Exome-capture RNA sequencing of decade-old breast cancers and matched decalcified bone metastases
Nolan Priedigkeit, … , Steffi Oesterreich, Adrian V. Lee
Nolan Priedigkeit, … , Steffi Oesterreich, Adrian V. Lee
Published September 7, 2017
Citation Information: JCI Insight. 2017;2(17):e95703. https://doi.org/10.1172/jci.insight.95703.
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Resource and Technical Advance Genetics Oncology

Exome-capture RNA sequencing of decade-old breast cancers and matched decalcified bone metastases

Abstract

Bone metastases (BoM) are a significant cause of morbidity in patients with estrogen receptor–positive (ER-positive) breast cancer; yet, characterizations of human specimens are limited. In this study, exome-capture RNA sequencing (ecRNA-seq) on aged (8–12 years), formalin-fixed, paraffin-embedded (FFPE), and decalcified cancer specimens was evaluated. Gene expression values and ecRNA-seq quality metrics from FFPE or decalcified tumor RNA showed minimal differences when compared with matched flash-frozen or nondecalcified tumors. ecRNA-seq was then applied on a longitudinal collection of 11 primary breast cancers and patient-matched synchronous or recurrent BoMs. Overtime, BoMs exhibited gene expression shifts to more Her2 and LumB PAM50 subtype profiles, temporally influenced expression evolution, recurrently dysregulated prognostic gene sets, and longitudinal expression alterations of clinically actionable genes, particularly in the CDK/Rb/E2F and FGFR signaling pathways. Taken together, this study demonstrates the use of ecRNA-seq on decade-old and decalcified specimens and defines recurrent longitudinal transcriptional remodeling events in estrogen-deprived breast cancers.

Authors

Nolan Priedigkeit, Rebecca J. Watters, Peter C. Lucas, Ahmed Basudan, Rohit Bhargava, William Horne, Jay K. Kolls, Zhou Fang, Margaret Q. Rosenzweig, Adam M. Brufsky, Kurt R. Weiss, Steffi Oesterreich, Adrian V. Lee

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Figure 3

Differentially expressed genes in patient-matched bone metastases.

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Differentially expressed genes in patient-matched bone metastases. (A) H...
(A) Heatmap (red, high relative expression; blue, low relative expression) of log2normCPM values from 207 differentially expressed genes (FDR-adjusted P value [padj] < 0.10, DESeq2) between primary tumors and patient-matched bone metastases. Heatmap is segregated into two sections; genes with log2 fold change >0 on top and genes with log2 fold change <0 on bottom. Each section is gene sorted by adjusted P values. (B) Disease-specific survival (DSS) outcome differences in ER-positive METABRIC tumors using boneMetSigUp (top) and boneMetSigDown (bottom) expression scores as strata. 95% confidence intervals are highlighted along with log-rank P values and associated risk tables.