A novel likely pathogenetic variant p.(Cys235Arg) of the MEN1 gene in multiple endocrine neoplasia type 1 with multifocal glucagonomas

Abstract

Purpose: Multiple endocrine neoplasia type 1 (MEN1) is a hereditary endocrine syndrome caused by pathogenic variants in MEN1 tumor suppressor gene. Diagnosis is commonly based on clinical criteria and confirmed by genetic testing. The objective of the present study was to report on a MEN1 case characterized by multiple pancreatic glucagonomas, with particular concern on the possible predisposing genetic defects.

Methods: While conducting an extensive review of the most recent scientific evidence on the unusual glucagonoma familial forms, we analyzed the MEN1 gene in a 35-year-old female with MEN1, as well as her son and daughter, using Sanger and next-generation sequencing (NGS) approaches. We additionally explored the functional and structural consequences of the identified variant using in silico analyses.

Results: NGS did not show any known pathogenic variant in the tested regions. However, a new non-conservative variant in exon 4 of MEN1 gene was found in heterozygosity in the patient and in her daughter, resulting in an amino acid substitution from hydrophobic cysteine to hydrophilic arginine at c.703T > C, p.(Cys235Arg). This variant is absent from populations databases and was never reported in full papers: its characteristics, together with the high specificity of the patient's clinical phenotype, pointed toward a possible causative role.

Conclusion: Our findings confirm the need for careful genetic analysis of patients with MEN1 and establish a likely pathogenic role for the new p.(Cys235Arg) variant, at least in the rare subset of MEN1 associated with glucagonomas.

Keywords: Adrenal gland adenoma; Familiar; Necrolytic migratory erythema; Neuroendocrine pancreatic tumor; Next-generation sequencing; Primary hyperparathyroidism.

Fig. 1

Timeline with relevant data from the clinical history

Fig. 2

Reverse and forward Sanger sequencing, confirming on a second DNA extraction from peripheral blood the c.703T > C nucleotide substitution (indicated by the arrow) in MEN1 exon 4 (NM_000244.3) identified by next-generation sequencing

Fig. 3

Sequence alignment of menin protein across 12 species (human amino acids from 224 to 246). Cysteine 235 is within the red rectangle

Fig. 4

Analysis of the structural impact of the missense variant recognizes for cysteine 235 of menin (sequence browser: O00255-1) highest buried and hydrophobicity indices suggesting a deleterious effect for p.Cys235Arg substitution (Missense3D)

Fig. 5

Crystallographic structure of the menin protein showing an "internal" (buried) position for the hydrophobic cysteine 235 and a high score of intolerability toward any amino acid substitution in this protein position with particular regard to hydrophilic and charged residues such as a basic arginine. The higher and red the bars are, the more the amino acid substitution is predicted not tolerated (Missense3D)

Fig. 6

Steric clash analysis of the menin protein with arginine at position 235, instead of cysteine, suggests a high rate of clashes that means bad side-chain placement, or possibly an incorrect backbone in the region (Phyre2)