Proteomic Biomarker Discovery: Review of the Science and Its Challenges with Clinical Samples
T. Hussain *
University of Hull-Hull, York Medical School and Hull and East Yorkshire Hospitals, NHS Trust, Castle Hill Hospital, Hull, UK.
L. Scaife
Postgraduate Medical Institute of the University of Hull, Hull York Medical School, Hull, UK.
V. Hodgkinson
Postgraduate Medical Institute of the University of Hull, Hull York Medical School, Hull, UK.
J. P. Kneeshaw
Breast Unit, Hull and East Yorkshire Hospitals NHS Trust, Hull, UK.
M. Lind
Postgraduate Medical Institute of the University of Hull, Hull York Medical School, Hull, UK and Queens Centre for Oncology and Haematology, Hull and East Yorkshire Hospitals NHS Trust, Hull, UK.
P. Drew
Postgraduate Medical Institute of the University of Hull, Hull York Medical School, Hull, UK.
L. Cawkwell
Postgraduate Medical Institute of the University of Hull, Hull York Medical School, Hull, UK.
*Author to whom correspondence should be addressed.
Abstract
Proteomics is a science that facilitates global analysis of protein expression, molecular interactions and functional states of protein in a cell, organ or organism under consideration. Protein at the molecular level represents the biological endpoint and therefore more suitable to assess cellular responses. Proteins biomarkers are routinely used in cancers for different purposes such as diagnosis, screening and predicting therapy responses. Proteomic science utilise both cell line models and clinical samples to make novel discoveries. Compared to cell lines, clinical samples provide more accurate representation of the tumour micro-environment, explore and identify stromal molecular targets. However, using clinical samples for biomarker discovery has its own challenges. In this review, we aim to provide clinicians an overview of the proteomic biomarker discovery pathway, examine the use of different clinical samples in proteomic research and highlight the limitations and challenges of using clinical samples with proteomic methods.
Keywords: Genomics, transcriptomics, proteomics, biomarker, tumour samples.