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Detappe A, Kunjachan S, Sancey L, Motto-Ros V, Biancur D, Drane P, Guieze R, Makrigiorgos GM, Tillement O, Langer R, Berbeco R. Corrigendum to "Corrigendum to 'Advanced multimodal nanoparticles delay tumor progression with clinical radiation therapy' [Journal of Controlled Release 238 (2016) 103-133]" [Journal of Controlled Release (year) Volume 329 (2021) Pages 1283-1285]. J Control Release 2024:S0168-3659(22)00860-4. [PMID: 38653589 DOI: 10.1016/j.jconrel.2022.12.046] [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: 04/25/2024]
Affiliation(s)
- Alexandre Detappe
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02215, USA; Lyon-1 University, Institut Lumière Matière, CNRS UMR5306, Lyon, France
| | - Sijumon Kunjachan
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02215, USA.
| | - Lucie Sancey
- Lyon-1 University, Institut Lumière Matière, CNRS UMR5306, Lyon, France
| | - Vincent Motto-Ros
- Lyon-1 University, Institut Lumière Matière, CNRS UMR5306, Lyon, France
| | - Douglas Biancur
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02215, USA
| | - Pascal Drane
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02215, USA
| | - Romain Guieze
- Division of Medical Oncology, Dana-Farber Cancer Institute, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02215, USA
| | - G Mike Makrigiorgos
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02215, USA
| | - Olivier Tillement
- Lyon-1 University, Institut Lumière Matière, CNRS UMR5306, Lyon, France
| | - Robert Langer
- Department of Chemical Engineering, David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Ross Berbeco
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02215, USA
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Parsons HA, Blewett T, Chu X, Sridhar S, Santos K, Xiong K, Abramson VG, Patel A, Cheng J, Brufsky A, Rhoades J, Force J, Liu R, Traina TA, Carey LA, Rimawi MF, Miller KD, Stearns V, Specht J, Falkson C, Burstein HJ, Wolff AC, Winer EP, Tayob N, Krop IE, Makrigiorgos GM, Golub TR, Mayer EL, Adalsteinsson VA. Circulating tumor DNA association with residual cancer burden after neoadjuvant chemotherapy in triple-negative breast cancer in TBCRC 030. Ann Oncol 2023; 34:899-906. [PMID: 37597579 PMCID: PMC10898256 DOI: 10.1016/j.annonc.2023.08.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 07/20/2023] [Accepted: 08/09/2023] [Indexed: 08/21/2023] Open
Abstract
BACKGROUND We aimed to examine circulating tumor DNA (ctDNA) and its association with residual cancer burden (RCB) using an ultrasensitive assay in patients with triple-negative breast cancer (TNBC) receiving neoadjuvant chemotherapy. PATIENTS AND METHODS We identified responders (RCB 0/1) and matched non-responders (RCB 2/3) from the phase II TBCRC 030 prospective study of neoadjuvant paclitaxel versus cisplatin in TNBC. We collected plasma samples at baseline, 3 weeks and 12 weeks (end of therapy). We created personalized ctDNA assays utilizing MAESTRO mutation enrichment sequencing. We explored associations between ctDNA and RCB status and disease recurrence. RESULTS Of 139 patients, 68 had complete samples and no additional neoadjuvant chemotherapy. Twenty-two were responders and 19 of those had sufficient tissue for whole-genome sequencing. We identified an additional 19 non-responders for a matched case-control analysis of 38 patients using a MAESTRO ctDNA assay tracking 319-1000 variants (median 1000 variants) to 114 plasma samples from 3 timepoints. Overall, ctDNA positivity was 100% at baseline, 79% at week 3 and 55% at week 12. Median tumor fraction (TFx) was 3.7 × 10-4 (range 7.9 × 10-7-4.9 × 10-1). TFx decreased 285-fold from baseline to week 3 in responders and 24-fold in non-responders. Week 12 ctDNA clearance correlated with RCB: clearance was observed in 10 of 11 patients with RCB 0, 3 of 8 with RCB 1, 4 of 15 with RCB 2 and 0 of 4 with RCB 3. Among six patients with known recurrence, five had persistent ctDNA at week 12. CONCLUSIONS Neoadjuvant chemotherapy for TNBC reduced ctDNA TFx by 285-fold in responders and 24-fold in non-responders. In 58% (22/38) of patients, ctDNA TFx dropped below the detection level of a commercially available test, emphasizing the need for sensitive tests. Additional studies will determine whether ctDNA-guided approaches can improve outcomes.
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Affiliation(s)
- H A Parsons
- Medical Oncology, Dana-Farber Cancer Institute, Boston; Breast Oncology Program, Dana-Farber Brigham Cancer Center, Boston; Harvard Medical School, Boston.
| | - T Blewett
- Broad Institute of MIT and Harvard, Cambridge
| | - X Chu
- Data Science, Dana-Farber Cancer Institute, Boston
| | - S Sridhar
- Broad Institute of MIT and Harvard, Cambridge
| | - K Santos
- Medical Oncology, Dana-Farber Cancer Institute, Boston
| | - K Xiong
- Broad Institute of MIT and Harvard, Cambridge
| | | | - A Patel
- Medical Oncology, Dana-Farber Cancer Institute, Boston
| | - J Cheng
- Broad Institute of MIT and Harvard, Cambridge
| | - A Brufsky
- University of Pittsburgh School of Medicine, Pittsburgh
| | - J Rhoades
- Broad Institute of MIT and Harvard, Cambridge
| | | | - R Liu
- Broad Institute of MIT and Harvard, Cambridge
| | - T A Traina
- Memorial Sloan Kettering Cancer Center, New York
| | - L A Carey
- The University of North Carolina Lineberger Comprehensive Cancer Center, Chapel Hill
| | - M F Rimawi
- Baylor College of Medicine Dan L. Duncan Comprehensive Cancer Center, Houston
| | - K D Miller
- Indiana University Melvin and Bren Simon Comprehensive Cancer Center, Indianapolis
| | - V Stearns
- Johns Hopkins Sidney Kimmel Comprehensive Cancer Center, Baltimore
| | - J Specht
- Seattle Cancer Care Alliance, Seattle
| | - C Falkson
- The University of Alabama at Birmingham, Birmingham
| | - H J Burstein
- Medical Oncology, Dana-Farber Cancer Institute, Boston; Breast Oncology Program, Dana-Farber Brigham Cancer Center, Boston; Harvard Medical School, Boston
| | - A C Wolff
- Johns Hopkins Sidney Kimmel Comprehensive Cancer Center, Baltimore
| | - E P Winer
- Medical Oncology, Dana-Farber Cancer Institute, Boston; Breast Oncology Program, Dana-Farber Brigham Cancer Center, Boston; Harvard Medical School, Boston
| | - N Tayob
- Data Science, Dana-Farber Cancer Institute, Boston
| | - I E Krop
- Medical Oncology, Dana-Farber Cancer Institute, Boston; Breast Oncology Program, Dana-Farber Brigham Cancer Center, Boston; Harvard Medical School, Boston
| | | | - T R Golub
- Broad Institute of MIT and Harvard, Cambridge
| | - E L Mayer
- Medical Oncology, Dana-Farber Cancer Institute, Boston; Breast Oncology Program, Dana-Farber Brigham Cancer Center, Boston; Harvard Medical School, Boston.
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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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Parsons HA, Blewett T, Chu X, Sridhar S, Santos K, Xiong K, Abramson VG, Patel A, Cheng J, Brufsky A, Rhoades J, Force J, Liu R, Traina TA, Carey LA, Rimawi MF, Miller KD, Stearns V, Specht J, Falkson C, Burstein HJ, Wolff AC, Winer EP, Tayob N, Krop IE, Makrigiorgos GM, Golub TR, Mayer EL, Adalsteinsson VA. Circulating tumor DNA association with residual cancer burden after neoadjuvant chemotherapy in triple-negative breast cancer in TBCRC 030. medRxiv 2023:2023.03.06.23286772. [PMID: 36945501 PMCID: PMC10029037 DOI: 10.1101/2023.03.06.23286772] [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: 03/11/2023]
Abstract
Purpose To examine circulating tumor DNA (ctDNA) and its association with residual cancer burden (RCB) using an ultrasensitive assay in patients with triple-negative breast cancer (TNBC) receiving neoadjuvant chemotherapy (NAT). Patients and Methods We identified responders (RCB-0/1) and matched non-responders (RCB-2/3) from the phase II TBCRC 030 prospective study of neoadjuvant paclitaxel vs. cisplatin in TNBC. We collected plasma samples at baseline, three weeks, and twelve weeks (end of therapy). We created personalized ctDNA assays utilizing MAESTRO mutation enrichment sequencing. We explored associations between ctDNA and RCB status and disease recurrence. Results Of 139 patients, 68 had complete samples and no additional NAT. Twenty-two were responders and 19 of those had sufficient tissue for whole-genome sequencing. We identified an additional 19 non-responders for a matched case-control analysis of 38 patients using a MAESTRO ctDNA assay tracking 319-1000 variants (median 1000) to 114 plasma samples from 3 timepoints. Overall, ctDNA positivity was 100% at baseline, 79% at week 3, and 55% at week 12. Median tumor fraction (TFx) was 3.7 × 10 -4 (range: 7.9 × 10 -7 to 4.9 × 10 -1 ). TFx decreased 285-fold from baseline to week 3 in responders and 24-fold in non-responders. Week 12 ctDNA clearance correlated with RCB: clearance was observed in 10/11 patients with RCB-0, 3/8 with RCB-1, 4/15 with RCB-2, and 0/4 with RCB-3. Among 6 patients with known recurrence five had persistent ctDNA at week 12. Conclusion NAT for TNBC reduced ctDNA TFx by 285-fold in responders and 24-fold in non-responders. In 58% (22/38) of patients, ctDNA TFx dropped below the detection level of a commercially available test, emphasizing the need for sensitive tests. Additional studies will determine if ctDNA-guided approaches can improve outcomes.
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Affiliation(s)
- Heather A. Parsons
- Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Breast Oncology Program, Dana-Farber Brigham Cancer Center, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | | | - Xiangying Chu
- Data Science, Dana-Farber Cancer Institute, Boston, MA, USA
| | | | - Katheryn Santos
- Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Kan Xiong
- Broad Institute of MIT and Harvard, Boston, MA, USA
| | | | - Ashka Patel
- Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Ju Cheng
- Broad Institute of MIT and Harvard, Boston, MA, USA
| | - Adam Brufsky
- University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | | | | | - Ruolin Liu
- Broad Institute of MIT and Harvard, Boston, MA, USA
| | | | - Lisa A. Carey
- The University of North Carolina Lineberger Comprehensive Cancer Center, Chapel Hill, NC, USA
| | - Mothaffar F. Rimawi
- Baylor College of Medicine Dan L. Duncan Comprehensive Cancer Center, Houston, TX, USA
| | - Kathy D. Miller
- Indiana University Melvin and Bren Simon Comprehensive Cancer Center, Indianapolis, IN, USA; Birmingham, AB, USA
| | - Vered Stearns
- Johns Hopkins Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD, USA
| | | | - Carla Falkson
- The University of Alabama at Birmingham, Birmingham, AL, USA
| | - Harold J. Burstein
- Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Breast Oncology Program, Dana-Farber Brigham Cancer Center, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Antonio C. Wolff
- Johns Hopkins Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD, USA
| | - Eric P. Winer
- Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Breast Oncology Program, Dana-Farber Brigham Cancer Center, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Nabihah Tayob
- Data Science, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Ian E. Krop
- Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Breast Oncology Program, Dana-Farber Brigham Cancer Center, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | | | | | - Erica L. Mayer
- Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Breast Oncology Program, Dana-Farber Brigham Cancer Center, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
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Kunjachan S, Detappe A, Kumar R, Ireland T, Cameron L, Biancur DE, Motto-Ros V, Sancey L, Sridhar S, Makrigiorgos GM, Berbeco RI. Retraction of: "Nanoparticle Mediated Tumor Vascular Disruption: A Novel Strategy in Radiation Therapy". Nano Lett 2022; 22:9216. [PMID: 36322509 PMCID: PMC9691526 DOI: 10.1021/acs.nanolett.2c03941] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
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Lyatskaya Y, Winey B, Kiger WS, Hurwitz M, Zygmanski P, Makrigiorgos GM, Bortfeld TR, Doppke KP, Lu X, Chin LM, Biggs P, Gierga DP. Combined clinical and research training in medical physics in a multi-institutional setting: 13-year experience of Harvard Medical Physics Residency Program. J Appl Clin Med Phys 2022; 24:e13806. [PMID: 36347055 PMCID: PMC9859991 DOI: 10.1002/acm2.13806] [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] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 09/11/2022] [Accepted: 09/15/2022] [Indexed: 11/09/2022] Open
Abstract
PURPOSE This manuscript describes the structure, management and outcomes of a multi-institutional clinical and research medical physics residency program (Harvard Medical Physics Residency Program, or HMPRP) to provide potentially useful information to the centers considering a multi-institutional approach for their training programs. METHODS Data from the program documents and public records was used to describe HMPRP and obtain statistics about participating faculty, enrolled residents, and graduates. Challenges associated with forming and managing a multi-institutional program and developed solutions for effective coordination between several clinical centers are described. RESULTS HMPRP was formed in 2009 and was accredited by the Commission on Accreditation of Medical Physics Education Programs (CAMPEP) in 2011. It is a 3-year therapy program, with a dedicated year of research and the 2 years of clinical training at three academic hospitals. A CAMPEP-accredited Certificate Program is embedded in HMPRP to allow enrolled residents to complete a formal didactic training in medical physics if necessary. The clinical training covers the material required by CAMPEP. In addition, training in protons, CyberKnife, MR-linac, and at network locations is included. The clinical training and academic record of the residents is outstanding. All graduates have found employment within clinical medical physics, mostly at large academic centers and graduates had a 100% pass rate at the oral American Board of Radiology exams. On average, three manuscripts per resident are published during residency, and multiple abstracts are presented at conferences. CONCLUSIONS A multi-institutional medical physics residency program can be successfully formed and managed. With a collaborative administrative structure, the program creates an environment for high-quality clinical training of the residents and high productivity in research. The main advantage of such program is access to a wide variety of resources. The main challenge is creating a structure for efficient management of multiple resources at different locations. This report may provide valuable information to centers considering starting a multi-institutional residency program.
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Affiliation(s)
- Yulia Lyatskaya
- Department of Radiation OncologyBrigham and Women's HospitalBostonMassachusettsUSA,Harvard Medical SchoolBostonMassachusettsUSA
| | - Brian Winey
- Department of Radiation OncologyMassachusetts General HospitalBostonMassachusettsUSA,Harvard Medical SchoolBostonMassachusettsUSA
| | - W. S. Kiger
- Department of Radiation OncologyBeth Israel Deaconess Medical CenterBostonMassachusettsUSA,Harvard Medical SchoolBostonMassachusettsUSA
| | - Martina Hurwitz
- Department of Radiation OncologyBeth Israel Deaconess Medical CenterBostonMassachusettsUSA,Harvard Medical SchoolBostonMassachusettsUSA
| | - Piotr Zygmanski
- Department of Radiation OncologyBrigham and Women's HospitalBostonMassachusettsUSA,Harvard Medical SchoolBostonMassachusettsUSA
| | - G. Mike Makrigiorgos
- Department of Radiation OncologyBrigham and Women's HospitalBostonMassachusettsUSA,Harvard Medical SchoolBostonMassachusettsUSA
| | - Thomas R. Bortfeld
- Department of Radiation OncologyMassachusetts General HospitalBostonMassachusettsUSA,Harvard Medical SchoolBostonMassachusettsUSA
| | - Karen P. Doppke
- Department of Radiation OncologyMassachusetts General HospitalBostonMassachusettsUSA,Harvard Medical SchoolBostonMassachusettsUSA
| | - Xing‐Qi Lu
- Department of Radiation OncologyBeth Israel Deaconess Medical CenterBostonMassachusettsUSA,Harvard Medical SchoolBostonMassachusettsUSA
| | - Lee M. Chin
- Department of Radiation OncologyBrigham and Women's HospitalBostonMassachusettsUSA,Harvard Medical SchoolBostonMassachusettsUSA
| | - Peter Biggs
- Department of Radiation OncologyMassachusetts General HospitalBostonMassachusettsUSA,Harvard Medical SchoolBostonMassachusettsUSA
| | - David P. Gierga
- Department of Radiation OncologyMassachusetts General HospitalBostonMassachusettsUSA,Harvard Medical SchoolBostonMassachusettsUSA
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Darbeheshti F, Yu F, Ahmed F, Adalsteinsson VA, Makrigiorgos GM. Recent Developments in Mutation Enrichment and Detection Technologies. Clin Chem 2022; 68:1250-1260. [PMID: 35716101 DOI: 10.1093/clinchem/hvac093] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 05/09/2022] [Indexed: 11/13/2022]
Abstract
BACKGROUND Presence of excess unaltered, wild-type DNA (wtDNA) providing information of little clinical value may often mask low-level mutations containing important diagnostic or therapeutic clues. This is a recurring hurdle in biotechnology and medicine, including cancer, prenatal diagnosis, infectious diseases, and organ transplantation. Mutation enrichment techniques that allow reduction of unwanted DNA to enable the detection of low-level mutations have emerged since the early 1990s. They are continuously being refined and updated with new technologies. The burgeoning interest in liquid biopsies for residual cancer monitoring, detection of resistance to therapy, and early cancer detection has driven an expanded interest in new and improved methodologies for practical and effective mutation enrichment and detection of low-level mutations of clinical relevance. CONTENT Newly developed mutation enrichment technologies are described and grouped according to the main principle of operation, PCR-blocking technologies, enzymatic methods, and physicochemical approaches. Special emphasis is given to technologies enabling pre-PCR blockage of wtDNA to bypass PCR errors [nuclease-assisted minor-allele enrichment assay with overlapping probes (NaME-PrO) and UV-mediated cross-linking minor allele enrichment (UVME)] or providing high multiplexity followed by next-generation sequencing [Minor allele enriched sequencing through recognition oligonucleotides (MAESTRO)]. SUMMARY This review summarizes technological developments in rare mutation enrichment over the last 12 years, complementing pre-2010 reviews on this topic. The expanding field of liquid biopsy calls for improved limits of detection (LOD) and highly parallel applications, along with the traditional requirements for accuracy, speed, and cost-effectiveness. The current technologies are reviewed with regards to these new requirements.
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Affiliation(s)
- Farzaneh Darbeheshti
- Department of Radiation Oncology, Dana Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Fangyan Yu
- Department of Radiation Oncology, Dana Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Farzana Ahmed
- Department of Radiation Oncology, Dana Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | | | - G Mike Makrigiorgos
- Department of Radiation Oncology, Dana Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
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Stergiopoulou D, Markou A, Tzanikou E, Ladas I, Makrigiorgos GM, Georgoulias V, Lianidou E. Abstract 5160: Development and analytical validation of a highly sensitive and specific NAPA assay for the detection of ESR1mutations in circulating tumor cells and plasma circulating tumor DNA. Cancer Res 2022. [DOI: 10.1158/1538-7445.am2022-5160] [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: A considerable number of estrogen receptor-positive breast cancer (ER+ BrCa) patients develop resistance to endocrine treatment. One of the most important resistance mechanisms is the presence of ESR1 mutations. The aim of the current study was the development and analytical validation of a highly sensitive and specific NaME-PrO-assisted ARMS (NAPA) assay for the detection of four ESR1 mutations (Y537S, Y537C, Y537N and D538G) in circulating tumor cells (CTCs) and corresponding plasma circulating tumor DNA (ctDNA) in patients with ER+ BrCa.
Methods: We first developed the assay and validated the analytical specificity, analytical sensitivity and reproducibility. We further evaluated the performance of the developed assay in CTCs and ctDNA derived from 13 ER+ BrCa primary tumor tissues and 64 liquid biopsy samples: 32 EpCAM-isolated cell fractions and 32 corresponding plasma cell free DNA (cfDNA) obtained at different time points from 8 ER+ metastatic breast cancer patients, during a 5-year follow-up period and peripheral blood from 11 healthy donors (HD). We further compared the performance of the ESR1 NAPA assay with drop-off droplet digital PCR (ddPCR), using identical samples.
Results: The developed assay is highly sensitive (detection of mutation-allelic-frequency of 0.5% for D538G and 0.1% for Y537S, Y537C, Y537N), and highly specific (0/13 mammoplasties and 0/11 HD for all mutations). In plasma ctDNA, ESR1 mutations were not identified at the baseline whereas the D538G mutation was detected in five sequential cfDNA samples during the follow-up period in the same patient. The developed assay gave comparable results with ddPCR, since the concordance between the ESR1 NAPA assay and drop-off ddPCR as evaluated using 32 identical cfDNA samples was 90.6% (29/32). In EpCAM-isolated cell fractions only the Y537C mutation was detected in one patient sample at baseline.
Conclusions: We present a low cost, highly specific, sensitive and robust assay for blood-based ESR1 profiling. The developed assay is fast, with a comparable sensitivity to ddPCR but has lower cost relative to ddPCR, and thus can be used as a fast screening method to classify patients as positive or negative for ESR1 mutations. Our results are consistent with reports that indicate that ESR1 mutations (especially D538G, Y537S) are associated with more aggressive disease.
Citation Format: Dimitra Stergiopoulou, Athina Markou, Eleni Tzanikou, Ioannis Ladas, G. Mike Makrigiorgos, Vassilis Georgoulias, Evi Lianidou. Development and analytical validation of a highly sensitive and specific NAPA assay for the detection of ESR1mutations in circulating tumor cells and plasma circulating tumor DNA [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 5160.
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Affiliation(s)
| | - Athina Markou
- 1National and Kapodistrian University of Athens, Athens, Greece
| | - Eleni Tzanikou
- 1National and Kapodistrian University of Athens, Athens, Greece
| | | | | | | | - Evi Lianidou
- 1National and Kapodistrian University of Athens, Athens, Greece
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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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10
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Yasmin-Karim S, Ziberi B, Wirtz J, Bih N, Moreau M, Mueller R, Anisworth V, Hesser J, Makrigiorgos GM, Chuong MD, Wei XX, Nguyen PL, Ngwa W. Boosting the Abscopal Effect Using Immunogenic Biomaterials With Varying Radiation Therapy Field Sizes. Int J Radiat Oncol Biol Phys 2022; 112:475-486. [PMID: 34530092 PMCID: PMC8750216 DOI: 10.1016/j.ijrobp.2021.09.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [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: 02/23/2021] [Revised: 08/31/2021] [Accepted: 09/03/2021] [Indexed: 02/03/2023]
Abstract
PURPOSE Persistent immunosuppression in the tumor microenvironment is a major limitation to boosting the abscopal effect, whereby radiation therapy at 1 site can lead to regression of tumors at distant sites. Here, we investigate the use of radiation and immunogenic biomaterials (IBM) targeting only the gross tumor volume/subvolume for boosting the abscopal effect in immunologically cold tumors. METHODS AND MATERIALS To evaluate the abscopal effect, 2 syngeneic contralateral tumors were implanted in each mouse, where only 1 tumor was treated. IBM was administered to the treated tumor with 1 fraction of radiation and results were compared, including as a function of different radiation therapy field sizes. The IBM was designed similar to fiducial markers using immunogenic polymer components loaded with anti-CD40 agonist. Tumor volumes of both treated and untreated tumors were measured over time, along with survival and corresponding immune cell responses. RESULTS Results showed that radiation with IBM administered to the gross tumor subvolume can effectively boost abscopal responses in both pancreatic and prostate cancers, significantly increasing survival (P < .0001 and P < .001, respectively). Results also showed equal or superior abscopal responses when using field sizes smaller than the gross tumor volume compared with irradiating the whole tumor volume. These results were buttressed by observation of higher infiltration of cytotoxic CD8+ T-lymphocytes in the treated tumors (P < .0001) and untreated tumors (P < .0001) for prostate cancer. Significantly higher infiltration was also observed in treated tumors (P < .0001) and untreated tumors P < .01) for pancreatic cancer. Moreover, the immune responses were accompanied by a positive shift of proinflammatory cytokines in both prostate and pancreatic tumors. CONCLUSIONS The approach targeting gross tumor subvolumes with radiation and IBM offers opportunity for boosting the abscopal effect while significantly minimizing healthy tissue toxicity. This approach proffers a radioimmunotherapy dose-painting strategy that can be developed for overcoming current barriers of immunosuppression especially for immunologically cold tumors.
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Affiliation(s)
- Sayeda Yasmin-Karim
- Dana Farber Cancer Institute, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, USA,Corresponding author: Name: Sayeda Yasmin-Karim, (S.Y.)
| | - Bashkim Ziberi
- Dana Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA,University of Tetova, Tetova, Republic of North Macedonia
| | - Johanna Wirtz
- Dana Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA,Medical Faculty of University Ulm, Ulm, Germany
| | - Noella Bih
- Dana Farber Cancer Institute, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Michele Moreau
- Dana Farber Cancer Institute, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, USA,University of Massachusetts, Lowell, Massachusetts, USA
| | - Romy Mueller
- Dana Farber Cancer Institute, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, USA,Data Analysis and Modeling in Medicine, Mannheim Institute for Intelligent Systems in Medicine (MIISM), Heidelberg University, 69117 Heidelberg, Germany
| | - Victoria Anisworth
- Dana Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA,University of Massachusetts, Lowell, Massachusetts, USA
| | - Juergen Hesser
- Data Analysis and Modeling in Medicine, Mannheim Institute for Intelligent Systems in Medicine (MIISM), Heidelberg University, 69117 Heidelberg, Germany
| | - G. Mike Makrigiorgos
- Dana Farber Cancer Institute, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Michael D Chuong
- Miami Cancer Institute, Baptist Health South Florida, Miami, Florida, USA
| | - Xiao Xiao Wei
- Dana Farber Cancer Institute, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Paul L. Nguyen
- Dana Farber Cancer Institute, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Wilfred Ngwa
- Dana Farber Cancer Institute, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, USA,University of Massachusetts, Lowell, Massachusetts, USA
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11
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Leong KW, Yu F, Makrigiorgos GM. Mutation enrichment in human DNA samples via UV-mediated cross-linking. Nucleic Acids Res 2021; 50:e32. [PMID: 34904676 PMCID: PMC8989544 DOI: 10.1093/nar/gkab1222] [Citation(s) in RCA: 3] [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: 06/03/2021] [Revised: 10/28/2021] [Accepted: 11/30/2021] [Indexed: 12/13/2022] Open
Abstract
Detection of low-level DNA mutations can reveal recurrent, hotspot genetic changes of clinical relevance to cancer, prenatal diagnostics, organ transplantation or infectious diseases. However, the high excess of wild-type (WT) alleles, which are concurrently present, often hinders identification of salient genetic changes. Here, we introduce UV-mediated cross-linking minor allele enrichment (UVME), a novel approach that incorporates ultraviolet irradiation (∼365 nm UV) DNA cross-linking either before or during PCR amplification. Oligonucleotide probes matching the WT target sequence and incorporating a UV-sensitive 3-cyanovinylcarbazole nucleoside modification are employed for cross-linking WT DNA. Mismatches formed with mutated alleles reduce DNA binding and UV-mediated cross-linking and favor mutated DNA amplification. UV can be applied before PCR and/or at any stage during PCR to selectively block WT DNA amplification and enable identification of traces of mutated alleles. This enables a single-tube PCR reaction directly from genomic DNA combining optimal pre-amplification of mutated alleles, which then switches to UV-mediated mutation enrichment-based DNA target amplification. UVME cross-linking enables enrichment of mutated KRAS and p53 alleles, which can be screened directly via Sanger sequencing, high-resolution melting, TaqMan genotyping or digital PCR, resulting in the detection of mutation allelic frequencies of 0.001–0.1% depending on the endpoint detection method. UV-mediated mutation enrichment provides new potential for mutation enrichment in diverse clinical samples.
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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, 450 Brookline Avenue, Boston, MA 02115, USA
| | - Fangyan Yu
- Department of Radiation Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, 450 Brookline Avenue, Boston, MA 02115, USA
| | - G Mike Makrigiorgos
- Department of Radiation Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, 450 Brookline Avenue, Boston, MA 02115, USA
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12
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Ahmed S, Bossenberger T, Nalichowski A, Bredfeldt JS, Bartlett S, Bertone K, Dominello M, Dziemianowicz M, Komajda M, Makrigiorgos GM, Marcus KJ, Ng A, Thomas M, Burmeister J. A bi-institutional multi-disciplinary failure mode and effects analysis (FMEA) for a Co-60 based total body irradiation technique. Radiat Oncol 2021; 16:224. [PMID: 34798879 PMCID: PMC8605584 DOI: 10.1186/s13014-021-01894-3] [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] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Accepted: 08/25/2021] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND We aim to assess the risks associated with total body irradiation (TBI) delivered using a commercial dedicated Co-60 irradiator, and to evaluate inter-institutional and inter-professional variations in the estimation of these risks. METHODS A failure mode and effects analysis (FMEA) was generated using guidance from the AAPM TG-100 report for quantitative estimation of prospective risk metrics. Thirteen radiation oncology professionals from two institutions rated possible failure modes (FMs) for occurrence (O), severity (S), and detectability (D) indices to generate a risk priority number (RPN). The FMs were ranked by descending RPN value. Absolute gross differences (AGD) in resulting RPN values and Jaccard Index (JI; for the top 20 FMs) were calculated. The results were compared between professions and institutions. RESULTS A total of 87 potential FMs (57, 15, 10, 3, and 2 for treatment, quality assurance, planning, simulation, and logistics respectively) were identified and ranked, with individual RPN ranging between 1-420 and mean RPN values ranging between 6 and 74. The two institutions shared 6 of their respective top 20 FMs. For various institutional and professional comparison pairs, the number of common FMs in the top 20 FMs ranged from 6 to 13, with JI values of 18-48%. For the top 20 FMs, the trend in inter-professional variability was institution-specific. The mean AGD values ranged between 12.5 and 74.5 for various comparison pairs. AGD values differed the most for medical physicists (MPs) in comparison to other specialties i.e. radiation oncologists (ROs) and radiation therapists (RTs) [MPs-vs-ROs: 36.3 (standard deviation SD = 34.1); MPs-vs-RTs: 41.2 (SD = 37.9); ROs-vs-RTs: 12.5 (SD = 10.8)]. Trends in inter-professional AGD values were similar for both institutions. CONCLUSION This inter-institutional comparison provides prospective risk analysis for a new treatment delivery unit and illustrates the institution-specific nature of FM prioritization, primarily due to operational differences. Despite being subjective in nature, the FMEA is a valuable tool to ensure the identification of the most significant risks, particularly when implementing a novel treatment modality. The creation of a bi-institutional, multidisciplinary FMEA for this unique TBI technique has not only helped identify potential risks but also served as an opportunity to evaluate clinical and safety practices from the perspective of both multiple professional roles and different institutions.
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Affiliation(s)
- Shahbaz Ahmed
- Department of Oncology, Wayne State University School of Medicine, Detroit, MI, USA.
| | - Todd Bossenberger
- Gershenson Radiation Oncology Center, Karmanos Cancer Center, Detroit, MI, USA
| | - Adrian Nalichowski
- Department of Oncology, Wayne State University School of Medicine, Detroit, MI, USA
- Gershenson Radiation Oncology Center, Karmanos Cancer Center, Detroit, MI, USA
| | - Jeremy S Bredfeldt
- Dana Farber/Brigham and Women's Cancer Center, Harvard Medical School, Boston, MA, USA
| | - Sarah Bartlett
- Dana Farber/Brigham and Women's Cancer Center, Harvard Medical School, Boston, MA, USA
| | - Kristen Bertone
- Dana Farber/Brigham and Women's Cancer Center, Harvard Medical School, Boston, MA, USA
| | - Michael Dominello
- Department of Oncology, Wayne State University School of Medicine, Detroit, MI, USA
| | - Mark Dziemianowicz
- Department of Oncology, Wayne State University School of Medicine, Detroit, MI, USA
| | - Melanie Komajda
- Gershenson Radiation Oncology Center, Karmanos Cancer Center, Detroit, MI, USA
| | - G Mike Makrigiorgos
- Dana Farber/Brigham and Women's Cancer Center, Harvard Medical School, Boston, MA, USA
| | - Karen J Marcus
- Dana Farber/Brigham and Women's Cancer Center, Harvard Medical School, Boston, MA, USA
| | - Andrea Ng
- Dana Farber/Brigham and Women's Cancer Center, Harvard Medical School, Boston, MA, USA
| | - Marvin Thomas
- Gershenson Radiation Oncology Center, Karmanos Cancer Center, Detroit, MI, USA
| | - Jay Burmeister
- Department of Oncology, Wayne State University School of Medicine, Detroit, MI, USA
- Gershenson Radiation Oncology Center, Karmanos Cancer Center, Detroit, MI, USA
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13
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Xiong K, Shea D, Rhoades J, Blewett T, Liu R, Bae J, Nguyen E, Makrigiorgos GM, Golub TR, Adalsteinsson V. Duplex-Repair enables highly accurate sequencing, despite DNA damage. Nucleic Acids Res 2021; 50:e1. [PMID: 34591958 PMCID: PMC8755016 DOI: 10.1093/nar/gkab855] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 09/07/2021] [Accepted: 09/13/2021] [Indexed: 11/28/2022] Open
Abstract
Accurate DNA sequencing is crucial in biomedicine. Underlying the most accurate methods is the assumption that a mutation is true if altered bases are present on both strands of the DNA duplex. We now show that this assumption can be wrong. We establish that current methods to prepare DNA for sequencing, via ‘End Repair/dA-Tailing,’ may substantially resynthesize strands, leading amplifiable lesions or alterations on one strand to become indiscernible from true mutations on both strands. Indeed, we discovered that 7–17% and 32–57% of interior ‘duplex base pairs’ from cell-free DNA and formalin-fixed tumor biopsies, respectively, could be resynthesized in vitro and potentially introduce false mutations. To address this, we present Duplex-Repair, and show that it limits interior duplex base pair resynthesis by 8- to 464-fold, rescues the impact of induced DNA damage, and affords up to 8.9-fold more accurate duplex sequencing. Our study uncovers a major Achilles’ heel in sequencing and offers a solution to restore high accuracy.
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Affiliation(s)
| | | | | | - Timothy Blewett
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Ruolin Liu
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Jin H Bae
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Erica Nguyen
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - G Mike Makrigiorgos
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Department of Radiation Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Todd R Golub
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
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14
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Yu F, Leong KW, Makrigiorgos A, Adalsteinsson VA, Ladas I, Ng K, Mamon H, Makrigiorgos GM. NGS-based identification and tracing of microsatellite instability from minute amounts DNA using inter-Alu-PCR. Nucleic Acids Res 2021; 49:e24. [PMID: 33290560 PMCID: PMC7913684 DOI: 10.1093/nar/gkaa1175] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 10/13/2020] [Accepted: 11/20/2020] [Indexed: 12/20/2022] Open
Abstract
Sensitive detection of microsatellite instability (MSI) in tissue or liquid biopsies using next generation sequencing (NGS) has growing prognostic and predictive applications in cancer. However, the complexities of NGS make it cumbersome as compared to established multiplex-PCR detection of MSI. We present a new approach to detect MSI using inter-Alu-PCR followed by targeted NGS, that combines the practical advantages of multiplexed-PCR with the breadth of information provided by NGS. Inter-Alu-PCR employs poly-adenine repeats of variable length present in every Alu element and provides a massively-parallel, rapid approach to capture poly-A-rich genomic fractions within short 80–150bp amplicons generated from adjacent Alu-sequences. A custom-made software analysis tool, MSI-tracer, enables Alu-associated MSI detection from tissue biopsies or MSI-tracing at low-levels in circulating-DNA. MSI-associated indels at somatic-indel frequencies of 0.05–1.5% can be detected depending on the availability of matching normal tissue and the extent of instability. Due to the high Alu copy-number in human genomes, a single inter-Alu-PCR retrieves enough information for identification of MSI-associated-indels from ∼100 pg circulating-DNA, reducing current limits by ∼2-orders of magnitude and equivalent to circulating-DNA obtained from finger-sticks. The combined practical and informational advantages of inter-Alu-PCR make it a powerful tool for identifying tissue-MSI-status or tracing MSI-associated-indels in liquid biopsies.
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Affiliation(s)
- Fangyan Yu
- Department of Radiation Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Ka Wai Leong
- Department of Radiation Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Alexander Makrigiorgos
- Department of Radiation Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | | | - Ioannis Ladas
- Department of Radiation Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Kimmie Ng
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medicine School, Boston, MA, USA
| | - Harvey Mamon
- Department of Radiation Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - G Mike Makrigiorgos
- Department of Radiation Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
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15
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Detappe A, Kunjachan S, Sancey L, Motto-Ros V, Biancur D, Drane P, Guieze R, Makrigiorgos GM, Tillement O, Langer R, Berbeco R. Corrigendum to "Advanced multimodal nanoparticles delay tumor progression withclinical radiation therapy" [Journal of Controlled Release 238 (2016) 103-133]. J Control Release 2021; 329:1283-1285. [PMID: 32977991 DOI: 10.1016/j.jconrel.2020.08.029] [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: 10/23/2022]
Affiliation(s)
- Alexandre Detappe
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02215, USA; Lyon-1 University, Institut Lumière Matière, CNRS UMR5306, Lyon, France
| | - Sijumon Kunjachan
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02215, USA
| | - Lucie Sancey
- Lyon-1 University, Institut Lumière Matière, CNRS UMR5306, Lyon, France
| | - Vincent Motto-Ros
- Lyon-1 University, Institut Lumière Matière, CNRS UMR5306, Lyon, France
| | - Douglas Biancur
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02215, USA
| | - Pascal Drane
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02215, USA
| | - Romain Guieze
- Division of Medical Oncology, Dana-Farber Cancer Institute, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02215, USA
| | - G Mike Makrigiorgos
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02215, USA
| | - Olivier Tillement
- Lyon-1 University, Institut Lumière Matière, CNRS UMR5306, Lyon, France
| | - Robert Langer
- Department of Chemical Engineering, David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Ross Berbeco
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02215, USA
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16
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Kunjachan S, Detappe A, Kumar R, Ireland T, Cameron L, Biancur DE, Motto-Ros V, Sancey L, Sridhar S, Makrigiorgos GM, Berbeco RI. Correction to "Nanoparticle Mediated Tumor Vascular Disruption: A Novel Strategy in Radiation Therapy". Nano Lett 2020; 20:6931. [PMID: 32787156 DOI: 10.1021/acs.nanolett.0c03032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
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17
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Virani NA, Kelada OJ, Kunjachan S, Detappe A, Kwon J, Hayashi J, Vazquez-Pagan A, Biancur DE, Ireland T, Kumar R, Sridhar S, Makrigiorgos GM, Berbeco RI. Noninvasive imaging of tumor hypoxia after nanoparticle-mediated tumor vascular disruption. PLoS One 2020; 15:e0236245. [PMID: 32706818 PMCID: PMC7380644 DOI: 10.1371/journal.pone.0236245] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Accepted: 07/01/2020] [Indexed: 01/09/2023] Open
Abstract
We have previously demonstrated that endothelial targeting of gold nanoparticles followed by external beam irradiation can cause specific tumor vascular disruption in mouse models of cancer. The induced vascular damage may lead to changes in tumor physiology, including tumor hypoxia, thereby compromising future therapeutic interventions. In this study, we investigate the dynamic changes in tumor hypoxia mediated by targeted gold nanoparticles and clinical radiation therapy (RT). By using noninvasive whole-body fluorescence imaging, tumor hypoxia was measured at baseline, on day 2 and day 13, post-tumor vascular disruption. A 2.5-fold increase (P<0.05) in tumor hypoxia was measured two days after combined therapy, resolving by day 13. In addition, the combination of vascular-targeted gold nanoparticles and radiation therapy resulted in a significant (P<0.05) suppression of tumor growth. This is the first study to demonstrate the tumor hypoxic physiological response and recovery after delivery of vascular-targeted gold nanoparticles followed by clinical radiation therapy in a human non-small cell lung cancer athymic Foxn1nu mouse model.
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Affiliation(s)
- Needa A. Virani
- Department of Radiation Oncology, Brigham and Women’s Hospital, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts, United States of America
- * E-mail:
| | - Olivia J. Kelada
- Department of Radiation Oncology, Brigham and Women’s Hospital, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts, United States of America
| | - Sijumon Kunjachan
- Department of Radiation Oncology, Brigham and Women’s Hospital, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts, United States of America
| | - Alexandre Detappe
- Department of Radiation Oncology, Brigham and Women’s Hospital, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts, United States of America
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston Massachusetts, United States of America
| | - Jihun Kwon
- Department of Radiation Oncology, Brigham and Women’s Hospital, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts, United States of America
- Department of Radiation Oncology, Hokkaido University, Sapporo, Japan
| | - Jennifer Hayashi
- Department of Radiation Oncology, Brigham and Women’s Hospital, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts, United States of America
- Nanomedicine Innovation Center and Department of Physics, Northeastern University, Boston, Massachusetts, United States of America
| | - Ana Vazquez-Pagan
- Department of Radiation Oncology, Brigham and Women’s Hospital, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts, United States of America
- Nanomedicine Innovation Center and Department of Physics, Northeastern University, Boston, Massachusetts, United States of America
| | - Douglas E. Biancur
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston Massachusetts, United States of America
| | - Thomas Ireland
- LA-ICP-MS and ICP-ES Laboratories, Boston University, Boston, Massachusetts, United States of America
| | - Rajiv Kumar
- Department of Radiation Oncology, Brigham and Women’s Hospital, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts, United States of America
- Nanomedicine Innovation Center and Department of Physics, Northeastern University, Boston, Massachusetts, United States of America
| | - Srinivas Sridhar
- Department of Radiation Oncology, Brigham and Women’s Hospital, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts, United States of America
- Nanomedicine Innovation Center and Department of Physics, Northeastern University, Boston, Massachusetts, United States of America
| | - G. Mike Makrigiorgos
- Department of Radiation Oncology, Brigham and Women’s Hospital, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts, United States of America
| | - Ross I. Berbeco
- Department of Radiation Oncology, Brigham and Women’s Hospital, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts, United States of America
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Herter-Sprie GS, Korideck H, Christensen CL, Herter JM, Rhee K, Berbeco RI, Bennett DG, Akbay EA, Kozono D, Mak RH, Makrigiorgos GM, Kimmelman AC, Wong KK. Author Correction: Image-guided radiotherapy platform using single nodule conditional lung cancer mouse models. Nat Commun 2020; 11:1835. [PMID: 32273495 DOI: 10.1038/s41467-020-15348-z] [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: 11/09/2022] Open
Abstract
An amendment to this paper has been published and can be accessed via a link at the top of the paper.
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Affiliation(s)
- Grit S Herter-Sprie
- Department of Medicine, Harvard Medical School, Boston, MA, 02115, USA.,Lowe Center for Thoracic Oncology, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA.,Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, 02215, MA, USA
| | - Houari Korideck
- Division of Medical Physics and Biophysics, Department of Radiation Oncology, Dana-Farber Cancer Institute, Brigham and Women's Hospital, Harvard Medical School, 450 Brookline Avenue, Boston, MA, 02215, USA
| | - Camilla L Christensen
- Department of Medicine, Harvard Medical School, Boston, MA, 02115, USA.,Lowe Center for Thoracic Oncology, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA.,Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, 02215, MA, USA
| | - Jan M Herter
- Center for Excellence in Vascular Biology,Department of Pathology, Brigham and Women's Hospitall, Harvard Medical School, Boston, MA, 02115, USA
| | - Kevin Rhee
- Department of Medicine, Harvard Medical School, Boston, MA, 02115, USA.,Lowe Center for Thoracic Oncology, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA.,Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, 02215, MA, USA
| | - Ross I Berbeco
- Division of Medical Physics and Biophysics, Department of Radiation Oncology, Dana-Farber Cancer Institute, Brigham and Women's Hospital, Harvard Medical School, 450 Brookline Avenue, Boston, MA, 02215, USA
| | - David G Bennett
- Department of Radiology, Harvard Medical School, Beth Israel Deaconess Medical Center, Boston, MA, 02215, USA.,PAREXEL International Corp., 195 West Street, Waltham, MA, USA
| | - Esra A Akbay
- Department of Medicine, Harvard Medical School, Boston, MA, 02115, USA.,Lowe Center for Thoracic Oncology, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA.,Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, 02215, MA, USA
| | - David Kozono
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Brigham and Women's Hospital, Harvard Medical School, 450 Brookline Avenue, Boston, MA, 02215, USA
| | - Raymond H Mak
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Brigham and Women's Hospital, Harvard Medical School, 450 Brookline Avenue, Boston, MA, 02215, USA
| | - G Mike Makrigiorgos
- Division of Medical Physics and Biophysics, Department of Radiation Oncology, Dana-Farber Cancer Institute, Brigham and Women's Hospital, Harvard Medical School, 450 Brookline Avenue, Boston, MA, 02215, USA
| | - Alec C Kimmelman
- Division of Genomic Stability and DNA Repair, Department of Radiation Oncology, Dana-Farber Cancer Institute, Brigham and Women's Hospital, Harvard Medical School, 450 Brookline Avenue, Boston, MA, 02215, USA.
| | - Kwok-Kin Wong
- Department of Medicine, Harvard Medical School, Boston, MA, 02115, USA. .,Lowe Center for Thoracic Oncology, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA. .,Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, 02215, MA, USA.
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19
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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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Markou A, Tzanikou E, Ladas I, Makrigiorgos GM, Lianidou E. Nuclease-Assisted Minor Allele Enrichment Using Overlapping Probes-Assisted Amplification-Refractory Mutation System: An Approach for the Improvement of Amplification-Refractory Mutation System-Polymerase Chain Reaction Specificity in Liquid Biopsies. Anal Chem 2019; 91:13105-13111. [PMID: 31538770 DOI: 10.1021/acs.analchem.9b03325] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Allele-specific polymerase chain reaction (PCR) (amplification-refractory mutation system, ARMS) is one of the most commonly used methods for mutation detection. However, a main limitation of ARMS-PCR is the false positive results obtained due to nonspecific priming that can take place with wild-type (WT) DNA, which often precludes detection of low-level mutations. To improve the analytical specificity of ARMS, we present here a new technology, NAPA: NaME-PrO-assisted ARMS, that overcomes the ARMS deficiency by adding a brief enzymatic step that reduces wild-type alleles just prior to ARMS. We performed this technology for the simultaneous detection of two hot-spot PIK3CA mutations (E545 K and H1047R) in circulating tumor cells (CTCs) and cell free DNA (cfDNA). The developed protocol could simultaneously detect mutation-allelic-frequency of 0.5% for PIK3CA exon 9 (E545 K) and 0.1% for PIK3CA exon 20 (H1047R) with high specificity. We further compared the developed NAPA assay with (a) ddPCR considered as the gold standard and (b) our previous assay based on the combination of allele-specific, asymmetric rapid PCR, and melting analysis. Our data show that the newly developed NAPA assay gives consistent results with both these assays (p = 0.001). The developed assay resolves the false positive signals issue derived through classic ARMS-PCR and provides an ideal combination of speed, accuracy, and versatility and should be easily applicable in routine diagnostic laboratories.
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Affiliation(s)
- Athina Markou
- Analysis of Circulating Tumor Cells, Laboratory of Analytical Chemistry, Department of Chemistry , University of Athens , Athens 15771 , Greece
| | - Elena Tzanikou
- Analysis of Circulating Tumor Cells, Laboratory of Analytical Chemistry, Department of Chemistry , University of Athens , Athens 15771 , Greece
| | - Ioannis Ladas
- Department of Radiation Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital , Harvard Medical School , Boston , Massachusetts 02115 , United States
| | - G Mike Makrigiorgos
- Department of Radiation Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital , Harvard Medical School , Boston , Massachusetts 02115 , United States
| | - Evi Lianidou
- Analysis of Circulating Tumor Cells, Laboratory of Analytical Chemistry, Department of Chemistry , University of Athens , Athens 15771 , Greece
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Makrigiorgos GM. Extreme PCR Meets High-Speed Melting: A Step Closer to Molecular Diagnostics "While You Wait". Clin Chem 2018; 65:217-219. [PMID: 30530717 DOI: 10.1373/clinchem.2018.298356] [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] [Received: 11/12/2018] [Accepted: 11/20/2018] [Indexed: 12/19/2022]
Affiliation(s)
- G Mike Makrigiorgos
- Department of Radiation Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA.
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22
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Fitarelli-Kiehl M, Yu F, Ashtaputre R, Leong KW, Ladas I, Supplee J, Paweletz C, Mitra D, Schoenfeld JD, Parangi S, Makrigiorgos GM. Denaturation-Enhanced Droplet Digital PCR for Liquid Biopsies. Clin Chem 2018; 64:1762-1771. [PMID: 30274976 DOI: 10.1373/clinchem.2018.293845] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Accepted: 09/04/2018] [Indexed: 12/14/2022]
Abstract
BACKGROUND Although interest in droplet-digital PCR technology (ddPCR) for cell-free circulating DNA (cfDNA) analysis is burgeoning, the technology is compromised by subsampling errors and the few clinical targets that can be analyzed from limited input DNA. The paucity of starting material acts as a "glass ceiling" in liquid biopsies because, irrespective how analytically sensitive ddPCR techniques are, detection limits cannot be improved past DNA input limitations. METHODS We applied denaturation-enhanced ddPCR (dddPCR) using fragmented genomic DNA (gDNA) with defined mutations. We then tested dddPCR on cfDNA from volunteers and patients with cancer for commonly-used mutations. gDNA and cfDNA were tested with and without end repair before denaturation and digital PCR. RESULTS By applying complete denaturation of double-stranded DNA before ddPCR droplet formation the number of positive droplets increased. dddPCR using gDNA resulted in a 1.9-2.0-fold increase in data-positive droplets, whereas dddPCR applied on highly-fragmented cfDNA resulted in a 1.6-1.7-fold increase. End repair of cfDNA before denaturation enabled cfDNA to display a 1.9-2.0-fold increase in data-positive signals, similar to gDNA. Doubling of data-positive droplets doubled the number of potential ddPCR assays that could be conducted from a given DNA input and improved ddPCR precision for cfDNA mutation detection. CONCLUSIONS dddPCR is a simple and useful modification in ddPCR that enables extraction of more information from low-input clinical samples with minor change in protocols. It should be applicable to all ddPCR platforms for mutation detection and, potentially, for gene copy-number analysis in cancer and prenatal screening.
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Affiliation(s)
- Mariana Fitarelli-Kiehl
- Department of Radiation Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| | - Fangyan Yu
- Department of Radiation Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| | - Ravina Ashtaputre
- Department of Radiation Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| | - Ka Wai Leong
- Department of Radiation Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| | - Ioannis Ladas
- Department of Radiation Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| | - Julianna Supplee
- Department of Medical Oncology and Belfer Institute for Applied Cancer Science, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
| | - Cloud Paweletz
- Department of Medical Oncology and Belfer Institute for Applied Cancer Science, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
| | - Devarati Mitra
- Department of Radiation Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| | - Jonathan D Schoenfeld
- Department of Radiation Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| | - Sareh Parangi
- Department of General & Gastrointestinal Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA
| | - G Mike Makrigiorgos
- Department of Radiation Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA;
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23
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Byrou S, Makrigiorgos GM, Christofides A, Kallikas I, Papasavva T, Kleanthous M. Fast Temperature-Gradient COLD PCR for the enrichment of the paternally inherited SNPs in cell free fetal DNA; an application to non-invasive prenatal diagnosis of β-thalassaemia. PLoS One 2018; 13:e0200348. [PMID: 30044883 PMCID: PMC6059429 DOI: 10.1371/journal.pone.0200348] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Accepted: 06/25/2018] [Indexed: 11/28/2022] Open
Abstract
Objective To develop a sensitive, specific, simple, cost-effective and reproducible platform for the non-invasive prenatal detection of paternally inherited alleles for β-thalassaemia. The development of such an assay is of major significance in order to replace currently-applied invasive methods containing inherent fetal loss risks. Methods We present a fast Temperature-Gradient Co-amplification at Lower Denaturation Temperature Polymerase Chain Reaction (fast TG COLD PCR) methodology for the detection of the paternally-inherited fetal alleles in maternal plasma. Two single-nucleotide polymorphisms (SNPs), rs7480526 (G/T) and rs968857 (G/A) that are located on the β-globin gene cluster and exhibit a high degree of heterozygosity in the Cypriot population were selected for evaluation. Seventeen maternal plasma samples from pregnancies at risk for β-thalassemia were analysed for the selected SNPs using the novel fast TG COLD PCR assay. Results Using fast TG COLD PCR, the paternally inherited allele in cell free fetal DNA was correctly determined for all the 17 maternal plasma samples tested, showing full agreement with the Chorionic Villus Sampling (CVS) analysis. Conclusions Our findings are encouraging and demonstrate the efficiency and sensitivity of fast TG COLD PCR in detecting the minor paternally-inherited fetal alleles in maternal plasma for the development of a NIPD assay for β-thalassaemia.
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Affiliation(s)
- Stefania Byrou
- Molecular Genetics Thalassaemia Department, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
- The Cyprus School of Molecular Medicine, Nicosia, Cyprus
| | - G. Mike Makrigiorgos
- Department of Radiation Oncology, Division of Medical Physics & Biophysics, Dana Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, United States of America
| | | | | | - Thessalia Papasavva
- Molecular Genetics Thalassaemia Department, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
- The Cyprus School of Molecular Medicine, Nicosia, Cyprus
- * E-mail:
| | - Marina Kleanthous
- Molecular Genetics Thalassaemia Department, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
- The Cyprus School of Molecular Medicine, Nicosia, Cyprus
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24
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Ladas I, Yu F, Leong K, Fitarelli-Kiehl M, Song C, Ashtaputre R, Kulke M, Mamon H, Makrigiorgos GM. Enhanced detection of microsatellite instability using pre-PCR elimination of wild-type DNA homo-polymers in tissue and liquid biopsies. Nucleic Acids Res 2018; 46:e74. [PMID: 29635638 PMCID: PMC6158611 DOI: 10.1093/nar/gky251] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [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: 02/05/2018] [Accepted: 03/28/2018] [Indexed: 02/06/2023] Open
Abstract
Detection of microsatellite-instability in colonoscopy-obtained polyps, as well as in plasma-circulating DNA, is frequently confounded by sensitivity issues due to co-existing excessive amounts of wild-type DNA. While also an issue for point mutations, this is particularly problematic for microsatellite changes, due to the high false-positive artifacts generated by polymerase slippage (stutter-bands). Here, we describe a nuclease-based approach, NaME-PrO, that uses overlapping oligonucleotides to eliminate unaltered micro-satellites at the genomic DNA level, prior to PCR. By appropriate design of the overlapping oligonucleotides, NaME-PrO eliminates WT alleles in long single-base homopolymers ranging from 10 to 27 nucleotides in length, while sparing targets containing variable-length indels at any position within the homopolymer. We evaluated 5 MSI targets individually or simultaneously, NR27, NR21, NR24, BAT25 and BAT26 using DNA from cell-lines, biopsies and circulating-DNA from colorectal cancer patients. NaME-PrO enriched altered microsatellites and detected alterations down to 0.01% allelic-frequency using high-resolution-melting, improving detection sensitivity by 500-1000-fold relative to current HRM approaches. Capillary-electrophoresis also demonstrated enhanced sensitivity and enrichment of indels 1-16 bases long. We anticipate application of this highly-multiplex-able method either with standard 5-plex reactions in conjunction with HRM/capillary electrophoresis or massively-parallel-sequencing-based detection of MSI on numerous targets for sensitive MSI-detection.
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Affiliation(s)
- Ioannis Ladas
- 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
| | - Ka Wai Leong
- Department of Radiation Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Mariana Fitarelli-Kiehl
- Department of Radiation Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Chen Song
- Department of Radiation Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Ravina Ashtaputre
- Department of Radiation Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Matthew Kulke
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Harvey Mamon
- Department of Radiation Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - G Mike Makrigiorgos
- Department of Radiation Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA,To whom correspondence should be addressed. Tel: +1 617 525 7122; Fax: +1 617 525 7122;
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25
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Guthier CV, D'Amico AV, King MT, Nguyen PL, Orio PF, Sridhar S, Makrigiorgos GM, Cormack RA. Determining optimal eluter design by modeling physical dose enhancement in brachytherapy. Med Phys 2018; 45:3916-3925. [PMID: 29905964 DOI: 10.1002/mp.13051] [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] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Revised: 05/30/2018] [Accepted: 06/06/2018] [Indexed: 11/05/2022] Open
Abstract
PURPOSE In situ drug release concurrent with radiation therapy has been proposed to enhance the therapeutic ratio of permanent prostate brachytherapy. Both brachytherapy sources and brachytherapy spacers have been proposed as potential eluters to release compounds, such as nanoparticles or chemotherapeutic agents. The relative effectiveness of the approaches has not been compared yet. This work models the physical dose enhancement of implantable eluters in conjunction with brachytherapy to determine which delivery mechanism provides greatest opportunity to enhance the therapeutic ratio. MATERIALS AND METHODS The combined effect of implanted eluters and radioactive sources were modeled in a manner that allowed the comparison of the relative effectiveness of different types of implantable eluters over a range of parameters. Prostate geometry, source, and spacer positions were extracted from treatment plans used for 125 I permanent prostate implants. Compound concentrations were calculated using steady-state solution to the diffusion equation including an elimination term characterized by the diffusion-elimination modulus (ϕb ). Does enhancement was assumed to be dependent on compound concentration up to a saturation concentration (csat ). Equivalent uniform dose (EUD) was used as an objective to determine the optimal configuration of eluters for a range of diffusion-elimination moduli, concentrations, and number of eluters. The compound delivery vehicle that produced the greatest enhanced dose was tallied for points in parameter space mentioned to determine the conditions under whether there are situations where one approach is preferable to the other. RESULTS The enhanced effect of implanted eluters was calculated for prostate volumes from 14 to 45 cm3 , ϕb from 0.01 to 4 mm-1 , csat from 0.05 to 7.5 times the steady-state compound concentration released from the surface of the eluter. The number of used eluters (ne ) was simulated from 10 to 60 eluters. For the region of (csat , Φ)-space that results in a large fraction of the gland being maximally sensitized, compound eluting spacers or sources produce equal increase in EUD. In the majority of the remaining (csat , Φ)-space, eluting spacers result in a greater EUD than sources even where sources often produce greater maximal physical dose enhancement. Placing eluting implants in planned locations throughout the prostate results in even greater enhancement than using only source or spacer locations. CONCLUSIONS Eluting brachytherapy spacers offer an opportunity to increase EUD during the routine brachytherapy process. Incorporating additional needle placements permits compound eluting spacer placement independent of source placement and thereby allowing a further increase in the therapeutic ratio. Additional work is needed to understand the in vivo spatial distribution of compound around eluters, and to incorporate time dependence of both compound release and radiation dose.
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Affiliation(s)
- C V Guthier
- Department of Radiation Oncology, Brigham and Women's Hospital and Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - A V D'Amico
- Department of Radiation Oncology, Brigham and Women's Hospital and Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - M T King
- Department of Radiation Oncology, Brigham and Women's Hospital and Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - P L Nguyen
- Department of Radiation Oncology, Brigham and Women's Hospital and Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - P F Orio
- Department of Radiation Oncology, Brigham and Women's Hospital and Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - S Sridhar
- Department of Radiation Oncology, Brigham and Women's Hospital and Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Nanomedicine Science and Technology Center, Northeastern University, Boston, MA, USA
| | - G M Makrigiorgos
- Department of Radiation Oncology, Brigham and Women's Hospital and Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - R A Cormack
- Department of Radiation Oncology, Brigham and Women's Hospital and Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
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Ladas I, Fitarelli-Kiehl M, Song C, Adalsteinsson VA, Parsons HA, Lin NU, Wagle N, Makrigiorgos GM. Multiplexed Elimination of Wild-Type DNA and High-Resolution Melting Prior to Targeted Resequencing of Liquid Biopsies. Clin Chem 2017; 63:1605-1613. [PMID: 28679646 PMCID: PMC5914173 DOI: 10.1373/clinchem.2017.272849] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [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: 02/27/2017] [Accepted: 05/12/2017] [Indexed: 02/06/2023]
Abstract
BACKGROUND The use of clinical samples and circulating cell-free DNA (cfDNA) collected from liquid biopsies for diagnostic and prognostic applications in cancer is burgeoning, and improved methods that reduce the influence of excess wild-type (WT) portion of the sample are desirable. Here we present enrichment of mutation-containing sequences using enzymatic degradation of WT DNA. Mutation enrichment is combined with high-resolution melting (HRM) performed in multiplexed closed-tube reactions as a rapid, cost-effective screening tool before targeted resequencing. METHODS We developed a homogeneous, closed-tube approach to use a double-stranded DNA-specific nuclease for degradation of WT DNA at multiple targets simultaneously. The No Denaturation Nuclease-assisted Minor Allele Enrichment with Probe Overlap (ND-NaME-PrO) uses WT oligonucleotides overlapping both strands on putative DNA targets. Under conditions of partial denaturation (DNA breathing), the oligonucleotide probes enhance double-stranded DNA-specific nuclease digestion at the selected targets, with high preference toward WT over mutant DNA. To validate ND-NaME-PrO, we used multiplexed HRM, digital PCR, and MiSeq targeted resequencing of mutated genomic DNA and cfDNA. RESULTS Serial dilution of KRAS mutation-containing DNA shows mutation enrichment by 10- to 120-fold and detection of allelic fractions down to 0.01%. Multiplexed ND-NaME-PrO combined with multiplexed PCR-HRM showed mutation scanning of 10-20 DNA amplicons simultaneously. ND-NaME-PrO applied on cfDNA from clinical samples enables mutation enrichment and HRM scanning over 10 DNA targets. cfDNA mutations were enriched up to approximately 100-fold (average approximately 25-fold) and identified via targeted resequencing. CONCLUSIONS Closed-tube homogeneous ND-NaME-PrO combined with multiplexed HRM is a convenient approach to efficiently enrich for mutations on multiple DNA targets and to enable prescreening before targeted resequencing.
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Affiliation(s)
- Ioannis Ladas
- Department of Radiation Oncology, Dana-Farber Cancer Institute and Brigham and Women’s Hospital, Harvard Medical School, Boston, MA
| | - Mariana Fitarelli-Kiehl
- Department of Radiation Oncology, Dana-Farber Cancer Institute and Brigham and Women’s Hospital, Harvard Medical School, Boston, MA
| | - Chen Song
- Department of Radiation Oncology, Dana-Farber Cancer Institute and Brigham and Women’s Hospital, Harvard Medical School, Boston, MA
| | | | - Heather A. Parsons
- Department of Medical Oncology, Dana-Farber Cancer Institute and Brigham and Women’s Hospital, Harvard Medical School, Boston, MA
| | - Nancy U. Lin
- Department of Medical Oncology, Dana-Farber Cancer Institute and Brigham and Women’s Hospital, Harvard Medical School, Boston, MA
| | - Nikhil Wagle
- Department of Medical Oncology, Dana-Farber Cancer Institute and Brigham and Women’s Hospital, Harvard Medical School, Boston, MA
| | - G. Mike Makrigiorgos
- Department of Radiation Oncology, Dana-Farber Cancer Institute and Brigham and Women’s Hospital, Harvard Medical School, Boston, MA,Correspondence: G. Mike Makrigiorgos, Ph.D., Brigham and Women’s Hospital, Level L2, Radiation Therapy, 75 Francis Street, Boston, MA 02115., Tel: 617-525-7122. Fax: 617-582-6037,
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van de Ven AL, Tangutoori S, Baldwin P, Qiao J, Gharagouzloo C, Seitzer N, Clohessy JG, Makrigiorgos GM, Cormack R, Pandolfi PP, Sridhar S. Nanoformulation of Olaparib Amplifies PARP Inhibition and Sensitizes PTEN/TP53-Deficient Prostate Cancer to Radiation. Mol Cancer Ther 2017; 16:1279-1289. [PMID: 28500233 DOI: 10.1158/1535-7163.mct-16-0740] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Revised: 03/09/2017] [Accepted: 04/28/2017] [Indexed: 12/17/2022]
Abstract
The use of PARP inhibitors in combination with radiotherapy is a promising strategy to locally enhance DNA damage in tumors. Here we show that radiation-resistant cells and tumors derived from a Pten/Trp53-deficient mouse model of advanced prostate cancer are rendered radiation sensitive following treatment with NanoOlaparib, a lipid-based injectable nanoformulation of olaparib. This enhancement in radiosensitivity is accompanied by radiation dose-dependent changes in γ-H2AX expression and is specific to NanoOlaparib alone. In animals, twice-weekly intravenous administration of NanoOlaparib results in significant tumor growth inhibition, whereas previous studies of oral olaparib as monotherapy have shown no therapeutic efficacy. When NanoOlaparib is administered prior to radiation, a single dose of radiation is sufficient to triple the median mouse survival time compared to radiation only controls. Half of mice treated with NanoOlaparib + radiation achieved a complete response over the 13-week study duration. Using ferumoxytol as a surrogate nanoparticle, MRI studies revealed that NanoOlaparib enhances the intratumoral accumulation of systemically administered nanoparticles. NanoOlaparib-treated tumors showed up to 19-fold higher nanoparticle accumulation compared to untreated and radiation-only controls, suggesting that the in vivo efficacy of NanoOlaparib may be potentiated by its ability to enhance its own accumulation. Together, these data suggest that NanoOlaparib may be a promising new strategy for enhancing the radiosensitivity of radiation-resistant tumors lacking BRCA mutations, such as those with PTEN and TP53 deletions. Mol Cancer Ther; 16(7); 1279-89. ©2017 AACR.
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Affiliation(s)
- Anne L van de Ven
- Department of Physics, Northeastern University, Boston, Massachusetts.,Nanomedicine Science & Technology Center, Northeastern University, Boston, Massachusetts
| | - Shifalika Tangutoori
- Nanomedicine Science & Technology Center, Northeastern University, Boston, Massachusetts.,Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Paige Baldwin
- Nanomedicine Science & Technology Center, Northeastern University, Boston, Massachusetts.,Department of Bioengineering, Northeastern University, Boston, Massachusetts
| | - Ju Qiao
- Department of Mechanical and Industrial Engineering, Northeastern University, Boston, Massachusetts
| | - Codi Gharagouzloo
- Department of Bioengineering, Northeastern University, Boston, Massachusetts
| | - Nina Seitzer
- Cancer Research Institute, Beth Israel Deaconess Cancer Center, Boston, Massachusetts
| | - John G Clohessy
- Cancer Research Institute, Beth Israel Deaconess Cancer Center, Boston, Massachusetts
| | - G Mike Makrigiorgos
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Robert Cormack
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Pier Paolo Pandolfi
- Cancer Research Institute, Beth Israel Deaconess Cancer Center, Boston, Massachusetts
| | - Srinivas Sridhar
- Department of Physics, Northeastern University, Boston, Massachusetts. .,Nanomedicine Science & Technology Center, Northeastern University, Boston, Massachusetts.,Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
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28
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Guthier CV, D'Amico AV, King MT, Nguyen PL, Orio PF, Sridhar S, Makrigiorgos GM, Cormack RA. Focal Radiosensitization of Brachytherapy: Determining the Optimal Design of Drug Eluting Implants. Brachytherapy 2017. [DOI: 10.1016/j.brachy.2017.04.224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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29
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Liu Y, Song C, Ladas I, Fitarelli-Kiehl M, Makrigiorgos GM. Methylation-sensitive enrichment of minor DNA alleles using a double-strand DNA-specific nuclease. Nucleic Acids Res 2017; 45:e39. [PMID: 27903892 PMCID: PMC5389605 DOI: 10.1093/nar/gkw1166] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [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: 07/12/2016] [Accepted: 11/08/2016] [Indexed: 02/06/2023] Open
Abstract
Aberrant methylation changes, often present in a minor allelic fraction in clinical samples such as plasma-circulating DNA (cfDNA), are potentially powerful prognostic and predictive biomarkers in human disease including cancer. We report on a novel, highly-multiplexed approach to facilitate analysis of clinically useful methylation changes in minor DNA populations. Methylation Specific Nuclease-assisted Minor-allele Enrichment (MS-NaME) employs a double-strand-specific DNA nuclease (DSN) to remove excess DNA with normal methylation patterns. The technique utilizes oligonucleotide-probes that direct DSN activity to multiple targets in bisulfite-treated DNA, simultaneously. Oligonucleotide probes targeting unmethylated sequences generate local double stranded regions resulting to digestion of unmethylated targets, and leaving methylated targets intact; and vice versa. Subsequent amplification of the targeted regions results in enrichment of the targeted methylated or unmethylated minority-epigenetic-alleles. We validate MS-NaME by demonstrating enrichment of RARb2, ATM, MGMT and GSTP1 promoters in multiplexed MS-NaME reactions (177-plex) using dilutions of methylated/unmethylated DNA and in DNA from clinical lung cancer samples and matched normal tissue. MS-NaME is a highly scalable single-step approach performed at the genomic DNA level in solution that combines with most downstream detection technologies including Sanger sequencing, methylation-sensitive-high-resolution melting (MS-HRM) and methylation-specific-Taqman-based-digital-PCR (digital Methylight) to boost detection of low-level aberrant methylation-changes.
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Affiliation(s)
- Yibin Liu
- Department of Radiation Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Chen Song
- Department of Radiation Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Ioannis Ladas
- Department of Radiation Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Mariana Fitarelli-Kiehl
- Department of Radiation Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - G. Mike Makrigiorgos
- Department of Radiation Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA,To whom correspondence should be addressed. Tel: +1 617 525 7122; Fax: +1 617 582 6037;
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Ven ALVD, Tangutoori S, Baldwin P, Qiao J, Gharagouzloo C, Seitzer N, Clohessy J, Korideck H, Makrigiorgos GM, Cormack R, Pandolfi PP, Sridhar S. Abstract B48: Prostate cancer pre-treatment with nanoformulated Olaparib overcomes radiation resistance. Cancer Res 2017. [DOI: 10.1158/1538-7445.epso16-b48] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [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
Prostate cancers with PTEN deletions are promising candidates for DNA repair inhibitors such as olaparib and talazoparib. Here we show that radiation-resistant cells and tumors derived from Ptenpc-/-;Trp53pc-/- mice are rendered radiation-sensitive following pre-treatment with liposomal nanoOlaparib. This enhancement in radiosensitivity is accompanied by radiation dose-dependent changes in γ-H2AX expression and is specific to nanoformulated Olaparib alone. In animals, twice-weekly intravenous administration of nanoOlaparib alone results in significant tumor growth inhibition. When nanoOlaparib is administered prior to radiation, we find that a single dose of radiation is sufficient to increase mouse survival time by as much as 10 weeks (study duration = 13 weeks). Using ferumoxytol as a surrogate nanoparticle, magnetic resonance imaging (MRI) studies revealed that nanoOlaparib administration enhances the ability of nanoparticles to accumulate in tumors. Compared to untreated and radiation-only controls, nanoOlaparib-treated tumors showed 18-fold higher nanoparticle accumulation, suggesting that the in vivo efficacy of nanoOlaparib may be potentiated by its ability to enhance its own accumulation in tumors.
Citation Format: Anne L. van de Ven, Shifalika Tangutoori, Paige Baldwin, Ju Qiao, Codi Gharagouzloo, Nina Seitzer, John Clohessy, Houari Korideck, G. Mike Makrigiorgos, Robert Cormack, Pier Paolo Pandolfi, Srinivas Sridhar. Prostate cancer pre-treatment with nanoformulated Olaparib overcomes radiation resistance. [abstract]. In: Proceedings of the AACR Special Conference on Engineering and Physical Sciences in Oncology; 2016 Jun 25-28; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2017;77(2 Suppl):Abstract nr B48.
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Affiliation(s)
| | | | | | - Ju Qiao
- 1Northeastern University, Boston, MA,
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31
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Song C, Liu Y, Fontana R, Makrigiorgos A, Mamon H, Kulke MH, Makrigiorgos GM. Elimination of unaltered DNA in mixed clinical samples via nuclease-assisted minor-allele enrichment. Nucleic Acids Res 2016; 44:e146. [PMID: 27431322 PMCID: PMC5100565 DOI: 10.1093/nar/gkw650] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Revised: 06/27/2016] [Accepted: 07/10/2016] [Indexed: 12/13/2022] Open
Abstract
Presence of excess unaltered, wild-type (WT) DNA providing no information of biological or clinical value often masks rare alterations containing diagnostic or therapeutic clues in cancer, prenatal diagnosis, infectious diseases or organ transplantation. With the surge of high-throughput technologies there is a growing demand for removing unaltered DNA over large pools-of-sequences. Here we present nuclease-assisted minor-allele enrichment with probe-overlap (NaME-PrO), a single-step approach with broad genome coverage that can remove WT-DNA from numerous sequences simultaneously, prior to genomic analysis. NaME-PrO employs a double-strand-DNA-specific nuclease and overlapping oligonucleotide-probes interrogating WT-DNA targets and guiding nuclease digestion to these sites. Mutation-containing DNA creates probe-DNA mismatches that inhibit digestion, thus subsequent DNA-amplification magnifies DNA-alterations at all selected targets. We demonstrate several-hundred-fold mutation enrichment in diverse human samples on multiple clinically relevant targets including tumor samples and circulating DNA in 50-plex reactions. Enrichment enables routine mutation detection at 0.01% abundance while by adjusting conditions it is possible to sequence mutations down to 0.00003% abundance, or to scan tumor-suppressor genes for rare mutations. NaME-PrO introduces a simple and highly parallel process to remove un-informative DNA sequences and unmask clinically and biologically useful alterations.
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Affiliation(s)
- Chen Song
- Department of Radiation Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Yibin Liu
- Department of Radiation Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Rachel Fontana
- Department of Radiation Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Alexander Makrigiorgos
- Department of Radiation Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Harvey Mamon
- Department of Radiation Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Matthew H Kulke
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA
| | - G 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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32
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Detappe A, Kunjachan S, Sancey L, Motto-Ros V, Biancur D, Drane P, Guieze R, Makrigiorgos GM, Tillement O, Langer R, Berbeco R. Advanced multimodal nanoparticles delay tumor progression with clinical radiation therapy. J Control Release 2016; 238:103-113. [PMID: 27423325 DOI: 10.1016/j.jconrel.2016.07.021] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Revised: 06/29/2016] [Accepted: 07/12/2016] [Indexed: 11/28/2022]
Abstract
Radiation therapy is a major treatment regimen for more than 50% of cancer patients. The collateral damage induced on healthy tissues during radiation and the minimal therapeutic effect on the organ-of-interest (target) is a major clinical concern. Ultra-small, renal clearable, silica based gadolinium chelated nanoparticles (SiGdNP) provide simultaneous MR contrast and radiation dose enhancement. The high atomic number of gadolinium provides a large photoelectric cross-section for increased photon interaction, even for high-energy clinical radiation beams. Imaging and therapy functionality of SiGdNP were tested in cynomolgus monkeys and pancreatic tumor-bearing mice models, respectively. A significant improvement in tumor cell damage (double strand DNA breaks), growth suppression, and overall survival under clinical radiation therapy conditions were observed in a human pancreatic xenograft model. For the first time, safe systemic administration and systematic renal clearance was demonstrated in both tested species. These findings strongly support the translational potential of SiGdNP for MR-guided radiation therapy in cancer treatment.
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Affiliation(s)
- Alexandre Detappe
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02215, USA; Lyon-1 University, Institut Lumière Matière, CNRS UMR5306, Lyon, France
| | - Sijumon Kunjachan
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02215, USA
| | - Lucie Sancey
- Lyon-1 University, Institut Lumière Matière, CNRS UMR5306, Lyon, France
| | - Vincent Motto-Ros
- Lyon-1 University, Institut Lumière Matière, CNRS UMR5306, Lyon, France
| | - Douglas Biancur
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02215, USA
| | - Pascal Drane
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02215, USA
| | - Romain Guieze
- Division of Medical Oncology, Dana-Farber Cancer Institute, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02215, USA
| | - G Mike Makrigiorgos
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02215, USA
| | - Olivier Tillement
- Lyon-1 University, Institut Lumière Matière, CNRS UMR5306, Lyon, France
| | - Robert Langer
- Department of Chemical Engineering, David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Ross Berbeco
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02215, USA
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Herter-Sprie GS, Koyama S, Korideck H, Hai J, Deng J, Li YY, Buczkowski KA, Grant AK, Ullas S, Rhee K, Cavanaugh JD, Neupane NP, Christensen CL, Herter JM, Makrigiorgos GM, Hodi FS, Freeman GJ, Dranoff G, Hammerman PS, Kimmelman AC, Wong KK. Synergy of radiotherapy and PD-1 blockade in Kras-mutant lung cancer. JCI Insight 2016; 1:e87415. [PMID: 27699275 DOI: 10.1172/jci.insight.87415] [Citation(s) in RCA: 117] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Radiation therapy (RT), a critical modality in the treatment of lung cancer, induces direct tumor cell death and augments tumor-specific immunity. However, despite initial tumor control, most patients suffer from locoregional relapse and/or metastatic disease following RT. The use of immunotherapy in non-small-cell lung cancer (NSCLC) could potentially change this outcome by enhancing the effects of RT. Here, we report significant (up to 70% volume reduction of the target lesion) and durable (up to 12 weeks) tumor regressions in conditional Kras-driven genetically engineered mouse models (GEMMs) of NSCLC treated with radiotherapy and a programmed cell death 1 antibody (αPD-1). However, while αPD-1 therapy was beneficial when combined with RT in radiation-naive tumors, αPD-1 therapy had no antineoplastic efficacy in RT-relapsed tumors and further induced T cell inhibitory markers in this setting. Furthermore, there was differential efficacy of αPD-1 plus RT among Kras-driven GEMMs, with additional loss of the tumor suppressor serine/threonine kinase 11/liver kinase B1 (Stk11/Lkb1) resulting in no synergistic efficacy. Taken together, our data provide evidence for a close interaction among RT, T cells, and the PD-1/PD-L1 axis and underscore the rationale for clinical combinatorial therapy with immune modulators and radiotherapy.
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Affiliation(s)
- Grit S Herter-Sprie
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA.,Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA.,Lowe Center for Thoracic Oncology
| | - Shohei Koyama
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA.,Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA.,Cancer Vaccine Center
| | - Houari Korideck
- Division of Medical Physics and Biophysics, and.,Department of Radiation Oncology, Dana-Farber Cancer Institute, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Josephine Hai
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA.,Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA.,Lowe Center for Thoracic Oncology
| | - Jiehui Deng
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA.,Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA.,Lowe Center for Thoracic Oncology
| | - Yvonne Y Li
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA.,Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA.,Lowe Center for Thoracic Oncology
| | - Kevin A Buczkowski
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA.,Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA.,Lowe Center for Thoracic Oncology
| | - Aaron K Grant
- Division of MRI Research, Department of Radiology, and
| | - Soumya Ullas
- Longwood Small Animal Imaging Facility, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Kevin Rhee
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA.,Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA.,Lowe Center for Thoracic Oncology
| | - Jillian D Cavanaugh
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA.,Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA.,Lowe Center for Thoracic Oncology
| | - Neermala Poudel Neupane
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA.,Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA.,Lowe Center for Thoracic Oncology
| | - Camilla L Christensen
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA.,Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA.,Lowe Center for Thoracic Oncology
| | - Jan M Herter
- Center for Excellence in Vascular Biology, Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - G Mike Makrigiorgos
- Division of Medical Physics and Biophysics, and.,Department of Radiation Oncology, Dana-Farber Cancer Institute, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - F Stephen Hodi
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA.,Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Gordon J Freeman
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA.,Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA.,Cancer Vaccine Center
| | - Glenn Dranoff
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA.,Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA.,Cancer Vaccine Center
| | - Peter S Hammerman
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA.,Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA.,Lowe Center for Thoracic Oncology
| | - Alec C Kimmelman
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA.,Division of Genomic Stability and DNA Repair, Dana-Farber Cancer Institute, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Kwok-Kin Wong
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA.,Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA.,Cancer Vaccine Center.,Department of Radiation Oncology, Dana-Farber Cancer Institute, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
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Yasmin-Karim S, Moreau M, Kumar R, Makrigiorgos GM, Hanlon J, Arnoldussen M, Hempstead J, Celli J, Ngwa W. SU-G-TeP3-05: In Vitro Demonstration of Endothelial Dose Enhancement Due to Gold Nanoparticles During Low-Voltage Radiotherapy. Med Phys 2016. [DOI: 10.1118/1.4957085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
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Brivio D, Zygmanski P, Arnoldussen M, Hanlon J, Chell E, Sajo E, Makrigiorgos GM, Ngwa W. Kilovoltage radiosurgery with gold nanoparticles for neovascular age-related macular degeneration (AMD): a Monte Carlo evaluation. Phys Med Biol 2015; 60:9203-13. [PMID: 26576672 DOI: 10.1088/0031-9155/60/24/9203] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
This work uses Monte Carlo radiation transport simulation to assess the potential benefits of gold nanoparticles (AuNP) in the treatment of neovascular age-related macular degeneration with stereotactic radiosurgery. Clinically, a 100 kVp x-ray beam of 4 mm diameter is aimed at the macula to deliver an ablative dose in a single fraction. In the transport model, AuNP accumulated at the bottom of the macula are targeted with a source representative of the clinical beam in order to provide enhanced dose to the diseased macular endothelial cells. It is observed that, because of the AuNP, the dose to the endothelial cells can be significantly enhanced, allowing for greater sparing of optic nerve, retina and other neighboring healthy tissue. For 20 nm diameter AuNP concentration of 32 mg g(-1), which has been shown to be achievable in vivo, a dose enhancement ratio (DER) of 1.97 was found to be possible, which could potentially be increased through appropriate optimization of beam quality and/or AuNP targeting. A significant enhancement in dose is seen in the vicinity of the AuNP layer within 30 μm, peaked at the AuNP-tissue interface. Different angular tilting of the 4 mm beam results in a similar enhancement. The DER inside and in the penumbra of the 4 mm irradiation-field are almost the same while the actual delivered dose is more than one order of magnitude lower outside the field leading to normal tissue sparing. The prescribed dose to macular endothelial cells can be delivered using almost half of the radiation allowing reduction of dose to the neighboring organs such as retina/optic nerve by 49% when compared to a treatment without AuNP.
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Affiliation(s)
- D Brivio
- Brigham and Woman's Hospital, Harvard Medical School, Boston, MA, USA. Dana Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
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36
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Kunjachan S, Detappe A, Kumar R, Ireland T, Cameron L, Biancur DE, Motto-Ros V, Sancey L, Sridhar S, Makrigiorgos GM, Berbeco RI. Nanoparticle Mediated Tumor Vascular Disruption: A Novel Strategy in Radiation Therapy. Nano Lett 2015; 15:7488-96. [PMID: 26418302 PMCID: PMC5507193 DOI: 10.1021/acs.nanolett.5b03073] [Citation(s) in RCA: 88] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
More than 50% of all cancer patients receive radiation therapy. The clinical delivery of curative radiation dose is strictly restricted by the proximal healthy tissues. We propose a dual-targeting strategy using vessel-targeted-radiosensitizing gold nanoparticles and conformal-image guided radiation therapy to specifically amplify damage in the tumor neoendothelium. The resulting tumor vascular disruption substantially improved the therapeutic outcome and subsidized the radiation/nanoparticle toxicity, extending its utility to intransigent or nonresectable tumors that barely respond to standard therapies.
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Affiliation(s)
- Sijumon Kunjachan
- Department of Radiation Oncology, Brigham and Women’s Hospital, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Alexandre Detappe
- Department of Radiation Oncology, Brigham and Women’s Hospital, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts 02115, United States
- Institut Lumière Matière, Université Claude Bernard Lyon1-CNRS, Université de Lyon, 69007 Lyon, France
| | - Rajiv Kumar
- Department of Radiation Oncology, Brigham and Women’s Hospital, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts 02115, United States
- Nanomedicine Science and Technology Center and Department of Physics, Northeastern University, Boston, Massachusetts 02115, United States
| | - Thomas Ireland
- LA-ICP-MS and ICP-ES Laboratories, Boston University, Boston, Massachusetts 02215, United States
| | - Lisa Cameron
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, United States
| | - Douglas E. Biancur
- Department of Radiation Oncology, Brigham and Women’s Hospital, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Vincent Motto-Ros
- Institut Lumière Matière, Université Claude Bernard Lyon1-CNRS, Université de Lyon, 69007 Lyon, France
| | - Lucie Sancey
- Institut Lumière Matière, Université Claude Bernard Lyon1-CNRS, Université de Lyon, 69007 Lyon, France
| | - Srinivas Sridhar
- Department of Radiation Oncology, Brigham and Women’s Hospital, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts 02115, United States
- Nanomedicine Science and Technology Center and Department of Physics, Northeastern University, Boston, Massachusetts 02115, United States
| | - G. Mike Makrigiorgos
- Department of Radiation Oncology, Brigham and Women’s Hospital, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Ross I. Berbeco
- Department of Radiation Oncology, Brigham and Women’s Hospital, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts 02115, United States
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Ngwa W, Ngoma T, Zietman A, Mayr N, Elzawawy A, Winningham TA, Balogun O, Enwerem-Bromson N, Ntizimira C, Olopade OI, Oluwole D, Odedina F, Williams M, Flanigan J, Asana L, Ngwa K, Avery S, Pollard JM, Roland T, Funwi-gabga N, Mbarika V, Hardenbergh P, Winkfield K, Pipman Y, Stefan C, Ngoma M, Mohammed S, Katz M, Erno S, Moni J, Fitzgerald T, Tonlaar N, Efstathiou J, Gierga D, Ayo C, Knaul F, Gospodarowicz M, Makrigiorgos GM, Nguyen PL. Closing the Cancer Divide Through Ubuntu: Information and Communication Technology-Powered Models for Global Radiation Oncology. Int J Radiat Oncol Biol Phys 2015; 94:440-9. [PMID: 26867873 DOI: 10.1016/j.ijrobp.2015.10.063] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2015] [Revised: 10/28/2015] [Accepted: 10/29/2015] [Indexed: 10/22/2022]
Affiliation(s)
- Wilfred Ngwa
- Department of Radiation Oncology, Dana Farber Cancer Institute, Brigham and Women's Hospital, and Harvard Medical School, Boston, Massachusetts; Department of Physics and Applied Physics, University of Massachusetts Lowell, Lowell, Massachusetts.
| | - Twalib Ngoma
- Department of Clinical Oncology, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - Anthony Zietman
- Department of Radiation Oncology, University of Washington School of Medicine, Seattle, Washington
| | - Nina Mayr
- Department of Radiation Oncology, Massachusetts General Hospital, and Harvard Medical School, Boston, Massachusetts
| | - Ahmed Elzawawy
- African Organization for Research and Training in Cancer, Rondebosch, South Africa
| | | | - Onyinye Balogun
- Department of Radiation Oncology, Weill Cornell Medical College, New York
| | - Nelly Enwerem-Bromson
- Program of Action for Cancer Therapy, International Atomic Energy Agency, Vienna, Austria
| | | | | | | | - Folakemi Odedina
- African Organization for Research and Training in Cancer, Rondebosch, South Africa; College of Pharmacy, University of Florida, Gainesville, Florida
| | - Makeda Williams
- Center for Global Health, National Cancer Institute, Rockville, Maryland
| | - John Flanigan
- Center for Global Health, National Cancer Institute, Rockville, Maryland
| | - Lydia Asana
- African Renaissance Ambassador Corporation, Orlando, Florida
| | - Kenneth Ngwa
- African Renaissance Ambassador Corporation, Orlando, Florida
| | - Stephen Avery
- Department of Radiation Oncology, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Julianne M Pollard
- Department of Radiation Physics, University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Teboh Roland
- Department of Radiation Oncology, Johns Hopkins University, Baltimore, Maryland
| | - Neba Funwi-gabga
- Southern Alberta Institute of Technology, Calgary, Alberta, Canada
| | - Victor Mbarika
- Information and Communication Technology University, Baton Rouge, Louisiana
| | | | - Karen Winkfield
- Department of Radiation Oncology, University of Washington School of Medicine, Seattle, Washington
| | - Yakov Pipman
- International Educational Activities Committee, American Association of Physicists in Medicine, College Park, Maryland
| | - Christina Stefan
- African Organization for Research and Training in Cancer, Rondebosch, South Africa; South African Medical Research Council, Cape Town, South Africa
| | - Mamsau Ngoma
- Ocean Road Cancer Institute, Dar Es Salaam, Tanzania
| | - Sulma Mohammed
- Department of Comparative Pathobiology and Purdue University Center for Cancer Research, Purdue University, West Lafayette, Indiana
| | | | - Sajo Erno
- Department of Physics and Applied Physics, University of Massachusetts Lowell, Lowell, Massachusetts
| | - Janaki Moni
- Department of Radiation Oncology, University of Massachusetts Medical School, Worcester, Massachusetts
| | - Thomas Fitzgerald
- Department of Radiation Oncology, University of Massachusetts Medical School, Worcester, Massachusetts
| | | | - Jason Efstathiou
- Department of Radiation Oncology, University of Washington School of Medicine, Seattle, Washington
| | - David Gierga
- Department of Radiation Oncology, University of Washington School of Medicine, Seattle, Washington
| | | | - Felicia Knaul
- Harvard Global Equity Initiative, Harvard Medical School, Boston, Massachusetts
| | - Mary Gospodarowicz
- Princess Margaret Cancer Centre, 610 University Avenue, M5G 2M9, Toronto, ON, Canada; Department of Radiation Oncology, University of Toronto, Toronto, ON, Canada
| | - G Mike Makrigiorgos
- Department of Radiation Oncology, Dana Farber Cancer Institute, Brigham and Women's Hospital, and Harvard Medical School, Boston, Massachusetts
| | - Paul L Nguyen
- Department of Radiation Oncology, Dana Farber Cancer Institute, Brigham and Women's Hospital, and Harvard Medical School, Boston, Massachusetts
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Song C, Castellanos-Rizaldos E, Bejar R, Ebert BL, Makrigiorgos GM. DMSO Increases Mutation Scanning Detection Sensitivity of High-Resolution Melting in Clinical Samples. Clin Chem 2015; 61:1354-62. [PMID: 26432802 DOI: 10.1373/clinchem.2015.245357] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2015] [Accepted: 08/17/2015] [Indexed: 02/02/2023]
Abstract
BACKGROUND Mutation scanning provides the simplest, lowest-cost method for identifying DNA variations on single PCR amplicons, and it may be performed before sequencing to avoid screening of noninformative wild-type samples. High-resolution melting (HRM) is the most commonly used method for mutation scanning. With PCR-HRM, however, mutations less abundant than approximately 3%-10% that can still be clinically significant may often be missed. Therefore, enhancing HRM detection sensitivity is important for mutation scanning and its clinical application. METHODS We used serial dilution of cell lines containing the TP53 exon 8 mutation to demonstrate the improvement in detection sensitivity for conventional-PCR-HRM in the presence of DMSO. We also conducted coamplification at lower denaturation temperature (COLD)-PCR with an extra step for cross-hybridization, followed by preferential denaturation and amplification at optimized critical temperature (full-COLD-PCR), to further enrich low-level mutations before HRM with or without DMSO, and we used droplet-digital PCR to derive the optimal conditions for mutation enrichment. Both conventional PCR-HRM and full-COLD-PCR-HRM with and without DMSO were used for mutation scanning of TP53 exon 8 in cancer samples containing known mutations and myelodysplastic syndrome samples with unknown mutations. Mutations in other genes were also examined. RESULTS The detection sensitivity of PCR-HRM scanning increases 2- to 5-fold in the presence of DMSO, depending on mutation type and sequence context, and can typically detect mutation abundance of approximately 1%. When mutation enrichment is applied during amplification with full-COLD-PCR followed by HRM in the presence of DMSO, mutations with 0.2%-0.3% abundance in TP53 exon 8 can be detected. CONCLUSIONS DMSO improves HRM mutation scanning sensitivity with saturating dyes. When full-COLD-PCR is used, followed by DMSO-HRM, the overall improvement is about 20-fold compared with conventional PCR-HRM.
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Affiliation(s)
- Chen Song
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| | - Elena Castellanos-Rizaldos
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| | - Rafael Bejar
- Division of Hematology and Oncology, UCSD Moores Cancer Center, La Jolla, CA
| | - Benjamin L Ebert
- Division of Hematology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| | - G Mike Makrigiorgos
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Brigham and Women's Hospital, Harvard Medical School, Boston, MA;
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Ngwa W, Kumar R, Sridhar S, Korideck H, Zygmanski P, Cormack RA, Berbeco R, Makrigiorgos GM. Targeted radiotherapy with gold nanoparticles: current status and future perspectives. Nanomedicine (Lond) 2015; 9:1063-82. [PMID: 24978464 DOI: 10.2217/nnm.14.55] [Citation(s) in RCA: 112] [Impact Index Per Article: 12.4] [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: 12/12/2022] Open
Abstract
Radiation therapy (RT) is the treatment of cancer and other diseases with ionizing radiation. The ultimate goal of RT is to destroy all the disease cells while sparing healthy tissue. Towards this goal, RT has advanced significantly over the past few decades in part due to new technologies including: multileaf collimator-assisted modulation of radiation beams, improved computer-assisted inverse treatment planning, image guidance, robotics with more precision, better motion management strategies, stereotactic treatments and hypofractionation. With recent advances in nanotechnology, targeted RT with gold nanoparticles (GNPs) is actively being investigated as a means to further increase the RT therapeutic ratio. In this review, we summarize the current status of research and development towards the use of GNPs to enhance RT. We highlight the promising emerging modalities for targeted RT with GNPs and the corresponding preclinical evidence supporting such promise towards potential clinical translation. Future prospects and perspectives are discussed.
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Affiliation(s)
- Wilfred Ngwa
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Brigham & Women's Hospital & Harvard Medical School, Boston, MA 02215, USA
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Abstract
This work investigates the dosimetric feasibility of employing gold nanoparticles (AuNPs) or carboplatin nano-particles (CNPs) to enhance radiotherapy (RT) treatment efficacy for ocular cancers: retinoblastoma (Rb) and choroidal melanoma (CM), during kV-energy internal and external beam radiotherapy. The results predict that substantial dose enhancement may be achieved by employing AuNPs or CNPs in conjunction with radiotherapy for ocular cancer using kV-energy photon beams. Brachytherapy sources yield higher dose enhancement than the external beam in kV energy range. However, the external beam has the advantage of being non-invasive.
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Affiliation(s)
| | - Erno Sajo
- University of Massachusetts Lowell, Lowell, MA, USA
| | - G Mike Makrigiorgos
- Department of Radiation Oncology, Brigham and Women's Hospital, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA USA
| | - Ross I Berbeco
- Department of Radiation Oncology, Brigham and Women's Hospital, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA USA
| | - Wilfred Ngwa
- University of Massachusetts Lowell, Lowell, MA, USA; Department of Radiation Oncology, Brigham and Women's Hospital, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA USA
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41
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Sinha N, Cifter G, Sajo E, Kumar R, Sridhar S, Nguyen PL, Cormack RA, Makrigiorgos GM, Ngwa W. Brachytherapy application with in situ dose painting administered by gold nanoparticle eluters. Int J Radiat Oncol Biol Phys 2014; 91:385-92. [PMID: 25482302 DOI: 10.1016/j.ijrobp.2014.10.001] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2014] [Revised: 09/24/2014] [Accepted: 10/01/2014] [Indexed: 10/24/2022]
Abstract
PURPOSE Recent studies show promise that administering gold nanoparticles (GNP) to tumor cells during brachytherapy could significantly enhance radiation damage to the tumor. A new strategy proposed for sustained administration of the GNP in prostate tumors is to load them into routinely used brachytherapy spacers for customizable in situ release after implantation. This in silico study investigated the intratumor biodistribution and corresponding dose enhancement over time due to GNP released from such GNP-loaded brachytherapy spacers (GBS). METHOD AND MATERIALS An experimentally determined intratumoral diffusion coefficient (D) for 10-nm nanoparticles was used to estimate D for other sizes by using the Stokes-Einstein equation. GNP concentration profiles, obtained using D, were then used to calculate the corresponding dose enhancement factor (DEF) for each tumor voxel, using dose painting-by-numbers approach, for times relevant to the considered brachytherapy sources' lifetimes. The investigation was carried out as a function of GNP size for the clinically applicable low-dose-rate brachytherapy sources iodine-125 (I-125), palladium-103 (Pd-103), and cesium-131 (Cs-131). RESULTS Results showed that dose enhancement to tumor voxels and subvolumes during brachytherapy can be customized by varying the size of GNP released or eluted from the GBS. For example, using a concentration of 7 mg/g GNP, significant DEF (>20%) could be achieved 5 mm from a GBS after 5, 12, 25, 46, 72, 120, and 195 days, respectively, for GNP sizes of 2, 5, 10, 20, 30, and 50 nm and for 80 nm when treating with I-125. CONCLUSIONS Analyses showed that using Cs-131 provides the highest dose enhancement to tumor voxels. However, given its relatively longer half-life, I-125 presents the most flexibility for customizing the dose enhancement as a function of GNP size. These findings provide a useful reference for further work toward development of potential new brachytherapy application with in situ dose painting administered via gold nanoparticle eluters for prostate cancer.
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Affiliation(s)
- Neeharika Sinha
- Department of Sciences, Wentworth Institute of Technology, Boston, Massachusetts
| | - Gizem Cifter
- Department of Physics and Applied Physics, University of Massachusetts, Lowell, Massachusetts; Department of Radiation Oncology, Dana-Farber Cancer Institute, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Erno Sajo
- Department of Physics and Applied Physics, University of Massachusetts, Lowell, Massachusetts
| | - Rajiv Kumar
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts; Electronic Materials Research Institute and Department of Physics, Northeastern University, Boston, Massachusetts
| | - Srinivas Sridhar
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts; Electronic Materials Research Institute and Department of Physics, Northeastern University, Boston, Massachusetts
| | - Paul L Nguyen
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Robert A Cormack
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | - G Mike Makrigiorgos
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Wilfred Ngwa
- Department of Physics and Applied Physics, University of Massachusetts, Lowell, Massachusetts; Department of Radiation Oncology, Dana-Farber Cancer Institute, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts.
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Affiliation(s)
- Derek M Murphy
- Department of Radiation Oncology Dana Farber Cancer Institute Brigham and Women's Hospital Harvard Medical School Boston MA
| | - Elena Castellanos-Rizaldos
- Department of Radiation Oncology Dana Farber Cancer Institute Brigham and Women's Hospital Harvard Medical School Boston MA
| | - G Mike Makrigiorgos
- Department of Radiation Oncology Dana Farber Cancer Institute Brigham and Women's Hospital Harvard Medical School Boston MA
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Castellanos-Rizaldos E, Milbury CA, Guha M, Makrigiorgos GM. COLD-PCR enriches low-level variant DNA sequences and increases the sensitivity of genetic testing. Methods Mol Biol 2014; 1102:623-39. [PMID: 24259002 DOI: 10.1007/978-1-62703-727-3_33] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Abstract
Detection of low-level mutations is important for cancer biomarker and therapy targets discovery, but reliable detection remains a technical challenge. The newly developed method of CO-amplification at Lower Denaturation temperature PCR (COLD-PCR) helps to circumvent this issue. This PCR-based technology preferentially enriches minor known or unknown variants present in samples with a high background of wild type DNA which often hampers the accurate identification of these minority alleles. This is a simple process that consists of lowering the temperature at the denaturation step during the PCR-cycling protocol (critical denaturation temperature, T c) and inducing DNA heteroduplexing during an intermediate step. COLD-PCR in its simplest forms does not need additional reagents or specific instrumentation and thus, can easily replace conventional PCR and at the same time improve the mutation detection sensitivity limit of downstream technologies. COLD-PCR can be applied in two basic formats: fast-COLD-PCR that can enrich T m-reducing mutations and full-COLD-PCR that can enrich all mutations, though it requires an intermediate cross-hybridization step that lengthens the thermocycling program. An improved version of full-COLD-PCR (improved and complete enrichment, ice-COLD-PCR) has also been described. Finally, most recently, we developed yet another form of COLD-PCR, temperature-tolerant-COLD-PCR, which gradually increases the denaturation temperature during the COLD-PCR reaction, enriching diverse targets using a single cycling program. This report describes practical considerations for application of fast-, full-, ice-, and temperature-tolerant-COLD-PCR for enrichment of mutations prior to downstream screening.
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Affiliation(s)
- Elena Castellanos-Rizaldos
- Division of DNA Repair and Genome Stability, Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
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Guha M, Castellanos-Rizaldos E, Makrigiorgos GM. DISSECT Method Using PNA-LNA Clamp Improves Detection of EGFR T790m Mutation. PLoS One 2013; 8:e67782. [PMID: 23805327 PMCID: PMC3689726 DOI: 10.1371/journal.pone.0067782] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2013] [Accepted: 05/22/2013] [Indexed: 11/19/2022] Open
Abstract
Non-small cell lung cancer (NSCLC) patients treated with small molecule EGFR inhibitors, such as gefitinib, frequently develop drug resistance due to the presence of secondary mutations like the T790M mutation on EGFR exon 20. These mutations may originate from small subclonal populations in the primary tumor that become dominant later on during treatment. In order to detect these low-level DNA variations in the primary tumor or to monitor their progress in plasma, it is important to apply reliable and sensitive mutation detection methods. Here, we combine two recently developed methodologies, Differential Strand Separation at Critical Temperature (DISSECT), with peptide nucleic acid-locked nucleic acid (PNA-LNA) polymerase chain reaction (PCR) for the detection of T790M EGFR mutation. DISSECT pre-enriches low-abundance T790M EGFR mutations from target DNA prior to implementing PNA-LNA PCR, a method that can detect 1 mutant allele in a background of 100–1000 wild type alleles. The combination of DISSECT and PNA-LNA PCR enables the detection of 1 mutant allele in a background of 10,000 wild type alleles. The combined DISSECT-PNA-LNA PCR methodology is amenable to adaptation for the sensitive detection of additional emerging resistance mutations in cancer.
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Affiliation(s)
- Minakshi Guha
- Division of DNA Repair and Genome Stability, Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Elena Castellanos-Rizaldos
- Division of DNA Repair and Genome Stability, Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, United States of America
| | - G. Mike Makrigiorgos
- Division of DNA Repair and Genome Stability, Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, United States of America
- Division of Medical Physics and Biophysics, Department of Radiation Oncology, Dana-Farber Cancer Institute, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- * E-mail:
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Guha M, Castellanos-Rizaldos E, Liu P, Mamon H, Makrigiorgos GM. Differential strand separation at critical temperature: a minimally disruptive enrichment method for low-abundance unknown DNA mutations. Nucleic Acids Res 2012; 41:e50. [PMID: 23258702 PMCID: PMC3561944 DOI: 10.1093/nar/gks1250] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [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] [Indexed: 02/05/2023] Open
Abstract
Detection of low-level DNA variations in the presence of wild-type DNA is important in several fields of medicine, including cancer, prenatal diagnosis and infectious diseases. PCR-based methods to enrich mutations during amplification have limited multiplexing capability, are mostly restricted to known mutations and are prone to polymerase or mis-priming errors. Here, we present Differential Strand Separation at Critical Temperature (DISSECT), a method that enriches unknown mutations of targeted DNA sequences purely based on thermal denaturation of DNA heteroduplexes without the need for enzymatic reactions. Target DNA is pre-amplified in a multiplex reaction and hybridized onto complementary probes immobilized on magnetic beads that correspond to wild-type DNA sequences. Presence of any mutation on the target DNA forms heteroduplexes that are subsequently denatured from the beads at a critical temperature and selectively separated from wild-type DNA. We demonstrate multiplexed enrichment by 100- to 400-fold for KRAS and TP53 mutations at multiple positions of the targeted sequence using two to four successive cycles of DISSECT. Cancer and plasma-circulating DNA samples containing traces of mutations undergo mutation enrichment allowing detection via Sanger sequencing or high-resolution melting. The simplicity, scalability and reliability of DISSECT make it a powerful method for mutation enrichment that integrates well with existing downstream detection methods.
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Affiliation(s)
- Minakshi Guha
- Division of DNA Repair and Genome Stability, Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
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Castellanos-Rizaldos E, Milbury CA, Makrigiorgos GM. Enrichment of mutations in multiple DNA sequences using COLD-PCR in emulsion. PLoS One 2012; 7:e51362. [PMID: 23236486 PMCID: PMC3516544 DOI: 10.1371/journal.pone.0051362] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2012] [Accepted: 11/01/2012] [Indexed: 01/04/2023] Open
Abstract
Background Multiplex detection of low-level mutant alleles in the presence of wild-type DNA would be useful for several fields of medicine including cancer, pre-natal diagnosis and infectious diseases. COLD-PCR is a recently developed method that enriches low-level mutations during PCR cycling, thus enhancing downstream detection without the need for special reagents or equipment. The approach relies on the differential denaturation of DNA strands which contain Tm-lowering mutations or mismatches, versus ‘homo-duplex’ wild-type DNA. Enabling multiplex-COLD-PCR that can enrich mutations in several amplicons simultaneously is desirable but technically difficult to accomplish. Here we describe the proof of principle of an emulsion-PCR based approach that demonstrates the feasibility of multiplexed-COLD-PCR within a single tube, using commercially available mutated cell lines. This method works best with short amplicons; therefore, it could potentially be used on highly fragmented samples obtained from biological material or FFPE specimens. Methods Following a multiplex pre-amplification of TP53 exons from genomic DNA, emulsions which incorporate the multiplex product, PCR reagents and primers specific for a given TP53 exon are prepared. Emulsions with different TP53 targets are then combined in a single tube and a fast-COLD-PCR program that gradually ramps up the denaturation temperature over several PCR cycles is applied (temperature-tolerant, TT-fast-eCOLD-PCR). The range of denaturation temperatures applied encompasses the critical denaturation temperature (Tc) corresponding to all the amplicons included in the reaction, resulting to a gradual enrichment of mutations within all amplicons encompassed by emulsion. Results Validation for TT-fast-eCOLD-PCR is provided for TP53 exons 6–9. Using dilutions of mutated cell-line into wild-type DNA, we demonstrate simultaneous mutation enrichment between 7 to 15-fold in all amplicons examined. Conclusions TT-fast-eCOLD-PCR expands the versatility of COLD-PCR and enables high-throughput enrichment of low-level mutant alleles over multiple sequences in a single tube.
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Affiliation(s)
- Elena Castellanos-Rizaldos
- Division of DNA Repair and Genome Stability, Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Coren Audrey Milbury
- Division of DNA Repair and Genome Stability, Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, United States of America
| | - G. Mike Makrigiorgos
- Division of DNA Repair and Genome Stability, Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, United States of America
- Division of Medical Physics and Biophysics, Department of Radiation Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- * E-mail:
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Berbeco RI, Korideck H, Ngwa W, Kumar R, Patel J, Sridhar S, Johnson S, Price BD, Kimmelman A, Makrigiorgos GM. DNA damage enhancement from gold nanoparticles for clinical MV photon beams. Radiat Res 2012; 178:604-8. [PMID: 23148509 DOI: 10.1667/rr3001.1] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
In this study, we quantify the relative damage enhancement due to the presence of gold nanoparticles (GNP) in vitro in a clinical 6 MV beam for various delivery parameters and depths. It is expected that depths and delivery modes that produce a larger proportions of low-energy photons will have a larger effect on the cell samples containing GNP. HeLa cells with and without 50 nm GNP were irradiated at depths of 1.5, 5, 10, 15 and 20 cm. Conventional beams with square aperture sizes 5, 10 and 15 cm at isocenter, and flattening filter free (FFF) beams were used. Relative DNA damage enhancement with GNP was evaluated by γ-H2AX staining. Statistically significant increases in DNA damage with GNP, compared to the absence of GNP, were observed for all depths and delivery modes. Relative to the shallowest depth, damage enhancement was observed to increase as a function of increasing depth for all deliveries. For the conventional (open field) delivery, DNA damage enhancement with GNP was seen to increase as a function of field size. For FFF delivery, a substantial increase in enhancement was found relative to the conventional field delivery. The measured relative DNA damage enhancement validates the theoretically predicted trends as a function of depth and delivery mode for clinical MV photon beams. The results of this study open new possibilities for the clinical development of gold nanoparticle-aided radiation therapy.
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Affiliation(s)
- Ross I Berbeco
- Department of Radiation Oncology, Division of Medical Physics and Biophysics, Brigham and Women's Hospital, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts, USA.
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Ngwa W, Korideck H, Kassis AI, Kumar R, Sridhar S, Makrigiorgos GM, Cormack RA. In vitro radiosensitization by gold nanoparticles during continuous low-dose-rate gamma irradiation with I-125 brachytherapy seeds. Nanomedicine 2012; 9:25-7. [PMID: 23041410 DOI: 10.1016/j.nano.2012.09.001] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2012] [Revised: 09/04/2012] [Accepted: 09/08/2012] [Indexed: 11/26/2022]
Abstract
UNLABELLED This communication reports the first experimental evidence of gold nanoparticle (AuNP) radiosensitization during continuous low-dose-rate (LDR) gamma irradiation with low-energy brachytherapy sources. HeLa cell cultures incubated with and without AuNP were irradiated with an I-125 seed plaque designed to produce a relatively homogeneous dose distribution in the plane of the cell culture slide. Four sets of irradiation experiments were conducted at low-dose rates ranging from 2.1 to 4.5cGy/h. Residual γH2AX was measured 24h after irradiation and used to compare radiation damage to the cells with and without AuNP. The data demonstrate that the biological effect when irradiating in the presence of 0.2mg/ml concentration of AuNP is about 70%-130% greater than without AuNP. Meanwhile, without radiation, the AuNP showed minimal effect on the cancer cells. These findings provide in vitro evidence that AuNP may be employed as radiosensitizers during continuous LDR brachytherapy. FROM THE CLINICAL EDITOR In this basic science paper, the application of gold nanoparticles as radiosensitizing agents for low dose rate gamma radiation therapy is discussed, demonstrating efficacy in cell culture models.
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Affiliation(s)
- Wilfred Ngwa
- Department of Radiation Oncology, Dana-Farber Cancer Institute, and Harvard Medical School, Boston, MA 02115, USA.
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Ngwa W, Makrigiorgos GM, Berbeco RI. Gold nanoparticle enhancement of stereotactic radiosurgery for neovascular age-related macular degeneration. Phys Med Biol 2012; 57:6371-80. [PMID: 22995994 DOI: 10.1088/0031-9155/57/20/6371] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Age-related macular degeneration (AMD) is the leading cause of blindness in developed countries for people over the age of 50. In this work, the dosimetric feasibility of using gold nanoparticles (AuNP) as radiosensitizers to enhance kilovoltage stereotactic radiosurgery for neovascular AMD is investigated. Microdosimetry calculations at the sub-cellular level were carried out to estimate the radiation dose enhancement to individual nuclei in neovascular AMD endothelial cells (nDEF) due to photon-induced photo-/Auger electrons from x-ray-irradiated AuNP. The nDEF represents the ratio of radiation doses to the endothelial cell nuclei with and without AuNP. The calculations were carried out for a range of feasible AuNP local concentrations using the clinically applicable 100 kVp x-ray beam parameters employed by a commercially available x-ray therapy system. The results revealed nDEF values of 1.30-3.26 for the investigated concentration range of 1-7 mg g(-1), respectively. In comparison, for the same concentration range, nDEF values of 1.32-3.40, 1.31-3.33, 1.29-3.19, 1.28-3.12 were calculated for 80, 90, 110 and 120 kVp x-rays, respectively. Meanwhile, calculations as a function of distance from the AuNP showed that the dose enhancement, for 100 kVp, is markedly confined to the targeted neovascular AMD endothelial cells where AuNP are localized. These findings provide impetus for considering the application of AuNP to enhance therapeutic efficacy during stereotactic radiosurgery for neovascular AMD.
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Affiliation(s)
- Wilfred Ngwa
- Department of Radiation Oncology, Division of Medical Physics and Biophysics, Brigham and Women's Hospital, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA 02115, USA.
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Castellanos-Rizaldos E, Liu P, Milbury CA, Guha M, Brisci A, Cremonesi L, Ferrari M, Mamon H, Makrigiorgos GM. Temperature-tolerant COLD-PCR reduces temperature stringency and enables robust mutation enrichment. Clin Chem 2012; 58:1130-8. [PMID: 22587896 DOI: 10.1373/clinchem.2012.183095] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
BACKGROUND Low-level mutations in clinical tumor samples often reside below mutation detection limits, thus leading to false negatives that may impact clinical diagnosis and patient management. COLD-PCR (coamplification at lower denaturation temperature PCR) is a technology that magnifies unknown mutations during PCR, thus enabling downstream mutation detection. However, a practical difficulty in applying COLD-PCR has been the requirement for strict control of the denaturation temperature for a given sequence, to within ±0.3 °C. This requirement precludes simultaneous mutation enrichment in sequences of substantially different melting temperature (T(m)) and limits the technique to a single sequence at a time. We present a temperature-tolerant (TT) approach (TT-COLD-PCR) that reduces this obstacle. METHODS We describe thermocycling programs featuring a gradual increase of the denaturation temperature during COLD-PCR. This approach enabled enrichment of mutations when the cycling achieves the appropriate critical denaturation temperature of each DNA amplicon that is being amplified. Validation was provided for KRAS (v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog) and TP53 (tumor protein p53) exons 6-9 by use of dilutions of mutated DNA, clinical cancer samples, and plasma-circulating DNA. RESULTS A single thermocycling program with a denaturation-temperature window of 2.5-3.0 °C enriches mutations in all DNA amplicons simultaneously, despite their different T(m)s. Mutation enrichments of 6-9-fold were obtained with TT-full-COLD-PCR. Higher mutation enrichments were obtained for the other 2 forms of COLD-PCR, fast-COLD-PCR, and ice-COLD-PCR. CONCLUSIONS Low-level mutations in diverse amplicons with different T(m)s can be mutation enriched via TT-COLD-PCR provided that their T(m)s fall within the denaturation-temperature window applied during amplification. This approach enables simultaneous enrichment of mutations in several amplicons and increases significantly the versatility of COLD-PCR.
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Affiliation(s)
- E Castellanos-Rizaldos
- Division of DNA Repair and Genome Stability, Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
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