Targeted profiling of human extrachromosomal DNA by CRISPR-CATCH.

Autor: Hung KL; Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA., Luebeck J; Bioinformatics and Systems Biology Graduate Program, University of California, San Diego, La Jolla, CA, USA.; Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA, USA., Dehkordi SR; Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA, USA., Colón CI; Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA.; Sarafan ChEM-H, Stanford University, Stanford, CA, USA.; Department of Pathology, Stanford University, Stanford, CA, USA., Li R; Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA., Wong IT; Sarafan ChEM-H, Stanford University, Stanford, CA, USA.; Department of Pathology, Stanford University, Stanford, CA, USA., Coruh C; Plant Molecular and Cellular Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA., Dharanipragada P; Division of Dermatology, Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, CA, USA., Lomeli SH; Division of Dermatology, Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, CA, USA., Weiser NE; Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA.; Department of Pathology, Stanford University, Stanford, CA, USA., Moriceau G; Division of Dermatology, Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, CA, USA., Zhang X; Division of Dermatology, Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, CA, USA., Bailey C; Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK., Houlahan KE; Department of Medicine, Division of Oncology, Stanford University School of Medicine, Stanford, CA, USA.; Department of Genetics, Stanford University, Stanford, CA, USA.; Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA., Yang W; Department of Medicine, Division of Oncology, Stanford University School of Medicine, Stanford, CA, USA.; Department of Genetics, Stanford University, Stanford, CA, USA.; Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA., González RC; Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany., Swanton C; Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK.; Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, University College London, London, UK.; University College London Hospitals NHS Trust, London, UK., Curtis C; Department of Medicine, Division of Oncology, Stanford University School of Medicine, Stanford, CA, USA.; Department of Genetics, Stanford University, Stanford, CA, USA.; Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA., Jamal-Hanjani M; Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, University College London, London, UK.; University College London Hospitals NHS Trust, London, UK., Henssen AG; Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany.; Experimental and Clinical Research Center (ECRC), Max Delbrück Center for Molecular Medicine and Charité-Universitätsmedizin Berlin, Berlin, Germany.; German Cancer Consortium (DKTK), partner site Berlin, and German Cancer Research Center DKFZ, Heidelberg, Germany.; Berlin Institute of Health, Berlin, Germany., Law JA; Plant Molecular and Cellular Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA., Greenleaf WJ; Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA.; Department of Genetics, Stanford University, Stanford, CA, USA., Lo RS; Division of Dermatology, Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, CA, USA.; Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California, USA.; Jonsson Comprehensive Cancer Center, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California, USA., Mischel PS; Sarafan ChEM-H, Stanford University, Stanford, CA, USA.; Department of Pathology, Stanford University, Stanford, CA, USA., Bafna V; Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA, USA., Chang HY; Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA. howchang@stanford.edu.; Department of Genetics, Stanford University, Stanford, CA, USA. howchang@stanford.edu.; Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA. howchang@stanford.edu.
Jazyk: angličtina
Zdroj: Nature genetics [Nat Genet] 2022 Nov; Vol. 54 (11), pp. 1746-1754. Date of Electronic Publication: 2022 Oct 17.
DOI: 10.1038/s41588-022-01190-0
Abstrakt: Extrachromosomal DNA (ecDNA) is a common mode of oncogene amplification but is challenging to analyze. Here, we adapt CRISPR-CATCH, in vitro CRISPR-Cas9 treatment and pulsed field gel electrophoresis of agarose-entrapped genomic DNA, previously developed for bacterial chromosome segments, to isolate megabase-sized human ecDNAs. We demonstrate strong enrichment of ecDNA molecules containing EGFR, FGFR2 and MYC from human cancer cells and NRAS ecDNA from human metastatic melanoma with acquired therapeutic resistance. Targeted enrichment of ecDNA versus chromosomal DNA enabled phasing of genetic variants, identified the presence of an EGFRvIII mutation exclusively on ecDNAs and supported an excision model of ecDNA genesis in a glioblastoma model. CRISPR-CATCH followed by nanopore sequencing enabled single-molecule ecDNA methylation profiling and revealed hypomethylation of the EGFR promoter on ecDNAs. We distinguished heterogeneous ecDNA species within the same sample by size and sequence with base-pair resolution and discovered functionally specialized ecDNAs that amplify select enhancers or oncogene-coding sequences.
(© 2022. The Author(s).)
Databáze: MEDLINE
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