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  • Review Article
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Antibody-based proteomics: fast-tracking molecular diagnostics in oncology

Nature Reviews Cancer volume 10, pages 605–617 (2010)Cite this article

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An Author Correction to this article was published on 24 March 2022

This article has been updated

Key Points

  • Personalization of cancer therapy requires the identification of unambiguous diagnostic, prognostic and predictive biomarkers to facilitate the accurate stratification of patients and the monitoring of responses to targeted therapies.

  • The systematic generation and validation of specific antibodies offers a high-throughput mechanism for the functional exploration of the proteome and a logical approach for fast-tracking the translation of identified biomarkers.

  • Multiple approaches exist, each with specific characteristics and advantages that are suitable for a wide range of applications, which capitalize on the inherent specificity and sensitivity of antibodies as affinity reagents.

  • The integration of antibody-based approaches with existing genomic and transcriptomic methods offers huge potential, and the clinical implementation of new high-throughput antibody-based approaches will depend on the integration of data across various platforms.

  • The clinical application of new antibody-based assays demonstrates their utility as accurate, sensitive and robust diagnostic and prognostic tests and has led to the development of a new approach, known as pathway diagnostics, which is likely to have a crucial role in the design of future molecular therapeutic trials.

Abstract

The effective implementation of personalized cancer therapeutic regimens depends on the successful identification and translation of informative biomarkers to aid clinical decision making. Antibody-based proteomics occupies a pivotal space in the cancer biomarker discovery and validation pipeline, facilitating the high-throughput evaluation of candidate markers. Although the clinical utility of these emerging technologies remains to be established, the traditional use of antibodies as affinity reagents in clinical diagnostic and predictive assays suggests that the rapid translation of such approaches is an achievable goal. Furthermore, in combination with, or as alternatives to, genomic and transcriptomic methods for patient stratification, antibody-based proteomics approaches offer the promise of additional insight into cancer disease states. In this Review, we discuss the current status of antibody-based proteomics and its contribution to the development of new assays that are crucial for the realization of individualized cancer therapy.

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Figure 1: Automated quantification of protein expression using immunohistochemistry and immunofluorescence.
Figure 2: Antibody-based proteomics and personalized cancer medicine.
Figure 3: Translating antibody-based assays into the clinic.

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Acknowledgements

The authors wish to acknowledge funding from Enterprise Ireland, the Health Research Board of Ireland (Programme Grant: Breast Cancer Metastasis: Biomarkers and Functional Mediators and a HRB Career Development Fellowship awarded to D.P.O'C.), the European Commission (in the context of the Marie Curie Industry-Academic Partnership and Pathways programme, Target-Melanoma), Science Foundation Ireland (in the context of the Strategic Research Cluster, Molecular Therapeutics for Cancer Ireland) and the Knut and Alice Wallenberg Foundation. The UCD Conway Institute is funded by the Programme for Research in Third Level Institutions, as administered by the Higher Education Authority of Ireland.

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Author notes

  1. Donal J. Brennan and Darran P. O'Connor: These authors contributed equally to this work.

Authors and Affiliations

  1. UCD School of Biomolecular and Biomedical Science, UCD Conway Institute, University College Dublin, Belfield, 4, Dublin, Ireland

    Donal J. Brennan, Darran P. O'Connor, Elton Rexhepaj & William M. Gallagher

  2. Department of Genetics and Pathology, Rudbeck Laboratory, Uppsala University, Uppsala, SE-751 85, Sweden

    Fredrik Ponten

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Correspondence to William M. Gallagher.

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D.J.B., E.R. and W.M.G. are co-inventors of a pending patent application relating to automated image analysis in oncology.

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DATABASES

National Cancer Institute Drug Dictionary

bevacizumab

erlotinib

fluorouracil

gefitinib

imatinib

irinotecan

leucovorin

pazopanib

PLX4032

sorafenib

Pathway Interaction Database 

AKT

EGFR

ERK

PTEN

STAT3

FURTHER INFORMATION

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CPTAC

Human Protein Atlas

Glossary

Reverse phase protein array

RPPA. Protein lysate dot blot in a high-density format on a solid surface that allows for multiple samples to be probed with the same antibody, or other affinity reagent, simultaneously.

Two-dimensional electrophoresis

2DE. Gel-based technique for the separation of proteins by isoelectric point in the first dimension (achieved by isoelectric focusing), followed by mass in the second dimension (achieved by SDS–PAGE). A higher resolution of protein separation is achieved compared with single dimension approaches.

Multi-dimensional liquid chromatography

Chomatographic separation in at least two dimensions, for example, reverse-phase chromatography followed by ion-exchange chromatography. Using additional dimensions increases the resolution of separation.

Tandem mass spectrometry

Often referred to as MS/MS, it uses two linked mass spectrometers to measure small amounts of proteins. Analytes are separated according to their mass and charge, with samples sorted and weighed in the first mass spectrometer, then fragmented in a collision cell, and fragments sorted and weighed in the second mass spectrometer.

Epitope mapping

Systematic identification and characterization of the minimum recognition domain for antibodies.

Sandwich-based assay

Antigen detection using surface-bound capture antibodies, followed by the application of the sample and subsequent detection using a second antibody raised against an alternative epitope on the same target protein.

Unsupervised analysis

A form of gene expression analysis that involves the discovery of empirical structure (patterns) in a given data set without taking into account any prior knowledge of the underlying biology. Gene expression patterns that are discovered in this manner should be unbiased.

Retrospective cohort

A study in which the medical records and possibly also the previous tissue specimens of groups of patients with a specific diagnosis (for example, breast cancer) are collected.

Prospective trial

A trial in which the participants or patients are identified, followed over time and the effects of different conditions on their eventual outcome are measured.

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Brennan, D., O'Connor, D., Rexhepaj, E. et al. Antibody-based proteomics: fast-tracking molecular diagnostics in oncology. Nat Rev Cancer 10, 605–617 (2010). https://doi.org/10.1038/nrc2902

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