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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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Multiplex profiling of serum proteins in solution using barcoded antibody fragments and next generation sequencing. Commun Biol 2020; 3:339. [PMID: 32620783 PMCID: PMC7334203 DOI: 10.1038/s42003-020-1068-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Accepted: 06/11/2020] [Indexed: 12/27/2022] Open
Abstract
The composition of serum proteins is reflecting the current health status and can, with the right tools, be used to detect early signs of disease, such as an emerging cancer. An earlier diagnosis of cancer would greatly increase the chance of an improved outcome for the patients. However, there is still an unmet need for proficient tools to decipher the information in the blood proteome, which calls for further technological development. Here, we present a proof-of-concept study that demonstrates an alternative approach for multiplexed protein profiling of serum samples in solution, using DNA barcoded scFv antibody fragments and next generation sequencing. The outcome shows high accuracy when discriminating samples derived from pancreatic cancer patients and healthy controls and represents a scalable alternative for serum analysis. Brofelth, Ekstrand et al use DNA barcoded scFv antibody fragments and next generation sequencing for multiplex profiling of proteins in serum from pancreatic cancer patients with high accuracy. This approach can potentially be used in high throughput precision diagnosis.
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Starr AE, Deeke SA, Li L, Zhang X, Daoud R, Ryan J, Ning Z, Cheng K, Nguyen LVH, Abou-Samra E, Lavallée-Adam M, Figeys D. Proteomic and Metaproteomic Approaches to Understand Host–Microbe Interactions. Anal Chem 2017; 90:86-109. [DOI: 10.1021/acs.analchem.7b04340] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Amanda E. Starr
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada
| | - Shelley A. Deeke
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada
| | - Leyuan Li
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada
| | - Xu Zhang
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada
| | - Rachid Daoud
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada
| | - James Ryan
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada
| | - Zhibin Ning
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada
| | - Kai Cheng
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada
| | - Linh V. H. Nguyen
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada
| | - Elias Abou-Samra
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada
| | - Mathieu Lavallée-Adam
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada
| | - Daniel Figeys
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada
- Molecular Architecture of Life Program, Canadian Institute for Advanced Research, Toronto, Ontario, M5G 1M1, Canada
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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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5
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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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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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8
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Intachai K, Singboottra P, Leksawasdi N, Kasinrerk W, Tayapiwatana C, Butr-Indr B. Enhanced Production of Functional Extracellular Single Chain Variable Fragment Against HIV-1 Matrix Protein fromEscherichia coliby Sequential Simplex Optimization. Prep Biochem Biotechnol 2014; 45:56-68. [DOI: 10.1080/10826068.2014.887580] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
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9
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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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