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Liu Y, Reed SC, Lo C, Choudhury AD, Parsons HA, Stover DG, Ha G, Gydush G, Rhoades J, Rotem D, Freeman S, Katz DW, Bandaru R, Zheng H, Fu H, Adalsteinsson VA, Kellis M. FinaleMe: Predicting DNA methylation by the fragmentation patterns of plasma cell-free DNA. Nat Commun 2024; 15:2790. [PMID: 38555308 PMCID: PMC10981715 DOI: 10.1038/s41467-024-47196-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 03/22/2024] [Indexed: 04/02/2024] Open
Abstract
Analysis of DNA methylation in cell-free DNA reveals clinically relevant biomarkers but requires specialized protocols such as whole-genome bisulfite sequencing. Meanwhile, millions of cell-free DNA samples are being profiled by whole-genome sequencing. Here, we develop FinaleMe, a non-homogeneous Hidden Markov Model, to predict DNA methylation of cell-free DNA and, therefore, tissues-of-origin, directly from plasma whole-genome sequencing. We validate the performance with 80 pairs of deep and shallow-coverage whole-genome sequencing and whole-genome bisulfite sequencing data.
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Affiliation(s)
- Yaping Liu
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA.
- Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, IL, 60611, USA.
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA.
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA.
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, 45229, USA.
- University of Cincinnati Center for Environmental Genetics, Cincinnati, OH, 45229, USA.
- University of Cincinnati Cancer Center, Cincinnati, OH, 45229, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.
- Massachusetts Institute of Technology, Computer Science and Artificial Intelligence Laboratory, Cambridge, MA, 02139, USA.
| | - Sarah C Reed
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- Medical Scientist Training Program, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Christopher Lo
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Atish D Choudhury
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- Dana-Farber Cancer Institute, Boston, MA, USA
| | | | | | - Gavin Ha
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Gregory Gydush
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Justin Rhoades
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Denisse Rotem
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Samuel Freeman
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - David W Katz
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
- Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, IL, 60611, USA
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
| | - Ravi Bandaru
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
- Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, IL, 60611, USA
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
| | - Haizi Zheng
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
| | - Hailu Fu
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
- Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, IL, 60611, USA
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
| | | | - Manolis Kellis
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.
- Massachusetts Institute of Technology, Computer Science and Artificial Intelligence Laboratory, Cambridge, MA, 02139, USA.
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2
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Liu Y, Reed SC, Lo C, Choudhury AD, Parsons HA, Stover DG, Ha G, Gydush G, Rhoades J, Rotem D, Freeman S, Katz D, Bandaru R, Zheng H, Fu H, Adalsteinsson VA, Kellis M. FinaleMe: Predicting DNA methylation by the fragmentation patterns of plasma cell-free DNA. bioRxiv 2024:2024.01.02.573710. [PMID: 38260558 PMCID: PMC10802291 DOI: 10.1101/2024.01.02.573710] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Analysis of DNA methylation in cell-free DNA (cfDNA) reveals clinically relevant biomarkers but requires specialized protocols and sufficient input material that limits its applicability. Millions of cfDNA samples have been profiled by genomic sequencing. To maximize the gene regulation information from the existing dataset, we developed FinaleMe, a non-homogeneous Hidden Markov Model (HMM), to predict DNA methylation of cfDNA and, therefore, tissues-of-origin directly from plasma whole-genome sequencing (WGS). We validated the performance with 80 pairs of deep and shallow-coverage WGS and whole-genome bisulfite sequencing (WGBS) data.
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Affiliation(s)
- Yaping Liu
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611
- Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, IL 60611
- Division of Human Genetics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229
- Division of Biomedical Informatics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229
- University of Cincinnati Center for Environmental Genetics, Cincinnati, OH 45229
- University of Cincinnati Cancer Center, Cincinnati, OH 45229
- Broad Institute of MIT and Harvard, Cambridge, MA 02142
- Massachusetts Institute of Technology, Computer Science and Artificial Intelligence Laboratory, Cambridge, MA 02139
| | - Sarah C. Reed
- Broad Institute of MIT and Harvard, Cambridge, MA 02142
| | | | - Atish D. Choudhury
- Broad Institute of MIT and Harvard, Cambridge, MA 02142
- Dana-Farber Cancer Institute, Boston, MA, USA
| | | | | | - Gavin Ha
- Broad Institute of MIT and Harvard, Cambridge, MA 02142
| | | | | | - Denisse Rotem
- Broad Institute of MIT and Harvard, Cambridge, MA 02142
| | | | - David Katz
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611
- Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, IL 60611
- Division of Human Genetics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229
| | - Ravi Bandaru
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611
- Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, IL 60611
- Division of Human Genetics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229
| | - Haizi Zheng
- Division of Human Genetics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229
| | - Hailu Fu
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611
- Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, IL 60611
- Division of Human Genetics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229
| | | | - Manolis Kellis
- University of Cincinnati Center for Environmental Genetics, Cincinnati, OH 45229
- University of Cincinnati Cancer Center, Cincinnati, OH 45229
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3
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Bae JH, Liu R, Roberts E, Nguyen E, Tabrizi S, Rhoades J, Blewett T, Xiong K, Gydush G, Shea D, An Z, Patel S, Cheng J, Sridhar S, Liu MH, Lassen E, Skytte AB, Grońska-Pęski M, Shoag JE, Evrony GD, Parsons HA, Mayer EL, Makrigiorgos GM, Golub TR, Adalsteinsson VA. Single duplex DNA sequencing with CODEC detects mutations with high sensitivity. Nat Genet 2023; 55:871-879. [PMID: 37106072 PMCID: PMC10181940 DOI: 10.1038/s41588-023-01376-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 03/21/2023] [Indexed: 04/29/2023]
Abstract
Detecting mutations from single DNA molecules is crucial in many fields but challenging. Next-generation sequencing (NGS) affords tremendous throughput but cannot directly sequence double-stranded DNA molecules ('single duplexes') to discern the true mutations on both strands. Here we present Concatenating Original Duplex for Error Correction (CODEC), which confers single duplex resolution to NGS. CODEC affords 1,000-fold higher accuracy than NGS, using up to 100-fold fewer reads than duplex sequencing. CODEC revealed mutation frequencies of 2.72 × 10-8 in sperm of a 39-year-old individual, and somatic mutations acquired with age in blood cells. CODEC detected genome-wide, clonal hematopoiesis mutations from single DNA molecules, single mutated duplexes from tumor genomes and liquid biopsies, microsatellite instability with 10-fold greater sensitivity and mutational signatures, and specific tumor mutations with up to 100-fold fewer reads. CODEC enables more precise genetic testing and reveals biologically significant mutations, which are commonly obscured by NGS errors.
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Affiliation(s)
- Jin H Bae
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Ruolin Liu
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Erica Nguyen
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Shervin Tabrizi
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Koch Institute for Integrative Cancer Research at MIT, Cambridge, MA, USA
- Massachusetts General Hospital, Boston, MA, USA
| | | | | | - Kan Xiong
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Douglas Shea
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Zhenyi An
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Sahil Patel
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Koch Institute for Integrative Cancer Research at MIT, Cambridge, MA, USA
- Massachusetts General Hospital, Boston, MA, USA
| | - Ju Cheng
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Mei Hong Liu
- Center for Human Genetics and Genomics, Departments of Pediatrics and Neuroscience & Physiology, New York University Grossman School of Medicine, New York City, NY, USA
| | | | | | - Marta Grońska-Pęski
- Center for Human Genetics and Genomics, Departments of Pediatrics and Neuroscience & Physiology, New York University Grossman School of Medicine, New York City, NY, USA
| | - Jonathan E Shoag
- University Hospitals Cleveland Medical Center, Case Western Reserve University School of Medicine, Case Comprehensive Cancer Center, Cleveland, OH, USA
| | - Gilad D Evrony
- Center for Human Genetics and Genomics, Departments of Pediatrics and Neuroscience & Physiology, New York University Grossman School of Medicine, New York City, NY, USA
| | | | | | | | - Todd R Golub
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
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4
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Gydush G, Nguyen E, Bae JH, Blewett T, Rhoades J, Reed SC, Shea D, Xiong K, Liu R, Yu F, Leong KW, Choudhury AD, Stover DG, Tolaney SM, Krop IE, Christopher Love J, Parsons HA, Mike Makrigiorgos G, Golub TR, Adalsteinsson VA. Massively parallel enrichment of low-frequency alleles enables duplex sequencing at low depth. Nat Biomed Eng 2022; 6:257-266. [PMID: 35301450 PMCID: PMC9089460 DOI: 10.1038/s41551-022-00855-9] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Accepted: 01/28/2022] [Indexed: 02/07/2023]
Abstract
The ability to assay large numbers of low-frequency mutations is useful in biomedicine, yet, the technical hurdles of sequencing multiple mutations at extremely high depth, with accuracy, limits their detection in clinical practice. Low-frequency mutations can typically be detected by increasing the sequencing depth, however this limits the number of loci that can be probed for simultaneously. Here, we report a technique to accurately track thousands of distinct mutations with minimal reads, termed MAESTRO (minor allele enriched sequencing through recognition oligonucleotides), which employs massively-parallel mutation enrichment to enable duplex sequencing to track up to 10,000 low-frequency mutations, yet requiring up to 100-fold less sequencing. We show that MAESTRO could inform the mutation validation of whole-exome sequencing and whole genome sequencing data from tumor samples, enable chimerism testing, and is suitable for the monitoring of minimal residual disease via liquid biopsies. MAESTRO may improve the breadth, depth, accuracy, and efficiency of sequencing-based mutational testing. Massively-parallel mutation enrichment enables the tracking of up to 10,000 low-frequency mutations, via duplex sequencing, requiring up to 100-fold less sequencing depth.
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Affiliation(s)
| | - Erica Nguyen
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Jin H Bae
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | | | | | - Douglas Shea
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Kan Xiong
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Ruolin Liu
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Fangyan Yu
- Department of Radiation Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Boston, MA, USA
| | - Ka Wai Leong
- Department of Radiation Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Boston, MA, USA.,Harvard Medical School, Boston, MA, USA
| | - Atish D Choudhury
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Harvard Medical School, Boston, MA, USA.,Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Daniel G Stover
- Ohio State University Comprehensive Cancer Center, Columbus, OH, USA
| | - Sara M Tolaney
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Ian E Krop
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - J Christopher Love
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Koch Institute for Integrative Cancer Research at MIT, Cambridge, MA, USA
| | - Heather A Parsons
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - G Mike Makrigiorgos
- Department of Radiation Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Boston, MA, USA.
| | - Todd R Golub
- Broad Institute of MIT and Harvard, Cambridge, MA, USA. .,Harvard Medical School, Boston, MA, USA. .,Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
| | - Viktor A Adalsteinsson
- Broad Institute of MIT and Harvard, Cambridge, MA, USA. .,Koch Institute for Integrative Cancer Research at MIT, Cambridge, MA, USA.
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5
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Pagès M, Rotem D, Gydush G, Reed S, Rhoades J, Ha G, Lo C, Fleharty M, Duran M, Jones R, Becker S, Haller M, Sinai CE, Goumnerova L, Golub TR, Love JC, Ligon KL, Wright KD, Adalsteinsson VA, Beroukhim R, Bandopadhayay P. Liquid biopsy detection of genomic alterations in pediatric brain tumors from cell-free DNA in peripheral blood, CSF, and urine. Neuro Oncol 2022; 24:1352-1363. [PMID: 34984433 PMCID: PMC9340641 DOI: 10.1093/neuonc/noab299] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND The ability to identify genetic alterations in cancers is essential for precision medicine; however, surgical approaches to obtain brain tumor tissue are invasive. Profiling circulating tumor DNA (ctDNA) in liquid biopsies has emerged as a promising approach to avoid invasive procedures. Here, we systematically evaluated the feasibility of profiling pediatric brain tumors using ctDNA obtained from plasma, cerebrospinal fluid (CSF), and urine. METHODS We prospectively collected 564 specimens (257 blood, 240 urine, and 67 CSF samples) from 258 patients across all histopathologies. We performed ultra-low-pass whole-genome sequencing (ULP-WGS) to assess copy number variations and estimate tumor fraction and developed a pediatric CNS tumor hybrid capture panel for deep sequencing of specific mutations and fusions. RESULTS ULP-WGS detected copy number alterations in 9/46 (20%) CSF, 3/230 (1.3%) plasma, and 0/153 urine samples. Sequencing detected alterations in 3/10 (30%) CSF, 2/74 (2.7%) plasma, and 0/2 urine samples. The only positive results were in high-grade tumors. However, most samples had insufficient somatic mutations (median 1, range 0-39) discoverable by the sequencing panel to provide sufficient power to detect tumor fractions of greater than 0.1%. CONCLUSIONS Children with brain tumors harbor very low levels of ctDNA in blood, CSF, and urine, with CSF having the most DNA detectable. Molecular profiling is feasible in a small subset of high-grade tumors. The level of clonal aberrations per genome is low in most of the tumors, posing a challenge for detection using whole-genome or even targeted sequencing methods. Substantial challenges therefore remain to genetically characterize pediatric brain tumors from liquid biopsies.
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Affiliation(s)
- Mélanie Pagès
- Dana-Farber/Boston Children’s Cancer and Blood Disorders Center, Boston, Massachusetts, USA,GHU-Paris—Sainte-Anne Hospital, Department of Neuropathology, Paris University, Paris, France,Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Denisse Rotem
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA
| | - Gregory Gydush
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA
| | - Sarah Reed
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA
| | - Justin Rhoades
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA
| | - Gavin Ha
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA
| | - Christopher Lo
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA
| | - Mark Fleharty
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA
| | - Madeleine Duran
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA
| | - Robert Jones
- Department of Oncologic Pathology, Dana Farber/Brigham and Women’s Cancer Center, Boston, Massachusetts, USA
| | - Sarah Becker
- Department of Oncologic Pathology, Dana Farber/Brigham and Women’s Cancer Center, Boston, Massachusetts, USA
| | - Michaela Haller
- Department of Oncologic Pathology, Dana Farber/Brigham and Women’s Cancer Center, Boston, Massachusetts, USA
| | - Claire E Sinai
- Department of Oncologic Pathology, Dana Farber/Brigham and Women’s Cancer Center, Boston, Massachusetts, USA
| | - Liliana Goumnerova
- Department of Neurosurgery, Boston Children’s Hospital, Boston, Massachusetts, USA
| | - Todd R Golub
- Dana-Farber/Boston Children’s Cancer and Blood Disorders Center, Boston, Massachusetts, USA,Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA
| | | | - Keith L Ligon
- Dana-Farber/Boston Children’s Cancer and Blood Disorders Center, Boston, Massachusetts, USA,Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA,Department of Neurosurgery, Boston Children’s Hospital, Boston, Massachusetts, USA
| | - Karen D Wright
- Karen Wright, MD, MS, Dana-Farber Cancer Institute, 450 Brookline Ave, Boston, MA 02115, USA ()
| | - Viktor A Adalsteinsson
- Viktor A. Adalsteinsson, PhD, Broad Institute, 450 Main Street, Cambridge, MA 02142, USA ()
| | - Rameen Beroukhim
- Corresponding Authors: Rameen Beroukhim, MD, PhD, Dana-Farber Cancer Institute, 450 Brookline Ave, Boston, MA 02115, USA ()
| | - Pratiti Bandopadhayay
- Pratiti Bandopadhayay, MBBS, PhD, Dana-Farber Cancer Institute, 450 Brookline Ave, Boston, MA 02115, USA ()
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6
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Francini E, Ou FS, Rhoades J, Wolfe EG, O’Connor EP, Ha G, Gydush G, Kelleher KM, Bhatt RS, Balk SP, Sweeney CJ, Adalsteinsson VA, Taplin ME, Choudhury AD. Circulating Cell-Free DNA as Biomarker of Taxane Resistance in Metastatic Castration-Resistant Prostate Cancer. Cancers (Basel) 2021; 13:4055. [PMID: 34439209 PMCID: PMC8391478 DOI: 10.3390/cancers13164055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 08/10/2021] [Indexed: 11/17/2022] Open
Abstract
There are no biomarkers predictive of resistance to docetaxel or cabazitaxel validated for patients with metastatic castration-resistant prostate cancer (mCRPC). We assessed the association between ABCB1 amplification and primary resistance to docetaxel or cabazitaxel for patients with mCRPC, using circulating cell-free DNA (cfDNA). Patients with ≥1 plasma sample drawn within 12 months before starting docetaxel (cohort A) or cabazitaxel (cohort B) for mCRPC were identified from the Dana-Farber Cancer Institute IRB approved database. Sparse whole genome sequencing was performed on the selected cfDNA samples and tumor fractions were estimated using the computational tool ichorCNA. We evaluated the association between ABCB1 amplification or other copy number alterations and primary resistance to docetaxel or cabazitaxel. Of the selected 176 patients, 45 samples in cohort A and 21 samples in cohort B had sufficient tumor content. No significant association was found between ABCB1 amplification and primary resistance to docetaxel (p = 0.58; odds ratio (OR) = 1.49) or cabazitaxel (p = 0.97; OR = 1.06). No significant association was found between exploratory biomarkers and primary resistance to docetaxel or cabazitaxel. In this study, ABCB1 amplification did not predict primary resistance to docetaxel or cabazitaxel for mCRPC. Future studies including ABCB1 amplification in a suite of putative biomarkers and a larger cohort may aid in drawing definitive conclusions.
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Affiliation(s)
- Edoardo Francini
- Department of Experimental and Clinical Medicine, University of Florence, 50134 Florence, Italy
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA; (E.P.O.); (G.H.); (K.M.K.); (C.J.S.); (M.-E.T.); (A.D.C.)
| | - Fang-Shu Ou
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN 55905, USA; (F.-S.O.); (E.G.W.)
| | - Justin Rhoades
- Eli and Edythe L. Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; (J.R.); (G.G.); (V.A.A.)
| | - Eric G. Wolfe
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN 55905, USA; (F.-S.O.); (E.G.W.)
| | - Edward P. O’Connor
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA; (E.P.O.); (G.H.); (K.M.K.); (C.J.S.); (M.-E.T.); (A.D.C.)
| | - Gavin Ha
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA; (E.P.O.); (G.H.); (K.M.K.); (C.J.S.); (M.-E.T.); (A.D.C.)
- Eli and Edythe L. Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; (J.R.); (G.G.); (V.A.A.)
| | - Gregory Gydush
- Eli and Edythe L. Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; (J.R.); (G.G.); (V.A.A.)
| | - Kaitlin M. Kelleher
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA; (E.P.O.); (G.H.); (K.M.K.); (C.J.S.); (M.-E.T.); (A.D.C.)
| | - Rupal S. Bhatt
- Beth Israel Deaconess Medical Center, Boston, MA 02215, USA; (R.S.B.); (S.P.B.)
| | - Steven P. Balk
- Beth Israel Deaconess Medical Center, Boston, MA 02215, USA; (R.S.B.); (S.P.B.)
| | - Christopher J. Sweeney
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA; (E.P.O.); (G.H.); (K.M.K.); (C.J.S.); (M.-E.T.); (A.D.C.)
| | - Viktor A. Adalsteinsson
- Eli and Edythe L. Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; (J.R.); (G.G.); (V.A.A.)
| | - Mary-Ellen Taplin
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA; (E.P.O.); (G.H.); (K.M.K.); (C.J.S.); (M.-E.T.); (A.D.C.)
| | - Atish D. Choudhury
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA; (E.P.O.); (G.H.); (K.M.K.); (C.J.S.); (M.-E.T.); (A.D.C.)
- Eli and Edythe L. Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; (J.R.); (G.G.); (V.A.A.)
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7
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White MD, Klein RH, Shaw B, Kim A, Subramanian M, Mora JL, Giobbie-Hurder A, Nagabhushan D, Jain A, Singh M, Kuter BM, Nayyar N, Bertalan MS, Stocking JH, Markson SC, Lastrapes M, Alvarez-Breckenridge C, Cahill DP, Gydush G, Rhoades J, Rotem D, Adalsteinsson VA, Mahar M, Kaplan A, Oh K, Sullivan RJ, Gerstner E, Carter SL, Brastianos PK. Detection of Leptomeningeal Disease Using Cell-Free DNA From Cerebrospinal Fluid. JAMA Netw Open 2021; 4:e2120040. [PMID: 34369989 PMCID: PMC8353541 DOI: 10.1001/jamanetworkopen.2021.20040] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Accepted: 05/05/2021] [Indexed: 12/27/2022] Open
Abstract
Importance Leptomeningeal disease (LMD) is a devastating complication of cancer that is frequently underdiagnosed owing to the low sensitivity of cerebrospinal fluid (CSF) cytologic assessment, the current benchmark diagnostic method. Improving diagnostic sensitivity may lead to improved treatment decisions. Objective To assess whether cell-free DNA (cfDNA) analysis of CSF may be used to diagnose LMD more accurately than cytologic analysis. Design, Setting, and Participants This diagnostic study conducted in a neuro-oncology clinic at 2 large, tertiary medical centers assessed the use of genomic sequencing of CSF samples obtained from 30 patients with suspected or confirmed LMD from 2015 through 2018 to identify tumor-derived cfDNA. From the same CSF samples, cytologic analyses were conducted, and the results of the 2 tests were compared. This study consisted of 2 patient populations: 22 patients with cytologically confirmed LMD without parenchymal tumors abutting their CSF and 8 patients with parenchymal brain metastases with no evidence of LMD. Patients were considered positive for the presence of LMD if previous CSF cytologic analysis was positive for malignant cells. The analysis was conducted from 2015 to 2018. Main Outcomes and Measures The primary outcome was the diagnostic accuracy of cfDNA analysis, defined as the number of tests that resulted in correct diagnoses out of the total number of tests assayed. Hypotheses were formed before data collection. Results In total, 30 patients (23 women [77%]; median age, 51 years [range, 28-81 years]), primarily presenting with metastatic solid malignant neoplasms, participated in this study. For 48 follow-up samples from patients previously diagnosed via cytologic analysis as having LMD with no parenchymal tumor abutting CSF, cfDNA findings were accurate in the assessment of LMD in 45 samples (94%; 95% CI, 83%-99%), whereas cytologic analysis was accurate in 36 samples (75%; 95% CI, 60%-86%), a significant difference (P = .02). Of 43 LMD-positive samples, CSF cfDNA analysis was sensitive to LMD in 40 samples (93%; 95% CI, 81%-99%), and cytologic analysis was sensitive to LMD in 31 samples (72%; 95% CI, 56%-85%), a significant difference (P = .02). For 3 patients with parenchymal brain metastases abutting the CSF and no suspicion of LMD, cytologic findings were negative for LMD in all 3 patients, whereas cfDNA findings were positive in all 3 patients. Conclusions and Relevance This diagnostic study found improved sensitivity and accuracy of cfDNA CSF testing vs cytologic assessment for diagnosing LMD with the exception of parenchymal tumors abutting CSF, suggesting improved ability to diagnosis LMD. Consideration of incorporating CSF cfDNA analysis into clinical care is warranted.
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Affiliation(s)
- Michael D. White
- Division of Neuro-Oncology, Massachusetts General Hospital, Harvard Medical School, Boston
- Cancer Center, Massachusetts General Hospital, Boston
- Division of Comprehensive Neurology, Massachusetts General Hospital, Harvard Medical School, Boston
- Division of Neuro-Oncology, University of Rochester School of Medicine, Rochester, New York
| | - Robert H. Klein
- Broad Institute of MIT and Harvard, Boston, Massachusetts
- Division of Computational Biology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Brian Shaw
- Department of Medicine, Harvard Medical School & Massachusetts General Hospital, Boston, Massachusetts
| | - Albert Kim
- Division of Neuro-Oncology, Massachusetts General Hospital, Harvard Medical School, Boston
- Cancer Center, Massachusetts General Hospital, Boston
| | - Megha Subramanian
- Department of Medicine, Harvard Medical School & Massachusetts General Hospital, Boston, Massachusetts
- Alnylam Pharmaceuticals, Cambridge, Massachusetts
| | - Joana L. Mora
- Cancer Center, Massachusetts General Hospital, Boston
- Broad Institute of MIT and Harvard, Boston, Massachusetts
- Department of Medicine, Harvard Medical School & Massachusetts General Hospital, Boston, Massachusetts
| | - Anita Giobbie-Hurder
- Division of Biostatistics, Department of Data Science, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Deepika Nagabhushan
- Department of Medicine, Harvard Medical School & Massachusetts General Hospital, Boston, Massachusetts
| | - Aarushi Jain
- Department of Medicine, Harvard Medical School & Massachusetts General Hospital, Boston, Massachusetts
| | - Mohini Singh
- Department of Medicine, Harvard Medical School & Massachusetts General Hospital, Boston, Massachusetts
| | - Benjamin M. Kuter
- Department of Medicine, Harvard Medical School & Massachusetts General Hospital, Boston, Massachusetts
- Boston University, Boston, Massachusetts
| | - Naema Nayyar
- Department of Medicine, Harvard Medical School & Massachusetts General Hospital, Boston, Massachusetts
| | - Mia S. Bertalan
- Cancer Center, Massachusetts General Hospital, Boston
- Department of Medicine, Harvard Medical School & Massachusetts General Hospital, Boston, Massachusetts
- Geisel School of Medicine, Dartmouth College, Dartmouth-Hitchcock Medical Center, Lebanon, New Hampshire
| | - Jackson H. Stocking
- Department of Medicine, Harvard Medical School & Massachusetts General Hospital, Boston, Massachusetts
- University of Colorado School of Medicine, Aurora
| | - Samuel C. Markson
- Broad Institute of MIT and Harvard, Boston, Massachusetts
- Division of Computational Biology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Matthew Lastrapes
- Broad Institute of MIT and Harvard, Boston, Massachusetts
- Division of Computational Biology, Dana-Farber Cancer Institute, Boston, Massachusetts
- University of Texas Health Science Center at Houston, Houston
| | - Christopher Alvarez-Breckenridge
- Broad Institute of MIT and Harvard, Boston, Massachusetts
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston
- The University of Texas MD Anderson Cancer Center, Houston
| | - Daniel P. Cahill
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston
| | - Gregory Gydush
- Broad Institute of MIT and Harvard, Boston, Massachusetts
| | - Justin Rhoades
- Broad Institute of MIT and Harvard, Boston, Massachusetts
| | - Denisse Rotem
- Broad Institute of MIT and Harvard, Boston, Massachusetts
- Tessera Therapeutics, Cambridge, Massachusetts
| | | | - Maura Mahar
- Division of Neuro-Oncology, Massachusetts General Hospital, Harvard Medical School, Boston
- Cancer Center, Massachusetts General Hospital, Boston
| | - Alexander Kaplan
- Department of Medicine, Harvard Medical School & Massachusetts General Hospital, Boston, Massachusetts
- University of Massachusetts, Boston, Massachusetts
| | - Kevin Oh
- Cancer Center, Massachusetts General Hospital, Boston
| | - Ryan J. Sullivan
- Cancer Center, Massachusetts General Hospital, Boston
- Broad Institute of MIT and Harvard, Boston, Massachusetts
- Department of Medicine, Harvard Medical School & Massachusetts General Hospital, Boston, Massachusetts
| | - Elizabeth Gerstner
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Boston
- Department of Radiology, Harvard Medical School, Harvard University, Boston, Massachusetts
| | - Scott L. Carter
- Broad Institute of MIT and Harvard, Boston, Massachusetts
- Division of Computational Biology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
| | - Priscilla K. Brastianos
- Cancer Center, Massachusetts General Hospital, Boston
- Broad Institute of MIT and Harvard, Boston, Massachusetts
- Department of Medicine, Harvard Medical School & Massachusetts General Hospital, Boston, Massachusetts
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8
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Parsons HA, Rhoades J, Reed SC, Gydush G, Ram P, Exman P, Xiong K, Lo CC, Li T, Fleharty M, Kirkner GJ, Rotem D, Cohen O, Yu F, Fitarelli-Kiehl M, Leong KW, Hughes ME, Rosenberg SM, Collins LC, Miller KD, Blumenstiel B, Trippa L, Cibulskis C, Neuberg DS, DeFelice M, Freeman SS, Lennon NJ, Wagle N, Ha G, Stover DG, Choudhury AD, Getz G, Winer EP, Meyerson M, Lin NU, Krop I, Love JC, Makrigiorgos GM, Partridge AH, Mayer EL, Golub TR, Adalsteinsson VA. Sensitive Detection of Minimal Residual Disease in Patients Treated for Early-Stage Breast Cancer. Clin Cancer Res 2020; 26:2556-2564. [PMID: 32170028 DOI: 10.1158/1078-0432.ccr-19-3005] [Citation(s) in RCA: 91] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Revised: 11/26/2019] [Accepted: 02/13/2020] [Indexed: 12/21/2022]
Abstract
PURPOSE Existing cell-free DNA (cfDNA) methods lack the sensitivity needed for detecting minimal residual disease (MRD) following therapy. We developed a test for tracking hundreds of patient-specific mutations to detect MRD with a 1,000-fold lower error rate than conventional sequencing. EXPERIMENTAL DESIGN We compared the sensitivity of our approach to digital droplet PCR (ddPCR) in a dilution series, then retrospectively identified two cohorts of patients who had undergone prospective plasma sampling and clinical data collection: 16 patients with ER+/HER2- metastatic breast cancer (MBC) sampled within 6 months following metastatic diagnosis and 142 patients with stage 0 to III breast cancer who received curative-intent treatment with most sampled at surgery and 1 year postoperative. We performed whole-exome sequencing of tumors and designed individualized MRD tests, which we applied to serial cfDNA samples. RESULTS Our approach was 100-fold more sensitive than ddPCR when tracking 488 mutations, but most patients had fewer identifiable tumor mutations to track in cfDNA (median = 57; range = 2-346). Clinical sensitivity was 81% (n = 13/16) in newly diagnosed MBC, 23% (n = 7/30) at postoperative and 19% (n = 6/32) at 1 year in early-stage disease, and highest in patients with the most tumor mutations available to track. MRD detection at 1 year was strongly associated with distant recurrence [HR = 20.8; 95% confidence interval, 7.3-58.9]. Median lead time from first positive sample to recurrence was 18.9 months (range = 3.4-39.2 months). CONCLUSIONS Tracking large numbers of individualized tumor mutations in cfDNA can improve MRD detection, but its sensitivity is driven by the number of tumor mutations available to track.
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Affiliation(s)
- Heather A Parsons
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.
| | - Justin Rhoades
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Sarah C Reed
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Gregory Gydush
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Priyanka Ram
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Pedro Exman
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Kan Xiong
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Christopher C Lo
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts.,Boston University School of Public Health, Boston, Massachusetts
| | - Tianyu Li
- Division of Biostatistics, Department of Data Sciences, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Mark Fleharty
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Gregory J Kirkner
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Denisse Rotem
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Ofir Cohen
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Fangyan Yu
- Department of Radiation Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Massachusetts
| | - Mariana Fitarelli-Kiehl
- Department of Radiation Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Massachusetts
| | - Ka Wai Leong
- Department of Radiation Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Massachusetts
| | - Melissa E Hughes
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Shoshana M Rosenberg
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Laura C Collins
- Department of Pathology, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, Massachusetts
| | - Kathy D Miller
- Indiana University Melvin and Bren Simon Cancer Center, Indianapolis, Indiana
| | | | - Lorenzo Trippa
- Division of Biostatistics, Department of Data Sciences, Dana-Farber Cancer Institute, Boston, Massachusetts
| | | | - Donna S Neuberg
- Division of Biostatistics, Department of Data Sciences, Dana-Farber Cancer Institute, Boston, Massachusetts
| | | | | | - Niall J Lennon
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Nikhil Wagle
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Gavin Ha
- Division of Public Health Services, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Daniel G Stover
- Medical Oncology, Ohio State University Comprehensive Cancer Center, Columbus, Ohio
| | - Atish D Choudhury
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Gad Getz
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Eric P Winer
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Matthew Meyerson
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Nancy U Lin
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Ian Krop
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - J Christopher Love
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts.,Koch Institute for Integrative Cancer Research at MIT, Cambridge, Massachusetts
| | - G Mike Makrigiorgos
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts.,Department of Radiation Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Massachusetts
| | - Ann H Partridge
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Erica L Mayer
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Todd R Golub
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts.,Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Howard Hughes Medical Institute, Chevy Chase, Maryland
| | - Viktor A Adalsteinsson
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts. .,Koch Institute for Integrative Cancer Research at MIT, Cambridge, Massachusetts
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9
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Leong KW, Yu F, Adalsteinsson VA, Reed S, Gydush G, Ladas I, Li J, Tantisira KG, Makrigiorgos GM. A nuclease-polymerase chain reaction enables amplification of probes used for capture-based DNA target enrichment. Nucleic Acids Res 2019; 47:e147. [PMID: 31598677 PMCID: PMC6902007 DOI: 10.1093/nar/gkz870] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Revised: 09/06/2019] [Accepted: 10/01/2019] [Indexed: 11/13/2022] Open
Abstract
DNA target enrichment via hybridization capture is a commonly adopted approach which remains expensive due in-part to using biotinylated-probe panels. Here we provide a novel isothermal amplification reaction to amplify rapidly existing probe panels without knowledge of the sequences involved, thereby decreasing a major portion of the overall sample preparation cost. The reaction employs two thermostable enzymes, BST-polymerase and duplex-specific nuclease DSN. DSN initiates random ‘nicks’ on double-stranded-DNA which enable BST to polymerize DNA by displacing the nicked-strand. Displaced strands re-hybridize and the process leads to an exponential chain-reaction generating biotinylated DNA fragments within minutes. When starting from single-stranded-DNA, DNA is first converted to double-stranded-DNA via terminal-deoxynucleotidyl-transferase (TdT) prior to initiation of BST–DSN reaction. Biotinylated probes generated by TdT–BST–DSN (TBD) reactions using panels of 33, 190 or 7186 DNA targets are used for hybrid-capture-based target enrichment from amplified circulating-DNA, followed by targeted re-sequencing. Polymerase-nuclease isothermal-chain-reactions generate random amplified probes with no apparent sequence dependence. One round of target-capture using TBD probes generates a modest on-target sequencing ratio, while two successive rounds of capture generate >80% on-target reads with good sequencing uniformity. TBD-reactions generate enough capture-probes to increase by approximately two to three orders-of-magnitude the target-enrichment experiments possible from an initial set of probes.
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Affiliation(s)
- Ka Wai Leong
- Department of Radiation Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Fangyan Yu
- Department of Radiation Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | | | - Sarah Reed
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Gregory Gydush
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Ioannis Ladas
- Department of Radiation Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Jiang Li
- The Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medicine School, Boston, MA 02142, USA
| | - Kelan G Tantisira
- The Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medicine School, Boston, MA 02142, USA
| | - Gerassimos Mike Makrigiorgos
- Department of Radiation Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
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10
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Pagès M, Rotem D, Gydush G, Reed S, Rhoades J, Ha G, Lo C, Tracy A, Jones R, Becker S, Haller M, Chi S, Kieran M, Goumnerova L, Love C, Ligon K, Wright K, Adalsteinsson V, Beroukhim R, Bandopadhayay P. GENE-07. LIQUID BIOPSY DETECTION OF GENOMIC ALTERATIONS IN PEDIATRIC BRAIN TUMORS FROM CELL-FREE DNA IN PERIPHERAL BLOOD, CSF, AND URINE. Neuro Oncol 2019. [DOI: 10.1093/neuonc/noz036.078] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Mélanie Pagès
- Dana-Farber Cancer Institute/Boston Children’s Cancer and Blood Disorders Center, Boston, MA, USA
| | | | | | | | | | - Gavin Ha
- Broad Institute, Cambridge, MA, USA
| | - Chris Lo
- Broad Institute, Cambridge, MA, USA
| | | | - Robert Jones
- Dana-Farber Cancer Institute/Boston Children’s Cancer and Blood Disorders Center, Boston, MA, USA
| | - Sarah Becker
- Dana-Farber Cancer Institute/Boston Children’s Cancer and Blood Disorders Center, Boston, MA, USA
| | - Michaela Haller
- Dana-Farber Cancer Institute/Boston Children’s Cancer and Blood Disorders Center, Boston, MA, USA
| | - Susan Chi
- Dana-Farber Cancer Institute/Boston Children’s Cancer and Blood Disorders Center, Boston, MA, USA
- Boston Children’s Hospital, Boston, MA, USA
| | - Mark Kieran
- Dana-Farber Cancer Institute/Boston Children’s Cancer and Blood Disorders Center, Boston, MA, USA
- Boston Children’s Hospital, Boston, MA, USA
| | - Liliana Goumnerova
- Dana-Farber Cancer Institute/Boston Children’s Cancer and Blood Disorders Center, Boston, MA, USA
- Boston Children’s Hospital, Boston, MA, USA
| | | | - Keith Ligon
- Dana-Farber Cancer Institute/Boston Children’s Cancer and Blood Disorders Center, Boston, MA, USA
- Broad Institute, Cambridge, MA, USA
- Boston Children’s Hospital, Boston, MA, USA
| | - Karen Wright
- Dana-Farber Cancer Institute/Boston Children’s Cancer and Blood Disorders Center, Boston, MA, USA
- Boston Children’s Hospital, Boston, MA, USA
| | - Viktor Adalsteinsson
- Broad Institute, Cambridge, MA, USA
- Massachussets Institute of Technology, Cambridge, MA, USA
| | - Rameen Beroukhim
- Dana-Farber Cancer Institute/Boston Children’s Cancer and Blood Disorders Center, Boston, MA, USA
- Broad Institute, Cambridge, MA, USA
| | - Pratiti Bandopadhayay
- Dana-Farber Cancer Institute/Boston Children’s Cancer and Blood Disorders Center, Boston, MA, USA
- Broad Institute, Cambridge, MA, USA
- Boston Children’s Hospital, Boston, MA, USA
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11
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Pages M, Rotem D, Gydush G, Reed S, Rhoades J, Ha G, Lo C, Tracy A, Jones R, Becker S, Haller M, Chi S, Kieran M, Goumnerova L, Love JC, Ligon K, Bandopadhayay P, Wright K, Adalsteinsson VA, Beroukhim R. INNV-22. LIQUID BIOPSY DETECTION OF GENOMIC ALTERATIONS IN PEDIATRIC BRAIN TUMORS FROM CELL FREE DNA IN PERIPHERAL BLOOD, CSF, AND URINE. Neuro Oncol 2018. [DOI: 10.1093/neuonc/noy148.595] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Mélanie Pages
- Dana-Farber Cancer Institute / Boston Childrens Cancer and Blood Disorders Center, Boston, MA, USA
| | | | | | | | | | - Gavin Ha
- Broad Institute, Cambridge, MA, USA
| | - Chris Lo
- Broad Institute, Cambridge, MA, USA
| | | | - Robert Jones
- Dana-Farber Cancer Institute / Boston Childrens Cancer and Blood Disorders Center, Boston, MA, USA
| | - Sarah Becker
- Dana-Farber Cancer Institute / Boston Childrens Cancer and Blood Disorders Center, Boston, MA, USA
| | - Michaela Haller
- Dana-Farber Cancer Institute / Boston Childrens Cancer and Blood Disorders Center, Boston, MA, USA
| | - Susan Chi
- Dana-Farber Cancer Institute / Boston Childrens Cancer and Blood Disorders Center / Boston Childrens Hospital, Boston, MA, USA
| | - Mark Kieran
- Dana-Farber Cancer Institute / Boston Childrens Cancer and Blood Disorders Center / Boston Childrens Hospital, Boston, MA, USA
| | - Liliana Goumnerova
- Dana-Farber Cancer Institute / Boston Childrens Cancer and Blood Disorders Center / Boston Childrens Hospital, Boston, MA, USA
| | | | - Keith Ligon
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | | | - Karen Wright
- Dana-Farber Cancer Institute / Boston Childrens Hospital, Boston, MA, USA
| | | | - Rameen Beroukhim
- Dana Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
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12
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Choudhury AD, Werner L, Francini E, Wei XX, Ha G, Freeman SS, Rhoades J, Reed SC, Gydush G, Rotem D, Lo C, Taplin ME, Harshman LC, Zhang Z, O'Connor EP, Stover DG, Parsons HA, Getz G, Meyerson M, Love JC, Hahn WC, Adalsteinsson VA. Tumor fraction in cell-free DNA as a biomarker in prostate cancer. JCI Insight 2018; 3:122109. [PMID: 30385733 DOI: 10.1172/jci.insight.122109] [Citation(s) in RCA: 79] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Accepted: 10/02/2018] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Tumor content in circulating cell-free DNA (cfDNA) is a promising biomarker, but longitudinal dynamics of tumor-derived and non-tumor-derived cfDNA through multiple courses of therapy have not been well described. METHODS CfDNA from 663 plasma samples from 140 patients with castration-resistant prostate cancer (CRPC) was subject to sparse whole genome sequencing. Tumor fraction (TFx) estimated using the computational tool ichorCNA was correlated with clinical features and responses to therapy. RESULTS TFx associated with the number of bone metastases (median TFx = 0.014 with no bone metastases, 0.047 with 1-3 bone metastases, 0.190 for 4+ bone metastases; P < 0.0001) and with visceral metastases (P < 0.0001). In multivariable analysis, TFx remained associated with metastasis location (P = 0.042); TFx was positively correlated with alkaline phosphatase (P = 0.0227) and negatively correlated with hemoglobin (Hgb) (P < 0.001), but it was not correlated with prostate specific antigen (PSA) (P = 0.75). Tumor-derived and non-tumor-derived cfDNA track together and do not increase with generalized tissue damage from chemotherapy or radiation at the time scales examined. All new treatments that led to ≥30% PSA decline at 6 weeks were associated with TFx decline when baseline TFx was >7%; however, TFx in patients being subsequently maintained on secondary hormonal therapy was quite dynamic. CONCLUSION TFx correlates with clinical features associated with overall survival in CRPC, and TFx decline is a promising biomarker for initial therapeutic response. TRIAL REGISTRATION Dana-Farber/Harvard Cancer Center (DF/HCC) protocol no. 18-135. FUNDING Wong Family Award in Translational Oncology, Dana Farber Cancer Institute Medical Oncology grant, Gerstner Family Foundation, Janssen Pharmaceuticals Inc., and Koch Institute Support (core) grant P30-CA14051 from the National Cancer Institute (NCI).
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Affiliation(s)
- Atish D Choudhury
- Dana-Farber Cancer Institute, Boston, Massachusetts, USA.,Harvard Medical School, Boston, Massachusetts, USA.,Eli and Edythe L. Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Lillian Werner
- Dana-Farber Cancer Institute, Boston, Massachusetts, USA.,Harvard Medical School, Boston, Massachusetts, USA
| | - Edoardo Francini
- Dana-Farber Cancer Institute, Boston, Massachusetts, USA.,Sapienza University of Rome, Rome, Italy
| | - Xiao X Wei
- Dana-Farber Cancer Institute, Boston, Massachusetts, USA.,Harvard Medical School, Boston, Massachusetts, USA
| | - Gavin Ha
- Dana-Farber Cancer Institute, Boston, Massachusetts, USA.,Eli and Edythe L. Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Samuel S Freeman
- Eli and Edythe L. Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Justin Rhoades
- Eli and Edythe L. Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Sarah C Reed
- Eli and Edythe L. Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Gregory Gydush
- Eli and Edythe L. Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Denisse Rotem
- Eli and Edythe L. Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Christopher Lo
- Eli and Edythe L. Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Mary-Ellen Taplin
- Dana-Farber Cancer Institute, Boston, Massachusetts, USA.,Harvard Medical School, Boston, Massachusetts, USA
| | - Lauren C Harshman
- Dana-Farber Cancer Institute, Boston, Massachusetts, USA.,Harvard Medical School, Boston, Massachusetts, USA
| | - Zhenwei Zhang
- Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | | | | | - Heather A Parsons
- Dana-Farber Cancer Institute, Boston, Massachusetts, USA.,Harvard Medical School, Boston, Massachusetts, USA.,Eli and Edythe L. Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Gad Getz
- Eli and Edythe L. Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.,Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Matthew Meyerson
- Dana-Farber Cancer Institute, Boston, Massachusetts, USA.,Harvard Medical School, Boston, Massachusetts, USA.,Eli and Edythe L. Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - J Christopher Love
- Eli and Edythe L. Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.,Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - William C Hahn
- Dana-Farber Cancer Institute, Boston, Massachusetts, USA.,Harvard Medical School, Boston, Massachusetts, USA.,Eli and Edythe L. Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Viktor A Adalsteinsson
- Eli and Edythe L. Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.,Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
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13
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Getz G, Cibulskis C, Leshchiner I, Hanna M, Livitz D, Slowik K, Levovitz C, Utro F, Rhrissorrakrai K, Rotem D, Gydush G, Reed SC, Rhoades J, Ha G, Freeman SS, Lo C, Fleharty M, Abreu J, Larkin K, Cipicchio M, Blumenstiel B, DeFelice M, Grimsby J, Hamilton S, Lennon N, Adalsteinsson VA, Parida L. Abstract 3001: Broad/IBM Project: Discovery of treatment resistance mechanisms through use of liquid biopsy genomics services. Cancer Res 2018. [DOI: 10.1158/1538-7445.am2018-3001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
The Broad/IBM Cancer Resistance Project has partnered with Broad Genomics to pilot the use of cutting edge sequencing technology for the analysis of cell free DNA in blood biopsies. Working closely with the Broad's Cancer Program, Broad Genomics has developed a suite of liquid biopsy sequencing products designed to provide optimal flexibility in conducting research studies with a broad range of applications including; biomarker discovery, treatment resistance monitoring, and detection of minimal residual disease (MRD) post-surgery. Cell-free DNA is extracted from the blood, and a dual unique-molecular-indexed library is created. From this library, low coverage whole genome (ultra-low-pass 0.1x coverage) data is generated to survey sample quality and evaluate the tumor fraction in the liquid specimen. Utilizing the same library, additional assays can be selected for processing based on the research aim (Targeted Panel Assays, MRD Detection or Whole Exomes). Since our approach utilizes the same genomic material for whole genome and targeted sequencing assays, it is possible to maximize the information learned from each valuable and limited liquid biopsy specimen. Our study design takes advantage of the discovery potential of combined tissue-based sequencing and serial liquid biopsy analysis to elucidate mechanisms of cancer resistance by tracking the evolution of clonal and subclonal populations in patients samples over time. This collaboration will utilize the ultra-low-pass sequencing and whole exome sequencing together with custom analysis pipelines to correlate the genomic events with patient clinical data. We aim to process 3,000 samples from 1,000 patients over the next 3 years. To date we have processed close to 500 samples through the ultra-low-pass pipeline and 100 samples through the whole exome sequencing pipeline (results to be provided).The ability to successfully investigate treatment resistant cancers from non-invasive liquid biopsies presents new opportunities for identifying markers, understanding dynamics and monitoring tumor dissemination and clonal evolution.
Citation Format: Gad Getz, Carrie Cibulskis, Ignaty Leshchiner, Megan Hanna, Dimitri Livitz, Kara Slowik, Chaya Levovitz, Filippo Utro, Kahn Rhrissorrakrai, Denisse Rotem, Gregory Gydush, Sarah C. Reed, Justin Rhoades, Gavin Ha, Samuel S. Freeman, Christopher Lo, Mark Fleharty, Justin Abreu, Katie Larkin, Michelle Cipicchio, Brendan Blumenstiel, Matt DeFelice, Jonna Grimsby, Susanna Hamilton, Niall Lennon, Viktor A. Adalsteinsson, Laxmi Parida. Broad/IBM Project: Discovery of treatment resistance mechanisms through use of liquid biopsy genomics services [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 3001.
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Affiliation(s)
- Gad Getz
- 1MGH Cancer Center and Broad Institute, Charlestown, MA
| | | | | | | | | | | | | | - Filippo Utro
- 3IBM T. J. Watson Research, Yorktown Heights, NY
| | | | | | | | | | | | - Gavin Ha
- 4Broad Institute, Harvard University, Cambridge, MA
| | | | | | | | | | | | | | | | | | | | | | | | | | - Laxmi Parida
- 3IBM T. J. Watson Research, Yorktown Heights, NY
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Freeman SS, Lin Z, Ha G, Leshchiner I, Rhoades J, Livitz D, Rosebrock D, Reed SC, Gydush G, Lo C, Rotem D, Choudhury AD, Stover DG, Parsons HA, Boehm JS, Love JC, Meyerson M, Grandgenett P, Hollingsworth MA, Adalsteinsson VA, Getz G. Abstract LB-225: Liquid biopsies identify trunk mutations and reflect multiple tumors in a patient. Cancer Res 2018. [DOI: 10.1158/1538-7445.am2018-lb-225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Introduction: Precision medicine approaches to guide therapy selection require routine sampling of tumors. However, tumor biopsies are not always accessible and may be confounded by spatial heterogeneity. Liquid biopsies, including analysis of cell-free DNA (cfDNA), present a non-invasive alternative which may reflect multiple tumors in the body. Previous studies have demonstrated exome-wide concordance between single-site tumor biopsies and cfDNA, but little is known about how cfDNA reflects multiple lesions within a patient. Here we sought to determine how cfDNA reflects the body-wide tumor phylogeny, which will inform the use of cfDNA for cancer precision medicine.
Methods: We identified 20 patients with pancreatic cancer who had undergone rapid autopsy. We then screened cfDNA tumor fraction and performed whole-exome sequencing of cfDNA and multiple tumor biopsies for 3 patients with cfDNA tumor fraction >10%. We inferred the tumor phylogeny and then developed a statistical approach to deconvolute the contributions to cfDNA from tumor phylogenetic nodes. Finally, we determined whether shared trunk mutations could be detected in cfDNA and tumor biopsies.
Results: For each patient, we found mutations shared between all sites and cfDNA, including putative driver mutations. We found mutations which were clonal in multiple regions were detectable in cfDNA, whereas mutations private to individual sites were never clonal in cfDNA. Through our deconvolution analysis, we found that cfDNA could not be modeled as a simple linear combination of individual sites, but rather that cfDNA represented multiple nodes in the inferred phylogeny. For two pancreatic adenocarcinoma patients, the inferred ancestor of the metastases had high estimated contribution (>70%) to cfDNA, while the ancestors of the primaries had lower contributions (<10%). Next, we considered trunk mutations, which originate earliest in the tumor phylogenetic tree. When we analyzed precision for detection of trunk mutations, we found on average, 71% of clonal mutations in metastases were truncal, while only 55% of clonal mutations in primary tumors were truncal. Due to copy number deletions, not all trunk mutations were detected in metastases. Finally, on average, cfDNA had equal or better precision than 83% of primaries and 88% of metastases, suggesting cfDNA may provide more accurate trunk SSNV calls than tumor biopsies.
Conclusions: Through analyzing cfDNA and synchronous tumor biopsies from the same patient, we find trunk mutations are enriched in cfDNA as compared to the average single-site biopsy. We also predict that cfDNA represents multiple nodes in the inferred phylogeny. In cases where tumor biopsies are inaccessible, we demonstrate that cfDNA might be a promising alternative to detect trunk SSNVs. These results suggest that cfDNA may be complementary to tumor biopsies for disease monitoring and treatment selection in personalized medicine.
Citation Format: Samuel S. Freeman, Ziao Lin, Gavin Ha, Ignaty Leshchiner, Justin Rhoades, Dimitri Livitz, Daniel Rosebrock, Sarah C. Reed, Gregory Gydush, Christopher Lo, Denisse Rotem, Atish D. Choudhury, Daniel G. Stover, Heather A. Parsons, Jesse S. Boehm, J Christopher Love, Matthew Meyerson, Paul Grandgenett, Michael A. Hollingsworth, Viktor A. Adalsteinsson, Gad Getz. Liquid biopsies identify trunk mutations and reflect multiple tumors in a patient [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr LB-225.
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Affiliation(s)
| | | | - Gavin Ha
- 2Dana-Farber Cancer Institute, Boston, MA
| | | | | | | | | | | | | | | | | | | | - Daniel G. Stover
- 3Ohio State University Comprehensive Cancer Center, Columbus, OH
| | | | | | | | | | | | | | | | - Gad Getz
- 6Massachusetts General Hospital, Boston, MA
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Pages M, Rotem D, Gydush G, Reed S, Rhoades J, Ha G, Lo C, Tracy A, Jones R, Becker S, Haller M, Chi S, Kieran M, Goumnerova L, Love JC, Ligon KL, Bandopadhayay P, Wright K, Adalsteinsson VA, Beroukhim R. TBIO-18. LIQUID BIOPSY DETECTION OF GENOMIC ALTERATIONS IN PEDIATRIC BRAIN TUMORS FROM CELL FREE DNA IN PERIPHERAL BLOOD, CSF, AND URINE. Neuro Oncol 2018. [DOI: 10.1093/neuonc/noy059.706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Melanie Pages
- Dana-Farber Cancer Institute/Boston Children’s Cancer and Blood Disorders Center, Boston, MA, USA
| | | | | | | | | | - Gavin Ha
- Broad Institute, Cambridge, MA, USA
| | - Chris Lo
- Broad Institute, Cambridge, MA, USA
| | | | - Robert Jones
- Dana-Farber Cancer Institute/Boston Children’s Cancer and Blood Disorders Center, Boston, MA, USA
| | - Sarah Becker
- Dana-Farber Cancer Institute/Boston Children’s Cancer and Blood Disorders Center, Boston, MA, USA
| | - Michaela Haller
- Dana-Farber Cancer Institute/Boston Children’s Cancer and Blood Disorders Center, Boston, MA, USA
| | - Susan Chi
- Dana-Farber Cancer Institute/Boston Children’s Cancer and Blood Disorders Center, Boston, MA, USA
- Boston Children’s Hospital, Boston, MA, USA
| | - Mark Kieran
- Dana-Farber Cancer Institute/Boston Children’s Cancer and Blood Disorders Center, Boston, MA, USA
- Boston Children’s Hospital, Boston, MA, USA
| | - Liliana Goumnerova
- Dana-Farber Cancer Institute/Boston Children’s Cancer and Blood Disorders Center, Boston, MA, USA
- Boston Children’s Hospital, Boston, MA, USA
| | | | - Keith L Ligon
- Dana-Farber Cancer Institute/Boston Children’s Cancer and Blood Disorders Center, Boston, MA, USA
- Boston Children’s Hospital, Boston, MA, USA
| | - Pratiti Bandopadhayay
- Dana-Farber Cancer Institute/Boston Children’s Cancer and Blood Disorders Center, Boston, MA, USA
- Boston Children’s Hospital, Boston, MA, USA
| | - Karen Wright
- Dana-Farber Cancer Institute/Boston Children’s Cancer and Blood Disorders Center, Boston, MA, USA
- Boston Children’s Hospital, Boston, MA, USA
| | - Viktor A Adalsteinsson
- Broad Institute, Cambridge, MA, USA
- Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Rameen Beroukhim
- Dana-Farber Cancer Institute/Boston Children’s Cancer and Blood Disorders Center, Boston, MA, USA
- Broad Institute, Cambridge, MA, USA
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Manier S, Park J, Capelletti M, Bustoros M, Freeman SS, Ha G, Rhoades J, Liu CJ, Huynh D, Reed SC, Gydush G, Salem KZ, Rotem D, Freymond C, Yosef A, Perilla-Glen A, Garderet L, Van Allen EM, Kumar S, Love JC, Getz G, Adalsteinsson VA, Ghobrial IM. Whole-exome sequencing of cell-free DNA and circulating tumor cells in multiple myeloma. Nat Commun 2018; 9:1691. [PMID: 29703982 PMCID: PMC5923255 DOI: 10.1038/s41467-018-04001-5] [Citation(s) in RCA: 128] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Accepted: 03/27/2018] [Indexed: 12/29/2022] Open
Abstract
Liquid biopsies including circulating tumor cells (CTCs) and cell-free DNA (cfDNA) have enabled minimally invasive characterization of many cancers, but are rarely analyzed together. Understanding the detectability and genomic concordance of CTCs and cfDNA may inform their use in guiding cancer precision medicine. Here, we report the detectability of cfDNA and CTCs in blood samples from 107 and 56 patients with multiple myeloma (MM), respectively. Using ultra-low pass whole-genome sequencing, we find both tumor fractions correlate with disease progression. Applying whole-exome sequencing (WES) to cfDNA, CTCs, and matched tumor biopsies, we find concordance in clonal somatic mutations (~99%) and copy number alterations (~81%) between liquid and tumor biopsies. Importantly, analyzing CTCs and cfDNA together enables cross-validation of mutations, uncovers mutations exclusive to either CTCs or cfDNA, and allows blood-based tumor profiling in a greater fraction of patients. Our study demonstrates the utility of analyzing both CTCs and cfDNA in MM. Circulating tumor cells (CTCs) and cell-free DNA (cfDNA) enables characterization of a patient’s cancer. Here, the authors analyse CTCs, cfDNA, and tumor biopsies from multiple myeloma patients to show these approaches are complementary for mutation detection, together enabling a greater fraction of patient tumors to be profiled.
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Affiliation(s)
- S Manier
- Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, 02115, USA.,Hematology Department, CHU, Univ. Lille, 59000, Lille, France.,INSERM UMR-S1172, 59000, Lille, France
| | - J Park
- Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, 02115, USA.,Brigham and Women's Hospital, Boston, MA, 02115, USA
| | - M Capelletti
- Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, 02115, USA
| | - M Bustoros
- Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, 02115, USA
| | - S S Freeman
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - G Ha
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - J Rhoades
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - C J Liu
- Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, 02115, USA
| | - D Huynh
- Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, 02115, USA
| | - S C Reed
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - G Gydush
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - K Z Salem
- Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, 02115, USA
| | - D Rotem
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - C Freymond
- Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, 02115, USA
| | - A Yosef
- Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, 02115, USA
| | - A Perilla-Glen
- Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, 02115, USA
| | - L Garderet
- Department of Hematology, St-Antoine University Hospital, Paris, 75000, France
| | - E M Van Allen
- Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, 02115, USA.,Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - S Kumar
- Department of Hematology, Mayo Clinic, Rochester, MN, 55902, USA
| | - J C Love
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - G Getz
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - V A Adalsteinsson
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.
| | - I M Ghobrial
- Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, 02115, USA. .,Brigham and Women's Hospital, Boston, MA, 02115, USA. .,Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.
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Stover DG, Parsons HA, Ha G, Freeman SS, Barry WT, Guo H, Choudhury AD, Gydush G, Reed SC, Rhoades J, Rotem D, Hughes ME, Dillon DA, Partridge AH, Wagle N, Krop IE, Getz G, Golub TR, Love JC, Winer EP, Tolaney SM, Lin NU, Adalsteinsson VA. Association of Cell-Free DNA Tumor Fraction and Somatic Copy Number Alterations With Survival in Metastatic Triple-Negative Breast Cancer. J Clin Oncol 2018; 36:543-553. [PMID: 29298117 PMCID: PMC5815405 DOI: 10.1200/jco.2017.76.0033] [Citation(s) in RCA: 143] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Purpose Cell-free DNA (cfDNA) offers the potential for minimally invasive genome-wide profiling of tumor alterations without tumor biopsy and may be associated with patient prognosis. Triple-negative breast cancer (TNBC) is characterized by few mutations but extensive somatic copy number alterations (SCNAs), yet little is known regarding SCNAs in metastatic TNBC. We sought to evaluate SCNAs in metastatic TNBC exclusively via cfDNA and determine if cfDNA tumor fraction is associated with overall survival in metastatic TNBC. Patients and Methods In this retrospective cohort study, we identified 164 patients with biopsy-proven metastatic TNBC at a single tertiary care institution who received prior chemotherapy in the (neo)adjuvant or metastatic setting. We performed low-coverage genome-wide sequencing of cfDNA from plasma. Results Without prior knowledge of tumor mutations, we determined tumor fraction of cfDNA for 96.3% of patients and SCNAs for 63.9% of patients. Copy number profiles and percent genome altered were remarkably similar between metastatic and primary TNBCs. Certain SCNAs were more frequent in metastatic TNBCs relative to paired primary tumors and primary TNBCs in publicly available data sets The Cancer Genome Atlas and METABRIC, including chromosomal gains in drivers NOTCH2, AKT2, and AKT3. Prespecified cfDNA tumor fraction threshold of ≥ 10% was associated with significantly worse metastatic survival (median, 6.4 v 15.9 months) and remained significant independent of clinicopathologic factors (hazard ratio, 2.14; 95% CI, 1.4 to 3.8; P < .001). Conclusion We present the largest genomic characterization of metastatic TNBC to our knowledge, exclusively from cfDNA. Evaluation of cfDNA tumor fraction was feasible for nearly all patients, and tumor fraction ≥ 10% is associated with significantly worse survival in this large metastatic TNBC cohort. Specific SCNAs are enriched and prognostic in metastatic TNBC, with implications for metastasis, resistance, and novel therapeutic approaches.
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Affiliation(s)
- Daniel G. Stover
- Daniel G. Stover, Ohio State University Comprehensive Cancer Center, Columbus, OH; Heather A. Parsons, Gavin Ha, William T. Barry, Hao Guo, Atish D. Choudhury, Melissa E. Hughes, Deborah A. Dillon, Ann H. Partridge, Nikhil Wagle, Ian E. Krop, Todd R. Golub, Eric P. Winer, Sara M. Tolaney, and Nancy U. Lin, Dana-Farber Cancer Institute; Gad Getz, Massachusetts General Hospital, Boston; Gavin Ha, Samuel S. Freeman, Atish D. Choudhury, Gregory Gydush, Sarah C. Reed, Justin Rhoades, Denisse Rotem, Nikhil Wagle, Gad Getz, Todd R. Golub, and Viktor A. Adalsteinsson, Broad Institute of Harvard and Massachusetts Institute of Technology; and J. Christopher Love, Massachusetts Institute of Technology, Cambridge, MA
| | - Heather A. Parsons
- Daniel G. Stover, Ohio State University Comprehensive Cancer Center, Columbus, OH; Heather A. Parsons, Gavin Ha, William T. Barry, Hao Guo, Atish D. Choudhury, Melissa E. Hughes, Deborah A. Dillon, Ann H. Partridge, Nikhil Wagle, Ian E. Krop, Todd R. Golub, Eric P. Winer, Sara M. Tolaney, and Nancy U. Lin, Dana-Farber Cancer Institute; Gad Getz, Massachusetts General Hospital, Boston; Gavin Ha, Samuel S. Freeman, Atish D. Choudhury, Gregory Gydush, Sarah C. Reed, Justin Rhoades, Denisse Rotem, Nikhil Wagle, Gad Getz, Todd R. Golub, and Viktor A. Adalsteinsson, Broad Institute of Harvard and Massachusetts Institute of Technology; and J. Christopher Love, Massachusetts Institute of Technology, Cambridge, MA
| | - Gavin Ha
- Daniel G. Stover, Ohio State University Comprehensive Cancer Center, Columbus, OH; Heather A. Parsons, Gavin Ha, William T. Barry, Hao Guo, Atish D. Choudhury, Melissa E. Hughes, Deborah A. Dillon, Ann H. Partridge, Nikhil Wagle, Ian E. Krop, Todd R. Golub, Eric P. Winer, Sara M. Tolaney, and Nancy U. Lin, Dana-Farber Cancer Institute; Gad Getz, Massachusetts General Hospital, Boston; Gavin Ha, Samuel S. Freeman, Atish D. Choudhury, Gregory Gydush, Sarah C. Reed, Justin Rhoades, Denisse Rotem, Nikhil Wagle, Gad Getz, Todd R. Golub, and Viktor A. Adalsteinsson, Broad Institute of Harvard and Massachusetts Institute of Technology; and J. Christopher Love, Massachusetts Institute of Technology, Cambridge, MA
| | - Samuel S. Freeman
- Daniel G. Stover, Ohio State University Comprehensive Cancer Center, Columbus, OH; Heather A. Parsons, Gavin Ha, William T. Barry, Hao Guo, Atish D. Choudhury, Melissa E. Hughes, Deborah A. Dillon, Ann H. Partridge, Nikhil Wagle, Ian E. Krop, Todd R. Golub, Eric P. Winer, Sara M. Tolaney, and Nancy U. Lin, Dana-Farber Cancer Institute; Gad Getz, Massachusetts General Hospital, Boston; Gavin Ha, Samuel S. Freeman, Atish D. Choudhury, Gregory Gydush, Sarah C. Reed, Justin Rhoades, Denisse Rotem, Nikhil Wagle, Gad Getz, Todd R. Golub, and Viktor A. Adalsteinsson, Broad Institute of Harvard and Massachusetts Institute of Technology; and J. Christopher Love, Massachusetts Institute of Technology, Cambridge, MA
| | - William T. Barry
- Daniel G. Stover, Ohio State University Comprehensive Cancer Center, Columbus, OH; Heather A. Parsons, Gavin Ha, William T. Barry, Hao Guo, Atish D. Choudhury, Melissa E. Hughes, Deborah A. Dillon, Ann H. Partridge, Nikhil Wagle, Ian E. Krop, Todd R. Golub, Eric P. Winer, Sara M. Tolaney, and Nancy U. Lin, Dana-Farber Cancer Institute; Gad Getz, Massachusetts General Hospital, Boston; Gavin Ha, Samuel S. Freeman, Atish D. Choudhury, Gregory Gydush, Sarah C. Reed, Justin Rhoades, Denisse Rotem, Nikhil Wagle, Gad Getz, Todd R. Golub, and Viktor A. Adalsteinsson, Broad Institute of Harvard and Massachusetts Institute of Technology; and J. Christopher Love, Massachusetts Institute of Technology, Cambridge, MA
| | - Hao Guo
- Daniel G. Stover, Ohio State University Comprehensive Cancer Center, Columbus, OH; Heather A. Parsons, Gavin Ha, William T. Barry, Hao Guo, Atish D. Choudhury, Melissa E. Hughes, Deborah A. Dillon, Ann H. Partridge, Nikhil Wagle, Ian E. Krop, Todd R. Golub, Eric P. Winer, Sara M. Tolaney, and Nancy U. Lin, Dana-Farber Cancer Institute; Gad Getz, Massachusetts General Hospital, Boston; Gavin Ha, Samuel S. Freeman, Atish D. Choudhury, Gregory Gydush, Sarah C. Reed, Justin Rhoades, Denisse Rotem, Nikhil Wagle, Gad Getz, Todd R. Golub, and Viktor A. Adalsteinsson, Broad Institute of Harvard and Massachusetts Institute of Technology; and J. Christopher Love, Massachusetts Institute of Technology, Cambridge, MA
| | - Atish D. Choudhury
- Daniel G. Stover, Ohio State University Comprehensive Cancer Center, Columbus, OH; Heather A. Parsons, Gavin Ha, William T. Barry, Hao Guo, Atish D. Choudhury, Melissa E. Hughes, Deborah A. Dillon, Ann H. Partridge, Nikhil Wagle, Ian E. Krop, Todd R. Golub, Eric P. Winer, Sara M. Tolaney, and Nancy U. Lin, Dana-Farber Cancer Institute; Gad Getz, Massachusetts General Hospital, Boston; Gavin Ha, Samuel S. Freeman, Atish D. Choudhury, Gregory Gydush, Sarah C. Reed, Justin Rhoades, Denisse Rotem, Nikhil Wagle, Gad Getz, Todd R. Golub, and Viktor A. Adalsteinsson, Broad Institute of Harvard and Massachusetts Institute of Technology; and J. Christopher Love, Massachusetts Institute of Technology, Cambridge, MA
| | - Gregory Gydush
- Daniel G. Stover, Ohio State University Comprehensive Cancer Center, Columbus, OH; Heather A. Parsons, Gavin Ha, William T. Barry, Hao Guo, Atish D. Choudhury, Melissa E. Hughes, Deborah A. Dillon, Ann H. Partridge, Nikhil Wagle, Ian E. Krop, Todd R. Golub, Eric P. Winer, Sara M. Tolaney, and Nancy U. Lin, Dana-Farber Cancer Institute; Gad Getz, Massachusetts General Hospital, Boston; Gavin Ha, Samuel S. Freeman, Atish D. Choudhury, Gregory Gydush, Sarah C. Reed, Justin Rhoades, Denisse Rotem, Nikhil Wagle, Gad Getz, Todd R. Golub, and Viktor A. Adalsteinsson, Broad Institute of Harvard and Massachusetts Institute of Technology; and J. Christopher Love, Massachusetts Institute of Technology, Cambridge, MA
| | - Sarah C. Reed
- Daniel G. Stover, Ohio State University Comprehensive Cancer Center, Columbus, OH; Heather A. Parsons, Gavin Ha, William T. Barry, Hao Guo, Atish D. Choudhury, Melissa E. Hughes, Deborah A. Dillon, Ann H. Partridge, Nikhil Wagle, Ian E. Krop, Todd R. Golub, Eric P. Winer, Sara M. Tolaney, and Nancy U. Lin, Dana-Farber Cancer Institute; Gad Getz, Massachusetts General Hospital, Boston; Gavin Ha, Samuel S. Freeman, Atish D. Choudhury, Gregory Gydush, Sarah C. Reed, Justin Rhoades, Denisse Rotem, Nikhil Wagle, Gad Getz, Todd R. Golub, and Viktor A. Adalsteinsson, Broad Institute of Harvard and Massachusetts Institute of Technology; and J. Christopher Love, Massachusetts Institute of Technology, Cambridge, MA
| | - Justin Rhoades
- Daniel G. Stover, Ohio State University Comprehensive Cancer Center, Columbus, OH; Heather A. Parsons, Gavin Ha, William T. Barry, Hao Guo, Atish D. Choudhury, Melissa E. Hughes, Deborah A. Dillon, Ann H. Partridge, Nikhil Wagle, Ian E. Krop, Todd R. Golub, Eric P. Winer, Sara M. Tolaney, and Nancy U. Lin, Dana-Farber Cancer Institute; Gad Getz, Massachusetts General Hospital, Boston; Gavin Ha, Samuel S. Freeman, Atish D. Choudhury, Gregory Gydush, Sarah C. Reed, Justin Rhoades, Denisse Rotem, Nikhil Wagle, Gad Getz, Todd R. Golub, and Viktor A. Adalsteinsson, Broad Institute of Harvard and Massachusetts Institute of Technology; and J. Christopher Love, Massachusetts Institute of Technology, Cambridge, MA
| | - Denisse Rotem
- Daniel G. Stover, Ohio State University Comprehensive Cancer Center, Columbus, OH; Heather A. Parsons, Gavin Ha, William T. Barry, Hao Guo, Atish D. Choudhury, Melissa E. Hughes, Deborah A. Dillon, Ann H. Partridge, Nikhil Wagle, Ian E. Krop, Todd R. Golub, Eric P. Winer, Sara M. Tolaney, and Nancy U. Lin, Dana-Farber Cancer Institute; Gad Getz, Massachusetts General Hospital, Boston; Gavin Ha, Samuel S. Freeman, Atish D. Choudhury, Gregory Gydush, Sarah C. Reed, Justin Rhoades, Denisse Rotem, Nikhil Wagle, Gad Getz, Todd R. Golub, and Viktor A. Adalsteinsson, Broad Institute of Harvard and Massachusetts Institute of Technology; and J. Christopher Love, Massachusetts Institute of Technology, Cambridge, MA
| | - Melissa E. Hughes
- Daniel G. Stover, Ohio State University Comprehensive Cancer Center, Columbus, OH; Heather A. Parsons, Gavin Ha, William T. Barry, Hao Guo, Atish D. Choudhury, Melissa E. Hughes, Deborah A. Dillon, Ann H. Partridge, Nikhil Wagle, Ian E. Krop, Todd R. Golub, Eric P. Winer, Sara M. Tolaney, and Nancy U. Lin, Dana-Farber Cancer Institute; Gad Getz, Massachusetts General Hospital, Boston; Gavin Ha, Samuel S. Freeman, Atish D. Choudhury, Gregory Gydush, Sarah C. Reed, Justin Rhoades, Denisse Rotem, Nikhil Wagle, Gad Getz, Todd R. Golub, and Viktor A. Adalsteinsson, Broad Institute of Harvard and Massachusetts Institute of Technology; and J. Christopher Love, Massachusetts Institute of Technology, Cambridge, MA
| | - Deborah A. Dillon
- Daniel G. Stover, Ohio State University Comprehensive Cancer Center, Columbus, OH; Heather A. Parsons, Gavin Ha, William T. Barry, Hao Guo, Atish D. Choudhury, Melissa E. Hughes, Deborah A. Dillon, Ann H. Partridge, Nikhil Wagle, Ian E. Krop, Todd R. Golub, Eric P. Winer, Sara M. Tolaney, and Nancy U. Lin, Dana-Farber Cancer Institute; Gad Getz, Massachusetts General Hospital, Boston; Gavin Ha, Samuel S. Freeman, Atish D. Choudhury, Gregory Gydush, Sarah C. Reed, Justin Rhoades, Denisse Rotem, Nikhil Wagle, Gad Getz, Todd R. Golub, and Viktor A. Adalsteinsson, Broad Institute of Harvard and Massachusetts Institute of Technology; and J. Christopher Love, Massachusetts Institute of Technology, Cambridge, MA
| | - Ann H. Partridge
- Daniel G. Stover, Ohio State University Comprehensive Cancer Center, Columbus, OH; Heather A. Parsons, Gavin Ha, William T. Barry, Hao Guo, Atish D. Choudhury, Melissa E. Hughes, Deborah A. Dillon, Ann H. Partridge, Nikhil Wagle, Ian E. Krop, Todd R. Golub, Eric P. Winer, Sara M. Tolaney, and Nancy U. Lin, Dana-Farber Cancer Institute; Gad Getz, Massachusetts General Hospital, Boston; Gavin Ha, Samuel S. Freeman, Atish D. Choudhury, Gregory Gydush, Sarah C. Reed, Justin Rhoades, Denisse Rotem, Nikhil Wagle, Gad Getz, Todd R. Golub, and Viktor A. Adalsteinsson, Broad Institute of Harvard and Massachusetts Institute of Technology; and J. Christopher Love, Massachusetts Institute of Technology, Cambridge, MA
| | - Nikhil Wagle
- Daniel G. Stover, Ohio State University Comprehensive Cancer Center, Columbus, OH; Heather A. Parsons, Gavin Ha, William T. Barry, Hao Guo, Atish D. Choudhury, Melissa E. Hughes, Deborah A. Dillon, Ann H. Partridge, Nikhil Wagle, Ian E. Krop, Todd R. Golub, Eric P. Winer, Sara M. Tolaney, and Nancy U. Lin, Dana-Farber Cancer Institute; Gad Getz, Massachusetts General Hospital, Boston; Gavin Ha, Samuel S. Freeman, Atish D. Choudhury, Gregory Gydush, Sarah C. Reed, Justin Rhoades, Denisse Rotem, Nikhil Wagle, Gad Getz, Todd R. Golub, and Viktor A. Adalsteinsson, Broad Institute of Harvard and Massachusetts Institute of Technology; and J. Christopher Love, Massachusetts Institute of Technology, Cambridge, MA
| | - Ian E. Krop
- Daniel G. Stover, Ohio State University Comprehensive Cancer Center, Columbus, OH; Heather A. Parsons, Gavin Ha, William T. Barry, Hao Guo, Atish D. Choudhury, Melissa E. Hughes, Deborah A. Dillon, Ann H. Partridge, Nikhil Wagle, Ian E. Krop, Todd R. Golub, Eric P. Winer, Sara M. Tolaney, and Nancy U. Lin, Dana-Farber Cancer Institute; Gad Getz, Massachusetts General Hospital, Boston; Gavin Ha, Samuel S. Freeman, Atish D. Choudhury, Gregory Gydush, Sarah C. Reed, Justin Rhoades, Denisse Rotem, Nikhil Wagle, Gad Getz, Todd R. Golub, and Viktor A. Adalsteinsson, Broad Institute of Harvard and Massachusetts Institute of Technology; and J. Christopher Love, Massachusetts Institute of Technology, Cambridge, MA
| | - Gad Getz
- Daniel G. Stover, Ohio State University Comprehensive Cancer Center, Columbus, OH; Heather A. Parsons, Gavin Ha, William T. Barry, Hao Guo, Atish D. Choudhury, Melissa E. Hughes, Deborah A. Dillon, Ann H. Partridge, Nikhil Wagle, Ian E. Krop, Todd R. Golub, Eric P. Winer, Sara M. Tolaney, and Nancy U. Lin, Dana-Farber Cancer Institute; Gad Getz, Massachusetts General Hospital, Boston; Gavin Ha, Samuel S. Freeman, Atish D. Choudhury, Gregory Gydush, Sarah C. Reed, Justin Rhoades, Denisse Rotem, Nikhil Wagle, Gad Getz, Todd R. Golub, and Viktor A. Adalsteinsson, Broad Institute of Harvard and Massachusetts Institute of Technology; and J. Christopher Love, Massachusetts Institute of Technology, Cambridge, MA
| | - Todd R. Golub
- Daniel G. Stover, Ohio State University Comprehensive Cancer Center, Columbus, OH; Heather A. Parsons, Gavin Ha, William T. Barry, Hao Guo, Atish D. Choudhury, Melissa E. Hughes, Deborah A. Dillon, Ann H. Partridge, Nikhil Wagle, Ian E. Krop, Todd R. Golub, Eric P. Winer, Sara M. Tolaney, and Nancy U. Lin, Dana-Farber Cancer Institute; Gad Getz, Massachusetts General Hospital, Boston; Gavin Ha, Samuel S. Freeman, Atish D. Choudhury, Gregory Gydush, Sarah C. Reed, Justin Rhoades, Denisse Rotem, Nikhil Wagle, Gad Getz, Todd R. Golub, and Viktor A. Adalsteinsson, Broad Institute of Harvard and Massachusetts Institute of Technology; and J. Christopher Love, Massachusetts Institute of Technology, Cambridge, MA
| | - J. Christopher Love
- Daniel G. Stover, Ohio State University Comprehensive Cancer Center, Columbus, OH; Heather A. Parsons, Gavin Ha, William T. Barry, Hao Guo, Atish D. Choudhury, Melissa E. Hughes, Deborah A. Dillon, Ann H. Partridge, Nikhil Wagle, Ian E. Krop, Todd R. Golub, Eric P. Winer, Sara M. Tolaney, and Nancy U. Lin, Dana-Farber Cancer Institute; Gad Getz, Massachusetts General Hospital, Boston; Gavin Ha, Samuel S. Freeman, Atish D. Choudhury, Gregory Gydush, Sarah C. Reed, Justin Rhoades, Denisse Rotem, Nikhil Wagle, Gad Getz, Todd R. Golub, and Viktor A. Adalsteinsson, Broad Institute of Harvard and Massachusetts Institute of Technology; and J. Christopher Love, Massachusetts Institute of Technology, Cambridge, MA
| | - Eric P. Winer
- Daniel G. Stover, Ohio State University Comprehensive Cancer Center, Columbus, OH; Heather A. Parsons, Gavin Ha, William T. Barry, Hao Guo, Atish D. Choudhury, Melissa E. Hughes, Deborah A. Dillon, Ann H. Partridge, Nikhil Wagle, Ian E. Krop, Todd R. Golub, Eric P. Winer, Sara M. Tolaney, and Nancy U. Lin, Dana-Farber Cancer Institute; Gad Getz, Massachusetts General Hospital, Boston; Gavin Ha, Samuel S. Freeman, Atish D. Choudhury, Gregory Gydush, Sarah C. Reed, Justin Rhoades, Denisse Rotem, Nikhil Wagle, Gad Getz, Todd R. Golub, and Viktor A. Adalsteinsson, Broad Institute of Harvard and Massachusetts Institute of Technology; and J. Christopher Love, Massachusetts Institute of Technology, Cambridge, MA
| | - Sara M. Tolaney
- Daniel G. Stover, Ohio State University Comprehensive Cancer Center, Columbus, OH; Heather A. Parsons, Gavin Ha, William T. Barry, Hao Guo, Atish D. Choudhury, Melissa E. Hughes, Deborah A. Dillon, Ann H. Partridge, Nikhil Wagle, Ian E. Krop, Todd R. Golub, Eric P. Winer, Sara M. Tolaney, and Nancy U. Lin, Dana-Farber Cancer Institute; Gad Getz, Massachusetts General Hospital, Boston; Gavin Ha, Samuel S. Freeman, Atish D. Choudhury, Gregory Gydush, Sarah C. Reed, Justin Rhoades, Denisse Rotem, Nikhil Wagle, Gad Getz, Todd R. Golub, and Viktor A. Adalsteinsson, Broad Institute of Harvard and Massachusetts Institute of Technology; and J. Christopher Love, Massachusetts Institute of Technology, Cambridge, MA
| | - Nancy U. Lin
- Daniel G. Stover, Ohio State University Comprehensive Cancer Center, Columbus, OH; Heather A. Parsons, Gavin Ha, William T. Barry, Hao Guo, Atish D. Choudhury, Melissa E. Hughes, Deborah A. Dillon, Ann H. Partridge, Nikhil Wagle, Ian E. Krop, Todd R. Golub, Eric P. Winer, Sara M. Tolaney, and Nancy U. Lin, Dana-Farber Cancer Institute; Gad Getz, Massachusetts General Hospital, Boston; Gavin Ha, Samuel S. Freeman, Atish D. Choudhury, Gregory Gydush, Sarah C. Reed, Justin Rhoades, Denisse Rotem, Nikhil Wagle, Gad Getz, Todd R. Golub, and Viktor A. Adalsteinsson, Broad Institute of Harvard and Massachusetts Institute of Technology; and J. Christopher Love, Massachusetts Institute of Technology, Cambridge, MA
| | - Viktor A. Adalsteinsson
- Daniel G. Stover, Ohio State University Comprehensive Cancer Center, Columbus, OH; Heather A. Parsons, Gavin Ha, William T. Barry, Hao Guo, Atish D. Choudhury, Melissa E. Hughes, Deborah A. Dillon, Ann H. Partridge, Nikhil Wagle, Ian E. Krop, Todd R. Golub, Eric P. Winer, Sara M. Tolaney, and Nancy U. Lin, Dana-Farber Cancer Institute; Gad Getz, Massachusetts General Hospital, Boston; Gavin Ha, Samuel S. Freeman, Atish D. Choudhury, Gregory Gydush, Sarah C. Reed, Justin Rhoades, Denisse Rotem, Nikhil Wagle, Gad Getz, Todd R. Golub, and Viktor A. Adalsteinsson, Broad Institute of Harvard and Massachusetts Institute of Technology; and J. Christopher Love, Massachusetts Institute of Technology, Cambridge, MA
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Stover DG, Parsons HA, Ha G, Freeman S, Barry B, Guo H, Choudhury A, Gydush G, Reed S, Rhoades J, Rotem D, Hughes ME, Dillon DA, Partridge AH, Wagle N, Krop IE, Getz G, Golub TA, Love JC, Winer EP, Tolaney SM, Lin NU, Adalsteinsson VA. Abstract GS3-07: Genome-wide copy number analysis of chemotherapy-resistant metastatic triple-negative breast cancer from cell-free DNA. Cancer Res 2018. [DOI: 10.1158/1538-7445.sabcs17-gs3-07] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Introduction:
Triple-negative breast cancer (TNBC) is a poor prognosis breast cancer subset characterized by relatively few mutations but extensive copy number alterations (CNAs). Cell-free DNA (cfDNA) offers the potential to overcome infrequent tumor biopsies in metastatic TNBC (mTNBC) and interrogate the genomics of chemotherapy resistance.
Methods:
506 archival or fresh plasma samples were identified from 164 patients with mTNBC who had previously received chemotherapy. We performed low coverage whole genome sequencing to determine genome-wide copy number and estimate 'tumor fraction' of cfDNA (TFx) using our recently-developed approach, ichorCNA. In patient samples with TFx >10%, we identified regions that were significantly gained or lost using GISTIC2.0. We compared CNAs of 20 paired primary-metastatic samples and also mTNBCs from cfDNA versus primary TNBCs from TCGA and METABRIC.
Results:
We successfully obtained high quality, low coverage whole genome sequencing data for 478 (94.5%) plasma samples from 158 patients, with 1 to 14 samples per patient. TFx and copy number profiles were highly concordant with paired metastatic biopsy (n=10, range 0-7 days from biopsy to blood draw) with sensitivity of 0.86 and specificity of 0.90 and reproducible in independently-processed blood draws (TFx intraclass correlation coefficient 0.984). Median overall survival from time of first blood draw was 8 months, and TFx was highly correlated independent of primary stage, primary receptor status, age at primary diagnosis, BRCA status, and metastatic line of therapy: adjusted hazard ratio between 4th and 1st quartiles = 2.14 (95% CI 1.40-3.28; p=0.00049). 101/158 patients (63.9%) had at least one sample with TFx >10%, our threshold for high confidence CNA calls. Copy number profiles and percent genome altered were remarkably similar between mTNBCs and primary TNBCs in TCGA and METABRIC (n=433), suggesting that large-scale chromosomal events are infrequent in TNBC metastatic progression. We identified chromosomal gains that demonstrated significant enrichment in mTNBCs relative to paired primary TNBCs (n=20) and also TCGA/METABRIC, including driver genes (NOTCH2, AKT2, AKT3) and putative antibody-drug conjugate targets. Finally, we identify a novel association of gains of 18q11 and/or 19p13 with poor metastatic prognosis, independent of clinicopathologic factors and TFx.
Conclusions:
Here, we present the first large-scale genomic characterization of metastatic TNBC to our knowledge, derived exclusively from cfDNA. 'Tumor fraction' of cfDNA is an independent prognostic marker in mTNBC. Primary and metastatic TNBC have remarkably similar copy number profiles yet we identify alterations enriched and prognostic in mTNBC. Collectively, these data have potential implications in the understanding of metastasis, therapeutic resistance, and novel therapeutic targets.
Citation Format: Stover DG, Parsons HA, Ha G, Freeman S, Barry B, Guo H, Choudhury A, Gydush G, Reed S, Rhoades J, Rotem D, Hughes ME, Dillon DA, Partridge AH, Wagle N, Krop IE, Getz G, Golub TA, Love JC, Winer EP, Tolaney SM, Lin NU, Adalsteinsson VA. Genome-wide copy number analysis of chemotherapy-resistant metastatic triple-negative breast cancer from cell-free DNA [abstract]. In: Proceedings of the 2017 San Antonio Breast Cancer Symposium; 2017 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2018;78(4 Suppl):Abstract nr GS3-07.
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Affiliation(s)
- DG Stover
- The Ohio State University Comprehensive Cancer Center, Columbus, OH; Dana-Farber Cancer Institute, Boston, MA; Broad Institute of Harvard and MIT, Cambridge, MA; Massachusetts Institute of Technology, Cambridge, MA
| | - HA Parsons
- The Ohio State University Comprehensive Cancer Center, Columbus, OH; Dana-Farber Cancer Institute, Boston, MA; Broad Institute of Harvard and MIT, Cambridge, MA; Massachusetts Institute of Technology, Cambridge, MA
| | - G Ha
- The Ohio State University Comprehensive Cancer Center, Columbus, OH; Dana-Farber Cancer Institute, Boston, MA; Broad Institute of Harvard and MIT, Cambridge, MA; Massachusetts Institute of Technology, Cambridge, MA
| | - S Freeman
- The Ohio State University Comprehensive Cancer Center, Columbus, OH; Dana-Farber Cancer Institute, Boston, MA; Broad Institute of Harvard and MIT, Cambridge, MA; Massachusetts Institute of Technology, Cambridge, MA
| | - B Barry
- The Ohio State University Comprehensive Cancer Center, Columbus, OH; Dana-Farber Cancer Institute, Boston, MA; Broad Institute of Harvard and MIT, Cambridge, MA; Massachusetts Institute of Technology, Cambridge, MA
| | - H Guo
- The Ohio State University Comprehensive Cancer Center, Columbus, OH; Dana-Farber Cancer Institute, Boston, MA; Broad Institute of Harvard and MIT, Cambridge, MA; Massachusetts Institute of Technology, Cambridge, MA
| | - A Choudhury
- The Ohio State University Comprehensive Cancer Center, Columbus, OH; Dana-Farber Cancer Institute, Boston, MA; Broad Institute of Harvard and MIT, Cambridge, MA; Massachusetts Institute of Technology, Cambridge, MA
| | - G Gydush
- The Ohio State University Comprehensive Cancer Center, Columbus, OH; Dana-Farber Cancer Institute, Boston, MA; Broad Institute of Harvard and MIT, Cambridge, MA; Massachusetts Institute of Technology, Cambridge, MA
| | - S Reed
- The Ohio State University Comprehensive Cancer Center, Columbus, OH; Dana-Farber Cancer Institute, Boston, MA; Broad Institute of Harvard and MIT, Cambridge, MA; Massachusetts Institute of Technology, Cambridge, MA
| | - J Rhoades
- The Ohio State University Comprehensive Cancer Center, Columbus, OH; Dana-Farber Cancer Institute, Boston, MA; Broad Institute of Harvard and MIT, Cambridge, MA; Massachusetts Institute of Technology, Cambridge, MA
| | - D Rotem
- The Ohio State University Comprehensive Cancer Center, Columbus, OH; Dana-Farber Cancer Institute, Boston, MA; Broad Institute of Harvard and MIT, Cambridge, MA; Massachusetts Institute of Technology, Cambridge, MA
| | - ME Hughes
- The Ohio State University Comprehensive Cancer Center, Columbus, OH; Dana-Farber Cancer Institute, Boston, MA; Broad Institute of Harvard and MIT, Cambridge, MA; Massachusetts Institute of Technology, Cambridge, MA
| | - DA Dillon
- The Ohio State University Comprehensive Cancer Center, Columbus, OH; Dana-Farber Cancer Institute, Boston, MA; Broad Institute of Harvard and MIT, Cambridge, MA; Massachusetts Institute of Technology, Cambridge, MA
| | - AH Partridge
- The Ohio State University Comprehensive Cancer Center, Columbus, OH; Dana-Farber Cancer Institute, Boston, MA; Broad Institute of Harvard and MIT, Cambridge, MA; Massachusetts Institute of Technology, Cambridge, MA
| | - N Wagle
- The Ohio State University Comprehensive Cancer Center, Columbus, OH; Dana-Farber Cancer Institute, Boston, MA; Broad Institute of Harvard and MIT, Cambridge, MA; Massachusetts Institute of Technology, Cambridge, MA
| | - IE Krop
- The Ohio State University Comprehensive Cancer Center, Columbus, OH; Dana-Farber Cancer Institute, Boston, MA; Broad Institute of Harvard and MIT, Cambridge, MA; Massachusetts Institute of Technology, Cambridge, MA
| | - G Getz
- The Ohio State University Comprehensive Cancer Center, Columbus, OH; Dana-Farber Cancer Institute, Boston, MA; Broad Institute of Harvard and MIT, Cambridge, MA; Massachusetts Institute of Technology, Cambridge, MA
| | - TA Golub
- The Ohio State University Comprehensive Cancer Center, Columbus, OH; Dana-Farber Cancer Institute, Boston, MA; Broad Institute of Harvard and MIT, Cambridge, MA; Massachusetts Institute of Technology, Cambridge, MA
| | - JC Love
- The Ohio State University Comprehensive Cancer Center, Columbus, OH; Dana-Farber Cancer Institute, Boston, MA; Broad Institute of Harvard and MIT, Cambridge, MA; Massachusetts Institute of Technology, Cambridge, MA
| | - EP Winer
- The Ohio State University Comprehensive Cancer Center, Columbus, OH; Dana-Farber Cancer Institute, Boston, MA; Broad Institute of Harvard and MIT, Cambridge, MA; Massachusetts Institute of Technology, Cambridge, MA
| | - SM Tolaney
- The Ohio State University Comprehensive Cancer Center, Columbus, OH; Dana-Farber Cancer Institute, Boston, MA; Broad Institute of Harvard and MIT, Cambridge, MA; Massachusetts Institute of Technology, Cambridge, MA
| | - NU Lin
- The Ohio State University Comprehensive Cancer Center, Columbus, OH; Dana-Farber Cancer Institute, Boston, MA; Broad Institute of Harvard and MIT, Cambridge, MA; Massachusetts Institute of Technology, Cambridge, MA
| | - VA Adalsteinsson
- The Ohio State University Comprehensive Cancer Center, Columbus, OH; Dana-Farber Cancer Institute, Boston, MA; Broad Institute of Harvard and MIT, Cambridge, MA; Massachusetts Institute of Technology, Cambridge, MA
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Adalsteinsson VA, Ha G, Freeman S, Choudhury AD, Stover DG, Parsons HA, Gydush G, Reed S, Loginov D, Livitz D, Rosebrock D, Leshchiner I, Cohen O, Oh C, Kim J, Stewart C, Rosenberg M, Ding H, Lloyd MR, Mahmud S, Helvie KE, Merrill MS, Santiago RA, O’Connor EP, Jeong SH, Kramkowski JF, Lohr JG, Polacek L, Oliver N, Marini L, Francis J, Harshman LC, Van Allen EM, Winer EP, Lin NU, Nakabayashi M, Taplin ME, Garraway LA, Golub TR, Boehm JS, Wagle N, Getz G, Meyerson M, Love CJ. Abstract LB-136: High concordance of whole-exome sequencing of cell-free DNA and matched biopsies enables genomic discovery in metastatic cancer. Cancer Res 2016. [DOI: 10.1158/1538-7445.am2016-lb-136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background: Circulating cell-free DNA (cfDNA) has largely been used to monitor blood for specific tumor mutations, but genome-wide discovery from cfDNA has not been well established. Here, we establish a scalable approach for whole-exome sequencing (WES) of cfDNA, making it possible to perform comprehensive genomic characterization of metastatic cancer in a routine and minimally-invasive manner.
Comprehensive genomic characterization of metastatic cancer stands to uncover novel alterations of clinical significance. A major challenge is that metastatic tumors are infrequently biopsied. Cell-free DNA is shed abundantly into the bloodstream from metastatic tumors, presenting an opportunity for genomic discovery in advanced cancers that are rarely biopsied in routine clinical care. We report an efficient process to qualify and sequence whole-exomes from cfDNA at scale and systematically compare the somatic mutations, indels, and copy number alterations detected in WES of cfDNA to WES of matched tumor biopsies.
Methods: We consented 86 patients with metastatic breast or prostate cancers for blood collection. We isolated cfDNA and germline DNA from blood and performed low coverage sequencing to estimate tumor content based on genome-wide copy number. We screened patient blood samples and prioritized those with higher tumor fractions for WES. In parallel, we analyzed cfDNA and germline DNA from healthy donors to calibrate our methods and assess false positive rate for genomic alterations.
Results: We found the vast majority of patients with metastatic prostate or breast cancer to have detectable tumor-derived cfDNA. WES of cfDNA from healthy donors revealed very low false positive rates for somatic mutations, indels and copy number alterations (SCNAs). By analyzing WES of cfDNA and tumor biopsies from dozens of patients with metastatic breast or prostate cancers, we established guidelines for the coverage and tumor fraction required for mutation discovery in WES of cfDNA. We found WES of cfDNA to uncover 91% of the clonal mutations, 59% of the subclonal mutations, and 75% of the SCNAs detected in WES of matched tumor biopsies. In several cases, we observed mutations exclusive to cfDNA that were confirmed in later blood draws, suggesting that cfDNA-exclusive mutations may be derived from unsampled metastases. In some cases, cfDNA revealed clinically actionable mutations that were not detected in matched tumor biopsies.
Conclusions: WES of cfDNA uncovers the majority of somatic mutations, indels, and SCNAs found in matched tumor biopsies of metastatic cancer. The high degree of concordance suggests that comprehensive sequencing of cfDNA can be leveraged for genomic discovery in settings where conventional biopsies are difficult to access. Furthermore, the detection of mutations in cfDNA that are not detected in concurrent biopsies suggests that cfDNA may be complementary to tumor biopsies for both translational studies and precision cancer medicine.
Citation Format: Viktor A. Adalsteinsson, Gavin Ha, Sam Freeman, Atish D. Choudhury, Daniel G. Stover, Heather A. Parsons, Gregory Gydush, Sarah Reed, Denis Loginov, Dimitri Livitz, Daniel Rosebrock, Ignat Leshchiner, Ofir Cohen, Coyin Oh, Jaegil Kim, Chip Stewart, Mara Rosenberg, Huiming Ding, Maxwell R. Lloyd, Sairah Mahmud, Karla E. Helvie, Margaret S. Merrill, Rebecca A. Santiago, Edward P. O’Connor, Seong H. Jeong, Joseph F. Kramkowski, Jens G. Lohr, Laura Polacek, Nelly Oliver, Lori Marini, Joshua Francis, Lauren C. Harshman, Eliezer M. Van Allen, Eric P. Winer, Nancy U. Lin, Mari Nakabayashi, Mary-Ellen Taplin, Levi A. Garraway, Todd R. Golub, Jesse S. Boehm, Nikhil Wagle, Gad Getz, Matthew Meyerson, Christopher J. Love. High concordance of whole-exome sequencing of cell-free DNA and matched biopsies enables genomic discovery in metastatic cancer. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr LB-136.
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Affiliation(s)
| | - Gavin Ha
- 2Dana-Farber Cancer Institute, Boston, MA
| | | | | | | | | | | | - Sarah Reed
- 1Broad Institute of MIT and Harvard, Cambridge, MA
| | | | | | | | | | - Ofir Cohen
- 1Broad Institute of MIT and Harvard, Cambridge, MA
| | - Coyin Oh
- 1Broad Institute of MIT and Harvard, Cambridge, MA
| | - Jaegil Kim
- 1Broad Institute of MIT and Harvard, Cambridge, MA
| | - Chip Stewart
- 1Broad Institute of MIT and Harvard, Cambridge, MA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Gad Getz
- 1Broad Institute of MIT and Harvard, Cambridge, MA
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Gaddes ER, Lee D, Gydush G, Wang Y, Dong C. Regulation of fibrin-mediated tumor cell adhesion to the endothelium using anti-thrombin aptamer. Exp Cell Res 2015; 339:417-26. [PMID: 26481421 DOI: 10.1016/j.yexcr.2015.10.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2015] [Revised: 09/29/2015] [Accepted: 10/09/2015] [Indexed: 12/27/2022]
Abstract
Molecular intervention during transient stages of various metastatic pathways may lead to development of promising therapeutic technologies. One of such involves soluble fibrin (sFn) that has been implicated as a cross-linker between circulating blood or tumor cells and endothelial cell receptors, promoting cell arrest on the endothelium during circulation. sFn generation is a result of thrombin-mediated fibrinogen (Fg) cleavage due to either vascular injuries or a tumor microenvironment. For cancer therapy, thrombin-mediated conversions of Fg to sFn thus serve as potential intervention points to decrease circulating tumor cell adhesion to the endothelium and subsequent metastatic events. The purpose of this work was to investigate the function of an anti-thrombin oligonucleotide aptamer in reducing tumor cell arrest. Both molecular and cellular interactions were examined to demonstrate the binding and inhibitory effects of anti-thrombin aptamer. The results show that the aptamer is capable of inhibiting thrombin-mediated Fg conversion, thereby reducing sFn-mediated tumor cell adhesion in a concentration-dependent manner. Notably, the aptamer is able to bind thrombin under dynamic flow conditions and reduce tumor cell adhesive events at various physiological shear rates. This study further indicates that oligonucleotide aptamers hold great promise as therapeutic regulators of tumor cell adhesion, and consequently, metastatic activity.
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Affiliation(s)
- Erin R Gaddes
- Department of Biomedical Engineering, The Pennsylvania State University, University Park, PA 16802, USA
| | - Deborah Lee
- Department of Biomedical Engineering, The Pennsylvania State University, University Park, PA 16802, USA
| | - Gregory Gydush
- Department of Biomedical Engineering, The Pennsylvania State University, University Park, PA 16802, USA
| | - Yong Wang
- Department of Biomedical Engineering, The Pennsylvania State University, University Park, PA 16802, USA
| | - Cheng Dong
- Department of Biomedical Engineering, The Pennsylvania State University, University Park, PA 16802, USA.
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Gaddes ER, Gydush G, Li S, Chen N, Dong C, Wang Y. Aptamer-based polyvalent ligands for regulated cell attachment on the hydrogel surface. Biomacromolecules 2015; 16:1382-9. [PMID: 25789558 DOI: 10.1021/acs.biomac.5b00165] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Natural biomolecules are often used to functionalize materials to achieve desired cell-material interactions. However, their applications can be limited owing to denaturation during the material functionalization process. Therefore, efforts have been made to develop synthetic ligands with polyvalence as alternatives to natural affinity biomolecules for the synthesis of functional materials and the control of cell-material interactions. This work was aimed at investigating the capability of a hydrogel functionalized with a novel polyvalent aptamer in inducing cell attachment in dynamic flow and releasing the attached cells in physiological conditions through a hybridization reaction. The results show that the polyvalent aptamer could induce cell attachment on the hydrogel in dynamic flow. Moreover, cell attachment on the hydrogel surface was significantly influenced by the value of shear stress. The cell density on the hydrogel was increased from 40 cells/mm(2) to nearly 700 cells/mm(2) when the shear stress was decreased from 0.05 to 0.005 Pa. After the attachment onto the hydrogel surface, approximately 95% of the cells could be triggered to detach within 20 min by using an oligonucleotide complementary sequence that displaced polyvalent aptamer strands from the hydrogel surface. While it was found that the cell activity was reduced, the live/dead staining results show that ≥98% of the detached cells were viable. Therefore, this work has suggested that the polyvalent aptamer is a promising synthetic ligand for the functionalization of materials for regulated cell attachment.
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Affiliation(s)
- Erin R Gaddes
- Department of Biomedical Engineering, Pennsylvania State University, University Park, Pennsylvania 16802-6804, United States
| | - Gregory Gydush
- Department of Biomedical Engineering, Pennsylvania State University, University Park, Pennsylvania 16802-6804, United States
| | - Shihui Li
- Department of Biomedical Engineering, Pennsylvania State University, University Park, Pennsylvania 16802-6804, United States
| | - Niancao Chen
- Department of Biomedical Engineering, Pennsylvania State University, University Park, Pennsylvania 16802-6804, United States
| | - Cheng Dong
- Department of Biomedical Engineering, Pennsylvania State University, University Park, Pennsylvania 16802-6804, United States
| | - Yong Wang
- Department of Biomedical Engineering, Pennsylvania State University, University Park, Pennsylvania 16802-6804, United States
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