Unmasking Intra-tumoral Heterogeneity and Clonal Evolution in NF1-MPNST

Abstract

Sarcomas are highly aggressive cancers that have a high propensity for metastasis, fail to respond to conventional therapies, and carry a poor 5-year survival rate. This is particularly true for patients with neurofibromatosis type 1 (NF1), in which 8%-13% of affected individuals will develop a malignant peripheral nerve sheath tumor (MPNST). Despite continued research, no effective therapies have emerged from recent clinical trials based on preclinical work. One explanation for these failures could be the lack of attention to intra-tumoral heterogeneity. Prior studies have relied on a single sample from these tumors, which may not be representative of all subclones present within the tumor. In the current study, samples were taken from three distinct areas within a single tumor from a patient with an NF1-MPNST. Whole exome sequencing, RNA sequencing, and copy number analysis were performed on each sample. A blood sample was obtained as a germline DNA control. Distinct mutational signatures were identified in different areas of the tumor as well as significant differences in gene expression among the spatially distinct areas, leading to an understanding of the clonal evolution within this patient. These data suggest that multi-regional sampling may be important for driver gene identification and biomarker development in the future.

Figure 1

Malignant peripheral nerve sheath tumor (MPNST) sampled areas. Area 1 shows an area centrally located in MPNST, Area 2 an area of hemorrhage, and Area 3 an area of necrosis.

Figure 2

H&E stained sections of the biopsy sites. H&E stained sections (20X) show areas (#1) of relatively uniform, spindled cells with fascicular growth pattern, characteristic for MPNST. Sampled area #2 shows evidence of hemorrhage within the tumor, a feature commonly seen in MPNST. Area #3 shows abundant tumor necrosis.

Figure 3

Location of NF1 germline variant. One intronic germline variant, NC_000017.11:g.31296270C>T (rs11080149). was identified and is depicted in this figure.

Figure 4

RNA-Seq Heatmap. Normalized read counts by counts per million (CPM) in differentially expressed genes are depicted here. Distinct gene expression profiles can be appreciated in each biopsied area. Each column is depicted as list of genes.

Figure 5

Copy Number Variation Plot. Copy number variation plots for each biopsied site demonstrate distinct copy number signatures.

Figure 6

Somatic Variant Waterfall Plot. All somatic variants displayed on a waterfall plot. Each row represents a gene. Distinct somatic variant signatures are appreciated.

Figure 7

Phylogenetic Tree. A predicted phylogenetic tree of the tumor subclones.