Role of gene expression arrays in sarcomas

Gene expression identifies heterogeneity of metastatic propensity in high-grade soft tissue sarcomas

BACKGROUND

Metastatic propensity of soft tissue sarcoma (STS) is heterogeneous and may be determined by gene expression patterns that do not correlate well with morphology. The authors have reported gene expression patterns that distinguish 2 broad classes of clear cell renal carcinoma (ccRCC-gene set), and other patterns that can distinguish heterogeneity of serous ovarian carcinoma (OVCA-gene set) and aggressive fibromatosis (AF-gene set); however, clinical follow-up data were not available for these samples.

METHODS

In the current study, gene expression patterns in 73 samples of high-grade STS were examined using spotted cDNA microarray slides that contained ∼16,000 unique UniGene clusters. Approximately 50% of the genes present in the ccRCC-, OVCA-, and AF-gene sets were also represented in the data from this chip set, and these were combined to form a composite gene set of 278 probes.

RESULTS

Hierarchical clustering using this composite gene set suggested the existence of subsets of the STS samples. Analysis revealed differences in the time to development of metastatic disease between the clusters defined by the first branch point of the clustering dendrogram (P = .005), and also among the 4 different clusters defined by the second branch points (P = .001).

CONCLUSIONS

This approach suggests the existence of >2 subsets of high-grade pleomorphic STS, each with distinct clinical behavior. A composite gene set such as that described here may be useful to stratify STS in clinical trials, and may be of practical utility in patient management.

Systematic therapy for unresectable or metastatic soft-tissue sarcomas: past, present, and future

Unresectable or metastatic disease occurs in 40% to 60% of soft-tissue sarcoma (STS) patients and portends a poor prognosis. For decades, doxorubicin has formed the backbone of systemic treatment, with response rates of approximately 26%. Patients progressing following first-line therapy were left with few proven options. No other cytotoxic chemotherapy agent or combination has demonstrated superiority to doxorubicin. Advances in targeted therapy of STS have been hindered by STS heterogeneity and poorly understood disease biology. Despite challenges, progress has been made in specific STS subtypes. Here, we highlight the challenges, progress, and lessons learned from STS trials published in the last 20 to 25 years.

Malignant fibrous histiocytoma--pleomorphic sarcoma, NOS gene expression, histology, and clinical course. A pilot study

PURPOSE

The new classification of malignant fibrous histiocytoma leaves only a small group of tumors without further line of differentiation, so-called pleomorphic sarcomas, not otherwise specified (NOS) as a pseudo-entity. This study focused on these tumors and analyzed the association of gene expression profiles to clinical outcome.

MATERIALS AND METHODS

Ten fresh samples of pleomorphic NOS sarcomas were evaluated histopathologically and by means of microarray analysis. Analysis of expression profiles was performed by clustering methods as well as by statistical analysis of primary vs recurrent tumors, irradiated vs nonirradiated tumors, tumors of patients above and below 60 years of age, male and female, and of tumors that developed metastatic or recurrent disease during the clinical course and those that did not.

RESULTS

Tumor clustering did not correlate to any histopathological or clinical finding. Detailed gene expression analysis showed a variety of genes whose upregulation (platelet-derived growth factor receptor alpha polypeptide, solute carrier family 39 member 14, solute carrier family 2 member 3, pleiotrophin, trophinin, pleckstrin and Sec7 domain containing 3, enolase 2, biglycan, SH3 and cysteine-rich domain, matrix metalloproteinases 16) and whose downregulation (tissue inhibitor of metalloproteinase 4, hairy/enhancer of split related with YRPW motif 2, protein tyrosine phosphatase receptor-type Z polypeptide 1, SH3 domain GRB2-like 2, microtubule-associated protein 7, potassium voltage-gated channel shaker-related subfamily member 1, RUN and FYVE domain containing 3, Sin3A-associated protein 18 kDa, proline-rich 4, calcium/calmodulin-dependent protein kinase ID, myeloid/lymphoid or mixed-lineage leukemia translocated to 3, insulin-like growth factor binding protein 5, nucleoside diphosphate-linked moiety X-type motif 9, NudC domain containing 3, imprinted in Prader-Willi syndrome, TAF6-like RNA polymerase II p300/CBP-associated factor 65 kDa, WD repeat and SOCS box-containing 2, adenosine diphosphate ribosylation factor 3, KRR1, proliferation-associated 2G4; CD36, complement component (3b/4b) receptor 1, solute carrier family 4 sodium bicarbonate cotransporter member 4, lipoprotein lipase (LPL), GATA binding protein 3, LPL, glutathione peroxidase 3, D: -aspartate oxidase, apolipoprotein E, sphingomyelin phosphodiesterase acid-like 3A) were associated with poor clinical outcome in terms of development of metastatic or recurrent disease.

CONCLUSIONS

The classification of these tumors may undergo further changes in the future. Gene expression profiling can provide additional information to categorize pleomorphic sarcoma (NOS) and reveal potential prognostic factors in this "entity."

Sarcoma

Sarcomas comprise a heterogeneous group of mesenchymal neoplasms. They can be grouped into 2 general categories, soft tissue sarcoma and primary bone sarcoma, which have different staging and treatment approaches. This review includes a discussion of both soft tissue sarcomas (malignant fibrous histiocytoma, liposarcoma, leiomyosarcoma, synovial sarcoma, dermatofibrosarcoma protuberans, angiosarcoma, Kaposi sarcoma, gastrointestinal stromal tumor, aggressive fibromatosis or desmoid tumor, rhabdomyosarcoma, and primary alveolar soft-part sarcoma) and primary bone sarcomas (osteosarcoma, Ewing sarcoma, giant cell tumor, and chondrosarcoma). The 3 most important prognostic variables are grade, size, and location of the primary tumor. The approach to a patient with a sarcoma begins with a biopsy that obtains adequate tissue for diagnosis without interfering with subsequent optimal definitive surgery. Subsequent treatment depends on the specific type of sarcoma. Because sarcomas are relatively uncommon yet comprise a wide variety of different entities, evaluation by oncology teams who have expertise in the field is recommended. Treatment and follow-up guidelines have been published by the National Comprehensive Cancer Network (www.nccn.org).