journal contribution
posted on 2023-03-31, 20:11 authored by Jennifer B. Dennison, Maria Shahmoradgoli, Wenbin Liu, Zhenlin Ju, Funda Meric-Bernstam, Charles M. Perou, Aysegul A. Sahin, Alana Welm, Steffi Oesterreich, Matthew J. Sikora, Robert E. Brown, Gordon B. Mills Statistical methods for RPPA; Supplemental references; Supplemental Figure S1: RPPA heatmap of TCGA cohort; Supplemental Figure S2: Diagram of RPPA proteins differentially expressed in Cluster II; Supplemental Figure S3: Expression of caveolin-1 by IHC in IDC; Supplemental Figure S4: Expression of E-cadherin by IHC in IDC; Supplemental Figure S5: Expression of RBM15 by IHC in IDC; Supplemental Figure S6: Association of RPPA subtypes with mRNA of selected genes; Supplemental Figure S7: Heatmap of RPPA protein expression of ER-pos breast cancer cell lines (IDC and ILC) and normal breast tissue; Supplemental Figure S8: Waterfall plots of RPPA proteins marked cancer or stroma derived in Reactive breast cancer (Cluster II); Supplemental Figure S9: Percent stroma as determined by compartment areas and cell counts; Supplemental Figure S10: Subtyping of MDACC ER-positive/HER2-negative breast cancers by RPPA; Supplemental Figure S11: Imaging summary for cell density and α-SMA scoring of TCGA cases; Supplemental Figure S12: Expression of α-SMA by IHC in ILC; Supplemental Figure S13: Expression of α-SMA by IHC of IDC; Supplemental Figure S14: Tumor purity, stromal scoring, EMT scoring, and immune scoring of RPPA subtypes; Supplemental Figure S15: Components of Nottingham grade for IDC; Supplemental Figure S16: RPPA heatmap of cases with matched normal tissues; Supplemental Table S1: The coefficient estimates of the final model using the core TCGA samples; Supplemental Table S2: The sensitivity, specificity and false discovery rate (FDR) from the test data sets using the final models from Table S1
Funding
Susan G. Komen
GlaxoSmithKline
American Cancer Society
Entertainment Industry Foundation
Breast Cancer Research Foundation
Susan G. Komen for the Cure
NIH
Joe and Jessie Crump Medical Research Fund
DoD Breast Cancer Research
BCRF
DoD BCRP Postdoctoral
NCI
History
ARTICLE ABSTRACT
Purpose: The current study evaluated associative effects of breast cancer cells with the tumor microenvironment and its influence on tumor behavior.Experimental Design: Formalin-fixed, paraffin-embedded tissue and matched protein lysates were evaluated from two independent breast cancer patient datasets (TCGA and MD Anderson). Reverse-phase protein arrays (RPPA) were utilized to create a proteomics signature to define breast tumor subtypes. Expression patterns of cell lines and normal breast tissues were utilized to determine markers that were differentially expressed in stroma and cancer cells. Protein localization and stromal contents were evaluated for matched cases by imaging.Results: A subtype of breast cancers designated “Reactive,” previously identified by RPPA that was not predicted by mRNA profiling, was extensively characterized. These tumors were primarily estrogen receptor (ER)-positive/human EGF receptor (HER)2-negative, low-risk cancers as determined by enrichment of low-grade nuclei, lobular or tubular histopathology, and the luminal A subtype by PAM50. Reactive breast cancers contained high numbers of stromal cells and the highest extracellular matrix content typically without infiltration of immune cells. For ER-positive/HER2-negative cancers, the Reactive classification predicted favorable clinical outcomes in the TCGA cohort (HR, 0.36; P < 0.05).Conclusions: A protein stromal signature in breast cancers is associated with a highly differentiated phenotype. The stromal compartment content and proteins are an extended phenotype not predicted by mRNA expression that could be utilized to subclassify ER-positive/HER2-negative breast cancers. Clin Cancer Res; 22(20); 5068–78. ©2016 AACR.
