Novel variants ensued genomic imprinting in familial central precocious puberty

Abstract

Introduction: Central precocious puberty (CPP) is characterized by the early onset of puberty and is associated with the critical processes involved in the pubertal switch. The puberty-related gene pool in the human genome is considerably large though few have been described in CPP. Within those genes, the genomic imprinting features of the MKRN3 and DLK1 genes add additional complexity to the understanding of the pathologic pathways. This study aimed to investigate the molecular etiology in the CPP cohort.

Methods: Eighteen familial CPP cases were investigated by Sanger sequencing for five CPP-related genes; DLK1, KISS1, KISS1R, MKRN3, and PROKR2. Segregation analysis was performed in all patients with pathogenic variants. Using an ELISA test, the functional pathogenicity of novel variants was also investigated in conjunction with serum delta-like 1 homolog (DLK1) concentrations.

Results: In three probands, a known variant in the MKRN3 gene (c.982C>T/p.(Arg328Cys)) and two novel variants in the DLK1 gene (c.357C>G/p.(Tyr119Ter) and c.67+78C>T) were identified. All three were inherited from the paternal allele. The individuals carrying the DLK1 variants had low detectable DLK1 levels in their serum.

Conclusions: The frequencies were 5.5% (1/18) for MKRN3 11% (2/18) for DLK1, and none for either KISS1, KISS1R, and PROKR2. Low serum DLK1 levels in affected individuals supported the relationship between here described novel DLK1 gene variants with CPP. Nonsense nature of c.357C>G/p.(Tyr119Ter) and an alteration in the evolutionarily conserved nucleotide c.67+78C>T suggested the disruptive nature of the variant's compatibility with CPP.

Keywords: DLK1; MKRN3; Central precocious puberty.

Fig. 1

Pedigrees and sequencing data of three families a CPP-3 (III.1), b CPP-4 (III.1), c CPP-18 (III.1)) identified with the MKRN3 and the DLK1 gene variants. Arrow indicates probands, the open square indicates; male, and the open circle indicates; female. The (/) symbols represent deceased family members. The black symbols represent affected individuals, and the black dots represent asymptomatic carriers according to the imprinted patterns of inheritance. Mothers (a—I.3 and II.1, b—II.1 and c—II.1) without the mutation exhibited normal pubertal timing

Fig. 2

DLK1 serum levels in affected family members (CPP-3, CPP-4), CPP-18 case, and control groups. Affecteds had low detectable DLK1 serum levels compared to the control group. The symbol * represents the range of the lowest and highest serum levels detected in affected individuals. The assay limit of sensitivity of ~ 10 ng/L

Fig. 3

Schematic structure of the MKRN3 protein (507 aa/Q13064-Uniprot). The variants were reported from Türkiye (white arrow) and disclosed in this study (black arrow). aa; amino acids, ZNF; Zinc-Finger domains, Cys-His; Makorin type zing finger domain

Fig. 4

Schematic representation of the DLK1 gene (a) and DLK1 peptide (P80370-Uniprot) (b). The protein structure has one signal peptide (1–23aa), six tandem epidermal growth factor (EGF)-like repeat domains (24–245 aa), an extracellular region (246–303aa), a transmembrane region (304–327aa), and a cytoplasmic region (328–383aa). TM transmembrane, aa amino acids, EGF-LD EGF-like extracellular domains. The DLK1 gene variants previously reported in the literature are shown in nucleotides and peptides. Novel variants revealed in this study are written in bold letters