Shreeve, Rebecca Louise (2015) Exploring complementary proteomic approaches for biomarker discovery in renal cell carcinoma. PhD thesis, University of Leeds.
Abstract
Renal cell carcinoma (RCC) is one of the top ten most common malignancies worldwide. The field of clinical proteomics has seen successes in recent years, and advancements in technology is making ever more possible the ability to answer clinical questions. This study used proteomics to investigate two key clinical questions in RCC biology. Firstly, two comparative studies were performed to investigate biomarkers that may predict response to sunitinib, the predominant drug used to treat metastatic RCC. Serum (12 patients) and FFPE tissue (16 patients) samples from sunitinib responding and non-responding patients were analysed by liquid chromatography-tandem mass spectrometry (LC-MS/MS), to discover novel markers of response. Two candidate biomarkers were initially validated using Western blot or immunohistochemistry. Two serum (IGFBP5, CDH1) and two FFPE tissue (CD70, hCAP18) proteins were identified as promising candidate biomarkers, initial validation of CD70 and hCAP18 was performed. Secondly, furthering the understanding of RCC biology may improve rational drug design and biomarker identification. Five cell lines carrying mutations of VHL, the predominant tumour suppressor gene in RCC, were compared to investigate the proteomic impact of VHL mutation. The scaffold protein IRS2 was identified as highly expressed in the absence of VHL, and this protein was initially validated by Western blot in in vitro cell lines. The techniques used in this study revealed logical biological alterations, of which three proteins were validated using an independent technique. Further validation of the identified proteins is on-going, with the hope that they may impact upon patient care. The advantages and disadvantages of the proteomic analysis of serum, FFPE tissue, and in vitro cell lines is discussed.
Metadata
Supervisors: | Banks, Roz and Vasudev, Naveen and Zougman, Alexandre and Selby, Peter |
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Keywords: | Renal Cell Carcinoma, biomarker, mass spectrometry, cancer, predictive, sunitinib, baseline, longitudinal, FFPE |
Awarding institution: | University of Leeds |
Academic Units: | The University of Leeds > Faculty of Medicine and Health (Leeds) The University of Leeds > Faculty of Medicine and Health (Leeds) > Institute of Molecular Medicine (LIMM) (Leeds) |
Identification Number/EthosID: | uk.bl.ethos.677290 |
Depositing User: | Miss Rebecca Louise Shreeve |
Date Deposited: | 04 Jan 2016 13:26 |
Last Modified: | 25 Mar 2021 16:45 |
Open Archives Initiative ID (OAI ID): | oai:etheses.whiterose.ac.uk:11120 |
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Supplementary Material
Filename: S1. Dot plots_Longitudinal serum.pdf
Description: S1_supplementary data: Longitudinal dot plots
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Supplementary Material
Filename: S2. Proteingroups_Longitudinal serum.xlsx
Description: S2_supplementary data: longitudinal serum protein groups
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Supplementary Material
Filename: S3. Stat analysis_Longitudinal serum.xls
Description: S3_supplementary data: longitudinal serum stat analysis
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Supplementary Material
Filename: S4. Dot plots_Baseline_serum.pdf
Description: S4_supp data: baseline serum dot plots
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Supplementary Material
Filename: S5. ProteinGroups_Baseline_serum.xlsx
Description: S5_supp data: baseline serum protein groups
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Supplementary Material
Filename: S6. Stat analysis_Baseline_serum.xls
Description: S6_supp data: baseline serum stat analysis
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Supplementary Material
Filename: S7. Protein groups_VHL plus minus.xlsx
Description: S7_supp data: VHL plus minus protein groups
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Supplementary Material
Filename: S8. Protein groups_IRS2 immunoprecipitation.xlsx
Description: S8_supp data: immunoprecipitation protein groups
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Supplementary Material
Filename: S9. Dot plots_VHL disease subtypes.pdf
Description: S9_supp data: VHL subtypes dot plots
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Supplementary Material
Filename: S10. Protein groups_VHL disease subtypes.xls
Description: S10_supp data: VHL subtypes protein groups
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Supplementary Material
Filename: S11. Stat analysis_VHL disease subtypes.xls
Description: S11_supp data: VHL subtype stat analysis
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Supplementary Material
Filename: S12. Dot plots_FFPE.pdf
Description: S12_supp data: FFPE dot plots
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Supplementary Material
Filename: S13. Protein groups_FFPE.xlsx
Description: S13_supp data: FFPE protein groups
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Supplementary Material
Filename: S14. Stat analysis_FFPE.xls
Description: S14_supp data: FFPE stat analysis
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Supplementary Material
Filename: Supplementary data files.docx
Description: Overview of supplementary file names
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