Genetic characterization of Solitary Fibrous Tumor and Pleomorphic Hyalinizing Angiectatic Tumor

Abstract

ABSTRACT

The genetic characteristics of two soft tissue tumors were investigated in the present study: pleomorphic hyalinizing angiectatic tumor (PHAT) and solitary fibrous tumor (SFT). PHAT is a benign soft tissue tumor of uncertain cellular origin and lineage of differentiation. Although PHAT is still poorly characterized at the genetic level, one reported case has shown a potential genetic overlap with two other soft tissue tumors - myxoinflammatory fibroblastic sarcoma (MIFS) and hemosiderotic fibrolipomatous (HFLT). MIFS and HFLT share a characteristic t(1;10)(p22;q24) with breakpoints in the TGFBR3 locus on chromosome 1 and near the MGEA5 locus on chromosome 10. To find out whether also PHAT is associated with this translocation, two cases were subjected to single nucleotide polymorphism (SNP) array and fluorescence in situ hybridization (FISH) analyses. None of them showed a t(1;10) or other types of rearrangement of the TGFBR3 or MGEA5 loci. Both tumors showed imbalances at SNP array analysis, but none was shared. Thus, the results indicate that PHAT is genetically distinguished from MIFS and HFLT, but further studies are needed to identify the salient genetic pathways involved in PHAT development. SFT is a rarely metastasizing soft tissue tumor that belongs to the group of fibroblastic/myofibroblastic tumors. Before the present study very little was known about the genetics of SFT, but cytogenetic data indicate a recurrent breakpoint in region 12q13-15. In this study, 30 patients with SFT were studied by cytogenetics, SNP array and FISH analysis. Subsequently, the study narrowed down to STAT6 and NAB2 as potential target genes for 12q13 rearrangements. The expression levels of both genes were investigated by global gene expression and quantitative real time PCR (qRT-PCR) showing different expression levels of the 5’ and 3’ ends of each gene. Two of the cases with 12q13 rearrangement were investigated for possible fusion genes by 5’ Rapid Amplification of cDNA Ends (RACE) PCR and reverse transcription PCR. RT-PCR analysis and sequencing of the amplified products revealed two novel NAB2/STAT6 fusion transcripts in which nucleotide 1846 (exon 6) of NAB2 was fused in-frame with nucleotide 2217(exon 18) of STAT6 in one and nucleotide 2112 (exon 17) of STAT6 in the other. The NAB2/STAT6 fusion was the result of a STAT6 inversion in the two cases. Most likely, the inversion and fusion of NAB2 with STAT6 is the primary hit in this tumor type.

Popular science summary:

Genetic characterization of Solitary Fibrous Tumor
and Pleomorphic Hyalinizing Angiectatic Tumor

The present study concerned the genetic characteristics of two soft tissue tumors: pleomorphic hyalinizing angiectatic tumor (PHAT) and solitary fibrous tumor (SFT).
PHAT is a benign soft tissue tumor of uncertain cellular origin and lineage of differentiation. Although PHAT is still poorly characterized at the genetic level, one reported case has shown a potential genetic overlap with two other soft tissue tumors. To evaluate this potential genetic association, two cases of PHAT were subjected to single nucleotide polymorphism (SNP) array and fluorescence in situ hybridization (FISH) analyses. The results of SNP array analysis showed different imbalances in the two cases; however none of them was recurrent or involved the regions of interest. Neither the FISH results supported the suggested genetic overlap between PHAT and the two other tumor types. Combined with the results from others, our findings indicate that most cases of PHAT probably develop through other genetic mechanisms.
SFT is a rarely metastasizing soft tissue tumor that belongs to the group of fibroblastic/myofibroblastic tumors. Before the present study very little was known about the genetics of SFT, but cytogenetic data indicated a recurrent breakpoint in chromosome 12 in a subset of the cases. In this study, 30 patients with SFT were studied by cytogenetics, SNP array and FISH analysis. Based on the results of these analyses, the study narrowed down to two potential target genes located in a recurrently involved region. The expression levels of the two genes were investigated by global gene expression and quantitative real time PCR (qRT-PCR), showing different expression levels of the 5’ and 3’ ends of each gene. Two of the cases with the recurrent rearrangement in the region of interest were investigated for possible fusion genes by 5’ Rapid Amplification of cDNA Ends (RACE) PCR and reverse transcription PCR. RT-PCR analysis and sequencing of the amplified products revealed in-frame transcripts corresponding to a novel fusion gene. Whereas both cases displayed transcripts corresponding to intronic breakpoints, one of the cases also showed a second transcript that suggested an exonic breakpoint in one of the two genes; the presence of two transcript suggest alternative splicing. The novel fusion is the result of an inversion at genomic level.

Advisor: Professor Fredrik Mertens
Master´s Degree project in Molecular Genetics: 60 credits in 2011-2012
Department of Biomedical Science, Lund University

• author: Mohajeri, Arezoo
• supervisor: Fredrik Mertens
• organization: Degree Projects in Molecular Biology
• course: MOBT19 20112
• year: 2012
• type: H2 - Master's Degree (Two Years)
• subject: Biology and Life Sciences
• language: English
• id: 3514375
• date added to LUP: 2013-02-20 15:16:46
• date last changed: 2013-03-26 14:40:41