Prostate cancer (PCa) molecular subtypes have been defined by essentially mutually exclusive events, including ETS gene fusions (most commonly involving ERG) and SPINK1 overexpression. Clinical assessment may aid in disease stratification, complementing available prognostic tests.
To determine the analytical validity and clinicopatholgic associations of microarray-based molecular subtyping.
Design, setting, and participants
We analyzed Affymetrix GeneChip expression profiles for 1577 patients from eight radical prostatectomy cohorts, including 1351 cases assessed using the Decipher prognostic assay (GenomeDx Biosciences, San Diego, CA, USA) performed in a laboratory with Clinical Laboratory Improvements Amendment certification. A microarray-based (m-) random forest ERG classification model was trained and validated. Outlier expression analysis was used to predict other mutually exclusive non-ERG ETS gene rearrangements (ETS+) or SPINK1 overexpression (SPINK1+).
Associations with clinical features and outcomes by multivariate logistic regression analysis and receiver operating curves.
Results and limitations
The m-ERG classifier showed 95% accuracy in an independent validation subset (155 samples). Across cohorts, 45% of PCas were classified as m-ERG+, 9% as m-ETS+, 8% as m-SPINK1+, and 38% as triple negative (m-ERG−/m-ETS−/m-SPINK1−). Gene expression profiling supports three underlying molecularly defined groups: m-ERG+, m-ETS+, and m-SPINK1+/triple negative. On multivariate analysis, m-ERG+ tumors were associated with lower preoperative serum prostate-specific antigen and Gleason scores, but greater extraprostatic extension (p < 0.001). m-ETS+ tumors were associated with seminal vesicle invasion (p = 0.01), while m-SPINK1+/triple negative tumors had higher Gleason scores and were more frequent in Black/African American patients (p < 0.001). Clinical outcomes were not significantly different among subtypes.
A clinically available prognostic test (Decipher) can also assess PCa molecular subtypes, obviating the need for additional testing. Clinicopathologic differences were found among subtypes based on global expression patterns.
Molecular subtyping of prostate cancer can be achieved using extra data generated from a clinical-grade, genome-wide expression-profiling prognostic assay (Decipher). Transcriptomic and clinical analysis support three distinct molecular subtypes: (1) m-ERG+, (2) m-ETS+, and (3) m-SPINK1+/triple negative (m-ERG−/m-ETS−/m-SPINK1−). Incorporation of subtyping into a clinically available assay may facilitate additional applications beyond routine prognosis.
Keywords: Prostate cancer, ERG, ETS, SPINK1, Microarray, Prognosis.
a Michigan Center for Translational Pathology, University of Michigan Medical School, Ann Arbor, MI, USA
b Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA
c Department of Urology, University of Michigan Medical School, Ann Arbor, MI, USA
d Comprehensive Cancer Center, University of Michigan Medical School, Ann Arbor, MI, USA
e GenomeDx Bioscience Inc., Vancouver, British Columbia, Canada
f Department of Radiation Oncology, University of Michigan Medical School, Ann Arbor, MI, USA
g Kimmel Cancer Center, Jefferson Medical College of Thomas Jefferson University, Philadelphia, PA, USA
h James Buchanan Brady Urological Institute, Johns Hopkins School of Medicine, Baltimore, MD, USA
i Glickman Urological & Kidney Institute, Cleveland Clinic, Cleveland, OH, USA
j Department of Urology, Mayo Clinic, Rochester, MN, USA
k Department of Pathology and Laboratory Medicine, Mayo Clinic, Rochester, MN, USA
Corresponding authors. Departments of Pathology and Urology, Michigan Center for Translational Pathology, University of Michigan Medical School, 1524 BSRB, 109 Zina Pitcher Place, Ann Arbor, MI 48109-2200, USA. Tel. +1 734 7641549; Fax: +1 734 6477950.Department of Radiation Oncology, Michigan Center for Translational Pathology, University of Michigan Medical School, 1500 East Medical Center Drive, UHB2C490-SPC5010, Ann Arbor, MI 48109-5010, USA. Tel. +1 734 9364302; Fax: +1 734 9367859.
© 2015 European Association of Urology, Published by Elsevier B.V.