Intron Variant Cause DICER1 Syndrome With Pleuropulmonary Blastoma

Abstract

DICER1 syndrome (OMIM 601200) is a rare autosomal dominant familial tumor susceptibility disorder with heterozygous DICER1 germline mutations. The most common tumor in clinical practice is pleuropulmonary blastoma. Pleuropulmonary blastoma is a rare pediatric lung tumor that begins during fetal lung development and is part of an inherited tumor syndrome. We found a patient with pleuropulmonary blastoma in clinical practice and performed whole-exome testing on him and his parents. The mutation is located at DICER1 gene, c. 1510-16G>A. The tested person has a heterozygous variation at this locus. The tested person's father has no variation at this locus, while the tested person's mother has a heterozygous variation at this locus. According to the ACMG guidelines, this mutation has been preliminarily determined as clinically significant (uncertain) PM2_Supporting: The frequency of this supporting variation in the normal population database is unknown; there is no report of correlation for this locus in the literature database, and the ClinVar database does not feature this locus. In point pathogenicity analysis results, analysis of splicing was carried out by Sanger sequencing and RT-PCR from peripheral blood and a minigene splicing assay, both of which showed a deletion of exon 10 resulting from the c. 1510-16G>A variant at the mRNA level. Bioinformatic analysis of the reported c. 1510-16G>A variant suggests that the variant is pathogenic. Based on the clinical characteristics of the patient and the functional verification of the gene variants, our pediatricians have finally diagnosed the infant with pleuropulmonary blastoma (OMIM 601200). Our findings expand the mutation spectrum leading to DICER1 deficiency-related diseases and provide accurate information for genetic counseling.

Keywords: DICER1 gene; DICER1 syndrome; minigene splicing assay; pleuropulmonary blastoma.

Figure 1

Functions of DICER1. Illustrative scheme showing the canonical (siRNA and pre-miRNA processing) and noncanonical functions (chromatin remodeling, DNA repair, ribonucleoprotein granule formation, apoptosis promotion, and viral dsRNA degradation) of DICER.

Figure 2

The Sanger sequencing results of the variant c.1510-16G>A. The Sanger sequencing showed that c.1510-16G>A was maternally inherited.

Figure 3

Splicing study of DICER1 c.1510-16G>A. (a) The Sanger sequencing of RT-PCR products based on peripheral blood samples of the proband. (b) Schematic of splicing sequence for DICER1 c.1510-16G>A; blue nucleotides were the deletion of exon 10 (115 bp). The amino acids corresponding to the base sequence encoding are highlighted in yellow. Base deletion can lead to nonsense mutations WT: wild type; MT: mutation type. (c) Use the SWISS-MODEL website (https://swissmodel.expasy.org/) to predict the tertiary structure of proteins corresponding to amino acid sequences.

Figure 4

Splicing study of DICER1 c.1510-16G>A by minigene assay. (a) Agarose gel electrophoresis results of RT-PCR for the plasmid expression. (b) The Sanger sequencing of RT-PCR for the plasmid expression. (c) Schematic of splicing for c.1510-16G>A. WT: wild type; MT: mutation type.

Figure 5

Schematic diagram for DICER1 and landscape of intronic mutation. DICER1 contains 7 important domains helicase, required for interaction with PRKRA and TARBP2, dicer dsRNA-binding fold, PAZ, RNaseIIIa, RNaseIIIb, and DRBM. The reported 27 intronic mutation in DICER1 is shown over the diagram. The variants reported are shown in black, and the variant identified in this study is in red.