High-resolution array CGH and gene expression profiling of alveolar soft part sarcoma.
OBJECTIVE
Alveolar soft part sarcoma (ASPS) is a soft tissue sarcoma with poor prognosis, and little molecular evidence exists for its origin, initiation, and progression. The aim of this study was to elucidate candidate molecular pathways involved in tumor pathogenesis.


METHODS
We employed high-throughput array comparative genomic hybridization (aCGH) and cDNA-Mediated Annealing, Selection, Ligation, and Extension Assay to profile the genomic and expression signatures of primary and metastatic ASPS from 17 tumors derived from 11 patients. We used an integrative bioinformatics approach to elucidate the molecular pathways associated with ASPS progression. FISH was performed to validate the presence of the t(X;17)(p11.2;q25) ASPL-TFE3 fusion and, hence, confirm the aCGH observations.


RESULTS
FISH analysis identified the ASPL-TFE3 fusion in all cases. aCGH revealed a higher number of numerical aberrations in metastatic tumors relative to primaries, but failed to identify consistent alterations in either group. Gene expression analysis highlighted 1,063 genes that were differentially expressed between the two groups. Gene set enrichment analysis identified 16 enriched gene sets (P < 0.1) associated with differentially expressed genes. Notable among these were several stem cell gene expression signatures and pathways related to differentiation. In particular, the paired box transcription factor PAX6 was upregulated in the primary tumors, along with several genes whose mouse orthologs have previously been implicated in Pax6 DNA binding during neural stem cell differentiation.


CONCLUSIONS
In addition to suggesting a tentative neural line of differentiation for ASPS, these results implicate transcriptional deregulation from fusion genes in the pathogenesis of ASPS.
Authors' Affiliations: Department of Pathology, Brigham and Women's Hospital, Harvard Medical School; Center for Molecular Oncologic Pathology, Dana-Farber Cancer Institute; Massachusetts General Hospital, Boston, Massachusetts; Carver College of Medicine, University of Iowa, Iowa City, Iowa; and Department of Pathology, St. James's Hospital, Dublin, Ireland.
Shamini
S
Selvarajah
Saumyadipta
S
Pyne
Eleanor
E
Chen
Ramakrishna
R
Sompallae
Azra H
AH
Ligon
Gunnlaugur P
GP
Nielsen
Glenn
G
Dranoff
Edward
E
Stack
Massimo
M
Loda
Richard
R
Flavin
D000328:Adult; D051778:Basic Helix-Loop-Helix Leucine Zipper Transcription Factors / Q000235:genetics; D055028:Comparative Genomic Hybridization; D005136:Eye Proteins / Q000235:genetics; D005260:Female; D020869:Gene Expression Profiling / Q000379:methods*; D057166:High-Throughput Screening Assays; D018398:Homeodomain Proteins / Q000235:genetics; D006801:Humans; D007150:Immunohistochemistry; D017404:In Situ Hybridization, Fluorescence; D047908:Intracellular Signaling Peptides and Proteins; D053208:Kaplan-Meier Estimate; D008297:Male; D008875:Middle Aged; D015514:Oncogene Proteins, Fusion / Q000235:genetics; D000071841:PAX6 Transcription Factor; D051761:Paired Box Transcription Factors / Q000235:genetics; D012097:Repressor Proteins / Q000235:genetics; D018234:Sarcoma, Alveolar Soft Part / Q000235:genetics* / Q000401:mortality; D055815:Young Adult
C422743:ASPSCR1 protein, human; D051778:Basic Helix-Loop-Helix Leucine Zipper Transcription Factors; D005136:Eye Proteins; D018398:Homeodomain Proteins; D047908:Intracellular Signaling Peptides and Proteins; D015514:Oncogene Proteins, Fusion; D000071841:PAX6 Transcription Factor; C000605730:PAX6 protein, human; D051761:Paired Box Transcription Factors; C000605732:Pax6 protein, mouse; D012097:Repressor Proteins; C069203:TFE3 protein, human