Fusion of the SEC31L1 and ALK genes in an inflammatory myofibroblastic tumor

Abstract

Inflammatory myofibroblastic tumor (IMT) is a neoplasm composed of myofibroblastic spindle cells and infiltrating inflammatory cells. Cytogenetic analyses have revealed that a subgroup of IMT, in particular among children and young adults, harbors clonal chromosomal rearrangements involving chromosome band 2p23. Further, molecular genetic studies have shown that these rearrangements target the ALK gene, serving as the 3 0 -partner in fusion genes with various translocation partners. In the present study, we describe the finding of a novel SEC31L1/ALK fusion gene in an intraabdominal IMT of a young man. G-band analysis revealed a translocation t(2;4)(p23;q21) and subsequent fluorescence in situ hybridization with locus-specific probes strongly indicated disruption of the ALK locus on chromosome 2. Immunostaining with monoclonal mouse anti-human CD246 ALK Protein showed diffuse cytoplasmic positivity. Using reverse primers for the ALK-gene, we could, by 5 0 -RACE methodology, amplify a single 1.2 kb fragment. Sequence analysis showed that the fragment was a hybrid cDNA product in which nt 3012 of SEC31L1 (NM_016211), located in band 4q21, was fused in-frame to nt 4080 of ALK (NM_004304). RT-PCR with two sets of primer pairs specific for SEC31L1 and ALK amplified two transcripts, which at sequencing corresponded to two types of chimeric SEC31L1/ALK transcripts. In the long, type I, transcript nt 3012 of SEC31L1 (NM_016211) was fused in-frame to nt 4080 of ALK. In the short, type II, transcript nt 2670 of SEC31L1 was fused in-frame to nt 4080 of ALK. Genomic PCR and subsequent sequencing showed that the breakpoints were located in intron 23 of SEC31L1 and intron 20 of ALK. ' 2005 Wiley-Liss, Inc.Key words: ALK gene fusion; SEC31L1; myofibroblastic tumor Inflammatory myofibroblastic tumor (IMT) is a distinctive neoplasm composed of varying proportions of myofibroblastic spindle cells, inflammatory cells and collagen fibers. IMTs can arise anywhere in the body, but are particularly common in the mesentery, omentum and lung. 1 Surgery with radical margins is usually curative, but in rare cases an IMT may metastasize. [2][3][4] Cytogenetic analyses have shown that a subset of IMTs harbors clonal chromosomal rearrangements involving band 2p23. In 1999, Griffin and co-workers demonstrated that such 2p23-rearrangements target the ALK locus and result in the creation of various fusion genes containing the catalytic domain of ALK. 5 So far, 6 ALK fusion partners have been described in IMTs: ATIC (at 2q35), CARS (at 11p15), CLTC (at 17q23), RANBP2 (at 2q13), TMP3 (at 1p23) and TMP4 (at 19p13) 2,6-12 Immunohistostochemical studies have detected ALK expression in 40-60% of IMTs. 11,12 In the present study, we describe the cytogenetic and molecular characterization of an IMT with a novel fusion gene, SEC31L1/ALK. Material and methods Case history and histopathologyA 23-year-old man was admitted to hospital, with a three-day history of fever and lower abdominal pain. Hemoglobin and white blood cell counts were normal and CRP slig...

ALK-positive large B-cell lymphomas with cryptic SEC31A-ALK and NPM1-ALK fusions

“…The molecular results were validated by metaphase FISH with fosmid probes flanking the SEC31A gene that confirmed a cryptic rearrangement of SEC31A associated with an insertion of its 5' end in the vicinity of the 3' end of ALK at 3q27, and duplication of this region on add (20) (Figure 1B; Online Supplementary Table S1). The latter aberration was additionally proved by FISH with probes covering the 5' end of SEC31A (WI2-2194A15 in red) and the 3' end of ALK (P1 clone 1111H1 in green) ( Figure 1B; Online Supplementary Table S1).…”

“…Remarkably, similar complex aberrations were detected in a case of IMT in which the SEC31A-ALK fusion was originally identified. 20 Whether another case of ALK + LBCL with a cryptic insertion of the 3' end of ALK at 4q22-24 reported by Stachurski et al, 21 targets SEC31A remains to be clarified. The duplication of the ALK fusion gene found in case 1 has been recurrently reported in ALK-positive lymphoma.…”

“…In the first case, the ALK-involving t(2;3)(p23;q27) masked the cryptic SEC31A-ALK fusion generated by an insertion of the 5' end of SEC31A (4q21) upstream of the 3' end of ALK. This rearrangement was associated with loss of the 5' end of ALK and duplication of SEC31A-ALK on der (20). In the second case with complex rearrangements of both chromosomes 2, a submicroscopic NPM1-ALK fusion created by insertion of the 3' end of ALK into the NPM1 locus was evidenced.…”

Utility of ALK-1 protein expression and ALK rearrangements in distinguishing inflammatory myofibroblastic tumor from malignant spindle cell lesions of the urinary bladder

“…4,5,7,9,[20][21][22][23][24][25][29][30][31][32] Cytogenetic and molecular analyses have demonstrated a number of ALK fusion gene partners, including RANBP2-ALK, TPM3-ALK, TPM4-ALK, CLTCALK, CARS-ALK and SEC31L1-ALK. 5,9,21,25,29,31 In the present study, ALK rearrangements were identified in 14 of 21 cases of inflammatory myofibroblastic tumor of the urinary bladder.…”

“…Rearrangements of ALK with various gene partners have been identified in inflammatory myofibroblastic tumor from a number of anatomic sites. [20][21][22][23][24] Each rearrangement is believed to result in the creation of novel gene fusions and subsequently leads to aberrant ALK activation. In the urinary bladder, a few series and case studies have reported cases of inflammatory myofibroblastic tumor exhibiting ALK rearrangements.…”