Recent findings from the human proteome project: opening the mass spectrometry toolbox to advance cancer diagnosis, surveillance and treatment

Abstract

The Human Proteome Project stands to eclipse the Human Genome Project in terms of scope, content and interpretation. Its outputs, in conjunction with recent developments across the proteomics community, provide new tools for cancer research with the potential of providing clinically relevant insights into the disease. These collectively may guide the development of future diagnosis, surveillance and treatment strategies. Having established a robust organizational framework within the international community, the Human Proteome Organization and the proteomics community at large have made significant advances in biomarker discovery, detection, molecular imaging and in exploring tumor heterogeneity. Here, the authors discuss some developments in cancer proteomics and how they can be implemented to reduce the global burden of the disease.

Keywords:

• biology
• cancer
• disease
• human proteome project
• proteomics

Financial & competing interests disclosure

This article was undertaken as part of the HUPO Biology and Disease Human Proteome Project as a Cancer HPP project. The authors have no other relevant affiliations or financial involvement with any organization or entity with a financial interest in or financial conflict with the subject matter or materials discussed in the manuscript apart from those disclosed.

Key issues

• Human proteome organization is an established, international proteomics community that has created a framework by which cancer researchers can provide translatable and reproducible insight into cancer biology under the auspices and standards of the Human Cancer Proteome Project.

• Reproducible determination of biomarker presence and concentration is now possible from resected tissue specimens as well as from feces or depleted patient plasma and urine samples.

• Selected reaction monitoring assay coordinates or any other relevant proteomic information regarding novel or established biomarkers must be deposited in a cancer-specific section of publicly accessible databases such as SRMAtlas for the field to reach its full potential.

• IMS is a growing field that represents tissue specimens in terms of overlapping molecular signatures, providing multiplexed visual representations of biomarker expression and their spatial distributions.

• The ideal of ’personalized medicine’ in cancer treatment requires accurate and comprehensive insight into the cellular composition and biomarker profile of a particular tumor, which may be afforded though the application of laser ablation inductively coupled plasma MS to clinical tissue biopsies.

• IMS can be employed for the multiplexed identification and characterization of cancer tissue specimens in a way that is supported by standard pathology.

• Both inter- and intra-tumoral heterogeneity remains a key problem in cancer treatment and research, requiring the development and adoption of uniform molecular phenotype classification systems.

• Proteomics is a field of molecular biology whose applications are continuing to expand and diversify, particularly as technological improvements allow the field to investigate new biological questions.

Notes