showing the greatest stability in K2E samples. Since pre-analytical variables differently affected extracellular vesicles and their miRNA content, they should be considered in each experimental setting and clinical routine.
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Affiliation(s)
- Martina Faraldi
- Laboratory of Experimental Biochemistry & Molecular Biology, IRCCS Istituto Ortopedico Galeazzi, Milan, Italy
| | - Marta Gomarasca
- Laboratory of Experimental Biochemistry & Molecular Biology, IRCCS Istituto Ortopedico Galeazzi, Milan, Italy
| | - Silvia Perego
- Laboratory of Experimental Biochemistry & Molecular Biology, IRCCS Istituto Ortopedico Galeazzi, Milan, Italy
| | - Veronica Sansoni
- Laboratory of Experimental Biochemistry & Molecular Biology, IRCCS Istituto Ortopedico Galeazzi, Milan, Italy
| | - Giuseppe Banfi
- Laboratory of Experimental Biochemistry & Molecular Biology, IRCCS Istituto Ortopedico Galeazzi, Milan, Italy
- Vita-Salute San Raffaele University, Milan, Italy
| | - Giovanni Lombardi
- Laboratory of Experimental Biochemistry & Molecular Biology, IRCCS Istituto Ortopedico Galeazzi, Milan, Italy
- Department of Athletics, Strength and Conditioning, Poznań University of Physical Education, Poznań, Poland
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6
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Horgan D, Ciliberto G, Conte P, Baldwin D, Seijo L, Montuenga LM, Paz-Ares L, Garassino M, Penault-Llorca F, Galli F, Ray-Coquard I, Querleu D, Capoluongo E, Banerjee S, Riegman P, Kerr K, Horbach B, Büttner R, Van Poppel H, Bjartell A, Codacci-Pisanelli G, Westphalen B, Calvo F, Koeva-Balabanova J, Hall S, Paradiso A, Kalra D, Cobbaert C, Varea Menendez R, Maravic Z, Fotaki V, Bennouna J, Cauchin E, Malats N, Gutiérrez-Ibarluzea I, Gannon B, Mastris K, Bernini C, Gallagher W, Buglioni S, Kent A, Munzone E, Belina I, Van Meerbeeck J, Duffy M, Sarnowska E, Jagielska B, Mee S, Curigliano G. Bringing Greater Accuracy to Europe's Healthcare Systems: The Unexploited Potential of Biomarker Testing in Oncology. Biomed Hub 2020; 5:182-223. [PMID: 33564664 DOI: 10.1159/000511209] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Accepted: 08/31/2020] [Indexed: 12/11/2022] Open
Abstract
Rapid and continuing advances in biomarker testing are not being matched by take-up in health systems, and this is hampering both patient care and innovation. It also risks costing health systems the opportunity to make their services more efficient and, over time, more economical. This paper sets out the potential of biomarker testing, the unfolding precision and range of possible diagnosis and prediction, and the many obstacles to adoption. It offers case studies of biomarker testing in breast, ovarian, prostate, lung, thyroid and colon cancers, and derives specific lessons as to the potential and actual use of each of them. It also draws lessons about how to improve access and alignment, and to remedy the data deficiencies that impede development. And it suggests solutions to outstanding issues - notably including funding and the tangled web of obtaining reimbursement or equivalent coverage that Europe's fragmented health system implies. It urges a European evolution towards an initial minimum testing scenario, which would guarantee universal access to a suite of biomarker tests for the currently most common conditions, and, further into the future, to an optimum testing scenario in which a much wider range of biomarker tests would be introduced and become part of a more sophisticated health system articulated around personalised medicine. For exploiting genomics to the full, it argues the need for a new policy framework for Europe. Biomarker testing is not an issue that can be treated in isolation, since the purpose of testing is to improve health. Its use is therefore always closely linked to specific health challenges and needs to be viewed in the broader policy context in the EU and more widely. The paper is the result of extensive engagement with experts and decision makers to develop the framework, and consequently represents a wide consensus of views on how healthcare systems should respond from push and pull factors at local, national and cross-border and EU level. It contains strong views and clear recommendations springing from the convictions of patients, clinicians, academics, medicines authorities, HTA bodies, payers, the diagnostic, pharmaceutical and ICT industries, and national policy makers.
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Affiliation(s)
- Denis Horgan
- European Alliance for Personalised Medicine, Brussels, Belgium
| | | | | | - David Baldwin
- University of Nottingham, Nottingham, United Kingdom
| | - Luis Seijo
- Clinica Universidad de Navarra, CIBERES, Madrid, Spain
| | - Luis M Montuenga
- Center for Applied Medical Research (CIMA), University of Navarra and CIBERONC and IdisNa, Pamplona, Spain
| | - Luis Paz-Ares
- Hospital Doce de Octubre and CIBERONC, Madrid, Spain
| | | | | | | | | | | | | | - Susana Banerjee
- The Royal Marsden NHS Foundation Trust, London, United Kingdom
| | | | - Keith Kerr
- Aberdeen University, Aberdeen, United Kingdom
| | | | | | | | | | | | - Benedikt Westphalen
- Grosshadern University Hospital, Ludwig-Maximilians University, Munich, Germany
| | | | | | | | | | - Dipak Kalra
- The European Institute for Innovation through Health Data (i∼HD), Gent, Belgium
| | - Christa Cobbaert
- European Federation of Clinical Chemistry and Laboratory Diagnostics, Milan, Italy
| | | | | | | | | | | | - Nuria Malats
- Spanish National Cancer Research Centre (CNIO) and CIBERONC, Madrid, Spain
| | - Iñaki Gutiérrez-Ibarluzea
- EuroScan International Network, Cologne, Germany.,BIOEF, Basque Foundation for Health Innovation and Research, Barakaldo, Spain
| | | | | | - Chiara Bernini
- European Alliance for Personalised Medicine, Brussels, Belgium
| | | | | | - Alastair Kent
- Independent Patient Advocate, London, United Kingdom
| | | | - Ivica Belina
- Coalition of Healthcare Association, Zagreb, Croatia
| | - Jan Van Meerbeeck
- Antwerp University and Antwerp University Hospital, Antwerp, Belgium
| | | | | | - Beata Jagielska
- Maria Skłodowska-Curie Institute of Oncology, Warsaw, Poland
| | - Sarah Mee
- AstraZeneca, Cambridge, United Kingdom
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7
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Wilson BM, Moran MM, Meagher MJ, Ross RD, Mashiatulla M, Virdi AS, Sumner DR. Early changes in serum osteocalcin and body weight are predictive of implant fixation in a rat model of implant loosening. J Orthop Res 2020; 38:1216-1227. [PMID: 31825107 PMCID: PMC7225033 DOI: 10.1002/jor.24563] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Accepted: 11/30/2019] [Indexed: 02/04/2023]
Abstract
Biomarkers are of interest to identify patients at risk for peri-implant osteolysis and aseptic loosening. We used a rat model of particle-induced peri-implant osteolysis to investigate if early changes in biomarkers were associated with subsequent implant fixation strength. Implants were placed in rat femora, which were then challenged with intra-articular knee injections of either clean polyethylene, lipopolysaccharide-doped polyethylene, or cobalt-chromium alloy particles, with particle-free vehicle serving as control (n ≥ 8 per group). Rats were weighed weekly, blood was collected at weeks 0, 3, 5, and 6, and locomotor behavior was assessed 4 days before study conclusion. Rats were euthanized 6 weeks post surgery. Week 6 serum was analyzed for five bone remodeling markers, while longitudinal serum was assessed for osteocalcin. Bone-implant contact, peri-implant trabecular architecture, and implant fixation strength were measured. Rats challenged with cobalt-chromium particles had a significant reduction in implant fixation strength compared with the vehicle-control group (P = .034). This group also had elevated serum osteocalcin (P = .005), depressed weight gain (P = .001) and less frequent rearing behavior (P = .029). Regardless of group, change in serum osteocalcin at week 3 (r = -.368; P = .046), change in weight at week 2 (r = .586; P < .001), as well as weight change at all other time intervals were associated with fixation strength. The finding that early alterations in serum osteocalcin and body weight were predictive of subsequent implant fixation strength supports continued investigation of biomarkers for early detection of peri-implant osteolysis and implant loosening. Further, change in biomarker levels was found to be more indicative of implant fixation status than any single measurement.
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Affiliation(s)
- Brittany M. Wilson
- Department of Cell & Molecular Medicine, Rush University Medical Center, Chicago, IL
| | - Meghan M. Moran
- Department of Cell & Molecular Medicine, Rush University Medical Center, Chicago, IL.,Department of Orthopedic Surgery, Rush University Medical Center, Chicago, IL
| | - Matthew J. Meagher
- Department of Cell & Molecular Medicine, Rush University Medical Center, Chicago, IL
| | - Ryan D. Ross
- Department of Cell & Molecular Medicine, Rush University Medical Center, Chicago, IL.,Department of Orthopedic Surgery, Rush University Medical Center, Chicago, IL
| | - Maleeha Mashiatulla
- Department of Cell & Molecular Medicine, Rush University Medical Center, Chicago, IL
| | - Amarjit S. Virdi
- Department of Cell & Molecular Medicine, Rush University Medical Center, Chicago, IL.,Department of Orthopedic Surgery, Rush University Medical Center, Chicago, IL
| | - D. Rick Sumner
- Department of Cell & Molecular Medicine, Rush University Medical Center, Chicago, IL.,Department of Orthopedic Surgery, Rush University Medical Center, Chicago, IL
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8
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Mind the gap! A survey of the challenges of biomarker commercialization. Drug Discov Today 2020; 25:22-26. [DOI: 10.1016/j.drudis.2019.09.015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Revised: 09/13/2019] [Accepted: 09/19/2019] [Indexed: 11/18/2022]
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Abstract
Abstract
Precision oncology aims to tailor clinical decisions specifically to patients with the objective of improving treatment outcomes. This can be achieved by leveraging omics information for accurate molecular characterization of tumors. Tumor tissue biopsies are currently the main source of information for molecular profiling. However, biopsies are invasive and limited in resolving spatiotemporal heterogeneity in tumor tissues. Alternative non-invasive liquid biopsies can exploit patient’s body fluids to access multiple layers of tumor-specific biological information (genomes, epigenomes, transcriptomes, proteomes, metabolomes, circulating tumor cells, and exosomes). Analysis and integration of these large and diverse datasets using statistical and machine learning approaches can yield important insights into tumor biology and lead to discovery of new diagnostic, predictive, and prognostic biomarkers. Translation of these new diagnostic tools into standard clinical practice could transform oncology, as demonstrated by a number of liquid biopsy assays already entering clinical use. In this review, we highlight successes and challenges facing the rapidly evolving field of cancer biomarker research.
Lay Summary
Precision oncology aims to tailor clinical decisions specifically to patients with the objective of improving treatment outcomes. The discovery of biomarkers for precision oncology has been accelerated by high-throughput experimental and computational methods, which can inform fine-grained characterization of tumors for clinical decision-making. Moreover, advances in the liquid biopsy field allow non-invasive sampling of patient’s body fluids with the aim of analyzing circulating biomarkers, obviating the need for invasive tumor tissue biopsies. In this review, we highlight successes and challenges facing the rapidly evolving field of liquid biopsy cancer biomarker research.
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10
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Sesler CL, Grigorenko EV. Analytical Validation of qPCR-Based Multivariate Index Assays in a Clinical Laboratory: Practical Challenges and Limitations. J Appl Lab Med 2019; 3:267-281. [PMID: 33636934 DOI: 10.1373/jalm.2017.025924] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Accepted: 04/02/2018] [Indexed: 11/06/2022]
Abstract
BACKGROUND Multivariate index assays (MIAs) to evaluate disease status and/or therapeutic efficacy are increasingly being used in clinical laboratories as laboratory-developed tests (LDTs). Before clinical use, diagnostic and analytical performance specifications of LDTs must be established. Several regulatory guidelines have been published that address specific components of validation procedures, but the interpretation for the analytical validation of MIAs is ambiguous and creates confusion when implementing a novel MIA in the clinical laboratory. CONTENT CLSI guidelines and published methods were evaluated to develop a validation strategy to establish analytical sensitivity, precision, specificity, and stability for qPCR-based MIAs. Limitations and challenges identified while evaluating guidelines and literature and implementing this strategy are discussed in this review, including sample sourcing and integrity, laboratory contamination, and sample throughput. Due to the diversity of qPCR-based MIAs, we discuss additional considerations for researchers intending to transfer MIAs to a clinical laboratory. SUMMARY A practical strategy to assess the analytical performance characteristics for validation of qPCR-based MIAs was developed and tested before diagnostic clinical use. Several important limitations, challenges, and considerations were identified during development of the analytical validation procedures that are not addressed in regulatory guidelines or published literature. The described strategy can provide insight for future developers of MIAs and clinical laboratories implementing MIAs as LDTs.
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11
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Corbacho-Alonso N, Rodríguez-Sánchez E, Martin-Rojas T, Mouriño-Alvarez L, Sastre-Oliva T, Hernandez-Fernandez G, Padial LR, Ruilope LM, Ruiz-Hurtado G, Barderas MG. Proteomic investigations into hypertension: what's new and how might it affect clinical practice? Expert Rev Proteomics 2019; 16:583-591. [PMID: 31195841 DOI: 10.1080/14789450.2019.1632197] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Introduction: Hypertension is a multifactorial disease that has, thus far, proven to be a difficult target for pharmacological intervention. The application of proteomic strategies may help to identify new biomarkers for the early diagnosis and prompt treatment of hypertension, in order to control blood pressure and prevent organ damage. Areas covered: Advances in proteomics have led to the discovery of new biomarkers to help track the pathophysiological processes implicated in hypertension. These findings not only help to better understand the nature of the disease, but will also contribute to the clinical needs for a timely diagnosis and more precise treatment. In this review, we provide an overview of new biomarkers identified in hypertension through the application of proteomic techniques, and we also discuss the difficulties and challenges in identifying biomarkers in this clinical setting. We performed a literature search in PubMed with the key words 'hypertension' and 'proteomics', and focused specifically on the most recent literature on the utility of proteomics in hypertension research. Expert opinion: There have been several promising biomarkers of hypertension identified by proteomics, but too few have been introduced to the clinic. Thus, further investigations in larger cohorts are necessary to test the feasibility of this strategy for patients. Also, this emerging field would profit from more collaboration between clinicians and researchers.
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Affiliation(s)
- N Corbacho-Alonso
- a Department of Vascular Physiopathology , Hospital Nacional de Paraplejicos (HNP), SESCAM , Toledo , Spain
| | - E Rodríguez-Sánchez
- b Cardiorenal Translational Laboratory , Instituto de Investigación i+12, Hospital Universitario 12 de Octubre , Madrid , Spain
| | - T Martin-Rojas
- a Department of Vascular Physiopathology , Hospital Nacional de Paraplejicos (HNP), SESCAM , Toledo , Spain
| | - L Mouriño-Alvarez
- a Department of Vascular Physiopathology , Hospital Nacional de Paraplejicos (HNP), SESCAM , Toledo , Spain
| | - T Sastre-Oliva
- a Department of Vascular Physiopathology , Hospital Nacional de Paraplejicos (HNP), SESCAM , Toledo , Spain
| | - G Hernandez-Fernandez
- a Department of Vascular Physiopathology , Hospital Nacional de Paraplejicos (HNP), SESCAM , Toledo , Spain
| | - L R Padial
- c Department of Cardiology , Hospital Virgen de la Salud, SESCAM , Toledo , Spain
| | - L M Ruilope
- b Cardiorenal Translational Laboratory , Instituto de Investigación i+12, Hospital Universitario 12 de Octubre , Madrid , Spain.,d Department of Preventive Medicine and Public Health, School of Medicine , Universidad Autónoma de Madrid/IdiPAZ and CIBER in Epidemiology and Public Health (CIBERESP) , Madrid , Spain.,e School of Doctoral Studies and Research , Universidad Europea de Madrid , Madrid , Spain
| | - G Ruiz-Hurtado
- b Cardiorenal Translational Laboratory , Instituto de Investigación i+12, Hospital Universitario 12 de Octubre , Madrid , Spain
| | - M G Barderas
- a Department of Vascular Physiopathology , Hospital Nacional de Paraplejicos (HNP), SESCAM , Toledo , Spain
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12
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Gohar F, McArdle A, Jones M, Callan N, Hernandez B, Kessel C, Miranda-Garcia M, Lavric M, Holzinger D, Pretzer C, Lainka E, Vastert SJ, de Roock S, FitzGerald O, Pennington SR, Foell D. Molecular signature characterisation of different inflammatory phenotypes of systemic juvenile idiopathic arthritis. Ann Rheum Dis 2019; 78:1107-1113. [DOI: 10.1136/annrheumdis-2019-215051] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Revised: 03/14/2019] [Accepted: 04/02/2019] [Indexed: 12/13/2022]
Abstract
ObjectivesThe International League of Associations for Rheumatology classification criteria define systemic juvenile idiopathic arthritis (SJIA) by the presence of fever, rash and chronic arthritis. Recent initiatives to revise current criteria recognise that a lack of arthritis complicates making the diagnosis early, while later a subgroup of patients develops aggressive joint disease. The proposed biphasic model of SJIA also implies a ‘window of opportunity’ to abrogate the development of chronic arthritis. We aimed to identify novel SJIA biomarkers during different disease phases.MethodsChildren with active SJIA were subgrouped clinically as systemic autoinflammatory disease with fever (SJIAsyst) or polyarticular disease (SJIApoly). A discovery cohort of n=10 patients per SJIA group, plus n=10 with infection, was subjected to unbiased label-free liquid chromatography mass spectrometry (LC-MS/MS) and immunoassay screens. In a separate verification cohort (SJIAsyst, n=45; SJIApoly, n=29; infection, n=32), candidate biomarkers were measured by multiple reaction monitoring MS (MRM-MS) and targeted immunoassays.ResultsSignatures differentiating the two phenotypes of SJIA could be identified. LC-MS/MS in the discovery cohort differentiated SJIAsyst from SJIApoly well, but less effectively from infection. Targeted MRM verified the discovery data and, combined with targeted immunoassays, correctly identified 91% (SJIAsyst vs SJIApoly) and 77% (SJIAsyst vs infection) of all cases.ConclusionsMolecular signatures differentiating two phenotypes of SJIA were identified suggesting shifts in underlying immunological processes in this biphasic disease. Biomarker signatures separating SJIA in its initial autoinflammatory phase from the main differential diagnosis (ie, infection) could aid early-stage diagnostic decisions, while markers of a phenotype switch could inform treat-to-target strategies.
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13
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Clerico A, Zaninotto M, Padoan A, Masotti S, Musetti V, Prontera C, Ndreu R, Zucchelli G, Passino C, Migliardi M, Plebani M. Evaluation of analytical performance of immunoassay methods for cTnI and cTnT: From theory to practice. Adv Clin Chem 2019; 93:239-262. [PMID: 31655731 DOI: 10.1016/bs.acc.2019.07.005] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Current guidelines worldwide recommend cardiac troponins I (cTnI) and T (cTnT) as the biomarkers of choice for the differential diagnosis of acute coronary syndrome (ACS), and the measurement of the 99th upper reference population limit (URL) value for cardiac troponins, with an imprecision of ≤10 CV%. Measuring the 99th URL of cTnI and cTnT is a challenging analytical task due to low biomarker concentrations present in healthy subjects. Therefore, since the year 2006, several manufacturers have established new generation cTnI and cTnT immunoassays with an improved analytical sensitivity in accordance with the quality specifications described in international guidelines, the more recent of which state that only immunoassays that meet the required quality specifications should be considered "high-sensitivity" methods. For the early diagnosis of ACS, and for the stratification of cardiovascular risk in cardiac patients and the general population, high-sensitivity methods should be employed. It is therefore important for laboratory professionals and clinicians to gain a thorough understanding of the analytical performances of immunoassay methods for cTnI and cTnT, especially at low to normal concentration ranges. The aim of the present study was to analyze critical aspects related to definition, analytical performance, pathophysiological interpretations, and the clinical relevance of high-sensitivity cardiac troponin assays.
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Affiliation(s)
- Aldo Clerico
- Fondazione CNR, Regione Toscana G. Monasterio and Scuola Superiore Sant'Anna, Pisa, Italy.
| | - Martina Zaninotto
- Department of Laboratory Medicine, University Hospital, Padova, Italy
| | - Andrea Padoan
- Department of Laboratory Medicine, University Hospital, Padova, Italy
| | - Silvia Masotti
- Fondazione CNR, Regione Toscana G. Monasterio and Scuola Superiore Sant'Anna, Pisa, Italy
| | - Veronica Musetti
- Fondazione CNR, Regione Toscana G. Monasterio and Scuola Superiore Sant'Anna, Pisa, Italy
| | - Concetta Prontera
- Fondazione CNR, Regione Toscana G. Monasterio and Scuola Superiore Sant'Anna, Pisa, Italy
| | - Rudina Ndreu
- QualiMedLab and CNR Clinical Physiology Institute, Pisa, Italy
| | | | - Claudio Passino
- Fondazione CNR, Regione Toscana G. Monasterio and Scuola Superiore Sant'Anna, Pisa, Italy
| | - Marco Migliardi
- S.C. Laboratorio Analisi, A.O. Ordine Mauriziano di Torino, Torino, Italy
| | - Mario Plebani
- Department of Laboratory Medicine, University Hospital, Padova, Italy
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14
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Aimo A, Januzzi JL, Vergaro G, Ripoli A, Latini R, Masson S, Magnoli M, Anand IS, Cohn JN, Tavazzi L, Tognoni G, Gravning J, Ueland T, Nymo SH, Rocca HPBL, Bayes-Genis A, Lupón J, de Boer RA, Yoshihisa A, Takeishi Y, Egstrup M, Gustafsson I, Gaggin HK, Eggers KM, Huber K, Tentzeris I, Wilson Tang WH, Grodin JL, Passino C, Emdin M. High-sensitivity troponin T, NT-proBNP and glomerular filtration rate: A multimarker strategy for risk stratification in chronic heart failure. Int J Cardiol 2018; 277:166-172. [PMID: 30416028 DOI: 10.1016/j.ijcard.2018.10.079] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Revised: 09/28/2018] [Accepted: 10/24/2018] [Indexed: 12/28/2022]
Abstract
BACKGROUND In a recent individual patient data meta-analysis, high-sensitivity troponin T (hs-TnT) emerged as robust predictor of prognosis in stable chronic heart failure (HF). In the same population, we compared the relative predictive performances of hs-TnT, N-terminal fraction of pro-B-type natriuretic peptide (NT-proBNP), hs-C-reactive protein (hs-CRP), and estimated glomerular filtration rate (eGFR) for prognosis. METHODS AND RESULTS 9289 patients (66 ± 12 years, 77% men, 85% LVEF <40%, 60% ischemic HF) were evaluated over a 2.4-year median follow-up. Median eGFR was 58 mL/min/1.73 m2 (interquartile interval 46-70; n = 9220), hs-TnT 16 ng/L (8-20; n = 9289), NT-proBNP 1067 ng/L (433-2470; n = 8845), and hs-CRP 3.3 mg/L (1.4-7.8; n = 7083). In a model including all 3 biomarkers, only hs-TnT and NT-proBNP were independent predictors of all-cause and cardiovascular mortality and cardiovascular hospitalization. hs-TnT was a stronger predictor than NT-proBNP: for example, the risk for all-cause death increased by 54% per doubling of hs-TnT vs. 24% per doubling of NT-proBNP. eGFR showed independent prognostic value from both hs-TnT and NT-proBNP. The best hs-TnT and NT-proBNP cut-offs for the prediction of all-cause death increased progressively with declining renal function (eGFR ≥ 90: hs-TnT 13 ng/L and NT-proBNP 825 ng/L; eGFR < 30: hs-TnT 40 ng/L and NT-proBNP 4608 ng/L). Patient categorization according to these cut-offs effectively stratified patient prognosis across all eGFR classes. CONCLUSIONS hs-TnT conveys independent prognostic information from NT-proBNP, while hs-CRP does not. Concomitant assessment of eGFR may further refine risk stratification. Patient classification according to hs-TnT and NT-proBNP cut-offs specific for the eGFR classes holds prognostic significance.
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Affiliation(s)
| | - James L Januzzi
- Massachusetts General Hospital, Harvard Clinical Research Institute, Boston, MA, USA
| | - Giuseppe Vergaro
- Scuola Superiore Sant'Anna, Pisa, Italy; Fondazione Toscana G. Monasterio, Pisa, Italy
| | | | - Roberto Latini
- Department of Cardiovascular Research, IRCCS - Istituto di Ricerche Farmacologiche - "Mario Negri", Milano, Italy
| | - Serge Masson
- Department of Cardiovascular Research, IRCCS - Istituto di Ricerche Farmacologiche - "Mario Negri", Milano, Italy
| | - Michela Magnoli
- Department of Cardiovascular Research, IRCCS - Istituto di Ricerche Farmacologiche - "Mario Negri", Milano, Italy
| | - Inder S Anand
- Division of Cardiovascular Medicine, University of Minnesota, Minneapolis, MN, USA; Department of Cardiology, VA Medical Centre, Minneapolis, MN, USA
| | - Jay N Cohn
- Division of Cardiovascular Medicine, University of Minnesota, Minneapolis, MN, USA
| | - Luigi Tavazzi
- GVM Hospitals of Care and Research, E.S. Health Science Foundation, Cotignola, Italy
| | - Gianni Tognoni
- Department of Cardiovascular Research, IRCCS - Istituto di Ricerche Farmacologiche - "Mario Negri", Milano, Italy
| | - Jørgen Gravning
- Department of Cardiology, Oslo University Hospital, Ullevål, Oslo, Norway; Centre for Heart Failure Research, University of Oslo, Oslo, Norway
| | - Thor Ueland
- Research Institute of Internal Medicine, Oslo University Hospital, Rikshospitalet, Oslo, Norway; Faculty of Medicine, University of Oslo, Oslo, Norway; K. G. Jebsen Thrombosis Research and Expertise Centre, University of Tromsø, Tromsø, Norway
| | - Ståle H Nymo
- Research Institute of Internal Medicine, Oslo University Hospital, Rikshospitalet, Oslo, Norway
| | | | | | - Josep Lupón
- Hospital Universitari Germans Trias i Pujol, Badalona, Barcelona, Spain
| | | | - Akiomi Yoshihisa
- Department of Cardiovascular Medicine, Fukushima Medical University, Fukushima, Japan
| | - Yasuchika Takeishi
- Department of Cardiovascular Medicine, Fukushima Medical University, Fukushima, Japan
| | - Michael Egstrup
- Department of Cardiology, Copenhagen University Hospital Rigshospitalet, Denmark
| | - Ida Gustafsson
- Department of Cardiology, Copenhagen University Hospital Rigshospitalet, Denmark
| | - Hanna K Gaggin
- Massachusetts General Hospital, Harvard Clinical Research Institute, Boston, MA, USA
| | - Kai M Eggers
- Department of Medical Sciences, Cardiology, Uppsala University, Uppsala, Sweden
| | - Kurt Huber
- Faculty of Internal Medicine, Wilhelminenspital and Sigmund Freud University, Medical School, Vienna, Austria
| | - Ioannis Tentzeris
- Faculty of Internal Medicine, Wilhelminenspital and Sigmund Freud University, Medical School, Vienna, Austria
| | - W H Wilson Tang
- Heart and Vascular Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Justin L Grodin
- Department of Internal Medicine, Division of Cardiology, University of Texas Southwestern Medical Centre, Dallas, TX, USA
| | - Claudio Passino
- Scuola Superiore Sant'Anna, Pisa, Italy; Fondazione Toscana G. Monasterio, Pisa, Italy
| | - Michele Emdin
- Scuola Superiore Sant'Anna, Pisa, Italy; Fondazione Toscana G. Monasterio, Pisa, Italy
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15
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Tan W, Yang M, Yang H, Zhou F, Shen W. Predicting the response to neoadjuvant therapy for early-stage breast cancer: tumor-, blood-, and imaging-related biomarkers. Cancer Manag Res 2018; 10:4333-4347. [PMID: 30349367 PMCID: PMC6188192 DOI: 10.2147/cmar.s174435] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Neoadjuvant therapy (NAT) has been used increasingly in patients with locally advanced or early-stage breast cancer. However, the accurate evaluation and prediction of response to NAT remain the great challenge. Biomarkers could prove useful to identify responders or nonresponders, or even to distinguish between early and delayed responses. These biomarkers could include markers from the tumor itself, such as versatile proteins, genes, and ribonucleic acids, various biological factors or peripheral blood cells, and clinical and pathological features. Possible predictive markers could also include multiple features from functional imaging, such as standard uptake values in positron emission tomography, apparent diffusion coefficient in magnetic resonance, or radiomics imaging biomarkers. In addition, cells that indirectly present the immune status of tumor cells and/or their host could also potentially be used as biomarkers, eg, tumor-infiltrating lymphocytes, tumor-associated macrophages, and myeloid-derived suppressor cells. Though numerous biomarkers have been widely investigated, only estrogen and/or progesterone receptors and human epidermal growth factor receptor have been proven to be reliable biomarkers to predict the response to NAT. They are the only biomarkers recommended in several international guidelines. The other aforementioned biomarkers warrant further validation studies. Some multigene profiling assays that are commercially available, eg, Oncotype DX and MammaPrint, should be used with caution when extrapolated to NAT settings. A panel of combined multilevel biomarkers might be able to predict the response to NAT more robustly than individual biomarkers. To establish such a panel and its prediction model, reliable methods and extensive clinical validation are warranted.
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Affiliation(s)
- Wenyong Tan
- Department of Oncology, Shenzhen Hospital of Southern Medical University, Shenzhen, People's Republic of China, ;
- Clinical Medical Research Center, The Second Clinical Medical College (Shenzhen People Hospital), Jinan University, Shenzhen, People's Republic of China,
| | - Ming Yang
- Shenzhen Jingmai Medical Scientific and Technique Company, Shenzhen, People's Republic of China
| | - Hongli Yang
- Clinical Medical Research Center, The Second Clinical Medical College (Shenzhen People Hospital), Jinan University, Shenzhen, People's Republic of China,
| | - Fangbin Zhou
- Clinical Medical Research Center, The Second Clinical Medical College (Shenzhen People Hospital), Jinan University, Shenzhen, People's Republic of China,
| | - Weixi Shen
- Department of Oncology, Shenzhen Hospital of Southern Medical University, Shenzhen, People's Republic of China, ;
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16
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Selby PJ, Banks RE, Gregory W, Hewison J, Rosenberg W, Altman DG, Deeks JJ, McCabe C, Parkes J, Sturgeon C, Thompson D, Twiddy M, Bestall J, Bedlington J, Hale T, Dinnes J, Jones M, Lewington A, Messenger MP, Napp V, Sitch A, Tanwar S, Vasudev NS, Baxter P, Bell S, Cairns DA, Calder N, Corrigan N, Del Galdo F, Heudtlass P, Hornigold N, Hulme C, Hutchinson M, Lippiatt C, Livingstone T, Longo R, Potton M, Roberts S, Sim S, Trainor S, Welberry Smith M, Neuberger J, Thorburn D, Richardson P, Christie J, Sheerin N, McKane W, Gibbs P, Edwards A, Soomro N, Adeyoju A, Stewart GD, Hrouda D. Methods for the evaluation of biomarkers in patients with kidney and liver diseases: multicentre research programme including ELUCIDATE RCT. PROGRAMME GRANTS FOR APPLIED RESEARCH 2018. [DOI: 10.3310/pgfar06030] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
BackgroundProtein biomarkers with associations with the activity and outcomes of diseases are being identified by modern proteomic technologies. They may be simple, accessible, cheap and safe tests that can inform diagnosis, prognosis, treatment selection, monitoring of disease activity and therapy and may substitute for complex, invasive and expensive tests. However, their potential is not yet being realised.Design and methodsThe study consisted of three workstreams to create a framework for research: workstream 1, methodology – to define current practice and explore methodology innovations for biomarkers for monitoring disease; workstream 2, clinical translation – to create a framework of research practice, high-quality samples and related clinical data to evaluate the validity and clinical utility of protein biomarkers; and workstream 3, the ELF to Uncover Cirrhosis as an Indication for Diagnosis and Action for Treatable Event (ELUCIDATE) randomised controlled trial (RCT) – an exemplar RCT of an established test, the ADVIA Centaur® Enhanced Liver Fibrosis (ELF) test (Siemens Healthcare Diagnostics Ltd, Camberley, UK) [consisting of a panel of three markers – (1) serum hyaluronic acid, (2) amino-terminal propeptide of type III procollagen and (3) tissue inhibitor of metalloproteinase 1], for liver cirrhosis to determine its impact on diagnostic timing and the management of cirrhosis and the process of care and improving outcomes.ResultsThe methodology workstream evaluated the quality of recommendations for using prostate-specific antigen to monitor patients, systematically reviewed RCTs of monitoring strategies and reviewed the monitoring biomarker literature and how monitoring can have an impact on outcomes. Simulation studies were conducted to evaluate monitoring and improve the merits of health care. The monitoring biomarker literature is modest and robust conclusions are infrequent. We recommend improvements in research practice. Patients strongly endorsed the need for robust and conclusive research in this area. The clinical translation workstream focused on analytical and clinical validity. Cohorts were established for renal cell carcinoma (RCC) and renal transplantation (RT), with samples and patient data from multiple centres, as a rapid-access resource to evaluate the validity of biomarkers. Candidate biomarkers for RCC and RT were identified from the literature and their quality was evaluated and selected biomarkers were prioritised. The duration of follow-up was a limitation but biomarkers were identified that may be taken forward for clinical utility. In the third workstream, the ELUCIDATE trial registered 1303 patients and randomised 878 patients out of a target of 1000. The trial started late and recruited slowly initially but ultimately recruited with good statistical power to answer the key questions. ELF monitoring altered the patient process of care and may show benefits from the early introduction of interventions with further follow-up. The ELUCIDATE trial was an ‘exemplar’ trial that has demonstrated the challenges of evaluating biomarker strategies in ‘end-to-end’ RCTs and will inform future study designs.ConclusionsThe limitations in the programme were principally that, during the collection and curation of the cohorts of patients with RCC and RT, the pace of discovery of new biomarkers in commercial and non-commercial research was slower than anticipated and so conclusive evaluations using the cohorts are few; however, access to the cohorts will be sustained for future new biomarkers. The ELUCIDATE trial was slow to start and recruit to, with a late surge of recruitment, and so final conclusions about the impact of the ELF test on long-term outcomes await further follow-up. The findings from the three workstreams were used to synthesise a strategy and framework for future biomarker evaluations incorporating innovations in study design, health economics and health informatics.Trial registrationCurrent Controlled Trials ISRCTN74815110, UKCRN ID 9954 and UKCRN ID 11930.FundingThis project was funded by the NIHR Programme Grants for Applied Research programme and will be published in full inProgramme Grants for Applied Research; Vol. 6, No. 3. See the NIHR Journals Library website for further project information.
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Affiliation(s)
- Peter J Selby
- Clinical and Biomedical Proteomics Group, Leeds Institute of Cancer and Pathology, University of Leeds, Leeds, UK
- Leeds Teaching Hospitals NHS Trust, Leeds, UK
| | - Rosamonde E Banks
- Clinical and Biomedical Proteomics Group, Leeds Institute of Cancer and Pathology, University of Leeds, Leeds, UK
| | - Walter Gregory
- Leeds Institute of Clinical Trials Research, University of Leeds, Leeds, UK
| | - Jenny Hewison
- Leeds Institute of Health Sciences, University of Leeds, Leeds, UK
| | - William Rosenberg
- Institute for Liver and Digestive Health, Division of Medicine, University College London, London, UK
| | - Douglas G Altman
- Centre for Statistics in Medicine, University of Oxford, Oxford, UK
| | - Jonathan J Deeks
- Institute of Applied Health Research, University of Birmingham, Birmingham, UK
| | - Christopher McCabe
- Department of Emergency Medicine, University of Alberta Hospital, Edmonton, AB, Canada
| | - Julie Parkes
- Primary Care and Population Sciences Academic Unit, University of Southampton, Southampton, UK
| | | | | | - Maureen Twiddy
- Leeds Institute of Health Sciences, University of Leeds, Leeds, UK
| | - Janine Bestall
- Leeds Institute of Health Sciences, University of Leeds, Leeds, UK
| | | | - Tilly Hale
- LIVErNORTH Liver Patient Support, Newcastle upon Tyne, UK
| | - Jacqueline Dinnes
- Institute of Applied Health Research, University of Birmingham, Birmingham, UK
| | - Marc Jones
- Leeds Institute of Clinical Trials Research, University of Leeds, Leeds, UK
| | | | | | - Vicky Napp
- Leeds Institute of Clinical Trials Research, University of Leeds, Leeds, UK
| | - Alice Sitch
- Institute of Applied Health Research, University of Birmingham, Birmingham, UK
| | - Sudeep Tanwar
- Institute for Liver and Digestive Health, Division of Medicine, University College London, London, UK
| | - Naveen S Vasudev
- Clinical and Biomedical Proteomics Group, Leeds Institute of Cancer and Pathology, University of Leeds, Leeds, UK
- Leeds Teaching Hospitals NHS Trust, Leeds, UK
| | - Paul Baxter
- Leeds Institute of Cardiovascular and Metabolic Medicine, University of Leeds, Leeds, UK
| | - Sue Bell
- Leeds Institute of Clinical Trials Research, University of Leeds, Leeds, UK
| | - David A Cairns
- Clinical and Biomedical Proteomics Group, Leeds Institute of Cancer and Pathology, University of Leeds, Leeds, UK
| | | | - Neil Corrigan
- Leeds Institute of Clinical Trials Research, University of Leeds, Leeds, UK
| | - Francesco Del Galdo
- Leeds Institute of Rheumatic and Musculoskeletal Medicine, University of Leeds, Leeds, UK
| | - Peter Heudtlass
- Leeds Institute of Clinical Trials Research, University of Leeds, Leeds, UK
| | - Nick Hornigold
- Clinical and Biomedical Proteomics Group, Leeds Institute of Cancer and Pathology, University of Leeds, Leeds, UK
| | - Claire Hulme
- Leeds Institute of Health Sciences, University of Leeds, Leeds, UK
| | - Michelle Hutchinson
- Clinical and Biomedical Proteomics Group, Leeds Institute of Cancer and Pathology, University of Leeds, Leeds, UK
| | - Carys Lippiatt
- Department of Specialist Laboratory Medicine, Leeds Teaching Hospitals NHS Trust, Leeds, UK
| | | | - Roberta Longo
- Leeds Institute of Health Sciences, University of Leeds, Leeds, UK
| | - Matthew Potton
- Leeds Institute of Clinical Trials Research, University of Leeds, Leeds, UK
| | - Stephanie Roberts
- Clinical and Biomedical Proteomics Group, Leeds Institute of Cancer and Pathology, University of Leeds, Leeds, UK
| | - Sheryl Sim
- Clinical and Biomedical Proteomics Group, Leeds Institute of Cancer and Pathology, University of Leeds, Leeds, UK
| | - Sebastian Trainor
- Clinical and Biomedical Proteomics Group, Leeds Institute of Cancer and Pathology, University of Leeds, Leeds, UK
| | - Matthew Welberry Smith
- Clinical and Biomedical Proteomics Group, Leeds Institute of Cancer and Pathology, University of Leeds, Leeds, UK
- Leeds Teaching Hospitals NHS Trust, Leeds, UK
| | - James Neuberger
- University Hospitals Birmingham NHS Foundation Trust, Birmingham, UK
| | | | - Paul Richardson
- Royal Liverpool and Broadgreen University Hospitals NHS Trust, Liverpool, UK
| | - John Christie
- Royal Devon and Exeter NHS Foundation Trust, Exeter, UK
| | - Neil Sheerin
- Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - William McKane
- Sheffield Teaching Hospitals NHS Foundation Trust, Sheffield, UK
| | - Paul Gibbs
- Portsmouth Hospitals NHS Trust, Portsmouth, UK
| | | | - Naeem Soomro
- Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | | | - Grant D Stewart
- NHS Lothian, Edinburgh, UK
- Academic Urology Group, University of Cambridge, Cambridge, UK
| | - David Hrouda
- Charing Cross Hospital, Imperial College Healthcare NHS Trust, London, UK
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17
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Nallagangula KS, Shashidhar KN, Lakshmaiah V, Muninarayana. Evolution of proteomic biomarker for chronic liver disease: Promise into reality. J Circ Biomark 2018; 7:1849454418777186. [PMID: 29854010 PMCID: PMC5971380 DOI: 10.1177/1849454418777186] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Accepted: 04/18/2018] [Indexed: 01/22/2023] Open
Abstract
Liver is the vital organ for synthesis of proteins whose concentration in blood reflects liver dysfunction. Variations in protein domain can generate clinically significant biomarkers. Biomarker pipeline includes discovery of candidates, qualification, verification, assay optimization, and validation. Advances in proteomic approach can discover protein biomarker candidates based on “up-or-down” regulation or fold change in expression which is correlated with disease state. Despite numerous biomarker candidates been discovered, only few are useful in clinical practice which indicates the need for well-established validation regimen. Hence, the main purpose of this review is to understand the protein biomarker development and pitfalls. Companion diagnostics provide insights into potential cost-effective diagnosis for chronic liver disease.
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Affiliation(s)
| | - K N Shashidhar
- Department of Biochemistry, Sri Devaraj Urs Medical College, SDUAHER, Karnataka, India
| | - V Lakshmaiah
- Department of Medicine, Sri Devaraj Urs Medical College, SDUAHER, Karnataka, India
| | - Muninarayana
- Department of Community Medicine, Sri Devaraj Urs Medical College, SDUAHER, Karnataka, India
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18
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Patil S, Majumdar B, Awan KH, Sarode GS, Sarode SC, Gadbail AR, Gondivkar S. Cancer oriented biobanks: A comprehensive review. Oncol Rev 2018; 12:357. [PMID: 30057691 PMCID: PMC6047884 DOI: 10.4081/oncol.2018.357] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Accepted: 04/11/2018] [Indexed: 01/12/2023] Open
Abstract
Biobanks provide a platform for innovative biomedical research and has improvised translational and personalized medicine to a great extent. Time 2009 published 10 ideas changing the world right now with biobanks on the list emphasizing its role in discovery and development of new therapeutic drugs. They form the cornerstone, providing resources for future investigations and biomarker discovery to understand the effects of genetic, environmental and lifestyle factors on human morbidity, mortality and health. The aim of this review paper is to understand the role of biobanking in cancer research, the challenges faced and strategies to overcome these, for long term and sustainable research in the field of oncology.
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Affiliation(s)
- Shankargouda Patil
- Department of Oral and Maxillofacial Surgery and Diagnostic Sciences, Division of Oral Pathology, College of Dentistry, Jazan University, Jazan, Saudi Arabia
| | - Barnali Majumdar
- Department of Oral Pathology and Microbiology, Bhojia Dental College & Hospital, Baddi, Himachal Pradesh, India
| | - Kamran Habib Awan
- College of Dental Medicine, Roseman University of Health Sciences, South Jordan, UT, USA
| | - Gargi S Sarode
- Department of Oral Pathology and Microbiology, Dr. D. Y. Patil Dental College and Hospital, Dr. D.Y. Patil Vidyapeeth, Maharashtra, India
| | - Sachin C Sarode
- Department of Oral Pathology and Microbiology, Dr. D. Y. Patil Dental College and Hospital, Dr. D.Y. Patil Vidyapeeth, Maharashtra, India
| | - Amol R Gadbail
- Department of Dentistry, Indira Gandhi Government Medical College, Nagpur, Maharashtra, India
| | - Shailesh Gondivkar
- Department of Oral Medicine and Radiology, Government Dental College & Hospital, Nagpur, Maharashtra, India
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19
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Justice AC, Erlandson KM, Hunt PW, Landay A, Miotti P, Tracy RP. Can Biomarkers Advance HIV Research and Care in the Antiretroviral Therapy Era? J Infect Dis 2018; 217:521-528. [PMID: 29165684 PMCID: PMC5853399 DOI: 10.1093/infdis/jix586] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Accepted: 11/13/2017] [Indexed: 12/22/2022] Open
Abstract
Despite achieving human immunodeficiency virus type 1 (HIV-1) RNA suppression below levels of detection and, for most, improved CD4+ T-cell counts, those aging with HIV experience excess low-level inflammation, hypercoagulability, and immune dysfunction (chronic inflammation), compared with demographically and behaviorally similar uninfected individuals. A host of biomarkers that are linked to chronic inflammation are also associated with HIV-associated non-AIDS-defining events, including cardiovascular disease, many forms of cancer, liver disease, renal disease, neurocognitive decline, and osteoporosis. Furthermore, chronic HIV infection may interact with long-term treatment toxicity and weight gain after ART initiation. These observations suggest that future biomarker-guided discovery and treatment may require attention to multiple biomarkers and, possibly, weighted indices. We are clinical trialists, epidemiologists, pragmatic trialists, and translational scientists. Together, we offer an operational definition of a biomarker and consider how biomarkers might facilitate progress along the translational pathway from therapeutic discovery to intervention trials and clinical management among people aging with or without HIV infection.
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Affiliation(s)
- Amy C Justice
- VA Connecticut Healthcare System West Haven, Yale University, New Haven, Connecticut
- School of Medicine, Yale University, New Haven, Connecticut
- School of Public Health, Yale University, New Haven, Connecticut
| | - Kristine M Erlandson
- Division of Infectious Diseases, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora
- Division of Geriatric Medicine, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora
| | - Peter W Hunt
- Division of Experimental Medicine, Department of Medicine, University of California–San Francisco
| | - Alan Landay
- Department of Microbial Pathogens and Immunity, Rush University Medical Center, Chicago, Illinois
| | - Paolo Miotti
- Office of AIDS Research, National Institutes of Health, Bethesda, Maryland
| | - Russell P Tracy
- Department of Pathology and Laboratory Medicine, University of Vermont Larner College of Medicine, Colchester
- Department of Biochemistry, University of Vermont Larner College of Medicine, Colchester
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A. Richard S. High-mobility group box 1 is a promising diagnostic and therapeutic monitoring biomarker in Cancers: A review. AIMS MOLECULAR SCIENCE 2018. [DOI: 10.3934/molsci.2018.4.183] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
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Mourino-Alvarez L, Baldan-Martin M, Rincon R, Martin-Rojas T, Corbacho-Alonso N, Sastre-Oliva T, Barderas MG. Recent advances and clinical insights into the use of proteomics in the study of atherosclerosis. Expert Rev Proteomics 2017; 14:701-713. [PMID: 28689450 DOI: 10.1080/14789450.2017.1353912] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
INTRODUCTION The application of new proteomics methods may help to identify new diagnostic/predictive molecular markers in an attempt to improve the clinical management of atherosclerosis. Areas covered: Technological advances in proteomics have enhanced its sensitivity and multiplexing capacity, as well as the possibility of studying protein interactions and tissue structure. These advances will help us better understand the molecular mechanisms at play in atherosclerosis as a biological system. Moreover, this should help identify new predictive/diagnostic biomarkers and therapeutic targets that may facilitate effective risk stratification and early diagnosis, with the ensuing rapid implementation of treatment. This review provides a comprehensive overview of the novel methods in proteomics, including state-of-the-art techniques, novel biological samples and applications for the study of atherosclerosis. Expert commentary: Collaboration between clinicians and researchers is crucial to further validate and introduce new molecular markers to manage atherosclerosis that are identified using the most up to date proteomic approaches.
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Affiliation(s)
- Laura Mourino-Alvarez
- a Department of Vascular Physiopathology , Hospital Nacional de Paraplejicos , Toledo , Spain
| | | | - Raul Rincon
- a Department of Vascular Physiopathology , Hospital Nacional de Paraplejicos , Toledo , Spain
| | - Tatiana Martin-Rojas
- a Department of Vascular Physiopathology , Hospital Nacional de Paraplejicos , Toledo , Spain
| | - Nerea Corbacho-Alonso
- a Department of Vascular Physiopathology , Hospital Nacional de Paraplejicos , Toledo , Spain
| | - Tamara Sastre-Oliva
- a Department of Vascular Physiopathology , Hospital Nacional de Paraplejicos , Toledo , Spain
| | - Maria G Barderas
- a Department of Vascular Physiopathology , Hospital Nacional de Paraplejicos , Toledo , Spain
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Ismail OZ, Bhayana V, Kadour M, Lepage N, Gowrishankar M, Filler G. Improving the translation of novel biomarkers to clinical practice: The story of cystatin C implementation in Canada. Clin Biochem 2017; 50:380-384. [DOI: 10.1016/j.clinbiochem.2017.01.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Revised: 01/10/2017] [Accepted: 01/10/2017] [Indexed: 10/20/2022]
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Ioannidis JPA, Bossuyt PMM. Waste, Leaks, and Failures in the Biomarker Pipeline. Clin Chem 2017; 63:963-972. [DOI: 10.1373/clinchem.2016.254649] [Citation(s) in RCA: 90] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Accepted: 11/30/2016] [Indexed: 01/05/2023]
Abstract
Abstract
BACKGROUND
The large, expanding literature on biomarkers is characterized by almost ubiquitous significant results, with claims about the potential importance, but few of these discovered biomarkers are used in routine clinical care.
CONTENT
The pipeline of biomarker development includes several specific stages: discovery, validation, clinical translation, evaluation, implementation (and, in the case of nonutility, deimplementation). Each of these stages can be plagued by problems that cause failures of the overall pipeline. Some problems are nonspecific challenges for all biomedical investigation, while others are specific to the peculiarities of biomarker research. Discovery suffers from poor methods and incomplete and selective reporting. External independent validation is limited. Selection for clinical translation is often shaped by nonrational choices. Evaluation is sparse and the clinical utility of many biomarkers remains unknown. The regulatory environment for biomarkers remains weak and guidelines can reach biased or divergent recommendations. Removing inefficient or even harmful biomarkers that have been entrenched in clinical care can meet with major resistance.
SUMMARY
The current biomarker pipeline is too prone to failures. Consideration of clinical needs should become a starting point for the development of biomarkers. Improvements can include the use of more stringent methodology, better reporting, larger collaborative studies, careful external independent validation, preregistration, rigorous systematic reviews and umbrella reviews, pivotal randomized trials, and implementation and deimplementation studies. Incentives should be aligned toward delivering useful biomarkers.
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Affiliation(s)
- John P A Ioannidis
- Departments of Medicine, Health Research and Policy, and Statistics, and the Meta-Research Innovation Center at Stanford (METRICS), Stanford University, Stanford, CA
| | - Patrick M M Bossuyt
- Department of Clinical Epidemiology, Biostatistics & Bioinformatics, Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands
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Clinical use of biomarkers in breast cancer: Updated guidelines from the European Group on Tumor Markers (EGTM). Eur J Cancer 2017; 75:284-298. [DOI: 10.1016/j.ejca.2017.01.017] [Citation(s) in RCA: 292] [Impact Index Per Article: 41.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2016] [Revised: 10/12/2016] [Accepted: 01/13/2017] [Indexed: 12/27/2022]
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Khare T, Khare S, Ibdah JA. Proteomics approaches for early detection and targeted therapy of hepatocellular carcinoma. World J Gastrointest Oncol 2017; 9:1-3. [PMID: 28144394 PMCID: PMC5241522 DOI: 10.4251/wjgo.v9.i1.1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Revised: 09/25/2016] [Accepted: 11/22/2016] [Indexed: 02/05/2023] Open
Abstract
Hepatocellular carcinoma (HCC) is one of the leading causes of cancer related mortality worldwide. HCC incidences have increased worldwide though more prevalent in Asia and Africa. Hepatitis B virus and hepatitis C virus infections are mostly responsible of increased number of HCC cases. Biomarkers can help early detection and improve treatment regimen in patients as advanced stage is chemo-refractive with limited treatment options. Potential of proteomics in finding new biomarkers for early detection has been explored more recently. Future developments in this area rely on how efficiently we manage vast amount of data generated by these techniques and speed up the clinical trials to improve patient care.
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Bioanalytical qualification of clinical biomarker assays in plasma using a novel multi-analyte Simple Plex™ platform. Bioanalysis 2016; 8:2415-2428. [DOI: 10.4155/bio-2016-0196] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Aim: Immune-checkpoint inhibitors are presumed to break down the tolerogenic state of immune cells by activating T-lymphocytes that release cytokines and enhance effector cell function for elimination of tumors. Measurement of cytokines is being pursued for better understanding of the mechanism of action of immune-checkpoint inhibitors, as well as to identify potential predictive biomarkers. Results: In this study, we show bioanalytical qualification of cytokine assays in plasma on a novel multi-analyte immunoassay platform, Simple Plex™. The qualified assays exhibited excellent sensitivity as evidenced by measurement of all samples within the quantifiable range. The accuracy and precision were 80–120% and 10%, respectively. Conclusion: The qualified assays will be useful in assessing mechanism of action cancer immunotherapies.
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Gohar F, Kessel C, Lavric M, Holzinger D, Foell D. Review of biomarkers in systemic juvenile idiopathic arthritis: helpful tools or just playing tricks? Arthritis Res Ther 2016; 18:163. [PMID: 27411444 PMCID: PMC4944486 DOI: 10.1186/s13075-016-1069-z] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Accepted: 06/29/2016] [Indexed: 01/28/2023] Open
Abstract
BACKGROUND Diagnosing systemic juvenile idiopathic arthritis (SJIA) can be extremely challenging if typical arthritis is lacking. A variety of biomarkers have been described for the diagnosis and management of SJIA. However, very few markers have been well-validated. In addition, increasing numbers of biomarkers are identified by high throughput or multi-marker panels. METHOD We identified diagnostic or prognostic biomarkers by systematic literature review, evaluating each according to a predefined level of verification, validation or clinical utility. Diagnostic biomarkers were those identifying SJIA versus (1) non-SJIA conditions or healthy controls (HC) or (2) other non-systemic JIA subtypes. Prognostic biomarkers were those specifically tested for the prediction of (1) disease flare, (2) increased disease activity +/- discrimination of active versus inactive disease, or (3) macrophage activation syndrome (MAS). RESULTS Fifty-five studies fulfilled the inclusion criteria identifying 68 unique biomarkers, of which 50/68 (74 %) were investigated by only a single research group. Candidate marker verification and clinical utility was evaluated according to whether markers were readily and reliably measurable, investigated by independent study groups, discovered by more than one method (i.e. verified markers) and validated in independent cohorts. This evaluation revealed diagnostic biomarkers of high interest for further evaluation in the diagnostic approach to SJIA that included heme oxygenase-1, interleukin-6 (IL-6), IL-12, IL-18, osteoprotegerin, S100 calcium-binding protein A12 (S100A12) and S100A8/A9. CONCLUSION In summary, a number of biomarkers were identified, though most had limited evidence for their use. However, our findings combined with the identified studies could inform validation studies, whether in single or multi-marker assays, which are urgently needed.
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Affiliation(s)
- Faekah Gohar
- Department of Paediatric Rheumatology and Immunology, University of Münster, Domagkstraße 3, D-48149, Münster, Germany
| | - Christoph Kessel
- Department of Paediatric Rheumatology and Immunology, University of Münster, Domagkstraße 3, D-48149, Münster, Germany
| | - Miha Lavric
- Department of Paediatric Rheumatology and Immunology, University of Münster, Domagkstraße 3, D-48149, Münster, Germany
| | - Dirk Holzinger
- Department of Paediatric Rheumatology and Immunology, University of Münster, Domagkstraße 3, D-48149, Münster, Germany
| | - Dirk Foell
- Department of Paediatric Rheumatology and Immunology, University of Münster, Domagkstraße 3, D-48149, Münster, Germany.
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Kawahara R, Bollinger JG, Rivera C, Ribeiro ACP, Brandão TB, Paes Leme AF, MacCoss MJ. A targeted proteomic strategy for the measurement of oral cancer candidate biomarkers in human saliva. Proteomics 2015; 16:159-73. [PMID: 26552850 DOI: 10.1002/pmic.201500224] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2015] [Revised: 08/27/2015] [Accepted: 11/04/2015] [Indexed: 12/31/2022]
Abstract
Head and neck cancers, including oral squamous cell carcinoma (OSCC), are the sixth most common malignancy in the world and are characterized by poor prognosis and a low survival rate. Saliva is oral fluid with intimate contact with OSCC. Besides non-invasive, simple, and rapid to collect, saliva is a potential source of biomarkers. In this study, we build an SRM assay that targets fourteen OSCC candidate biomarker proteins, which were evaluated in a set of clinically-derived saliva samples. Using Skyline software package, we demonstrated a statistically significant higher abundance of the C1R, LCN2, SLPI, FAM49B, TAGLN2, CFB, C3, C4B, LRG1, SERPINA1 candidate biomarkers in the saliva of OSCC patients. Furthermore, our study also demonstrated that CFB, C3, C4B, SERPINA1 and LRG1 are associated with the risk of developing OSCC. Overall, this study successfully used targeted proteomics to measure in saliva a panel of biomarker candidates for OSCC.
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Affiliation(s)
- Rebeca Kawahara
- Laboratório de Espectrometria de Massas, Laboratório Nacional de Biociências, LNBio, CNPEM, Campinas, Brazil
| | - James G Bollinger
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington, USA
| | - César Rivera
- Laboratório de Espectrometria de Massas, Laboratório Nacional de Biociências, LNBio, CNPEM, Campinas, Brazil
| | - Ana Carolina P Ribeiro
- Instituto do Câncer do Estado de São Paulo, Octavio Frias de Oliveira, São Paulo, Brazil
| | - Thaís Bianca Brandão
- Instituto do Câncer do Estado de São Paulo, Octavio Frias de Oliveira, São Paulo, Brazil
| | - Adriana F Paes Leme
- Laboratório de Espectrometria de Massas, Laboratório Nacional de Biociências, LNBio, CNPEM, Campinas, Brazil
| | - Michael J MacCoss
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington, USA
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Matrix Metalloproteinases and Their Inhibitors in Chronic Obstructive Pulmonary Disease. Arch Immunol Ther Exp (Warsz) 2015; 64:177-93. [DOI: 10.1007/s00005-015-0375-5] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Accepted: 09/25/2015] [Indexed: 01/04/2023]
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microRNA regulation of peritoneal cavity homeostasis in peritoneal dialysis. BIOMED RESEARCH INTERNATIONAL 2015; 2015:929806. [PMID: 26495316 PMCID: PMC4606405 DOI: 10.1155/2015/929806] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/22/2015] [Accepted: 08/09/2015] [Indexed: 12/20/2022]
Abstract
Preservation of peritoneal cavity homeostasis and peritoneal membrane function is critical for long-term peritoneal dialysis (PD) treatment. Several microRNAs (miRNAs) have been implicated in the regulation of key molecular pathways driving peritoneal membrane alterations leading to PD failure. miRNAs regulate the expression of the majority of protein coding genes in the human genome, thereby affecting most biochemical pathways implicated in cellular homeostasis. In this review, we report published findings on miRNAs and PD therapy, with emphasis on evidence for changes in peritoneal miRNA expression during long-term PD treatment. Recent work indicates that PD effluent- (PDE-) derived cells change their miRNA expression throughout the course of PD therapy, contributing to the loss of peritoneal cavity homeostasis and peritoneal membrane function. Changes in miRNA expression profiles will alter regulation of key molecular pathways, with the potential to cause profound effects on peritoneal cavity homeostasis during PD treatment. However, research to date has mainly adopted a literature-based miRNA-candidate methodology drawing conclusions from modest numbers of patient-derived samples. Therefore, the study of miRNA expression during PD therapy remains a promising field of research to understand the mechanisms involved in basic peritoneal cell homeostasis and PD failure.
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Circulating HMGB1 and RAGE as Clinical Biomarkers in Malignant and Autoimmune Diseases. Diagnostics (Basel) 2015; 5:219-53. [PMID: 26854151 PMCID: PMC4665591 DOI: 10.3390/diagnostics5020219] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Revised: 06/01/2015] [Accepted: 06/05/2015] [Indexed: 12/18/2022] Open
Abstract
High molecular group box 1 (HMGB1) is a highly conserved member of the HMG-box-family; abundantly expressed in almost all human cells and released in apoptosis; necrosis or by activated immune cells. Once in the extracellular space, HMGB1 can act as a danger associated molecular pattern (DAMP), thus stimulating or inhibiting certain functions of the immune system; depending on the “combinatorial cocktail” of the surrounding milieu. HMGB1 exerts its various functions through binding to a multitude of membrane-bound receptors such as TLR-2; -4 and -9; IL-1 and RAGE (receptor for advanced glycation end products); partly complex-bound with intracellular fragments like nucleosomes. Soluble RAGE in the extracellular space, however, acts as a decoy receptor by binding to HMGB1 and inhibiting its effects. This review aims to outline today’s knowledge of structure, intra- and extracellular functions including mechanisms of release and finally the clinical relevance of HMGB1 and RAGE as clinical biomarkers in therapy monitoring, prediction and prognosis of malignant and autoimmune disease.
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de la Cuesta F, Mourino-Alvarez L, Baldan-Martin M, Moreno-Luna R, Barderas MG. Contribution of proteomics to the management of vascular disorders. TRANSLATIONAL PROTEOMICS 2015. [DOI: 10.1016/j.trprot.2014.10.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
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Chahrour O, Cobice D, Malone J. Stable isotope labelling methods in mass spectrometry-based quantitative proteomics. J Pharm Biomed Anal 2015; 113:2-20. [PMID: 25956803 DOI: 10.1016/j.jpba.2015.04.013] [Citation(s) in RCA: 174] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2015] [Revised: 04/05/2015] [Accepted: 04/08/2015] [Indexed: 02/04/2023]
Abstract
Mass-spectrometry based proteomics has evolved as a promising technology over the last decade and is undergoing a dramatic development in a number of different areas, such as; mass spectrometric instrumentation, peptide identification algorithms and bioinformatic computational data analysis. The improved methodology allows quantitative measurement of relative or absolute protein amounts, which is essential for gaining insights into their functions and dynamics in biological systems. Several different strategies involving stable isotopes label (ICAT, ICPL, IDBEST, iTRAQ, TMT, IPTL, SILAC), label-free statistical assessment approaches (MRM, SWATH) and absolute quantification methods (AQUA) are possible, each having specific strengths and weaknesses. Inductively coupled plasma mass spectrometry (ICP-MS), which is still widely recognised as elemental detector, has recently emerged as a complementary technique to the previous methods. The new application area for ICP-MS is targeting the fast growing field of proteomics related research, allowing absolute protein quantification using suitable elemental based tags. This document describes the different stable isotope labelling methods which incorporate metabolic labelling in live cells, ICP-MS based detection and post-harvest chemical label tagging for protein quantification, in addition to summarising their pros and cons.
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Affiliation(s)
| | - Diego Cobice
- Spectroscopy Group, Analytical Services, Almac, UK
| | - John Malone
- Spectroscopy Group, Analytical Services, Almac, UK
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Duffy MJ, Sturgeon CM, Sölétormos G, Barak V, Molina R, Hayes DF, Diamandis EP, Bossuyt PMM. Validation of new cancer biomarkers: a position statement from the European group on tumor markers. Clin Chem 2015; 61:809-20. [PMID: 25882892 DOI: 10.1373/clinchem.2015.239863] [Citation(s) in RCA: 75] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2015] [Accepted: 04/02/2015] [Indexed: 11/06/2022]
Abstract
BACKGROUND Biomarkers are playing increasingly important roles in the detection and management of patients with cancer. Despite an enormous number of publications on cancer biomarkers, few of these biomarkers are in widespread clinical use. CONTENT In this review, we discuss the key steps in advancing a newly discovered cancer candidate biomarker from pilot studies to clinical application. Four main steps are necessary for a biomarker to reach the clinic: analytical validation of the biomarker assay, clinical validation of the biomarker test, demonstration of clinical value from performance of the biomarker test, and regulatory approval. In addition to these 4 steps, all biomarker studies should be reported in a detailed and transparent manner, using previously published checklists and guidelines. Finally, all biomarker studies relating to demonstration of clinical value should be registered before initiation of the study. SUMMARY Application of the methodology outlined above should result in a more efficient and effective approach to the development of cancer biomarkers as well as the reporting of cancer biomarker studies. With rigorous application, all stakeholders, and especially patients, would be expected to benefit.
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Affiliation(s)
- Michael J Duffy
- Clinical Research Centre, St Vincent's University Hospital and UCD School of Medicine and Medical Science, Conway Institute of Bimolecular and Biomedical Research, University College Dublin, Dublin, Ireland;
| | - Catharine M Sturgeon
- Department of Clinical Biochemistry, Royal Infirmary of Edinburgh, Edinburgh, United Kingdom
| | - György Sölétormos
- Department of Clinical Biochemistry, University of Copenhagen North Zealand Hospital, Hillerød, Denmark
| | - Vivian Barak
- Oncology Department, Hadassah University Hospital, Jerusalem, Israel
| | - Rafael Molina
- Hospital Clinic, University of Barcelona, Barcelona, Spain
| | - Daniel F Hayes
- University of Michigan Comprehensive Cancer Center, Ann Arbor, MI
| | - Eleftherios P Diamandis
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Patrick M M Bossuyt
- Department of Clinical Epidemiology, Biostatistics and Bioinformatics, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
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Murphy L, Prencipe M, Gallagher WM, Watson RW. Commercialized biomarkers: new horizons in prostate cancer diagnostics. Expert Rev Mol Diagn 2015; 15:491-503. [DOI: 10.1586/14737159.2015.1011622] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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Phelix CF, Villareal G, LeBaron RG, Roberson DJ. Biomarkers from biosimulations: Transcriptome-To-Reactome™ Technology for individualized medicine. ANNUAL INTERNATIONAL CONFERENCE OF THE IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. ANNUAL INTERNATIONAL CONFERENCE 2015; 2014:3452-5. [PMID: 25570733 DOI: 10.1109/embc.2014.6944365] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
We validated a model of the TGF-β signaling pathway using reactions from Reactome. Using a patentpending technique, gene expression profiles from individual patients are used to determine model parameters. Gene expression profiles from 45 women, normal, or benign tumor and malignant breast cancer were used as training and validating sets for assessing clinical sensitivity and specificity. Biomarkers were identified from the biosimulation results using sensitivity analyses and derivative properties from the model. A membrane signaling marker had sensitivity of 80% and specificity of 60%; while a nuclear transcription factor marker had sensitivity of 80% and specificity of 90% to predict malignancy. Use of Fagan's nomogram increased probability from 7.5% for positive mammogram to 39% with positive results of the biosimulation for the nuclear marker. Our technology will allow researchers to identify and develop biomarkers and assist clinicians in diagnostic and treatment decision making.
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Hepburn S, Banks RE, Thompson D. Protein Biomarker Research in UK Hospital Clinical Biochemistry Laboratories: A Survey of Current Practice and Views. Clin Biochem Rev 2014; 35:115-33. [PMID: 25210209 PMCID: PMC4159780] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
BACKGROUND With the increasing drive for more and better disease biomarkers to underpin the stratified or personalised medicine agenda, clinical biochemistry laboratories should be ideally placed to play a major role in their translation into clinical practice. However, little is known about the current extent of biomarker-related research activity in UK National Health Service clinical biochemistry departments. METHODS In December 2010, an online questionnaire was sent to active UK members of the Association for Clinical Biochemistry (ACB) to determine the extent of their current research activity and involvement in protein biomarker discovery and translation, including an assessment of the awareness of proteomics. RESULTS A total of 198 eligible responses (19% response rate) was received from across the UK. Of a further 50 eligible people who responded to a follow-up for initial non-responders, most cited insufficient knowledge about the topic as the reason for non-response (24% total response rate). The results illustrate the highly skilled nature of the workforce with many having experience in a research environment (75%) with postgraduate qualifications. However, more than half spend <10% of their time undertaking research in their current role, and many (61%) would like to be more research active. Encouragingly, approximately a third were involved in biomarker discovery activities, even though for <10% of their time, with slightly more reporting involvement in biomarker translation. CONCLUSIONS Although there are people with the necessary skills and desire to be involved in biomarker research in clinical biochemistry departments, their involvement is small, predominantly due to issues with capacity and resources. It is likely that the majority of biomarker programmes will therefore continue to be carried out by a small number of academic groups, hopefully with collaborative input from hospital laboratories.
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Affiliation(s)
- Sophie Hepburn
- Department of Blood Sciences, Leeds Teaching Hospitals NHS Trust
- Clinical and Biomedical Proteomics Group, Leeds Institute of Molecular Medicine, St James’s University Hospital, Leeds, UK
| | - Rosamonde E Banks
- Clinical and Biomedical Proteomics Group, Leeds Institute of Molecular Medicine, St James’s University Hospital, Leeds, UK
| | - Douglas Thompson
- Department of Blood Sciences, Leeds Teaching Hospitals NHS Trust
- Clinical and Biomedical Proteomics Group, Leeds Institute of Molecular Medicine, St James’s University Hospital, Leeds, UK
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Yu JP, Xu XG, Ma RJ, Qin SN, Wang CR, Wang XB, Li M, Li MS, Ma Q, Xu WW. Development of a clinical chemiluminescent immunoassay for serum GPC3 and simultaneous measurements alone with AFP and CK19 in diagnosis of hepatocellular carcinoma. J Clin Lab Anal 2014; 29:85-93. [PMID: 24687454 DOI: 10.1002/jcla.21733] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2013] [Accepted: 11/21/2013] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Glypican-3 (GPC3) is an oncofetal antigen that shows great promise as a biomarker for diagnosis of hepatocellular carcinoma (HCC), but there is no reliable kit that can be used to detect it in clinics. The aim of this study is to develop a stable performance kit for GPC3 detection in clinics. DESIGN AND METHODS The paired antibodies were identified through cycle-screening methods based on our previous research. Then, a double antibodies sandwich chemiluminescent immunoassay for detecting serum GPC3 was developed. The performance of the developed GPC3 diagnostic kit was evaluated by detecting the concentration of serum GPC3 and assessing its single or combined use with alpha fetoprotein (AFP) and cytokeratin 19 fragment (CK19) for HCC diagnosis. RESULTS The assay demonstrated a linear range of 10-800 ng/ml, the cross-reactivity rate at 0.018% (AFP), 0.020% (carcino-embryonic antigen), and 0.021% (CK19), respectively. The minimum detectable concentration was 0.05 ng/ml; the intraassay coefficient of variation (CV) and interassay CV were both less than 10%, with good stability and reproducibility. GPC3 has a high sensitivity (54.2%) and specificity (99.4%) in diagnosing HCC. The level of GPC3 in HCC was robust higher than that in healthy or other liver diseases' sera (108.67 ± 230.04 ng/ml vs. 3.99 ± 7.68 ng/ml). The diagnostic sensitivity of GPC3 single or combined with CK19 and AFP for HCC was evaluated, and the rates were 54.2 and 90.6%, respectively. CONCLUSIONS An applicable chemiluminescent immunoassay with stable performance against GPC3 in diagnosing HCC has been established and the combination of GPC3 with CK19 and AFP could improve the diagnostic sensitivity for HCC.
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Affiliation(s)
- Juan-Ping Yu
- Institute of Antibody Engineering, School of Biotechnology, Southern Medical University, Guangzhou, P.R. China
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A practical guide to epidemiological practice and standards in the identification and validation of diagnostic markers using a bladder cancer example. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2014; 1844:145-55. [DOI: 10.1016/j.bbapap.2013.07.018] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2012] [Revised: 07/23/2013] [Accepted: 07/30/2013] [Indexed: 12/14/2022]
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Abstract
Hormone determinations are of central importance to the practice of Clinical Endocrinology, and ensuring their correct use and performance is a multidisciplinary responsibility involving clinicians, laboratory staff, manufacturers of diagnostic systems and healthcare regulatory agencies. All these professional groups have, therefore, an interest in external quality assessment (EQA) as an audit tool that can identify areas where use of tests in routine practice requires improvement to reduce risks to patients. This chapter reviews the principles of EQA, and outlines its strengths and limitations, illustrated with example data from the UK National External Quality Assessment Service (UK NEQAS). The immunological nature of many hormone assays, often further complicated by heterogeneity of analyte structure and lack of suitable calibrators, presents special problems for the designers of EQA schemes in ensuring that specimens are appropriate and that target values are accurate. Laboratory users of EQA should have sufficient knowledge of the characteristics of the EQA schemes in which they participate to make informed interpretation of their data. The trend since the 1980s for in-house assays designed in individual laboratories to be superseded by automated assays provided by a small number of diagnostics manufacturers places a special responsibility on manufacturers to ensure reliable assay design and calibration. In collaboration with other parties EQA can help identify priorities for improved assay design and calibration. Although traditionally the focus of EQA has been on assessing the analytical phase it can also make some assessment of other important aspects of performance, e.g. the consistency of reference ranges and how results are interpreted. Overall, EQA has a valuable role both in laboratory accreditation and as an educational resource, thereby helping to ensure and improve the quality of laboratory services that support patient care.
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Affiliation(s)
- Catharine M Sturgeon
- UK NEQAS [Edinburgh], Department of Laboratory Medicine, Royal Infirmary of Edinburgh, Edinburgh EH16 4SA, UK.
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Kift RL, Messenger MP, Wind TC, Hepburn S, Wilson M, Thompson D, Smith MW, Sturgeon C, Lewington AJ, Selby PJ, Banks RE. A comparison of the analytical performance of five commercially available assays for neutrophil gelatinase-associated lipocalin using urine. Ann Clin Biochem 2013; 50:236-44. [PMID: 23605129 DOI: 10.1258/acb.2012.012117] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
BACKGROUND Neutrophil gelatinase-associated lipocalin (NGAL) is a promising biomarker for acute kidney injury that is beginning to be used in clinical practice in addition to research studies. The current study describes an independent validation and comparison of five commercially available NGAL assays, focusing on urine samples. This is an essential step in the translation of this marker to clinical use in terms of allowing valid inter-study comparison and generation of robust results. METHODS Two CE (Conformité Européenne)-marked assays, the NGAL Test (BioPorto) on Siemens ADVIA(®) 1800 and the ARCHITECT Urine NGAL assay on i2000SR (Abbott Laboratories), and three research-use-only (RUO) ELISAs (R&D Systems, Hycult and BioPorto) were evaluated. Imprecision, parallelism, recovery, selectivity, limit of quantitation (LOQ), vulnerability to interference and hook effect were assessed and inter-assay agreement was determined using 68 urine samples from patients with various renal diseases and healthy controls. RESULTS The Abbott and R&D Systems assays demonstrated satisfactory performance for all parameters tested. However for the other three assays evaluated, problems were identified with LOQ (BioPorto/ADVIA(®)), parallelism (BioPorto ELISA) or several parameters (Hycult). Between-method agreement varied with the Hycult assay in particular being markedly different and highlighting issues with standardization and form of NGAL measured. CONCLUSIONS Variability exists between the five NGAL assays in terms of their performance and this should be taken into account when interpreting results from the various clinical or research studies measuring urinary NGAL.
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Affiliation(s)
- Rebecca L Kift
- Blood Sciences, Leeds General Infirmary, Great George Street, Leeds KS1 3EX, UK
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Xiang D, Zhang H, Bai J, Ma J, Li M, Gao W, Zhang X, Gao J, Wang C. Particle-enhanced turbidimetric immunoassay for determination of serum neutrophil gelatinase-associated lipocalin on the Roche Cobas c501 analyzer. Clin Biochem 2013; 46:1756-60. [DOI: 10.1016/j.clinbiochem.2013.09.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2013] [Revised: 09/10/2013] [Accepted: 09/12/2013] [Indexed: 11/30/2022]
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Füzéry AK, Levin J, Chan MM, Chan DW. Translation of proteomic biomarkers into FDA approved cancer diagnostics: issues and challenges. Clin Proteomics 2013; 10:13. [PMID: 24088261 PMCID: PMC3850675 DOI: 10.1186/1559-0275-10-13] [Citation(s) in RCA: 274] [Impact Index Per Article: 24.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2013] [Accepted: 08/31/2013] [Indexed: 12/22/2022] Open
Abstract
Tremendous efforts have been made over the past few decades to discover novel cancer biomarkers for use in clinical practice. However, a striking discrepancy exists between the effort directed toward biomarker discovery and the number of markers that make it into clinical practice. One of the confounding issues in translating a novel discovery into clinical practice is that quite often the scientists working on biomarker discovery have limited knowledge of the analytical, diagnostic, and regulatory requirements for a clinical assay. This review provides an introduction to such considerations with the aim of generating more extensive discussion for study design, assay performance, and regulatory approval in the process of translating new proteomic biomarkers from discovery into cancer diagnostics. We first describe the analytical requirements for a robust clinical biomarker assay, including concepts of precision, trueness, specificity and analytical interference, and carryover. We next introduce the clinical considerations of diagnostic accuracy, receiver operating characteristic analysis, positive and negative predictive values, and clinical utility. We finish the review by describing components of the FDA approval process for protein-based biomarkers, including classification of biomarker assays as medical devices, analytical and clinical performance requirements, and the approval process workflow. While we recognize that the road from biomarker discovery, validation, and regulatory approval to the translation into the clinical setting could be long and difficult, the reward for patients, clinicians and scientists could be rather significant.
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Affiliation(s)
- Anna K Füzéry
- Department of Pathology, Johns Hopkins University, School of Medicine, Baltimore, MD 21287, USA.
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Duffy MJ, Crown J. Companion biomarkers: paving the pathway to personalized treatment for cancer. Clin Chem 2013; 59:1447-56. [PMID: 23656699 DOI: 10.1373/clinchem.2012.200477] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
BACKGROUND Companion biomarkers are biomarkers that are used in combination with specific therapies and that prospectively help predict likely response or severe toxicity. In this article we review the role of companion biomarkers in guiding treatment in patients with cancer. CONTENT In addition to the established companion biomarkers such as estrogen receptors and HER2 (human epidermal growth factor receptor 2) in breast cancer, several new companion biomarkers have become available in recent years. These include v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog (KRAS) mutations for the selection of patients with advanced colorectal cancer who are unlikely to benefit from anti-epidermal growth factor receptor antibodies (cetuximab or panitumumab), epidermal growth factor receptor (EGFR) mutations for selecting patients with advanced non-small cell lung cancer (NSCLC) for treatment with tyrosine kinase inhibitors (gefitinib or erlotinib), v-raf murine sarcoma viral oncogene homolog B1 (BRAF) mutations for selecting patients with advanced melanoma for treatment with anti-BRAF agents (vemurafenib and dabrafenib), and anaplastic lymphoma receptor tyrosine kinase (ALK) translocations for identifying patients with NSCLC likely to benefit from crizotinib. SUMMARY The availability of companion biomarkers should improve drug efficacy, decrease toxicity, and lead to a more individualized approach to cancer treatment.
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Affiliation(s)
- Michael J Duffy
- UCD School of Medicine and Medical Science, Conway Institute, University College Dublin, Ireland
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Wood SL, Knowles MA, Thompson D, Selby PJ, Banks RE. Proteomic studies of urinary biomarkers for prostate, bladder and kidney cancers. Nat Rev Urol 2013; 10:206-18. [PMID: 23443013 DOI: 10.1038/nrurol.2013.24] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Urine is an ideal body fluid for the detection of protein markers produced by urological cancers as it can be sampled noninvasively and contains secreted and directly shed proteins from the prostate, bladder and kidney. Major challenges of working with urine include high inter-individual and intra-individual variability, low protein concentration, the presence of salts and the dynamic range of protein expression. Despite these challenges, significant progress is being made using modern proteomic methods to identify and characterize protein-based markers for urological cancers. The development of robust, easy-to-use clinical tests based on novel biomarkers has the potential to impact upon diagnosis, prognosis and monitoring and could revolutionize the treatment and management of these cancers.
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Affiliation(s)
- Steven L Wood
- Wolfson Molecular Imaging Centre, 27 Palatine Road, Withington, Manchester M20 3LJ, UK.
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Abstract
Cardiovascular diseases constitute the largest of death in developed countries, being atherosclerosis the major contributor. Atherosclerosis is a process of chronic inflammation, characterized by the accumulation of lipids, cells, and fibrous elements in medium and large arteries. There is a continuum in atherosclerotic cardiovascular pathology that extends from the initial endothelial damage to diseases such as angina, myocardial infarction, and stroke. The extent of inflammation, proteolysis, calcification, and neovascularization influences the development of advanced lesions (atheroma plaques) on the arteries. Plaque rupture and the ensuing thrombosis cause the acute complications of atherosclerosis, i.e., myocardial infarction and cerebral ischemia. Thus, identification of early biomarkers of plaque unstability and susceptibility to rupture is of capital importance in preventing acute events. In recent years proteomics has been successfully applied to study proteins involved in these pathological processes. Thus, proteomic studies have been carried out focusing on different elements such as vascular tissues (arteries), artery layers, cells looking at proteomes and secretomes, plasma/serum, exosomes, lipoproteins, and metabolites. This chapter will provide an overview of latest advances in proteomic studies of atherosclerosis and related vascular diseases.
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Affiliation(s)
- Maria G Barderas
- Department of Vascular Physiopathology, SESCAM, Hospital Nacional de Parapléjicos, Toledo, Spain
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Torsetnes SB, Nordlund MS, Paus E, Halvorsen TG, Reubsaet L. Digging deeper into the field of the small cell lung cancer tumor marker ProGRP: a method for differentiation of its isoforms. J Proteome Res 2012. [PMID: 23190087 DOI: 10.1021/pr300751j] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In this paper, we have used a newly developed immunocapture and LC-MS method to demonstrate for the first time the presence of protein isoforms 1 and 3 of the small cell lung cancer (SCLC) marker progastrin-releasing peptide (ProGRP) in sera. In addition, the method allows for indirect determination of the relative presence of the other known isoform of ProGRP, also known as ProGRP isoform 2. This new method is able to determine total ProGRP as a marker in sera at clinically relevant levels and to differentiate between isoforms at the low-pM level through combining selective sample preparation by immunoextraction, tryptic digestion, and separation followed by detection with LC-SRM-MS of the signature peptides, NLLGLIEAK (total ProGRP), LSAPGSQR (ProGRP isoform 1), and DLVDSLLQVLNVK (ProGRP isoform 3), with accuracies ≤ 25% for lower limit of quantification (LLOQ) and precisions ≤ 33%. By analyzing serum samples from four patients diagnosed with SCLC using the here described new and fully validated method, the ability is shown to both determine total ProGRP concentration and to differentiate between ProGRP isoforms 1 and 3 in one single run. Quantification of various ProGRP isoforms in one single run may be helpful for further understanding of the underlying biochemical processes in SCLC and differentiation of small cell lung cancer.
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Affiliation(s)
- Silje Bøen Torsetnes
- Department of Pharmaceutical Chemistry, School of Pharmacy, University of Oslo, Oslo, Norway
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Sölétormos G, Duffy MJ, Hayes DF, Sturgeon CM, Barak V, Bossuyt PM, Diamandis EP, Gion M, Hyltoft-Petersen P, Lamerz RM, Nielsen DL, Sibley P, Tholander B, Tuxen MK, Bonfrer JMG. Design of tumor biomarker-monitoring trials: a proposal by the European Group on Tumor Markers. Clin Chem 2012; 59:52-9. [PMID: 23034139 DOI: 10.1373/clinchem.2011.180778] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
A major application of tumor biomarkers is in serial monitoring of cancer patients, but there are no published guidelines on how to evaluate biomarkers for this purpose. The European Group on Tumor Markers has convened a multidisciplinary panel of scientists to develop guidance on the design of such monitoring trials. The panel proposes a 4-phase model for biomarker-monitoring trials analogous to that in use for the investigation of new drugs. In phase I, biomarker kinetics and correlation with tumor burden are assessed. Phase II evaluates the ability of the biomarker to identify, exclude, and/or predict a change in disease status. In phase III, the effectiveness of tumor biomarker-guided intervention is assessed by measuring patient outcome in randomized trials. Phase IV consists of an audit of the long-term effects after biomarker monitoring has been included into standard patient care. Systematic well-designed evaluations of biomarkers for monitoring may provide a stronger evidence base that might enable their earlier use in evaluating responses to cancer therapy.
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Affiliation(s)
- György Sölétormos
- Department of Clinical Biochemistry, Hillerød Hospital, University of Copenhagen, Hillerød, Denmark
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Vidal M, Chan DW, Gerstein M, Mann M, Omenn GS, Tagle D, Sechi S. The human proteome - a scientific opportunity for transforming diagnostics, therapeutics, and healthcare. Clin Proteomics 2012; 9:6. [PMID: 22583803 PMCID: PMC3388576 DOI: 10.1186/1559-0275-9-6] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2012] [Accepted: 05/14/2012] [Indexed: 11/16/2022] Open
Abstract
A National Institutes of Health (NIH) workshop was convened in Bethesda, MD on September 26–27, 2011, with representative scientific leaders in the field of proteomics and its applications to clinical settings. The main purpose of this workshop was to articulate ways in which the biomedical research community can capitalize on recent technology advances and synergize with ongoing efforts to advance the field of human proteomics. This executive summary and the following full report describe the main discussions and outcomes of the workshop.
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Affiliation(s)
- Marc Vidal
- University of Michigan, Ann Arbor, MI, USA.
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Affiliation(s)
- David J Brenner
- Center for Radiological Research, Columbia University Medical Center, New York, New York 10032, USA
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