Proteomic analysis of archival breast cancer clinical specimens identifies biological subtypes with distinct survival outcomes

Karama Asleh,Dongxia Gao,Gian Luca Negri,Gregg B Morin,Christopher S Hughes,Shane Colborne,Stephen K L Chia,Sandra E Spencer Miko,Torsten O Nielsen,C Blake Gilks,Xiu Q Wang

doi:10.1038/s41467-022-28524-0

Abstract

Despite advances in genomic classification of breast cancer, current clinical tests and treatment decisions are commonly based on protein level information. Formalin-fixed paraffin-embedded (FFPE) tissue specimens with extended clinical outcomes are widely available. Here, we perform comprehensive proteomic profiling of 300 FFPE breast cancer surgical specimens, 75 of each PAM50 subtype, from patients diagnosed in 2008-2013 (n = 178) and 1986-1992 (n = 122) with linked clinical outcomes. These two cohorts are analyzed separately, and we quantify 4214 proteins across all 300 samples. Within the aggressive PAM50-classified basal-like cases, proteomic profiling reveals two groups with one having characteristic immune hot expression features and highly favorable survival. Her2-Enriched cases separate into heterogeneous groups differing by extracellular matrix, lipid metabolism, and immune-response features. Within 88 triple-negative breast cancers, four proteomic clusters display features of basal-immune hot, basal-immune cold, mesenchymal, and luminal with disparate survival outcomes. Our proteomic analysis characterizes the heterogeneity of breast cancer in a clinically-applicable manner, identifies potential biomarkers and therapeutic targets, and provides a resource for clinical breast cancer classification.

Highlights

Despite advances in genomic classification of breast cancer, current clinical tests and treatment decisions are commonly based on protein level information
Samples were assembled with an original aim to be analyzed as one cohort, the mass spectrometry (MS) data were obtained per this design, from patients diagnosed with invasive breast cancer using tissue obtained prior to adjuvant systemic therapy in 2008–2013 (n = 178; the 08–13 cohort) and 1986–1992 (n = 122; the 86–92 cohort)
Digested peptides were labeled with a stable isotope labeled tandem mass tag (TMT) and the whole cohort was run in TMT-11-multiplex sets; each set had two of each PAM50 subtype, one normal sample, a standard SuperMix, and a pool of all samples (Supplementary Fig. 1b, Supplementary Data 1a)

Summary

Introduction

Despite advances in genomic classification of breast cancer, current clinical tests and treatment decisions are commonly based on protein level information. We perform comprehensive proteomic profiling of 300 FFPE breast cancer surgical specimens, 75 of each PAM50 subtype, from patients diagnosed in 2008-2013 (n = 178) and 1986-1992 (n = 122) with linked clinical outcomes These two cohorts are analyzed separately, and we quantify 4214 proteins across all 300 samples. RNA-based gene signature[4,5], are increasingly used as a goldstandard to identify intrinsic breast cancer subtypes and recommend biomarkers for clinical use[6,7] These classifications do not always guide therapeutic choices, due to the extensive heterogeneity that still characterizes breast cancers beyond their DNA or RNA profiles, especially within the aggressive subgroup of triple-negative breast cancer (TNBC)[8,9,10,11,12]. To classify breast tumors in a more in-depth and comprehensive manner, the Clinical Proteomic Tumor Analysis

Methods

Results

Conclusion