Biology subjects

Kanu, N.

Publications and source records attributed to Kanu, N..

4 recordsLinked to original sources

bioRxiv2024

Extrachromosomal DNA driven oncogene spatial heterogeneity and evolution in glioblastoma

Oncogene amplification on extrachromosomal DNA (ecDNA) is strongly associated with treatment resistance and shorter survival for patients with cancer, including patients with glioblastoma. The non-chromosomal inheritance of ecDNA during cell division is a major contributor to intratumoral genetic heterogeneity. At present, the spatial dynamics of ecDNA, and the impact on tumor evolutionary trajectories, are not well understood. Here, we investigate the spatial-temporal evolution of ecDNA and its clinical impact by analyzing tumor samples from 94 treatment-naive human IDH-wildtype glioblastoma patients. We developed a spatial-temporal computational model of ecDNA positive tumors ( SPECIES) that integrates whole-genome sequencing, multi-region DNA FISH, and nascent RNAscope, to provide unique insight into the spatial dynamics of ecDNA evolution. Random segregation in combination with positive selection of ecDNAs induce large, predictable spatial patterns of cell-to-cell ecDNA copy number variation that are highly dependent on the oncogene encoded on the circular DNA. EGFR ecDNAs often reach high mean copy number (mean of 50 copies per tumor cell), are under strong positive selection (mean selection coefficient, s > 2) and do not co-amplify other oncogenes on the same ecDNA particles. In contrast, PDGFRA ecDNAs have lower mean copy number (mean of 15 copies per cell), are under weaker positive selection and frequently co-amplify other oncogenes on the same ecDNA. Evolutionary modeling suggests that EGFR ecDNAs often accumulate prior to clonal expansion. EGFR structural variants, including vIII and c-terminal deletions are under strong positive selection, are found exclusively on ecDNA, and are intermixed with wild-type EGFR ecDNAs. Simulations show EGFRvIII ecDNA likely arises after ecDNA formation in a cell with high wild-type EGFR copy number (> 10) before the onset of the most recent clonal expansion. This remains true even in cases of co-selection and co-amplification of multiple oncogenic ecDNA species in a subset of patients. Overall, our results suggest a potential time window in which early ecDNA detection may provide an opportunity for more effective intervention. HighlightsO_LIecDNA is the most common mechanism of focal oncogene amplification in IDHwt glioblastoma. C_LIO_LIEGFR and its variants on ecDNA are particularly potent, likely arising early in tumor development, providing a strong oncogenic stimulus to drive tumorigenesis. C_LIO_LIWild-type and variant EGFR ecDNA heteroplasmy (co-occurrence) is common with EGFRvIII or c-terminal deletions being derived from EGFR wild-type ecDNA prior to the most recent clonal expansion. C_LIO_LITumors with ecDNA amplified EGFR versus PDGFRA exhibit different evolutionary trajectories. C_LIO_LISPECIES model can infer spatial evolutionary dynamics of ecDNA in cancer. C_LIO_LIA delay between ecDNA accumulation and subsequent oncogenic mutation may give a therapeutic window for early intervention. C_LI

cancer biology↗

bioRxiv2020

Targeted cancer therapy induces APOBEC fuelling the evolution of drug resistance

Introductory paragraphThe clinical success of targeted cancer therapy is limited by drug resistance that renders cancers lethal in patients1-4. Human tumours can evolve therapy resistance by acquiring de novo genetic alterations and increased heterogeneity via mechanisms that remain incompletely understood1. Here, through parallel analysis of human clinical samples, tumour xenograft and cell line models and murine model systems, we uncover an unanticipated mechanism of therapy-induced adaptation that fuels the evolution of drug resistance. Targeted therapy directed against EGFR and ALK oncoproteins in lung cancer induced adaptations favoring apolipoprotein B mRNA-editing enzyme, catalytic polypeptide (APOBEC)-mediated genome mutagenesis. In human oncogenic EGFR-driven and ALK-driven lung cancers and preclinical models, EGFR or ALK inhibitor treatment induced the expression and DNA mutagenic activity of APOBEC3B via therapy-mediated activation of NF-{kappa}B signaling. Moreover, targeted therapy also mediated downregulation of certain DNA repair enzymes such as UNG2, which normally counteracts APOBEC-catalyzed DNA deamination events. In mutant EGFR-driven lung cancer mouse models, APOBEC3B was detrimental to tumour initiation and yet advantageous to tumour progression during EGFR targeted therapy, consistent with TRACERx data demonstrating subclonal enrichment of APOBEC-mediated mutagenesis. This study reveals how cancers adapt and drive genetic diversity in response to targeted therapy and identifies APOBEC deaminases as future targets for eliciting more durable clinical benefit to targeted cancer therapy.

cancer biology↗

bioRxiv2020

Copy number-aware deconvolution of tumor-normal DNA methylation profiles

Aberrant methylation is a hallmark of cancer, but bulk tumor data is confounded by admixed normal cells and copy number changes. Here, we introduce Copy number-Aware Methylation Deconvolution Analysis of Cancers (CAMDAC; https://github.com/VanLoo-lab/CAMDAC), which outputs tumor purity, allele-specific copy number and deconvolved methylation estimates. We apply CAMDAC to 122 multi-region samples from 38 TRACERx non-small cell lung cancers profiled by reduced representation bisulfite sequencing. CAMDAC copy number profiles parallel those derived from genome sequencing and highlight widespread chromosomal instability. Deconvolved polymorphism-independent methylation rates enable unbiased tumor-normal and tumor-tumor differential methylation calling. Read-phasing validates CAMDAC methylation rates and directly links genotype and epitype. We show increased epigenetic instability in adenocarcinoma vs. squamous cell carcinoma, frequent hypermethylation at sites carrying somatic mutations, and parallel copy number losses and methylation changes at imprinted loci. Unlike bulk methylomes, CAMDAC profiles recapitulate tumor phylogenies and evidence distinct patterns of epigenetic heterogeneity in lung cancer.

genomics↗

bioRxiv2020

Cisplatin is more mutagenic than carboplatin or oxaliplatin at equitoxic concentrations

Platinum-based drugs are a mainstay of cancer chemotherapy. However, their mutagenic effect can increase tumour heterogeneity, contribute to the evolution of treatment resistance, and also induce secondary malignancies. We coupled whole genome sequencing with phenotypic investigations on two cell line models to compare the magnitude and understand the mechanism of mutagenicity of cisplatin, carboplatin and oxaliplatin. Cisplatin induced significantly more base substitution mutations than carboplatin or oxaliplatin when used at equitoxic concentrations on human TK6 or chicken DT40 cells, and also induced the highest number of short insertions and deletions. Assessment through histone H2AX phosphorylation and single cell agarose gel electrophoresis suggested that cisplatin caused more DNA damage than carboplatin or oxaliplatin. The analysis of base substitution spectra revealed that all three tested platinum drugs elicit both a direct mutagenic effect at purine dinucleotides, and an indirect effect of accelerating endogenous mutagenic processes. Whereas the direct mutagenic effect correlated with the level of DNA damage caused, the indirect mutagenic effects were equal. The different mutagenicity and DNA damaging effect of equitoxic platinum drug treatments suggests that DNA damage independent mechanisms significantly contribute to their cytotoxicity. Thus, the comparatively high mutagenicity of cisplatin should be taken into account in the design of chemotherapeutic regimens.

bioinformatics↗