Mass Spectrometry-Based Protein Biomarker Discovery in Pancreatic Cancer

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Mass Spectrometry-Based Protein Biomarker Discovery in Pancreatic Cancer. / Zhou, Qimin.

Lund : Lund University, Faculty of Medicine, 2020. 84 s.

Forskningsoutput: AvhandlingDoktorsavhandling (sammanläggning)

Harvard

Zhou, Q 2020, 'Mass Spectrometry-Based Protein Biomarker Discovery in Pancreatic Cancer', Doktor, Institutionen för kliniska vetenskaper, Lund, Lund.

APA

Zhou, Q. (2020). Mass Spectrometry-Based Protein Biomarker Discovery in Pancreatic Cancer. Lund: Lund University, Faculty of Medicine.

CBE

Zhou Q. 2020. Mass Spectrometry-Based Protein Biomarker Discovery in Pancreatic Cancer. Lund: Lund University, Faculty of Medicine. 84 s.

MLA

Vancouver

Zhou Q. Mass Spectrometry-Based Protein Biomarker Discovery in Pancreatic Cancer. Lund: Lund University, Faculty of Medicine, 2020. 84 s. (Lund University, Faculty of Medicine Doctoral Dissertation Series; 2020:47).

Author

Zhou, Qimin. / Mass Spectrometry-Based Protein Biomarker Discovery in Pancreatic Cancer. Lund : Lund University, Faculty of Medicine, 2020. 84 s.

RIS

TY - THES

T1 - Mass Spectrometry-Based Protein Biomarker Discovery in Pancreatic Cancer

AU - Zhou, Qimin

N1 - Defense details Date: 2020-04-28 Time: 13:00 Place: Föreläsningssal 3, Centralblocket, Entrégatan 7, Skånes Universitetssjukhus i Lund External reviewer (s) Name: Sund, Malin Title: Professor Affiliation: Department of Surgical and Perioperative Sciences, Umeå University, Umeå, Sweden

PY - 2020

Y1 - 2020

N2 - Background: Pancreatic cancer has the lowest survival rate among all the major cancer types. Although recent decades have seen advances in diagnostic imaging, surgical techniques, perioperative care and oncological treatment, this has not been translated into major improvements in clinical outcome. The 5-year survival rate remains less than 10% for all stages. One important unmet clinical need is biomarkers of clinical utility that can be used for early detection, prognostication and guidance of treatment.Aim: The aim of this thesis was to develop and validate protein biomarkers for diagnosis, prognosis and prediction of treatment response in pancreatic cancer.Methods: Mass spectrometry (MS)-based proteomic profiling of fresh frozen tissue specimens from pancreatic cancer patients and control subjects was conducted to identify potential protein biomarkers. These were subsequently verified by targeted proteomics (parallel reaction monitoring (PRM)) and bioinformatic analysis. Selected biomarker candidates were further validated in larger patient cohorts by tissue microarray-based immunohistochemistry studies, serum immunoassay measurements and in vitro experiments.Results/conclusions:(I) A proteolytic digestion protocol was optimised for MS-based proteomics studies. Urea in-solution digestion at room temperature (24 ± 2 °C) was found to be superior to traditional proteolysis at 37 °C, presenting several advantages such as fewer experimentally-induced post-translational modifications (carbamylation and pyroglutamic acid modifications), increased identification of peptides and proteins, and improved protein quantification by reducing coefficients of variations.(II) Some 165 potential protein biomarkers were identified in pancreatic cancer tissues and a panel of 45 biomarker candidates was verified by targeted MS. The novel protein BASP1 was significantly associated with favourable survival and positive response to adjuvant chemotherapy in pancreatic cancer patients. Bioinformatic analysis indicated that BASP1 interacts with Wilms tumour protein WT1. Patients with negative BASP1 and high WT1 expression had the poorest outcomes.(III) Prognostic analysis of YAP1 demonstrated a significant correlation with lower survival, at both mRNA expression levels (TCGA cohort) and protein expression levels (Lund cohort). Inhibiting the YAP1/TEAD interaction interfered with the expression of AREG, CTGF, CYR61 and MSLN in pancreatic cancer cells, which suggests that YAP1 transcriptional activity may affect the evolution and persistence of a fibrotic tumour microenvironment.(IV) Expression of AGP1 in pancreatic cancer tissues is significantly correlated with poor survival. Circulating levels of AGP1 and CA 19-9 yielded a high diagnostic accuracy (AUC 0.963) for discrimination of resectable pancreatic cancer patients against healthy controls.

AB - Background: Pancreatic cancer has the lowest survival rate among all the major cancer types. Although recent decades have seen advances in diagnostic imaging, surgical techniques, perioperative care and oncological treatment, this has not been translated into major improvements in clinical outcome. The 5-year survival rate remains less than 10% for all stages. One important unmet clinical need is biomarkers of clinical utility that can be used for early detection, prognostication and guidance of treatment.Aim: The aim of this thesis was to develop and validate protein biomarkers for diagnosis, prognosis and prediction of treatment response in pancreatic cancer.Methods: Mass spectrometry (MS)-based proteomic profiling of fresh frozen tissue specimens from pancreatic cancer patients and control subjects was conducted to identify potential protein biomarkers. These were subsequently verified by targeted proteomics (parallel reaction monitoring (PRM)) and bioinformatic analysis. Selected biomarker candidates were further validated in larger patient cohorts by tissue microarray-based immunohistochemistry studies, serum immunoassay measurements and in vitro experiments.Results/conclusions:(I) A proteolytic digestion protocol was optimised for MS-based proteomics studies. Urea in-solution digestion at room temperature (24 ± 2 °C) was found to be superior to traditional proteolysis at 37 °C, presenting several advantages such as fewer experimentally-induced post-translational modifications (carbamylation and pyroglutamic acid modifications), increased identification of peptides and proteins, and improved protein quantification by reducing coefficients of variations.(II) Some 165 potential protein biomarkers were identified in pancreatic cancer tissues and a panel of 45 biomarker candidates was verified by targeted MS. The novel protein BASP1 was significantly associated with favourable survival and positive response to adjuvant chemotherapy in pancreatic cancer patients. Bioinformatic analysis indicated that BASP1 interacts with Wilms tumour protein WT1. Patients with negative BASP1 and high WT1 expression had the poorest outcomes.(III) Prognostic analysis of YAP1 demonstrated a significant correlation with lower survival, at both mRNA expression levels (TCGA cohort) and protein expression levels (Lund cohort). Inhibiting the YAP1/TEAD interaction interfered with the expression of AREG, CTGF, CYR61 and MSLN in pancreatic cancer cells, which suggests that YAP1 transcriptional activity may affect the evolution and persistence of a fibrotic tumour microenvironment.(IV) Expression of AGP1 in pancreatic cancer tissues is significantly correlated with poor survival. Circulating levels of AGP1 and CA 19-9 yielded a high diagnostic accuracy (AUC 0.963) for discrimination of resectable pancreatic cancer patients against healthy controls.

KW - pancreatic cancer

KW - proteomics

KW - mass spectrometry

KW - biomarkers

KW - diagnosis

KW - prognosis

KW - prediction

KW - BASP1

KW - WT1

KW - YAP1

KW - AGP1

M3 - Doctoral Thesis (compilation)

SN - 978-91-7619-908-4

T3 - Lund University, Faculty of Medicine Doctoral Dissertation Series

PB - Lund University, Faculty of Medicine

CY - Lund

ER -