Germline nonsense mutation and somatic inactivation of SMARCA4/BRG1 in a family with rhabdoid tumor predisposition syndrome

Abstract

Rhabdoid tumors of early infancy are highly aggressive with consequent poor prognosis. Most cases show inactivation of the SMARCB1 (also known as INI1 and hSNF5) tumor suppressor, a core member of the ATP-dependent SWI/SNF chromatin-remodeling complex. Familial cases, described as rhabdoid tumor predisposition syndrome (RTPS), have been linked to heterozygous SMARCB1 germline mutations. We identified inactivation of another member of the SWI/SNF chromatin-remodeling complex, its ATPase subunit SMARCA4 (also known as BRG1), due to a SMARCA4/BRG1 germline mutation and loss of heterozygosity by uniparental disomy in the tumor cells of two sisters with rhabdoid tumors lacking SMARCB1 mutations. SMARCA4 is thus a second member of the SWI/SNF complex involved in cancer predisposition. Its general involvement in other tumor entities remains to be established.

Figure 1

Synopsis of Clinical and Molecular Data of the Investigated Family (A) T1-weighted imaging with contrast demonstrates in axial, coronal, and sagittal planes (from left) a cerebellopontine angle tumor with a heterogeneous enhancement pattern and infiltration of the brainstem indicative of a highly malignant neoplasm in patient III-2. (B) MRI and CT imaging of patient III-3 demonstrates a large right flank mass originating from the kidney with metastases to the lungs (yellow arrows) and mediastinum. (C) Pedigree of the investigated family and segregation of the SMARCA4 nonsense mutation. The unaffected sibling, individual III-1, was not available for investigation. (D) Domain structure of normal SMARCA4 and of the derived p.R1189X truncation mutant. The truncated protein would lack the C-terminal part of the ATPase subunit, the AT hook, and the Bromo domain.

Figure 2

SMARCA4 Immunohistochemistry and Molecular Studies (A) Identification of the nonsense mutation p.R1189X (c.3565C>T) in germline DNA, detection of loss of heterozygosity in tumor DNA (Tu-DNA), and low concentration mutant cDNA obtained by RT PCR from patient III-3's immortalized B cells compared to the heterozygous state seen in genomic germline DNA (gDNA). (B) Copy-neutral loss of heterozygosity in 19p containing the SMARCA4 locus in the RT of patient III-2. 100K SNP array (GeneChip Human Mapping 100K Set, Affymetrix; Santa Clara, CA, USA) mapping was performed on DNA derived from the RT of patient III-2, as well as from germline DNA of the father (II-1, for comparison). Analysis of chromosome 19 is displayed with black dots (raw copy-number data smoothed by a median filter) and a red line showing copy-number estimations derived from the Copy Number Analyser for GeneChip (2 = balanced) of the RT of patient III-2 (the gain in 19q derived from a known copy-number variant). Heterozygous calls are indicated by green dots (RT of III-2) and blue dots (germline DNA of the father, II-1). In contrast to II-1, the RT of III-2 shows loss of heterozygosity in 19p (gray shaded area, chr19: 341,341–13,425,865 bp), containing the SMARCA4 gene at chr19:10,932,598–11,033,958 (based on the May 2004 UCSC Genome Browser; hg17). (C–E) Immunohistochemistry. Tumor cells from both case individuals (C: patient III-2, AT/RT; D: patient III-3, RTK) lack SMARCA4 staining; immunoreactivity remains restricted to the vasculature. In contrast, 14 sporadic AT/RT (E) (representative staining result) as well as a panel of embryonal tumors (inset) display nuclear SMARCA4 staining. (F) Lack of expression of truncated mutant SMARCA4 in immortalized B cell lines of patient III-3 in comparison to B cells of her mother (II-2) and of a normal control (N). Arrow points to truncated recombinant mutant SMARCA4 (rm) overexpressed in the SMARCA4-negative cell line NCI H1299. −C: nontransfected NCI H1299 as negative control. (G) Expression of two naturally occurring splice variants of SMARCA4 (one without exon 27 and one including exon 27), both harboring the p.R1189X mutation, in comparison to recombinant WT SMARCA4 in different cell lines. 1 and 7: nontransfected HELA cells constitutively expressing SMARCA4, 2–6: 293-EBNA cells constitutively expressing SMARCA4 (2: mock transfection, 3: WT SMARCA4 long splice variant, 4: mutant SMARCA4 long splice variant, 5: WT SMARCA4 short splice variant, 6: mutant SMARCA4 short splice variant). 8–12: NCI-H1299 cells lacking constitutive SMARCA4 expression (8: mock transfection, 9: WT SMARCA4 long splice variant, 10: mutant SMARCA4 long splice variant, 11: WT SMARCA4 short splice variant, 12: mutant SMARCA4 short splice variant). The truncated mutant p.R1189X fragment is expressed under a strong cytomegalovirus promoter and is clearly separated from WT SMARCA4 by electrophoresis. Size differences between the long and the short SMARCA4 splice variants are not visible because of limited electrophoretic resolution.