Genomic Patterns of Malignant Peripheral Nerve Sheath Tumor (MPNST) Evolution Correlate with Clinical Outcome and Are Detectable in Cell-Free DNA

Abstract

Malignant peripheral nerve sheath tumor (MPNST), an aggressive soft-tissue sarcoma, occurs in people with neurofibromatosis type 1 (NF1) and sporadically. Whole-genome and multiregional exome sequencing, transcriptomic, and methylation profiling of 95 tumor samples revealed the order of genomic events in tumor evolution. Following biallelic inactivation of NF1, loss of CDKN2A or TP53 with or without inactivation of polycomb repressive complex 2 (PRC2) leads to extensive somatic copy-number aberrations (SCNA). Distinct pathways of tumor evolution are associated with inactivation of PRC2 genes and H3K27 trimethylation (H3K27me3) status. Tumors with H3K27me3 loss evolve through extensive chromosomal losses followed by whole-genome doubling and chromosome 8 amplification, and show lower levels of immune cell infiltration. Retention of H3K27me3 leads to extensive genomic instability, but an immune cell-rich phenotype. Specific SCNAs detected in both tumor samples and cell-free DNA (cfDNA) act as a surrogate for H3K27me3 loss and immune infiltration, and predict prognosis.

Significance: MPNST is the most common cause of death and morbidity for individuals with NF1, a relatively common tumor predisposition syndrome. Our results suggest that somatic copy-number and methylation profiling of tumor or cfDNA could serve as a biomarker for early diagnosis and to stratify patients into prognostic and treatment-related subgroups. This article is highlighted in the In This Issue feature, p. 517.

Figure 1.

Genomic and pathology classification of MPNSTs. A, Overview of the experimental design and technologies utilized in this study. The GeM cohort consists of 95 tumor samples from 90 tumors (61 NF1-related and 29 sporadic), including 7 tumor samples without FFPE available for pathology review and confirmation of main tumor diagnosis. B, Relationship between NF1 status, biallelic inactivation of CDKN2A, and the PRC2 complex. The numbers on top of the bars indicate the total number of tumors in each group. C, Clinical information, histopathologic features and mutations in driver genes in the GeM cohort. Precursor lesions are marked by arrowheads. Sample labels not marked by an arrowhead correspond to high-grade MPNSTs. ANNUBP, atypical neurofibromatous neoplasms of uncertain biological potential; CN, copy number; GL, germline; INDEL, insertions and deletion; PV, pathogenic variant; RNA-seq, RNA sequencing; S, sporadic; SNV, single-nucleotide variants.

Figure 2.

MPNSTs stratify into two clinically and biologically distinct groups according to H3K27me3 status. A, Pathways related to immune activation are downregulated in tumors with loss of H3K27me3 estimated. B, Immune score analysis reveals decreased immune infiltration according to H3K27me3 status. C, Tumors with retention and loss of H3K27me3 are characterized by high levels of somatic copy-number alterations. D, Tumors with loss of H3K27me3 show significantly higher levels of genome-wide LOH as compared with tumors with retention of H3K27me3. E, Genome-wide analysis of the fraction of tumors showing amplification (black) and LOH (orange) based on H3K27me3 status. Representative copy-number profiles for tumors with loss of H3K27me3 showing near-haploidization (F) followed by WGD and chromosome 8q amplification (G). Box plots in B–D show the median, first, and third quartiles (boxes), and the whiskers encompass observations within a distance of 1.5 × the interquartile range from the first and third quartiles. Amp., amplification; chrom., chromosome.

Figure 3.

Recurrent copy-number aberrations predict patient outcome and are detected in cfDNA from NF1 patients. A, Kaplan–Meier plot showing the overall survival for NF1 individuals with high-grade MPNSTs stratified according to chromosome 5q LOH. B, Hazard ratios with 95% confidence intervals and P values computed using Cox proportional-hazards regression. C, Kaplan–Meier plot showing the overall survival for NF1 individuals with high-grade MPNSTs based on the amplification of chromosome 8q. D, Copy-number profiles estimated using ultra-low-pass WGS of cfDNA from patients with MPNST.

Figure 4.

MPNST evolution and intratumor heterogeneity. A, Phylogenetic tree inferred from SNVs detected using WGS data for a neurofibroma and a high-grade MPNST sample from individual TOR_002. Scale bar, 700 SNVs. B, Rearrangement profiles of a neurofibroma (top) and a high-grade MPNST (bottom) from patient TOR_002. The genomic position of CDKN2A, EED, TP53, and NF1 is shown at the top. Both tumors show biallelic inactivation of CDKNA and NF1 mediated by SVs. Total and minor copy-number values are shown in black and blue, respectively. Somatic events common to both tumors (NF1 deletion and 24 SNVs) and private to each of them are shown. C, Sequencing coverage calculated at 500 bp windows at the CDKN2A locus for the neurofibroma (top) and the high-grade MPNST (bottom). Dots corresponding to windows mapping to CDKN2A are shown in red. D, Difference in the timing of WGD events relative to the clonal expansion between MPNSTs with loss and retention of H3K27me3. ***, P < 0.001; two-sided Wilcoxon rank sum test. Phylogenetic trees inferred from SNVs detected using multiregional sequencing data from fresh-frozen samples for a neurofibroma (E), MPNSTs with loss (F), and retention (G) of H3K27me3. Each region (R) is arbitrarily named with a number. The scale bars indicate the number of SNVs. H, Genome-wide total copy-number profiles estimated using whole-exome sequencing data for a neurofibroma and MPNSTs with loss of H3K27me3. I, Genome-wide total copy-number profiles estimated using whole-exome sequencing data for MPNSTs with retention of H3K27me3. Box plots in D show the median, first, and third quartiles (boxes), and the whiskers encompass observations within a distance of 1.5 × the interquartile range from the first and third quartiles. Chrom., chromosome; MRCA, most recent common ancestor.

Figure 5.

Pathways of MPNST evolution. Schematic representation of the order and timing of events involved in the evolution of MPNSTs. Copy-number signatures predominant in specific karyotypic configurations are shown. chrom., chromosome; isochrom., isochromosome; PRC2, polycomb repressive complex 2.