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Wang S, Sun Y, Zeng T, Wu Y, Ding L, Zhang X, Zhang L, Huang X, Li H, Yang X, Ni Y, Hu Q. Impact of preanalytical freezing delay time on the stability of metabolites in oral squamous cell carcinoma tissue samples. Metabolomics 2022; 18:82. [PMID: 36282338 DOI: 10.1007/s11306-022-01943-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Accepted: 10/11/2022] [Indexed: 12/29/2022]
Abstract
INTRODUCTION Metabolite stability is critical for tissue metabolomics. However, changes in metabolites in tissues over time from the operating room to the laboratory remain underexplored. OBJECTIVES In this study, we evaluated the effect of postoperative freezing delay time on the stability of metabolites in normal and oral squamous cell carcinoma (OSCC) tissues. METHODS Tumor and paired normal tissues from five OSCC patients were collected after surgical resection, and samples was sequentially quenched in liquid nitrogen at 30, 40, 50, 60, 70, 80, 90 and 120 min (80 samples). Untargeted metabolic analysis by liquid chromatography-mass spectrometry/mass spectrometry in positive and negative ion modes was used to identify metabolic changes associated with delayed freezing time. The trends of metabolite changes at 30-120 and 30-60 min of delayed freezing were analyzed. RESULTS 190 metabolites in 36 chemical classes were detected. After delayed freezing for 120 min, approximately 20% of the metabolites changed significantly in normal and tumor tissues, and differences in the metabolites were found in normal and tumor tissues. After a delay of 60 min, 29 metabolites had changed significantly in normal tissues, and 84 metabolites had changed significantly in tumor tissues. In addition, we constructed three tissue freezing schemes based on the observed variation trends in the metabolites. CONCLUSION Delayed freezing of tissue samples has a certain impact on the stability of metabolites. For metabolites with significant changes, we suggest that the freezing time of tissues be reasonably selected according to the freezing schemes and the actual clinical situation.
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Affiliation(s)
- Shuai Wang
- Department of Oral and Maxillofacial Surgery, Nanjing Stomatological Hospital, Medical School of Nanjing University, Nanjing, 210008, Jiangsu, China
- Central Laboratory of Stomatology, Nanjing Stomatological Hospital, Medical School of Nanjing University, Nanjing, 210008, Jiangsu, China
| | - Yawei Sun
- Department of Oral and Maxillofacial Surgery, Nanjing Stomatological Hospital, Medical School of Nanjing University, Nanjing, 210008, Jiangsu, China
| | - Tao Zeng
- State Key Lab of Pharmaceutical Biotechnology, College of Life Sciences, Nanjing University, Nanjing, 210008, Jiangsu, China
| | - Yan Wu
- Department of Oral Pathology, Nanjing Stomatological Hospital, Medical School of Nanjing University, Nanjing, 210008, Jiangsu, China
- Central Laboratory of Stomatology, Nanjing Stomatological Hospital, Medical School of Nanjing University, Nanjing, 210008, Jiangsu, China
| | - Liang Ding
- Central Laboratory of Stomatology, Nanjing Stomatological Hospital, Medical School of Nanjing University, Nanjing, 210008, Jiangsu, China
| | - Xiaoxin Zhang
- Central Laboratory of Stomatology, Nanjing Stomatological Hospital, Medical School of Nanjing University, Nanjing, 210008, Jiangsu, China
| | - Lei Zhang
- Department of Oral Pathology, Nanjing Stomatological Hospital, Medical School of Nanjing University, Nanjing, 210008, Jiangsu, China
| | - Xiaofeng Huang
- Department of Oral Pathology, Nanjing Stomatological Hospital, Medical School of Nanjing University, Nanjing, 210008, Jiangsu, China
| | - Huiling Li
- Department of Oral Pathology, Nanjing Stomatological Hospital, Medical School of Nanjing University, Nanjing, 210008, Jiangsu, China
| | - Xihu Yang
- Department of Oral and Maxillofacial Surgery, Affiliated Hospital of Jiangsu University, Zhenjiang, 212001, Jiangsu, China
| | - Yanhong Ni
- Central Laboratory of Stomatology, Nanjing Stomatological Hospital, Medical School of Nanjing University, Nanjing, 210008, Jiangsu, China.
| | - Qingang Hu
- Department of Oral and Maxillofacial Surgery, Nanjing Stomatological Hospital, Medical School of Nanjing University, Nanjing, 210008, Jiangsu, China.
- Central Laboratory of Stomatology, Nanjing Stomatological Hospital, Medical School of Nanjing University, Nanjing, 210008, Jiangsu, China.
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Mathieson W, Mommaerts K, Trouet JM, Mathay C, Guan P, Carithers LJ, Rohrer D, Valley DR, Blanski A, Jewell S, Moore HM, Betsou F. Cold Ischemia Score: An mRNA Assay for the Detection of Extended Cold Ischemia in Formalin-Fixed, Paraffin-Embedded Tissue. J Histochem Cytochem 2019; 67:159-168. [PMID: 30562131 PMCID: PMC6393842 DOI: 10.1369/0022155418819967] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Accepted: 11/26/2018] [Indexed: 02/08/2023] Open
Abstract
Although there are thousands of formalin-fixed paraffin-embedded (FFPE) tissue blocks potentially available for scientific research, many are of questionable quality, partly due to unknown preanalytical variables. We analyzed FFPE tissue biospecimens as part of the National Cancer Institute (NCI) Biospecimen Preanalytical Variables program to identify mRNA markers denoting cold ischemic time. The mRNA was extracted from colon, kidney, and ovary cancer FFPE blocks (40 patients, 10-12 hr fixation time) with 1, 2, 3, and 12 hr cold ischemic times, then analyzed using qRT-PCR for 23 genes selected following a literature search. No genes tested could determine short ischemic times (1-3 hr). However, a combination of three unstable genes normalized to a more stable gene could generate a "Cold Ischemia Score" that could distinguish 1 to 3 hr cold ischemia from 12 hr cold ischemia with 62% sensitivity and 84% specificity.
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Affiliation(s)
| | | | | | | | - Ping Guan
- National Cancer Institute, Bethesda, Maryland
| | | | | | | | | | | | | | - Fay Betsou
- Integrated Biobank of Luxembourg, Luxembourg
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Abstract
Prostate cancer is the second most common malignancy, and the fifth leading cause of cancer-related death among men, worldwide. A major unsolved clinical challenge in prostate cancer is the ability to accurately distinguish indolent cancer types from the aggressive ones. Reprogramming of metabolism is now a widely accepted hallmark of cancer development, where cancer cells must be able to convert nutrients to biomass while maintaining energy production. Metabolomics is the large-scale study of small molecules, commonly known as metabolites, within cells, biofluids, tissues, or organisms. Nuclear magnetic resonance (NMR) spectroscopy is commonly applied in metabolomics studies of cancer. This chapter provides protocols for NMR-based metabolomics of cell cultures, biofluids (serum and urine), and intact tissue, with concurrent advice for optimal biobanking and sample preparation procedures.
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Broeckx V, Boonen K, Pringels L, Sagaert X, Prenen H, Landuyt B, Schoofs L, Maes E. Comparison of multiple protein extraction buffers for GeLC-MS/MS proteomic analysis of liver and colon formalin-fixed, paraffin-embedded tissues. MOLECULAR BIOSYSTEMS 2016; 12:553-65. [PMID: 26676081 DOI: 10.1039/c5mb00670h] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Formalin-fixed paraffin-embedded (FFPE) tissue specimens represent a potential valuable source of samples for clinical research. Since these specimens are banked in hospital archives, large cohorts of samples can be collected in short periods of time which can all be linked with a patients' clinical history. Therefore, the use of FFPE tissue in protein biomarker discovery studies gains interest. However, despite the growing number of FFPE proteome studies in the literature, there is a lack of a FFPE proteomics standard operating procedure (SOP). One of the challenging steps in the development of such a SOP is the ability to obtain an efficient and repeatable extraction of full length FFPE proteins. In this study, the protein extraction efficiency of eight protein extraction buffers is critically compared with GeLC-MS/MS (1D gel electrophoresis followed by in-gel digestion and LC-MS/MS). The data variation caused by using these extraction buffers was investigated since the variation is a very important aspect when using FFPE tissue as a source for biomarker detection. In addition, a qualitative comparison was made between the protein extraction efficiency and repeatability for FFPE tissue and fresh frozen tissue.
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Affiliation(s)
- Valérie Broeckx
- Research Group of Functional Genomics and Proteomics, Department of Biology, University of Leuven, Zoological Institute, Naamsestraat 59, 3000 Leuven, Belgium.
| | - Kurt Boonen
- Research Group of Functional Genomics and Proteomics, Department of Biology, University of Leuven, Zoological Institute, Naamsestraat 59, 3000 Leuven, Belgium.
| | - Lentel Pringels
- Research Group of Functional Genomics and Proteomics, Department of Biology, University of Leuven, Zoological Institute, Naamsestraat 59, 3000 Leuven, Belgium.
| | - Xavier Sagaert
- Centre for Translational Cell and Tissue Research, University Hospital of Leuven, Herestraat 49, 3000 Leuven, Belgium
| | - Hans Prenen
- Department of Gastro-Enterology, Digestive Oncology Unit, University Hospital of Leuven, Herestraat 49, 3000 Leuven, Belgium
| | - Bart Landuyt
- Research Group of Functional Genomics and Proteomics, Department of Biology, University of Leuven, Zoological Institute, Naamsestraat 59, 3000 Leuven, Belgium.
| | - Liliane Schoofs
- Research Group of Functional Genomics and Proteomics, Department of Biology, University of Leuven, Zoological Institute, Naamsestraat 59, 3000 Leuven, Belgium.
| | - Evelyne Maes
- Flemish Institute for Technological Research (VITO), Boeretang 200, 2400 Mol, Belgium and Centre for Proteomics, University of Antwerp/Flemish Institute for Technological Research (VITO), Groenenborgerlaan 171, 2020 Antwerp, Belgium
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Hu ZC, Tang B, Guo D, Zhang J, Liang YY, Ma D, Zhu JY. Expression of insulin-like growth factor-1 receptor in keloid and hypertrophic scar. Clin Exp Dermatol 2014; 39:822-8. [PMID: 25154292 PMCID: PMC4232319 DOI: 10.1111/ced.12407] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/01/2014] [Indexed: 11/29/2022]
Abstract
BACKGROUND Keloid and hypertrophic scar (HS) are two pathological forms of excessive dermal fibrosis, which are due to aberrant wound-healing responses. Accumulating evidence suggests that aberrant activity of growth factors and increased numbers of growth factor receptors play an important role in the formation of pathological scar. AIM We examined the expression level of insulin-like growth factor-1 receptor (IGF-IR) in keloid, HS and normal skin. METHODS IGF-IR expression was analyzed by immunohistochemistry, real-time PCR and western blotting on tissues and fibroblasts from 30 patients, comprising 10 patients with keloid and 20 with HS (10 with immature and 10 with mature HS), and from 10 age-matched and sex-matched healthy controls. RESULTS Immunoreactivity to IGF-IR was found in dermal fibroblasts of keloid (90%), immature HS, (80%) and mature HS (30%), but not in normal skin. There was no statistically significant difference in immunoreactivity scores between keloid and immature HS, but there was a significant difference (P < 0.01) between mature and immature HS. Real-time PCR and western blot analysis confirmed that there was high expression of IGF-IR in keloid and immature HS fibroblasts, but not in mature HS or normal skin fibroblasts. IGF-IR was expressed in the overlying epidermis, and there was no significant difference between the groups. CONCLUSIONS IGF-IR may be involved in the pathogenesis of keloid and HS. Given that IGF-IR are predominantly expressed on dermal fibroblasts, targeting of IGF-IR in fibroblasts may be of benefit to prevent scarring.
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Affiliation(s)
- Z-C Hu
- Department of Burns, First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
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Thompson SM, Craven RA, Nirmalan NJ, Harnden P, Selby PJ, Banks RE. Impact of pre-analytical factors on the proteomic analysis of formalin-fixed paraffin-embedded tissue. Proteomics Clin Appl 2013; 7:241-51. [PMID: 23027712 DOI: 10.1002/prca.201200086] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2012] [Accepted: 08/15/2012] [Indexed: 12/14/2022]
Abstract
Formalin-fixed paraffin-embedded (FFPE) tissue samples represent a tremendous potential resource for biomarker discovery, with large numbers of samples in hospital pathology departments and links to clinical information. However, the cross-linking of proteins and nucleic acids by formalin fixation has hampered analysis and proteomic studies have been restricted to using frozen tissue, which is more limited in availability as it needs to be collected specifically for research. This means that rare disease subtypes cannot be studied easily. Recently, improved extraction techniques have enabled analysis of FFPE tissue by a number of proteomic techniques. As with all clinical samples, pre-analytical factors are likely to impact on the results obtained, although overlooked in many studies. The aim of this review is to discuss the various pre-analytical factors, which include warm and cold ischaemic time, size of sample, fixation duration and temperature, tissue processing conditions, length of storage of archival tissue and storage conditions, and to review the studies that have considered these factors in more detail. In those areas where investigations are few or non-existent, illustrative examples of the possible importance of specific factors have been drawn from studies using frozen tissue or from immunohistochemical studies of FFPE tissue.
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Affiliation(s)
- Seonaid M Thompson
- Clinical and Biomedical Proteomics Group, Leeds Institute of Molecular Medicine, St. James's University Hospital, United Kingdom
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Betsou F, Gunter E, Clements J, DeSouza Y, Goddard KAB, Guadagni F, Yan W, Skubitz A, Somiari S, Yeadon T, Chuaqui R. Identification of evidence-based biospecimen quality-control tools: a report of the International Society for Biological and Environmental Repositories (ISBER) Biospecimen Science Working Group. J Mol Diagn 2013; 15:3-16. [PMID: 23195791 PMCID: PMC5707193 DOI: 10.1016/j.jmoldx.2012.06.008] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2012] [Revised: 06/11/2012] [Accepted: 06/20/2012] [Indexed: 01/20/2023] Open
Abstract
Control of biospecimen quality that is linked to processing is one of the goals of biospecimen science. Consensus is lacking, however, regarding optimal sample quality-control (QC) tools (ie, markers and assays). The aim of this review was to identify QC tools, both for fluid and solid-tissue samples, based on a comprehensive and critical literature review. The most readily applicable tools are those with a known threshold for the preanalytical variation and a known reference range for the QC analyte. Only a few meaningful markers were identified that meet these criteria, such as CD40L for assessing serum exposure at high temperatures and VEGF for assessing serum freeze-thawing. To fully assess biospecimen quality, multiple QC markers are needed. Here we present the most promising biospecimen QC tools that were identified.
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Kultima K, Sköld K, Borén M. Biomarkers of disease and post-mortem changes - Heat stabilization, a necessary tool for measurement of protein regulation. J Proteomics 2011; 75:145-59. [PMID: 21708298 DOI: 10.1016/j.jprot.2011.06.009] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2011] [Revised: 05/25/2011] [Accepted: 06/07/2011] [Indexed: 12/25/2022]
Abstract
This review focuses on post sampling changes and how the Stabilizor system has been used to control this natural biological process and potential implications on cancer-specific biomarkers due to post sampling changes. Tissue sampling is a major traumatic event that can have drastic effects within a very short timeframe at the molecular level [1] resulting in loss of sample quality due to post-mortem changes. A heat-stabilization technology, using the Stabilizor system, has been developed to quickly and permanently abolish the enzymatic activity that causes these changes post-sampling and so preserve sample quality. The Stabilizor system has been shown to give better sample quality when analyzing a variety of tissues in various proteomic workflows. In this paper we discuss the impact of using heat-stabilized tissue in different proteomic applications. Based on our observations regarding the overlap between commonly changing proteins and proteins found to change post-mortem we also highlight a group of proteins of particular interest in cancer studies.
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Affiliation(s)
- Kim Kultima
- Analytical Chemistry, Department of Physical and Analytical Chemistry, Uppsala University, 75124, Uppsala, Sweden
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Gao X, Pang J, Li LY, Liu WP, Di JM, Sun QP, Fang YQ, Liu XP, Pu XY, He D, Li MT, Su ZL, Li BY. Expression profiling identifies new function of collapsin response mediator protein 4 as a metastasis-suppressor in prostate cancer. Oncogene 2010; 29:4555-66. [PMID: 20543870 DOI: 10.1038/onc.2010.213] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Metastasis is the chief cause of mortality from cancer, but the mechanisms leading to metastasis are poorly understood. We used a proteomics approach to screen for metastasis-associated proteins and found that collapsin response mediator protein-4 (CRMP4) expression was inversely associated with the lymph node metastasis of prostate cancer (PCa). Subsequent in vitro and in vivo studies revealed that overexpression of CRMP4 not only suppressed the invasion ability of PCa cells, but also strongly inhibited tumor metastasis in an animal model. Furthermore, methylation of a CpG island within the promoter region of the CRMP4 gene is responsible for downregulation of CRMP4 expression. Thus, in this study, we show new function of CRMP4 as a metastasis-suppressor in PCa. The findings provide new mechanistic insights into metastasis and therapeutic potential for this most common male cancer.
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Affiliation(s)
- X Gao
- Department of Urology, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, China.
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10
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Pang J, Liu WP, Liu XP, Li LY, Fang YQ, Sun QP, Liu SJ, Li MT, Su ZL, Gao X. Profiling protein markers associated with lymph node metastasis in prostate cancer by DIGE-based proteomics analysis. J Proteome Res 2010; 9:216-26. [PMID: 19894759 DOI: 10.1021/pr900953s] [Citation(s) in RCA: 79] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Current predictive tools and imaging modalities are not accurate enough for preoperative diagnosis of lymph node metastatic prostate cancer (LNM PCa). Proteomic analysis is introduced to screen potential biomarkers for early detection of LNM PCa. In our initial study, protein samples from localized and LNM PCa as well as benign prostatic hyperplasia tissues were analyzed using two-dimensional fluorescence difference in gel electrophoresis (2-D DIGE) coupled with MALDI-TOF/TOF MS. We identified 58 proteins that were differentially expressed in the LNM PCa group relative to the localized PCa group. Six of these proteins, e-FABP5, MCCC2, PPA2, Ezrin, SLP2, and SM22, are functionally relevant to cancer metastasis. Expression of these proteins was therefore further validated in tissue samples from the original cohort and also from a larger, independent cohort of patients using real time PCR, Western blotting, and immunohistochemistry staining. In addition, the serum levels of e-FABP5 were also examined by ELISA. Relative to localized PCa tissues, LNM PCa tissues had increased expression of e-FABP5, MCCC2, PPA2, Ezrin, and SLP2 and decreased expression of SM22. Patients with LNM PCa had significantly higher levels of serum e-FABP5. This study presents evidence that increased expression of e-FABP5, MCCC2, PPA2, Ezrin, and SLP2 and decreased expression of SM22 are useful diagnostic markers for the existence of LNM PCa.
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Affiliation(s)
- Jun Pang
- Department of Urology, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou 510630, China
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Jackson DH, Banks RE. Banking of clinical samples for proteomic biomarker studies: A consideration of logistical issues with a focus on pre-analytical variation. Proteomics Clin Appl 2010; 4:250-70. [DOI: 10.1002/prca.200900220] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2009] [Revised: 12/20/2009] [Accepted: 12/20/2009] [Indexed: 01/07/2023]
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Mandal N, Heegaard S, Prause JU, Honoré B, Vorum H. Ocular proteomics with emphasis on two-dimensional gel electrophoresis and mass spectrometry. Biol Proced Online 2009; 12:56-88. [PMID: 21406065 PMCID: PMC3055252 DOI: 10.1007/s12575-009-9019-7] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2009] [Accepted: 09/28/2009] [Indexed: 01/30/2023] Open
Abstract
The intention of this review is to provide an overview of current methodologies employed in the rapidly developing field of ocular proteomics with emphasis on sample preparation, two-dimensional polyacrylamide gel electrophoresis (2D-PAGE) and mass spectrometry (MS). Appropriate sample preparation for the diverse range of cells and tissues of the eye is essential to ensure reliable results. Current methods of protein staining for 2D-PAGE, protein labelling for two-dimensional difference gel electrophoresis, gel-based expression analysis and protein identification by MS are summarised. The uses of gel-free MS-based strategies (MuDPIT, iTRAQ, ICAT and SILAC) are also discussed. Proteomic technologies promise to shed new light onto ocular disease processes that could lead to the discovery of strong novel biomarkers and therapeutic targets useful in many ophthalmic conditions.
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Affiliation(s)
- Nakul Mandal
- Eye Pathology Section, Department of Neuroscience and Pharmacology, University of Copenhagen, Copenhagen, Denmark
- Department of Medical Biochemistry, Aarhus University, Aarhus, Denmark
| | - Steffen Heegaard
- Eye Pathology Section, Department of Neuroscience and Pharmacology, University of Copenhagen, Copenhagen, Denmark
| | - Jan Ulrik Prause
- Eye Pathology Section, Department of Neuroscience and Pharmacology, University of Copenhagen, Copenhagen, Denmark
| | - Bent Honoré
- Department of Medical Biochemistry, Aarhus University, Aarhus, Denmark
| | - Henrik Vorum
- Department of Medical Biochemistry, Aarhus University, Aarhus, Denmark
- Department of Ophthalmology, Aalborg Hospital, Aarhus University Hospital, Aalborg, Denmark
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Mojica WD. Importance of cell-procurement methods in transforming personalized cancer treatment from concept to reality. Per Med 2009; 6:33-43. [PMID: 29783382 DOI: 10.2217/17410541.6.1.33] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The much-anticipated promise of personalized cancer care is to deliver therapies best suited for a patient based on the knowledge of that individual's genetics and tumor characteristics. This transformative approach will require many changes in the scientific and medical community, one of the most fundamental being the direct study of human tissue biospecimens. Biospecimens will be integral to the elucidation of biomarkers that will help identify and serve as potential diagnostic, prognostic and therapeutic targets in cancer. Despite the vast repositories of fixed-tissue biospecimens that are in existence, a number of flaws exist that hinder their reliable use as instruments from which to enable personalized cancer research and clinical care. A new view of biospecimen worth in the future will mandate that the molecules within its cells are reflective of their in vivo state, and not altered by external variables introduced during the excision and processing of the biospecimen. Research on biospecimen collection is a legitimate field of study that will be necessary for personalized cancer care to become a reality.
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Affiliation(s)
- Wilfrido D Mojica
- University at Buffalo, State University of New York, Department of Pathology, 100 High Street, Buffalo NY 14203, USA.
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Riegman PHJ, Morente MM, Betsou F, de Blasio P, Geary P. Biobanking for better healthcare. Mol Oncol 2008; 2:213-22. [PMID: 19383342 PMCID: PMC5527804 DOI: 10.1016/j.molonc.2008.07.004] [Citation(s) in RCA: 171] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2008] [Revised: 07/18/2008] [Accepted: 07/21/2008] [Indexed: 12/12/2022] Open
Abstract
Translational cancer research is highly dependent of large series of cases including high quality samples and their associated data. Comprehensive Cancer Centers should be involved in networks to enable large-scale multi-center research projects between the centers [Ringborg, U., de Valeriola, D., van Harten, W., Llombart-Bosch, A., Lombardo, C., Nilsson, K., Philip, T., Pierotti, M.A., Riegman, P., Saghatchian, M., Storme, G., Tursz, T., Verellen, D, 2008. Improvement of European translational cancer research. Collaboration between comprehensive cancer centers. Tumori 94, 143-146.]. Combating cancer knows many frontiers. Research is needed for prevention as well as better care for those who have acquired the disease. This implies that human samples for cancer research need to be sourced from distinct forms of biobanking. An easier access to these samples for the scientific community is considered as the main bottleneck for research for health, and biobanks are the most adequate site to try to resolve this issue [Ozols, R.F., Herbst, R.S., Colson, Y.L., Gralow, J., Bonner, J., Curran Jr., W.J., Eisenberg, B.L., Ganz, P.A., Kramer, B.S., Kris, M.G., Markman, M., Mayer, R.J., Raghavan, D., Reaman, G.H., Sawaya, R., Schilsky, R.L., Schuchter, L.M., Sweetenham, J.W., Vahdat, L.T., Winn, R.J., and the American Society of Clinical Oncology, 2007. Clinical cancer advances 2006: major research advances in cancer treatment, prevention, and screening: a report from the American Society of Clinical Oncology. J. Clin. Oncol. 25, 146-162.]. However, biobanks should not be considered a static activity. On the contrary, biobanking is a young discipline [Morente, M.M., Fernandez, P.L., de Alava, E. Biobanking: old activity or young discipline? Semin. Diagn. Pathol., in press.], which need continuously evolve according to the permanent development of new techniques and new scientific goals. To accomplish current requirements of the scientific community biobanks need to face some essential challenges including an appropriate design, harmonized and more suitable procedures, and sustainability, all of them in the framework of their ethic, legal and social dimensions. This review therefore presents an overview on these issues, based on the works and discussions of the Marble Arch International Working Group on Biobanking for Biomedical Research, integrated by experts in biobanking from five continents.
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Affiliation(s)
- Peter H J Riegman
- Department of Pathology, Josephine Nefkens Institute, Erasmus Medical Center, Be 235b, Dr Molwaterplein 50, 3015 GE Rotterdam, The Netherlands.
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Editorial Comment. J Urol 2008. [DOI: 10.1016/j.juro.2008.04.121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Nirmalan NJ, Harnden P, Selby PJ, Banks RE. Mining the archival formalin-fixed paraffin-embedded tissue proteome: opportunities and challenges. MOLECULAR BIOSYSTEMS 2008; 4:712-20. [PMID: 18563244 DOI: 10.1039/b800098k] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The significant potential of tissue-based proteomic biomarker studies can be restricted by difficulties in accessing samples in optimal fresh-frozen form. While archival formalin-fixed tissue collections with attached clinical and outcome data represent a valuable alternate resource, the use of formalin as a fixative which induces protein cross-linking, has generally been assumed to render them unsuitable for proteomic studies. However, this view has been challenged recently with the publication of several papers accomplishing variable degrees of heat-induced reversal of cross-links. Although still in its infancy and requiring the quantitative optimisation of several critical parameters, formalin-fixed tissue proteomics holds promise as a powerful tool for biomarker-driven translational research. Here, we critically review the current status of research in the field, highlighting challenges which need to be addressed for robust quantitative application of protocols to ensure confident high impact inferences can be made.
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Affiliation(s)
- Niroshini J Nirmalan
- Clinical and Biomedical Proteomics Group, Cancer Research UK Clinical Centre, St James's University Hospital, Beckett Street, Leeds, UK
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Jackson D, Craven RA, Hutson RC, Graze I, Lueth P, Tonge RP, Hartley JL, Nickson JA, Rayner SJ, Johnston C, Dieplinger B, Hubalek M, Wilkinson N, Perren TJ, Kehoe S, Hall GD, Daxenbichler G, Dieplinger H, Selby PJ, Banks RE. Proteomic profiling identifies afamin as a potential biomarker for ovarian cancer. Clin Cancer Res 2008; 13:7370-9. [PMID: 18094419 DOI: 10.1158/1078-0432.ccr-07-0747] [Citation(s) in RCA: 75] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
PURPOSE To discover and validate serum glycoprotein biomarkers in ovarian cancer using proteomic-based approaches. EXPERIMENTAL DESIGN Serum samples from a "discovery set" of 20 patients with ovarian cancer or benign ovarian cysts or healthy volunteers were compared by fluorescence two-dimensional differential in-gel electrophoresis and parallel lectin-based two-dimensional profiling. Validation of a candidate biomarker was carried out with Western blotting and immunoassay (n = 424). RESULTS Twenty-six proteins that changed significantly were identified by mass spectrometric sequencing. One of these, confirmed by Western blotting, was afamin, a vitamin E binding protein, with two isoforms decreasing in patients with ovarian cancer. Validation using cross-sectional samples from 303 individuals (healthy controls and patients with benign, borderline, or malignant ovarian conditions and other cancers) assayed by ELISA showed significantly decreased total afamin concentrations in patients with ovarian cancer compared with healthy controls (P = 0.002) and patients with benign disease (P = 0.046). However, the receiver operating characteristic areas for total afamin for the comparison of ovarian cancer with healthy controls or benign controls were only 0.67 and 0.60, respectively, with comparable figures for CA-125 being 0.92 and 0.88 although corresponding figures for a subgroup of samples analyzed by isoelectric focusing for afamin isoform 2 were 0.85 and 0.79. Analysis of a further 121 samples collected prospectively from 9 patients pretreatment through to relapse indicated complementarity of afamin with CA-125, including two cases in whom CA-125 was noninformative. CONCLUSIONS Afamin shows potential complementarity with CA-125 in longitudinal monitoring of patients with ovarian cancer, justifying prospective larger-scale investigation. Changes in specific isoforms may provide further information.
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Affiliation(s)
- David Jackson
- Cancer Research UK Clinical Centre, St James's University Hospital, Leeds, United Kingdom
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