Characterization of anticancer drug resistance by reverse-phase protein array: new targets and strategies

ABSTRACT

Introduction

Drug resistance is the main barrier to achieving cancer cures with medical therapy. Cancer drug resistance occurs, in part, due to adaptation of the tumor and microenvironment to therapeutic stress at a proteomic level. Reverse-phase protein arrays (RPPA) are well suited to proteomic analysis of drug resistance due to high sample throughput, sensitive detection of phosphoproteins, and validation for a large number of critical cellular pathways.

Areas covered

This review summarizes contributions of RPPA to understanding and combating drug resistance. In particular, contributions of RPPA to understanding resistance to PARP inhibitors, BRAF inhibitors, immune checkpoint inhibitors, and breast cancer investigational therapies are discussed. Articles reviewed were identified by MEDLINE, Scopus, and Cochrane search for keywords ‘proteomics,’ ‘reverse-phase protein array,’ ‘drug resistance,’ ‘PARP inhibitor,’ ‘BRAF inhibitor,’ ‘immune checkpoint inhibitor,’ and ‘I-SPY’ spanning October 1, 1960 – October 1, 2021.

Expert opinion

Precision oncology has thus far failed to convert the armament of targeted therapies into durable responses for most patients, highlighting that genetic sequencing alone is insufficient to guide therapy selection and overcome drug resistance. Combined genomic and proteomic analyses paired with creative drug combinations and dosing strategies hold promise for maturing precision oncology into an era of improved patient outcomes.

KEYWORDS:

• Proteomics
• reverse-phase protein array
• RPPA
• drug resistance
• adaptive resistance
• precision oncology
• PARP inhibitor
• BRAF inhibitor
• immune checkpoint inhibitor

Article highlights

• Reverse-phase protein arrays (RPPA) have enabled the high-throughput measurement of expression and post-translational modification of up to 500 proteins of high biological and clinical significance in low-volume samples including serum, plasma, and lysates from cultured cells, fine need aspirates, fresh tissue, frozen tissue, formalin-fixed paraffin-embedded tissue, and laser capture microdissected specimens.

• RPPA has been applied in the pre-clinical setting to generate hypotheses regarding mechanisms of drug resistance and strategies to overcome drug resistance that have subsequently been validated in clinical trials. Notable examples include combination PARP inhibition and PI3K pathway inhibition to impart sensitivity to PARP inhibitors in the BRCA-wildtype setting, and combination BRAF inhibition and mTOR pathway inhibition to restore sensitivity to BRAF inhibitors in heavily pretreated patients with BRAF-mutant tumors. Newer areas of RPPA investigation include resistance to targeted breast cancer therapies and immune checkpoint inhibitors, with clinical trials designed to overcome drug resistance in these settings both underway and expected soon.

• RPPA has been applied directly in the clinical setting to identify potential biomarkers in completed and ongoing window of opportunity clinical trials and adaptive clinical trials. In this setting, RPPA is used to analyze pre- and on-treatment patient biopsy specimens to characterize the molecular underpinnings of differential patient response to treatment.

• Genomic analyses alone have thus far been limited in their ability to describe and predict patient responses to targeted therapy. Genomic analyses have been demonstrated to poorly characterize intracellular protein levels and activities, making proteomics a critical companion to genomics in the goal to understand and devise new strategies to overcome cancer drug resistance.

Declaration of interests

G.B. Mills discloses the following interests: AstraZeneca, Chrysallis Biotechnology, Ellipses Pharma, ImmunoMET, Infinity, Ionis, Lilly, Medacorp, Nanostring, PDX Pharmaceuticals, Signalchem Lifesciences, Tarveda, Turbine, Zentalis Pharmaceuticals (scientific advisory board/consultancy); Catena Pharmaceuticals, ImmunoMet, SignalChem, Tarveda, Turbine (stock/options/financial); and HRD assay to Myriad Genetics, DSP patents with Nanostring (licensed techonology). 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.

Reviewer disclosures

Peer reviewers on this manuscript have no relevant financial or other relationships to disclose.

Additional information

Funding

This manuscript was funded by a kind gift from the Miriam and Sheldon Adelson Medical Research Foundation, the Breast Cancer Research Foundation grant BCRF 21110, and NIH/NCI grant CA217685.