Final Report Summary - TRANSBIOBC (Translation of novel Biomarkers for Bladder Cancer for clinical outcome prediction)
Executive Summary:
Currently, clinical diagnosis and monitoring of urinary bladder cancer (UBC) relies on invasive, highly costly cystoscopy. Additionally, due to high recurrence rates, UBC treatment is associated with frequent follow-up of patients, making it one of the most costly types of cancer in terms of management cost. The TransBioBC project was based on the identification of novel biomarkers (BM) for UBC detection in urine and powerful technological platforms (capillary electrophoresis mass spectrometry; CE-MS and micro-capillary ELISA; mELISA), as extensive foreground work of the involved partners in the framework of FP7 EU projects DECanBio and GENINCA. The objective of TransBioBC was to translate this foreground into valuable products and to specifically employ the involved technologies (CE-MS and micro-ELISA), represented by the participating SMEs (MOS, DS), for the development of non-invasive urine tests for routine monitoring of UBC. The experimental workflow included:
a) Assuring platform and assay analytical performance according to regulatory guidelines,
b) Analysis of well characterized clinical samples from existing sufficiently powered UBC cohorts in a two-phase approach (phase I: targeting definition of optimized BM combinations for the specific contexts of use; and phase II: validation of the latter in existing prospectively collected urine samples);
c) Development of database platforms integrating biomarker and clinical information;
d) Thorough analysis of the biomarker added value;
e) Development of a prototype kit for quantification in urine of the optimal UBC biomarker (s);
f) Biomarker multi-stakeholder dissemination and exploitation plans.
Tested biomarkers included peptide biomarker profiles defined by CE-MS (Theodorescu et al., Lancet Oncol 7, 230, 2006), as well as proteins associated with UBC based on high resolution mass spectrometry analysis of urine, including SPARC (Secreted Protein Acidic and Rich in Cysteine), profilin 1, histone 2B (Frantzi et al., J Proteome Res. 12, 3969 2013, Zoidakis et al, Mol Cell Proteomics;11(4):M111.009449 2012). Following collection of proper ethics approvals, extensive analytical performance analysis indicated interference of ELISA assays by urine matrix for the vast majority of tested biomarkers, with the main exceptions of SPARC (ELISA; PLOS One, 11(2):e0149471, 2016) and vitamin D binding protein (VDBP; micro-ELISA). Further quantification of SPARC (BRFAA) in the prospectively collected ISBLaC study (CNIO) (n=488), supported the marker discriminatory potential for mainly invasive UBC and an association with tumor relapse. Nevertheless, hematuria was found as a cofounder for biomarker measurements. Similarly, results from micro-ELISA also provided discrimination for UBC, nevertheless at sub-optimal diagnostic rates. Based on these technical difficulties encountered with ELISA, mass spectrometry based assays (multiple reaction monitoring-MRM) were developed for the quantification of these UBC protein biomarkers. MRM assays were found to exhibit superior performance in comparison to ELISA, being impacted to a lower extent by hematuria, nevertheless measurements of SPARC, NMP22 (Nuclear Matrix Protein 22), profilin1 and VASP (Vasodilator-Stimulated Phosphoprotein) in the ISBLaC cohort provided overall lower diagnostic accuracies in comparison to the CE-MS peptides.
In parallel, 1433 urine samples from various clinical centres were analysed using CE-MS in Phase I, and 712 in Phase II. The former included a discovery and test set to refine previously described biomarkers for specific use in primary diagnosis and detection of tumor relapse. Support vector machine models based on 116 (primary diagnosis) and 106 (tumor relapse) peptides provided AUC of 0.87 (n=270, test set) and 0.75 (n=211, test set), respectively. The peptide biomarkers outperformed cytology, providing complementary information to the latter (combination of both tests resulted in an AUC of 0.90; Frantzi et al., Clin Cancer Res. 22, 4077, 2016).
Further validation of these optimal classifiers was performed in a phase II study involving blinded analysis by CE-MS of a total of 712 samples from prospectively collected samples – (Radboud University Nijmegen (Netherlands) and University of Barcelona (Spain). Based on the results, a prototype kit for the measurement of the CE-MS UBC biomarkers was developed including detailed manuals for use and distributed to collaborating clinical centers. In parallel, besides the highly ranked publication in Clinical Cancer Research, results were disseminated to the scientific community via presentations to relevant meetings as well as by contacting patient groups, and by generating and distributing TransBioBC flyers. Contacts with pharma companies were established, currently addressing potential use of the TransBioBC markers in clinical trials. Health economic calculations were performed suggesting the cost-effectiveness of the biomarkers in UBC management.
TransBioBC enabled the establishment of a novel non-invasive approach for UBC detection especially during UBC surveillance with anticipated positive impact on UBC management. In addition, acquired know-how (on MRM assays, data management) open new avenues in biomarker research for UBC and other diseases alike.
Project Context and Objectives:
please see attached
Project Results:
please see attached
Potential Impact:
please see attached
List of Websites:
http://transbiobc.org/
Currently, clinical diagnosis and monitoring of urinary bladder cancer (UBC) relies on invasive, highly costly cystoscopy. Additionally, due to high recurrence rates, UBC treatment is associated with frequent follow-up of patients, making it one of the most costly types of cancer in terms of management cost. The TransBioBC project was based on the identification of novel biomarkers (BM) for UBC detection in urine and powerful technological platforms (capillary electrophoresis mass spectrometry; CE-MS and micro-capillary ELISA; mELISA), as extensive foreground work of the involved partners in the framework of FP7 EU projects DECanBio and GENINCA. The objective of TransBioBC was to translate this foreground into valuable products and to specifically employ the involved technologies (CE-MS and micro-ELISA), represented by the participating SMEs (MOS, DS), for the development of non-invasive urine tests for routine monitoring of UBC. The experimental workflow included:
a) Assuring platform and assay analytical performance according to regulatory guidelines,
b) Analysis of well characterized clinical samples from existing sufficiently powered UBC cohorts in a two-phase approach (phase I: targeting definition of optimized BM combinations for the specific contexts of use; and phase II: validation of the latter in existing prospectively collected urine samples);
c) Development of database platforms integrating biomarker and clinical information;
d) Thorough analysis of the biomarker added value;
e) Development of a prototype kit for quantification in urine of the optimal UBC biomarker (s);
f) Biomarker multi-stakeholder dissemination and exploitation plans.
Tested biomarkers included peptide biomarker profiles defined by CE-MS (Theodorescu et al., Lancet Oncol 7, 230, 2006), as well as proteins associated with UBC based on high resolution mass spectrometry analysis of urine, including SPARC (Secreted Protein Acidic and Rich in Cysteine), profilin 1, histone 2B (Frantzi et al., J Proteome Res. 12, 3969 2013, Zoidakis et al, Mol Cell Proteomics;11(4):M111.009449 2012). Following collection of proper ethics approvals, extensive analytical performance analysis indicated interference of ELISA assays by urine matrix for the vast majority of tested biomarkers, with the main exceptions of SPARC (ELISA; PLOS One, 11(2):e0149471, 2016) and vitamin D binding protein (VDBP; micro-ELISA). Further quantification of SPARC (BRFAA) in the prospectively collected ISBLaC study (CNIO) (n=488), supported the marker discriminatory potential for mainly invasive UBC and an association with tumor relapse. Nevertheless, hematuria was found as a cofounder for biomarker measurements. Similarly, results from micro-ELISA also provided discrimination for UBC, nevertheless at sub-optimal diagnostic rates. Based on these technical difficulties encountered with ELISA, mass spectrometry based assays (multiple reaction monitoring-MRM) were developed for the quantification of these UBC protein biomarkers. MRM assays were found to exhibit superior performance in comparison to ELISA, being impacted to a lower extent by hematuria, nevertheless measurements of SPARC, NMP22 (Nuclear Matrix Protein 22), profilin1 and VASP (Vasodilator-Stimulated Phosphoprotein) in the ISBLaC cohort provided overall lower diagnostic accuracies in comparison to the CE-MS peptides.
In parallel, 1433 urine samples from various clinical centres were analysed using CE-MS in Phase I, and 712 in Phase II. The former included a discovery and test set to refine previously described biomarkers for specific use in primary diagnosis and detection of tumor relapse. Support vector machine models based on 116 (primary diagnosis) and 106 (tumor relapse) peptides provided AUC of 0.87 (n=270, test set) and 0.75 (n=211, test set), respectively. The peptide biomarkers outperformed cytology, providing complementary information to the latter (combination of both tests resulted in an AUC of 0.90; Frantzi et al., Clin Cancer Res. 22, 4077, 2016).
Further validation of these optimal classifiers was performed in a phase II study involving blinded analysis by CE-MS of a total of 712 samples from prospectively collected samples – (Radboud University Nijmegen (Netherlands) and University of Barcelona (Spain). Based on the results, a prototype kit for the measurement of the CE-MS UBC biomarkers was developed including detailed manuals for use and distributed to collaborating clinical centers. In parallel, besides the highly ranked publication in Clinical Cancer Research, results were disseminated to the scientific community via presentations to relevant meetings as well as by contacting patient groups, and by generating and distributing TransBioBC flyers. Contacts with pharma companies were established, currently addressing potential use of the TransBioBC markers in clinical trials. Health economic calculations were performed suggesting the cost-effectiveness of the biomarkers in UBC management.
TransBioBC enabled the establishment of a novel non-invasive approach for UBC detection especially during UBC surveillance with anticipated positive impact on UBC management. In addition, acquired know-how (on MRM assays, data management) open new avenues in biomarker research for UBC and other diseases alike.
Project Context and Objectives:
please see attached
Project Results:
please see attached
Potential Impact:
please see attached
List of Websites:
http://transbiobc.org/
