Integrative genomic analysis of salivary duct carcinoma

Abstract

Salivary duct carcinoma (SDC) is one of the most aggressive subtypes of salivary gland cancers. Conventional chemotherapy and/or radiation have shown only limited clinical efficacy in the treatment of recurrent or metastatic SDC. Currently, clinically approved targeted-therapeutics are not generally applicable except in very limited cases, and there exists a strong need for the development of treatment against this unique tumor type. To further interrogate genomic features of SDC, we have conducted multi-omic profiling of the SDC to describe the genomic alterations prevalent in this disease. Whole-genome sequencing, whole exome-sequencing and transcriptome sequencing were performed on a discovery cohort of 10 SDC samples. Targeted genomic profiling was performed in additional 32 SDC samples to support the findings obtained from the original discovery cohort. The cancer cohort was characterized by an average mutation burden of 85 somatic exonic mutations per tumor sample. The cohort harbored a mutational signature of BRCA and APOBEC/AID. Several genes, including TP53, RB1, SMAD4, HRAS, APC, PIK3CA and GNAQ were recurrently somatically altered in SDC. A novel fusion gene, generated by genomic rearrangement, MYB-NHSL1, was also noted. Our findings represent a significant layer in the systematic understanding of potentially clinically useful genomic and molecular targets for a subset of recurrent/metastatic SDC.

Figure 1

Clinico-pathological characterization and genetic aberrations across 42 salivary duct carcinomas. The clinic-pathological features were depicted in the top panel. The first row indicates gender, the second row smoking-status and the third row Androgen Receptor staining. The panel in the middle is the heatmap representation of individual mutations present in 42 salivary duct cancer samples in association with information from the top panel. It shows the mutational types in a given sample and in a given gene in 2-dimensional matrix format. (Left) Percentage of mutations in each gene in the cohort. (Right) List of recurrently mutated genes. The panel in the bottom is the heatmap of somatic copy number alterations (SCNAs) of SDC samples in association with panels in the top and in the middle. Significant SCNAs are shown. SCNAs were categorized into 4 different classes, depending on the degree of SCNAs; deletion, copy-loss, copy-gain and amplification.

Figure 2

Functional profiling and network analysis of SDC somatic mutations. Ordered list of somatic mutations frequently observed in SDC were used as input for characterizing the gene list. Molecular processes functionally enriched in SDC were annotated in the clustered nodes of the network, the analyses of which is described in the method section.

Figure 3

Mutational signature analysis of SDC. (A) Mutational signature analysis of SDC cohort. Point mutations of SDC samples were aggregated to form a set of ‘ensemble SDC mutations’. This ensemble mutation set was used in mutation signature analysis to decipher representative signatures in SDC cohort. (B) Contribution of mutation signatures to each SDC sample. Somatic mutations identified from genomic sequencing of SDC samples were subjected to mutation signature analysis per sample. Patterns of 1937 single-nucleotide mutations in 10 SDC samples were analyzed and the contribution of each signature to the mutagenesis of SDC samples are shown. X-axis is the name of sample and y-axis is the relative contribution of mutation signature normalized per sample. (C) Comparison of mutation rate between samples with and without APOBEC/AID signatures. The number of somatic mutations in the exonic region of SDC between groups with and without APOBEC/AID signatures (signature 2,13/9) were compared and presented in the box-plot.

Figure 4

MYB-NSHL1 fusion gene in SDC. (A) Representation of DNA rearrangements in MYB-NHSL1 fusion SDC samples. MYB and NHSL1 genes are located in the same chromosome 6, separated by around 3.2 megabase. The complex genomic DNA rearrangement event involving chromosome 6 relocates MYB and MHSL1 gene in reverse orientation, producing the MYB-NHSL1 fusion gene. (B) MYB-NHSL1 fusion identified from RNA-sequencing. 60 split-reads that span the MYB-NHSL1 junction are depicted. (C) MYB-NHSL1 rearrangement-specific PCR reaction from genomic DNA derived from SDC patients. Sequencing chromatogram of a patient spanning the fusion junction. Sample 1 is the SDC sample harboring MYB-NSHL1 and sample 2 is a control SDC sample.