A Technical Assessment of the Utility of Reverse Phase Protein Arrays for the Study of the Functional Proteome in Non-microdissected Human Breast Cancers
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Discussion
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Implication
Validation study demonstrates reliable functional proteome profiling by reverse phase protein arrays in non-microdissected breast cancer, highlighting clinical utility for prognostic classification.
Key Points
- To assess the analytical robustness, stability, and clinical utility of reverse phase protein arrays (RPPA) for profiling the functional proteome in non-microdissected human breast tumors.
- Validated 82 antibodies recognizing kinase and steroid signaling proteins for RPPA, assessing intraslide and interslide coefficients of variability.
- Tested pre-analytical stability of functional proteomic fingerprints in resected tumor samples kept at room temperature for up to 24 hours before freezing.
- Assessed intratumoral versus intertumoral heterogeneity and classified 128 non-microdissected breast cancer specimens to compare RPPA with immunohistochemistry and transcriptomic profiling.
- Intraslide and interslide coefficients of variability were <15%, and while 21 of 82 proteins exhibited time-dependent instability between 6 and 24 hours, overall proteomic fingerprints remained robust across 24 hours at room temperature.
- Intratumoral protein expression variability was markedly lower than intertumoral variability, allowing reproducible and accurate prediction of patient outcomes from multiple tumor sites.
- RPPA exhibited superior dynamic range compared to immunohistochemistry and classified 128 breast cancers into six distinct prognostic subgroups that correlated significantly with transcriptional subtypes.
Cite This Study
Hennessy et al. (2010) studied this question.