Transcriptomes define distinct subgroups of salivary gland adenoid cystic carcinoma with different driver mutations and outcomes

Abstract

The relative rarity of salivary gland adenoid cystic carcinoma (ACC) and its slow growing yet aggressive nature has complicated the development of molecular markers for patient stratification. To analyze molecular differences linked to the protracted disease course of ACC and metastases that form 5 or more years after diagnosis, detailed RNA-sequencing (RNA-seq) analysis was performed on 68 ACC tumor samples, starting with archived, formalin-fixed paraffin-embedded (FFPE) samples up to 25 years old, so that clinical outcomes were available. A statistical peak-finding approach was used to classify the tumors that expressed MYB or MYBL1, which had overlapping gene expression signatures, from a group that expressed neither oncogene and displayed a unique phenotype. Expression of MYB or MYBL1 was closely correlated to the expression of the SOX4 and EN1 genes, suggesting that they are direct targets of Myb proteins in ACC tumors. Unsupervised hierarchical clustering identified a subgroup of approximately 20% of patients with exceptionally poor overall survival (median less than 30 months) and a unique gene expression signature resembling embryonic stem cells. The results provide a strategy for stratifying ACC patients and identifying the high-risk, poor-outcome group that are candidates for personalized therapies.

N-Terminal Truncated Myb with New Transcriptional Activity Produced Through Use of an Alternative MYB Promoter in Salivary Gland Adenoid Cystic Carcinoma

“…Transcriptional regulation of the MYB gene has not been studied in detail in ACC tumors, but in most tissues and tumor types, transcription of the gene initiates upstream of exon 1 at the normal promoter, designated here as TSS1 (Transcription Start Site 1, Figure 1A) [12,13]. Detailed analyses of RNA-sequencing (RNA-seq) studies of ACC tumors [7,8] have revealed that nearly all ACC tumors have very few reads aligned to the first exon of the MYB gene, suggesting an anomaly in its transcriptional regulation in ACC. In addition to the normal TSS1 promoter, several additional regulatory elements have been described in the MYB gene.…”

“…In addition, an infrequently used alternative promoter, designated here as TSS2, is located just upstream of exon 2 ( Figure 1A) [18,19]. We visually inspected the RNA-seq reads from two frozen ACC tumors (T73 and T9; clinical information [7]). Figure 1A shows a genome browser view of the RNA-seq coverage of the first four exons of the MYB gene.…”

“…ACC tumors have one of the highest rates of perineural invasion [5], a condition where tumor cells invade the surrounding nerves, which is associated with local tumor recurrence [6]. Recent studies have revealed previously unappreciated diversity amongst ACC tumors, with gene expression analyses exposing a poor-outcome patient group with a median survival of little more than two years [7]. Consequently, even after treatment, ACC patients face uncertain outcomes due to the likelihood for local recurrence, distant metastases, lack of targeted therapeutics, and intrinsic tumor diversity.…”

“…The NFIB gene is a common translocation partner, creating t(6;9) and t(8;9) fusions for the MYB and MYBL1 genes, respectively. However, less frequent translocations involving other genes also occur, suggesting that NFIB is not an obligatory fusion target [7]. Instead, the chromosomal translocations are thought to activate the expression of the MYB (or MYBL1) gene by recruiting distant enhancers that interact with the MYB promoter [11], implicating enhancer hijacking as a primary mechanism activating the MYB gene in ACC tumors.…”

Molecular features of adenoid cystic carcinoma with an emphasis on microRNA expression

“…18). However, in contrast to studies on gene expression of ACC, no difference in outcome was identified between these two groups (240). Although the survival curve of Group 1 had a somewhat steeper decline than that of Group 2, it remains speculative whether additional cases would have revealed a difference.…”