Whole-Exome Sequencing Reveals High Prevalence of Germline Alterations in Neuroendocrine Neoplasms

Beyond syndromic tumor-predisposing conditions, germline susceptibility to neuroendocrine neoplasms (NENs) is not well understood. Familial clustering of cases and the co-occurrence of additional malignancies in patients suggest that additional, thus far unrecognized, germline predispositions to NEN development may exist.

We conducted whole-exome sequencing of germline and somatic DNA from a prospective cohort of patients with NENs (n=144) treated at The Ohio State University. Gene ontology analysis was performed using the DAVID algorithm. Multiplex immunofluorescence (mIF) was conducted on samples with germline MUTYH (gMUTYH) alterations. Clinical data from patients with gMUTYH alterations who were treated with immune checkpoint inhibition (ICI) were also abstracted.

A total of 144 samples were sequenced, revealing 3,400 variants, including 75 pathogenic and 99 likely pathogenic. Pathogenic/likely pathogenic variants were found in 78% of patients (112/144), across 127 genes. Pathogenic variants alone were identified in 45% (65/144), across 57 genes. Recurrent alterations were detected in 37 genes (frequency, false discovery rate), including MEN1 (5%; 1.22E-17), MUTYH (5%; 0.003), PKD1 (5%; 0.003), ATP4A (4%; 0.04), and PAH (4%; 0.003). The 3 most commonly involved pathways were DNA repair (26%), cellular calcium signaling (14%), and epigenetic regulation (7%). gMUTYH alterations were associated with high somatic tumor mutational burden in 3 of 6 patients. Among 5 subjects with gMUTYH, 2 showed a high levels of CD3+ and CD11c+ immune infiltration on mIF. Separately, we reported 2 cases of gMUTYH-altered NENs with robust responses to ICI.

Approximately 45% of patients with NENs harbor pathogenic germline variants on whole-exome sequencing. A subset of patients with gMUTYH alterations demonstrate a high tumor mutational burden, rich immune infiltration, and significant responses to ICI.