Human cells have twenty-three pairs of chromosomes but in cancer, genes can be amplified in chromosomes or in circular extrachromosomal DNA (ECDNA), whose frequency and functional significance are not understood1–4. We performed whole genome sequencing, structural modeling and cytogenetic analyses of 17 different cancer types, including 2572 metaphases, and developed ECdetect to conduct unbiased integrated ECDNA detection and analysis. ECDNA was found in nearly half of human cancers varying by tumor type, but almost never in normal cells. Driver oncogenes were amplified most commonly on ECDNA, elevating transcript level. Mathematical modeling predicted that ECDNA amplification elevates oncogene copy number and increases intratumoral heterogeneity more effectively than chromosomal amplification, which we validated by quantitative analyses of cancer samples. These results suggest that ECDNA contributes to accelerated evolution in cancer.

Intratumoral heterogeneity contributes to cancer drug resistance, but the underlying mechanisms are not understood. Single-cell analyses of patient-derived models and clinical samples from glioblastoma patients treated with epidermal growth factor receptor (EGFR) tyrosine kinase inhibitors (TKIs) demonstrate that tumor cells reversibly up-regulate or suppress mutant EGFR expression, conferring distinct cellular phenotypes to reach an optimal equilibrium for growth. Resistance to EGFR TKIs is shown to occur by elimination of mutant EGFR from extrachromosomal DNA. After drug withdrawal, reemergence of clonal EGFR mutations on extrachromosomal DNA follows. These results indicate a highly specific, dynamic, and adaptive route by which cancers can evade therapies that target oncogenes maintained on extrachromosomal DNA.

Precision oncology hinges on linking tumor genotype with druggable enzymatic dependencies1, however targeting the frequently dysregulated metabolic landscape of cancer has proven to be a major challenge2. Here we show that tissue context is the major determinant of NAD metabolic pathway dependence in cancer. By analyzing over 7000 tumors and 2600 matched normal samples of 19 tissue types, coupled with mathematical modeling and extensive in vitro and in vivo analyses, we identify a simple and actionable set of "rules". If the rate limiting enzyme of de novo NAD synthesis, NAPRT, is highly expressed in a normal tissue type, cancers that arise from that tissue will have a high frequency of NAPRT amplification and will be completely and irreversibly dependent on NAPRT for survival. Tumors arising from normal tissues that do not highly express NAPRT are entirely dependent on the NAD Salvage-pathway for survival. We identify the previously unknown enhancer that underlies this dependence. NAPRT amplification is demonstrated to generate an absolute, pharmacologically actionable tumor cell dependence for survival; dependence on NAMPT generated through enhancer remodeling is subject to resistance through NMRK1-dependent NAD synthesis. These results identify a central role for tissue context §

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Highlights d Phosphorylation of PTEN at tyrosine 240 (pY240) by FGFR2 mediates IR resistance d pY240-PTEN plays a critical role in DNA damage repair d pY240-PTEN associates with chromatin DNA through interaction with Ki-67 d Blocking pY240-PTEN using FGFR inhibitors sensitizes tumors to ionizing radiation