Molecular Heterogeneity in Pediatric Malignant Rhabdoid Tumors in Patients With Multi-Organ Involvement

Abstract

Rhabdoid tumors (RTs) of the brain (atypical teratoid/rhabdoid tumor; AT/RT) and extracranial sites (most often the kidney; RTK) are malignant tumors predominantly occurring in children, frequently those with SMARCB1 germline alterations. Here we present data from seven RTs from three pediatric patients who all had multi-organ involvement. The tumors were analyzed using a multimodal molecular approach, which included exome sequencing of tumor and germline comparator and RNA sequencing and DNA array-based methylation profiling of tumors. SMARCB1 germline alterations were identified in all patients and in all tumors. We observed a second hit in SMARCB1 via chr22 loss of heterozygosity. By methylation profiling, all tumors were classified as rhabdoid tumors with a corresponding subclassification within the MYC, TYR, or SHH AT/RT subgroups. Using RNA-seq gene expression clustering, we recapitulated the classification of known AT/RT subgroups. Synchronous brain and kidney tumors from the same patient showed different patterns of either copy number variants, single-nucleotide variants, and/or genome-wide DNA methylation, suggestive of non-clonal origin. Furthermore, we demonstrated that a lung and abdominal metastasis from two patients shared overlapping molecular features with the patient's primary kidney tumor, indicating the likely origin of the metastasis. In addition to the SMARCB1 events, we identified other whole-chromosome events and single-nucleotide variants in tumors, but none were found to be prognostic, diagnostic, or offer therapeutic potential for rhabdoid tumors. While our findings are of biological interest, there may also be clinical value in comprehensive molecular profiling in patients with multiple rhabdoid tumors, particularly given the potential prognostic and therapeutic implications for different rhabdoid tumor subgroups demonstrated in recent clinical trials and other large cohort studies.

Keywords: DNA methylation array; SMARCB1; atypical teratoid/rhabdoid tumor (AT/RT); malignant rhabdoid tumor (MRT); next-generation sequencing.

Figure 1

–3Clonality analysis. River plots showing the composition of clones in multiple tumor samples plus matched normal blood (germline) sample. Vertical lines indicate a sample, labeled on the X-axis. Colored circles indicate the origins of a clone from a single cell, either of the germline (black) or a preceding clone. Colored outlines show the cellularity of clones (Y-axis) in each sample. The percentages shown (in white or black text) indicate the cellularity of a tumor clone in each sample that was identified, excluding the cells of any descendant clones. Clone percentages sum up to the total tumor cellularity of a sample. The samples are arranged to most clearly visualize clonal descent but do not represent a formal time-series. The copy number variants, loss-of-heterozygosity events, and single-nucleotide variants identified in the tumor samples as well as relevant germline predisposition variants are listed on the right and colored by which clone they belong to.

Figure 2

River plots show the composition of clones in multiple tumor samples plus matched normal blood (germline) sample. Vertical lines indicate a sample, labeled on the X-axis. Colored circles indicate the origins of a clone from a single cell, either of the germline (black) or a preceding clone. Colored outlines show the cellularity of clones (Y-axis) in each sample. Percentages shown (in white or black text) indicate the cellularity of a tumor clone in each sample that was identified, excluding the cells of any descendant clones. Clone percentages sum to the total tumor cellularity of a sample. Samples are arranged to most clearly visualize clonal descent but do not represent a formal time-series. Copy number variants (CNVs), loss-of-heterozygosity events (LOH), and single nucleotide variants (SNVs) identified in the tumor samples, as well as relevant germline predisposition variants, are listed on the right and colored by which clone they belong to.

Figure 3

River plots show the composition of clones in multiple tumor samples plus matched normal blood (germline) sample. Vertical lines indicate a sample, labeled on the X-axis. Colored circles indicate the origins of a clone from a single cell, either of the germline (black) or a preceding clone. Colored outlines show the cellularity of clones (Y-axis) in each sample. Percentages shown (in white or black text) indicate the cellularity of a tumor clone in each sample that was identified, excluding the cells of any descendant clones. Clone percentages sum to the total tumor cellularity of a sample. Samples are arranged to most clearly visualize clonal descent but do not represent a formal time-series. Copy number variants (CNVs), loss-of-heterozygosity events (LOH), and single nucleotide variants (SNVs) identified in the tumor samples, as well as relevant germline predisposition variants, are listed on the right and colored by which clone they belong to.