Reverse-Phase Protein Array (RPPA)

Overview

Reverse-phase protein array (RPPA) is a high-throughput antibody-based platform for quantifying protein and phosphoprotein expression levels across many samples simultaneously. Lysates from tumor tissue are arrayed on nitrocellulose slides and probed with validated antibodies; signal intensity is normalized and used to estimate relative protein abundance. RPPA enables pathway-level proteomics in large cohorts.

Used by

  • Applied to 214 GBM samples (171 antibodies) as part of TCGA GBM 2013 multi-platform analysis; 127/171 antibodies correlated with transcriptomic subtype; revealed non-linear genotype-to-signaling relationships (e.g., RTK-amplified samples had lower downstream p-AKT/S6K/MAPK signaling than expected) PMID:24120142
  • Reverse-phase protein array (RPPA) applied to TCGA bladder carcinoma samples for protein and phosphoprotein expression profiling; contributed to multi-platform pathway-level characterization identifying therapeutic targets in 69% of tumors PMID:24476821
  • Applied as one of five molecular platforms in the TCGA HCC integrated characterisation of 196 patients alongside DNA copy number, methylation, mRNA, and miRNA PMID:24798001
  • RPPA profiling of gastric adenocarcinomas (stad_tcga_pub) revealed elevated EGFR pY1068 phosphorylation in the CIN subtype and IL-12 signalling in EBV-positive tumors; used alongside six other molecular platforms PMID:25079317
  • RPPA on 181 of 230 lung adenocarcinomas (luad_tcga_pub) identified three mTOR activation patterns (basal; STK11-low/AMPK-low; high p-AKT/PIK3CA mutation), demonstrating that pathway-state biomarkers complement DNA-based stratification PMID:25079552
  • Applied in TCGA PTC study to resolve proteomic differences between BVL (BRAFV600E-driven, high MEK/ERK activation) and RL (RAS-driven, elevated p90RSK phosphorylation, TSC2 inhibition, BCL2 over-expression) subtypes PMID:25417114
  • Applied in TCGA HNSC multi-platform profiling (n=279) for protein-level characterization, integrated with genomic subtypes to characterize therapeutic targets across the atypical/mesenchymal/basal/classical expression subtypes PMID:25631445
  • Reverse-phase protein array (RPPA, 181 cancer-related proteins/phosphoproteins) on 202 melanoma samples revealed pathway-specific signaling differences: phospho-MEK/ERK elevated in BRAF/RAS subtypes, highest KIT protein in Triple-WT, highest CRAF in NF1 subtype. PMID:26091043
  • Applied to 633 of 817 breast tumor samples in the TCGA ILC/IDC study; quantified 180+ proteins including phospho-AKT S473/T308, total/phospho-EGFR, pSTAT3 Y705, p70S6K T389; revealed that ILC has the highest average pAKT of any breast subtype, matching HER2+ and Basal-like IDC despite predominantly Luminal A classification PMID:26451490
  • Reverse phase protein array profiling performed on 152 of 333 primary prostate adenocarcinomas in the TCGA molecular taxonomy study as part of multi-platform molecular characterization PMID:26544944.
  • Applied to 473 glioma samples in the TCGA pan-glioma study for protein-level pathway analysis complementing genomic and transcriptomic data PMID:26824661
  • Reverse-phase protein array (RPPA) profiled 113 oesophageal/gastric tumors in the TCGA esophageal/stomach study; ESCC2 showed elevated cleaved Caspase-7; RPPA helped distinguish ESCC subtypes PMID:28052061.
  • RPPA applied to 173 PCPG tumors in the TCGA PCPG study; RPPA cluster 3 (RAS-MAPK signaling) enriched in kinase signaling subtype; MAML3 fusion-positive tumors showed elevated β-catenin, DVL3, and GSK3 by RPPA PMID:28162975.
  • Applied to 343/412 BLCA tumors with 208 antibodies; five proteomic clusters with distinct outcomes (p=0.019) identified, including HER2-high clusters proposed for trastuzumab and an EGFR-high cluster for EGFR inhibitors PMID:28988769
  • Applied to 206 TCGA sarcomas for protein expression profiling; STLMS showed highest PD-L1 expression among sarcoma subtypes (p=4×10⁻⁵ vs ULMS) PMID:29100075

Notes

  • Coverage is limited to antibodies in the validated panel; cannot detect novel proteins or isoforms without prior selection.
  • Non-linear genotype-to-protein relationships observed in GBM (e.g., PI3K-mutant samples with lower p-AKT than PI3K-WT) highlight the complexity of translating genomic to proteomic signals.
  • Widely used in TCGA pan-cancer studies for pathway activation profiling.

Sources

This page was processed by crosslinker on 2026-05-14. - PMID:24476821

This page was processed by crosslinker on 2026-05-14. - PMID:24798001

This page was processed by crosslinker on 2026-05-14. - PMID:25079317

This page was processed by crosslinker on 2026-05-14. - PMID:25079552

This page was processed by crosslinker on 2026-05-14. - PMID:25417114

This page was processed by crosslinker on 2026-05-14. - PMID:25631445

This page was processed by crosslinker on 2026-05-14. - PMID:26091043

This page was processed by crosslinker on 2026-05-14. - PMID:26451490

This page was processed by crosslinker on 2026-05-14. - PMID:26544944

This page was processed by wiki-cli on 2026-05-14. - PMID:26824661

This page was processed by wiki-cli on 2026-05-14. - PMID:28052061

This page was processed by wiki-cli on 2026-05-14. - PMID:28162975

This page was processed by wiki-cli on 2026-05-14. - PMID:28988769

This page was processed by entity-page-writer on 2026-05-15. - PMID:29100075

This page was processed by entity-page-writer on 2026-05-15.