Novel Chromosomal Rearrangements and Break Points at the t(6;9) in Salivary Adenoid Cystic Carcinoma: Association with MYB–NFIB Chimeric Fusion, MYB Expression, and Clinical Outcome

Abstract

Objective To investigate the molecular-genetic heterogeneity associated with the t(6:9) in adenoid cystic carcinoma (ACC) and correlate the findings with patient clinical outcome. Experimental Design Multi-molecular and genetic techniques complemented with massive pair-ended sequencing and SNP array analyses were used on tumor specimens from 30 new and 52 previously RT-PCR analyzed fusion transcript negative ACCs. MYB mRNA expression level was determined by quantitative RT-PCR. The results of 102 tumors (30 new and 72 previously reported cases) were correlated with the clinicopathologic factors and patients’ survival. Results The FISH analysis showed 34/82 (41.5%) fusion positive tumors and molecular techniques identified fusion transcripts in 21 of the 82 (25.6%) tumors. Detailed FISH analysis of 11 out the 15 tumors with gene fusion without transcript formation showed translocation of NFIB sequences to proximal or distal sites of the MYB gene. Massive pair-end sequencing of a subset of tumors confirmed the proximal translocation to an NFIB sequence and led to the identification of a new fusion gene (NFIB-AIG1) in one of the tumors. Overall, MYB-NFIB gene fusion rate by FISH was in 52.9% while fusion transcript forming incidence was 38.2%. Significant statistical association between the 5′ MYB transcript expression and patient survival was found. Conclusions We conclude that: 1) t(6;9) results in a complex genetic and molecular alterations in ACC, 2) MYB-NFIB gene fusion may not always be associated with chimeric transcript formation, 3) non-canonical MYB, NFIB gene fusions occur in a subset of tumors, 4) high MYB expression correlates with worse patient survival.

Whole exome sequencing of adenoid cystic carcinoma

“…MYB-NFIB fusion status was investigated using a combination of fusion transcript sequencing, qRT-PCR, FISH, and 3′ rapid amplification of cDNA ends (3′ RACE), as described previously (25). The particular data supporting a scoring of MYB activation in any given sample are given in Supplemental Detection of copy number variation.…”

Fusion Oncogenes in Salivary Gland Tumors: Molecular and Clinical Consequences

“…Detailed genomic characterization (including next generation sequencing) of several such cases have revealed insertions of a segment from 9p23-p22.3, including the 3 0 -part of NFIB, immediately centromeric to the MYB locus ( Fig. 3) [9,20,21]. In these cases we can only speculate that enhancer elements upstream of MYB perhaps in combination with other regulatory elements in the 3 0 -part of NFIB and its flanking sequences may contribute to the activation of MYB.…”

Adenoid Cystic Carcinoma: Clinical and Molecular Features

“…Though there is some disagreement in the literature regarding the percent of ACC tumors harboring this molecular alteration, most subsequent studies have shown that the majority of ACC have a disrupted MYB gene and/ or evidence of a MYB-NFIB fusion RNA transcript [32][33][34][35][36]. One of the largest independent cohorts separate from the Stenman group came from a study at Stanford University, where 37 cases of ACC were studied by fluorescence in situ hybridization (FISH) of the MYB and NFIB loci, with 65 % of cases showing abnormalities of these loci [34].…”