Glioblastoma (GBM) is a prototypical heterogeneous brain tumor refractory to conventional

Glioblastoma (GBM) is a prototypical heterogeneous brain tumor refractory to conventional therapy. can be broadly classified into linear recurrences that share extensive genetic similarity with the primary Sivelestat sodium salt
tumor and can be directly traced to one of its specific sectors and divergent recurrences that share few genetic alterations with the primary tumor and originate from cells that branched off early during tumorigenesis. Our study provides mechanistic insights into how genetic alterations in primary tumors impact the ensuing evolution of tumor cells and the emergence of subclonal heterogeneity. The presence of multiple cancer cell clones within a single tumor has been explained as a Darwinian process in which different clones compete for limited resources and the most Sivelestat sodium salt phenotypically fit Sivelestat sodium salt cells eventually prevail (Greaves and Maley 2012; Yates and Campbell 2012; Aparicio and Caldas 2013). It has been suggested that such heterogeneity allows a tumor to respond to local and systemic selective pressures such as those exerted by therapeutic interventions (Nowak and Sigmund 2004; Greaves and Maley 2012; Bozic et al. 2013). For example the presence of subclonal driver mutations in cancer cells was indicative of rapid disease progression in chronic lymphocytic leukemia (Landau et al. 2013). Using single-cell sequencing or massively parallel sequencing clonal architectures ranging from complex polyclonal structures to monoclonal tumors have Sivelestat sodium salt been described in cancer lineages such as those of the breast kidney and blood (Navin et al. 2011; Ding et al. 2012; Shah et al. 2012; Landau et al. 2013; Gerlinger et al. 2014). Distinct subclonal tumor cell populations relating to mosaic amplification of receptor tyrosine kinases were reported in glioblastoma (GBM) suggesting a similarly dynamic architecture for this disease (Snuderl et al. 2011; Nickel et al. 2012; Szerlip et al. 2012; Sottoriva et al. 2013). GBM is the most common malignant brain tumor in adults (Van Meir et al. 2010; Dunn et al. 2012) and is standardly treated with surgical resection followed by concomitant radiotherapy and administration of the alkylating agent temozolomide (TMZ) (Stupp et al. 2005). Despite this aggressive treatment regimen the median time to disease recurrence is 6.9 mo with >90% of GBM tumors recurring at the original site (Wen and Kesari 2008). Therapy targeting the epidermal growth factor receptor variant III (EGFRvIII) led to an improved overall survival time among patients with GBM; however 82 of these patients lost EGFRvIII expression when the tumor recurred which suggests a competitive advantage for non-EGFRvIII expressing clones in these tumors (Sampson et al. Rabbit Polyclonal to ATP5H. 2010). Achieving a better understanding of the clonal structure of cancer cells is thus of vital importance and may inform the development of additional targeted therapies for rapidly lethal forms of cancer such as GBM. Here we analyzed genomic profiles of 252 GBM samples from The Cancer Genome Atlas (TCGA) (Brennan et al. 2013) and 60 biopsies taken from 23 pairs of pre- and post-treatment GBMs to understand (1) the intratumoral clonal compositions of primary GBM; and (2) how GBM responds to therapeutic intervention. Our results provide a molecular portrait of GBM recurrence. Results Sample characteristics and mutation calling In this study we performed an analysis of genomic data from 252 untreated GBM samples from The Cancer Genome Atlas (cohort I). To study tumor responses to treatment we obtained a second cohort of tumor samples for which we collected pairs of primary and first recurrent GBM samples from 21 patients and added pairs of secondary GBM and next disease occurrence samples from two patients (cohort II). Prior to disease recurrence 21 patients in cohort II had received radiotherapy and 17 of them had also received adjuvant TMZ. A variety of treatments including carmustine and anti-inflammatory agents were administered to the remaining patients in cohort II. An R132 mutation was detected in two cases. The clinical data for cohort II is summarized in Supplemental Table 1. Integrative analysis identifies clonal and subclonal mutations To investigate the clonal architecture of GBM we classified somatic mutations into clonal and subclonal categories by integrating variant allele fraction DNA copy number genotype and tumor purity (Methods). We used PyClone a Bayesian clustering method that simultaneously estimates the distribution of the cellular frequency for each mutation (Roth et al. 2014). After correcting for.