1. ¹Department of Pathology, Stanford University Medical Center, Stanford, CA, USA
2. ²Department of Pathology, Genetic Pathology Evaluation Centre, Vancouver General Hospital and British Columbia Cancer Agency, Vancouver, British Columbia, Canada
3. ³Department of Statistics, Stanford University Medical Center, Stanford, CA, USA
4. ⁴Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
5. ⁵Department of Biochemistry, Stanford University Medical Center, Stanford, CA, USA
6. ⁶Department of Surgery, The University of California, San Francisco, CA, USA
7. ⁷Department of Anatomic Pathology, Pathology and Laboratory Medicine Institute, The Cleveland Clinic and the Cleveland Clinic Lerner College of Medicine, Case Western Reserve University, Cleveland, OH, USA
8. ⁸Department of Pathology and Laboratory Service, Palo Alto Veterans Affairs Health Care System, Palo Alto, CA, USA

Correspondence: Professor M van de Rijn, Department of Pathology, Stanford University Medical Center, 300 Pasteur Drive, L235, Stanford, CA 94305, USA. E-mail: mrijn@stanford.edu

Received 22 May 2009; Revised 14 August 2009; Accepted 4 September 2009; Published online 9 November 2009.

Abstract

Leiomyosarcoma (LMS) is a soft tissue tumor with a significant degree of morphologic and molecular heterogeneity. We used integrative molecular profiling to discover and characterize molecular subtypes of LMS. Gene expression profiling was performed on 51 LMS samples. Unsupervised clustering showed three reproducible LMS clusters. Array comparative genomic hybridization (aCGH) was performed on 20 LMS samples and showed that the molecular subtypes defined by gene expression showed distinct genomic changes. Tumors from the 'muscle-enriched' cluster showed significantly increased copy number changes (P=0.04). A majority of the muscle-enriched cases showed loss at 16q24, which contains Fanconi anemia, complementation group A, known to have an important role in DNA repair, and loss at 1p36, which contains PRDM16, of which loss promotes muscle differentiation. Immunohistochemistry (IHC) was performed on LMS tissue microarrays (n=377) for five markers with high levels of messenger RNA in the muscle-enriched cluster (ACTG2, CASQ2, SLMAP, CFL2 and MYLK) and showed significantly correlated expression of the five proteins (all pairwise P<0.005). Expression of the five markers was associated with improved disease-specific survival in a multivariate Cox regression analysis (P<0.04). In this analysis that combined gene expression profiling, aCGH and IHC, we characterized distinct molecular LMS subtypes, provided insight into their pathogenesis, and identified prognostic biomarkers.