We describe a novel gene fusion, EWSR1-CREM, identified in 3 cases of clear cell carcinoma (CCC) using anchored multiplex polymerase chain reaction, a next-generation sequencing-based technique. CCC is a low-grade salivary tumor recently characterized to have EWSR1-ATF1 fusions in the majority of cases. Three cases of malignant tumor presenting in the base of tongue, lung, and nasopharynx were studied. All cases shared a clear cell morphology with hyalinized stroma, presence of mucin and p63 positivity and were initially diagnosed as mucoepidermoid carcinoma but were negative for evidence of any of the expected gene fusions. Anchored multiplex polymerase chain reaction demonstrated a EWSR1-CREM fusion in all 3 cases to confirm a diagnosis of CCC. This finding is biologically justified as CREM and ATF1 both belong to the CREB family of transcription factors. EWSR1-CREM fusions have not been previously reported in CCC and have only rarely been reported in other tumors. We show that the ability to discover novel gene variants with next-generation sequencing-based assays has clinical utility in the pathologic classification of fusion gene-associated tumors.

Pulmonary hyalinizing granulomas (PHGs) are unusual fibrosclerotic inflammatory lung lesions. The organ-based manifestations of the recently defined IgG4-related sclerosing disease typically show dense fibrosis and heavy lymphoplasmacytic infiltrates. IgG4-related sclerosing disease is also defined by increased serum IgG4 levels and increased tissue levels of IgG4-positive plasma cells. The morphologic features of PHG overlap with those seen in IgG4-related sclerosing disease, and this suggests that PHG may be a form of IgG4-related sclerosing disease. We present a case of a 51-year-old man with a history of sarcoidosis who presented with slowly enlarging pulmonary nodules. Histologic evaluation of one of the nodules yielded a diagnosis of PHG. Further investigation demonstrated both elevated serum IgG4 and elevated tissue IgG4-positive plasma cells in the PHG. In previous reports, lesions that are now considered part of IgG4-related sclerosing disease were documented in patients also diagnosed with PHG, although these reports date from before the description of IgG4 sclerosing disease. This case provides the first definitive evidence that PHG is part of the spectrum of IgG4-related sclerosing disease.

Metastatic adenoid cystic carcinomas (ACCs) can cause significant morbidity and mortality. Because of their slow growth and relative rarity, there is limited evidence for systemic therapy regimens. Recently, molecular profiling studies have begun to reveal the genetic landscape of these poorly understood cancers, and new treatment possibilities are beginning to emerge. The objective is to use whole-genome and transcriptome sequencing and analysis to better understand the genetic alterations underlying the pathology of metastatic and rare ACCs and determine potentially actionable therapeutic targets. We report five cases of metastatic ACC, not originating in the salivary glands, in patients enrolled in the Personalized Oncogenomics (POG) Program at the BC Cancer Agency. Genomic workup included whole-genome and transcriptome sequencing, detailed analysis of tumor alterations, and integration with existing knowledge of drug–target combinations to identify potential therapeutic targets. Analysis reveals low mutational burden in these five ACC cases, and mutation signatures that are commonly observed in multiple cancer types. Notably, the only recurrent structural aberration identified was the well-described MYB-NFIB fusion that was present in four of five cases, and one case exhibited a closely related MYBL1-NFIB fusion. Recurrent mutations were also identified in BAP1 and BCOR, with additional mutations in individual samples affecting NOTCH1 and the epigenetic regulators ARID2, SMARCA2, and SMARCB1. Copy changes were rare, and they included amplification of MYC and homozygous loss of CDKN2A in individual samples. Genomic analysis revealed therapeutic targets in all five cases and served to inform a therapeutic choice in three of the cases to date.

No abstract