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Embracing Project Optimus: Can we Leverage Evolutionary Theory to Optimize Dosing in Oncology? Pharm Res 2022; 39:3259-3265. [PMID: 36056271 PMCID: PMC9789176 DOI: 10.1007/s11095-022-03380-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 08/25/2022] [Indexed: 12/27/2022]
Abstract
Project Optimus is a US Food and Drug Administration (FDA) initiative to reform dose selection in oncology drug development. Here, we focus on tumor evolution, a broadly observed phenomenon that invariably leads to therapeutic failure and disease relapse, and its effect on the exposure-response (E-R) relationships of oncology drugs. We propose a greater emphasis on tumor evolution during clinical development to facilitate the selection of optimal doses for molecularly targeted therapies and immunotherapies in oncology.
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52
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Inferring parameters of cancer evolution in chronic lymphocytic leukemia. PLoS Comput Biol 2022; 18:e1010677. [DOI: 10.1371/journal.pcbi.1010677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 11/16/2022] [Accepted: 10/24/2022] [Indexed: 11/06/2022] Open
Abstract
As a cancer develops, its cells accrue new mutations, resulting in a heterogeneous, complex genomic profile. We make use of this heterogeneity to derive simple, analytic estimates of parameters driving carcinogenesis and reconstruct the timeline of selective events following initiation of an individual cancer, where two longitudinal samples are available for sequencing. Using stochastic computer simulations of cancer growth, we show that we can accurately estimate mutation rate, time before and after a driver event occurred, and growth rates of both initiated cancer cells and subsequently appearing subclones. We demonstrate that in order to obtain accurate estimates of mutation rate and timing of events, observed mutation counts should be corrected to account for clonal mutations that occurred after the founding of the tumor, as well as sequencing coverage. Chronic lymphocytic leukemia (CLL), which often does not require treatment for years after diagnosis, presents an optimal system to study the untreated, natural evolution of cancer cell populations. When we apply our methodology to reconstruct the individual evolutionary histories of CLL patients, we find that the parental leukemic clone typically appears within the first fifteen years of life.
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Malapelle U, Pisapia P, Pepe F, Russo G, Buono M, Russo A, Gomez J, Khorshid O, Mack PC, Rolfo C, Troncone G. The evolving role of liquid biopsy in lung cancer. Lung Cancer 2022; 172:53-64. [PMID: 35998482 DOI: 10.1016/j.lungcan.2022.08.004] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2022] [Revised: 07/22/2022] [Accepted: 08/05/2022] [Indexed: 12/20/2022]
Abstract
Liquid biopsy has revolutionized the management of cancer patients. In particular, liquid biopsy-based testing has proven to be highly beneficial for identifying actionable cancer markers, especially when solid tissue biopsies are insufficient or unattainable. Beyond the predictive role, liquid biopsy may be a useful tool for comprehensive tumor genotyping, identification of emergent resistance mechanisms, monitoring of minimal residual disease, early detection, and cancer interception. The application of next generation sequencing to liquid biopsy has led to the "quantum leap" of predictive molecular pathology. Here, we review the evolving role of liquid biopsy in lung cancer.
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Affiliation(s)
- Umberto Malapelle
- Department of Public Health, University of Naples Federico II, Naples, Italy.
| | - Pasquale Pisapia
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Francesco Pepe
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Gianluca Russo
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Mauro Buono
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | | | - Jorge Gomez
- Center for Thoracic Oncology, Tisch Cancer Institute, Mount Sinai Medical System & Icahn School of Medicine, New York, NY, USA
| | - Ola Khorshid
- National Cancer Institute, Cairo University, Cairo, Egypt
| | - Philip C Mack
- Center for Thoracic Oncology, Tisch Cancer Institute, Mount Sinai Medical System & Icahn School of Medicine, New York, NY, USA
| | - Christian Rolfo
- Center for Thoracic Oncology, Tisch Cancer Institute, Mount Sinai Medical System & Icahn School of Medicine, New York, NY, USA
| | - Giancarlo Troncone
- Department of Public Health, University of Naples Federico II, Naples, Italy
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Kunimasa K, Nishino K, Sato Y, Mori M, Ihara S, Suzuki H, Nagatomo I, Kumagai T, Morishima T, Imamura F. Fragment size and dynamics of EGFR-mutated tumor-derived DNA provide prognostic information regarding EGFR-TKI efficacy in patients with EGFR-mutated NSCLC. Sci Rep 2022; 12:13544. [PMID: 35941190 PMCID: PMC9360008 DOI: 10.1038/s41598-022-17848-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 08/02/2022] [Indexed: 02/06/2023] Open
Abstract
Circulating tumor DNA (ctDNA)-based next-generation sequencing (NGS) is a complementary and alternative test to tissue-based NGS. We performed NGS analysis of ctDNA samples collected from patients with EGFR-mutated non-small cell lung cancer (NSCLC) who received osimertinib; the samples were collected after second-line treatment, before osimertinib treatment, one week and one month after osimertinib treatment, and at the time of resistance formation. We examinedthe correlation with osimertinib efficacy. From January to December 2018, 34 patients with EGFR-mutated NSCLC harboring EGFR T790M mutations were enrolled, and a total of 132 peripheral blood samples were collected. The fragment sizes of EGFR-mutated ctDNAs were significantly shorter than that of their corresponding normal fragments. Osimertinib treatment of patients with shorter EGFR-mutated ctDNA fragments resulted in shorter progression-free survival (PFS). The disappearance time of EGFR-mutated fragment fractions and clonal evolution patterns (new driver mutation group, additional mutation group vs. attenuation group) were each associated with the PFS achieved with osimertinib treatment; however,multivariate analysis revealed that only shorter EGFR-mutated ctDNA fragments were associated with the PFS resulting from osimertinib treatment. EGFR-mutated ctDNA fragment size, time of disappearance of these fragments, and clonal evolution pattern were related to the effects of osimertinib. In particular, short EGFR-mutated ctDNA fragmentation may be closely related to osimertinib efficacy prediction.
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Affiliation(s)
- Kei Kunimasa
- Department of Thoracic Oncology, Osaka International Cancer Institute, 3-1-69 Otemae Chuoku, Osaka City, Osaka, 541-8567, Japan.
| | - Kazumi Nishino
- Department of Thoracic Oncology, Osaka International Cancer Institute, 3-1-69 Otemae Chuoku, Osaka City, Osaka, 541-8567, Japan
| | | | - Masahide Mori
- Department of Thoracic Oncology, Osaka Toneyama Medical Center, Osaka, Japan
| | - Shoichi Ihara
- Department of Respiratory Medicine, Osaka Police Hospital, Osaka, Japan
| | - Hidekazu Suzuki
- Department of Thoracic Oncology, Osaka Habikino Medical Center, Osaka, Japan
| | - Izumi Nagatomo
- Department of Respiratory Medicine and Clinical Immunology, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Toru Kumagai
- Department of Thoracic Oncology, Osaka International Cancer Institute, 3-1-69 Otemae Chuoku, Osaka City, Osaka, 541-8567, Japan
| | | | - Fumio Imamura
- Department of Thoracic Oncology, Osaka International Cancer Institute, 3-1-69 Otemae Chuoku, Osaka City, Osaka, 541-8567, Japan
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Haseltine JM, Offin M, Flynn JR, Zhang Z, Lebow ES, Aziz K, Makhnin A, Eichholz J, Lim LP, Li M, Isbell JM, Gomez DR, Li BT, Rimner A. Tumor volume as a predictor of cell free DNA mutation detection in advanced non-small cell lung cancer. Transl Lung Cancer Res 2022; 11:1578-1590. [PMID: 36090640 PMCID: PMC9459617 DOI: 10.21037/tlcr-22-164] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 06/14/2022] [Indexed: 01/13/2023]
Abstract
Background Cell free DNA (cfDNA) is an exciting biomarker with applications across the cancer care continuum. Determinants of cfDNA shedding dynamics remain an active research area. We performed a detailed analysis of tumor volume and factors associated with detection of cfDNA mutations. Methods Patients with advanced non-small cell lung cancers (NSCLCs) were prospectively enrolled on a plasma biomarker protocol. Next generation sequencing (NGS) was performed using a validated, bias-corrected, hybrid-capture panel assay of lung cancer-associated genes. Volume of tumor in different subsites and total tumor volume were determined through manual volume delineation using PET/CT and brain magnetic resonance imaging (MRI) imaging. The primary endpoint was detection of cfDNA mutation; secondary endpoints were overall survival (OS) and variant allele frequency (VAF). Results There were 110 patients included, 78 of whom had at least one mutation detected. Median total tumor volume for the entire cohort, patients with mutation detected, and patients with no mutation detected were 66 mL (range, 2-1,383 mL), 76 mL (range, 5-1,383 mL), and 45 mL (range, 2-460 mL), respectively (P=0.002; mutation detected vs. not). The optimal total tumor volume threshold to predict increased probability of mutation detection was 65 mL (P=0.006). Total tumor volume greater than 65 mL was a significant predictor of mutation detection on multivariate analysis (OR: 4.30, P=0.003). Significant predictors of OS were age (HR: 1.04, P=0.002), detection of cfDNA mutation (HR: 2.11, P=0.024), and presence of bone metastases (HR: 1.66, P=0.047). Conclusions Total tumor volume greater than 65 mL was associated with cfDNA mutation detection in patients with advanced NSCLC.
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Affiliation(s)
- Justin M. Haseltine
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Michael Offin
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jessica R. Flynn
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Zhigang Zhang
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Emily S. Lebow
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Khaled Aziz
- Department of Radiation Oncology, Johns Hopkins Hospital, Baltimore, MD, USA
| | - Alex Makhnin
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jordan Eichholz
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Lee P. Lim
- Resolution Bioscience, Agilent Technologies, Kirkland, WA, USA
| | - Mark Li
- Resolution Bioscience, Agilent Technologies, Kirkland, WA, USA
| | - James M. Isbell
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Daniel R. Gomez
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Bob T. Li
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Andreas Rimner
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
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Dobre EG, Constantin C, Neagu M. Skin Cancer Research Goes Digital: Looking for Biomarkers within the Droplets. J Pers Med 2022; 12:jpm12071136. [PMID: 35887633 PMCID: PMC9323323 DOI: 10.3390/jpm12071136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 07/12/2022] [Accepted: 07/12/2022] [Indexed: 12/24/2022] Open
Abstract
Skin cancer, which includes the most frequent malignant non-melanoma carcinomas (basal cell carcinoma, BCC, and squamous cell carcinoma, SCC), along with the difficult to treat cutaneous melanoma (CM), pose important worldwide issues for the health care system. Despite the improved anti-cancer armamentarium and the latest scientific achievements, many skin cancer patients fail to respond to therapies, due to the remarkable heterogeneity of cutaneous tumors, calling for even more sophisticated biomarker discovery and patient monitoring approaches. Droplet digital polymerase chain reaction (ddPCR), a robust method for detecting and quantifying low-abundance nucleic acids, has recently emerged as a powerful technology for skin cancer analysis in tissue and liquid biopsies (LBs). The ddPCR method, being capable of analyzing various biological samples, has proved to be efficient in studying variations in gene sequences, including copy number variations (CNVs) and point mutations, DNA methylation, circulatory miRNome, and transcriptome dynamics. Moreover, ddPCR can be designed as a dynamic platform for individualized cancer detection and monitoring therapy efficacy. Here, we present the latest scientific studies applying ddPCR in dermato-oncology, highlighting the potential of this technology for skin cancer biomarker discovery and validation in the context of personalized medicine. The benefits and challenges associated with ddPCR implementation in the clinical setting, mainly when analyzing LBs, are also discussed.
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Affiliation(s)
- Elena-Georgiana Dobre
- Faculty of Biology, University of Bucharest, Splaiul Independentei 91–95, 050095 Bucharest, Romania;
- Correspondence:
| | - Carolina Constantin
- Immunology Department, “Victor Babes” National Institute of Pathology, 050096 Bucharest, Romania;
- Pathology Department, Colentina Clinical Hospital, 020125 Bucharest, Romania
| | - Monica Neagu
- Faculty of Biology, University of Bucharest, Splaiul Independentei 91–95, 050095 Bucharest, Romania;
- Immunology Department, “Victor Babes” National Institute of Pathology, 050096 Bucharest, Romania;
- Pathology Department, Colentina Clinical Hospital, 020125 Bucharest, Romania
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Zhang M, Feng Y, Qu C, Meng M, Li W, Ye M, Li S, Li S, Ma Y, Wu N, Jia S. Comparison of the somatic mutations between circulating tumor DNA and tissue DNA in Chinese patients with non-small cell lung cancer. Int J Biol Markers 2022; 37:386-394. [PMID: 35791673 DOI: 10.1177/03936155221099036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
BACKGROUND Non-invasive liquid biopsies of circulating tumor DNA (ctDNA) is a rapidly growing field in the research of non-small cell lung cancer (NSCLC). In this study, factors affecting the concordance of mutations in paired plasma and tissue and the detection rate of ctDNA in real-world Chinese patients with NSCLC were identified. METHODS Peripheral blood and paired formalin-fixed paraffin-embedded tumor tissue samples from 125 NSCLC patients were collected and analyzed by sequencing 15 genes. Serological biomarkers were tested by immunoassay. RESULTS The overall concordance between tumor and plasma samples and the detection rate of somatic mutations in ctDNA was 69.2% and 78.4%, respectively. The concordance and detection rate raised with clinical stage were stage I: 14.3%, 14.3%; stage II: 53.3%, 60.0%; stage III: 71.4%, 78.1%; stage IV: 74.1%, 85.2%. With increased tumor diameter, the concordance and detection rate raised from 33.33% to 71.64% and 33.33% to 80.8%, respectively. For patients with partial response, stable disease, progressive disease, and who were treatment-naïve, the concordance and detection rates were 0.0%, 62.7%, 75.2, 73.6%, and 16.7%, 61.9%, 83.3%, 86.5%, respectively. Serological markers: CEA, CA125, NSE, and CYFRA21-1 were significantly higher for patients with detectable somatic alterations in ctDNA than in those who were ctDNA negative (17.08 ng/mL vs. 3.95 ng/mL, 21.63 U/mL vs. 18.27 U/mL, 17.68 U/mL vs. 14.14 U/mL, and 6.55 U/mL vs. 3.81 U/mL, respectively). CONCLUSION Advanced-stage, treatment naïve or poor therapy outcome, and large tumor size were associated with a high concordance and detection rate. Patients with detectable mutations in ctDNA had a higher level of carcinoembryonic antigen, CA125, NSE, and CYFRA21-1.
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Affiliation(s)
- Meng Zhang
- Department of Molecular Diagnostics, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), 12519Peking University Cancer Hospital and Institute, Beijing, China
| | - Yi Feng
- Department of Molecular Diagnostics, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), 12519Peking University Cancer Hospital and Institute, Beijing, China
| | - Changda Qu
- Department of Molecular Diagnostics, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), 12519Peking University Cancer Hospital and Institute, Beijing, China
| | - Meizhu Meng
- Department of Molecular Diagnostics, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), 12519Peking University Cancer Hospital and Institute, Beijing, China
| | - Wenmei Li
- Department of Molecular Diagnostics, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), 12519Peking University Cancer Hospital and Institute, Beijing, China
| | - Meiying Ye
- Department of Molecular Diagnostics, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), 12519Peking University Cancer Hospital and Institute, Beijing, China
| | - Sisi Li
- Department of Molecular Diagnostics, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), 12519Peking University Cancer Hospital and Institute, Beijing, China
| | - Shaolei Li
- Department of Thoracic Surgery II, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), 12519Peking University Cancer Hospital and Institute, Beijing, China
| | - Yuanyuan Ma
- Department of Thoracic Surgery II, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), 12519Peking University Cancer Hospital and Institute, Beijing, China
| | - Nan Wu
- Department of Thoracic Surgery II, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), 12519Peking University Cancer Hospital and Institute, Beijing, China
| | - Shuqin Jia
- Department of Molecular Diagnostics, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), 12519Peking University Cancer Hospital and Institute, Beijing, China
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Gerratana L, Movarek M, Wehbe F, Katam N, Mahalingam D, Donahue J, Shah A, Chae YK, Mulcahy M, Tsarwhas D, Villaflor V, Kalyan A, Hussein M, Patel J, Chandra S, Platanias LC, Gradishar W, Cristofanilli M, Behdad A. Genomic Landscape of Advanced Solid Tumors in Circulating Tumor DNA and Correlation With Tissue Sequencing: A Single Institution's Experience. JCO Precis Oncol 2022; 6:e2100289. [PMID: 35772051 DOI: 10.1200/po.21.00289] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
PURPOSE Circulating tumor DNA (ctDNA) has emerged as a promising noninvasive biomarker for baseline characterization and longitudinal monitoring of a tumor throughout disease management. The aim of this study was to evaluate the utility of ctDNA across a wide spectrum of tumor types. METHODS We retrospectively identified 1,763 patients with advanced cancers who had next-generation sequencing of ctDNA or tumor tissue completed by a designated commercial assay at Northwestern University. RESULTS ctDNA identified at least one gene alteration in 90% of patients. The number of detected alterations (NDA) and mutant allele frequency (MAF) of the most frequently mutated genes varied significantly across tumor types, with the highest MAF observed in gastric, colorectal, and breast cancers and the highest NDA observed in colorectal, lung squamous, and ovarian/endometrial cancers. TP53 was the most mutated gene in all tumor types. PIK3CA, ERBB2, BRCA1, and FGFR1 alterations were associated with breast cancer, and ESR1 mutations were exclusively detected in this tumor type. Colorectal cancer was characterized by alterations in KRAS and APC mutations, whereas KRAS, EGFR, PIK3CA, and BRAF mutations were common in lung adenocarcinoma. Concordance between blood and tissue sequencing was notably observed for truncal gene alterations (eg, APC and KRAS), whereas low concordance was often observed in genes associated with treatment resistance mechanisms (eg, RB1 and NF1). Tumor mutational burden (TMB) varied significantly across tumor types, and patients with high MAF or NDA had a significantly higher TMB score with one of the investigated platforms. CONCLUSION The study provided new insights into the ctDNA mutational landscape across solid tumors, suggesting new hypotheses-generating data and caveats for future histotype-agnostic workflows integrated with tissue-based biomarkers such as TMB.
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Affiliation(s)
- Lorenzo Gerratana
- Division of Hematology and Oncology, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL.,Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, IL.,Department of Medicine, University of Udine, Udine, Italy.,Department of Medical Oncology, Centro di Riferimento Oncologico (CRO), IRCCS, Aviano, Italy
| | - Michael Movarek
- Department of Medicine, Division of Hematology-Oncology, Weill Cornell Medicine/New York-Presbyterian Hospital, New York, NY
| | - Firas Wehbe
- Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, IL
| | - Neelima Katam
- Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, IL
| | - Devalingam Mahalingam
- Division of Hematology and Oncology, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL.,Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, IL
| | - Jeannine Donahue
- Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, IL
| | - Ami Shah
- Division of Hematology and Oncology, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL.,Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, IL
| | - Young K Chae
- Division of Hematology and Oncology, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL.,Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, IL
| | - Mary Mulcahy
- Division of Hematology and Oncology, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL.,Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, IL
| | - Dean Tsarwhas
- Division of Hematology and Oncology, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL.,Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, IL
| | - Victoria Villaflor
- Division of Hematology and Oncology, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL.,Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, IL
| | - Aparna Kalyan
- Division of Hematology and Oncology, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL.,Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, IL
| | - Maha Hussein
- Division of Hematology and Oncology, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL.,Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, IL
| | - Jyoti Patel
- Division of Hematology and Oncology, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL.,Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, IL
| | - Sunandana Chandra
- Division of Hematology and Oncology, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL.,Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, IL
| | - Leonidas C Platanias
- Division of Hematology and Oncology, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL.,Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, IL
| | - William Gradishar
- Division of Hematology and Oncology, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL.,Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, IL
| | - Massimo Cristofanilli
- Division of Hematology and Oncology, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL.,Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, IL.,Department of Medicine, Division of Hematology-Oncology, Weill Cornell Medicine/New York-Presbyterian Hospital, New York, NY
| | - Amir Behdad
- Division of Hematology and Oncology, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL.,Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, IL.,Department of Pathology, Northwestern University Feinberg School of Medicine, Chicago, IL
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Cui Z, Li D, Yang W, Fan K, Liu H, Wen F, Li L, Dong L, Wang G, Wu W. An electrochemical biosensor based on few-layer MoS 2 nanosheets for highly sensitive detection of tumor marker ctDNA. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2022; 14:1956-1962. [PMID: 35531866 DOI: 10.1039/d2ay00467d] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
An electrochemical biosensor based on few-layer molybdenum disulfide (MoS2) nanosheets was fabricated for the highly sensitive detection of tumor marker circulating tumor DNA (ctDNA) in this paper. The MoS2 nanosheets with few layers were prepared by the shear stripping. Compared with the mechanical stripping method and the lithium ion intercalation method, this method is simpler to operate, and the prepared MoS2 nanosheets had good electrochemical activity. The biosensing platform was fabricated based on the discriminative affinity of MoS2 nanosheets towards single-stranded DNA (ssDNA) and double-stranded DNA (dsDNA). Methylene blue (MB) was used as the signal molecule. The results showed that the detection of ctDNA by this sensor showed an excellent linear relationship in the concentration range of 1.0 × 10-7 M to 1.0 × 10-16 M, and the detection limit was 2.5 × 10-18 M. In addition, this sensor exhibited outstanding stability and specificity. This strategy provides an alternative approach for ctDNA detection and an effective sensing strategy for future in vitro cancer diagnosis by label-free detection.
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Affiliation(s)
- Zhilian Cui
- Ministry of Education Engineering Research Center of Smart Microsensors and Microsystems, Hangzhou Dianzi University, Hangzhou, 310018, China.
- School of Electronics and Information, Hangzhou Dianzi University, Hangzhou, 310018, China
| | - Dujuan Li
- Ministry of Education Engineering Research Center of Smart Microsensors and Microsystems, Hangzhou Dianzi University, Hangzhou, 310018, China.
- School of Electronics and Information, Hangzhou Dianzi University, Hangzhou, 310018, China
| | - Weihuang Yang
- Ministry of Education Engineering Research Center of Smart Microsensors and Microsystems, Hangzhou Dianzi University, Hangzhou, 310018, China.
- School of Electronics and Information, Hangzhou Dianzi University, Hangzhou, 310018, China
| | - Kai Fan
- School of Automation, Hangzhou Dianzi University, Hangzhou, 310018, China
| | - Hongying Liu
- School of Automation, Hangzhou Dianzi University, Hangzhou, 310018, China
| | - Fei Wen
- Ministry of Education Engineering Research Center of Smart Microsensors and Microsystems, Hangzhou Dianzi University, Hangzhou, 310018, China.
- School of Electronics and Information, Hangzhou Dianzi University, Hangzhou, 310018, China
| | - Lili Li
- Ministry of Education Engineering Research Center of Smart Microsensors and Microsystems, Hangzhou Dianzi University, Hangzhou, 310018, China.
- School of Electronics and Information, Hangzhou Dianzi University, Hangzhou, 310018, China
| | - Linxi Dong
- Ministry of Education Engineering Research Center of Smart Microsensors and Microsystems, Hangzhou Dianzi University, Hangzhou, 310018, China.
- School of Electronics and Information, Hangzhou Dianzi University, Hangzhou, 310018, China
| | - Gaofeng Wang
- Ministry of Education Engineering Research Center of Smart Microsensors and Microsystems, Hangzhou Dianzi University, Hangzhou, 310018, China.
- School of Electronics and Information, Hangzhou Dianzi University, Hangzhou, 310018, China
| | - Wei Wu
- Ministry of Education Engineering Research Center of Smart Microsensors and Microsystems, Hangzhou Dianzi University, Hangzhou, 310018, China.
- School of Electronics and Information, Hangzhou Dianzi University, Hangzhou, 310018, China
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The History and Future of Basic and Translational Cell-Free DNA Research at a Glance. Diagnostics (Basel) 2022; 12:diagnostics12051192. [PMID: 35626347 PMCID: PMC9139999 DOI: 10.3390/diagnostics12051192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 04/29/2022] [Accepted: 05/03/2022] [Indexed: 11/30/2022] Open
Abstract
We discuss the early history of the structure of DNA and its involvement in gene structure as well as its mobility in and between cells and between tissues in the form of circulating cell-free DNA (cfDNA). This is followed by a view of the present status of the studies on cfDNA and clinical applications of circulating cell-free tumor DNA (ctDNA). The future developments and roles of ctDNA are also considered.
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Nie W, Wang ZJ, Zhang K, Li B, Cai YR, Wen FC, Zhang D, Bai YZ, Zhang XY, Wang SY, Cheng L, Zhong H, Liu L, Wang J, Han BH. ctDNA-adjusted bTMB as a predictive biomarker for patients with NSCLC treated with PD-(L)1 inhibitors. BMC Med 2022; 20:170. [PMID: 35509036 PMCID: PMC9069852 DOI: 10.1186/s12916-022-02360-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/09/2022] [Accepted: 03/29/2022] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND In non-small cell lung cancer (NSCLC) patients receiving immune checkpoint inhibitors (ICIs), higher blood tumor mutational burden (bTMB) was usually associated with better progression-free survival (PFS) and objective response rate (ORR). However, the association between bTMB and overall survival (OS) benefit remains undefined. It has been reported that patients harboring a high level of circulating tumor DNA (ctDNA) had poor survival. We hypothesized that ctDNA-adjusted bTMB might predict OS benefit in NSCLC patients receiving ICIs. METHODS Our study was retrospectively performed in three cohorts, including OAK and POPLAR cohort (n = 853), Shanghai and Wuhan (SH&WH) cohort (n = 44), and National Cancer Center (NCC) cohort (n = 47). Durable clinical benefit (DCB) was defined as PFS lasting ≥ 6 months. The cutoff value of ctDNA-adjusted bTMB for DCB prediction was calculated based on a receiver operating characteristic curve. Interaction between treatments and ctDNA-adjusted bTMB was assessed. RESULTS The bTMB score was significantly associated with tumor burden, while no association was observed between ctDNA-adjusted bTMB with tumor burden. In the OAK and POPLAR cohort, significantly higher ORR (P = 0.020) and DCB (P < 0.001) were observed in patients with high ctDNA-adjusted bTMB than those with low ctDNA-adjusted bTMB. Importantly, the interactions between ctDNA-adjusted bTMB and treatments were significant for OS (interaction P = 0.019) and PFS (interaction P = 0.002). In the SH&WH cohort, the interactions between ctDNA-adjusted bTMB and treatment were marginally significant for OS (interaction P = 0.081) and PFS (interaction P = 0.062). Similar result was demonstrated in the NCC cohort. CONCLUSIONS Our study indicated that ctDNA-adjusted bTMB might predict OS benefit in NSCLC patients receiving ICIs. The potential of ctDNA-adjusted bTMB as a noninvasive predictor for immunotherapy should be confirmed in future studies.
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Affiliation(s)
- Wei Nie
- Department of Pulmonary Medicine, Shanghai Chest Hospital, Shanghai Jiaotong University, Shanghai, 200030, China
| | - Zhi-Jie Wang
- State Key Laboratory of Molecular Oncology, Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Kai Zhang
- Cancer Center, Wuhan Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Bing Li
- Department of DataScience, Burning Rock Biotech, Guangzhou, China
| | - Yi-Ran Cai
- Department of DataScience, Burning Rock Biotech, Guangzhou, China
| | - Feng-Cai Wen
- The Medical Department, 3D Medicines Inc., Shanghai, China
| | - Ding Zhang
- The Medical Department, 3D Medicines Inc., Shanghai, China
| | - Yue-Zong Bai
- The Medical Department, 3D Medicines Inc., Shanghai, China
| | - Xue-Yan Zhang
- Department of Pulmonary Medicine, Shanghai Chest Hospital, Shanghai Jiaotong University, Shanghai, 200030, China
| | - Shu-Yuan Wang
- Department of Pulmonary Medicine, Shanghai Chest Hospital, Shanghai Jiaotong University, Shanghai, 200030, China
| | - Lei Cheng
- Department of Pulmonary Medicine, Shanghai Chest Hospital, Shanghai Jiaotong University, Shanghai, 200030, China
| | - Hua Zhong
- Department of Pulmonary Medicine, Shanghai Chest Hospital, Shanghai Jiaotong University, Shanghai, 200030, China.
| | - Li Liu
- Cancer Center, Wuhan Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China.
| | - Jie Wang
- State Key Laboratory of Molecular Oncology, Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.
| | - Bao-Hui Han
- Department of Pulmonary Medicine, Shanghai Chest Hospital, Shanghai Jiaotong University, Shanghai, 200030, China.
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Donker HC, Schuuring E, Heitzer E, Groen HJ. Decoding circulating tumor DNA to identify durable benefit from immunotherapy in lung cancer. Lung Cancer 2022; 170:52-57. [DOI: 10.1016/j.lungcan.2022.05.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 05/17/2022] [Accepted: 05/23/2022] [Indexed: 11/28/2022]
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Sepich-Poore GD, Guccione C, Laplane L, Pradeu T, Curtius K, Knight R. Cancer's second genome: Microbial cancer diagnostics and redefining clonal evolution as a multispecies process: Humans and their tumors are not aseptic, and the multispecies nature of cancer modulates clinical care and clonal evolution: Humans and their tumors are not aseptic, and the multispecies nature of cancer modulates clinical care and clonal evolution. Bioessays 2022; 44:e2100252. [PMID: 35253252 PMCID: PMC10506734 DOI: 10.1002/bies.202100252] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2021] [Revised: 01/31/2022] [Accepted: 02/16/2022] [Indexed: 12/13/2022]
Abstract
The presence and role of microbes in human cancers has come full circle in the last century. Tumors are no longer considered aseptic, but implications for cancer biology and oncology remain underappreciated. Opportunities to identify and build translational diagnostics, prognostics, and therapeutics that exploit cancer's second genome-the metagenome-are manifold, but require careful consideration of microbial experimental idiosyncrasies that are distinct from host-centric methods. Furthermore, the discoveries of intracellular and intra-metastatic cancer bacteria necessitate fundamental changes in describing clonal evolution and selection, reflecting bidirectional interactions with non-human residents. Reconsidering cancer clonality as a multispecies process similarly holds key implications for understanding metastasis and prognosing therapeutic resistance while providing rational guidance for the next generation of bacterial cancer therapies. Guided by these new findings and challenges, this Review describes opportunities to exploit cancer's metagenome in oncology and proposes an evolutionary framework as a first step towards modeling multispecies cancer clonality. Also see the video abstract here: https://youtu.be/-WDtIRJYZSs.
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Affiliation(s)
| | - Caitlin Guccione
- Division of Biomedical Informatics, Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
- Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA 92093, USA
- Department of Pediatrics, University of California San Diego, La Jolla, CA 92093, USA
| | - Lucie Laplane
- Institut d’histoire et de philosophie des sciences et des techniques (UMR8590), CNRS & Panthéon-Sorbonne University, 75006 Paris, France
- Hematopoietic stem cells and the development of myeloid malignancies (UMR1287), Gustave Roussy Cancer Campus, 94800 Villejuif, France
| | - Thomas Pradeu
- ImmunoConcept (UMR5164), CNRS & University of Bordeaux, 33076 Bordeaux Cedex, France
| | - Kit Curtius
- Division of Biomedical Informatics, Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
- Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA 92093, USA
| | - Rob Knight
- Department of Bioengineering, University of California San Diego, La Jolla, CA 92093, USA
- Department of Pediatrics, University of California San Diego, La Jolla, CA 92093, USA
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA 92093, USA
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Clinical validation of a next-generation sequencing-based multi-cancer early detection "liquid biopsy" blood test in over 1,000 dogs using an independent testing set: The CANcer Detection in Dogs (CANDiD) study. PLoS One 2022; 17:e0266623. [PMID: 35471999 PMCID: PMC9041869 DOI: 10.1371/journal.pone.0266623] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 03/23/2022] [Indexed: 12/11/2022] Open
Abstract
Cancer is the leading cause of death in dogs, yet there are no established screening paradigms for early detection. Liquid biopsy methods that interrogate cancer-derived genomic alterations in cell-free DNA in blood are being adopted for multi-cancer early detection in human medicine and are now available for veterinary use. The CANcer Detection in Dogs (CANDiD) study is an international, multi-center clinical study designed to validate the performance of a novel multi-cancer early detection “liquid biopsy” test developed for noninvasive detection and characterization of cancer in dogs using next-generation sequencing (NGS) of blood-derived DNA; study results are reported here. In total, 1,358 cancer-diagnosed and presumably cancer-free dogs were enrolled in the study, representing the range of breeds, weights, ages, and cancer types seen in routine clinical practice; 1,100 subjects met inclusion criteria for analysis and were used in the validation of the test. Overall, the liquid biopsy test demonstrated a 54.7% (95% CI: 49.3–60.0%) sensitivity and a 98.5% (95% CI: 97.0–99.3%) specificity. For three of the most aggressive canine cancers (lymphoma, hemangiosarcoma, osteosarcoma), the detection rate was 85.4% (95% CI: 78.4–90.9%); and for eight of the most common canine cancers (lymphoma, hemangiosarcoma, osteosarcoma, soft tissue sarcoma, mast cell tumor, mammary gland carcinoma, anal sac adenocarcinoma, malignant melanoma), the detection rate was 61.9% (95% CI: 55.3–68.1%). The test detected cancer signal in patients representing 30 distinct cancer types and provided a Cancer Signal Origin prediction for a subset of patients with hematological malignancies. Furthermore, the test accurately detected cancer signal in four presumably cancer-free subjects before the onset of clinical signs, further supporting the utility of liquid biopsy as an early detection test. Taken together, these findings demonstrate that NGS-based liquid biopsy can offer a novel option for noninvasive multi-cancer detection in dogs.
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Wu M, Shen H, Wang Z, Kanu N, Chen K. Research Progress on Postoperative Minimal/Molecular Residual Disease Detection in Lung Cancer. Chronic Dis Transl Med 2022; 8:83-90. [PMID: 35774426 PMCID: PMC9215711 DOI: 10.1002/cdt3.10] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 12/22/2021] [Indexed: 12/05/2022] Open
Abstract
Lung cancer is the leading cause of cancer‐related deaths worldwide. Approximately 10%–50% of patients experience relapse after radical surgery, which may be attributed to the persistence of minimal/molecular residual disease (MRD). Circulating tumor DNA (ctDNA), a common liquid biopsy approach, has been demonstrated to have significant clinical merit. In this study, we review the evidence supporting the use of ctDNA for MRD detection and discuss the potential clinical applications of postoperative MRD detection, including monitoring recurrence, guiding adjuvant treatment, and driving clinical trials in lung cancer. We will also discuss the problems that prevent the routine application of ctDNA MRD detection. Multi‐analyte methods and identification of specific genetic and molecular alterations, especially methylation, are effective detection strategies and show considerable prospects for future development. Interventional prospective studies based on ctDNA detection are needed to determine whether the application of postoperative MRD detection can improve the clinical outcomes of lung cancer patients, and the accuracy, sensitivity, specificity, and robustness of different detection methods still require optimization and refinement.
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Affiliation(s)
- Manqi Wu
- Department of Thoracic Surgery Peking University People's Hospital, Peking University Beijing 100044 China
| | - Haifeng Shen
- Department of Thoracic Surgery Peking University People's Hospital, Peking University Beijing 100044 China
| | - Ziyang Wang
- Department of Thoracic Surgery Peking University People's Hospital, Peking University Beijing 100044 China
| | - Nnennaya Kanu
- Cancer Research UK Lung Cancer Centre of Excellence University College London Cancer Institute, University College London 72 Huntley St London WC1E 6DD UK
| | - Kezhong Chen
- Department of Thoracic Surgery Peking University People's Hospital, Peking University Beijing 100044 China
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Øgaard N, Reinert T, Henriksen TV, Frydendahl A, Aagaard E, Ørntoft MBW, Larsen MØ, Knudsen AR, Mortensen FV, Andersen CL. Tumour-agnostic circulating tumour DNA analysis for improved recurrence surveillance after resection of colorectal liver metastases: A prospective cohort study. Eur J Cancer 2022; 163:163-176. [DOI: 10.1016/j.ejca.2021.12.026] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 12/20/2021] [Accepted: 12/23/2021] [Indexed: 12/15/2022]
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67
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Kolesar J, Peh S, Thomas L, Baburaj G, Mukherjee N, Kantamneni R, Lewis S, Pai A, Udupa KS, Kumar An N, Rangnekar VM, Rao M. Integration of liquid biopsy and pharmacogenomics for precision therapy of EGFR mutant and resistant lung cancers. Mol Cancer 2022; 21:61. [PMID: 35209919 PMCID: PMC8867675 DOI: 10.1186/s12943-022-01534-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 02/07/2022] [Indexed: 11/22/2022] Open
Abstract
The advent of molecular profiling has revolutionized the treatment of lung cancer by comprehensively delineating the genomic landscape of the epidermal growth factor receptor (EGFR) gene. Drug resistance caused by EGFR mutations and genetic polymorphisms of drug metabolizing enzymes and transporters impedes effective treatment of EGFR mutant and resistant lung cancer. This review appraises current literature, opportunities, and challenges associated with liquid biopsy and pharmacogenomic (PGx) testing as precision therapy tools in the management of EGFR mutant and resistant lung cancers. Liquid biopsy could play a potential role in selection of precise tyrosine kinase inhibitor (TKI) therapies during different phases of lung cancer treatment. This selection will be based on the driver EGFR mutational status, as well as monitoring the development of potential EGFR mutations arising during or after TKIs treatment, since some of these new mutations may be druggable targets for alternative TKIs. Several studies have identified the utility of liquid biopsy in the identification of EGFR driver and acquired resistance with good sensitivities for various blood-based biomarkers. With a plethora of sequencing technologies and platforms available currently, further evaluations using randomized controlled trials (RCTs) in multicentric, multiethnic and larger patient cohorts could enable optimization of liquid-based assays for the detection of EGFR mutations, and support testing of CYP450 enzymes and drug transporter polymorphisms to guide precise dosing of EGFR TKIs.
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Affiliation(s)
- Jill Kolesar
- Department of Pharmacy Practice & Science, University of Kentucky, Lexington, KY, 40536, USA
| | - Spencer Peh
- Department of Pharmacy Practice & Science, University of Kentucky, Lexington, KY, 40536, USA
| | - Levin Thomas
- Department of Pharmacy Practice, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India
| | - Gayathri Baburaj
- Department of Pharmacy Practice, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India
| | - Nayonika Mukherjee
- Department of Pharmacy Practice, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India
| | - Raveena Kantamneni
- Department of Pharmacy Practice, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India
| | - Shirley Lewis
- Department of Radiotherapy and Oncology, Kasturba Medical College, Manipal Comprehensive Cancer Care Centre, Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India
| | - Ananth Pai
- Department of Medical Oncology, Kasturba Medical College, Manipal Comprehensive Cancer Care Centre, Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India
| | - Karthik S Udupa
- Department of Medical Oncology, Kasturba Medical College, Manipal Comprehensive Cancer Care Centre, Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India
| | - Naveena Kumar An
- Department of Surgical Oncology, Kasturba Medical College, Manipal Comprehensive Cancer Care Centre, Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India
| | - Vivek M Rangnekar
- Markey Cancer Centre and Department of Radiation Medicine, University of Kentucky, Lexington, KY, 40536, USA
| | - Mahadev Rao
- Department of Pharmacy Practice, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India.
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Eisenhardt AE, Schmid A, Esser J, Brugger Z, Lausch U, Kiefer J, Braig M, Runkel A, Wehrle J, Claus R, Bronsert P, Leithner A, Liegl-Atzwanger B, Zeller J, Papini R, von Laffert M, Pfitzner BM, Koulaxouzidis G, Giunta RE, Eisenhardt SU, Braig D. Targeted next-generation sequencing of circulating free DNA enables non-invasive tumor detection in myxoid liposarcomas. Mol Cancer 2022; 21:50. [PMID: 35164780 PMCID: PMC8842903 DOI: 10.1186/s12943-022-01523-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 01/26/2022] [Indexed: 12/17/2022] Open
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69
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Stadler JC, Belloum Y, Deitert B, Sementsov M, Heidrich I, Gebhardt C, Keller L, Pantel K. Current and Future Clinical Applications of ctDNA in Immuno-Oncology. Cancer Res 2022; 82:349-358. [PMID: 34815256 PMCID: PMC9397642 DOI: 10.1158/0008-5472.can-21-1718] [Citation(s) in RCA: 59] [Impact Index Per Article: 29.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 10/06/2021] [Accepted: 11/09/2021] [Indexed: 01/07/2023]
Abstract
Testing peripheral blood for circulating tumor DNA (ctDNA) offers a minimally invasive opportunity to diagnose, characterize, and monitor the disease in individual cancer patients. ctDNA can reflect the actual tumor burden and specific genomic state of disease and thus might serve as a prognostic and predictive biomarker for immune checkpoint inhibitor (ICI) therapy. Recent studies in various cancer entities (e.g., melanoma, non-small cell lung cancer, colon cancer, and urothelial cancer) have shown that sequential ctDNA analyses allow for the identification of responders to ICI therapy, with a significant lead time to imaging. ctDNA assessment may also help distinguish pseudoprogression under ICI therapy from real progression. Developing dynamic changes in ctDNA concentrations as a potential surrogate endpoint of clinical efficacy in patients undergoing adjuvant immunotherapy is ongoing. Besides overall ctDNA burden, further ctDNA characterization can help uncover tumor-specific determinants (e.g., tumor mutational burden and microsatellite instability) of responses or resistance to immunotherapy. In future studies, standardized ctDNA assessments need to be included in interventional clinical trials across cancer entities to demonstrate the clinical utility of ctDNA as a biomarker for personalized cancer immunotherapy.
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Affiliation(s)
- Julia-Christina Stadler
- Department of Tumor Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.,Department of Dermatology and Venereology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.,Mildred Scheel Cancer Career Center HaTriCS4, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Yassine Belloum
- Department of Tumor Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Benjamin Deitert
- Department of Tumor Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Mark Sementsov
- Department of Tumor Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Isabel Heidrich
- Department of Tumor Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.,Department of Dermatology and Venereology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.,Mildred Scheel Cancer Career Center HaTriCS4, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Christoffer Gebhardt
- Department of Dermatology and Venereology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Laura Keller
- Department of Tumor Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.,Corresponding Authors: Klaus Pantel, Institute for Tumor Biologie, University Medical Center Hamburg-Eppendorf, Martinistrasse 52, Hamburg, Hamburg, 20246, Germany. E-mail: ; and Laura Keller, E-mail:
| | - Klaus Pantel
- Department of Tumor Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.,Corresponding Authors: Klaus Pantel, Institute for Tumor Biologie, University Medical Center Hamburg-Eppendorf, Martinistrasse 52, Hamburg, Hamburg, 20246, Germany. E-mail: ; and Laura Keller, E-mail:
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Serial ctDNA analysis predicts clinical progression in patients with advanced urothelial carcinoma. Br J Cancer 2022; 126:430-439. [PMID: 35046520 PMCID: PMC8810988 DOI: 10.1038/s41416-021-01648-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2021] [Revised: 10/28/2021] [Accepted: 11/22/2021] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Targeted sequencing of circulating tumour DNA (ctDNA) is a promising tool to monitor dynamic changes in the variant allele frequencies (VAF) of genomic alterations and predict clinical outcomes in patients with advanced urothelial carcinoma (UC). METHODS We performed targeted sequencing of 182 serial ctDNA samples from 53 patients with advanced UC. RESULTS Serial ctDNA-derived metrics predicted the clinical outcomes in patients with advanced UC. Combining serial ctDNA aggregate VAF (aVAF) values with clinical factors, including age, sex, and liver metastasis, improved the performance of prognostic models. An increase of the ctDNA aVAF by ≥1 in serial ctDNA samples predicted disease progression within 6 months in 90% of patients. The majority of patients with aVAFs ≤0.7 in three consecutive ctDNA samples achieved durable clinical responses (≥6 months). CONCLUSIONS Serial ctDNA analysis predicts disease progression and enables dynamic monitoring to guide precision medicine in patients with advanced UC.
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71
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Sanz-Garcia E, Zhao E, Bratman SV, Siu LL. Monitoring and adapting cancer treatment using circulating tumor DNA kinetics: Current research, opportunities, and challenges. SCIENCE ADVANCES 2022; 8:eabi8618. [PMID: 35080978 PMCID: PMC8791609 DOI: 10.1126/sciadv.abi8618] [Citation(s) in RCA: 54] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Circulating tumor DNA (ctDNA) has emerged as a biomarker with wide-ranging applications in cancer management. While its role in guiding precision medicine in certain tumors via noninvasive detection of susceptibility and resistance alterations is now well established, recent evidence has pointed to more generalizable use in treatment monitoring. Quantitative changes in ctDNA levels over time (i.e., ctDNA kinetics) have shown potential as an early indicator of therapeutic efficacy and could enable treatment adaptation. However, ctDNA kinetics are complex and heterogeneous, affected by tumor biology, host physiology, and treatment factors. This review outlines the current preclinical and clinical knowledge of ctDNA kinetics in cancer and how early on-treatment changes in ctDNA levels could be applied in clinical research to collect evidence to support implementation in daily practice.
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Affiliation(s)
- Enrique Sanz-Garcia
- Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, Ontario, Canada
| | - Eric Zhao
- Department of Radiation Oncology, Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, Ontario, Canada
| | - Scott V. Bratman
- Department of Radiation Oncology, Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Lillian L. Siu
- Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, Ontario, Canada
- Corresponding author.
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72
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Foo J, Basanta D, Rockne RC, Strelez C, Shah C, Ghaffarian K, Mumenthaler SM, Mitchell K, Lathia JD, Frankhouser D, Branciamore S, Kuo YH, Marcucci G, Vander Velde R, Marusyk A, Hang S, Hari K, Jolly MK, Hatzikirou H, Poels K, Spilker M, Shtylla B, Robertson-Tessi M, Anderson ARA. Roadmap on plasticity and epigenetics in cancer. Phys Biol 2022; 19. [PMID: 35078159 PMCID: PMC9190291 DOI: 10.1088/1478-3975/ac4ee2] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 01/25/2022] [Indexed: 11/22/2022]
Abstract
The role of plasticity and epigenetics in shaping cancer evolution and response to therapy has taken center stage with recent technological advances including single cell sequencing. This roadmap article is focused on state-of-the-art mathematical and experimental approaches to interrogate plasticity in cancer, and addresses the following themes and questions: is there a formal overarching framework that encompasses both non-genetic plasticity and mutation-driven somatic evolution? How do we measure and model the role of the microenvironment in influencing/controlling non-genetic plasticity? How can we experimentally study non-genetic plasticity? Which mathematical techniques are required or best suited? What are the clinical and practical applications and implications of these concepts?
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Affiliation(s)
- Jasmine Foo
- University of Minnesota System, School of Mathematics, Minneapolis, Minnesota, 55455-2020, UNITED STATES
| | - David Basanta
- Integrated Mathematical Oncology, H Lee Moffitt Cancer Center and Research Center Inc, H Lee Moffitt Cancer Center and Research Institute, 12902 Magnolia Drive, MRC-3 West/IMO, Tampa, Florida 33612USA, Tampa, Florida, 33612-9416, UNITED STATES
| | - Russell C Rockne
- Computational and Quantitative Medicine; Division of Mathematical Oncology, Beckman Research Institute, 1500 E Duarte Rd, Rose Vogel Building (74), Duarte, California, 91010, UNITED STATES
| | - Carly Strelez
- Lawrence J. Ellison Institute , Transformative Medicine, Los Angeles, CA 90064, UNITED STATES
| | - Curran Shah
- Lawrence J. Ellison Institute , Transformative Medicine, Los Angeles, CA 90064, UNITED STATES
| | - Kimya Ghaffarian
- Lawrence J. Ellison Institute , Transformative Medicine, Los Angeles, CA 90064, UNITED STATES
| | - Shannon M Mumenthaler
- Lawrence J. Ellison Institute , Transformative Medicine, Los Angeles, CA 90064, UNITED STATES
| | - Kelly Mitchell
- Department of Cardiovascular & Metabolic Sciences, Cleveland Clinic, Lerner Research Institute, Cleveland, Ohio, 44195-5243, UNITED STATES
| | - Justin D Lathia
- Department of Cardiovascular & Metabolic Sciences, Cleveland Clinic, Lerner Research Institute, Cleveland, Ohio, 44195-5243, UNITED STATES
| | - David Frankhouser
- Computational and Quantitative Medicine; Division of Mathematical Oncology, Beckman Research Institute, 1500 E Duarte Rd, Rose Vogel Building (74), Duarte, California, 91010, UNITED STATES
| | - Sergio Branciamore
- Computational and Quantitative Medicine; Division of Mathematical Oncology, Beckman Research Institute, 1500 E Duarte Rd, Rose Vogel Building (74), Duarte, California, 91010, UNITED STATES
| | - Ya-Huei Kuo
- Hematologic Malignancies Translational Science, City of Hope National Medical Center, Beckman Research Institute, 1500 E Duarte Rd, Rose Vogel Building (74), Duarte, California, 91010, UNITED STATES
| | - Guido Marcucci
- Hematologic Malignancies Translational Science, City of Hope National Medical Center, Beckman Research Institute, 1500 E Duarte Rd, Rose Vogel Building (74), Duarte, California, 91010, UNITED STATES
| | - Robert Vander Velde
- Department of Cancer Physiology, H Lee Moffitt Cancer Center and Research Center Inc, H Lee Moffitt Cancer Center and Research Institute, 12902 Magnolia Drive, MRC-3 West/IMO, Tampa, Florida 33612USA, Tampa, Florida, 33612-9416, UNITED STATES
| | - Andriy Marusyk
- Cancer Physiology, Moffitt Cancer Center, 12902 USF Magnolia Drive, Tampa, Florida, 33612, UNITED STATES
| | - Sui Hang
- Institute for Systems Biology, Systems Biology, WA , WA 98109, UNITED STATES
| | - Kishore Hari
- Indian Institute of Science, 560012 Bangalore, Bangalore, 560012, INDIA
| | - Mohit Kumar Jolly
- Centre for BioSystems Science and Engineering,, Indian Institute of Science, 560012 Bangalore, Bangalore, 560012, INDIA
| | - Haralampos Hatzikirou
- Khalifa University, P.O. Box: 127788, Abu Dhabi, Abu Dhabi, NA, UNITED ARAB EMIRATES
| | - Kamrine Poels
- Early Clinical Development, Pfizer Global Research and Development, Early Clinical Development, Groton, Connecticut, 06340, UNITED STATES
| | - Mary Spilker
- Medicine Design, Pfizer Global Research and Development, Medicine Design, Groton, Connecticut, 06340, UNITED STATES
| | - Blerta Shtylla
- Early Clinical Development, Pfizer Global Research and Development, Early Clinical Development, Groton, Connecticut, 06340, UNITED STATES
| | - Mark Robertson-Tessi
- Integrated Mathematical Oncology Department, Moffitt Cancer Center, 12902 USF Magnolia Drive, Tampa, Florida, 33612, UNITED STATES
| | - Alexander R A Anderson
- Integrated Mathematical Oncology, Moffitt Cancer Center, Co-Director of Integrated Mathematical Oncology, 12902 Magnolia Drive, SRB 4 Rm 24000H, Tampa, Florida 33612, Tampa, 33612, UNITED STATES
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73
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Mead EA, Boulghassoul-Pietrzykowska N, Wang Y, Anees O, Kinstlinger NS, Lee M, Hamza S, Feng Y, Pietrzykowski AZ. Non-Invasive microRNA Profiling in Saliva can Serve as a Biomarker of Alcohol Exposure and Its Effects in Humans. Front Genet 2022; 12:804222. [PMID: 35126468 PMCID: PMC8812725 DOI: 10.3389/fgene.2021.804222] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 12/13/2021] [Indexed: 12/14/2022] Open
Abstract
Alcohol Use Disorder (AUD) is one of the most prevalent mental disorders worldwide. Considering the widespread occurrence of AUD, a reliable, cheap, non-invasive biomarker of alcohol consumption is desired by healthcare providers, clinicians, researchers, public health and criminal justice officials. microRNAs could serve as such biomarkers. They are easily detectable in saliva, which can be sampled from individuals in a non-invasive manner. Moreover, microRNAs expression is dynamically regulated by environmental factors, including alcohol. Since excessive alcohol consumption is a hallmark of alcohol abuse, we have profiled microRNA expression in the saliva of chronic, heavy alcohol abusers using microRNA microarrays. We observed significant changes in salivary microRNA expression caused by excessive alcohol consumption. These changes fell into three categories: downregulated microRNAs, upregulated microRNAs, and microRNAs upregulated de novo. Analysis of these combinatorial changes in microRNA expression suggests dysregulation of specific biological pathways leading to impairment of the immune system and development of several types of epithelial cancer. Moreover, some of the altered microRNAs are also modulators of inflammation, suggesting their contribution to pro-inflammatory mechanisms of alcohol actions. Establishment of the cellular source of microRNAs in saliva corroborated these results. We determined that most of the microRNAs in saliva come from two types of cells: leukocytes involved in immune responses and inflammation, and buccal cells, involved in development of epithelial, oral cancers. In summary, we propose that microRNA profiling in saliva can be a useful, non-invasive biomarker allowing the monitoring of alcohol abuse, as well as alcohol-related inflammation and early detection of cancer.
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Affiliation(s)
- Edward A. Mead
- Laboratory of Adaptation, Reward and Addiction, Department of Animal Sciences, Rutgers University, New Brunswick, NJ, United States
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- *Correspondence: Edward A. Mead,
| | - Nadia Boulghassoul-Pietrzykowska
- Laboratory of Adaptation, Reward and Addiction, Department of Animal Sciences, Rutgers University, New Brunswick, NJ, United States
- Mayo Clinic Health System, NWWI, Barron, WI, United States
- Department of Medicine, Capital Health, Trenton, NJ, United States
- Weight and Life MD, Hamilton, NJ, United States
| | - Yongping Wang
- Laboratory of Adaptation, Reward and Addiction, Department of Animal Sciences, Rutgers University, New Brunswick, NJ, United States
- Holmdel Township School, Holmdel, NJ, United States
| | - Onaiza Anees
- Laboratory of Adaptation, Reward and Addiction, Department of Animal Sciences, Rutgers University, New Brunswick, NJ, United States
- Virginia Commonwealth University Health, CMH Behavioral Health, South Hill, VA, United States
| | - Noah S. Kinstlinger
- Laboratory of Adaptation, Reward and Addiction, Department of Animal Sciences, Rutgers University, New Brunswick, NJ, United States
- Albert Einstein College of Medicine, Bronx, NY, United States
| | - Maximillian Lee
- Laboratory of Adaptation, Reward and Addiction, Department of Animal Sciences, Rutgers University, New Brunswick, NJ, United States
- George Washington University, School of Medicine and Health Sciences, Washington DC, MA, United States
| | - Shireen Hamza
- Laboratory of Adaptation, Reward and Addiction, Department of Animal Sciences, Rutgers University, New Brunswick, NJ, United States
- Department of the History of Science, Harvard University, Cambridge, MA, United States
| | - Yaping Feng
- Waksman Genomics Core Facility, Rutgers University, Piscataway, NJ, United States
- Bioinformatics Department, Admera Health, South Plainfield, NJ, United States
| | - Andrzej Z. Pietrzykowski
- Laboratory of Adaptation, Reward and Addiction, Department of Animal Sciences, Rutgers University, New Brunswick, NJ, United States
- Weight and Life MD, Hamilton, NJ, United States
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Fournier L, de Geus-Oei LF, Regge D, Oprea-Lager DE, D’Anastasi M, Bidaut L, Bäuerle T, Lopci E, Cappello G, Lecouvet F, Mayerhoefer M, Kunz WG, Verhoeff JJC, Caruso D, Smits M, Hoffmann RT, Gourtsoyianni S, Beets-Tan R, Neri E, deSouza NM, Deroose CM, Caramella C. Twenty Years On: RECIST as a Biomarker of Response in Solid Tumours an EORTC Imaging Group - ESOI Joint Paper. Front Oncol 2022; 11:800547. [PMID: 35083155 PMCID: PMC8784734 DOI: 10.3389/fonc.2021.800547] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2021] [Accepted: 11/30/2021] [Indexed: 12/15/2022] Open
Abstract
Response evaluation criteria in solid tumours (RECIST) v1.1 are currently the reference standard for evaluating efficacy of therapies in patients with solid tumours who are included in clinical trials, and they are widely used and accepted by regulatory agencies. This expert statement discusses the principles underlying RECIST, as well as their reproducibility and limitations. While the RECIST framework may not be perfect, the scientific bases for the anticancer drugs that have been approved using a RECIST-based surrogate endpoint remain valid. Importantly, changes in measurement have to meet thresholds defined by RECIST for response classification within thus partly circumventing the problems of measurement variability. The RECIST framework also applies to clinical patients in individual settings even though the relationship between tumour size changes and outcome from cohort studies is not necessarily translatable to individual cases. As reproducibility of RECIST measurements is impacted by reader experience, choice of target lesions and detection/interpretation of new lesions, it can result in patients changing response categories when measurements are near threshold values or if new lesions are missed or incorrectly interpreted. There are several situations where RECIST will fail to evaluate treatment-induced changes correctly; knowledge and understanding of these is crucial for correct interpretation. Also, some patterns of response/progression cannot be correctly documented by RECIST, particularly in relation to organ-site (e.g. bone without associated soft-tissue lesion) and treatment type (e.g. focal therapies). These require specialist reader experience and communication with oncologists to determine the actual impact of the therapy and best evaluation strategy. In such situations, alternative imaging markers for tumour response may be used but the sources of variability of individual imaging techniques need to be known and accounted for. Communication between imaging experts and oncologists regarding the level of confidence in a biomarker is essential for the correct interpretation of a biomarker and its application to clinical decision-making. Though measurement automation is desirable and potentially reduces the variability of results, associated technical difficulties must be overcome, and human adjudications may be required.
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Affiliation(s)
- Laure Fournier
- Imaging Group, European Organisation of Research and Treatment in Cancer (EORTC), Brussels, Belgium
- European Society of Oncologic Imaging (ESOI), European Society of Radiology, Vienna, Austria
- Université de Paris, Assistance Publique–Hôpitaux de Paris (AP-HP), Hopital europeen Georges Pompidou, Department of Radiology, Paris Cardiovascular Research Center (PARCC) Unité Mixte de Recherche (UMRS) 970, Institut national de la santé et de la recherche médicale (INSERM), Paris, France
| | - Lioe-Fee de Geus-Oei
- Imaging Group, European Organisation of Research and Treatment in Cancer (EORTC), Brussels, Belgium
- Department of Radiology, Leiden University Medical Center, Leiden, Netherlands
- Biomedical Photonic Imaging Group, University of Twente, Enschede, Netherlands
| | - Daniele Regge
- European Society of Oncologic Imaging (ESOI), European Society of Radiology, Vienna, Austria
- Department of Surgical Sciences, University of Turin, Turin, Italy
- Radiology Unit, Candiolo Cancer Institute, Fondazione del Piemonte per l’Oncologia-Istituto Di Ricovero e Cura a Carattere Scientifico (FPO-IRCCS), Turin, Italy
| | - Daniela-Elena Oprea-Lager
- Imaging Group, European Organisation of Research and Treatment in Cancer (EORTC), Brussels, Belgium
- Department of Radiology & Nuclear Medicine, Cancer Centre Amsterdam, Amsterdam University Medical Centers [Vrije Universiteit (VU) University], Amsterdam, Netherlands
| | - Melvin D’Anastasi
- European Society of Oncologic Imaging (ESOI), European Society of Radiology, Vienna, Austria
- Medical Imaging Department, Mater Dei Hospital, University of Malta, Msida, Malta
| | - Luc Bidaut
- Imaging Group, European Organisation of Research and Treatment in Cancer (EORTC), Brussels, Belgium
- College of Science, University of Lincoln, Lincoln, United Kingdom
| | - Tobias Bäuerle
- European Society of Oncologic Imaging (ESOI), European Society of Radiology, Vienna, Austria
- Institute of Radiology, University Hospital Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Egesta Lopci
- Imaging Group, European Organisation of Research and Treatment in Cancer (EORTC), Brussels, Belgium
- Nuclear Medicine Unit, Istituto Di Ricovero e Cura a Carattere Scientifico (IRCCS) – Humanitas Research Hospital, Milan, Italy
| | - Giovanni Cappello
- Department of Surgical Sciences, University of Turin, Turin, Italy
- Radiology Unit, Candiolo Cancer Institute, Fondazione del Piemonte per l’Oncologia-Istituto Di Ricovero e Cura a Carattere Scientifico (FPO-IRCCS), Turin, Italy
| | - Frederic Lecouvet
- Imaging Group, European Organisation of Research and Treatment in Cancer (EORTC), Brussels, Belgium
- Department of Radiology, Institut de Recherche Expérimentale et Clinique (IREC), Cliniques Universitaires Saint Luc, Université Catholique de Louvain (UCLouvain), Brussels, Belgium
| | - Marius Mayerhoefer
- European Society of Oncologic Imaging (ESOI), European Society of Radiology, Vienna, Austria
- Department of Radiology, Memorial Sloan Kettering Cancer Center, New York, NY, United States
- Department of Biomedical Imaging and Image-guided Therapy, Medical University of Vienna, Vienna, Austria
| | - Wolfgang G. Kunz
- Imaging Group, European Organisation of Research and Treatment in Cancer (EORTC), Brussels, Belgium
- European Society of Oncologic Imaging (ESOI), European Society of Radiology, Vienna, Austria
- Department of Radiology, University Hospital, Ludwig Maximilian University (LMU) Munich, Munich, Germany
| | - Joost J. C. Verhoeff
- Imaging Group, European Organisation of Research and Treatment in Cancer (EORTC), Brussels, Belgium
- Department of Radiotherapy, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
| | - Damiano Caruso
- European Society of Oncologic Imaging (ESOI), European Society of Radiology, Vienna, Austria
- Department of Medical-Surgical Sciences and Translational Medicine, Sapienza University of Rome, Rome, Italy
| | - Marion Smits
- Imaging Group, European Organisation of Research and Treatment in Cancer (EORTC), Brussels, Belgium
- Department of Radiology & Nuclear Medicine, Erasmus MC, University Medical Centre Rotterdam, Rotterdam, Netherlands
- Brain Tumour Centre, Erasmus Medical Centre (MC) Cancer Institute, Rotterdam, Netherlands
| | - Ralf-Thorsten Hoffmann
- European Society of Oncologic Imaging (ESOI), European Society of Radiology, Vienna, Austria
- Institute and Policlinic for Diagnostic and Interventional Radiology, University Hospital, Carl-Gustav-Carus Technical University Dresden, Dresden, Germany
| | - Sofia Gourtsoyianni
- European Society of Oncologic Imaging (ESOI), European Society of Radiology, Vienna, Austria
- Department of Radiology, School of Medicine, National and Kapodistrian University of Athens, Areteion Hospital, Athens, Greece
| | - Regina Beets-Tan
- European Society of Oncologic Imaging (ESOI), European Society of Radiology, Vienna, Austria
- Department of Radiology, The Netherlands Cancer Institute, Amsterdam, Netherlands
- School For Oncology and Developmental Biology (GROW) School for Oncology and Developmental Biology, Maastricht University, Maastricht, Netherlands
| | - Emanuele Neri
- European Society of Oncologic Imaging (ESOI), European Society of Radiology, Vienna, Austria
- Diagnostic and Interventional Radiology, Department of Translational Research and of New Surgical and Medical Technologies, University of Pisa, Pisa, Italy
| | - Nandita M. deSouza
- Imaging Group, European Organisation of Research and Treatment in Cancer (EORTC), Brussels, Belgium
- Division of Radiotherapy and Imaging, The Institute of Cancer Research and Royal Marsden National Health Service (NHS) Foundation Trust, London, United Kingdom
- European Imaging Biomarkers Alliance (EIBALL), European Society of Radiology, Vienna, Austria
- Quantitative Imaging Biomarkers Alliance, Radiological Society of North America, Oak Brook, IL, United States
| | - Christophe M. Deroose
- Imaging Group, European Organisation of Research and Treatment in Cancer (EORTC), Brussels, Belgium
- Nuclear Medicine, University Hospitals Leuven, Leuven, Belgium
- Nuclear Medicine & Molecular Imaging, Department of Imaging and Pathology, Katholieke Universiteit (KU) Leuven, Leuven, Belgium
| | - Caroline Caramella
- Imaging Group, European Organisation of Research and Treatment in Cancer (EORTC), Brussels, Belgium
- Radiology Department, Hôpital Marie Lannelongue, Groupe Hospitalier Paris Saint Joseph Centre International des Cancers Thoraciques, Université Paris-Saclay, Le Plessis-Robinson, France
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75
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Symonds EL, Pedersen SK, Yeo B, Al Naji H, Byrne SE, Roy A, Young GP. Assessment of tumor burden and response to therapy in patients with colorectal cancer using a quantitative ctDNA test for methylated BCAT1/IKZF1. Mol Oncol 2022; 16:2031-2041. [PMID: 35000264 PMCID: PMC9120880 DOI: 10.1002/1878-0261.13178] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 11/10/2021] [Accepted: 01/07/2022] [Indexed: 11/22/2022] Open
Abstract
Failure of colorectal cancer (CRC) treatment is due to residual disease, and its timely identification is critical for patient survival. Detecting CRC‐associated mutations in patient circulating cell‐free DNA is confounded by tumor mutation heterogeneity, requiring primary tumor sequencing to identify relevant mutations. In this study, we assessed BCAT1 and IKZF1 methylation levels to quantify circulating tumor DNA (ctDNA) and investigated whether this method can be used to assess tumor burden and efficacy of therapy. In 175 patients with CRC who were ctDNA‐positive pretreatment, ctDNA levels were higher with advancing stage (P < 0.05) and correlated with tumor diameter (r = 0.35, P < 0.001) and volume (r = 0.58, P < 0.01). After completion of treatment (median of 70 days [IQR 49‐109] after surgery, +/− radiotherapy, +/− chemotherapy), ctDNA levels were reduced in 98% (47/48) and were undetectable in 88% (42/48) of patients tested. For those with incomplete adjuvant chemotherapy after surgery, roughly half remained ctDNA‐positive (11/21, 52.4%). The presence of ctDNA after treatment was associated with disease progression (HR 9.7, 95%CI 2.5‐37.6) compared to no ctDNA. Assaying blood for ctDNA methylated in BCAT1/IKZF1 has the potential for identifying residual disease due to treatment failure, informing a potential need for therapy adjustment in advanced disease.
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Affiliation(s)
- Erin L Symonds
- Bowel Health Service, Flinders Medical Centre, Bedford Park, SA.,Cancer Research, Flinders Health and Medical Research Institute, Flinders University, Bedford Park, SA
| | - Susanne K Pedersen
- Cancer Research, Flinders Health and Medical Research Institute, Flinders University, Bedford Park, SA.,Clinical Genomics Pty Ltd, North Ryde
| | - Bernita Yeo
- Department of Medicine, College of Medicine and Public Health, Flinders University, Bedford Park, SA
| | - Hiba Al Naji
- Department of Medicine, College of Medicine and Public Health, Flinders University, Bedford Park, SA
| | - Susan E Byrne
- Cancer Research, Flinders Health and Medical Research Institute, Flinders University, Bedford Park, SA
| | - Amitesh Roy
- Department of Oncology, Flinders Medical Centre, Bedford Park, SA
| | - Graeme P Young
- Cancer Research, Flinders Health and Medical Research Institute, Flinders University, Bedford Park, SA
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76
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Abouali H, Hosseini SA, Purcell E, Nagrath S, Poudineh M. Recent Advances in Device Engineering and Computational Analysis for Characterization of Cell-Released Cancer Biomarkers. Cancers (Basel) 2022; 14:288. [PMID: 35053452 PMCID: PMC8774172 DOI: 10.3390/cancers14020288] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 12/21/2021] [Accepted: 01/04/2022] [Indexed: 02/04/2023] Open
Abstract
During cancer progression, tumors shed different biomarkers into the bloodstream, including circulating tumor cells (CTCs), extracellular vesicles (EVs), circulating cell-free DNA (cfDNA), and circulating tumor DNA (ctDNA). The analysis of these biomarkers in the blood, known as 'liquid biopsy' (LB), is a promising approach for early cancer detection and treatment monitoring, and more recently, as a means for cancer therapy. Previous reviews have discussed the role of CTCs and ctDNA in cancer progression; however, ctDNA and EVs are rapidly evolving with technological advancements and computational analysis and are the subject of enormous recent studies in cancer biomarkers. In this review, first, we introduce these cell-released cancer biomarkers and briefly discuss their clinical significance in cancer diagnosis and treatment monitoring. Second, we present conventional and novel approaches for the isolation, profiling, and characterization of these markers. We then investigate the mathematical and in silico models that are developed to investigate the function of ctDNA and EVs in cancer progression. We convey our views on what is needed to pave the way to translate the emerging technologies and models into the clinic and make the case that optimized next-generation techniques and models are needed to precisely evaluate the clinical relevance of these LB markers.
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Affiliation(s)
- Hesam Abouali
- Department of Electrical and Computer Engineering, University of Waterloo, Waterloo, ON N2L 3G1, Canada; (H.A.); (S.A.H.)
| | - Seied Ali Hosseini
- Department of Electrical and Computer Engineering, University of Waterloo, Waterloo, ON N2L 3G1, Canada; (H.A.); (S.A.H.)
| | - Emma Purcell
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI 48109-2800, USA; (E.P.); (S.N.)
| | - Sunitha Nagrath
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI 48109-2800, USA; (E.P.); (S.N.)
| | - Mahla Poudineh
- Department of Electrical and Computer Engineering, University of Waterloo, Waterloo, ON N2L 3G1, Canada; (H.A.); (S.A.H.)
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77
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Boniface CT, Spellman PT. Blood, Toil, and Taxoteres: Biological Determinates of Treatment-Induce ctDNA Dynamics for Interpreting Tumor Response. Pathol Oncol Res 2022; 28:1610103. [PMID: 35665409 PMCID: PMC9160182 DOI: 10.3389/pore.2022.1610103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/02/2021] [Accepted: 04/29/2022] [Indexed: 11/23/2022]
Abstract
Collection and analysis of circulating tumor DNA (ctDNA) is one of the few methods of liquid biopsy that measures generalizable and tumor specific molecules, and is one of the most promising approaches in assessing the effectiveness of cancer care. Clinical assays that utilize ctDNA are commercially available for the identification of actionable mutations prior to treatment and to assess minimal residual disease after treatment. There is currently no clinical ctDNA assay specifically intended to monitor disease response during treatment, partially due to the complex challenge of understanding the biological sources of ctDNA and the underlying principles that govern its release. Although studies have shown pre- and post-treatment ctDNA levels can be prognostic, there is evidence that early, on-treatment changes in ctDNA levels are more accurate in predicting response. Yet, these results also vary widely among cohorts, cancer type, and treatment, likely due to the driving biology of tumor cell proliferation, cell death, and ctDNA clearance kinetics. To realize the full potential of ctDNA monitoring in cancer care, we may need to reorient our thinking toward the fundamental biological underpinnings of ctDNA release and dissemination from merely seeking convenient clinical correlates.
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Affiliation(s)
- Christopher T. Boniface
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, United States
- Cancer Early Detection Advanced Research Center, Knight Cancer Institute, Oregon Health & Science University, Portland, OR, United States
- *Correspondence: Christopher T. Boniface, ; Paul T. Spellman,
| | - Paul T. Spellman
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, United States
- Cancer Early Detection Advanced Research Center, Knight Cancer Institute, Oregon Health & Science University, Portland, OR, United States
- *Correspondence: Christopher T. Boniface, ; Paul T. Spellman,
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78
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Adams E, Sepich-Poore GD, Miller-Montgomery S, Knight R. Using All Our Genomes: Blood-based Liquid Biopsies for the Early Detection of Cancer. VIEW 2022; 3:20200118. [PMID: 35872970 PMCID: PMC9307139 DOI: 10.1002/viw.20200118] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2021] [Accepted: 10/22/2021] [Indexed: 02/02/2023] Open
Abstract
The pursuit of highly sensitive and specific cancer diagnostics based on cell-free (cf) nucleic acids isolated from minimally invasive liquid biopsies has been an area of intense research and commercial effort for at least two decades. Most of these tests detect cancer-specific mutations or epigenetic modifications on circulating DNA derived from tumor cells (ctDNA). Although recent FDA approvals of both single and multi-analyte liquid biopsy companion diagnostic assays are proof of the tremendous progress made in this domain, using ctDNA for the diagnosis of early-stage (stage I/II) cancers remains challenging due to several factors, such as low mutational allele frequency in circulation, overlapping profiles in genomic alterations among diverse cancers, and clonal hematopoiesis. This review discusses these analytical challenges, interim solutions, and the opportunity to complement ctDNA diagnostics with microbiome-aware analyses that may mitigate several existing ctDNA assay limitations.
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Affiliation(s)
| | - Gregory D Sepich-Poore
- Micronoma, Inc., San Diego, CA, USA
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
| | | | - Rob Knight
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA
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79
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Ribba B, Roller A, Helms HJ, Stern M, Bleul C. Circulating tumor DNA: Opportunities and challenges for pharmacometric approaches. Front Pharmacol 2022; 13:1058220. [PMID: 36968790 PMCID: PMC10030934 DOI: 10.3389/fphar.2022.1058220] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 12/01/2022] [Indexed: 03/29/2023] Open
Abstract
To support further development of model-informed drug development approaches leveraging circulating tumor DNA (ctDNA), we performed an exploratory analysis of the relationships between treatment-induced changes to ctDNA levels, clinical response and tumor size dynamics in patients with cancer treated with checkpoint inhibitors and targeted therapies. This analysis highlights opportunities for pharmacometrics approaches such as for optimizing sampling design strategies. It also highlights challenges related to the nature of the data and associated variability overall emphasizing the importance of mechanistic modeling studies of the underlying biology of ctDNA processes such as shedding, release and clearance and their relationships with tumor size dynamic and treatment effects.
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80
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Cell-Free-DNA-Based Copy Number Index Score in Epithelial Ovarian Cancer-Impact for Diagnosis and Treatment Monitoring. Cancers (Basel) 2021; 14:cancers14010168. [PMID: 35008332 PMCID: PMC8750971 DOI: 10.3390/cancers14010168] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 12/16/2021] [Accepted: 12/20/2021] [Indexed: 12/02/2022] Open
Abstract
Simple Summary The prognosis of ovarian cancer is dependent on the tumor stage and the development of chemotherapy resistance. Using low-coverage cell-free tumor DNA sequencing, we were able to determine the chromosomal instability (CI) of tumors that are frequently found in patients with primary advanced and recurrent high-grade ovarian cancer from a blood sample. We were able to show that the CI could be used for the reliable detection of ovarian cancer in comparison to healthy controls. Moreover, we showed that the CI was significantly associated with the prognostic and predictive clinical measures in primary and recurrent ovarian cancer. The high diagnostic accuracy of the tumor CI derived from cfDNA analysis might lead to the optimization of main prognostic determinants in patients with ovarian cancer. As the CI is a characteristic feature in high-grade ovarian cancer, no upfront tumor tissue analysis is required to identify genomic alterations for targeted sequencing of cfDNA, if the herein described low-coverage sequencing and CNI-Score determination is used. Abstract Background: Chromosomal instability, a hallmark of cancer, results in changes in the copy number state. These deviant copy number states can be detected in the cell-free DNA (cfDNA) and provide a quantitative measure of the ctDNA levels by converting cfDNA next-generation sequencing results into a genome-wide copy number instability score (CNI-Score). Our aim was to determine the role of the CNI-Score in detecting epithelial ovarian cancer (EOC) and its role as a marker to monitor the response to treatment. Methods: Blood samples were prospectively collected from 109 patients with high-grade EOC. cfDNA was extracted and analyzed using a clinical-grade assay designed to calculate a genome-wide CNI-Score from low-coverage sequencing data. Stored data from 241 apparently healthy controls were used as a reference set. Results: Comparison of the CNI-Scores of primary EOC patients versus controls yielded sensitivities of 91% at a specificity of 95% to detect OC, respectively. Significantly elevated CNI-Scores were detected in primary (median: 87, IQR: 351) and recurrent (median: 346, IQR: 1891) blood samples. Substantially reduced CNI-Scores were detected after primary debulking surgery. Using a cut-off of 24, a diagnostic sensitivity of 87% for primary and recurrent EOC was determined at a specificity of 95%. CNI-Scores above this threshold were detected in 21/23 primary tumor (91%), 36/42 of platinum-eligible recurrent (85.7%), and 19/22 of non-platinum-eligible recurrent (86.3%) samples, respectively. Conclusion: ctDNA-quantification based on genomic instability determined by the CNI-Score was a biomarker with high diagnostic accuracy in high-grade EOC. The applied assay might be a promising tool for diagnostics and therapy monitoring, as it requires no a priori information about the tumor.
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81
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Wan JCM, Mughal TI, Razavi P, Dawson SJ, Moss EL, Govindan R, Tan IB, Yap YS, Robinson WA, Morris CD, Besse B, Bardelli A, Tie J, Kopetz S, Rosenfeld N. Liquid biopsies for residual disease and recurrence. MED 2021; 2:1292-1313. [PMID: 35590147 DOI: 10.1016/j.medj.2021.11.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 09/27/2021] [Accepted: 10/29/2021] [Indexed: 02/07/2023]
Abstract
Detection of minimal residual disease in patients with cancer, who are in complete remission with no cancer cells detectable, has the potential to improve recurrence-free survival through treatment selection. Studies analyzing circulating tumor DNA (ctDNA) in patients with solid tumors suggest the potential to accurately predict and detect relapse, enabling treatment strategies that may improve clinical outcomes. Over the past decade, assays for ctDNA detection in plasma samples have steadily increased in sensitivity and specificity. These are applied for the detection of residual disease after treatment and for earlier detection of recurrence. Novel clinical trials are now assessing how assays for "residual disease and recurrence" (RDR) may influence current treatment paradigms and potentially change the landscape of risk classification for cancer recurrence. In this review, we appraise the progress of RDR detection using ctDNA and consider the emerging role of liquid biopsy in the monitoring and management of solid tumors.
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Affiliation(s)
| | - Tariq Imdadali Mughal
- Tufts University School of Medicine, Boston, MA 02111, USA; University of Buckingham, Buckingham MK18 1EG, UK
| | - Pedram Razavi
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | | | - Esther Louise Moss
- Leicester Cancer Research Centre, College of Life Sciences, University of Leicester, Leicester LE1 7RH, UK; Department of Gynaecological Oncology, University Hospitals of Leicester NHS Trust, Leicester General Hospital, Leicester LE5 4PW, UK
| | | | - Iain Beehuat Tan
- Division of Medical Oncology, National Cancer Centre Singapore, 169610 Singapore, Singapore
| | - Yoon-Sim Yap
- Division of Medical Oncology, National Cancer Centre Singapore, 169610 Singapore, Singapore
| | | | | | - Benjamin Besse
- Department of Cancer Medicine, Institut Gustave Roussy Cancer Center, 94805 Villejuif, France
| | - Alberto Bardelli
- Candiolo Cancer Institute, FPO-IRCCS, 10060 Candiolo TO, Italy; Department of Oncology, University of Turin, 10060 Candiolo TO, Italy
| | - Jeanne Tie
- Peter MacCallum Cancer Center, Melbourne, VIC 3000, Australia; Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
| | - Scott Kopetz
- MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Nitzan Rosenfeld
- Inivata, Cambridge CB22 3FH, UK; Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, UK; Cancer Research UK Cambridge Centre, Cambridge CB2 0RE, UK.
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82
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Sunami K, Bando H, Yatabe Y, Naito Y, Takahashi H, Tsuchihara K, Toyooka S, Mimori K, Kohsaka S, Uetake H, Kinoshita I, Komine K, Takeda M, Hayashida T, Tamura K, Nishio K, Yamamoto N. Appropriate use of cancer comprehensive genome profiling assay using circulating tumor DNA. Cancer Sci 2021; 112:3911-3917. [PMID: 34128569 PMCID: PMC8409307 DOI: 10.1111/cas.15022] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Revised: 06/08/2021] [Accepted: 06/09/2021] [Indexed: 01/11/2023] Open
Abstract
Comprehensive genomic profiling (CGP) is being increasingly used for the routine clinical management of solid cancers. In July 2018, the use of tumor tissue-based CGP assays became available for all solid cancers under the universal health insurance system in Japan. Several restrictions presently exist, such as patient eligibility and limitations on the opportunities to perform such assays. The clinical implementation of CGP based on plasma circulating tumor DNA (ctDNA) is also expected to raise issues regarding the selection and use of tissue DNA and ctDNA CGP. A Joint Task Force for the Promotion of Cancer Genome Medicine comprised of three Japanese cancer-related societies has formulated a policy proposal for the appropriate use of plasma CGP (in Japanese), available at https://www.jca.gr.jp/researcher/topics/2021/files/20210120.pdf, http://www.jsco.or.jp/jpn/user_data/upload/File/20210120.pdf, and https://www.jsmo.or.jp/file/dl/newsj/2765.pdf. Based on these recommendations, the working group has summarized the respective advantages and cautions regarding the use of tissue DNA CGP and ctDNA CGP with reference to the advice of a multidisciplinary expert panel, the preferred use of plasma specimens over tissue, and multiple ctDNA testing. These recommendations have been prepared to maximize the benefits of performing CGP assays and might be applicable in other countries and regions.
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Affiliation(s)
- Kuniko Sunami
- Department of Laboratory MedicineNational Cancer Center HospitalTokyoJapan
| | - Hideaki Bando
- Department of Clinical OncologyAichi Cancer Center HospitalNagoyaJapan
| | - Yasushi Yatabe
- Department of Diagnostic PathologyNational Cancer Center HospitalDivision of Molecular PathologyNational Cancer Center Research InstituteTokyoJapan
| | - Yoichi Naito
- Department of Medical OncologyNational Cancer Center Hospital EastKashiwaJapan
| | - Hideaki Takahashi
- Department of Hepatobiliary and Pancreatic OncologyNational Cancer Center Hospital EastKashiwaJapan
| | - Katsuya Tsuchihara
- Division of Translational InformaticsExploratory Oncology Research and Clinical Trial CenterNational Cancer CenterKashiwaJapan
| | - Shinichi Toyooka
- Department of General Thoracic Surgery and Breast and Endocrine SurgeryOkayama University Graduate School of Medicine, Dentistry, and Pharmaceutical SciencesOkayamaJapan
| | | | - Shinji Kohsaka
- Division of Cellular SignalingNational Cancer Center Research InstituteTokyoJapan
| | - Hiroyuki Uetake
- Department of Clinical ResearchNational Disaster Medical CenterTokyoJapan
| | - Ichiro Kinoshita
- Division of Clinical Cancer GenomicsHokkaido University HospitalSapporoJapan
| | - Keigo Komine
- Department of Clinical OncologyTohoku University HospitalSendaiJapan
| | - Masayuki Takeda
- Department of Cancer Genomics and Medical OncologyNara Medical UniversityNaraJapan
| | - Tetsu Hayashida
- Department of SurgeryKeio University School of MedicineTokyoJapan
| | - Kenji Tamura
- Department of Medical OncologyShimane University HospitalIzumoJapan
| | - Kazuto Nishio
- Department of Genome BiologyKindai University Faculty of MedicineOsakasayamaJapan
| | - Noboru Yamamoto
- Department of Experimental TherapeuticsNational Cancer Center HospitalTokyoJapan
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83
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Lin C, Liu X, Zheng B, Ke R, Tzeng CM. Liquid Biopsy, ctDNA Diagnosis through NGS. Life (Basel) 2021; 11:life11090890. [PMID: 34575039 PMCID: PMC8468354 DOI: 10.3390/life11090890] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 08/08/2021] [Accepted: 08/11/2021] [Indexed: 12/15/2022] Open
Abstract
Liquid biopsy with circulating tumor DNA (ctDNA) profiling by next-generation sequencing holds great promise to revolutionize clinical oncology. It relies on the basis that ctDNA represents the real-time status of the tumor genome which contains information of genetic alterations. Compared to tissue biopsy, liquid biopsy possesses great advantages such as a less demanding procedure, minimal invasion, ease of frequent sampling, and less sampling bias. Next-generation sequencing (NGS) methods have come to a point that both the cost and performance are suitable for clinical diagnosis. Thus, profiling ctDNA by NGS technologies is becoming more and more popular since it can be applied in the whole process of cancer diagnosis and management. Further developments of liquid biopsy ctDNA testing will be beneficial for cancer patients, paving the way for precision medicine. In conclusion, profiling ctDNA with NGS for cancer diagnosis is both biologically sound and technically convenient.
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Affiliation(s)
- Chen Lin
- School of Medicine, Huaqiao University, Quanzhou 362021, China; (C.L.); (X.L.)
| | - Xuzhu Liu
- School of Medicine, Huaqiao University, Quanzhou 362021, China; (C.L.); (X.L.)
| | - Bingyi Zheng
- Translational Medicine Research Center, School of Pharmaceutical Sciences, Xiamen University, Xiamen 361102, China;
- Xiamen Key Laboratory of Cancer Cell Theranostics and Clinical Translation, Xiamen 361102, China
| | - Rongqin Ke
- School of Medicine, Huaqiao University, Quanzhou 362021, China; (C.L.); (X.L.)
- Correspondence: (R.K.); (C.-M.T.)
| | - Chi-Meng Tzeng
- Translational Medicine Research Center, School of Pharmaceutical Sciences, Xiamen University, Xiamen 361102, China;
- Xiamen Key Laboratory of Cancer Cell Theranostics and Clinical Translation, Xiamen 361102, China
- Correspondence: (R.K.); (C.-M.T.)
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84
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Bredno J, Lipson J, Venn O, Aravanis AM, Jamshidi A. Clinical correlates of circulating cell-free DNA tumor fraction. PLoS One 2021; 16:e0256436. [PMID: 34432811 PMCID: PMC8386888 DOI: 10.1371/journal.pone.0256436] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Accepted: 08/08/2021] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND Oncology applications of cell-free DNA analysis are often limited by the amount of circulating tumor DNA and the fraction of cell-free DNA derived from tumor cells in a blood sample. This circulating tumor fraction varies widely between individuals and cancer types. Clinical factors that influence tumor fraction have not been completely elucidated. METHODS AND FINDINGS Circulating tumor fraction was determined for breast, lung, and colorectal cancer participant samples in the first substudy of the Circulating Cell-free Genome Atlas study (CCGA; NCT02889978; multi-cancer early detection test development) and was related to tumor and patient characteristics. Linear models were created to determine the influence of tumor size combined with mitotic or metabolic activity (as tumor mitotic volume or excessive lesion glycolysis, respectively), histologic type, histologic grade, and lymph node status on tumor fraction. For breast and lung cancer, tumor mitotic volume and excessive lesion glycolysis (primary lesion volume scaled by percentage positive for Ki-67 or PET standardized uptake value minus 1.0, respectively) were the only statistically significant covariates. For colorectal cancer, the surface area of tumors invading beyond the subserosa was the only significant covariate. The models were validated with cases from the second CCGA substudy and show that these clinical correlates of circulating tumor fraction can predict and explain the performance of a multi-cancer early detection test. CONCLUSIONS Prognostic clinical variables, including mitotic or metabolic activity and depth of invasion, were identified as correlates of circulating tumor DNA by linear models that relate clinical covariates to tumor fraction. The identified correlates indicate that faster growing tumors have higher tumor fractions. Early cancer detection from assays that analyze cell-free DNA is determined by circulating tumor fraction. Results support that early detection is particularly sensitive for faster growing, aggressive tumors with high mortality, many of which have no available screening today.
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Affiliation(s)
- Joerg Bredno
- GRAIL, Inc., Menlo Park, California, United States of America
| | - Jafi Lipson
- GRAIL, Inc., Menlo Park, California, United States of America
| | - Oliver Venn
- GRAIL, Inc., Menlo Park, California, United States of America
| | | | - Arash Jamshidi
- GRAIL, Inc., Menlo Park, California, United States of America
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85
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Brett JO, Spring LM, Bardia A, Wander SA. ESR1 mutation as an emerging clinical biomarker in metastatic hormone receptor-positive breast cancer. Breast Cancer Res 2021; 23:85. [PMID: 34392831 PMCID: PMC8365900 DOI: 10.1186/s13058-021-01462-3] [Citation(s) in RCA: 114] [Impact Index Per Article: 38.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Accepted: 07/20/2021] [Indexed: 11/10/2022] Open
Abstract
In metastatic hormone receptor-positive breast cancer, ESR1 mutations are a common cause of acquired resistance to the backbone of therapy, estrogen deprivation by aromatase inhibition. How these mutations affect tumor sensitivity to established and novel therapies are active areas of research. These therapies include estrogen receptor-targeting agents, such as selective estrogen receptor modulators, covalent antagonists, and degraders (including tamoxifen, fulvestrant, and novel agents), and combination therapies, such as endocrine therapy plus CDK4/6, PI3K, or mTORC1 inhibition. In this review, we summarize existing knowledge surrounding the mechanisms of action of ESR1 mutations and roles in resistance to aromatase inhibition. We then analyze the recent literature on how ESR1 mutations affect outcomes in estrogen receptor-targeting and combination therapies. For estrogen receptor-targeting therapies such as tamoxifen and fulvestrant, ESR1 mutations cause relative resistance in vitro but do not clearly lead to resistance in patients, making novel agents in this category promising. Regarding combination therapies, ESR1 mutations nullify any aromatase inhibitor component of the combination. Thus, combinations using endocrine alternatives to aromatase inhibition, or combinations where the non-endocrine component is efficacious as monotherapy, are still effective against ESR1 mutations. These results emphasize the importance of investigating combinatorial resistance, challenging as these efforts are. We also discuss future directions and open questions, such as studying the differences among distinct ESR1 mutations, asking how to adjust clinical decisions based on molecular surveillance testing, and developing novel therapies that are effective against ESR1 mutations.
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Affiliation(s)
- Jamie O Brett
- Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Laura M Spring
- Harvard Medical School, Boston, MA, USA
- Department of Medical Oncology, Massachusetts General Hospital Cancer Center, 55 Fruit Street, Boston, MA, 02114, USA
| | - Aditya Bardia
- Harvard Medical School, Boston, MA, USA
- Department of Medical Oncology, Massachusetts General Hospital Cancer Center, 55 Fruit Street, Boston, MA, 02114, USA
| | - Seth A Wander
- Harvard Medical School, Boston, MA, USA.
- Department of Medical Oncology, Massachusetts General Hospital Cancer Center, 55 Fruit Street, Boston, MA, 02114, USA.
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86
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Ahn J, Heo S, Lee J, Bang D. Introduction to Single-Cell DNA Methylation Profiling Methods. Biomolecules 2021; 11:1013. [PMID: 34356635 PMCID: PMC8301785 DOI: 10.3390/biom11071013] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 07/05/2021] [Accepted: 07/06/2021] [Indexed: 02/06/2023] Open
Abstract
DNA methylation is an epigenetic mechanism that is related to mammalian cellular differentiation, gene expression regulation, and disease. In several studies, DNA methylation has been identified as an effective marker to identify differences between cells. In this review, we introduce single-cell DNA-methylation profiling methods, including experimental strategies and approaches to computational data analysis. Furthermore, the blind spots of the basic analysis and recent alternatives are briefly described. In addition, we introduce well-known applications and discuss future development.
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Affiliation(s)
- Jongseong Ahn
- Department of Chemistry, Yonsei University, Seoul 03722, Korea; (J.A.); (S.H.)
| | - Sunghoon Heo
- Department of Chemistry, Yonsei University, Seoul 03722, Korea; (J.A.); (S.H.)
| | - Jihyun Lee
- Department of Clinical Pharmacology and Therapeutics, College of Medicine, Kyung Hee University, Seoul 02447, Korea
- Department of Biomedical Science and Technology, Kyung Hee University, Seoul 02447, Korea
| | - Duhee Bang
- Department of Chemistry, Yonsei University, Seoul 03722, Korea; (J.A.); (S.H.)
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87
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Perspectives for circulating tumor DNA in clinical management of colorectal cancer. Int J Clin Oncol 2021; 26:1420-1430. [PMID: 34185174 DOI: 10.1007/s10147-021-01937-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 05/11/2021] [Indexed: 10/21/2022]
Abstract
Growing evidence has demonstrated that circulating tumor DNA (ctDNA) detection in colorectal cancer might be a promising approach to address current important clinical questions. During chemotherapy for metastatic colorectal cancer, tumor cells acquire potential resistance by generating additional somatic mutations related to therapeutic resistance. ctDNA can capture the tumor landscape, including heterogeneity, which might provide the opportunity for additional treatment options. Moreover, ctDNA detection is advantageous, because it can monitor tumor heterogeneity serially, in a non-invasive manner. ctDNA is considered valid for detecting minimal residual disease after a curable resection. By utilizing ctDNA detection, adjuvant chemotherapy for patients with stage II-III colorectal cancer might be omitted for patients at low risk of recurrence; or conversely, adjuvant chemotherapy might be highly recommended for patients at high risk, based on ctDNA findings. During multidisciplinary treatments for locally advanced rectal cancer, it is essential to monitor the responses to sequential treatments to make appropriate decisions. Currently, these decisions are mainly based on radiological or pathological findings. ctDNA can add value by providing the real-time status of locally advanced rectal cancer. In this review, we summarized the current evidence and discussed future strategies for using ctDNA in the treatment of colorectal cancer.
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88
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Haring CT, Brummel C, Bhambhani C, Jewell B, Neal MH, Bhangale A, Casper K, Malloy K, McLean S, Shuman A, Stucken C, Rosko A, Prince M, Bradford C, Eisbruch A, Mierzwa M, Tewari M, Worden FP, Swiecicki PL, Spector ME, Brenner JC. Implementation of human papillomavirus circulating tumor DNA to identify recurrence during treatment de-escalation. Oral Oncol 2021; 121:105332. [PMID: 34140235 DOI: 10.1016/j.oraloncology.2021.105332] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Accepted: 05/05/2021] [Indexed: 11/18/2022]
Affiliation(s)
- Catherine T Haring
- University of Michigan, Department of Otolaryngology- Head and Neck Surgery, United States
| | - Collin Brummel
- University of Michigan, Department of Otolaryngology- Head and Neck Surgery, United States
| | - Chandan Bhambhani
- University of Michigan, Department of Internal Medicine, Division of Hematology and Oncology, United States
| | - Brittany Jewell
- University of Michigan, Department of Otolaryngology- Head and Neck Surgery, United States
| | - Molly Heft Neal
- University of Michigan, Department of Otolaryngology- Head and Neck Surgery, United States
| | - Apurva Bhangale
- University of Michigan, Department of Otolaryngology- Head and Neck Surgery, United States
| | - Keith Casper
- University of Michigan, Department of Otolaryngology- Head and Neck Surgery, United States; University of Michigan, Rogel Cancer Center, United States
| | - Kelly Malloy
- University of Michigan, Department of Otolaryngology- Head and Neck Surgery, United States; University of Michigan, Rogel Cancer Center, United States
| | - Scott McLean
- University of Michigan, Department of Otolaryngology- Head and Neck Surgery, United States; University of Michigan, Rogel Cancer Center, United States
| | - Andrew Shuman
- University of Michigan, Department of Otolaryngology- Head and Neck Surgery, United States; University of Michigan, Rogel Cancer Center, United States
| | - Chaz Stucken
- University of Michigan, Department of Otolaryngology- Head and Neck Surgery, United States; University of Michigan, Rogel Cancer Center, United States
| | - Andrew Rosko
- University of Michigan, Department of Otolaryngology- Head and Neck Surgery, United States; University of Michigan, Rogel Cancer Center, United States
| | - Mark Prince
- University of Michigan, Department of Otolaryngology- Head and Neck Surgery, United States; University of Michigan, Rogel Cancer Center, United States
| | - Carol Bradford
- University of Michigan, Department of Otolaryngology- Head and Neck Surgery, United States; University of Michigan, Rogel Cancer Center, United States
| | - Avraham Eisbruch
- University of Michigan, Department of Radiation Oncology, United States; University of Michigan, Rogel Cancer Center, United States
| | - Michelle Mierzwa
- University of Michigan, Department of Radiation Oncology, United States; University of Michigan, Rogel Cancer Center, United States
| | - Muneesh Tewari
- University of Michigan, Department of Internal Medicine, Division of Hematology and Oncology, United States; University of Michigan, Rogel Cancer Center, United States
| | - Francis P Worden
- University of Michigan, Department of Internal Medicine, Division of Hematology and Oncology, United States; University of Michigan, Rogel Cancer Center, United States
| | - Paul L Swiecicki
- University of Michigan, Department of Internal Medicine, Division of Hematology and Oncology, United States; University of Michigan, Rogel Cancer Center, United States
| | - Matthew E Spector
- University of Michigan, Department of Otolaryngology- Head and Neck Surgery, United States; University of Michigan, Rogel Cancer Center, United States
| | - J Chad Brenner
- University of Michigan, Department of Otolaryngology- Head and Neck Surgery, United States; University of Michigan, Rogel Cancer Center, United States; University of Michigan, Department of Pharmacology, United States.
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Masfarré L, Vidal J, Fernández-Rodríguez C, Montagut C. ctDNA to Guide Adjuvant Therapy in Localized Colorectal Cancer (CRC). Cancers (Basel) 2021; 13:2869. [PMID: 34201274 PMCID: PMC8226638 DOI: 10.3390/cancers13122869] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Revised: 05/30/2021] [Accepted: 06/02/2021] [Indexed: 12/15/2022] Open
Abstract
Currently, the standard treatment for patients with localized colorectal cancer (CRC) includes surgical resection followed by adjuvant chemotherapy based on clinicopathological features. Recurrence risk stratification in those patients is of utmost importance to guide clinicians to avoid both under- and overtreatment. Recently, the concept of minimal residual disease (MRD) has emerged as the detection of circulating tumor DNA (ctDNA) carrying tumor-specific genomic or epigenomic alterations in the bloodstream of patients after surgery. Emerging studies described how the detection of MRD is a powerful prognostic biomarker to identify patients at higher risk of recurrence and who will potentially benefit the most from a systemic adjuvant treatment. Based on that unprecedented finding, several clinical trials involving stage II and III CRC patients are ongoing evaluating the impact of ctDNA guided treatment by escalating or deescalating adjuvant chemotherapy based on ctDNA MRD detection. This review provides a critical overview of current perspectives of liquid biopsy in early-stage CRC including technical, biological, and clinical key points, as well as ongoing ctDNA-based clinical trials that ultimately aim to improve clinical outcomes of patients with CRC.
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Affiliation(s)
- Laura Masfarré
- Medical Oncology Department, Hospital del Mar, 08003 Barcelona, Spain; (L.M.); (J.V.)
| | - Joana Vidal
- Medical Oncology Department, Hospital del Mar, 08003 Barcelona, Spain; (L.M.); (J.V.)
- Cancer Research Program, FIMIM, Hospital del Mar, 08003 Barcelona, Spain
| | | | - Clara Montagut
- Medical Oncology Department, Hospital del Mar, 08003 Barcelona, Spain; (L.M.); (J.V.)
- Cancer Research Program, FIMIM, Hospital del Mar, 08003 Barcelona, Spain
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90
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Filipska M, Rosell R. Mutated circulating tumor DNA as a liquid biopsy in lung cancer detection and treatment. Mol Oncol 2021; 15:1667-1682. [PMID: 33969622 PMCID: PMC8169447 DOI: 10.1002/1878-0261.12983] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Revised: 04/30/2021] [Accepted: 05/07/2021] [Indexed: 12/12/2022] Open
Abstract
Over the past decade, substantial developments have been made in the detection of circulating tumor DNA (ctDNA)-cell-free DNA (cfDNA) fragments released into the circulation from tumor cells and displaying the genetic alterations of those cells. As such, ctDNA detected in liquid biopsies serves as a powerful tool for cancer patient stratification, therapy guidance, detection of resistance, and relapse monitoring. In this Review, we describe lung cancer diagnosis and monitoring strategies using ctDNA detection technologies and compile recent evidence regarding lung cancer-related mutation detection in liquid biopsy. We focus not only on epidermal growth factor receptor (EGFR) alterations, but also on significant co-mutations that shed more light on novel ctDNA-based liquid biopsy applications. Finally, we discuss future perspectives of early-cancer detection and clonal hematopoiesis filtering strategies, with possible inclusion of microbiome-driven liquid biopsy.
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Affiliation(s)
- Martyna Filipska
- Germans Trias i Pujol Research Institute and HospitalBadalonaSpain
- Autonomous University of BarcelonaCerdanyola del VallesSpain
| | - Rafael Rosell
- Germans Trias i Pujol Research Institute and HospitalBadalonaSpain
- Autonomous University of BarcelonaCerdanyola del VallesSpain
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91
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Lee S, Park YS, Chang WJ, Choi JY, Lim A, Kim B, Lee SB, Lee JW, Kim SH, Kim J, Kwak JM, Yoon KC, Lee SH, Kim YH. Clinical Implication of Liquid Biopsy in Colorectal Cancer Patients Treated with Metastasectomy. Cancers (Basel) 2021; 13:cancers13092231. [PMID: 34066481 PMCID: PMC8125778 DOI: 10.3390/cancers13092231] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2021] [Revised: 04/26/2021] [Accepted: 05/04/2021] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND & AIMS The application of circulating tumor DNA (ctDNA) has been studied for predicting recurrent disease after surgery and treatment response during systemic treatment. Metastasectomy can be curative for well-selected patients with metastatic colorectal cancer (mCRC). This prospective study investigated the ctDNA level before and after metastasectomy in patients with mCRC to explore its potential as a predictive biomarker. METHODS We collected data on 98 metastasectomies for mCRC performed from March 2017 to February 2020. Somatic mutations in the primary and metastatic tumors were identified and tumor-informed ctDNAs were selected by ultra-deep targeted sequencing. Plasma samples were mandatorily collected before and 3-4 weeks after metastasectomy and serially, if patients agreed. RESULTS Data on 67 of 98 metastasectomies (58 patients) meeting the criteria were collected. ctDNA was detected in 9 (29%) of 31 cases treated with upfront metastasectomy and in 7 (19.4%) of 36 cases treated with metastasectomy after upfront chemotherapy. The detection rate of ctDNA was higher in liver metastasis (p = 0.0045) and tumors measuring ≥1 cm (p = 0.0183). ctDNA was less likely to be detected if the response to chemotherapy was good. After metastasectomy, ctDNA was found in 4 (6%) cases with rapid progressive disease. CONCLUSION The biological factors affecting the ctDNA shedding from the tumor should be considered when applying ctDNA assays in a clinical setting. After metastasectomy for oligometastatic lesions in good responders of chemotherapy, most ctDNA was cleared or existed below the detection level. To assist clinical decision making after metastasectomy for mCRC using ctDNA, further studies for improving specific outcomes are needed.
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Affiliation(s)
- Soohyeon Lee
- Division of Medical Oncology and Hematology, Department of Internal Medicine, Korea University College of Medicine, Seoul 02841, Korea; (S.L.); (W.-J.C.); (J.Y.C.); (A.L.)
| | - Young-Soo Park
- Korea University Cancer Research Institute, Korea University College of Medicine, Seoul 02841, Korea; (Y.-S.P.); (B.K.); (S.-B.L.); (J.-W.L.)
| | - Won-Jin Chang
- Division of Medical Oncology and Hematology, Department of Internal Medicine, Korea University College of Medicine, Seoul 02841, Korea; (S.L.); (W.-J.C.); (J.Y.C.); (A.L.)
| | - Jung Yoon Choi
- Division of Medical Oncology and Hematology, Department of Internal Medicine, Korea University College of Medicine, Seoul 02841, Korea; (S.L.); (W.-J.C.); (J.Y.C.); (A.L.)
| | - Ahreum Lim
- Division of Medical Oncology and Hematology, Department of Internal Medicine, Korea University College of Medicine, Seoul 02841, Korea; (S.L.); (W.-J.C.); (J.Y.C.); (A.L.)
| | - Boyeon Kim
- Korea University Cancer Research Institute, Korea University College of Medicine, Seoul 02841, Korea; (Y.-S.P.); (B.K.); (S.-B.L.); (J.-W.L.)
| | - Saet-Byeol Lee
- Korea University Cancer Research Institute, Korea University College of Medicine, Seoul 02841, Korea; (Y.-S.P.); (B.K.); (S.-B.L.); (J.-W.L.)
| | - Jong-Won Lee
- Korea University Cancer Research Institute, Korea University College of Medicine, Seoul 02841, Korea; (Y.-S.P.); (B.K.); (S.-B.L.); (J.-W.L.)
| | - Seon-Hahn Kim
- Department of Surgery, Korea University College of Medicine, Seoul 02841, Korea; (S.-H.K.); (J.K.); (J.-M.K.); (K.-C.Y.)
| | - Jin Kim
- Department of Surgery, Korea University College of Medicine, Seoul 02841, Korea; (S.-H.K.); (J.K.); (J.-M.K.); (K.-C.Y.)
| | - Jung-Myun Kwak
- Department of Surgery, Korea University College of Medicine, Seoul 02841, Korea; (S.-H.K.); (J.K.); (J.-M.K.); (K.-C.Y.)
| | - Kyung-Chul Yoon
- Department of Surgery, Korea University College of Medicine, Seoul 02841, Korea; (S.-H.K.); (J.K.); (J.-M.K.); (K.-C.Y.)
| | - Sung-Ho Lee
- Department of Thoracic and Cardiovascular Surgery, Korea University College of Medicine, Seoul 02841, Korea;
| | - Yeul Hong Kim
- Division of Medical Oncology and Hematology, Department of Internal Medicine, Korea University College of Medicine, Seoul 02841, Korea; (S.L.); (W.-J.C.); (J.Y.C.); (A.L.)
- Korea University Cancer Research Institute, Korea University College of Medicine, Seoul 02841, Korea; (Y.-S.P.); (B.K.); (S.-B.L.); (J.-W.L.)
- Correspondence: ; Tel.: +82-2-920-5569; Fax: +82-2-926-4534
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92
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Koval AP, Blagodatskikh KA, Kushlinskii NE, Shcherbo DS. The Detection of Cancer Epigenetic Traces in Cell-Free DNA. Front Oncol 2021; 11:662094. [PMID: 33996585 PMCID: PMC8118693 DOI: 10.3389/fonc.2021.662094] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Accepted: 04/12/2021] [Indexed: 12/23/2022] Open
Abstract
Nucleic acid fragments found in blood circulation originate mostly from dying cells and carry signs pointing to specific features of the parental cell types. Deciphering these clues may be transformative for numerous research and clinical applications but strongly depends on the development and implementation of robust analytical methods. Remarkable progress has been achieved in the reliable detection of sequence alterations in cell-free DNA while decoding epigenetic information from methylation and fragmentation patterns requires more sophisticated approaches. This review discusses the currently available strategies for detecting and analyzing the epigenetic marks in the liquid biopsies.
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Affiliation(s)
- Anastasia P Koval
- Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Konstantin A Blagodatskikh
- Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Nikolay E Kushlinskii
- Laboratory of Clinical Biochemistry, N.N. Blokhin Cancer Research Medical Center of Oncology, Moscow, Russia
| | - Dmitry S Shcherbo
- Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia
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93
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Vidal J, Casadevall D, Bellosillo B, Pericay C, Garcia-Carbonero R, Losa F, Layos L, Alonso V, Capdevila J, Gallego J, Vera R, Salud A, Martin-Richard M, Nogué M, Cillán E, Maurel J, Faull I, Raymond V, Fernández-Martos C, Montagut C. Clinical Impact of Presurgery Circulating Tumor DNA after Total Neoadjuvant Treatment in Locally Advanced Rectal Cancer: A Biomarker Study from the GEMCAD 1402 Trial. Clin Cancer Res 2021; 27:2890-2898. [PMID: 33727257 DOI: 10.1158/1078-0432.ccr-20-4769] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 02/06/2021] [Accepted: 03/10/2021] [Indexed: 11/16/2022]
Abstract
PURPOSE Total neoadjuvant treatment (TNT) is a valid strategy for patients with high-risk locally advanced rectal cancer (LARC). Biomarkers of response to TNT are an unmet clinical need. We aimed to determine the value of circulating tumor DNA (ctDNA) to predict tumor response, recurrence, and survival in patients with LARC treated with TNT. EXPERIMENTAL DESIGN The GEMCAD 1402 was a phase II randomized, multicentric clinical trial that randomized 180 patients with LARC to modified schedule of fluorouracil, leucovorin, and oxaliplatin (mFOLFOX6) +/- aflibercept, followed by chemoradiation and surgery. Plasma samples were collected at baseline and after TNT within 48 hours before surgery (presurgery). An ultrasensitive assay that integrates genomic and epigenomic cancer signatures was used to assess ctDNA status. ctDNA results were correlated with variables of local tumor response in the surgery sample, local/systemic recurrence, and survival. RESULTS A total of 144 paired plasma samples from 72 patients were included. ctDNA was detectable in 83% of patients at baseline and in 15% following TNT (presurgery). No association was found between ctDNA status and pathologic response. Detectable presurgery ctDNA was significantly associated with systemic recurrence, shorter disease-free survival (HR, 4; P = 0.033), and shorter overall survival (HR, 23; P < 0.0001). CONCLUSIONS In patients with LARC treated with TNT, presurgery ctDNA detected minimal metastatic disease identifying patients at high risk of distant recurrence and death. This study sets the basis for prospective clinical trials that use liquid biopsy to personalize the therapeutic approach following TNT.
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Affiliation(s)
- Joana Vidal
- Department of Medical Oncology, Hospital del Mar - IMIM, CIBERONC, Barcelona, Spain
| | - David Casadevall
- Department of Medical Oncology, Hospital del Mar - IMIM, CIBERONC, Barcelona, Spain
| | | | - Carles Pericay
- Department of Medical Oncology, Complex Sanitari Parc Tauli, Sabadell, Spain
| | - Rocio Garcia-Carbonero
- Department of Medical Oncology, Hospital Universitario Doce de Octubre, Imas12, UCM, CNIO, CIBERONC, Madrid, Spain
| | - Ferran Losa
- Department of Medical Oncology, Hospital, Sant Joan Despí-Moises Broggi, Sant Joan Despí, Spain
| | - Laia Layos
- Department of Medical Oncology, Hospital Universitari Germans Trias i Pujol, Institut Català d'Oncologia, Badalona, Spain
| | - Vicente Alonso
- Department of Medical Oncology, Hospital Universitario Miguel Servet, IISA, CIBERONC, Zaragoza, Spain
| | - Jaume Capdevila
- Department of Medical Oncology, Hospital Universitari Vall d'Hebron, Barcelona, Spain
| | - Javier Gallego
- Department of Medical Oncology, Hospital General Universitario de Elche, Elche, Spain
| | - Ruth Vera
- Department of Medical Oncology, Complejo Hospitalario de Navarra, Instituto de investigaciones Sanitarias de Navarra (IdISNA), Pamplona, Navarra, Spain
| | - Antonieta Salud
- Department of Medical Oncology, Hospital Arnau de Vilanova de Lleida, Lleida, Spain
| | - Marta Martin-Richard
- Department of Medical Oncology, Hospital Santa Creu i Sant Pau, Barcelona, Spain
| | - Miguel Nogué
- Department of Medical Oncology, Hospital de Granollers, Granollers, Spain
| | - Elena Cillán
- Department of Medical Oncology, Hospital Sant Joan de Déu Fundació Althaia, Manresa, Spain
| | - Joan Maurel
- Department of Medical Oncology, Hospital Clìnic i Provincial de Barcelona, Barcelona, Spain
| | - Iris Faull
- Guardant Health, Redwood City, California
| | | | | | - Clara Montagut
- Department of Medical Oncology, Hospital del Mar - IMIM, CIBERONC, Barcelona, Spain.
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94
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Ruiz-Bañobre J, Goel A. Genomic and epigenomic biomarkers in colorectal cancer: From diagnosis to therapy. Adv Cancer Res 2021; 151:231-304. [PMID: 34148615 DOI: 10.1016/bs.acr.2021.02.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Colorectal cancer (CRC) is the second leading cause of cancer-related deaths in the United States. Despite ongoing efforts aimed at increasing screening for CRC and early detection, and development of more effective therapeutic regimens, the overall morbidity and mortality from this malignancy remains a clinical challenge. Therefore, identifying and developing genomic and epigenomic biomarkers that can improve CRC diagnosis and help predict response to current therapies are of paramount importance for improving survival outcomes in CRC patients, sparing patients from toxicity associated with current regimens, and reducing the economic burden associated with these treatments. Although efforts to develop biomarkers over the past decades have achieved some success, the recent availability of high-throughput analytical tools, together with the use of machine learning algorithms, will likely hasten the development of more robust diagnostic biomarkers and improved guidance for clinical decision-making in the coming years. In this chapter, we provide a systematic and comprehensive overview on the current status of genomic and epigenomic biomarkers in CRC, and comment on their potential clinical significance in the management of patients with this fatal malignancy, including in the context of precision medicine.
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Affiliation(s)
- Juan Ruiz-Bañobre
- Medical Oncology Department, University Clinical Hospital of Santiago de Compostela, University of Santiago de Compostela (USC), CIBERONC, Santiago de Compostela, Spain; Translational Medical Oncology Group (Oncomet), Health Research Institute of Santiago (IDIS), University Clinical Hospital of Santiago de Compostela, University of Santiago de Compostela (USC), CIBERONC, Santiago de Compostela, Spain
| | - Ajay Goel
- Department of Molecular Diagnostics and Experimental Therapeutics, Beckman Research Institute of City of Hope Comprehensive Cancer Center, Duarte, CA, United States.
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Lam VK, Zhang J, Wu CC, Tran HT, Li L, Diao L, Wang J, Rinsurongkawong W, Raymond VM, Lanman RB, Lewis J, Roarty EB, Roth J, Swisher S, Lee JJ, Gibbons DL, Papadimitrakopoulou VA, Heymach JV. Genotype-Specific Differences in Circulating Tumor DNA Levels in Advanced NSCLC. J Thorac Oncol 2020; 16:601-609. [PMID: 33388476 DOI: 10.1016/j.jtho.2020.12.011] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 12/03/2020] [Accepted: 12/13/2020] [Indexed: 12/12/2022]
Abstract
INTRODUCTION Plasma-based circulating tumor DNA (ctDNA) is an established biomarker for molecular profiling with emerging applications in disease monitoring in multiple tumor types, including, NSCLC. However, determinants of ctDNA shedding and correlation with tumor burden are incompletely understood, particularly in advanced-stage disease. METHODS We retrospectively analyzed ctDNA-based and tissue-based genomic data and imaging from 144 patients with NSCLC. Tumor burden was quantified with computed tomography (CT) and brain magnetic resonance imaging for the overall cohort and 18F-fludeoxyglucose positron emission tomography-CT in a subset of patients. RESULTS There was a moderate but statistically significant correlation between ctDNA variant allele frequency and multiple imaging measures of tumor burden such as CT volume (rho = 0.34, p ≤ 0.0001) and metabolic tumor volume (rho = 0.36, p = 0.003). This correlation was strongest in KRAS-mutant tumors (rho = 0.56, p ≤ 0.001), followed by TP53 mutants (rho = 0.43, p ≤ 0.0001), and weakest in EGFR-mutated (EGFR+) tumors (rho = 0.24, p = 0.077). EGFR+ tumors with EGFR copy number gain had significantly higher variant allele frequency than EGFR+ without copy number gain (p ≤ 0.00001). In multivariable analysis, TP53 and EGFR mutations, visceral metastasis, and tumor burden were independent predictors of increased ctDNA shedding. CONCLUSIONS Levels of detectable ctDNA were affected not only by tumor burden but also by tumor genotype. The genotype-specific differences observed may be due to variations in DNA shedding and cellular turnover. These findings have implications for the emerging use of ctDNA in NSCLC disease monitoring and early detection.
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Affiliation(s)
- Vincent K Lam
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jianjun Zhang
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Carol C Wu
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Hai T Tran
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Lerong Li
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Lixia Diao
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jing Wang
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Waree Rinsurongkawong
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | | | | | - Jeff Lewis
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Emily B Roarty
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jack Roth
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Stephen Swisher
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - J Jack Lee
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Don L Gibbons
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | | | - John V Heymach
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas.
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