Identification of Novel PAX3-MAML3 Fusion Gene in Low Grade Sinonasal Sarcoma with Neural and Myogenic Features by Transcriptome Analysis
Xiaoke Wang, Rondell P Graham, Jean E Lewis, Jason T Lewis, Michele R Erickson-Johnson, Michael Yaszemski, Yan Asmann, Jin Jen, Avudaippan Maran, Melissa L Lonzo, Andre M Oliveira. Mayo Clinic, Rochester, MN
Background: Low-grade sinonasal sarcoma with neural and myogenic features (LGSS) is a recently described spindle cell sarcoma of the sinonasal tract characterized by concomitant neural and myogenic differentiation (Lewis JT et al., 2011). In this study we show that the fusion gene PAX3-MAML3 due to the translocation t(2;4)(q37.1;q31.3) is a recurrent and specific molecular finding of these tumors.
Design: Twenty-two LGSS cases were retrieved from Mayo Clinic tissue archives and referring institutions. The histologic features and immunohistochemical profile of all cases were reviewed for diagnostic confirmation. Cytogenetic analysis was performed on two examples in which fresh tissue was available. RNA was extracted from cultured cells and cDNA libraries were prepared using TruSeq RNA Sample Prep Kit (Illumina Inc, San Diego). Global transcriptome sequencing analysis was performed using HiSeq 2000 sequencer (Ilumina Inc). Potential fusion genes were investigated using the SnowShoes-FTD algorithm for paired end mRNA-Seq data (Asmann Y et al., 2011). High throughput sequence results were confirmed at the genomic level by FISH, and at the transcriptional level by RT-PCR and direct Sanger sequencing on available FFPEs. Fifteen distinct tumors and normal tissues were used as negative controls.
Results: Global transcriptome sequencing analysis identified the fusion of PAX3 exon 7 to the mastermind-like 3 (MAML3) exon 2 in one index tumor with t(2;4). FISH and RT-PCR analyses confirmed the PAX3-MAML3 fusion in 14 (of 22 cases; 63%). Furthermore, PAX3 rearrangements only (without MAML3 involvement) were found in 7 cases (32%), consistent with the presence of alternate PAX3 fusion genes. A single case showed MAML3 rearrangement only. All controls, including six alveolar rhabdomyosarcomas, were negative for this novel fusion.
Conclusions: Our study identified the novel PAX3-MAML3 as a recurrent fusion gene event in LGSS. PAX3 rearrangement without MAML3 rearrangement was identified in a subset of cases, implying the presence of alternate PAX3 fusion genes. The structure of PAX3-MAML3 fusion protein is predicted to retain the paired box and homeobox DNA binding domains of PAX3 and the transactivation domain of MAML3. However, it is still unclear whether the developmental roles of PAX3 and MAML3 may explain the biphenotypic profile of LGSS. Finally, the identification of PAX3-MAML3 can be used as a novel diagnostic biomarker for LGSS.
Category: Bone & Soft Tissue
Tuesday, March 5, 2013 8:45 AM
Proffered Papers: Section G, Tuesday Morning