Fig. 4: Parallel evolution of LMS tumors.

The clinical courses of two patients with LMS are shown (samples per patient >3). For the phylogenies, larger circles represent major clones, whereas smaller circles represent subclones. The color of each clone represents a distinct clone population. The clonal trajectory and final composition are shown per sample. Branch lengths are proportional to Treeomics mutation assignments. (a) Patient Ab6 was treated with radiofrequency ablation (RFA) and chemotherapy (chemo). They had three tumors at three separate time points (T1, T2, and T3). The primary tumor at diagnosis (Dx) was located in the small intestine, while the first metastatic relapse (MR1) was located in the liver. The second metastatic relapse (MR2) was multifocal and detected in the vastus lateralis (thigh muscle). MR2 was bisected and biopsies were taken from five distinct sections from both foci (Regions/Re 1–5). Following bulk (Dx, MR1) and multiregion (MR2) sequencing, phylogenetic reconstruction can be seen on the right. Early substitutions in TP53, RB1 and CREBBP, as well as LOH events of chromosomes 10 (PTEN), 13 (RB1), and 17 (TP53) are observed in the founder clone of this patient’s tumors. Chromosome 11 kataegis events and an SPEN deletion were common to Dx and MR2, but not MR1. Genome doubling and chromosome X kataegis occurred only in MR2. Metastatic multifocal nodes greatly resemble each other. Using clock-like mutagenesis, the Dx and MR1 diverge approximately 30 years pre-diagnosis in these patients, while Dx and MR2 diverge approximately 25 years pre-diagnosis. (b) Patient Ab11 was treated with radiation therapy (RT) and had two tumors at two separate time points (T1 and T2). The Dx was located at the posterior aspect of the right kidney and inferior vena cava. This tumor was bisected en face and biopsies were taken from four regions. The metastatic relapses (MR1-3) were taken from the liver. Following bulk (T2: MR1-3) and multiregion (T1: Dx, Regions/Re1-4) sequencing, phylogenetic reconstruction can be seen on the right. Much like Ab6, early losses of chromosomes 10, 13, and 17 are observed. Also seen early are AXIN1 and TET2 point mutations, an ATRX deletion, and a RB1 translocation. Chromosome 2 kataegis events are unique to Dx, while chr 6 chromothripsis events are unique to MR1-3. A chromosome12 kataegis event occurs only in 2/3 liver metastases. Using clock-like mutagenesis, Dx and MR1-3 diverge approximately 15 years pre-diagnosis in this patient.