Loss of functionSMAD4nonstop mutations in human cancer

Abstract

BackgroundSMAD4is a tumour suppressor gene that is mutated in a variety of cancers.SMAD4nonstop mutations, which convert stop codons to sense codons that extend transcription, have been identified in genomic databases but have not been characterised in human pathology samples. The frequency ofSMAD4nonstop mutations and the consequences of nonstop mutations on SMAD4 protein expression are unknown.MethodsWe retrospectively analysed our cancer sequencing database of 38,002 tumour specimens and evaluated the spectrum ofSMAD4mutations. SMAD4 protein expression was evaluated by immunohistochemistry in tumours withSMAD4nonstop mutations.ResultsIn total, 1956SMAD4mutations were identified in 1822 tumours.SMAD4mutations were most common in tumours of the gastrointestinal tract and included nonsense variants (n = 344), frameshift indels (n = 258), splice site variants (n = 104), and missense variants at codon R361 (n = 245). In a subset of cases with immunohistochemistry, SMAD4 expression was lost in 23 of 25 tumours (92%) with protein truncating variants and in 7 of 27 tumours (26%) with missense variants. Four cases harbouredSMAD4nonstop mutations.SMAD4nonstop mutations were identified in two pancreatic adenocarcinomas, one colonic adenocarcinoma, and one non‐small cell lung carcinoma. Immunohistochemistry demonstrated loss of SMAD4 protein expression in each of the four tumours withSMAD4nonstop mutations.ConclusionSMAD4nonstop mutations are associated with loss of SMAD4 protein expression in multiple tumour types.SMAD4nonstop mutations should be clinically interpreted as pathogenic loss of function alterations when identified in cancer sequencing panels.