Author

P. S. Mischel

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Cancer Biology· 14

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Organism:human· 12 Approach:statistical model· 10 Research Focus:cancer & tumor microenvironment· 6 Research Focus:clustering· 6 Approach:experimental assay· 6 Assay:whole-genome sequencing· 5 Research Focus:differential expression· 4 Research Focus:gene regulatory network inference· 4

Frequent Co-Authors

V. Bafna· 12 shared H. Y. Chang· 8 shared J. Luebeck· 6 shared K. L. Hung· 6 shared I. T.-L. Wong· 5 shared S. Wu· 5 shared J. T. Lange· 4 shared E. J. Curtis· 3 shared

Activity by Year

2019-2024 · peak 5/yr

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10 top collaborators · 39 mutual co-author links

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12 shared papersCancer Biology

V. Bafna

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14 papers

Recent·Most cited

Rampant transcription replication conflict creates therapeutic vulnerability in extrachromosomal DNA containing cancers

J. Tang, N. E. Weiser, G. Wang, S. Chowdhry, E. J. Curtis, Y. Zhao, I. T.-L. Wong, G. K. Marinov, R. Li, P. Hanoian, E. Tse, R. Hansen, J. Plum, A. Steffy, S. Milutinovic, , H. Y. Chang

This paper identifies transcription-replication conflict as a vulnerability in ecDNA-containing cancers and demonstrates that CHK1 inhibition selectively kills these tumors.

bioRxiv · Mar 29, 2024 · PreprintCancer Biology

CoRAL accurately resolves extrachromosomal DNA genomestructures with long-read sequencing

K. Zhu, M. G. Jones, J. Luebeck, X. Bu, H. Yi, K. L. Hung, I. T.-L. Wong, S. Zhang, P. S. Mischel, H. Y. Chang, V. Bafna

CoRAL improves ecDNA structure reconstruction using long-read sequencing, outperforming short-read methods in simulations and cell-line datasets.

bioRxiv · Feb 15, 2024Cancer Biology

Breakage fusion bridge cycles drive high oncogene copy number, but not intratumoral genetic heterogeneity or rapid cancer genome change

S. R. Dehkordi, I. T.-L. Wong, J. Ni, J. Luebeck, K. Zhu, G. Prasad, L. Krockenberger, G. Xu, B. Chowdhury, U. Rajkumar, A. Caplin, D. Muliaditan, C. Coruh, Q. Jin, K. Turner, , V. Bafna

The paper introduces OM2BFB, an algorithm detecting BFB amplifications using OGMs, showing high precision and recall, and finds BFB events are common in certain cancers but not linked to intratumoral heterogeneity or rapid genome change.

bioRxiv · Dec 12, 2023 · PreprintCancer Biology

Disparate pathways for extrachromosomal DNA biogenesis and genomic DNA repair

J. C. Rose, I. T.-L. Wang, B. Daniel, M. G. Jones, K. E. Yost, K. L. Hung, E. J. Curtis, P. S. Mischel, H. Chang

This study uses a CRISPR-based method to investigate ecDNA formation, showing efficient circularization and distinct repair pathways for ecDNA and chromosomal scars.

bioRxiv · Oct 22, 2023Cancer Biology

Coordinated inheritance of extrachromosomal DNA species in human cancer cells

K. L. Hung, M. G. Jones, I. T.-L. Wong, J. T. Lange, J. Luebeck, E. Scanu, B. J. He, L. Brückner, R. Li, R. C. Gonzalez, R. Schmargon, J. R. Dörr, J. A. Belk, V. Bafna, B. Werner, , H. Y. Chang

This study shows that multiple extrachromosomal DNA species are coordinately inherited in cancer cells through mitotic co-segregation, enabling oncogene cooperation and guiding therapeutic strategies.

bioRxiv · Jul 18, 2023 · PreprintCancer Biology

Transcriptional immune suppression and upregulation of double stranded DNA damage and repair repertoires in ecDNA-containing tumors

M. S. Lin, S.-Y. Jo, J. Luebeck, H. Y. Chang, S. Wu, P. S. Mischel, V. Bafna

The paper identifies transcriptional correlates of ecDNA in tumors, showing upregulation of DNA repair and downregulation of immune pathways.

bioRxiv · Apr 24, 2023Cancer Biology

Targeted profiling of human extrachromosomal DNA by CRISPR-CATCH

K. L. Hung, J. Luebeck, S. R. Dehkordi, C. Coruh, J. A. Law, W. J. Greenleaf, P. S. Mischel, V. Bafna, H. Y. Chang

This study introduces CRISPR-CATCH, a method to purify and analyze extrachromosomal DNA, revealing hypomethylation and structural details of ecDNA in cancer cells.

bioRxiv · Nov 28, 2021Cancer Biology

The landscape of extrachromosomal circular DNA in medulloblastoma

O. S. Chapman, J. Luebeck, S. Wani, A. Tiwari, M. Pagadala, S. Wang, J. D. Larson, J. T. Lange, I. T.-L. Wong, S. R. Dehkordi, S. Chandran, M. Adam, Y. Lin, E. Juarez, J. T. Robinson, , L. Chavez

This study identifies ecDNA in 18% of medulloblastoma patients, linking it to higher relapse and mortality rates and suggesting enhancer rewiring as an oncogenic mechanism.

bioRxiv · Oct 18, 2021 · PreprintCancer Biology

Principles of ecDNA random inheritance drive rapid genome change and therapy resistance in human cancers

J. T. Lange, C. Y. Chen, Y. Pichugin, F. Xie, J. Tang, K. L. Hung, K. E. Yost, Q. Shi, M. L. Erb, U. Rajkumar, S. Wu, C. Swanton, Z. Liu, W. Huang, H. Y. Chang, , P. S. Mischel

bioRxiv · Jun 11, 2021 · PreprintCancer Biology

Comprehensive analysis of clustered mutations in cancer reveals recurrent APOBEC3 mutagenesis of ecDNA

E. N. Bergstrom, J.-C. Luebeck, M. Petljak, V. Bafna, P. S. Mischel, R. Harris, L. B. Alexandrov

The paper analyzes clustered mutations in 2,583 cancer genomes, identifying APOBEC3-driven mutagenesis on ecDNA as a significant contributor to cancer evolution.

bioRxiv · May 27, 2021Cancer Biology

Targeting Glioblastoma Signaling and Metabolism with A Re-Purposed Brain-Penetrant Drug

J. Bi, A. Khan, J. Tang, S. Wu, W. Zhang, R. C. Gimple, T. Koga, A. M. Armando, S. Miki, H. Yang, B. Prager, E. J. Curtis, D. A. Wainwright, F. B. Furnari, J. N. Rich, , P. S. Mischel

This study identifies fluoxetine as a potential therapy for glioblastoma by inhibiting SMPD1 and enhancing temozolomide efficacy, with real-world evidence suggesting improved survival.

bioRxiv · Mar 16, 2021Cancer Biology

EcDNA hubs drive cooperative intermolecular oncogene expression

K. L. Hung, K. E. Yost, L. Xie, S. Wu, J. T. Lange, C. V. Duffy, K. Kraft, J. Tang, Q. Shi, J. C. Rose, M. R. Corces, J. M. Granja, R. Li, U. Rajkumar, R. Tjian, , H. Y. Chang

The paper identifies ecDNA hubs as nuclear structures that drive cooperative oncogene expression through intermolecular enhancer-promoter interactions and shows BET inhibitors can disrupt these hubs and kill cancer cells.

bioRxiv · Nov 19, 2020Cancer Biology

Frequent extrachromosomal oncogene amplification drives aggressive tumors

H. Kim, N. Nguyen, K. Turner, S. Wu, J. Liu, V. Deshpande, S. Namburi, H. Y. Chang, C. Beck, P. S. Mischel, V. Bafna, R. G. W. Verhaak

This study shows that extrachromosomal DNA amplification of oncogenes is common in human cancers and is associated with worse patient outcomes.

bioRxiv · Nov 28, 2019 · PreprintCancer Biology

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

T. Koga, J. A. Benitez, I. A. Chaim, S. Markmiller, A. D. Parisian, R. F. Hevner, K. M. Turner, F. M. Hessenauer, M. D'Antonio, N.-p. D. Nguyen, S. Saberi, J. Ma, S. Miki, A. D. Boyer, J. Ravits, , F. B. Furnari

This paper introduces cancer avatar models using genetically engineered hiPSCs to study tumor development and heterogeneity in glioblastoma.

bioRxiv · Oct 25, 2019Cancer Biology