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Kuci Emruli V, Liljedahl L, Axelsson U, Richter C, Theorin L, Bjartell A, Lilja H, Donovan J, Neal D, Hamdy FC, Borrebaeck CAK. Identification of a serum biomarker signature associated with metastatic prostate cancer. Proteomics Clin Appl 2021; 15:e2000025. [PMID: 33580906 DOI: 10.1002/prca.202000025] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Revised: 01/10/2021] [Accepted: 01/11/2021] [Indexed: 12/24/2022]
Abstract
PURPOSE Improved early diagnosis and determination of aggressiveness of prostate cancer (PC) is important to select suitable treatment options and to decrease over-treatment. The conventional marker is total prostate specific antigen (PSA) levels in blood, but lacks specificity and ability to accurately discriminate indolent from aggressive disease. EXPERIMENTAL DESIGN In this study, we sought to identify a serum biomarker signature associated with metastatic PC. We measured 157 analytes in 363 serum samples from healthy subjects, patients with non-metastatic PC and patients with metastatic PC, using a recombinant antibody microarray. RESULTS A signature consisting of 69 proteins differentiating metastatic PC patients from healthy controls was identified. CONCLUSIONS AND CLINICAL RELEVANCE The clinical value of this biomarker signature requires validation in larger independent patient cohorts before providing a new prospect for detection of metastatic PC.
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Affiliation(s)
- Venera Kuci Emruli
- Department of Immunotechnology and CREATE Health Translational Cancer Center, Lund University, Lund, Sweden
| | - Leena Liljedahl
- Department of Immunotechnology and CREATE Health Translational Cancer Center, Lund University, Lund, Sweden
| | - Ulrika Axelsson
- Department of Immunotechnology and CREATE Health Translational Cancer Center, Lund University, Lund, Sweden
| | - Corinna Richter
- Department of Immunotechnology and CREATE Health Translational Cancer Center, Lund University, Lund, Sweden
| | - Lisa Theorin
- Department of Immunotechnology and CREATE Health Translational Cancer Center, Lund University, Lund, Sweden
| | - Anders Bjartell
- Department of Urology, Skåne University Hospital, Malmö, Sweden.,Department of Translational Medicine, Lund University, Malmö, Sweden
| | - Hans Lilja
- Department of Translational Medicine, Lund University, Malmö, Sweden.,Department of Laboratory Medicine, Surgery, and Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA.,The Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK
| | - Jenny Donovan
- Bristol Medical School, University of Bristol, Bristol, UK
| | - David Neal
- The Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK
| | - Freddie C Hamdy
- The Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK
| | - Carl A K Borrebaeck
- Department of Immunotechnology and CREATE Health Translational Cancer Center, Lund University, Lund, Sweden
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2
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Delfani P, Sturfelt G, Gullstrand B, Carlsson A, Kassandra M, Borrebaeck CAK, Bengtsson AA, Wingren C. Deciphering systemic lupus erythematosus-associated serum biomarkers reflecting apoptosis and disease activity. Lupus 2016; 26:373-387. [PMID: 27694630 DOI: 10.1177/0961203316669240] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Systemic lupus erythematosus (SLE) is a severe chronic inflammatory autoimmune connective tissue disease. Despite major efforts, SLE remains a poorly understood disease with unpredictable course, unknown etiology and complex pathogenesis. Apoptosis combined with deficiency in clearing apoptotic cells is an important etiopathogenic event in SLE, which could contribute to the increased load of potential autoantigen(s); however, the lack of disease-specific protein signatures deciphering SLE and the underlying biological processes is striking and represents a key limitation. In this retrospective pilot study, we explored the immune system as a specific sensor for disease, in order to advance our understanding of SLE. To this end, we determined multiplexed serum protein expression profiles of crude SLE serum samples, using antibody microarrays. The aim was to identify differential immunoprofiles, or snapshots of the immune response modulated by the disease, reflecting apoptosis, a key process in the etiology of SLE and disease activity. The results showed that multiplexed panels of SLE-associated serum biomarkers could be decoded, in particular reflecting disease activity, but potentially the apoptosis process as well. While the former biomarkers could display a potential future use for prognosis, the latter biomarkers might help shed further light on the apoptosis process taking place in SLE.
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Affiliation(s)
- P Delfani
- 1 Department of Immunotechnology and CREATE Health, Lund University, Lund, Sweden
| | - G Sturfelt
- 2 Department of Clinical Sciences, Rheumatology Section, Lund University Hospital, Lund University, Lund, Sweden
| | - B Gullstrand
- 2 Department of Clinical Sciences, Rheumatology Section, Lund University Hospital, Lund University, Lund, Sweden
| | - A Carlsson
- 1 Department of Immunotechnology and CREATE Health, Lund University, Lund, Sweden
| | - M Kassandra
- 1 Department of Immunotechnology and CREATE Health, Lund University, Lund, Sweden
| | - C A K Borrebaeck
- 1 Department of Immunotechnology and CREATE Health, Lund University, Lund, Sweden
| | - A A Bengtsson
- 2 Department of Clinical Sciences, Rheumatology Section, Lund University Hospital, Lund University, Lund, Sweden
| | - C Wingren
- 1 Department of Immunotechnology and CREATE Health, Lund University, Lund, Sweden
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3
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Delfani P, Dexlin Mellby L, Nordström M, Holmér A, Ohlsson M, Borrebaeck CAK, Wingren C. Technical Advances of the Recombinant Antibody Microarray Technology Platform for Clinical Immunoproteomics. PLoS One 2016; 11:e0159138. [PMID: 27414037 PMCID: PMC4944972 DOI: 10.1371/journal.pone.0159138] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Accepted: 06/28/2016] [Indexed: 01/30/2023] Open
Abstract
In the quest for deciphering disease-associated biomarkers, high-performing tools for multiplexed protein expression profiling of crude clinical samples will be crucial. Affinity proteomics, mainly represented by antibody-based microarrays, have during recent years been established as a proteomic tool providing unique opportunities for parallelized protein expression profiling. But despite the progress, several main technical features and assay procedures remains to be (fully) resolved. Among these issues, the handling of protein microarray data, i.e. the biostatistics parts, is one of the key features to solve. In this study, we have therefore further optimized, validated, and standardized our in-house designed recombinant antibody microarray technology platform. To this end, we addressed the main remaining technical issues (e.g. antibody quality, array production, sample labelling, and selected assay conditions) and most importantly key biostatistics subjects (e.g. array data pre-processing and biomarker panel condensation). This represents one of the first antibody array studies in which these key biostatistics subjects have been studied in detail. Here, we thus present the next generation of the recombinant antibody microarray technology platform designed for clinical immunoproteomics.
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Affiliation(s)
- Payam Delfani
- Department of Immunotechnology and CREATE Health, Lund University, Medicon Village, Lund, Sweden
| | - Linda Dexlin Mellby
- Department of Immunotechnology and CREATE Health, Lund University, Medicon Village, Lund, Sweden
- Immunovia AB, Lund, Sweden
| | | | | | - Mattias Ohlsson
- Computational Biology & Biological Physics, Department of Astronomy and Theoretical Physics, Lund University, Lund, Sweden
| | - Carl A. K. Borrebaeck
- Department of Immunotechnology and CREATE Health, Lund University, Medicon Village, Lund, Sweden
| | - Christer Wingren
- Department of Immunotechnology and CREATE Health, Lund University, Medicon Village, Lund, Sweden
- * E-mail:
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4
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Gerdtsson AS, Wingren C, Persson H, Delfani P, Nordström M, Ren H, Wen X, Ringdahl U, Borrebaeck CAK, Hao J. Plasma protein profiling in a stage defined pancreatic cancer cohort - Implications for early diagnosis. Mol Oncol 2016; 10:1305-16. [PMID: 27522951 DOI: 10.1016/j.molonc.2016.07.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2016] [Revised: 07/01/2016] [Accepted: 07/04/2016] [Indexed: 12/30/2022] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is a disease where detection preceding clinical symptoms significantly increases the life expectancy of patients. In this study, a recombinant antibody microarray platform was used to analyze 213 Chinese plasma samples from PDAC patients and normal control (NC) individuals. The cohort was stratified according to disease stage, i.e. resectable disease (stage I/II), locally advanced (stage III) and metastatic disease (stage IV). Support vector machine analysis showed that all PDAC stages could be discriminated from controls and that the accuracy increased with disease progression, from stage I to IV. Patients with stage I/II PDAC could be discriminated from NC with high accuracy based on a plasma protein signature, indicating a possibility for early diagnosis and increased detection rate of surgically resectable tumors.
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Affiliation(s)
- Anna Sandström Gerdtsson
- Department of Immunotechnology, CREATE Health Translational Cancer Center, Medicon Village bldg. 406, Lund University, SE 223 81 Lund, Sweden.
| | - Christer Wingren
- Department of Immunotechnology, CREATE Health Translational Cancer Center, Medicon Village bldg. 406, Lund University, SE 223 81 Lund, Sweden.
| | - Helena Persson
- Department of Immunotechnology, CREATE Health Translational Cancer Center, Medicon Village bldg. 406, Lund University, SE 223 81 Lund, Sweden.
| | - Payam Delfani
- Department of Immunotechnology, CREATE Health Translational Cancer Center, Medicon Village bldg. 406, Lund University, SE 223 81 Lund, Sweden.
| | | | - He Ren
- Tianjin Medical University Cancer Institute & Hospital, Huan-Hu-Xi Road, Ti-Huan-Bei, He Xi District, Tianjin 300060, PR China.
| | - Xin Wen
- Tianjin Medical University Cancer Institute & Hospital, Huan-Hu-Xi Road, Ti-Huan-Bei, He Xi District, Tianjin 300060, PR China.
| | - Ulrika Ringdahl
- Department of Immunotechnology, CREATE Health Translational Cancer Center, Medicon Village bldg. 406, Lund University, SE 223 81 Lund, Sweden.
| | - Carl A K Borrebaeck
- Department of Immunotechnology, CREATE Health Translational Cancer Center, Medicon Village bldg. 406, Lund University, SE 223 81 Lund, Sweden.
| | - Jihui Hao
- Tianjin Medical University Cancer Institute & Hospital, Huan-Hu-Xi Road, Ti-Huan-Bei, He Xi District, Tianjin 300060, PR China.
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Genetic methods of antibody generation and their use in immunohistochemistry. Methods 2014; 70:20-7. [DOI: 10.1016/j.ymeth.2014.02.031] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2013] [Revised: 01/22/2014] [Accepted: 02/21/2014] [Indexed: 12/18/2022] Open
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6
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Petersson L, Berthet Duroure N, Auger A, Dexlin-Mellby L, Borrebaeck CA, Ait Ikhlef A, Wingren C. Generation of miniaturized planar ecombinant antibody arrays using a microcantilever-based printer. NANOTECHNOLOGY 2014; 25:275104. [PMID: 24960426 DOI: 10.1088/0957-4484/25/27/275104] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Miniaturized (Ø 10 μm), multiplexed (>5-plex), and high-density (>100 000 spots cm(-2)) antibody arrays will play a key role in generating protein expression profiles in health and disease. However, producing such antibody arrays is challenging, and it is the type and range of available spotters which set the stage. This pilot study explored the use of a novel microspotting tool, Bioplume(TM)-consisting of an array of micromachined silicon cantilevers with integrated microfluidic channels-to produce miniaturized, multiplexed, and high-density planar recombinant antibody arrays for protein expression profiling which targets crude, directly labelled serum. The results demonstrated that 16-plex recombinant antibody arrays could be produced-based on miniaturized spot features (78.5 um(2), Ø 10 μm) at a 7-125-times increased spot density (250 000 spots cm(-2)), interfaced with a fluorescent-based read-out. This prototype platform was found to display adequate reproducibility (spot-to-spot) and an assay sensitivity in the pM range. The feasibility of the array platform for serum protein profiling was outlined.
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Affiliation(s)
- Linn Petersson
- Department of Immunotechnology, Lund University, Medicon Village, SE-22381 Lund, Sweden. CREATE Health, Lund University, Medicon Village, SE-22381 Lund, Sweden
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Taussig MJ, Schmidt R, Cook EA, Stoevesandt O. Development of proteome-wide binding reagents for research and diagnostics. Proteomics Clin Appl 2014; 7:756-66. [PMID: 24178846 DOI: 10.1002/prca.201300060] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2013] [Revised: 09/09/2013] [Accepted: 09/10/2013] [Indexed: 01/11/2023]
Abstract
Alongside MS, antibodies and other specific protein-binding molecules have a special place in proteomics as affinity reagents in a toolbox of applications for determining protein location, quantitative distribution and function (affinity proteomics). The realisation that the range of research antibodies available, while apparently vast is nevertheless still very incomplete and frequently of uncertain quality, has stimulated projects with an objective of raising comprehensive, proteome-wide sets of protein binders. With progress in automation and throughput, a remarkable number of recent publications refer to the practical possibility of selecting binders to every protein encoded in the genome. Here we review the requirements of a pipeline of production of protein binders for the human proteome, including target prioritisation, antigen design, 'next generation' methods, databases and the approaches taken by ongoing projects in Europe and the USA. While the task of generating affinity reagents for all human proteins is complex and demanding, the benefits of well-characterised and quality-controlled pan-proteome binder resources for biomedical research, industry and life sciences in general would be enormous and justify the effort. Given the technical, personnel and financial resources needed to fulfil this aim, expansion of current efforts may best be addressed through large-scale international collaboration.
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Affiliation(s)
- Michael J Taussig
- Protein Technology Group, The Babraham Institute, Cambridge, UK; Cambridge Protein Arrays Ltd, Babraham Research Campus, Cambridge, UK
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8
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Pauly F, Smedby KE, Jerkeman M, Hjalgrim H, Ohlsson M, Rosenquist R, Borrebaeck CAK, Wingren C. Identification of B-cell lymphoma subsets by plasma protein profiling using recombinant antibody microarrays. Leuk Res 2014; 38:682-90. [PMID: 24754901 DOI: 10.1016/j.leukres.2014.03.010] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2014] [Revised: 03/13/2014] [Accepted: 03/15/2014] [Indexed: 12/14/2022]
Abstract
B-cell lymphoma (BCL) heterogeneity represents a key issue, often making the classification and clinical management of these patients challenging. In this pilot study, we outlined the first resolved view of BCL disease heterogeneity on the protein level by deciphering disease-associated plasma biomarkers, specific for chronic lymphocytic leukemia, diffuse large B-cell lymphoma, follicular lymphoma, and mantle cell lymphoma, using recombinant antibody microarrays targeting mainly immunoregulatory proteins. The results showed the BCLs to be heterogeneous, and revealed potential novel subgroups of each BCL. In the case of diffuse large B-cell lymphoma, we also indicated a link between the novel subgroups and survival.
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Affiliation(s)
- Frida Pauly
- Department of Immunotechnology, Lund University, Lund, Sweden; CREATE Health, Lund University, Lund, Sweden
| | - Karin E Smedby
- Department of Medicine Solna, Clinical Epidemiology Unit, Karolinska Institutet, Stockholm, Sweden
| | - Mats Jerkeman
- Department of Oncology, Skåne University Hospital, Lund, Sweden
| | - Henrik Hjalgrim
- Department of Epidemiology Research, Statens Serum Institute, Copenhagen, Denmark
| | - Mattias Ohlsson
- Computational Biology & Biological Physics, Department of Astronomy and Theoretical Physics, Lund University, Lund, Sweden; CREATE Health, Lund University, Lund, Sweden
| | - Richard Rosenquist
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Carl A K Borrebaeck
- Department of Immunotechnology, Lund University, Lund, Sweden; CREATE Health, Lund University, Lund, Sweden
| | - Christer Wingren
- Department of Immunotechnology, Lund University, Lund, Sweden; CREATE Health, Lund University, Lund, Sweden.
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9
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Pauly F, Dexlin-Mellby L, Ek S, Ohlin M, Olsson N, Jirström K, Dictor M, Schoenmakers S, Borrebaeck CAK, Wingren C. Protein Expression Profiling of Formalin-Fixed Paraffin-Embedded Tissue Using Recombinant Antibody Microarrays. J Proteome Res 2013; 12:5943-53. [DOI: 10.1021/pr4003245] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Frida Pauly
- Department of Immunotechnology, Lund University, Medicon Village, Lund, Sweden
- CREATE Health, Lund University, Medicon Village, Lund, Sweden
| | - Linda Dexlin-Mellby
- Department of Immunotechnology, Lund University, Medicon Village, Lund, Sweden
- CREATE Health, Lund University, Medicon Village, Lund, Sweden
| | - Sara Ek
- Department of Immunotechnology, Lund University, Medicon Village, Lund, Sweden
- CREATE Health, Lund University, Medicon Village, Lund, Sweden
| | - Mats Ohlin
- Department of Immunotechnology, Lund University, Medicon Village, Lund, Sweden
- CREATE Health, Lund University, Medicon Village, Lund, Sweden
| | - Niclas Olsson
- Department of Immunotechnology, Lund University, Medicon Village, Lund, Sweden
- CREATE Health, Lund University, Medicon Village, Lund, Sweden
| | - Karin Jirström
- Department of Clinical Sciences, Pathology, Lund University, Skåne University Hospital, Lund, Sweden
| | - Michael Dictor
- Department of Clinical Sciences, Pathology, Lund University, Skåne University Hospital, Lund, Sweden
| | | | - Carl A. K. Borrebaeck
- Department of Immunotechnology, Lund University, Medicon Village, Lund, Sweden
- CREATE Health, Lund University, Medicon Village, Lund, Sweden
| | - Christer Wingren
- Department of Immunotechnology, Lund University, Medicon Village, Lund, Sweden
- CREATE Health, Lund University, Medicon Village, Lund, Sweden
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Holm A, Wu W, Lund-Johansen F. Antibody array analysis of labelled proteomes: how should we control specificity? N Biotechnol 2011; 29:578-85. [PMID: 21840428 DOI: 10.1016/j.nbt.2011.07.008] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2011] [Revised: 07/26/2011] [Accepted: 07/27/2011] [Indexed: 11/15/2022]
Abstract
Researchers who use protein binders in multiplexed assays can be divided into two camps. One believes that arrays with proteome-wide coverage will become a reality once we have developed binders for all proteins. The sceptics claim that detection with immobilized protein binders and sample labelling will not provide the required specificity. In this article, we review the evidence showing that antibody array analysis of labelled samples can provide meaningful data and discuss the issues raised by the sceptics. We argue that direct the evidence for monospecificity has yet to be published. This will require assays designed to resolve the proteins captured by each binder. One option is to combine array measurement with protein separation. We have developed an assay where labelled sample proteins are separated by size exclusion chromatography (SEC) before contact with microsphere-based arrays (Size-MAP; size exclusion chromatography-resolved microsphere-based affinity proteomics). The effect is an 'antibody array Western blot' where reactivity of immobilized binders is resolved against the size of the proteins in the sample. We show that Size-MAP is useful to discriminate monospecific- and polyreactive antibodies and for automatic detection of reacting with the same target. The possibility to test specificity directly in array-based measurement should be useful to select the best binders and to determine whether the DNA microarray for the proteome is a realistic goal or not.
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Affiliation(s)
- Anders Holm
- Department of Immunology, Clinic of Specialized Medicine and Surgery Oslo University Hospital, Rikshospitalet, N-0027 Oslo, Norway
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