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    University - Scholar Department: Pathology Position: Postdoctoral Scholar

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  • Mail Code: 5324

All Publications

  • EcDNA-borne structural variants drive oncogenic fusion transcript amplification. Cell Yi, H., Zhang, S., Swinderman, J., Wang, Y., Kanakaveti, V., Hung, K. L., Tsz-Lo Wong, I., Srinivasan, S., Curtis, E. J., Bhargava-Shah, A., Li, R., Jones, M. G., Luebeck, J., Bailey, C., Zhao, Y., Belk, J. A., Kraft, K., Shi, Q., Yan, X., Pritchard, S. K., Mahajan, K. S., Liang, F., Jamal-Hanjani, M., Felsher, D. W., Gilbert, L. A., Bafna, V., Mischel, P. S., Chang, H. Y. 2026

    Abstract

    Extrachromosomal DNA (ecDNA) amplifications are key drivers of human cancers. Here, we show that ecDNAs are major platforms for generating and amplifying oncogene fusion transcripts across diverse cancer types. By integrating analysis of whole-genome and transcriptome sequences from tumor samples and cancer cell lines of a wide variety of tissue types, we reveal that ecDNAs have the highest rate of oncogene fusion events of any copy-number alteration. Focusing on the most common ecDNA fusion hotspot, we find that fusion of the 5' end of the long noncoding RNA gene, PVT1-with exon 1 joined to diverse 3' partners-confers increased RNA stability, potentially via an SRSF1-dependent mechanism, and enhances MYC-dependent transcription and cancer cell survival. These results demonstrate that ecDNA fosters genome instability and frequent oncogene fusion formation in cancer.

    View details for DOI 10.1016/j.cell.2025.12.009

    View details for PubMedID 41506267

  • Enhancer activation from transposable elements in extrachromosomal DNA. Nature cell biology Kraft, K., Murphy, S. E., Jones, M. G., Shi, Q., Bhargava-Shah, A., Luong, C., Hung, K. L., He, B. J., Li, R., Park, S. K., Montgomery, M. T., Weiser, N. E., Wang, Y., Luebeck, J., Bafna, V., Boeke, J. D., Mischel, P. S., Boettiger, A. N., Chang, H. Y. 2025

    Abstract

    Extrachromosomal DNA (ecDNA) drives oncogene amplification and intratumoural heterogeneity in aggressive cancers. While transposable element reactivation is common in cancer, its role on ecDNA remains unexplored. Here we map the 3D architecture of MYC-amplified ecDNA in colorectal cancer cells and identify 68 ecDNA-interacting elements-genomic loci enriched for transposable elements that are frequently integrated onto ecDNA. We focus on an L1M4a1#LINE/L1 fragment co-amplified with MYC, which functions only in the ecDNA-amplified context. Using CRISPR-CATCH, CRISPR interference and reporter assays, we confirm its presence on ecDNA, enhancer activity and essentiality for cancer cell fitness. These findings reveal that repetitive elements can be reactivated and co-opted as functional rather than inactive sequences on ecDNA, potentially driving oncogene expression and tumour evolution. Our study uncovers a mechanism by which ecDNA harnesses repetitive elements to shape cancer phenotypes, with implications for diagnosis and therapy.

    View details for DOI 10.1038/s41556-025-01788-6

    View details for PubMedID 41120733

    View details for PubMedCentralID 7484012

  • Enhancing transcription-replication conflict targets ecDNA-positive cancers. Nature Tang, J., Weiser, N. E., Wang, G., Chowdhry, S., Curtis, E. J., Zhao, Y., Wong, I. T., Marinov, G. K., Li, R., Hanoian, P., Tse, E., Mojica, S. G., Hansen, R., Plum, J., Steffy, A., Milutinovic, S., Meyer, S. T., Luebeck, J., Wang, Y., Zhang, S., Altemose, N., Curtis, C., Greenleaf, W. J., Bafna, V., Benkovic, S. J., Pinkerton, A. B., Kasibhatla, S., Hassig, C. A., Mischel, P. S., Chang, H. Y. 2024; 635 (8037): 210-218

    Abstract

    Extrachromosomal DNA (ecDNA) presents a major challenge for cancer patients. ecDNA renders tumours treatment resistant by facilitating massive oncogene transcription and rapid genome evolution, contributing to poor patient survival1-7. At present, there are no ecDNA-specific treatments. Here we show that enhancing transcription-replication conflict enables targeted elimination of ecDNA-containing cancers. Stepwise analyses of ecDNA transcription reveal pervasive RNA transcription and associated single-stranded DNA, leading to excessive transcription-replication conflicts and replication stress compared with chromosomal loci. Nucleotide incorporation on ecDNA is markedly slower, and replication stress is significantly higher in ecDNA-containing tumours regardless of cancer type or oncogene cargo. pRPA2-S33, a mediator of DNA damage repair that binds single-stranded DNA, shows elevated localization on ecDNA in a transcription-dependent manner, along with increased DNA double strand breaks, and activation of the S-phase checkpoint kinase, CHK1. Genetic or pharmacological CHK1 inhibition causes extensive and preferential tumour cell death in ecDNA-containing tumours. We advance a highly selective, potent and bioavailable oral CHK1 inhibitor, BBI-2779, that preferentially kills ecDNA-containing tumour cells. In a gastric cancer model containing FGFR2 amplified on ecDNA, BBI-2779 suppresses tumour growth and prevents ecDNA-mediated acquired resistance to the pan-FGFR inhibitor infigratinib, resulting in potent and sustained tumour regression in mice. Transcription-replication conflict emerges as a target for ecDNA-directed therapy, exploiting a synthetic lethality of excess to treat cancer.

    View details for DOI 10.1038/s41586-024-07802-5

    View details for PubMedID 39506153

  • HLTF disrupts Cas9-DNA post-cleavage complexes to allow DNA break processing. Nature communications Reginato, G., Dello Stritto, M. R., Wang, Y., Hao, J., Pavani, R., Schmitz, M., Halder, S., Morin, V., Cannavo, E., Ceppi, I., Braunshier, S., Acharya, A., Ropars, V., Charbonnier, J. B., Jinek, M., Nussenzweig, A., Ha, T., Cejka, P. 2024; 15 (1): 5789

    Abstract

    The outcome of CRISPR-Cas-mediated genome modifications is dependent on DNA double-strand break (DSB) processing and repair pathway choice. Homology-directed repair (HDR) of protein-blocked DSBs requires DNA end resection that is initiated by the endonuclease activity of the MRE11 complex. Using reconstituted reactions, we show that Cas9 breaks are unexpectedly not directly resectable by the MRE11 complex. In contrast, breaks catalyzed by Cas12a are readily processed. Cas9, unlike Cas12a, bridges the broken ends, preventing DSB detection and processing by MRE11. We demonstrate that Cas9 must be dislocated after DNA cleavage to allow DNA end resection and repair. Using single molecule and bulk biochemical assays, we next find that the HLTF translocase directly removes Cas9 from broken ends, which allows DSB processing by DNA end resection or non-homologous end-joining machineries. Mechanistically, the activity of HLTF requires its HIRAN domain and the release of the 3'-end generated by the cleavage of the non-target DNA strand by the Cas9 RuvC domain. Consequently, HLTF removes the H840A but not the D10A Cas9 nickase. The removal of Cas9 H840A by HLTF explains the different cellular impact of the two Cas9 nickase variants in human cells, with potential implications for gene editing.

    View details for DOI 10.1038/s41467-024-50080-y

    View details for PubMedID 38987539

    View details for PubMedCentralID PMC11237066