Paul S. Mischel YOU? Author Swipe

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Enhancer activation from transposable elements in extrachromosomal DNA Open

Katerina Kraft, Sedona E. Murphy, Matthew G. Jones, Quanming Shi, Aarohi Bhargava-Shah , et al. · 2025

Genetic elements promote retention of extrachromosomal DNA in cancer cells Open

Venkat Sankar, King L. Hung, Aditi Gnanasekar, Ivy Tsz-Lo Wong, Quanming Shi , et al. · 2025

Extrachromosomal DNA (ecDNA) is a prevalent and devastating form of oncogene amplification in cancer 1,2 . Circular megabase-sized ecDNAs lack centromeres and segregate stochastically during cell division 3–6 yet persist over many generati…

Supplementary Figures from Extrachromosomal DNA–Driven Oncogene Spatial Heterogeneity and Evolution in Glioblastoma Open

Imran Noorani, Magnus Haughey, Jens Luebeck, Andrew Rowan, Eva Grönroos , et al. · 2025

Supplementary Figures 1 to 34, detailing additional analyses.

Figure 5 from Extrachromosomal DNA–Driven Oncogene Spatial Heterogeneity and Evolution in Glioblastoma Open

Imran Noorani, Magnus Haughey, Jens Luebeck, Andrew Rowan, Eva Grönroos , et al. · 2025

Selection dynamics of EGFR SVs on ecDNA. A, A subclonal EGFRvIII variant on ecDNA in the tumor of patient A23. B, Variant heteroplasmy in the core region of all samples across the GB-UK and PCAWG cohorts, which …

Figure 3 from Extrachromosomal DNA–Driven Oncogene Spatial Heterogeneity and Evolution in Glioblastoma Open

Imran Noorani, Magnus Haughey, Jens Luebeck, Andrew Rowan, Eva Grönroos , et al. · 2025

SPECIES spatial modeling of ecDNA evolution. A and B, DNA FISH staining of two representative GBM samples from the GB-UK cohort, revealing (A) EGFR- and (B) PDGFRA-ecDNA. EGFR-ecDNA seem to …

Data from Extrachromosomal DNA–Driven Oncogene Spatial Heterogeneity and Evolution in Glioblastoma Open

Imran Noorani, Magnus Haughey, Jens Luebeck, Andrew Rowan, Eva Grönroos , et al. · 2025

Oncogenes amplified on extrachromosomal DNA (ecDNA) contribute to treatment resistance and poor survival across cancers. Currently, the spatiotemporal evolution of ecDNA remains poorly understood. In this study, we integrate computational …

Figure 4 from Extrachromosomal DNA–Driven Oncogene Spatial Heterogeneity and Evolution in Glioblastoma Open

Imran Noorani, Magnus Haughey, Jens Luebeck, Andrew Rowan, Eva Grönroos , et al. · 2025

ecDNA accumulation in genetically engineered in vivo and ex vivo murine models. A, Neural stem cells were propagated within the SVZ of genetically engineered mice for 4 months. B,Myc-ecDNAs were in…

Supplementary Methods from Extrachromosomal DNA–Driven Oncogene Spatial Heterogeneity and Evolution in Glioblastoma Open

Imran Noorani, Magnus Haughey, Jens Luebeck, Andrew Rowan, Eva Grönroos , et al. · 2025

Supplementary Methods, providing details about methodology used throughout the study.

Figure 6 from Extrachromosomal DNA–Driven Oncogene Spatial Heterogeneity and Evolution in Glioblastoma Open

Imran Noorani, Magnus Haughey, Jens Luebeck, Andrew Rowan, Eva Grönroos , et al. · 2025

Simulating multi-ecDNA dynamics in vivo.A, DNA FISH and nascent RNAscope images from the tumor of patient A5, showing the coexistence of both EGFR-ecDNA and PDGFRA-ecDNA. B, Circular structures of three d…

Figure 1 from Extrachromosomal DNA–Driven Oncogene Spatial Heterogeneity and Evolution in Glioblastoma Open

Imran Noorani, Magnus Haughey, Jens Luebeck, Andrew Rowan, Eva Grönroos , et al. · 2025

Workflow of the study analysis. A, A total of 94 IDHwt GBMs were analyzed (35 from the PCAWG cohort and 59 from the GB-UK cohort). B, The core region of all patient tumors was analyzed using WGS, and GB-UK patient tumo…

Figure 2 from Extrachromosomal DNA–Driven Oncogene Spatial Heterogeneity and Evolution in Glioblastoma Open

Imran Noorani, Magnus Haughey, Jens Luebeck, Andrew Rowan, Eva Grönroos , et al. · 2025

Diversity and high copy numbers of ecDNA in IDHwt GBMs. A, Focal copy-number amplifications across the GB-UK and PCAWG cohorts, categorized by amplicon type [ecDNA, breakage–fusion–bridge (BFB) cycle, linear]. Only tumors con…

Extrachromosomal DNA–Driven Oncogene Spatial Heterogeneity and Evolution in Glioblastoma Open

Imran Noorani, Magnus Haughey, Jens Luebeck, Andrew Rowan, Eva Grönroos , et al. · 2025

Oncogenes amplified on extrachromosomal DNA (ecDNA) contribute to treatment resistance and poor survival across cancers. Currently, the spatiotemporal evolution of ecDNA remains poorly understood. In this study, we integrate computational …

Applying multilevel selection to understand cancer evolution and progression Open

Lucie Laplane, Annie Lamoureux, Harley I. Richker, Gissel Marquez Alcaraz, Angelo Fortunato , et al. · 2025

Natural selection occurs at multiple levels of organization in cancer. At an organismal level, natural selection has led to the evolution of diverse tumor suppression mechanisms, while at a cellular level, it favors traits that promote cel…

Extrachromosomal DNA: shaping the evolutionary dynamics of cancer Open

Magnus Haughey, Imran Noorani, Charles Swanton, Paul S. Mischel, Benjamin Werner · 2025

Cancers are complex, diverse, and elusive, with extrachromosomal DNA (ecDNA) recently emerging as a crucial player in driving the evolution of about 20% of all tumors. In this review we discuss open questions concerning the evolutionary ro…

Oxidative stress is a shared characteristic of ME/CFS and Long COVID. Open

Vishnu Shankar, Julie Wilhelmy, Ellis J. Curtis, Basil Michael, Layla Cervantes , et al. · 2025

Over 65 million individuals worldwide are estimated to have Long COVID (LC), a complex multisystemic condition marked by fatigue, post-exertional malaise, and other symptoms resembling myalgic encephalomyelitis/chronic fatigue syndrome (ME…

Accurate Prediction of ecDNA in Interphase Cancer Cells using Deep Neural Networks Open

Utkrisht Rajkumar, Gino Prasad, Ellis J. Curtis, Ivy Tsz-Lo Wong, Xiaowei Yan , et al. · 2025

Oncogene amplification is a key driver of cancer pathogenesis and is often mediated by extrachromosomal DNA (ecDNA). EcDNA amplifications are associated with increased pathogenicity of cancer and poorer outcomes for patients. EcDNA can be …

Data from A Guide to Extrachromosomal DNA: Cancer’s Dynamic Circular Genome Open

Natasha E. Weiser, Thomas B.K. Watkins, Howard Y. Chang, Paul S. Mischel · 2025

Focal amplifications of oncogenes are important cancer drivers. They can occur on chromosomes or in the context of circular extrachromosomal DNA (ecDNA). Many key features of ecDNAs were described in the 1960s to 1980s, including their “un…

Figure S1 from A Guide to Extrachromosomal DNA: Cancer’s Dynamic Circular Genome Open

Natasha E. Weiser, Thomas B.K. Watkins, Howard Y. Chang, Paul S. Mischel · 2025

Summary of key differences between ecDNA and eccDNA

Data from Spatial–Temporal Diversity of Extrachromosomal DNA Shapes Urothelial Carcinoma Evolution and the Tumor Immune Microenvironment Open

Wei Lv, Yuchen Zeng, Conghui Li, Yuan Liang, Huiying Tao , et al. · 2025

Extrachromosomal DNA (ecDNA) presents a promising target for cancer therapy; however, its spatial–temporal diversity and influence on tumor evolution and the immune microenvironment remain largely unclear. We apply computational methods to…

Supplementary Figures 1-12 from Spatial–Temporal Diversity of Extrachromosomal DNA Shapes Urothelial Carcinoma Evolution and the Tumor Immune Microenvironment Open

Wei Lv, Yuchen Zeng, Conghui Li, Yuan Liang, Huiying Tao , et al. · 2025

Supplementary Figure 1. Prevalence of ecDNA in human cancers. Supplementary Figure 2. Characteristics of ecDNA. Supplementary Figure 3. ecDNA drives massive oncogene expression in UC. Supplementary Figure 4. ecDNA can arise in flat urothel…

Supplementary Tables 1-24 from Spatial–Temporal Diversity of Extrachromosomal DNA Shapes Urothelial Carcinoma Evolution and the Tumor Immune Microenvironment Open

Wei Lv, Yuchen Zeng, Conghui Li, Yuan Liang, Huiying Tao , et al. · 2025

Table_S1. Study cohort. Table_S2. The sample composition of each dataset. Table_S3. Patient information. Table_S4. Whole genome sequencing (WGS) datasets. 1,411 UC whole genomes. Table_S5. Whole exome sequencing (WES) datasets. Table_S6. R…

A Guide to Extrachromosomal DNA: Cancer’s Dynamic Circular Genome Open

Natasha E. Weiser, Thomas B.K. Watkins, Howard Y. Chang, Paul S. Mischel · 2025

Focal amplifications of oncogenes are important cancer drivers. They can occur on chromosomes or in the context of circular extrachromosomal DNA (ecDNA). Many key features of ecDNAs were described in the 1960s to 1980s, including their “un…

Unified molecular approach for spatial epigenome, transcriptome, and cell lineages Open

Yung‐Hsin Huang, Julia A. Belk, Ruochi Zhang, Natasha E. Weiser, Zachary Chiang , et al. · 2025

Spatial epigenomics and multiomics can provide fine-grained insights into cellular states but their widespread adoption is limited by the requirement for bespoke slides and capture chemistries for each data modality. Here, we present SPati…

Oncogene Silencing via ecDNA Micronucleation Open

Lotte Brückner, Robin Xu, Jun Tang, Alexander M. Herrmann, Ivy Tsz-Lo Wong , et al. · 2025

Extrachromosomal DNA (ecDNA) is a common source of oncogene amplification across many types of cancer. The non-Mendelian inheritance of ecDNA contributes to heterogeneous tumour genomes that rapidly evolve to resist treatment. Here, using …

EcDNA-borne PVT1 fusion stabilizes oncogenic mRNAs Open

Hyerim Yi, Shu Zhang, Jason Swinderman, Yanbo Wang, Vishnupriya Kanakaveti , et al. · 2025

Summary Extrachromosomal DNA (ecDNA) amplifications are prevalent drivers of human cancers. We show that ecDNAs exhibit elevated structural variants leading to gene fusions that produce oncogene fusion transcripts. The long noncoding RNA (…

Inhibition of human-HPV hybrid ecDNA enhancers reduces oncogene expression and tumor growth in oropharyngeal cancer Open

Takuya Nakagawa, Jens Luebeck, Kaiyuan Zhu, Joshua T. Lange, Roman Šášik , et al. · 2025

Extrachromosomal circular DNA (ecDNA) has been found in most types of human cancers, and ecDNA incorporating viral genomes has recently been described, specifically in human papillomavirus (HPV)-mediated oropharyngeal cancer (OPC). However…

Spatial–Temporal Diversity of Extrachromosomal DNA Shapes Urothelial Carcinoma Evolution and the Tumor Immune Microenvironment Open

Wei Lv, Yuchen Zeng, Conghui Li, Yuan Liang, Huiying Tao , et al. · 2025

Extrachromosomal DNA (ecDNA) presents a promising target for cancer therapy; however, its spatial–temporal diversity and influence on tumor evolution and the immune microenvironment remain largely unclear. We apply computational methods to…

Breakage fusion bridge cycles drive high oncogene number with moderate intratumoural heterogeneity Open

Siavash R. Dehkordi, Ivy Tsz-Lo Wong, Jing Ni, Jens Luebeck, Kaiyuan Zhu , et al. · 2025

Oncogene amplification is a key driver of cancer pathogenesis. Both breakage fusion bridge (BFB) cycles and extrachromosomal DNA (ecDNA) can lead to high oncogene copy numbers, but the impact of BFB amplifications on intratumoral heterogen…

Supplementary Data Set 1 from Disparate Pathways for Extrachromosomal DNA Biogenesis and Genomic DNA Repair Open

John C. Rose, Julia A. Belk, Ivy Tsz-Lo Wong, Jens Luebeck, Hudson T. Horn , et al. · 2025

sgRNA, primer, and probe sequences.

Data from Disparate Pathways for Extrachromosomal DNA Biogenesis and Genomic DNA Repair Open

John C. Rose, Julia A. Belk, Ivy Tsz-Lo Wong, Jens Luebeck, Hudson T. Horn , et al. · 2025

Oncogene amplification on extrachromosomal DNA (ecDNA) is a pervasive driver event in cancer, yet our understanding of how ecDNA forms is limited. In this study, we couple a CRISPR-based method for ecDNA induction with extensive characteri…

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