Whole-genome and multisector exome sequencing of primary and post-treatment glioblastoma reveals patterns of tumor evolution

Abstract

Glioblastoma (GBM) is a prototypical heterogeneous brain tumor refractory to conventional therapy. A small residual population of cells escapes surgery and chemoradiation, resulting in a typically fatal tumor recurrence ∼7 mo after diagnosis. Understanding the molecular architecture of this residual population is critical for the development of successful therapies. We used whole-genome sequencing and whole-exome sequencing of multiple sectors from primary and paired recurrent GBM tumors to reconstruct the genomic profile of residual, therapy resistant tumor initiating cells. We found that genetic alteration of the p53 pathway is a primary molecular event predictive of a high number of subclonal mutations in glioblastoma. The genomic road leading to recurrence is highly idiosyncratic but can be broadly classified into linear recurrences that share extensive genetic similarity with the primary 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.

Clonal Heterogeneity and Tumor Evolution: Past, Present, and the Future

“…Such studies may also allow new insights into the processes generating diversity and reveal how constraints to tumor evolution may be exploited, leveraging an adaptive immune response, permitting proactive management of cancers. (Nikbakht et al, 2016); Neuroblastoma (Eleveld et al, 2015); low-grade gliomba/glioblastoma multiforme Kim et al, 2015;Wang et al, 2016); breast cancer (Yates et al, 2015); clear cell renal cell carcinoma (Gerlinger et al, 2014a); multiple myeloma (Bolli et al, 2014); lung adenocarcinomas (de Bruin et al, 2014;Zhang et al, 2014);…”

“…Predominantly this likely reflects the fact that distinct mutational processes may operate at different times in tumor evolution (de Bruin et al, 2014;McGranahan et al, 2015;Nik-Zainal et al, 2012). Indeed, the most notable outliers with regard to high subclonal mutational burden, but low clonal burden, are low-grade gliomas that recur as glioblastomas after treatment with the alkylating agent temozolomide Kim et al, 2015). In this case, the abundance of subclonal mutations can be directly linked to therapyinduced mutations that are compounded by loss of mismatch repair machinery.…”

“…Just as genotoxic damage can foster the emergence of drug resistant cells and histological transformation of the tumor into a high-grade recurrence Kim et al, 2015), the stroma can also be adversely affected by genotoxic agents to support the survival of cancer cells in the face of such selection pressures. Genotoxic therapy can promote the microenvironmental secretion of WNT16B that reduces the impact of cytotoxic therapy upon prostate cancer cells in vivo (Sun et al, 2012).…”

“…As the resolution of cancer evolutionary analyses improves, the number of examples of parallel evolution increases, including but not limited to events involving EGFR in glioblastoma (Francis et al, 2014;Kim et al, 2015), TP53 and ATRX in glioma , activation of the MAPK pathway in multiple myeloma (Bolli et al, 2014;Melchor et al, 2014), NOTCH1 and GNPTAB recurrent mutations in esophageal adenocarcinoma (Murugaesu et al, 2015), SMO mutations in medulloblastoma (Morrissy et al, 2016), distinct AR amplification events in prostate cancer (Gundem et al, 2015), KMTD2D and CREBBP mutations in follicular lymphoma (Okosun et al, 2014) and PTEN and TP53 mutations, FGFR2 amplifications and RUNX1 deletions in primary breast cancer (Yates et al, 2015), as well as distinct CCNE1 amplifications in ovarian cancers (McPherson et al, 2016). In clear cell renal carcinoma, an early clonal event is 3p loss of heterozygosity, which appears to prime the tumor for second hits in SETD2, PBRM1 and BAP1 (all of which are encoded on chromosome 3p) later in tumor evolution (Gerlinger et al, 2014a).…”

Molecular Diagnosis of Diffuse Gliomas through Sequencing of Cell-Free Circulating Tumor DNA from Cerebrospinal Fluid

“…However, characterization of cancer is challenged by evolving intratumor heterogeneity, which requires thorough and continuous analysis of genomic complexity over time. This is particularly relevant in brain malignancies where the genomic landscape changes in response to treatment or during relapse (7,8). However, availability of glioma samples for characterization and correct diagnosis can be challenging.…”