Discordant inheritance of chromosomal and extrachromosomal DNA elements contributes to dynamic disease evolution in glioblastoma

Abstract

To understand how genomic heterogeneity of glioblastoma contributes to the poor response to therapy characteristic of this disease, we performed DNA and RNA sequencing on GBM tumor samples and the neurospheres and orthotopic xenograft models derived from them. We used the resulting data set to show that somatic driver alterations including single nucleotide variants, focal DNA alterations, and oncogene amplification on extrachromosomal DNA (ecDNA) elements were in majority propagated from tumor to model systems. In several instances, ecDNAs and chromosomal alterations demonstrated divergent inheritance patterns and clonal selection dynamics during cell culture and xenografting. We infer that ecDNA inherited unevenly between offspring cells, a characteristic that affects the oncogenic potential of cells with more or fewer ecDNAs. Longitudinal patient tumor profiling found that oncogenic ecDNAs are frequently retained throughout the course of disease. Our analysis shows that extrachromosomal elements allow rapid increase of genomic heterogeneity during glioblastoma evolution, independent of chromosomal DNA alterations.

Cancer avatars derived from genetically engineered pluripotent stem cells allow for longitudinal assessment of tumor development

“…6E). This supports a clonally unstable nature of the TP53 -/-;PDGFRA Δ 8-9 model, where genomic instability or ecDNA could be driving dynamic accelerated clonal evolution29,30 .iHGG tumors confirm features characteristic of patient tumor samples.We also applied unsupervised Louvain clustering of PTEN -/-;NF1 -/-iHGG secondary tumors (Fig. 7ai) and, in parallel, TP53 -/-;PDGFRA Δ 8-9 iHGG secondary tumors(Fig.…”

Primary and recurrent glioma patient-derived orthotopic xenografts (PDOX) represent relevant patient avatars for precision medicine

“…Subclonal fractions were also retained in longitudinal models of patients LIH0192 and LIH0347, although certain fluctuations in cellular prevalence were observed (Figure 3f, Figure S3e). Interestingly, we also observed evolutionary dynamics in EGFR amplicons (Figure S3f), arising most probably from evolutionary trajectories of extrachromosomal double minutes 51 . In summary, glioma PDOXs largely recapitulate genetic aberrations and genetic heterogeneity of parental tumors.…”

“…Most glioma PDX models are derived by subcutaneous implantation of tumor fragments 66,67 , which may not accurately mimic the complex and distinctive brain microenvironment. As direct implantation of tissue fragments to rodent brains is challenging, GBM orthotopic xenografts usually rely on single cell dissociation followed by in vitro cultures prior to xenotransplantation 51,66,[68][69][70] , where cultures are often maintained for unspecified time and passage number. To minimize the loss of tissue architecture and heterogeneity, which may lead to clonal selection and adaptation 71,72 , we derive organoids from mechanically minced glioma tissue, which is only briefly maintained in culture without any in vitro passaging.…”

“…Interestingly, we report a case of EGFR variant selection, observed both upon tumor relapse in patients as well as upon xenografting. This may be linked to high levels of EGFR amplification and the presence of extrachromosomal double minute structures, which are known to show evolutionary dynamics 51 . In rare cases PDOX models showed engraftment or expansion of specific genetic clones, with distinct gene amplifications or mutations, differing from the originating tumor.…”

Cell-Free eccDNAs: A New Type of Nucleic Acid Component for Liquid Biopsy?

“…For example, DMs, exclusively found in tumor cells (13) and drug-resistance cells (43), significantly elevate the active gene transcripts to promote tumor progression. Because of their self-replication and uneven segregation, DMs are related to tumor cell heterogeneity and adaptation (44). In a recent study, extrachromosomal gene amplification was proved to drive tumor evolution and heterogeneity, with higher efficiency than the intrachromosomal gene amplification (40).…”