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Alba-Bernal A, Godoy-Ortiz A, Domínguez-Recio ME, López-López E, Quirós-Ortega ME, Sánchez-Martín V, Roldán-Díaz MD, Jiménez-Rodríguez B, Peralta-Linero J, Bellagarza-García E, Troyano-Ramos L, Garrido-Ruiz G, Hierro-Martín MI, Vicioso L, González-Ortiz Á, Linares-Valencia N, Velasco-Suelto J, Carbajosa G, Garrido-Aranda A, Lavado-Valenzuela R, Álvarez M, Pascual J, Comino-Méndez I, Alba E. Increased blood draws for ultrasensitive ctDNA and CTCs detection in early breast cancer patients. NPJ Breast Cancer 2024; 10:36. [PMID: 38750090 PMCID: PMC11096188 DOI: 10.1038/s41523-024-00642-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2023] [Accepted: 05/01/2024] [Indexed: 05/18/2024] Open
Abstract
Early breast cancer patients often experience relapse due to residual disease after treatment. Liquid biopsy is a methodology capable of detecting tumor components in blood, but low concentrations at early stages pose challenges. To detect them, next-generation sequencing has promise but entails complex processes. Exploring larger blood volumes could overcome detection limitations. Herein, a total of 282 high-volume plasma and blood-cell samples were collected for dual ctDNA/CTCs detection using a single droplet-digital PCR assay per patient. ctDNA and/or CTCs were detected in 100% of pre-treatment samples. On the other hand, post-treatment positive samples exhibited a minimum variant allele frequency of 0.003% for ctDNA and minimum cell number of 0.069 CTCs/mL of blood, surpassing previous investigations. Accurate prediction of residual disease before surgery was achieved in patients without a complete pathological response. A model utilizing ctDNA dynamics achieved an area under the ROC curve of 0.92 for predicting response. We detected disease recurrence in blood in the three patients who experienced a relapse, anticipating clinical relapse by 34.61, 9.10, and 7.59 months. This methodology provides an easily implemented alternative for ultrasensitive residual disease detection in early breast cancer patients.
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Affiliation(s)
- Alfonso Alba-Bernal
- Unidad de Gestion Clinica Intercentros de Oncologia Medica, Hospitales Universitarios Regional y Virgen de la Victoria, 29010, Malaga, Spain
- The Biomedical Research Institute of Málaga (IBIMA-CIMES-UMA), 29010, Malaga, Spain
- Andalusia-Roche Network in Precision Medical Oncology, 41092, Sevilla, Spain
| | - Ana Godoy-Ortiz
- Unidad de Gestion Clinica Intercentros de Oncologia Medica, Hospitales Universitarios Regional y Virgen de la Victoria, 29010, Malaga, Spain
- The Biomedical Research Institute of Málaga (IBIMA-CIMES-UMA), 29010, Malaga, Spain
- Centro de Investigacion Biomedica en Red de Cancer (CIBERONC - CB16/12/00481), 28029, Madrid, Spain
| | - María Emilia Domínguez-Recio
- Unidad de Gestion Clinica Intercentros de Oncologia Medica, Hospitales Universitarios Regional y Virgen de la Victoria, 29010, Malaga, Spain
- The Biomedical Research Institute of Málaga (IBIMA-CIMES-UMA), 29010, Malaga, Spain
| | - Esperanza López-López
- Unidad de Gestion Clinica Intercentros de Oncologia Medica, Hospitales Universitarios Regional y Virgen de la Victoria, 29010, Malaga, Spain
- The Biomedical Research Institute of Málaga (IBIMA-CIMES-UMA), 29010, Malaga, Spain
| | - María Elena Quirós-Ortega
- Unidad de Gestion Clinica Intercentros de Oncologia Medica, Hospitales Universitarios Regional y Virgen de la Victoria, 29010, Malaga, Spain
- The Biomedical Research Institute of Málaga (IBIMA-CIMES-UMA), 29010, Malaga, Spain
- Andalusia-Roche Network in Precision Medical Oncology, 41092, Sevilla, Spain
| | - Victoria Sánchez-Martín
- Unidad de Gestion Clinica Intercentros de Oncologia Medica, Hospitales Universitarios Regional y Virgen de la Victoria, 29010, Malaga, Spain
- Centro de Investigacion Biomedica en Red de Cancer (CIBERONC - CB16/12/00481), 28029, Madrid, Spain
| | - María Dunia Roldán-Díaz
- Unidad de Gestion Clinica Intercentros de Oncologia Medica, Hospitales Universitarios Regional y Virgen de la Victoria, 29010, Malaga, Spain
- The Biomedical Research Institute of Málaga (IBIMA-CIMES-UMA), 29010, Malaga, Spain
| | - Begoña Jiménez-Rodríguez
- Unidad de Gestion Clinica Intercentros de Oncologia Medica, Hospitales Universitarios Regional y Virgen de la Victoria, 29010, Malaga, Spain
- The Biomedical Research Institute of Málaga (IBIMA-CIMES-UMA), 29010, Malaga, Spain
- Centro de Investigacion Biomedica en Red de Cancer (CIBERONC - CB16/12/00481), 28029, Madrid, Spain
| | - Jesús Peralta-Linero
- Unidad de Gestion Clinica Intercentros de Oncologia Medica, Hospitales Universitarios Regional y Virgen de la Victoria, 29010, Malaga, Spain
- The Biomedical Research Institute of Málaga (IBIMA-CIMES-UMA), 29010, Malaga, Spain
| | - Estefanía Bellagarza-García
- Unidad de Gestion Clinica Intercentros de Oncologia Medica, Hospitales Universitarios Regional y Virgen de la Victoria, 29010, Malaga, Spain
| | - Laura Troyano-Ramos
- Unidad de Gestion Clinica Intercentros de Oncologia Medica, Hospitales Universitarios Regional y Virgen de la Victoria, 29010, Malaga, Spain
| | - Guadalupe Garrido-Ruiz
- Radiology Department, Hospital Clinico Universitario Virgen de la Victoria de Malaga, 29010, Malaga, Spain
| | - M Isabel Hierro-Martín
- The Biomedical Research Institute of Málaga (IBIMA-CIMES-UMA), 29010, Malaga, Spain
- Unidad de Gestion Clinica Provincial de Anatomia Patologica de Malaga, Hospital Clinico Universitario Virgen de la Victoria de Malaga, 29010, Malaga, Spain
- University of Málaga, Faculty of Medicine, 29010, Malaga, Spain
| | - Luis Vicioso
- The Biomedical Research Institute of Málaga (IBIMA-CIMES-UMA), 29010, Malaga, Spain
- Unidad de Gestion Clinica Provincial de Anatomia Patologica de Malaga, Hospital Clinico Universitario Virgen de la Victoria de Malaga, 29010, Malaga, Spain
- University of Málaga, Faculty of Medicine, 29010, Malaga, Spain
| | - Álvaro González-Ortiz
- Unidad de Gestion Clinica Intercentros de Oncologia Medica, Hospitales Universitarios Regional y Virgen de la Victoria, 29010, Malaga, Spain
| | - Noelia Linares-Valencia
- Unidad de Gestion Clinica Intercentros de Oncologia Medica, Hospitales Universitarios Regional y Virgen de la Victoria, 29010, Malaga, Spain
- The Biomedical Research Institute of Málaga (IBIMA-CIMES-UMA), 29010, Malaga, Spain
| | - Jesús Velasco-Suelto
- Unidad de Gestion Clinica Intercentros de Oncologia Medica, Hospitales Universitarios Regional y Virgen de la Victoria, 29010, Malaga, Spain
- The Biomedical Research Institute of Málaga (IBIMA-CIMES-UMA), 29010, Malaga, Spain
| | - Guillermo Carbajosa
- Unidad de Gestion Clinica Intercentros de Oncologia Medica, Hospitales Universitarios Regional y Virgen de la Victoria, 29010, Malaga, Spain
- University of Málaga, Faculty of Medicine, 29010, Malaga, Spain
| | - Alicia Garrido-Aranda
- Unidad de Gestion Clinica Intercentros de Oncologia Medica, Hospitales Universitarios Regional y Virgen de la Victoria, 29010, Malaga, Spain
- The Biomedical Research Institute of Málaga (IBIMA-CIMES-UMA), 29010, Malaga, Spain
- Andalusia-Roche Network in Precision Medical Oncology, 41092, Sevilla, Spain
- Laboratorio de biologia molecular del cancer (LBMC), Centro de investigaciones medico-sanitarias (CIMES-UMA), 29010, Malaga, Spain
| | - Rocío Lavado-Valenzuela
- Unidad de Gestion Clinica Intercentros de Oncologia Medica, Hospitales Universitarios Regional y Virgen de la Victoria, 29010, Malaga, Spain
- The Biomedical Research Institute of Málaga (IBIMA-CIMES-UMA), 29010, Malaga, Spain
- Andalusia-Roche Network in Precision Medical Oncology, 41092, Sevilla, Spain
- Centro de Investigacion Biomedica en Red de Cancer (CIBERONC - CB16/12/00481), 28029, Madrid, Spain
- Laboratorio de biologia molecular del cancer (LBMC), Centro de investigaciones medico-sanitarias (CIMES-UMA), 29010, Malaga, Spain
| | - Martina Álvarez
- The Biomedical Research Institute of Málaga (IBIMA-CIMES-UMA), 29010, Malaga, Spain
- Andalusia-Roche Network in Precision Medical Oncology, 41092, Sevilla, Spain
- Centro de Investigacion Biomedica en Red de Cancer (CIBERONC - CB16/12/00481), 28029, Madrid, Spain
- University of Málaga, Faculty of Medicine, 29010, Malaga, Spain
- Laboratorio de biologia molecular del cancer (LBMC), Centro de investigaciones medico-sanitarias (CIMES-UMA), 29010, Malaga, Spain
| | - Javier Pascual
- Unidad de Gestion Clinica Intercentros de Oncologia Medica, Hospitales Universitarios Regional y Virgen de la Victoria, 29010, Malaga, Spain
- The Biomedical Research Institute of Málaga (IBIMA-CIMES-UMA), 29010, Malaga, Spain
- Andalusia-Roche Network in Precision Medical Oncology, 41092, Sevilla, Spain
- Centro de Investigacion Biomedica en Red de Cancer (CIBERONC - CB16/12/00481), 28029, Madrid, Spain
| | - Iñaki Comino-Méndez
- Unidad de Gestion Clinica Intercentros de Oncologia Medica, Hospitales Universitarios Regional y Virgen de la Victoria, 29010, Malaga, Spain.
- The Biomedical Research Institute of Málaga (IBIMA-CIMES-UMA), 29010, Malaga, Spain.
- Andalusia-Roche Network in Precision Medical Oncology, 41092, Sevilla, Spain.
- Centro de Investigacion Biomedica en Red de Cancer (CIBERONC - CB16/12/00481), 28029, Madrid, Spain.
| | - Emilio Alba
- Unidad de Gestion Clinica Intercentros de Oncologia Medica, Hospitales Universitarios Regional y Virgen de la Victoria, 29010, Malaga, Spain
- The Biomedical Research Institute of Málaga (IBIMA-CIMES-UMA), 29010, Malaga, Spain
- Andalusia-Roche Network in Precision Medical Oncology, 41092, Sevilla, Spain
- Centro de Investigacion Biomedica en Red de Cancer (CIBERONC - CB16/12/00481), 28029, Madrid, Spain
- University of Málaga, Faculty of Medicine, 29010, Malaga, Spain
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Hashimoto T, Nakamura Y, Oki E, Kobayashi S, Yuda J, Shibuki T, Bando H, Yoshino T. Bridging horizons beyond CIRCULATE-Japan: a new paradigm in molecular residual disease detection via whole genome sequencing-based circulating tumor DNA assay. Int J Clin Oncol 2024; 29:495-511. [PMID: 38551727 PMCID: PMC11043144 DOI: 10.1007/s10147-024-02493-4] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2024] [Accepted: 02/16/2024] [Indexed: 04/26/2024]
Abstract
Circulating tumor DNA (ctDNA) is the fraction of cell-free DNA in patient blood that originates from a tumor. Advances in DNA sequencing technologies and our understanding of the molecular biology of tumors have increased interest in exploiting ctDNA to facilitate detection of molecular residual disease (MRD). Analysis of ctDNA as a promising MRD biomarker of solid malignancies has a central role in precision medicine initiatives exemplified by our CIRCULATE-Japan project involving patients with resectable colorectal cancer. Notably, the project underscores the prognostic significance of the ctDNA status at 4 weeks post-surgery and its correlation to adjuvant therapy efficacy at interim analysis. This substantiates the hypothesis that MRD is a critical prognostic indicator of relapse in patients with colorectal cancer. Despite remarkable advancements, challenges endure, primarily attributable to the exceedingly low ctDNA concentration in peripheral blood, particularly in scenarios involving low tumor shedding and the intrinsic error rates of current sequencing technologies. These complications necessitate more sensitive and sophisticated assays to verify the clinical utility of MRD across all solid tumors. Whole genome sequencing (WGS)-based tumor-informed MRD assays have recently demonstrated the ability to detect ctDNA in the parts-per-million range. This review delineates the current landscape of MRD assays, highlighting WGS-based approaches as the forefront technique in ctDNA analysis. Additionally, it introduces our upcoming endeavor, WGS-based pan-cancer MRD detection via ctDNA, in our forthcoming project, SCRUM-Japan MONSTAR-SCREEN-3.
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Affiliation(s)
- Tadayoshi Hashimoto
- Translational Research Support Office, National Cancer Center Hospital East, Kashiwa, Japan
- Department of Gastroenterology and Gastrointestinal Oncology, National Cancer Center Hospital East, 6-5-1 Kashiwanoha, Kashiwa, Chiba, 277-8577, Japan
| | - Yoshiaki Nakamura
- Translational Research Support Office, National Cancer Center Hospital East, Kashiwa, Japan
- Department of Gastroenterology and Gastrointestinal Oncology, National Cancer Center Hospital East, 6-5-1 Kashiwanoha, Kashiwa, Chiba, 277-8577, Japan
| | - Eiji Oki
- Department of Surgery and Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Shin Kobayashi
- Department of Hepatobiliary and Pancreatic Surgery, National Cancer Center Hospital East, Kashiwa, Japan
| | - Junichiro Yuda
- Department of Hematology, National Cancer Center Hospital East, Kashiwa, Japan
| | - Taro Shibuki
- Translational Research Support Office, National Cancer Center Hospital East, Kashiwa, Japan
| | - Hideaki Bando
- Translational Research Support Office, National Cancer Center Hospital East, Kashiwa, Japan
- Department of Gastroenterology and Gastrointestinal Oncology, National Cancer Center Hospital East, 6-5-1 Kashiwanoha, Kashiwa, Chiba, 277-8577, Japan
| | - Takayuki Yoshino
- Department of Gastroenterology and Gastrointestinal Oncology, National Cancer Center Hospital East, 6-5-1 Kashiwanoha, Kashiwa, Chiba, 277-8577, Japan.
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Yoshinami T. Perspectives for the clinical application of ctDNA analysis to breast cancer drug therapy. Breast Cancer 2024:10.1007/s12282-024-01571-9. [PMID: 38649655 DOI: 10.1007/s12282-024-01571-9] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Accepted: 03/14/2024] [Indexed: 04/25/2024]
Abstract
Circulating tumor DNA (ctDNA) consists of DNA fragments released from cancer cells into the blood circulation with quick clearance. Analysis of ctDNA can enable real-time assessment of the presence of cancer cells and their genomic characteristics. Therefore, ctDNA is expected to be one of the most useful biomarkers for cancer. In recent years, several ultra-sensitive assays for ctDNA analysis have been developed, and many clinical trials are using these assays to investigate the efficacy of ctDNA-based therapeutic strategies. In the perioperative phase, real-time identification of minimal residual disease at the molecular level with ctDNA analysis can help evaluate the risk of recurrence to inform escalation or de-escalation of perioperative drug therapy. Many trials have examined whether therapeutic strategies using ctDNA analysis to predict treatment efficacy or resistance to molecular targeted agents can improve prognosis in metastatic breast cancer. In this review, we discuss the most recent ctDNA assays, the significance of introducing ctDNA assays to clinical practice, and the research on their application in perioperative and metastatic phases.
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Affiliation(s)
- Tetsuhiro Yoshinami
- Department of Breast and Endocrine Surgery, Graduate School of Medicine, Osaka University, Osaka, Japan.
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4
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Davidson BA, Miranda AX, Reed SC, Bergman RE, Kemp JDJ, Reddy AP, Pantone MV, Fox EK, Dorand RD, Hurley PJ, Croessmann S, Park BH. An in vitro CRISPR screen of cell-free DNA identifies apoptosis as the primary mediator of cell-free DNA release. Commun Biol 2024; 7:441. [PMID: 38600351 PMCID: PMC11006667 DOI: 10.1038/s42003-024-06129-1] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Accepted: 03/29/2024] [Indexed: 04/12/2024] Open
Abstract
ABTRACT Clinical circulating cell-free DNA (cfDNA) testing is now routine, however test accuracy remains limited. By understanding the life-cycle of cfDNA, we might identify opportunities to increase test performance. Here, we profile cfDNA release across a 24-cell line panel and utilize a cell-free CRISPR screen (cfCRISPR) to identify mediators of cfDNA release. Our panel outlines two distinct groups of cell lines: one which releases cfDNA fragmented similarly to clinical samples and purported as characteristic of apoptosis, and another which releases larger fragments associated with vesicular or necrotic DNA. Our cfCRISPR screens reveal that genes mediating cfDNA release are primarily involved with apoptosis, but also identify other subsets of genes such as RNA binding proteins as potential regulators of cfDNA release. We observe that both groups of cells lines identified primarily produce cfDNA through apoptosis. These results establish the utility of cfCRISPR, genetically validate apoptosis as a major mediator of DNA release in vitro, and implicate ways to improve cfDNA assays.
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Affiliation(s)
- Brad A Davidson
- Division of Hematology, Oncology, Department of Medicine, Vanderbilt University Medical Center and the Vanderbilt-Ingram Cancer Center, Nashville, TN, USA
| | - Adam X Miranda
- Division of Hematology, Oncology, Department of Medicine, Vanderbilt University Medical Center and the Vanderbilt-Ingram Cancer Center, Nashville, TN, USA
| | - Sarah C Reed
- Division of Hematology, Oncology, Department of Medicine, Vanderbilt University Medical Center and the Vanderbilt-Ingram Cancer Center, Nashville, TN, USA
- Medical Scientist Training Program, Vanderbilt University, Nashville, TN, USA
| | - Riley E Bergman
- Division of Hematology, Oncology, Department of Medicine, Vanderbilt University Medical Center and the Vanderbilt-Ingram Cancer Center, Nashville, TN, USA
- Medical Scientist Training Program, Vanderbilt University, Nashville, TN, USA
| | - Justin D J Kemp
- Division of Hematology, Oncology, Department of Medicine, Vanderbilt University Medical Center and the Vanderbilt-Ingram Cancer Center, Nashville, TN, USA
| | - Anvith P Reddy
- Division of Hematology, Oncology, Department of Medicine, Vanderbilt University Medical Center and the Vanderbilt-Ingram Cancer Center, Nashville, TN, USA
- Medical Scientist Training Program, Vanderbilt University, Nashville, TN, USA
| | - Morgan V Pantone
- Division of Hematology, Oncology, Department of Medicine, Vanderbilt University Medical Center and the Vanderbilt-Ingram Cancer Center, Nashville, TN, USA
| | - Ethan K Fox
- Division of Hematology, Oncology, Department of Medicine, Vanderbilt University Medical Center and the Vanderbilt-Ingram Cancer Center, Nashville, TN, USA
| | - R Dixon Dorand
- Division of Hematology, Oncology, Department of Medicine, Vanderbilt University Medical Center and the Vanderbilt-Ingram Cancer Center, Nashville, TN, USA
| | - Paula J Hurley
- Division of Hematology, Oncology, Department of Medicine, Vanderbilt University Medical Center and the Vanderbilt-Ingram Cancer Center, Nashville, TN, USA
| | - Sarah Croessmann
- Division of Hematology, Oncology, Department of Medicine, Vanderbilt University Medical Center and the Vanderbilt-Ingram Cancer Center, Nashville, TN, USA
| | - Ben Ho Park
- Division of Hematology, Oncology, Department of Medicine, Vanderbilt University Medical Center and the Vanderbilt-Ingram Cancer Center, Nashville, TN, USA.
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Abbasi AB, Wu V, Lang JE, Esserman LJ. Precision Oncology in Breast Cancer Surgery. Surg Oncol Clin N Am 2024; 33:293-310. [PMID: 38401911 DOI: 10.1016/j.soc.2023.12.011] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/26/2024]
Abstract
Outcomes for patients with breast cancer have improved over time due to increased screening and the availability of more effective therapies. It is important to recognize that breast cancer is a heterogeneous disease that requires treatment based on molecular characteristics. Early endpoints such as pathologic complete response correlate with event-free survival, allowing the opportunity to consider de-escalation of certain cancer treatments to avoid overtreatment. This article discusses clinical trials of tailoring treatment (eg, I-SPY2) and screening (eg, WISDOM) to individual patients based on their unique risk features.
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Affiliation(s)
- Ali Benjamin Abbasi
- Department of Surgery, San Francisco Breast Care Center, University of California, Box 1710, UCSF, San Francisco, CA 94143, USA
| | - Vincent Wu
- Department of Surgery, Cleveland Clinic Breast Services, 9500 Euclid Avenue, A80, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Julie E Lang
- Department of Surgery, Cleveland Clinic Breast Services, 9500 Euclid Avenue, A80, Cleveland Clinic, Cleveland, OH 44195, USA.
| | - Laura J Esserman
- Department of Surgery, San Francisco Breast Care Center, University of California, Box 1710, UCSF, San Francisco, CA 94143, USA
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Merryman RW, Rhoades J, Xiong K, Redd RA, Antel K, An HH, McDonough M, Guerrero L, Crnjac A, Sridhar S, Blewett T, Cheng J, Dahi PB, Nieto Y, Joyce RM, Chen Y, Herrera AF, Armand P, Murakami M, Adalsteinsson VA. Comparison of whole-genome and immunoglobulin-based circulating tumor DNA assays in diffuse large B-cell lymphoma. Hemasphere 2024; 8:e47. [PMID: 38566803 PMCID: PMC10983020 DOI: 10.1002/hem3.47] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 12/30/2023] [Accepted: 01/24/2024] [Indexed: 04/04/2024] Open
Affiliation(s)
- Reid W. Merryman
- Department of Medical OncologyDana‐Farber Cancer InstituteBostonMassachusettsUSA
| | - Justin Rhoades
- Gerstner Center for Cancer DiagnosticsBroad InstituteCambridgeMassachusettsUSA
| | - Kan Xiong
- Gerstner Center for Cancer DiagnosticsBroad InstituteCambridgeMassachusettsUSA
| | - Robert A. Redd
- Department of Data ScienceDana‐Farber Cancer InstituteBostonMassachusettsUSA
| | - Katherine Antel
- Department of Medical OncologyDana‐Farber Cancer InstituteBostonMassachusettsUSA
- Institute for Infectious Disease and Molecular MedicineUniversity of Cape TownCape TownSouth Africa
| | - Hyun Hwan An
- Department of Medical OncologyDana‐Farber Cancer InstituteBostonMassachusettsUSA
| | - Mikaela McDonough
- Department of Medical OncologyDana‐Farber Cancer InstituteBostonMassachusettsUSA
| | - Liliana Guerrero
- Department of Medical OncologyDana‐Farber Cancer InstituteBostonMassachusettsUSA
| | - Andela Crnjac
- Gerstner Center for Cancer DiagnosticsBroad InstituteCambridgeMassachusettsUSA
| | - Sainetra Sridhar
- Gerstner Center for Cancer DiagnosticsBroad InstituteCambridgeMassachusettsUSA
| | - Timothy Blewett
- Gerstner Center for Cancer DiagnosticsBroad InstituteCambridgeMassachusettsUSA
| | - Ju Cheng
- Gerstner Center for Cancer DiagnosticsBroad InstituteCambridgeMassachusettsUSA
| | - Parastoo B. Dahi
- Department of Medicine, Adult Bone Marrow Transplant ServiceMemorial Sloan‐Kettering Cancer CenterNew York CityNew YorkUSA
| | - Yago Nieto
- Department of Stem Cell Transplantation and Cellular TherapyThe University of Texas MD Anderson Cancer CenterHoustonTexasUSA
| | - Robin M. Joyce
- Department of Hematologic MalignancyBeth Israel Deaconess Medical CenterBostonMassachusettsUSA
| | - Yi‐Bin Chen
- Bone Marrow Transplantation ProgramMassachusetts General HospitalBostonMassachusettsUSA
| | - Alex F. Herrera
- Department of Hematology and Hematopoietic Cell TransplantationCity of Hope National Medical CenterDuarteCaliforniaUSA
| | - Philippe Armand
- Department of Medical OncologyDana‐Farber Cancer InstituteBostonMassachusettsUSA
| | - Mark Murakami
- Department of Medical OncologyDana‐Farber Cancer InstituteBostonMassachusettsUSA
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7
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Efthymiou V, Queenan N, Haas M, Naegele S, Goss D, Faden DL. Circulating Tumor DNA in the Immediate Postoperative Setting. Ann Surg Oncol 2024; 31:2319-2325. [PMID: 38190058 DOI: 10.1245/s10434-023-14860-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 12/17/2023] [Indexed: 01/09/2024]
Abstract
BACKGROUND Circulating tumor DNA (ctDNA) has emerged as an accurate real-time biomarker of disease status across many solid tumor types. Most studies evaluating the utility of ctDNA have focused on time points weeks to months after surgery, which, for many cancer types, is significantly later than decision-making time points for adjuvant treatment. In this systematic review, we summarize the state of the literature on the feasibility of using ctDNA as a biomarker in the immediate postoperative period. METHODS We performed a systematic review evaluating the early kinetics, defined here as 3 days of ctDNA in patients who underwent curative-intent surgery. RESULTS Among the 2057 studies identified, eight cohort studies met the criteria for evaluation. Across six different cancer types, all studies showed an increased risk of cancer recurrence in patients with detectable ctDNA in the immediate postoperative period. CONCLUSION While ctDNA clearance kinetics appear to vary based on tumor type, across all studies detectable ctDNA after surgery was predictive of recurrence, suggesting early postoperative time points could be feasibly used for determining minimal residual disease. However, larger studies need to be performed to better understand the precise kinetics of ctDNA clearance across different cancer types as well as to determine optimal postoperative time points.
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Affiliation(s)
- Vasileios Efthymiou
- Department of Otolaryngology-Head and Neck Surgery, Massachusetts Eye and Ear, Boston, MA, USA
| | - Natalia Queenan
- Department of Otolaryngology-Head and Neck Surgery, Massachusetts Eye and Ear, Boston, MA, USA
| | - Markus Haas
- Department of Otolaryngology-Head and Neck Surgery, Massachusetts Eye and Ear, Boston, MA, USA
| | - Saskia Naegele
- Department of Otolaryngology-Head and Neck Surgery, Massachusetts Eye and Ear, Boston, MA, USA
| | - Deborah Goss
- Department of Otolaryngology-Head and Neck Surgery, Massachusetts Eye and Ear, Boston, MA, USA
| | - Daniel L Faden
- Department of Otolaryngology-Head and Neck Surgery, Massachusetts Eye and Ear, Boston, MA, USA.
- Harvard Medical School, Boston, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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8
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Lynce F, Mainor C, Donahue RN, Geng X, Jones G, Schlam I, Wang H, Toney NJ, Jochems C, Schlom J, Zeck J, Gallagher C, Nanda R, Graham D, Stringer-Reasor EM, Denduluri N, Collins J, Chitalia A, Tiwari S, Nunes R, Kaltman R, Khoury K, Gatti-Mays M, Tarantino P, Tolaney SM, Swain SM, Pohlmann P, Parsons HA, Isaacs C. Adjuvant nivolumab, capecitabine or the combination in patients with residual triple-negative breast cancer: the OXEL randomized phase II study. Nat Commun 2024; 15:2691. [PMID: 38538574 PMCID: PMC10973408 DOI: 10.1038/s41467-024-46961-x] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 03/15/2024] [Indexed: 04/04/2024] Open
Abstract
Chemotherapy and immune checkpoint inhibitors have a role in the post-neoadjuvant setting in patients with triple-negative breast cancer (TNBC). However, the effects of nivolumab, a checkpoint inhibitor, capecitabine, or the combination in changing peripheral immunoscore (PIS) remains unclear. This open-label randomized phase II OXEL study (NCT03487666) aimed to assess the immunologic effects of nivolumab, capecitabine, or the combination in terms of the change in PIS (primary endpoint). Secondary endpoints included the presence of ctDNA, toxicity, clinical outcomes at 2-years and association of ctDNA and PIS with clinical outcomes. Forty-five women with TNBC and residual invasive disease after standard neoadjuvant chemotherapy were randomized to nivolumab, capecitabine, or the combination. Here we show that a combination of nivolumab plus capecitabine leads to a greater increase in PIS from baseline to week 6 (91%) compared with nivolumab (47%) or capecitabine (53%) alone (log-rank p = 0.08), meeting the pre-specified primary endpoint. In addition, the presence of circulating tumor DNA (ctDNA) is associated with disease recurrence, with no new safety signals in the combination arm. Our results provide efficacy and safety data on this combination in TNBC and support further development of PIS and ctDNA analyses to identify patients at high risk of recurrence.
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Affiliation(s)
- Filipa Lynce
- Division of 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.
| | - Candace Mainor
- MedStar Georgetown University Hospital, Washington, DC, USA
| | - Renee N Donahue
- Center for Immuno-Oncology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Xue Geng
- Georgetown University, Washington, DC, USA
| | | | - Ilana Schlam
- MedStar Washington Hospital Center, Washington, DC, USA
- Tufts Medical Center, Boston, MA, USA
| | | | - Nicole J Toney
- Center for Immuno-Oncology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Caroline Jochems
- Center for Immuno-Oncology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Jeffrey Schlom
- Center for Immuno-Oncology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Jay Zeck
- MedStar Georgetown University Hospital, Washington, DC, USA
| | | | | | - Deena Graham
- Hackensack University Medical Center, Hackensack, NJ, USA
| | | | | | - Julie Collins
- MedStar Georgetown University Hospital, Washington, DC, USA
- AstraZeneca, Arlington, VA, USA
| | - Ami Chitalia
- MedStar Washington Hospital Center, Washington, DC, USA
| | - Shruti Tiwari
- MedStar Washington Hospital Center, Washington, DC, USA
| | - Raquel Nunes
- Johns Hopkins Sidney Kimmel Cancer Center, Baltimore, MD, USA
- AstraZeneca, Arlington, VA, USA
| | | | - Katia Khoury
- University of Alabama at Birmingham, Birmingham, AL, USA
| | | | - Paolo Tarantino
- Division of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Sara M Tolaney
- Division of 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
| | | | - Paula Pohlmann
- MedStar Georgetown University Hospital, Washington, DC, USA
| | - Heather A Parsons
- Division of 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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9
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Conforti F, Pala L, De Pas T, Zattarin E, Catania C, Cocorocchio E, Rossi G, Laszlo D, Colleoni M, Zambelli A, Hortobagyi GN, Cortes J, Piccart MJ, Dowsett M, Gelber RD, Viale G. Fine-Tuning Adjuvant Endocrine Therapy for Early-Stage Breast Cancer: An Expert Consensus on Open Issues for Future Research. Clin Cancer Res 2024; 30:1093-1103. [PMID: 37906083 DOI: 10.1158/1078-0432.ccr-23-1836] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 08/29/2023] [Accepted: 10/19/2023] [Indexed: 11/02/2023]
Abstract
After decades of research, improving the efficacy of adjuvant endocrine therapy (ET) for early-stage breast cancer becomes increasingly difficult. Beyond technological breakthroughs and the availability of new classes of drugs, further improvement of adjuvant ET will require applying a rigorous research approach in poorly investigated areas. We critically discuss some key principles that should inform future research to improve ET efficacy, including identifying specific subgroups of patients who can benefit from escalating or de-escalating approaches, optimizing available and new treatment strategies for different clinical contexts, and dissecting the direct and indirect biological effects of therapeutic interventions. Four main issues regarding adjuvant ET were identified as relevant areas, where a better application of such principles can provide positive results in the near future: (i) tailoring the optimal duration of adjuvant ET, (ii) optimizing ovarian function suppression for premenopausal women, (iii) dissecting the biological effects of estrogen receptor manipulation, and (iv) refining the selection of patients to candidate for treatments escalation.
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Affiliation(s)
- Fabio Conforti
- Department of Medical Oncology, Cliniche Humanitas Gavazzeni, Bergamo, Italy
| | - Laura Pala
- Department of Medical Oncology, Cliniche Humanitas Gavazzeni, Bergamo, Italy
| | - Tommaso De Pas
- Department of Medical Oncology, Cliniche Humanitas Gavazzeni, Bergamo, Italy
| | - Emma Zattarin
- Department of Medical Oncology, Cliniche Humanitas Gavazzeni, Bergamo, Italy
| | - Chiara Catania
- Department of Medical Oncology, Cliniche Humanitas Gavazzeni, Bergamo, Italy
| | - Emilia Cocorocchio
- Department of Medical Oncology, Cliniche Humanitas Gavazzeni, Bergamo, Italy
| | - Giovanna Rossi
- Department of Medical Oncology, Cliniche Humanitas Gavazzeni, Bergamo, Italy
| | - Daniele Laszlo
- Department of Medical Oncology, Cliniche Humanitas Gavazzeni, Bergamo, Italy
| | - Marco Colleoni
- Division of Medical Senology, IEO, European Institute of Oncology IRCCS, Milan, Italy
| | - Alberto Zambelli
- Department of Biomedical Sciences, Humanitas University, Milan, Italy
- IRCCS Humanitas Research Hospital, Humanitas Cancer Center, Milan, Italy
| | - Gabriel N Hortobagyi
- Department of Breast Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Javier Cortes
- International Breast Cancer Center, Pangaea Oncology, Quironsalud Group, Madrid and Barcelona, Spain
- Universidad Europea de Madrid, Faculty of Biomedical and Health Sciences, Department of Medicine, Madrid, Spain
| | - Martine J Piccart
- Institut Jules Bordet, Université Libre de Bruxelles, Brussels, Belgium
| | - Mitch Dowsett
- Breast Unit, Royal Marsden Hospital, London, United Kingdom
| | - Richard D Gelber
- Department of Data Science, Division of Biostatistics, Dana-Farber Cancer Institute, Harvard Medical School, Harvard T.H. Chan School of Public Health, and Frontier Science Foundation, Boston, Massachusetts
| | - Giuseppe Viale
- Department of Pathology, IEO, European Institute of Oncology, IRCCS, Milan, Italy
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10
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Northcott J, Bartha G, Harris J, Li C, Navarro FC, Pyke RM, Hong M, Zhang Q, Ma S, Chen TX, Lai J, Udar N, Saldivar JS, Ayash E, Anderson J, Li J, Cui T, Le T, Chow R, Velasco RJ, Mallo C, Santiago R, Bruce RC, Goodman LJ, Chen Y, Norton D, Chen RO, Lyle JM. Analytical validation of NeXT Personal®, an ultra-sensitive personalized circulating tumor DNA assay. Oncotarget 2024; 15:200-218. [PMID: 38484152 PMCID: PMC10939476 DOI: 10.18632/oncotarget.28565] [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] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Accepted: 02/12/2024] [Indexed: 03/17/2024] Open
Abstract
We describe the analytical validation of NeXT Personal®, an ultra-sensitive, tumor-informed circulating tumor DNA (ctDNA) assay for detecting residual disease, monitoring therapy response, and detecting recurrence in patients diagnosed with solid tumor cancers. NeXT Personal uses whole genome sequencing of tumor and matched normal samples combined with advanced analytics to accurately identify up to ~1,800 somatic variants specific to the patient's tumor. A personalized panel is created, targeting these variants and then used to sequence cell-free DNA extracted from patient plasma samples for ultra-sensitive detection of ctDNA. The NeXT Personal analytical validation is based on panels designed from tumor and matched normal samples from two cell lines, and from 123 patients across nine cancer types. Analytical measurements demonstrated a detection threshold of 1.67 parts per million (PPM) with a limit of detection at 95% (LOD95) of 3.45 PPM. NeXT Personal showed linearity over a range of 0.8 to 300,000 PPM (Pearson correlation coefficient = 0.9998). Precision varied from a coefficient of variation of 12.8% to 3.6% over a range of 25 to 25,000 PPM. The assay targets 99.9% specificity, with this validation study measuring 100% specificity and in silico methods giving us a confidence interval of 99.92 to 100%. In summary, this study demonstrates NeXT Personal as an ultra-sensitive, highly quantitative and robust ctDNA assay that can be used to detect residual disease, monitor treatment response, and detect recurrence in patients.
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Affiliation(s)
| | | | | | - Conan Li
- Personalis, Inc., Fremont, CA 94555, USA
| | | | | | | | - Qi Zhang
- Personalis, Inc., Fremont, CA 94555, USA
| | - Shuyuan Ma
- Personalis, Inc., Fremont, CA 94555, USA
| | | | - Janet Lai
- Personalis, Inc., Fremont, CA 94555, USA
| | - Nitin Udar
- Personalis, Inc., Fremont, CA 94555, USA
| | | | - Erin Ayash
- Personalis, Inc., Fremont, CA 94555, USA
| | | | - Jiang Li
- Personalis, Inc., Fremont, CA 94555, USA
| | - Tiange Cui
- Personalis, Inc., Fremont, CA 94555, USA
| | - Tu Le
- Personalis, Inc., Fremont, CA 94555, USA
| | | | | | | | | | | | | | - Yi Chen
- Personalis, Inc., Fremont, CA 94555, USA
| | - Dan Norton
- Personalis, Inc., Fremont, CA 94555, USA
| | | | - John M. Lyle
- Personalis, Inc., Fremont, CA 94555, USA
- Co-last authors
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11
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Nader-Marta G, Monteforte M, Agostinetto E, Cinquini M, Martins-Branco D, Langouo M, Llombart-Cusac A, Cortés J, Ignatiadis M, Torri V, Apolone G, Cappelletti V, Pruneri G, de Azambuja E, Di Cosimo S. Circulating tumor DNA for predicting recurrence in patients with operable breast cancer: a systematic review and meta-analysis. ESMO Open 2024; 9:102390. [PMID: 38460249 PMCID: PMC10940943 DOI: 10.1016/j.esmoop.2024.102390] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 01/25/2024] [Accepted: 01/26/2024] [Indexed: 03/11/2024] Open
Abstract
BACKGROUND The incorporation of circulating tumor DNA (ctDNA) into the management of operable breast cancer (BC) has been hampered by the heterogeneous results from different studies. We aimed to assess the prognostic value of ctDNA in patients with operable (non metastatic) BC. MATERIALS AND METHODS A systematic search of databases (PubMed/Medline, Embase, and CENTRAL) and conference proceedings was conducted to identify studies reporting the association of ctDNA detection with disease-free survival (DFS) and overall survival (OS) in patients with stage I-III BC. Log-hazard ratios (HRs) were pooled at each timepoint of ctDNA assessment (baseline, after neoadjuvant therapy, and follow-up). ctDNA assays were classified as primary tumor-informed and non tumor-informed. RESULTS Of the 3174 records identified, 57 studies including 5779 patients were eligible. In univariate analyses, ctDNA detection was associated with worse DFS at baseline [HR 2.98, 95% confidence interval (CI) 1.92-4.63], after neoadjuvant therapy (HR 7.69, 95% CI 4.83-12.24), and during follow-up (HR 14.04, 95% CI 7.55-26.11). Similarly, ctDNA detection at all timepoints was associated with worse OS (at baseline: HR 2.76, 95% CI 1.60-4.77; after neoadjuvant therapy: HR 2.72, 95% CI 1.44-5.14; and during follow-up: HR 9.19, 95% CI 3.26-25.90). Similar DFS and OS results were observed in multivariate analyses. Pooled HRs were numerically higher when ctDNA was detected at the end of neoadjuvant therapy or during follow-up and for primary tumor-informed assays. ctDNA detection sensitivity and specificity for BC recurrence ranged from 0.31 to 1.0 and 0.7 to 1.0, respectively. The mean lead time from ctDNA detection to overt recurrence was 10.81 months (range 0-58.9 months). CONCLUSIONS ctDNA detection was associated with worse DFS and OS in patients with operable BC, particularly when detected after treatment and using primary tumor-informed assays. ctDNA detection has a high specificity for anticipating BC relapse.
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Affiliation(s)
- G Nader-Marta
- Academic Trials Promoting Team (ATPT), Institut Jules Bordet, Hôpital Universitaire de Bruxelles (HUB), Université Libre de Bruxelles (U.L.B), Brussels, Belgium.
| | - M Monteforte
- Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Milan, Italy
| | - E Agostinetto
- Academic Trials Promoting Team (ATPT), Institut Jules Bordet, Hôpital Universitaire de Bruxelles (HUB), Université Libre de Bruxelles (U.L.B), Brussels, Belgium. https://twitter.com/ElisaAgostinett
| | - M Cinquini
- Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Milan, Italy
| | - D Martins-Branco
- Academic Trials Promoting Team (ATPT), Institut Jules Bordet, Hôpital Universitaire de Bruxelles (HUB), Université Libre de Bruxelles (U.L.B), Brussels, Belgium. https://twitter.com/DMBranco
| | - M Langouo
- Medical Oncology Department, Institut Jules Bordet, Hôpital Universitaire de Bruxelles (HUB), Université Libre de Bruxelles (U.L.B), Brussels, Belgium
| | - A Llombart-Cusac
- Medica Scientia Innovation Research (MEDSIR), Barcelona, Spain; Medica Scientia Innovation Research (MEDSIR), Ridgewood, New Jersey, USA; Arnau de Vilanova Hospital; Universidad Católica de Valencia, Valencia, Spain
| | - J Cortés
- Medica Scientia Innovation Research (MEDSIR), Barcelona, Spain; Medica Scientia Innovation Research (MEDSIR), Ridgewood, New Jersey, USA; International Breast Cancer Center (IBCC), Pangaea Oncology, Quiron Group, Barcelona, Spain; Department of Medicine, Faculty of Biomedical and Health Sciences, Universidad Europea de Madrid, Madrid, Spain. https://twitter.com/JavierCortesMD
| | - M Ignatiadis
- Academic Trials Promoting Team (ATPT), Institut Jules Bordet, Hôpital Universitaire de Bruxelles (HUB), Université Libre de Bruxelles (U.L.B), Brussels, Belgium; Medical Oncology Department, Institut Jules Bordet, Hôpital Universitaire de Bruxelles (HUB), Université Libre de Bruxelles (U.L.B), Brussels, Belgium. https://twitter.com/MIgnatiadis
| | - V Torri
- Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Milan, Italy. https://twitter.com/ValterTorri
| | - G Apolone
- Scientific Directorate, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - V Cappelletti
- Department of Advanced Diagnostics, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - G Pruneri
- Department of Advanced Diagnostics, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy; University of Milan, School of Medicine, Milan, Italy. https://twitter.com/PruneriG
| | - E de Azambuja
- Academic Trials Promoting Team (ATPT), Institut Jules Bordet, Hôpital Universitaire de Bruxelles (HUB), Université Libre de Bruxelles (U.L.B), Brussels, Belgium; Medical Oncology Department, Institut Jules Bordet, Hôpital Universitaire de Bruxelles (HUB), Université Libre de Bruxelles (U.L.B), Brussels, Belgium. https://twitter.com/E_de_Azambuja
| | - S Di Cosimo
- Department of Advanced Diagnostics, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy. https://twitter.com/serenadicosimo
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12
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Blewett T, Rhoades J, Liu R, Xiong K, Sridhar S, Crnjac A, Cheng J, Lawless AR, Frederick DT, Flaherty KT, Makrigiorgos GM, Adalsteinsson VA. MAESTRO-Pool Enables Highly Parallel and Specific Mutation-Enrichment Sequencing for Minimal Residual Disease Detection in Cohort Studies. Clin Chem 2024; 70:434-443. [PMID: 38069911 PMCID: PMC10847667 DOI: 10.1093/clinchem/hvad203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Accepted: 10/19/2023] [Indexed: 02/08/2024]
Abstract
BACKGROUND Tracing patient-specific tumor mutations in cell-free DNA (cfDNA) for minimal residual disease (MRD) detection is promising but challenging. Assaying more mutations and cfDNA stands to improve MRD detection but requires highly accurate, efficient sequencing methods and proper calibration to prevent false detection with bespoke tests. METHODS MAESTRO (Minor Allele Enriched Sequencing Through Recognition Oligonucleotides) uses mutation-specific oligonucleotide probes to enrich cfDNA libraries for tumor mutations and enable their accurate detection with minimal sequencing. A new approach, MAESTRO-Pool, which entails pooling MAESTRO probes for all patients and applying these to all samples from all patients, was used to screen for 22 333 tumor mutations from 9 melanoma patients in 98 plasma samples. This enabled quantification of MRD detection in patient-matched samples and false detection in unmatched samples from other patients. To detect MRD, a new dynamic MRD caller was used that computes a probability for MRD detection based on the number of mutations and cfDNA molecules sequenced, thereby calibrating for variations in each bespoke test. RESULTS MAESTRO-Pool enabled sensitive detection of MRD down to 0.78 parts per million (ppm), reflecting a 10- to 100-fold improvement over existing tests. Of the 8 MRD positive samples with ultra-low tumor fractions <10 ppm, 7 were either in upward-trend preceding recurrence or downward-trend aligning with response. Of 784 patient-unmatched tests, only one was found as MRD positive (tumor fraction = 2.7 ppm), suggesting high specificity. CONCLUSIONS MAESTRO-Pool enables massively parallel, tumor-informed MRD testing with concurrent benchmarking of bespoke MRD tests. Meanwhile, our new MRD caller enables more mutations and cfDNA molecules to be tested without compromising specificity. These improve the ability for detecting traces of MRD from blood.
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Affiliation(s)
- Timothy Blewett
- Gerstner Center for Cancer Diagnostics, Broad Institute of MIT and Harvard, Cambridge, MA, United States
| | - Justin Rhoades
- Gerstner Center for Cancer Diagnostics, Broad Institute of MIT and Harvard, Cambridge, MA, United States
| | - Ruolin Liu
- Gerstner Center for Cancer Diagnostics, Broad Institute of MIT and Harvard, Cambridge, MA, United States
| | - Kan Xiong
- Gerstner Center for Cancer Diagnostics, Broad Institute of MIT and Harvard, Cambridge, MA, United States
| | - Sainetra Sridhar
- Gerstner Center for Cancer Diagnostics, Broad Institute of MIT and Harvard, Cambridge, MA, United States
| | - Andjela Crnjac
- Gerstner Center for Cancer Diagnostics, Broad Institute of MIT and Harvard, Cambridge, MA, United States
| | - Ju Cheng
- Gerstner Center for Cancer Diagnostics, Broad Institute of MIT and Harvard, Cambridge, MA, United States
| | - Aleigha R Lawless
- Massachusetts General Hospital Cancer Center, Department of Medicine, Massachusetts General Hospital, Boston, MA, United States
| | - Dennie T Frederick
- Gerstner Center for Cancer Diagnostics, Broad Institute of MIT and Harvard, Cambridge, MA, United States
| | - Keith T Flaherty
- Massachusetts General Hospital Cancer Center, Department of Medicine, Massachusetts General Hospital, Boston, MA, United States
| | - Gerassimos Mike Makrigiorgos
- Department of Radiation Oncology, Dana-Farber Cancer Institute and Brigham and Women’s Hospital, Boston, MA, United States
| | - Viktor A Adalsteinsson
- Gerstner Center for Cancer Diagnostics, Broad Institute of MIT and Harvard, Cambridge, MA, United States
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13
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Fan W, Xia Z, Chen R, Lin D, Li F, Zheng Y, Luo J, Xiong Y, Yu P, Gao W, Gong Y, Zhang F, Zhang S, Li L. Circulating tumor DNA analysis predicts recurrence and avoids unnecessary adjuvant chemotherapy in I-IV colorectal cancer. Ther Adv Med Oncol 2024; 16:17588359231220607. [PMID: 38282662 PMCID: PMC10822076 DOI: 10.1177/17588359231220607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 11/21/2023] [Indexed: 01/30/2024] Open
Abstract
Background Circulating tumor DNA (ctDNA) has emerged as a biomarker that can define the risk of recurrence after curative-intent surgery for patients with colorectal cancer (CRC). However, beyond the predictive power of postoperative ctDNA detection, the efficacy and potential limitations of ctDNA detection urgently need to be fully elucidated in a large cohort of CRC. Objectives To define potentially cured CRC patients through ctDNA monitoring following surgery. Design A prospective, multicenter, observational study. Methods We enrolled 309 patients with stages I-IV CRC who underwent definitive surgery. Tumor tissues were sequenced by a custom-designed next-generation sequencing panel to identify somatic mutations. Plasma was analyzed using a ctDNA-based molecular residual disease (MRD) assay which integrated tumor-genotype-informed and tumor-genotype-naïve ctDNA analysis. The turnaround time of the assay was 10-14 days. Results Postoperative ctDNA was detected in 5.4%, 13.8%, 15%, and 30% of patients with stage I, II, III, and IV disease, respectively, and in 17.5% of all longitudinal samples. Patients with positive postsurgery MRD had a higher recurrence rate than those with negative postsurgery MRD [hazard ratio (HR), 13.17; p < 0.0001], producing a sensitivity of 64.6%, a specificity of 94.8%, a positive predictive value (PPV) of 75.6%, and a negative predictive value (NPV) of 91.5%. Furthermore, patients with positive longitudinal MRD also had a significantly higher recurrence rate (HR, 14.44; p < 0.0001), with increased sensitivity (75.0%), specificity (94.9%), PPV (79.6%), and NPV (93.4%). Subgroup analyses revealed that adjuvant therapy did not confer superior survival for patients with undetectable or detectable MRD. In addition, MRD detection was less effective in identifying lung-only and peritoneal metastases. Conclusion Postoperative ctDNA status is a strong predictor of recurrence independent of stage and microsatellite instability status. Longitudinal undetectable MRD could be used to define the potentially cured population in CRC patients undergoing curative-intent surgery.
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Affiliation(s)
- Wenhua Fan
- Department of Colorectal Surgery, Sun Yat-Sen University Cancer Center, Guangzhou, China
- Collaborative Innovation Center for Cancer Medicine, State Key Laboratory of Oncology in South China, Sun Yat-Sen University Cancer Center, Guangzhou, China
| | - Zhiyuan Xia
- Department of Colorectal & Anal Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | | | - Dagui Lin
- Department of Colorectal Surgery, Sun Yat-Sen University Cancer Center, Guangzhou, China
- Collaborative Innovation Center for Cancer Medicine, State Key Laboratory of Oncology in South China, Sun Yat-Sen University Cancer Center, Guangzhou, China
| | - Fang Li
- Geneplus-Beijing, Beijing, China
| | - Yang Zheng
- Department of General Surgery, The First Affiliated Hospital of Shantou University Medical College, Shantou, China
| | - Jiongyong Luo
- Department of General Surgery, The First Affiliated Hospital of Shantou University Medical College, Shantou, China
| | | | | | - Wei Gao
- Geneplus-Beijing, Beijing, China
| | | | - Feiran Zhang
- Department of General Surgery, The First Affiliated Hospital of Shantou University Medical College, No. 57 Changping Road, Jinping District, Shantou, Guangdong 515041, China
| | - Sen Zhang
- Department of Colorectal & Anal Surgery, The First Affiliated Hospital of Guangxi Medical University, No. 6 Shuangyong Road, Nanning 530021, China
| | - Liren Li
- Department of Colorectal Surgery, Sun Yat-Sen University Cancer Center, Guangzhou, China
- Collaborative Innovation Center for Cancer Medicine, State Key Laboratory of Oncology in South China, Sun Yat-Sen University Cancer Center, 651 Dongfeng Road East, Guangzhou 510060, China
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14
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Martin-Alonso C, Tabrizi S, Xiong K, Blewett T, Sridhar S, Crnjac A, Patel S, An Z, Bekdemir A, Shea D, Wang ST, Rodriguez-Aponte S, Naranjo CA, Rhoades J, Kirkpatrick JD, Fleming HE, Amini AP, Golub TR, Love JC, Bhatia SN, Adalsteinsson VA. Priming agents transiently reduce the clearance of cell-free DNA to improve liquid biopsies. Science 2024; 383:eadf2341. [PMID: 38236959 DOI: 10.1126/science.adf2341] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Accepted: 12/01/2023] [Indexed: 01/23/2024]
Abstract
Liquid biopsies enable early detection and monitoring of diseases such as cancer, but their sensitivity remains limited by the scarcity of analytes such as cell-free DNA (cfDNA) in blood. Improvements to sensitivity have primarily relied on enhancing sequencing technology ex vivo. We sought to transiently augment the level of circulating tumor DNA (ctDNA) in a blood draw by attenuating its clearance in vivo. We report two intravenous priming agents given 1 to 2 hours before a blood draw to recover more ctDNA. Our priming agents consist of nanoparticles that act on the cells responsible for cfDNA clearance and DNA-binding antibodies that protect cfDNA. In tumor-bearing mice, they greatly increase the recovery of ctDNA and improve the sensitivity for detecting small tumors.
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Affiliation(s)
- Carmen Martin-Alonso
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Harvard-MIT Division of Health Sciences and Technology, Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Shervin Tabrizi
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Department of Radiation Oncology, Massachusetts General Hospital, Boston, MA 02114, USA
- Harvard Medical School, Boston, MA 02115, USA
| | - Kan Xiong
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Timothy Blewett
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | - Andjela Crnjac
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Sahil Patel
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Division of Pulmonary and Critical Care, Department of Medicine, Massachusetts General Hospital, Boston, MA 02124, USA
| | - Zhenyi An
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Ahmet Bekdemir
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Douglas Shea
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Shih-Ting Wang
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Sergio Rodriguez-Aponte
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Christopher A Naranjo
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Justin Rhoades
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Jesse D Kirkpatrick
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Harvard-MIT Division of Health Sciences and Technology, Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Heather E Fleming
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Ava P Amini
- Microsoft Research, Cambridge, MA 02142, USA
| | - Todd R Golub
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Harvard Medical School, Boston, MA 02115, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - J Christopher Love
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Sangeeta N Bhatia
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Harvard-MIT Division of Health Sciences and Technology, Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
- Wyss Institute at Harvard University, Boston, MA 02215, USA
- Howard Hughes Medical Institute, Cambridge, MA 02138, USA
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15
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Dong Q, Chen C, Hu Y, Zhang W, Yang X, Qi Y, Zhu C, Chen X, Shen X, Ji W. Clinical application of molecular residual disease detection by circulation tumor DNA in solid cancers and a comparison of technologies: review article. Cancer Biol Ther 2023; 24:2274123. [PMID: 37955635 PMCID: PMC10653633 DOI: 10.1080/15384047.2023.2274123] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Accepted: 08/04/2023] [Indexed: 11/14/2023] Open
Abstract
Molecular residual disease (MRD), detected by circulating tumor DNA (ctDNA) can be involved in the entire process of solid tumor management, including recurrence prediction, efficacy evaluation, and risk stratification. Currently, the detection technologies are divided into two main categories, as follows: tumor-agnostic and tumor informed. Tumor-informed assay obtains mutation information by sequencing tumor tissue samples before blood MRD monitoring, followed by formulation of a personalized MRD panel. Tumor-agnostic assays are carried out using a fixed panel without the mutation information from primary tumor tissue. The choice of testing strategy may depend on the level of evidence from ongoing randomized clinical trials, investigator preference, cost-effectiveness, patient economics, and availability of tumor tissue. The review describes the difference between tumor informed and tumor agnostic detection. In addition, the clinical application of ctDNA MRD in solid tumors was introduced, with emphasis on lung cancer, colorectal cancer, Urinary system cancer, and breast cancer.
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Affiliation(s)
- Qiantong Dong
- Department of Gastrointestinal Surveillance, The Second Affiliated Hospital and Yuying Children’s Hospital of Wenzhou Medical University, Lucheng District, Wenzhou, Zhejiang, China
| | - Chenbin Chen
- Department of Gastrointestinal Surveillance, The Second Affiliated Hospital and Yuying Children’s Hospital of Wenzhou Medical University, Lucheng District, Wenzhou, Zhejiang, China
- Department of Gastrointestinal Surveillance, The First Affiliated Hospital of Wenzhou Medical University, Ouhai District, Wenzhou City, Zhejiang, China
| | - Yuanbo Hu
- Department of Gastrointestinal Surveillance, The Second Affiliated Hospital and Yuying Children’s Hospital of Wenzhou Medical University, Lucheng District, Wenzhou, Zhejiang, China
- Department of Gastrointestinal Surveillance, The First Affiliated Hospital of Wenzhou Medical University, Ouhai District, Wenzhou City, Zhejiang, China
| | - Weiteng Zhang
- Department of Gastrointestinal Surveillance, The Second Affiliated Hospital and Yuying Children’s Hospital of Wenzhou Medical University, Lucheng District, Wenzhou, Zhejiang, China
| | - Xinxin Yang
- Department of Gastrointestinal Surveillance, The First Affiliated Hospital of Wenzhou Medical University, Ouhai District, Wenzhou City, Zhejiang, China
| | - Yingxue Qi
- The Medical Department, Jiangsu Simcere Diagnostics Co.Ltd, The state Key Laboratory of Neurology and Oncology Drug Development, Nanjing, China
| | - Chan Zhu
- The Medical Department, Jiangsu Simcere Diagnostics Co.Ltd, The state Key Laboratory of Neurology and Oncology Drug Development, Nanjing, China
| | - Xiaodong Chen
- Department of Gastrointestinal Surveillance, The Second Affiliated Hospital and Yuying Children’s Hospital of Wenzhou Medical University, Lucheng District, Wenzhou, Zhejiang, China
| | - Xian Shen
- Department of Gastrointestinal Surveillance, The Second Affiliated Hospital and Yuying Children’s Hospital of Wenzhou Medical University, Lucheng District, Wenzhou, Zhejiang, China
- Department of Gastrointestinal Surveillance, The First Affiliated Hospital of Wenzhou Medical University, Ouhai District, Wenzhou City, Zhejiang, China
| | - Weiping Ji
- Department of Gastrointestinal Surveillance, The Second Affiliated Hospital and Yuying Children’s Hospital of Wenzhou Medical University, Lucheng District, Wenzhou, Zhejiang, China
- Department of Gastrointestinal Surveillance, The First Affiliated Hospital of Wenzhou Medical University, Ouhai District, Wenzhou City, Zhejiang, China
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16
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Alix-Panabières C, Marchetti D, Lang JE. Liquid biopsy: from concept to clinical application. Sci Rep 2023; 13:21685. [PMID: 38066040 PMCID: PMC10709452 DOI: 10.1038/s41598-023-48501-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2023] Open
Affiliation(s)
- Catherine Alix-Panabières
- Laboratory of Rare Circulating Human Cells (LCCRH), University Medical Center of Montpellier, Montpellier, France.
- CREEC/CANECEV, MIVEGEC (CREES), Université de Montpellier, CNRS, IRD, Montpellier, France.
- European Liquid Biopsy Society (ELBS), Hamburg, Germany.
- Institut Universitaire de Recherche Clinique (IURC), 641, avenue du Doyen Gaston Giraud, 34093, Montpellier Cedex 5, France.
| | - Dario Marchetti
- Departments of Internal Medicine and Pathology, The University of New Mexico Health Sciences Center, UNM Comprehensive Cancer Center, MSC07 4025, 1 University of New Mexico, Albuquerque, NM, 87131, USA
| | - Julie E Lang
- Breast Surgery and Cancer Biology, Cleveland Clinic, 9500 Euclid Ave, A80, Cleveland, OH, 44195, USA
- Case Comprehensive Cancer Center, Cleveland Clinic, 9500 Euclid Ave, A80, Cleveland, OH, 44195, USA
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17
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Lynce F, Mainor C, Donahue RN, Geng X, Jones G, Schlam I, Wang H, Toney NJ, Jochems C, Schlom J, Zeck J, Gallagher C, Nanda R, Graham D, Stringer-Reasor EM, Denduluri N, Collins J, Chitalia A, Tiwari S, Nunes R, Kaltman R, Khoury K, Gatti-Mays M, Tarantino P, Tolaney SM, Swain SM, Pohlmann P, Parsons HA, Isaacs C. Adjuvant nivolumab, capecitabine or the combination in patients with residual triple-negative breast cancer: the OXEL randomized phase II study. medRxiv 2023:2023.12.04.23297559. [PMID: 38105958 PMCID: PMC10723519 DOI: 10.1101/2023.12.04.23297559] [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: 12/19/2023]
Abstract
Chemotherapy and immune checkpoint inhibitors have a role in the post-neoadjuvant setting in patients with triple-negative breast cancer (TNBC). However, the effects of nivolumab, a checkpoint inhibitor, capecitabine, or the combination in changing peripheral immunoscore (PIS) remains unclear. This open-label randomized phase II OXEL study (NCT03487666) aimed to assess the immunologic effects of nivolumab, capecitabine, or the combination in terms of the change in PIS (primary endpoint). Secondary endpoints include the presence of ctDNA, toxicity, clinical outcomes at 2-years and association of ctDNA and PIS with clinical outcomes. Forty-five women with TNBC and residual invasive disease after standard neoadjuvant chemotherapy were randomized to nivolumab, capecitabine, or the combination. Here we show that a combination of nivolumab plus capecitabine leads to a greater increase in PIS from baseline to week 6 (91%) compared with nivolumab (47%) or capecitabine (53%) alone (log-rank p = 0.08), meeting the pre-specified primary endpoint. In addition, the presence of circulating tumor DNA (ctDNA) was associated with disease recurrence, with no new safety signals in the combination arm. Our results provide efficacy and safety data on this combination in TNBC and support further development of PIS and ctDNA analyses to identify patients at high risk of recurrence.
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Affiliation(s)
- Filipa Lynce
- Division of 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
| | - Candace Mainor
- MedStar Georgetown University Hospital, Washington, DC, USA
| | - Renee N. Donahue
- Center for Immuno-Oncology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Xue Geng
- Georgetown University, Washington, DC
| | - Greg Jones
- NeoGenomics, Research Triangle Park, NC, USA
| | - Ilana Schlam
- MedStar Washington Hospital Center, Washington, DC, USA
- Tufts Medical Center, Boston, MA, USA
| | | | - Nicole J. Toney
- Center for Immuno-Oncology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Caroline Jochems
- Center for Immuno-Oncology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Jeffrey Schlom
- Center for Immuno-Oncology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Jay Zeck
- MedStar Georgetown University Hospital, Washington, DC, USA
| | | | | | - Deena Graham
- Hackensack University Medical Center, Hackensack, NJ, USA
| | | | | | - Julie Collins
- MedStar Georgetown University Hospital, Washington, DC, USA
| | - Ami Chitalia
- MedStar Washington Hospital Center, Washington, DC, USA
| | - Shruti Tiwari
- MedStar Washington Hospital Center, Washington, DC, USA
| | - Raquel Nunes
- Johns Hopkins Sidney Kimmel Cancer Center, Baltimore, MD, USA
| | | | - Katia Khoury
- University of Alabama at Birmingham, Birmingham, AL, USA
| | | | - Paolo Tarantino
- Division of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Sara M. Tolaney
- Division of 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
| | | | - Paula Pohlmann
- MedStar Georgetown University Hospital, Washington, DC, USA
| | - Heather A. Parsons
- Division of 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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18
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Zavarykina TM, Lomskova PK, Pronina IV, Khokhlova SV, Stenina MB, Sukhikh GT. Circulating Tumor DNA Is a Variant of Liquid Biopsy with Predictive and Prognostic Clinical Value in Breast Cancer Patients. Int J Mol Sci 2023; 24:17073. [PMID: 38069396 PMCID: PMC10706922 DOI: 10.3390/ijms242317073] [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] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 11/24/2023] [Accepted: 11/27/2023] [Indexed: 12/18/2023] Open
Abstract
This paper introduces the reader to the field of liquid biopsies and cell-free nucleic acids, focusing on circulating tumor DNA (ctDNA) in breast cancer (BC). BC is the most common type of cancer in women, and progress with regard to treatment has been made in recent years. Despite this, there remain a number of unresolved issues in the treatment of BC; in particular, early detection and diagnosis, reliable markers of response to treatment and for the prediction of recurrence and metastasis, especially for unfavorable subtypes, are needed. It is also important to identify biomarkers for the assessment of drug resistance and for disease monitoring. Our work is devoted to ctDNA, which may be such a marker. Here, we describe its main characteristics and potential applications in clinical oncology. This review considers the results of studies devoted to the analysis of the prognostic and predictive roles of various methods for the determination of ctDNA in BC patients. Currently known epigenetic changes in ctDNA with clinical significance are reviewed. The possibility of using ctDNA as a predictive and prognostic marker for monitoring BC and predicting the recurrence and metastasis of cancer is also discussed, which may become an important part of a precision approach to the treatment of BC.
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Affiliation(s)
- Tatiana M. Zavarykina
- N.M. Emanuel Institute of Biochemical Physics of the Russian Academy of Sciences, Moscow 119334, Russia;
- “B.I. Kulakov National Medical Research Center of Obstetrics, Gynecology, and Perinatology of Ministry of Health of the Russian Federation, Moscow 117997, Russia; (S.V.K.); (G.T.S.)
| | - Polina K. Lomskova
- N.M. Emanuel Institute of Biochemical Physics of the Russian Academy of Sciences, Moscow 119334, Russia;
| | - Irina V. Pronina
- Institute of General Pathology and Pathophysiology, Moscow 125315, Russia;
| | - Svetlana V. Khokhlova
- “B.I. Kulakov National Medical Research Center of Obstetrics, Gynecology, and Perinatology of Ministry of Health of the Russian Federation, Moscow 117997, Russia; (S.V.K.); (G.T.S.)
| | - Marina B. Stenina
- “N.N. Blokhin National Medical Research Center of Oncology of Ministry of Health of the Russian Federation, Moscow 115522, Russia;
| | - Gennady T. Sukhikh
- “B.I. Kulakov National Medical Research Center of Obstetrics, Gynecology, and Perinatology of Ministry of Health of the Russian Federation, Moscow 117997, Russia; (S.V.K.); (G.T.S.)
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19
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Keup C, Kimmig R, Kasimir-Bauer S. The Diversity of Liquid Biopsies and Their Potential in Breast Cancer Management. Cancers (Basel) 2023; 15:5463. [PMID: 38001722 PMCID: PMC10670968 DOI: 10.3390/cancers15225463] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 11/10/2023] [Accepted: 11/14/2023] [Indexed: 11/26/2023] Open
Abstract
Analyzing blood as a so-called liquid biopsy in breast cancer (BC) patients has the potential to adapt therapy management. Circulating tumor cells (CTCs), extracellular vesicles (EVs), cell-free DNA (cfDNA) and other blood components mirror the tumoral heterogeneity and could support a range of clinical decisions. Multi-cancer early detection tests utilizing blood are advancing but are not part of any clinical routine yet. Liquid biopsy analysis in the course of neoadjuvant therapy has potential for therapy (de)escalation.Minimal residual disease detection via serial cfDNA analysis is currently on its way. The prognostic value of blood analytes in early and metastatic BC is undisputable, but the value of these prognostic biomarkers for clinical management is controversial. An interventional trial confirmed a significant outcome benefit when therapy was changed in case of newly emerging cfDNA mutations under treatment and thus showed the clinical utility of cfDNA analysis for therapy monitoring. The analysis of PIK3CA or ESR1 variants in plasma of metastatic BC patients to prescribe targeted therapy with alpesilib or elacestrant has already arrived in clinical practice with FDA-approved tests available and is recommended by ASCO. The translation of more liquid biopsy applications into clinical practice is still pending due to a lack of knowledge of the analytes' biology, lack of standards and difficulties in proving clinical utility.
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Affiliation(s)
- Corinna Keup
- Department of Gynecology and Obstetrics, University Hospital of Essen, 45147 Essen, Germany
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20
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Medford AJ, Moy B, Spring LM, Hurvitz SA, Turner NC, Bardia A. Molecular Residual Disease in Breast Cancer: Detection and Therapeutic Interception. Clin Cancer Res 2023; 29:4540-4548. [PMID: 37477704 DOI: 10.1158/1078-0432.ccr-23-0757] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 05/12/2023] [Accepted: 07/10/2023] [Indexed: 07/22/2023]
Abstract
Breast cancer remains a leading cause of cancer-related death in women despite screening and therapeutic advances. Early detection allows for resection of local disease; however, patients can develop metastatic recurrences years after curative treatment. There is no reliable blood-based monitoring after curative therapy, and radiographic evaluation for metastatic disease is performed only in response to symptoms. Advances in circulating tumor DNA (ctDNA) assays have allowed for a potential option for blood-based monitoring. The detection of ctDNA in the absence of overt metastasis or recurrent disease indicates molecular evidence of cancer, defined as molecular residual disease (MRD). Multiple studies have shown that MRD detection is strongly associated with disease recurrence, with a lead time prior to clinical evidence of recurrence of many months. Importantly, it is still unclear whether treatment changes in response to ctDNA detection will improve outcomes. There are currently ongoing trials evaluating the efficacy of therapy escalation in the setting of MRD, and these studies are being conducted in all major breast cancer subtypes. Additional therapies under study include CDK4/6 inhibitors, PARP inhibitors, HER2-targeted therapies, and immunotherapy. This review will summarize the underlying scientific principles of various MRD assays, their known prognostic roles in early breast cancer, and the ongoing clinical trials assessing the efficacy of therapy escalation in the setting of MRD.
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Affiliation(s)
- Arielle J Medford
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, Massachusetts
| | - Beverly Moy
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, Massachusetts
| | - Laura M Spring
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, Massachusetts
| | - Sara A Hurvitz
- University of California Los Angeles, David Geffen School of Medicine, Los Angeles, California
| | - Nicholas C Turner
- The Royal Marsden NHS Foundation Trust, Breast Cancer Now Research Centre, The Institute of Cancer Research, London, United Kingdom
| | - Aditya Bardia
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, Massachusetts
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21
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Efthymiou V, Queenan N, Haas M, Naegele S, Goss D, Faden DL. circulating tumor DNA in the immediate post-operative setting. medRxiv 2023:2023.09.30.23296390. [PMID: 37873394 PMCID: PMC10593016 DOI: 10.1101/2023.09.30.23296390] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Background Circulating tumor DNA (ctDNA) has emerged as an accurate real-time biomarker of disease status across most solid tumor types. Most studies evaluating the utility of ctDNA have focused on time points weeks to months after surgery, which for many cancer types, is significantly later than decision-making time points for adjuvant treatment. In this systematic review, we summarize the state of the literature on the feasibility of using ctDNA as a biomarker in the immediate postoperative period. Methods We performed a systematic review evaluating the early kinetics, defined here as three days, of ctDNA in patients who underwent curative-intent surgery across several cancer types. Results Among the 2057 studies identified, we evaluated eight cohort studies with ctDNA levels measured within the first three days after surgery. Across six different cancer types, all studies showed an increased risk of cancer recurrence in patients with a positive early postoperative ctDNA level. Discussion While ctDNA clearance kinetics appear to vary based on tumor type, across all studies- detectable ctDNA after surgery was predictive of recurrence, suggesting early postoperative timepoints could be feasibly used for determining minimal residual disease. However, larger studies need to be performed to better understand the precise kinetics of ctDNA clearance across different cancer types as well as to determine optimal postoperative time points. Synopsis This systematic review analyzed the use of ctDNA as a biomarker for minimal residual disease detection in the early postoperative setting and found that ctDNA detection within three days after surgery is associated with an increased risk of recurrence.
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Affiliation(s)
- Vasileios Efthymiou
- Department of Otolaryngology-Head and Neck Surgery Massachusetts Eye and Ear, Boston, Massachusetts
| | - Natalia Queenan
- Department of Otolaryngology-Head and Neck Surgery Massachusetts Eye and Ear, Boston, Massachusetts
| | - Markus Haas
- Department of Otolaryngology-Head and Neck Surgery Massachusetts Eye and Ear, Boston, Massachusetts
| | - Saskia Naegele
- Department of Otolaryngology-Head and Neck Surgery Massachusetts Eye and Ear, Boston, Massachusetts
| | - Deborah Goss
- Department of Otolaryngology-Head and Neck Surgery Massachusetts Eye and Ear, Boston, Massachusetts
| | - Daniel L. Faden
- Department of Otolaryngology-Head and Neck Surgery Massachusetts Eye and Ear, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
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22
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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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23
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Medford AJ, Denault EN, Moy B, Parsons HA, Bardia A. Circulating Tumor DNA in Breast Cancer: Current and Future Applications. Clin Breast Cancer 2023; 23:687-692. [PMID: 37438196 DOI: 10.1016/j.clbc.2023.06.008] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 06/14/2023] [Accepted: 06/17/2023] [Indexed: 07/14/2023]
Abstract
The assessment of plasma for circulating tumor DNA (ctDNA) via liquid biopsy has revolutionized our understanding of breast cancer pathogenesis and evolution. Historically, genotyping evaluation of breast cancer required invasive tissue biopsy, limiting potential for serial evaluation over the treatment course of advanced breast cancer, and not allowing for assessment for residual disease in early breast cancer after resection. However, technological advances over the years have led to an increase in the clinical use of ctDNA as a liquid biopsy for genotype-matched therapy selection and monitoring for patients undergoing treatment for advanced breast cancer. Furthermore, increasingly sensitive assays are being developed to facilitate detection of molecular evidence of residual or recurrent disease in localized breast cancer after definitive therapy. In this review, we discuss the current and future applications of ctDNA in breast cancer. Rational applications of ctDNA offer the potential to further refine patient-centered care and personalize treatment based on molecularly defined risk assessments for patients with breast cancer.
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Affiliation(s)
- Arielle J Medford
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA; Broad Institute of MIT & Harvard, Cambridge, MA.
| | - Elyssa N Denault
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA
| | - Beverly Moy
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA
| | | | - Aditya Bardia
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA
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Ganesan S. Treating Early and Often: Targeted Therapeutics in the Adjuvant Setting. JCO Precis Oncol 2023; 7:e2300551. [PMID: 38096471 PMCID: PMC10730077 DOI: 10.1200/po.23.00551] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Accepted: 11/01/2023] [Indexed: 12/18/2023] Open
Affiliation(s)
- Shridar Ganesan
- Rutgers Cancer Institute of New Jersey, Department of Medicine and Pharmacology, Rutgers Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, New Brunswick, NJ
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25
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Nishio K, Sakai K, Nishio M, Seto T, Visseren-Grul C, Carlsen M, Matsui T, Enatsu S, Nakagawa K. Impact of ramucirumab plus erlotinib on circulating cell-free DNA from patients with untreated metastatic non-small cell lung cancer with EGFR-activating mutations (RELAY phase 3 randomized study). Transl Lung Cancer Res 2023; 12:1702-1716. [PMID: 37691865 PMCID: PMC10483085 DOI: 10.21037/tlcr-22-736] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 07/20/2023] [Indexed: 09/12/2023]
Abstract
Background An exploratory, proof-of-concept, liquid biopsy addendum to examine biomarkers within cell-free DNA (cfDNA) in the RELAY phase 3, randomized, double-blind, placebo-controlled study was conducted. RELAY showed improved progression-free survival (PFS) with ramucirumab (RAM), a human immunoglobulin G1 vascular endothelial growth factor receptor 2 antagonist, plus erlotinib (ERL), a tyrosine kinase inhibitor, compared with placebo (PL) plus ERL. Methods Treatment-naïve patients with endothelial growth factor receptor (EGFR)-mutated metastatic non-small cell lung cancer were randomized (1:1) to RAM + ERL or PL + ERL. Plasma samples were collected at baseline, on treatment, and at 30-day post-study treatment discontinuation follow-up. Baseline and treatment-emergent gene alterations and EGFR-activating mutation allele counts were investigated by next-generation sequencing (NGS) and droplet digital polymerase chain reaction (ddPCR), respectively. cfDNA concentration and fragment size were evaluated by real-time polymerase chain reaction and the BioAnalyzer. Patients with a valid baseline plasma sample were included (70 RAM + ERL, 61 PL + ERL). Results TP53 mutation was the most frequently co-occurring baseline gene alteration (43%). Post-study treatment discontinuation EGFR T790M mutation rates were 54.5% (6/11) and 41.2% (7/17) by ddPCR, and 22.2% (2/9) and 29.4% (5/17) by NGS, in the RAM + ERL and PL + ERL arms, respectively. EGFR-activating mutation allele count decreased at Cycle 4 in both treatment arms and was sustained at follow-up with RAM + ERL. PFS improved for patients with no detectable EGFR-activating mutation at Cycle 4 vs. those with detectable EGFR-activating mutation. Total cfDNA concentration increased from baseline at Cycle 4 and through to follow-up with RAM + ERL. cfDNA fragment size was similar between treatment arms at baseline [mean (standard deviation) base pairs: RAM + ERL, 173.4 (2.6); PL + ERL, 172.9 (3.2)] and was shorter at Cycle 4 with RAM + ERL vs. PL + ERL [169.5 (2.8) vs. 174.1 (3.3), respectively; P<0.0001]. Baseline vs. Cycle 4 paired analysis showed a decrease in cfDNA fragment size for 84% (48/57) and 23% (11/47) of patient samples in the RAM + ERL and PL + ERL arms, respectively. Conclusions EGFR-activating mutation allele count was suppressed, total cfDNA concentration increased, and short fragment-sized cfDNA increased with RAM + ERL, suggesting the additional anti-tumor effect of RAM may contribute to the PFS benefit observed in RELAY with RAM + ERL vs. PL + ERL. Trial Registration ClinicalTrials.gov; identifier: NCT02411448.
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Affiliation(s)
- Kazuto Nishio
- Department of Genome Biology, Kindai University Faculty of Medicine, Osaka, Japan
| | - Kazuko Sakai
- Department of Genome Biology, Kindai University Faculty of Medicine, Osaka, Japan
| | - Makoto Nishio
- Department of Thoracic Medical Oncology, The Cancer Institute Hospital of Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Takashi Seto
- National Hospital Organization Kyushu Cancer Center, Fukuoka, Japan
| | | | | | | | | | - Kazuhiko Nakagawa
- Department of Medical Oncology, Kindai University Faculty of Medicine, Osaka, Japan
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26
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Zhu L, Xu R, Yang L, Shi W, Zhang Y, Liu J, Li X, Zhou J, Bing P. Minimal residual disease (MRD) detection in solid tumors using circulating tumor DNA: a systematic review. Front Genet 2023; 14:1172108. [PMID: 37636270 PMCID: PMC10448395 DOI: 10.3389/fgene.2023.1172108] [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] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 04/20/2023] [Indexed: 08/29/2023] Open
Abstract
Minimal residual disease (MRD) refers to a very small number of residual tumor cells in the body during or after treatment, representing the persistence of the tumor and the possibility of clinical progress. Circulating tumor DNA (ctDNA) is a DNA fragment actively secreted by tumor cells or released into the circulatory system during the process of apoptosis or necrosis of tumor cells, which emerging as a non-invasive biomarker to dynamically monitor the therapeutic effect and prediction of recurrence. The feasibility of ctDNA as MRD detection and the revolution in ctDNA-based liquid biopsies provides a potential method for cancer monitoring. In this review, we summarized the main methods of ctDNA detection (PCR-based Sequencing and Next-Generation Sequencing) and their advantages and disadvantages. Additionally, we reviewed the significance of ctDNA analysis to guide the adjuvant therapy and predict the relapse of lung, breast and colon cancer et al. Finally, there are still many challenges of MRD detection, such as lack of standardization, false-negatives or false-positives results make misleading, and the requirement of validation using large independent cohorts to improve clinical outcomes.
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Affiliation(s)
- Lemei Zhu
- Hunan Key Laboratory of the Research and Development of Novel Pharmaceutical Preparations, Changsha, China
- Academician Workstation, Changsha Medical University, Changsha, China
- School of Public Health, Changsha Medical University, Changsha, China
| | - Ran Xu
- Geneis Beijing Co., Ltd., Beijing, China
| | | | - Wei Shi
- Geneis Beijing Co., Ltd., Beijing, China
| | - Yuan Zhang
- Hunan Key Laboratory of the Research and Development of Novel Pharmaceutical Preparations, Changsha, China
- Academician Workstation, Changsha Medical University, Changsha, China
- School of Public Health, Changsha Medical University, Changsha, China
| | - Juan Liu
- Hunan Key Laboratory of the Research and Development of Novel Pharmaceutical Preparations, Changsha, China
- Academician Workstation, Changsha Medical University, Changsha, China
- School of Public Health, Changsha Medical University, Changsha, China
| | - Xi Li
- Department of Orthopedics, Xiangya Hospital Central South University, Changsha, China
| | - Jun Zhou
- Hunan Key Laboratory of the Research and Development of Novel Pharmaceutical Preparations, Changsha, China
- Academician Workstation, Changsha Medical University, Changsha, China
| | - Pingping Bing
- Hunan Key Laboratory of the Research and Development of Novel Pharmaceutical Preparations, Changsha, China
- Academician Workstation, Changsha Medical University, Changsha, China
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27
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Santini D, Botticelli A, Galvano A, Iuliani M, Incorvaia L, Gristina V, Taffon C, Foderaro S, Paccagnella E, Simonetti S, Fazio F, Scagnoli S, Pomati G, Pantano F, Perrone G, De Falco E, Russo A, Spinelli GP. Network approach in liquidomics landscape. J Exp Clin Cancer Res 2023; 42:193. [PMID: 37542343 PMCID: PMC10401883 DOI: 10.1186/s13046-023-02743-9] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 06/27/2023] [Indexed: 08/06/2023] Open
Abstract
Tissue-based biopsy is the present main tool to explore the molecular landscape of cancer, but it also has many limits to be frequently executed, being too invasive with the risk of side effects. These limits and the ability of cancer to constantly evolve its genomic profile, have recently led to the need of a less invasive and more accurate alternative, such as liquid biopsy. By searching Circulating Tumor Cells and residues of their nucleic acids or other tumor products in body fluids, especially in blood, but also in urine, stools and saliva, liquid biopsy is becoming the future of clinical oncology. Despite the current lack of a standardization for its workflows, that makes it hard to be reproduced, liquid biopsy has already obtained promising results for cancer screening, diagnosis, prognosis, and risk of recurrence.Through a more accessible molecular profiling of tumors, it could become easier to identify biomarkers predictive of response to treatment, such as EGFR mutations in non-small cell lung cancer and KRAS mutations in colorectal cancer, or Microsatellite Instability and Mismatch Repair as predictive markers of pembrolizumab response.By monitoring circulating tumor DNA in longitudinal repeated sampling of blood we could also predict Minimal Residual Disease and the risk of recurrence in already radically resected patients.In this review we will discuss about the current knowledge of limitations and strengths of the different forms of liquid biopsies for its inclusion in normal cancer management, with a brief nod to their newest biomarkers and its future implications.
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Affiliation(s)
- Daniele Santini
- Oncologia Medica A, Policlinico Umberto 1, La Sapienza Università Di Roma, Rome, Italy
| | - Andrea Botticelli
- Oncologia Medica A, Policlinico Umberto 1, La Sapienza Università Di Roma, Rome, Italy
| | - Antonio Galvano
- Section of Medical Oncology, Department of Surgical, Oncological and Oral Sciences, University of Palermo, Palermo, Italy
| | - Michele Iuliani
- Medical Oncology, Fondazione Policlinico Universitario Campus Bio-Medico, Department of Medicine and Surgery, Università Campus Bio-Medico Di Roma, Selcetta, Italy
| | - Lorena Incorvaia
- Section of Medical Oncology, Department of Surgical, Oncological and Oral Sciences, University of Palermo, Palermo, Italy
| | - Valerio Gristina
- Section of Medical Oncology, Department of Surgical, Oncological and Oral Sciences, University of Palermo, Palermo, Italy
| | - Chiara Taffon
- Anatomical Pathology Operative Research Unit, Fondazione Policlinico Universitario Campus Bio-Medico, Rome, Italy
- Department of Medicine and Surgery, Research Unit of Anatomical Pathology, Università Campus Bio-Medico Di Roma, Rome, Italy
| | - Simone Foderaro
- Medical Oncology, Fondazione Policlinico Universitario Campus Bio-Medico, Department of Medicine and Surgery, Università Campus Bio-Medico Di Roma, Selcetta, Italy
| | - Elisa Paccagnella
- Department of Medical Surgical Sciences and Biotechnologies, Sapienza University of Rome, C.So Della Repubblica 79, 04100, Latina, Italy
| | - Sonia Simonetti
- Medical Oncology, Fondazione Policlinico Universitario Campus Bio-Medico, Department of Medicine and Surgery, Università Campus Bio-Medico Di Roma, Selcetta, Italy
| | - Federico Fazio
- UOC Oncologia Territoriale, Polo Pontino, La Sapienza Università Di Roma, Latina, Italy.
| | - Simone Scagnoli
- Oncologia Medica A, Policlinico Umberto 1, La Sapienza Università Di Roma, Rome, Italy
| | | | - Francesco Pantano
- Medical Oncology, Fondazione Policlinico Universitario Campus Bio-Medico, Department of Medicine and Surgery, Università Campus Bio-Medico Di Roma, Selcetta, Italy
| | - Giuseppe Perrone
- Anatomical Pathology Operative Research Unit, Fondazione Policlinico Universitario Campus Bio-Medico, Rome, Italy
- Department of Medicine and Surgery, Research Unit of Anatomical Pathology, Università Campus Bio-Medico Di Roma, Rome, Italy
| | - Elena De Falco
- Department of Medical Surgical Sciences and Biotechnologies, Sapienza University of Rome, C.So Della Repubblica 79, 04100, Latina, Italy
- Mediterranea Cardiocentro, 80122, Naples, Italy
| | - Antonio Russo
- Section of Medical Oncology, Department of Surgical, Oncological and Oral Sciences, University of Palermo, Palermo, Italy
| | - Gian Paolo Spinelli
- UOC Oncologia Territoriale, Polo Pontino, La Sapienza Università Di Roma, Latina, Italy
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Ryoo SB, Heo S, Lim Y, Lee W, Cho SH, Ahn J, Kang JK, Kim SY, Kim HP, Bang D, Kang SB, Yu CS, Oh ST, Park JW, Jeong SY, Kim YJ, Park KJ, Han SW, Kim TY. Personalised circulating tumour DNA assay with large-scale mutation coverage for sensitive minimal residual disease detection in colorectal cancer. Br J Cancer 2023; 129:374-381. [PMID: 37280413 PMCID: PMC10338477 DOI: 10.1038/s41416-023-02300-3] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 04/25/2023] [Accepted: 05/02/2023] [Indexed: 06/08/2023] Open
Abstract
BACKGROUND Postoperative minimal residual disease (MRD) detection using circulating-tumour DNA (ctDNA) requires a highly sensitive analysis platform. We have developed a tumour-informed, hybrid-capture ctDNA sequencing MRD assay. METHODS Personalised target-capture panels for ctDNA detection were designed using individual variants identified in tumour whole-exome sequencing of each patient. MRD status was determined using ultra-high-depth sequencing data of plasma cell-free DNA. The MRD positivity and its association with clinical outcome were analysed in Stage II or III colorectal cancer (CRC). RESULTS In 98 CRC patients, personalised panels for ctDNA sequencing were built from tumour data, including a median of 185 variants per patient. In silico simulation showed that increasing the number of target variants increases MRD detection sensitivity in low fractions (<0.01%). At postoperative 3-week, 21.4% of patients were positive for MRD by ctDNA. Postoperative positive MRD was strongly associated with poor disease-free survival (DFS) (adjusted hazard ratio 8.40, 95% confidence interval 3.49-20.2). Patients with a negative conversion of MRD after adjuvant therapy showed significantly better DFS (P < 0.001). CONCLUSION Tumour-informed, hybrid-capture-based ctDNA assay monitoring a large number of patient-specific mutations is a sensitive strategy for MRD detection to predict recurrence in CRC.
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Affiliation(s)
- Seung-Bum Ryoo
- Department of Surgery, Seoul National University Hospital, Seoul, Korea
| | | | | | | | | | - Jongseong Ahn
- IMBdx, Seoul, Korea
- Department of Chemistry, Yonsei University, Seoul, Korea
| | | | | | | | - Duhee Bang
- Department of Chemistry, Yonsei University, Seoul, Korea
| | - Sung-Bum Kang
- Department of Surgery, Seoul National University Bundang Hospital, Seongnam, Korea
| | - Chang Sik Yu
- Department of Surgery, Asan Medical Center, Seoul, Korea
| | - Seong Taek Oh
- Department of Surgery, The Catholic University of Korea Uijeongbu St. Mary's Hospital, Uijeongbu, Korea
| | - Ji Won Park
- Department of Surgery, Seoul National University Hospital, Seoul, Korea
| | - Seung-Yong Jeong
- Department of Surgery, Seoul National University Hospital, Seoul, Korea
| | - Young-Joon Kim
- Department of Biochemistry, Yonsei University, Seoul, Korea
| | - Kyu Joo Park
- Department of Surgery, Seoul National University Hospital, Seoul, Korea
| | - Sae-Won Han
- Department of Internal Medicine, Seoul National University Hospital, Seoul, Korea.
- Cancer Research Institute, Seoul National University, Seoul, Korea.
| | - Tae-You Kim
- IMBdx, Seoul, Korea
- Department of Internal Medicine, Seoul National University Hospital, Seoul, Korea
- Cancer Research Institute, Seoul National University, Seoul, Korea
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29
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Cohen SA, Liu MC, Aleshin A. Practical recommendations for using ctDNA in clinical decision making. Nature 2023; 619:259-268. [PMID: 37438589 DOI: 10.1038/s41586-023-06225-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 05/16/2023] [Indexed: 07/14/2023]
Abstract
The continuous improvement in cancer care over the past decade has led to a gradual decrease in cancer-related deaths. This is largely attributed to improved treatment and disease management strategies. Early detection of recurrence using blood-based biomarkers such as circulating tumour DNA (ctDNA) is being increasingly used in clinical practice. Emerging real-world data shows the utility of ctDNA in detecting molecular residual disease and in treatment-response monitoring, helping clinicians to optimize treatment and surveillance strategies. Many studies have indicated ctDNA to be a sensitive and specific biomarker for recurrence. However, most of these studies are largely observational or anecdotal in nature, and peer-reviewed data regarding the use of ctDNA are mainly indication-specific. Here we provide general recommendations on the clinical utility of ctDNA and how to interpret ctDNA analysis in different treatment settings, especially in patients with solid tumours. Specifically, we provide an understanding around the implications, strengths and limitations of this novel biomarker and how to best apply the results in clinical practice.
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Affiliation(s)
- Stacey A Cohen
- Fred Hutchinson Cancer Center, Seattle, WA, USA.
- University of Washington, Seattle, WA, USA.
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30
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Vlataki K, Antonouli S, Kalyvioti C, Lampri E, Kamina S, Mauri D, Harissis HV, Magklara A. Circulating Tumor DNA in the Management of Early-Stage Breast Cancer. Cells 2023; 12:1573. [PMID: 37371043 DOI: 10.3390/cells12121573] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 05/24/2023] [Accepted: 06/01/2023] [Indexed: 06/29/2023] Open
Abstract
Liquid biopsies refer to the isolation and analysis of tumor-derived biological material from body fluids, most commonly blood, in order to provide clinically valuable information for the management of cancer patients. Their non-invasive nature allows to overcome the limitations of tissue biopsy and complement the latter in guiding therapeutic decision-making. In the past years, several studies have demonstrated that circulating tumor DNA (ctDNA) detection can be used in the clinical setting to improve patient prognosis and monitor therapy response, especially in metastatic cancers. With the advent of significant technological advances in assay development, ctDNA can now be accurately and reliably identified in early-stage cancers despite its low levels in the bloodstream. In this review, we discuss the most important studies that highlight the potential clinical utility of ctDNA in early-stage breast cancer focusing on early diagnosis, detection of minimal residual disease and prediction of metastatic relapse. We also offer a concise description of the most sensitive techniques that are deemed appropriate for ctDNA detection in early-stage cancer and we examine their advantages and disadvantages, as they have been employed in various studies. Finally, we discuss future perspectives on how ctDNA could be better integrated into the everyday oncology practice.
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Affiliation(s)
- Katerina Vlataki
- Department of Clinical Chemistry, Faculty of Medicine, University of Ioannina, 45110 Ioannina, Greece
| | - Sevastiani Antonouli
- Department of Clinical Chemistry, Faculty of Medicine, University of Ioannina, 45110 Ioannina, Greece
| | - Christina Kalyvioti
- Breast Unit, Department of Surgery, University Hospital of Ioannina, 45500 Ioannina, Greece
| | - Evangeli Lampri
- Department of Pathology, University Hospital of Ioannina, 45500 Ioannina, Greece
| | - Sevasti Kamina
- Department of Pathology, University Hospital of Ioannina, 45500 Ioannina, Greece
| | - Davide Mauri
- Department of Medical Oncology, University Hospital of Ioannina, 45500 Ioannina, Greece
| | - Haralampos V Harissis
- Breast Unit, Department of Surgery, University Hospital of Ioannina, 45500 Ioannina, Greece
| | - Angeliki Magklara
- Department of Clinical Chemistry, Faculty of Medicine, University of Ioannina, 45110 Ioannina, Greece
- Biomedical Research Institute, Foundation for Research and Technology, 45110 Ioannina, Greece
- Institute of Biosciences, University Research Center of Ioannina (URCI), 45110 Ioannina, Greece
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31
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Singh H, Klempner SJ, Melnitchouk N, Chander DP, Negrea OG, Patel AK, Schlechter BL, Rubinson DA, Huffman BM, Nambiar C, Remland J, Andrews E, Leahy ME, Brais LK, Enzinger PC, Mamon HJ, Giannakis M, Meyerhardt JA, Ng K, Perez KJ, Aguirre AJ, Clark JW, Cleary JM, Wolpin BM. Highly Sensitive Circulating Tumor DNA Assay Aids Clinical Management of Radiographically Occult Isolated Peritoneal Metastases in Patients With GI Cancer. JCO Precis Oncol 2023; 7:e2200572. [PMID: 37343200 DOI: 10.1200/po.22.00572] [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] [Received: 10/14/2022] [Revised: 03/09/2023] [Accepted: 05/22/2023] [Indexed: 06/23/2023] Open
Abstract
PURPOSE GI cancers commonly spread to the peritoneal cavity, particularly from primary adenocarcinomas of the stomach and appendix. Peritoneal metastases are difficult to visualize on cross-sectional imaging and cause substantial morbidity and mortality. The purpose of this study was to determine whether serial highly sensitive tumor-informed circulating tumor DNA (ctDNA) measurements could longitudinally track changes in disease burden and inform clinical care. METHODS This was a retrospective case series of patients with gastric or appendiceal adenocarcinoma and isolated peritoneal disease that was radiographically occult. Patients underwent quantitative tumor-informed ctDNA testing (Signatera) as part of routine clinical care. No interventions were prespecified based on ctDNA results. RESULTS Of 13 patients studied, the median age was 65 (range, 45-75) years, with 7 (54%) women, 5 (38%) patients with gastric, and 8 (62%) patients with appendiceal adenocarcinoma. Eight (62%) patients had detectable ctDNA at baseline measurement, with median value 0.13 MTM/mL (range, 0.06-11.68), and assay was technically unsuccessful in two cases with appendiceal cancer because of limited tumor tissue. Five (100%) patients with gastric cancer and 3 (50%) patients with appendiceal cancer had detectable ctDNA at baseline. Although baseline levels of ctDNA were low, longitudinal assessment tracked with changes in disease burden among patients undergoing chemotherapy for metastatic disease. In two patients undergoing surveillance after definitive surgical management of gastric adenocarcinoma, detection of ctDNA prompted diagnosis of isolated peritoneal disease. CONCLUSION Quantitative tumor-informed serial ctDNA testing aids clinical management of patients with isolated peritoneal disease. Low levels of baseline ctDNA suggest a role for highly sensitive ctDNA approaches over panel-based testing. Further exploration of this approach should be considered in patients with isolated peritoneal malignant disease.
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Affiliation(s)
- Harshabad Singh
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
- Department of Medicine, Brigham and Women's Hospital, Boston, MA
- Harvard Medical School, Boston, MA
| | - Samuel J Klempner
- Harvard Medical School, Boston, MA
- Massachusetts General Hospital Cancer Center, Boston, MA
| | - Nelya Melnitchouk
- Harvard Medical School, Boston, MA
- Department of Surgery, Brigham and Women's Hospital, Boston, MA
| | - Deepak P Chander
- Dana-Farber Cancer Institute at South Shore Hospital, Weymouth, MA
| | | | - Anuj K Patel
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
- Department of Medicine, Brigham and Women's Hospital, Boston, MA
- Harvard Medical School, Boston, MA
| | - Benjamin L Schlechter
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
- Department of Medicine, Brigham and Women's Hospital, Boston, MA
- Harvard Medical School, Boston, MA
| | - Douglas A Rubinson
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
- Department of Medicine, Brigham and Women's Hospital, Boston, MA
- Harvard Medical School, Boston, MA
| | - Brandon M Huffman
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
- Department of Medicine, Brigham and Women's Hospital, Boston, MA
- Harvard Medical School, Boston, MA
| | - Chetan Nambiar
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Joshua Remland
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Elizabeth Andrews
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Megan E Leahy
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Lauren K Brais
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Peter C Enzinger
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
- Department of Medicine, Brigham and Women's Hospital, Boston, MA
- Harvard Medical School, Boston, MA
| | - Harvey J Mamon
- Harvard Medical School, Boston, MA
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Marios Giannakis
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
- Department of Medicine, Brigham and Women's Hospital, Boston, MA
- Harvard Medical School, Boston, MA
| | - Jeffrey A Meyerhardt
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
- Department of Medicine, Brigham and Women's Hospital, Boston, MA
- Harvard Medical School, Boston, MA
| | - Kimmie Ng
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
- Department of Medicine, Brigham and Women's Hospital, Boston, MA
- Harvard Medical School, Boston, MA
| | - Kimberly J Perez
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
- Department of Medicine, Brigham and Women's Hospital, Boston, MA
- Harvard Medical School, Boston, MA
| | - Andrew J Aguirre
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
- Department of Medicine, Brigham and Women's Hospital, Boston, MA
- Harvard Medical School, Boston, MA
| | - Jeffrey W Clark
- Harvard Medical School, Boston, MA
- Massachusetts General Hospital Cancer Center, Boston, MA
| | - James M Cleary
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
- Department of Medicine, Brigham and Women's Hospital, Boston, MA
- Harvard Medical School, Boston, MA
| | - Brian M Wolpin
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
- Department of Medicine, Brigham and Women's Hospital, Boston, MA
- Harvard Medical School, Boston, MA
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32
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Morganti S, Parsons HA, Lin NU, Grinshpun A. Liquid biopsy for brain metastases and leptomeningeal disease in patients with breast cancer. NPJ Breast Cancer 2023; 9:43. [PMID: 37225714 DOI: 10.1038/s41523-023-00550-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 05/12/2023] [Indexed: 05/26/2023] Open
Abstract
A significant subset of patients with metastatic breast cancer develops brain metastasis. As efficacy of systemic therapies has improved and patients live longer with metastatic breast cancer, the incidence of breast cancer brain metastases has increased. Brain metastases pose a clinical challenge in diagnosis, treatment, and monitoring across all breast cancer subtypes, and better tools are needed. Liquid biopsy, which enables minimally invasive sampling of a patient's cancer, has the potential to shed light on intra-cranial tumor biology and to improve patient care by enabling therapy tailoring. Here we review current evidence for the clinical validity of liquid biopsy in patients with breast cancer brain metastases, with a focus on circulating tumor cells and circulating tumor DNA.
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Affiliation(s)
- Stefania Morganti
- 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
- Broad Institute of MIT and Harvard, Boston, MA, USA
| | - 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
- Broad Institute of MIT and Harvard, Boston, MA, USA
| | - Nancy U Lin
- 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
| | - Albert Grinshpun
- 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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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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Sun Y, Zhu C, Xu F, Cui S, Guan X. Circulating Tumor DNA as a Novel Biomarker Optimizing Treatment for Triple Negative Breast Cancer. Clin Breast Cancer 2023; 23:339-349. [PMID: 36966079 DOI: 10.1016/j.clbc.2023.02.012] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 01/23/2023] [Accepted: 02/26/2023] [Indexed: 03/05/2023]
Abstract
Triple-negative breast cancer is a sub-type of clinically and molecularly heterogeneous malignant disease with a worse prognosis and earlier recurrence than HER2-amplified or hormone-receptor positive breast cancer. Because of the lack of personalized therapy, genetic information is essential to early diagnosing, identifying the high risk of recurrence, guiding therapeutic management, and monitoring treatment efficiency. Circulating tumor DNA (ctDNA) is a novel noninvasive, timely, and tumor specified biomarker that reliably reflects the comprehensive tumor genetic profiles. Thus, it holds significant expectations in personalized therapy, including accurate diagnosis, treatment monitoring, and early detection of recurrence of TNBC. In this review, we summarize the results from recent and ongoing ctDNA-based biomarker-driven clinical trials, with respect to ctDNA analysis' predictive role, in adjuvant, neo-adjuvant, and metastatic settings. Collectively, we anticipate that ctDNA will ultimately be integrated into the management of TNBC to foster precise treatment.
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Affiliation(s)
- Yue Sun
- Department of Oncology, The First Affiliated Hospital with Nanjing Medical University, Nanjing, China
| | - Chengjun Zhu
- Department of Oncology, The First Affiliated Hospital with Nanjing Medical University, Nanjing, China
| | - Feng Xu
- Department of Oncology, The First Affiliated Hospital with Nanjing Medical University, Nanjing, China
| | - Shiyun Cui
- Department of Oncology, The First Affiliated Hospital with Nanjing Medical University, Nanjing, China
| | - Xiaoxiang Guan
- Department of Oncology, The First Affiliated Hospital with Nanjing Medical University, Nanjing, China.
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Cui S, Liu W, Wang W, Miao K, Guan X. Advances in the Diagnosis and Prognosis of Minimal Residual Lesions of Breast Cancer. Pathol Res Pract 2023; 245:154428. [PMID: 37028109 DOI: 10.1016/j.prp.2023.154428] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Revised: 03/23/2023] [Accepted: 03/25/2023] [Indexed: 03/30/2023]
Abstract
PURPOSE To review the latest research of minimal residual disease (MRD) in breast cancer as well as some emerging or potential detection methods for MRD in breast cancer. METHODS Springer, Wiley, and PubMed databases were searched for the electronic literature with search terms of breast cancer, minimal residual disease, circulating tumor cells (CTCs), circulating tumor DNA (ctDNA), exosomes, etc. RESULTS: Minimal residual disease refers to the occult micrometastasis or minimal residual lesions detected in patients with tumor after radical treatment. An early and dynamic monitoring of breast cancer MRD can contribute to clinical treatment decision-making, improving the diagnosis accuracy and prognosis of breast cancer patients. The updated knowledge regarding MRD in breast cancer diagnosis and prognosis were summarized, followed by the review of several emerging or potential detection technologies for MRD in breast cancer. With the developed new MRD detection technologies referring to CTCs, ctDNA and exosomes, the role of MRD in breast cancer has been growingly verified, which is expected to serve as a new risk stratification factor and prognostic indicator for breast cancer. CONCLUSION This paper systematically reviews the research progress, opportunities and challenges in MRD in breast cancer in recent years.
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Affiliation(s)
- Shiyun Cui
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, Jiangsu, China
| | - Weici Liu
- The First School of Clinical Medicine, Nanjing Medical University, Nanjing 210029, Jiangsu, China
| | - Wenxiang Wang
- School of Basic Medical Sciences, Nanjing Medical University, Nanjing 210029, Jiangsu, China
| | - Keyan Miao
- Medical College, Soochow University, Suzhou 215123, Jiangsu, China
| | - Xiaoxiang Guan
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, Jiangsu, China.
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Turner NC, Swift C, Jenkins B, Kilburn L, Coakley M, Beaney M, Fox L, Goddard K, Garcia-Murillas I, Proszek P, Hall P, Harper-Wynne C, Hickish T, Kernaghan S, Macpherson IR, Okines AFC, Palmieri C, Perry S, Randle K, Snowdon C, Stobart H, Wardley AM, Wheatley D, Waters S, Winter MC, Hubank M, Allen SD, Bliss JM. Results of the c-TRAK TN trial: a clinical trial utilising ctDNA mutation tracking to detect molecular residual disease and trigger intervention in patients with moderate- and high-risk early-stage triple-negative breast cancer. Ann Oncol 2023; 34:200-211. [PMID: 36423745 DOI: 10.1016/j.annonc.2022.11.005] [Citation(s) in RCA: 33] [Impact Index Per Article: 33.0] [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: 07/14/2022] [Revised: 11/04/2022] [Accepted: 11/08/2022] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND Post-treatment detection of circulating tumour DNA (ctDNA) in early-stage triple-negative breast cancer (TNBC) patients predicts high risk of relapse. c-TRAK TN assessed the utility of prospective ctDNA surveillance in TNBC and the activity of pembrolizumab in patients with ctDNA detected [ctDNA positive (ctDNA+)]. PATIENTS AND METHODS c-TRAK TN, a multicentre phase II trial, with integrated prospective ctDNA surveillance by digital PCR, enrolled patients with early-stage TNBC and residual disease following neoadjuvant chemotherapy, or stage II/III with adjuvant chemotherapy. ctDNA surveillance comprised three-monthly blood sampling to 12 months (18 months if samples were missed due to coronavirus disease), and ctDNA+ patients were randomised 2 : 1 to intervention : observation. ctDNA results were blinded unless patients were allocated to intervention, when staging scans were done and those free of recurrence were offered pembrolizumab. A protocol amendment (16 September 2020) closed the observation group; all subsequent ctDNA+ patients were allocated to intervention. Co-primary endpoints were (i) ctDNA detection rate and (ii) sustained ctDNA clearance rate on pembrolizumab (NCT03145961). RESULTS Two hundred and eight patients registered between 30 January 2018 and 06 December 2019, 185 had tumour sequenced, 171 (92.4%) had trackable mutations, and 161 entered ctDNA surveillance. Rate of ctDNA detection by 12 months was 27.3% (44/161, 95% confidence interval 20.6% to 34.9%). Seven patients relapsed without prior ctDNA detection. Forty-five patients entered the therapeutic component (intervention n = 31; observation n = 14; one observation patient was re-allocated to intervention following protocol amendment). Of patients allocated to intervention, 72% (23/32) had metastases on staging at the time of ctDNA+, and 4 patients declined pembrolizumab. Of the five patients who commenced pembrolizumab, none achieved sustained ctDNA clearance. CONCLUSIONS c-TRAK TN is the first prospective study to assess whether ctDNA assays have clinical utility in guiding therapy in TNBC. Patients had a high rate of metastatic disease on ctDNA detection. Findings have implications for future trial design, emphasising the importance of commencing ctDNA testing early, with more sensitive and/or frequent ctDNA testing regimes.
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Affiliation(s)
- N C Turner
- Breast Cancer Now Research Centre, The Institute of Cancer Research, London, UK; Breast Unit, The Royal Marsden Hospital, London, UK.
| | - C Swift
- The Institute of Cancer Research, London, UK; The Royal Marsden NHS Foundation Trust, Sutton, Surrey, UK
| | - B Jenkins
- Clinical Trials and Statistics Unit, The Institute of Cancer Research, London, UK
| | - L Kilburn
- Clinical Trials and Statistics Unit, The Institute of Cancer Research, London, UK
| | - M Coakley
- The Institute of Cancer Research, London, UK; The Royal Marsden NHS Foundation Trust, Sutton, Surrey, UK
| | - M Beaney
- The Institute of Cancer Research, London, UK
| | - L Fox
- Clinical Trials and Statistics Unit, The Institute of Cancer Research, London, UK
| | - K Goddard
- Clinical Trials and Statistics Unit, The Institute of Cancer Research, London, UK
| | | | - P Proszek
- NIHR Centre for Molecular Pathology, Royal Marsden Hospital, London, UK
| | - P Hall
- University of Edinburgh, Edinburgh, UK
| | - C Harper-Wynne
- Maidstone Hospital, Maidstone and Tunbridge Wells NHS Trust, Maidstone, UK
| | - T Hickish
- University Hospitals Dorset NHS Foundation Trust, Bournemouth, UK
| | - S Kernaghan
- Clinical Trials and Statistics Unit, The Institute of Cancer Research, London, UK
| | | | - A F C Okines
- Breast Unit, The Royal Marsden Hospital, London, UK
| | - C Palmieri
- Clatterbridge Cancer Centre NHS Trust, Liverpool, Wirral, UK
| | - S Perry
- Clinical Trials and Statistics Unit, The Institute of Cancer Research, London, UK
| | - K Randle
- Independent Cancer Patients' Voice, London, UK
| | - C Snowdon
- Clinical Trials and Statistics Unit, The Institute of Cancer Research, London, UK
| | - H Stobart
- Independent Cancer Patients' Voice, London, UK
| | - A M Wardley
- Outreach Research & Innovation Group Ltd, Manchester, UK
| | - D Wheatley
- Royal Cornwall Hospitals NHS Trust, Truro, UK
| | - S Waters
- Velindre Cancer Centre, Velindre University NHS Trust, Cardiff, UK
| | - M C Winter
- Sheffield Teaching Hospitals NHS Foundation Trust, Weston Park Hospital, Sheffield, UK
| | - M Hubank
- The Institute of Cancer Research, London, UK; The Royal Marsden NHS Foundation Trust, Sutton, Surrey, UK
| | - S D Allen
- The Royal Marsden NHS Foundation Trust, Sutton, Surrey, UK
| | - J M Bliss
- Clinical Trials and Statistics Unit, The Institute of Cancer Research, London, UK
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Vellanki PJ, Ghosh S, Pathak A, Fusco MJ, Bloomquist EW, Tang S, Singh H, Philip R, Pazdur R, Beaver JA. Regulatory implications of ctDNA in immuno-oncology for solid tumors. J Immunother Cancer 2023; 11:e005344. [PMID: 36796877 PMCID: PMC9936292 DOI: 10.1136/jitc-2022-005344] [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] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/14/2022] [Indexed: 02/18/2023] Open
Abstract
In the era of precision oncology, use of circulating tumor DNA (ctDNA) is emerging as a minimally invasive approach for the diagnosis and management of patients with cancer and as an enrichment tool in clinical trials. In recent years, the US Food and Drug Administration has approved multiple ctDNA-based companion diagnostic assays for the safe and effective use of targeted therapies and ctDNA-based assays are also being developed for use with immuno-oncology-based therapies. For early-stage solid tumor cancers, ctDNA may be particularly important to detect molecular residual disease (MRD) to support early implementation of adjuvant or escalated therapy to prevent development of metastatic disease. Clinical trials are also increasingly using ctDNA MRD for patient selection and stratification, with an ultimate goal of improving trial efficiency through use of an enriched patient population. Standardization and harmonization of ctDNA assays and methodologies, along with further clinical validation of ctDNA as a prognostic and predictive biomarker, are necessary before ctDNA may be considered as an efficacy-response biomarker to support regulatory decision making.
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Affiliation(s)
- Paz J Vellanki
- Center for Drug Evaluation and Research, US Food and Drug Administration, Silver Spring, Maryland, USA
| | - Soma Ghosh
- Center for Devices and Radiological Health, US Food and Drug Administration, Silver Spring, Maryland, USA
| | - Anand Pathak
- Center for Devices and Radiological Health, US Food and Drug Administration, Silver Spring, Maryland, USA
| | - Michael J Fusco
- Center for Drug Evaluation and Research, US Food and Drug Administration, Silver Spring, Maryland, USA
| | - Erik W Bloomquist
- Center for Drug Evaluation and Research, US Food and Drug Administration, Silver Spring, Maryland, USA
| | - Shenghui Tang
- Center for Drug Evaluation and Research, US Food and Drug Administration, Silver Spring, Maryland, USA
| | - Harpreet Singh
- Center for Drug Evaluation and Research, US Food and Drug Administration, Silver Spring, Maryland, USA
- Oncology Center of Excellence, US Food and Drug Administration, Silver Spring, Maryland, USA
| | - Reena Philip
- Oncology Center of Excellence, US Food and Drug Administration, Silver Spring, Maryland, USA
| | - Richard Pazdur
- Oncology Center of Excellence, US Food and Drug Administration, Silver Spring, Maryland, USA
| | - Julia A Beaver
- Oncology Center of Excellence, US Food and Drug Administration, Silver Spring, Maryland, USA
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Ramdhani D, Listiani N, Sriyani ME, Maria W E, Watabe H, Mustarichie R, Fitri Kusuma SA, Janitra RS. Estrogen receptor targeting with genistein radiolabeled Technetium-99(m) as radiotracer of breast cancer: Its optimization, characterization, and predicting stability constants by DFT calculation. Heliyon 2023; 9:e13169. [PMID: 36747562 DOI: 10.1016/j.heliyon.2023.e13169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2022] [Revised: 01/19/2023] [Accepted: 01/20/2023] [Indexed: 01/23/2023] Open
Abstract
Objective Genistein is an isoflavone molecule with a high affinity for estrogen receptors (ER), which could lead to the mechanism of selective estrogen receptor modulators (SERMs) in breast cancer. Genistein labeling with technetium-99m can be a new promising strategy for diagnostic breast cancer. In this research, we evaluate the physicochemical characteristics of the [99mTc]Tc-genistein complex and describe the optimal labeling method parameters. We also calculated density functional theory to study the stability constants to support complex formation analysis (DFT). Methods The genistein was directly labeled with 99mTc, and its stability as well as its potential for usage as a radiotracer were all investigated. DFT calculations with thermodynamic cycles to determine chemical coordination models and calculate thermodynamic constants of complex more accurately. Results The radiochemical purity of [99mTc]Tc-genistein showed a high yield of 93.25% ± 0.30% and had good physicochemical properties. The stability of the Tc(IV)-genistein complex was confirmed by DFT calculations at a value of 99.0822. Conclusions As a result, [99mTc]Tc-genistein could be a potential radiotracer kit for SPECT imaging of breast cancer.
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Tabrizi S, Martin-Alonso C, Xiong K, Blewett T, Sridhar S, An Z, Patel S, Rodriguez-Aponte S, Naranjo CA, Wang ST, Shea D, Golub TR, Bhatia SN, Adalsteinsson V, Love JC. An intravenous DNA-binding priming agent protects cell-free DNA and improves the sensitivity of liquid biopsies. bioRxiv 2023:2023.01.13.523947. [PMID: 36711455 PMCID: PMC9882106 DOI: 10.1101/2023.01.13.523947] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Blood-based, or "liquid," biopsies enable minimally invasive diagnostics but have limits on sensitivity due to scarce cell-free DNA (cfDNA). Improvements to sensitivity have primarily relied on enhancing sequencing technology ex vivo . Here, we sought to augment the level of circulating tumor DNA (ctDNA) detected in a blood draw by attenuating the clearance of cfDNA in vivo . We report a first-in-class intravenous DNA-binding priming agent given 2 hours prior to a blood draw to recover more cfDNA. The DNA-binding antibody minimizes nuclease digestion and organ uptake of cfDNA, decreasing its clearance at 1 hour by over 150-fold. To improve plasma persistence and limit potential immune interactions, we abrogated its Fc-effector function. We found that it protects GC-rich sequences and DNase-hypersensitive sites, which are ordinarily underrepresented in cfDNA. In tumor-bearing mice, priming improved tumor DNA recovery by 19-fold and sensitivity for detecting cancer from 6% to 84%. These results suggest a novel method to enhance the sensitivity of existing DNA-based cancer testing using blood biopsies.
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Martin-Alonso C, Tabrizi S, Xiong K, Blewett T, Patel S, An Z, Sridhar S, Bekdemir A, Shea D, Amini AP, Wang ST, Kirkpatrick J, Rhoades J, Golub TR, Love JC, Adalsteinsson VA, Bhatia SN. A nanoparticle priming agent reduces cellular uptake of cell-free DNA and enhances the sensitivity of liquid biopsies. bioRxiv 2023:2023.01.13.524003. [PMID: 36711603 PMCID: PMC9882213 DOI: 10.1101/2023.01.13.524003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Liquid biopsies are enabling minimally invasive monitoring and molecular profiling of diseases across medicine, but their sensitivity remains limited by the scarcity of cell-free DNA (cfDNA) in blood. Here, we report an intravenous priming agent that is given prior to a blood draw to increase the abundance of cfDNA in circulation. Our priming agent consists of nanoparticles that act on the cells responsible for cfDNA clearance to slow down cfDNA uptake. In tumor-bearing mice, this agent increases the recovery of circulating tumor DNA (ctDNA) by up to 60-fold and improves the sensitivity of a ctDNA diagnostic assay from 0% to 75% at low tumor burden. We envision that this priming approach will significantly improve the performance of liquid biopsies across a wide range of clinical applications in oncology and beyond.
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Koo KM. Multifunctional Hybrid Nanozymes for Magnetic Enrichment and Bioelectrocatalytic Sensing of Circulating Tumor RNA during Minimal Residual Disease Monitoring. Catalysts 2023; 13:178. [DOI: 10.3390/catal13010178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Iron oxide nanozymes are a form of nanomaterial with both superparamagnetic and enzyme-mimicking properties. Ongoing research efforts have been made to create multifunctional iron oxide hybrid nanozymes with auxiliary properties through biomolecular modifications. Such iron oxide hybrid nanozymes can be useful for rapid and cost-effective analysis of circulating tumor nucleic acids (ctNAs) in patient liquid biopsies during minimal residual disease (MRD) monitoring of cancer recurrence. Herein, the use of streptavidin-modified iron oxide hybrid nanozymes is reported for magnetic enrichment and bioelectrocatalytic sensing of three prostate cancer (PCa) ctRNA biomarkers with high detection specificity and sensitivity (10 copies) over an ultrabroad dynamic range (five orders of magnitude). Furthermore, the feasibility of ctRNA analysis for pre- and post-cancer treatment MRD monitoring is demonstrated using PCa urinary liquid biopsy samples.
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Darbeheshti F, Makrigiorgos GM. Enzymatic Methods for Mutation Detection in Cancer Samples and Liquid Biopsies. Int J Mol Sci 2023; 24. [PMID: 36674433 DOI: 10.3390/ijms24020923] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Revised: 12/28/2022] [Accepted: 12/29/2022] [Indexed: 01/06/2023] Open
Abstract
Low-level tumor somatic DNA mutations in tissue and liquid biopsies obtained from cancer patients can have profound implications for development of metastasis, prognosis, choice of treatment, follow-up, or early cancer detection. Unless detected, such low-frequency DNA alterations can misinform patient management decisions or become missed opportunities for personalized medicine. Next-generation sequencing technologies and digital-PCR can resolve low-level mutations but require access to specialized instrumentation, time, and resources. Enzymatic-based approaches to detection of low-level mutations provide a simple, straightforward, and affordable alternative to enrich and detect such alterations and is broadly available to low-resource laboratory settings. This review summarizes the traditional uses of enzymatic mutation detection and describes the latest exciting developments, potential, and applications with specific reference to the field of liquid biopsy in cancer.
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Dabbs DJ, Huang RS, Ross JS. Novel markers in breast pathology. Histopathology 2023; 82:119-139. [PMID: 36468266 DOI: 10.1111/his.14770] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 08/07/2022] [Accepted: 08/08/2022] [Indexed: 12/12/2022]
Abstract
Breast pathology is an ever-expanding database of information which includes markers, or biomarkers, that detect or help treat the disease as prognostic or predictive information. This review focuses on these aspects of biomarkers which are grounded in immunohistochemistry, liquid biopsies and next-generation sequencing.
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Affiliation(s)
- David J Dabbs
- PreludeDx, Laguna Hills, CA, USA.,Department of Pathology, University of Pittsburgh, Board Member, CASI (Consortium for Analytical Standardization in Immunohistochemistry), Pittsburgh, PA, USA
| | - Richard S Huang
- Clinical Development, Foundation Medicine, Cambridge, MA, USA
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Doebley AL, Ko M, Liao H, Cruikshank AE, Santos K, Kikawa C, Hiatt JB, Patton RD, De Sarkar N, Collier KA, Hoge ACH, Chen K, Zimmer A, Weber ZT, Adil M, Reichel JB, Polak P, Adalsteinsson VA, Nelson PS, MacPherson D, Parsons HA, Stover DG, Ha G. A framework for clinical cancer subtyping from nucleosome profiling of cell-free DNA. Nat Commun 2022; 13:7475. [PMID: 36463275 PMCID: PMC9719521 DOI: 10.1038/s41467-022-35076-w] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Accepted: 11/17/2022] [Indexed: 12/05/2022] Open
Abstract
Cell-free DNA (cfDNA) has the potential to inform tumor subtype classification and help guide clinical precision oncology. Here we develop Griffin, a framework for profiling nucleosome protection and accessibility from cfDNA to study the phenotype of tumors using as low as 0.1x coverage whole genome sequencing data. Griffin employs a GC correction procedure tailored to variable cfDNA fragment sizes, which generates a better representation of chromatin accessibility and improves the accuracy of cancer detection and tumor subtype classification. We demonstrate estrogen receptor subtyping from cfDNA in metastatic breast cancer. We predict estrogen receptor subtype in 139 patients with at least 5% detectable circulating tumor DNA with an area under the receive operator characteristic curve (AUC) of 0.89 and validate performance in independent cohorts (AUC = 0.96). In summary, Griffin is a framework for accurate tumor subtyping and can be generalizable to other cancer types for precision oncology applications.
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Affiliation(s)
- Anna-Lisa Doebley
- Division of Public Health Sciences and Human Biology, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Molecular and Cellular Biology Graduate Program, University of Washington, Seattle, WA, USA
- Medical Scientist Training Program, University of Washington, Seattle, WA, USA
| | - Minjeong Ko
- Division of Public Health Sciences and Human Biology, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Hanna Liao
- Molecular and Cellular Biology Graduate Program, University of Washington, Seattle, WA, USA
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - A Eden Cruikshank
- Division of Public Health Sciences and Human Biology, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Molecular and Cellular Biology Graduate Program, University of Washington, Seattle, WA, USA
| | | | - Caroline Kikawa
- Medical Scientist Training Program, University of Washington, Seattle, WA, USA
| | - Joseph B Hiatt
- Division of Public Health Sciences and Human Biology, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Division of Medical Oncology, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Robert D Patton
- Division of Public Health Sciences and Human Biology, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Navonil De Sarkar
- Division of Public Health Sciences and Human Biology, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | | | - Anna C H Hoge
- Division of Public Health Sciences and Human Biology, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Katharine Chen
- Molecular and Cellular Biology Graduate Program, University of Washington, Seattle, WA, USA
| | - Anat Zimmer
- Division of Public Health Sciences and Human Biology, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Zachary T Weber
- Ohio State University Comprehensive Cancer Center, Columbus, OH, USA
| | - Mohamed Adil
- Division of Public Health Sciences and Human Biology, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Jonathan B Reichel
- Division of Public Health Sciences and Human Biology, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
| | - Paz Polak
- Department of Oncological Sciences, Icahn School of Medicine, Mount Sinai, New York, NY, USA
| | | | - Peter S Nelson
- Division of Public Health Sciences and Human Biology, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Division of Medical Oncology, Department of Medicine, University of Washington, Seattle, WA, USA
- Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
| | - David MacPherson
- Division of Public Health Sciences and Human Biology, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | | | - Daniel G Stover
- Ohio State University Comprehensive Cancer Center, Columbus, OH, USA
| | - Gavin Ha
- Division of Public Health Sciences and Human Biology, Fred Hutchinson Cancer Center, Seattle, WA, USA.
- Department of Genome Sciences, University of Washington, Seattle, WA, USA.
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA.
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He W, Xiao Y, Yan S, Zhu Y, Ren S. Cell-free DNA in the management of prostate cancer: Current status and future prospective. Asian J Urol 2022. [PMID: 37538150 PMCID: PMC10394290 DOI: 10.1016/j.ajur.2022.11.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Objective With the escalating prevalence of prostate cancer (PCa) in China, there is an urgent demand for novel diagnostic and therapeutic approaches. Extensive investigations have been conducted on the clinical implementation of circulating free DNA (cfDNA) in PCa. This review aims to provide a comprehensive overview of the present state of cfDNA as a biomarker for PCa and to examine its merits and obstacles for future clinical utilization. Methods Relevant peer-reviewed manuscripts on cfDNA as a PCa marker were evaluated by PubMed search (2010-2022) to evaluate the roles of cfDNA in PCa diagnosis, prognosis, and prediction, respectively. Results cfDNA is primarily released from cells undergoing necrosis and apoptosis, allowing for non-invasive insight into the genomic, transcriptomic, and epigenomic alterations within various PCa disease states. Next-generation sequencing, among other detection methods, enables the assessment of cfDNA abundance, mutation status, fragment characteristics, and epigenetic modifications. Multidimensional analysis based on cfDNA can facilitate early detection of PCa, risk stratification, and treatment monitoring. However, standardization of cfDNA detection methods is still required to expedite its clinical application. Conclusion cfDNA provides a non-invasive, rapid, and repeatable means of acquiring multidimensional information from PCa patients, which can aid in guiding clinical decisions and enhancing patient management. Overcoming the application barriers of cfDNA necessitates increased data sharing and international collaboration.
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Yang Y, Zhang J, Li JY, Xu L, Wang SN, Zhang JQ, Xun Z, Xia Y, Cao JB, Liu Y, Shi LY, Li W, Shi YL, He YG, Gu DJ, Yu ZY, Chen K, Lan J. The ctDNA-based postoperative molecular residual disease status in different subtypes of early-stage breast cancer. Gland Surg 2022; 11:1924-1935. [PMID: 36654951 PMCID: PMC9840987 DOI: 10.21037/gs-22-634] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 12/12/2022] [Indexed: 12/28/2022]
Abstract
Background Breast cancer is a highly heterogeneous disease. Early-stage, non-metastatic breast cancer is considered curable after definitive treatment. Early detection of tumor recurrence and metastasis through sensitive biomarkers is helpful for guiding clinical decision-making and early intervention in second-line treatment, which could improve patient prognosis and survival. Methods In this real-world study, we retrospectively analyzed 82 patients with stages I to III breast cancer who had been analyzed by molecular residual disease (MRD) assay. A total of 82 tumor tissues and 224 peripheral blood samples were collected and detected by next-generation sequencing (NGS) based on a 1,021-gene panel in this study. Results MRD positivity was detected in 18 of 82 patients (22.0%). The hormone receptor-/human epidermal growth factor receptor 2+ (HR-/HER2+) subgroup had the highest postoperative MRD detection rate at 30.8% (4/13). The BRCA2 and SLX4 genes were significantly enriched in all patients in the MRD positive group and FGFR1 amplification was significantly enriched in the MRD negative group with HR+/HER2-. The number of single nucleotide variants (SNVs) in tissue samples of MRD-positive patients was higher than that of MRD-negative patients (11.94 vs. 8.50 SNVs/sample). Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis showed that there was a similar biological function of the tumor-mutated genes in the 2 MRD status groups. Conclusions This real-world study confirmed that patient samples of primary tumor tissue with different MRD status and molecular subtypes had differential genetic features, which may be used to predict patients at high risk for recurrence.
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Affiliation(s)
- Yang Yang
- Medical College of Soochow University, Suzhou, China
| | - Jie Zhang
- Department of Gynecology & Obstetrics, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Jiao-Yang Li
- Department of Ultrasound, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Lu Xu
- Department of General Surgery, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Si-Ning Wang
- Medical College of Soochow University, Suzhou, China
| | - Jun-Qi Zhang
- Medical College of Soochow University, Suzhou, China
| | - Zhou Xun
- Medical College of Soochow University, Suzhou, China
| | - Yu Xia
- Department of General Surgery, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Jian-Bo Cao
- Department of General Surgery, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Yang Liu
- Department of General Surgery, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Li-Yan Shi
- Department of Oncology, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Wei Li
- Department of Oncology, The First Affiliated Hospital of Soochow University, Suzhou, China
| | | | - Yuan-Ge He
- Geneplus-Beijing Institute, Beijing, China
| | - De-Jian Gu
- Geneplus-Beijing Institute, Beijing, China
| | - Zheng-Yuan Yu
- Department of Oncology, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Kai Chen
- Department of Oncology, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Jing Lan
- Department of General Surgery, The First Affiliated Hospital of Soochow University, Suzhou, China
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Műzes G, Bohusné Barta B, Szabó O, Horgas V, Sipos F. Cell-Free DNA in the Pathogenesis and Therapy of Non-Infectious Inflammations and Tumors. Biomedicines 2022; 10:biomedicines10112853. [PMID: 36359370 PMCID: PMC9687442 DOI: 10.3390/biomedicines10112853] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Revised: 10/31/2022] [Accepted: 11/07/2022] [Indexed: 11/09/2022] Open
Abstract
The basic function of the immune system is the protection of the host against infections, along with the preservation of the individual antigenic identity. The process of self-tolerance covers the discrimination between self and foreign antigens, including proteins, nucleic acids, and larger molecules. Consequently, a broken immunological self-tolerance results in the development of autoimmune or autoinflammatory disorders. Immunocompetent cells express pattern-recognition receptors on their cell membrane and cytoplasm. The majority of endogenous DNA is located intracellularly within nuclei and mitochondria. However, extracellular, cell-free DNA (cfDNA) can also be detected in a variety of diseases, such as autoimmune disorders and malignancies, which has sparked interest in using cfDNA as a possible biomarker. In recent years, the widespread use of liquid biopsies and the increasing demand for screening, as well as monitoring disease activity and therapy response, have enabled the revival of cfDNA research. The majority of studies have mainly focused on the function of cfDNA as a biomarker. However, research regarding the immunological consequences of cfDNA, such as its potential immunomodulatory or therapeutic benefits, is still in its infancy. This article discusses the involvement of various DNA-sensing receptors (e.g., absent in melanoma-2; Toll-like receptor 9; cyclic GMP-AMP synthase/activator of interferon genes) in identifying host cfDNA as a potent danger-associated molecular pattern. Furthermore, we aim to summarize the results of the experimental studies that we recently performed and highlight the immunomodulatory capacity of cfDNA, and thus, the potential for possible therapeutic consideration.
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Affiliation(s)
| | | | | | | | - Ferenc Sipos
- Correspondence: ; Tel.: +36-20-478-0752; Fax: +36-1-266-0816
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Abstract
PURPOSE OF REVIEW Triple-negative breast cancer (TNBC) has been conventionally associated with poor prognosis, as a result of limited therapeutic options. In the early setting, prognosis is informed by clinical-pathological factors; for patients receiving neoadjuvant treatments, pathological complete response (pCR) is the strongest factor. In this review, we mapped the landscape of clinical trials in the postneoadjuvant space, and identified three patterns of clinical trial design. RECENT FINDINGS For patients at higher risk, effective postneoadjuvant treatments are of paramount importance to address a high clinical need. Postneoadjuvant risk-adapted treatments have demonstrated to improve survival in patients at high of recurrence. SUMMARY Patients at high risk have indication for adjuvant treatment intensification, informed by baseline clinical, pathological or molecular factors (type 1 approach), on the presence, extent and molecular characteristics of the residual disease at the time of surgery (type 2) or on risk factors assessed in the postsurgical setting (type 3), for example, circulating tumour DNA. Most of the past trials were based on type 2 approaches, for example, with capecitabine and Olaparib. Few trials were based on a type 1 approach, notably pembrolizumab for early TNBC. The clinical validity of type 3 approaches is under investigation in several ongoing trials.
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Affiliation(s)
- Dario Trapani
- Department of Medical Oncology, Dana-Farber Cancer Institute
- Harvard Medical School, Boston, Massachusetts
| | - Emanuela Ferraro
- Breast Medicine Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Federica Giugliano
- Division of Early Drug Development for Innovative Therapies, European Institute of Oncology IRCCS, Milan, Italy
- Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
| | - Luca Boscolo Bielo
- Division of Early Drug Development for Innovative Therapies, European Institute of Oncology IRCCS, Milan, Italy
- Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
| | - Giuseppe Curigliano
- Division of Early Drug Development for Innovative Therapies, European Institute of Oncology IRCCS, Milan, Italy
- Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
| | - Harold J Burstein
- Department of Medical Oncology, Dana-Farber Cancer Institute
- Harvard Medical School, Boston, Massachusetts
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Valenza C, Trapani D, Curigliano G. Circulating tumour DNA dynamics for assessment of molecular residual disease and for intercepting resistance in breast cancer. Curr Opin Oncol 2022; 34:595-605. [PMID: 36083118 DOI: 10.1097/cco.0000000000000905] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
PURPOSE OF REVIEW Longitudinal evaluation of circulating tumour DNA (ctDNA) represents a promising tool for monitoring tumour evolution. In patients with breast cancer, ctDNA dynamics for the assessment of molecular residual disease (MRD) and resistances may, respectively, help clinicians in treatment modulation of adjuvant treatments, and in anticipating resistance to ongoing treatments and switch treatments before clinical progression, to improve disease control. Anyway, the introduction of this dynamic biomarker into clinical practice requires the demonstration of analytical validity, clinical validity and clinical utility. RECENT FINDINGS In early breast cancer setting, several observational studies demonstrated the clinical validity of MRD monitoring through ctDNA in identifying patients at a higher risk of relapse, but many clinical trials evaluating the clinical utility are still ongoing, and few data resulted in inconclusive results.Instead, ctDNA dynamics for intercepting resistance have not been fully evaluated in terms of clinical validity, because monitoring schedules of most observational studies are not intensive. The only trial assessing their clinical utility (PADA-1) demonstrated a benefit in terms of progression-free survival, portraying a new landscape for clinical trials in this space. SUMMARY Rigorous clinical trials with adequate assays and patient-relevant endpoints are paramount to demonstrate the clinical utility of ctDNA dynamics and eventually increase clinical outcomes.
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Affiliation(s)
- Carmine Valenza
- Division of New Drugs and Early Drug Development for Innovative Therapies, European Institute of Oncology, IRCCS
- Department of Oncology and Haematology, University of Milan, Milan, Italy
| | - Dario Trapani
- Division of New Drugs and Early Drug Development for Innovative Therapies, European Institute of Oncology, IRCCS
| | - Giuseppe Curigliano
- Division of New Drugs and Early Drug Development for Innovative Therapies, European Institute of Oncology, IRCCS
- Department of Oncology and Haematology, University of Milan, Milan, Italy
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