1
|
Li Y, Li Q, Cao Z, Wu J. Multicenter proteome-wide Mendelian randomization study identifies causal plasma proteins in melanoma and non-melanoma skin cancers. Commun Biol 2024; 7:857. [PMID: 39003418 PMCID: PMC11246481 DOI: 10.1038/s42003-024-06538-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Accepted: 07/03/2024] [Indexed: 07/15/2024] Open
Abstract
This study addresses the diagnostic and therapeutic challenges in malignant melanoma (MM) and non-melanoma skin cancers (NMSC). We aim to identify circulating proteins causally linked to MM and NMSC traits using a multicenter Mendelian randomization (MR) framework. We utilized large-scale cis-MR to estimate the impact of numerous plasma proteins on MM, NMSC, squamous cell carcinoma (SCC), and basal cell carcinoma (BCC). To ensure robustness, additional analyses like MR Steiger and Bayesian colocalization are conducted, followed by replication through meta-analytical methods. The associations between identified proteins and outcomes are also validated at the tissue level using Transcriptome-Wide Association Study methods. Furthermore, a protein-protein interaction analysis is conducted to explore the relationship between identified proteins and existing cancer medication targets. The MR analysis has identified associations of 13 plasma proteins with BCC, 2 with SCC, and 1 with MM. Specifically, ASIP and KRT5 are associated with BCC, with ASIP also potentially targeting MM. CTSS and TNFSF8 are identified as promising druggability candidates for BCC. This multidimensional approach nominates ASIP, KRT5, CTSS, and TNFSF8 as potential diagnostic and therapeutic targets for skin cancers.
Collapse
Affiliation(s)
- Yajia Li
- Department of Dermatology, Xiangya Hospital, Central South University, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Qiangxiang Li
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Ziqin Cao
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China.
- Department of Spine Surgery and Orthopaedics, Xiangya Hospital, Central South University, Changsha, China.
| | - Jianhuang Wu
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China.
- Department of Spine Surgery and Orthopaedics, Xiangya Hospital, Central South University, Changsha, China.
| |
Collapse
|
2
|
Gómez-Peregrina D, Cicala CM, Serrano C. Monitoring advanced gastrointestinal stromal tumor with circulating tumor DNA. Curr Opin Oncol 2024; 36:282-290. [PMID: 38726808 DOI: 10.1097/cco.0000000000001040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2024]
Abstract
PURPOSE OF REVIEW This review explores the role of circulating tumor (ct)DNA as a biomarker for clinical decision-making and monitoring purposes in metastatic gastrointestinal stromal tumor (GIST) patients. We discuss key insights from recent clinical trials and anticipate the future perspectives of ctDNA profiling within the clinical landscape of GIST. RECENT FINDINGS The identification and molecular characterization of KIT/platelet-derived growth factor receptor alpha (PDGFRA) mutations from ctDNA in metastatic GIST is feasible and reliable. Such identification through ctDNA serves as a predictor of clinical outcomes to tyrosine-kinase inhibitors (TKIs) in metastatic patients. Additionally, conjoined ctDNA analysis from clinical trials reveal the evolving mutational landscapes and increase in intratumoral heterogeneity across treatment lines. Together, this data positions ctDNA determination as a valuable tool for monitoring disease progression and guiding therapy in metastatic patients. These collective efforts culminated in the initiation of a ctDNA-based randomized clinical trial in GIST, marking a significant milestone in integrating ctDNA testing into the clinical care of GIST patients. SUMMARY The dynamic field of ctDNA technologies is rapidly evolving and holds significant promise for research. Several trials have successfully validated the clinical utility of ctDNA in metastatic GIST, laying the foundations for its prospective integration into the routine clinical management of GIST patients.
Collapse
Affiliation(s)
- David Gómez-Peregrina
- Sarcoma Translational Research Laboratory, Vall d'Hebron Institute of Oncology (VHIO)
| | - Carlo Maria Cicala
- Sarcoma Translational Research Laboratory, Vall d'Hebron Institute of Oncology (VHIO)
- Department of Medical Oncology, Vall d'Hebron University Hospital, Barcelona, Spain
| | - César Serrano
- Sarcoma Translational Research Laboratory, Vall d'Hebron Institute of Oncology (VHIO)
- Department of Medical Oncology, Vall d'Hebron University Hospital, Barcelona, Spain
| |
Collapse
|
3
|
Levit LA, Garrett-Mayer E, Peppercorn J, Ratain MJ. Critical importance of correctly defining and reporting secondary endpoints when assessing the ethics of research biopsies. Clin Trials 2024:17407745241244753. [PMID: 38654414 DOI: 10.1177/17407745241244753] [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: 04/26/2024]
Abstract
This article reviews the implementation challenges to the American Society of Clinical Oncology's ethical framework for including research biopsies in oncology clinical trials. The primary challenges to implementation relate to the definitions of secondary endpoints, the scientific and regulatory framework, and the incentive structure that encourages inclusion of biopsies. Principles of research stewardship require that the clinical trials community correctly articulate the scientific goals of any research biopsies, especially those that are required for the patient to enroll on a trial and receive an investigational agent. Furthermore, it is important to sufficiently justify the characterization of secondary (as distinguished from exploratory) endpoints, protect the interest of research participants, and report accurate and complete information to ClinicalTrials.gov and the published literature.
Collapse
Affiliation(s)
- Laura A Levit
- Center for Research and Analytics, American Society of Clinical Oncology, Alexandria, VA, USA
| | - Elizabeth Garrett-Mayer
- Center for Research and Analytics, American Society of Clinical Oncology, Alexandria, VA, USA
| | | | | |
Collapse
|
4
|
Schenker MP, Silverman SG, Mayo-Smith WW, Khorasani R, Glazer DI. Clinical indications, safety, and effectiveness of percutaneous image-guided adrenal mass biopsy: an 8-year retrospective analysis in 160 patients. Abdom Radiol (NY) 2024; 49:1231-1240. [PMID: 38430264 DOI: 10.1007/s00261-024-04211-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 01/17/2024] [Accepted: 01/17/2024] [Indexed: 03/03/2024]
Abstract
PURPOSE To assess indications, safety, and effectiveness of percutaneous adrenal mass biopsy in contemporary practice. METHODS This institutional review board-approved, retrospective study included all patients undergoing percutaneous image-guided adrenal mass biopsies at an academic health system from January 6, 2015, to January 6, 2023. Patient demographics, biopsy indications, mass size, laboratory data, pathology results, and complications were recorded. Final diagnoses were based on pathology or ≥ 1 year of imaging follow-up when biopsy specimens did not yield malignant tissue. Test performance calculations excluded repeat biopsies. Continuous variables were compared with Student's t test, dichotomous variables with chi-squared test. RESULTS A total of 160 patients underwent 186 biopsies. Biopsies were indicated to diagnose metastatic disease (139/186; 74.7%), for oncologic research only (27/186; 14.5%), diagnose metastatic disease and oncologic research (15/186; 8%), and diagnose an incidental adrenal mass (5/186; 2.7%). Biopsy specimens were diagnostic in 154 patients (96.3%) and non-diagnostic in 6 (3.8%). Diagnostic biopsies yielded malignant tissue (n = 136), benign adrenal tissue (n = 12), and benign adrenal neoplasms (n = 6) with sensitivity = 98.6% (136/138), specificity = 100% (16/16), positive predictive value = 100% (136/136), and negative predictive value = 88.9% (16/18). Adverse events followed 11/186 procedures (5.9%) and most minor (7/11, 63.6%). The adverse event rate was similar whether tissue was obtained for clinical or research purposes (10/144; 6.9% vs. 1/42; 2.4%, p = 0.27), despite more specimens obtained for research (5.8 vs. 3.7, p < 0.001). CONCLUSION Percutaneous adrenal mass biopsy is safe, accurate, and utilized almost exclusively to diagnose metastatic disease or for oncologic research. The negative predictive value is high when diagnostic tissue samples are obtained. Obtaining specimens for research does not increase adverse event risk.
Collapse
Affiliation(s)
- Matthew P Schenker
- Department of Radiology, Brigham and Women's Hospital, Harvard Medical School, 75 Francis Street, Boston, MA, 02115, USA
| | - Stuart G Silverman
- Department of Radiology, Brigham and Women's Hospital, Harvard Medical School, 75 Francis Street, Boston, MA, 02115, USA
| | - William W Mayo-Smith
- Department of Radiology, Brigham and Women's Hospital, Harvard Medical School, 75 Francis Street, Boston, MA, 02115, USA
| | - Ramin Khorasani
- Department of Radiology, Brigham and Women's Hospital, Harvard Medical School, 75 Francis Street, Boston, MA, 02115, USA
- Center for Evidence-Based Imaging, Department of Radiology, Brigham and Women's Hospital, Harvard Medical School, 1620 Tremont Street, Boston, MA, 02120, USA
| | - Daniel I Glazer
- Department of Radiology, Brigham and Women's Hospital, Harvard Medical School, 75 Francis Street, Boston, MA, 02115, USA.
- Center for Evidence-Based Imaging, Department of Radiology, Brigham and Women's Hospital, Harvard Medical School, 1620 Tremont Street, Boston, MA, 02120, USA.
| |
Collapse
|
5
|
Ruan D, Fang J, Teng X. Efficient 18F-fluorodeoxyglucose positron emission tomography/computed tomography-based machine learning model for predicting epidermal growth factor receptor mutations in non-small cell lung cancer. THE QUARTERLY JOURNAL OF NUCLEAR MEDICINE AND MOLECULAR IMAGING : OFFICIAL PUBLICATION OF THE ITALIAN ASSOCIATION OF NUCLEAR MEDICINE (AIMN) [AND] THE INTERNATIONAL ASSOCIATION OF RADIOPHARMACOLOGY (IAR), [AND] SECTION OF THE SOCIETY OF... 2024; 68:70-83. [PMID: 35420272 DOI: 10.23736/s1824-4785.22.03441-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
BACKGROUND Beyond the human eye's limitations, radiomics provides more information that can be used for diagnosis. We develop a personalized and efficient model based on 18F-fluorodeoxyglucose (18F-FDG) positron emission tomography/computed tomography (PET/CT) to predict epidermal growth factor receptor (EGFR) mutations to help identify which non-small cell cancer (NSCLC) patients are candidates for EGFR-tyrosine kinase inhibitors (TKIs) therapy. METHODS We retrospectively included 100 patients with NSCLC and randomized them according to 70 patients in the training group and 30 patients in the validation group. The least absolute shrinkage and selection operator logistic regression (LLR) algorithm and support vector machine (SVM) classifier were used to build the models and predict whether EGFR is mutated or not. The predictive efficacy of the LLR algorithm-based model and the SVM classifier-based model was evaluated by plotting the receiver operating characteristic (ROC) curves and calculating the area under the curve (AUC). RESULTS The AUC, sensitivity and specificity of our radiomics model by LLR algorithm were 0.792, 0.967, and 0.600 for the training group and 0.643, 1.00, and 0.378 for the validation group, respectively, in predicting EGFR mutations. The AUC was 0.838 for the training group and 0.696 for the validation group after combining radiomics features with clinical features. The prediction results based on the SVM classifier showed that the validation group had the best performance when based on radial kernel function with AUC, sensitivity, and specificity of 0.741, 0.667, and 0.825, respectively. CONCLUSIONS Radiomics models based on 18F-FDG PET/CT modeled with different machine learning algorithms can improve the predictive efficacy of the models. Models that combine clinical features are more clinically valuable.
Collapse
Affiliation(s)
- Dan Ruan
- Department of Nuclear Medicine, Xiamen Branch, Zhongshan Hospital, Fudan University, Fujian, China -
| | - Janyao Fang
- Department of Nuclear Medicine, Xiamen Branch, Zhongshan Hospital, Fudan University, Fujian, China
| | - Xinyu Teng
- Department of Nuclear Medicine, Xiamen Branch, Zhongshan Hospital, Fudan University, Fujian, China
| |
Collapse
|
6
|
Najafi S, Majidpoor J, Mortezaee K. Liquid biopsy in colorectal cancer. Clin Chim Acta 2024; 553:117674. [PMID: 38007059 DOI: 10.1016/j.cca.2023.117674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2023] [Revised: 11/16/2023] [Accepted: 11/20/2023] [Indexed: 11/27/2023]
Abstract
Liquid biopsy refers to a set of pathological samples retrieved from non-solid sources, such as blood, cerebrospinal fluid, urine, and saliva through non-invasive or minimally invasive approaches. In the recent decades, an increasing number of studies have focused on clinical applications and improving technological investigation of liquid biopsy biosources for diagnostic goals particularly in cancer. Materials extracted from these sources and used for medical evaluations include cells like circulating tumor cells (CTCs), tumor-educated platelets (TEPs), cell-free nucleic acids released by cells, such as circulating tumor DNA (ctDNA), cell-free DNA (cfDNA), cell-free RNA (cfRNA), and exosomes. Playing significant roles in the pathogenesis of human malignancies, analysis of these sources can provide easier access to genetic and transcriptomic information of the cancer tissue even better than the conventional tissue biopsy. Notably, they can represent the inter- and intra-tumoral heterogeneity and accordingly, liquid biopsies demonstrate strengths for improving diagnosis in early detection and screening, monitoring and follow-up after therapies, and personalization of therapeutical strategies in various types of human malignancies. In this review, we aim to discuss the roles, functions, and analysis approaches of liquid biopsy sources and their clinical implications in human malignancies with a focus on colorectal cancer.
Collapse
Affiliation(s)
- Sajad Najafi
- Department of Medical Biotechnology, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran; Cellular and Molecular Biology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Jamal Majidpoor
- Department of Anatomy, School of Medicine, Infectious Diseases Research Center, Gonabad University of Medical Sciences, Gonabad, Iran
| | - Keywan Mortezaee
- Department of Anatomy, School of Medicine, Kurdistan University of Medical Sciences, Sanandaj, Iran.
| |
Collapse
|
7
|
Moura PC, Raposo M, Vassilenko V. Breath biomarkers in Non-Carcinogenic diseases. Clin Chim Acta 2024; 552:117692. [PMID: 38065379 DOI: 10.1016/j.cca.2023.117692] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 12/02/2023] [Accepted: 12/03/2023] [Indexed: 12/19/2023]
Abstract
The analysis of volatile organic compounds (VOCs) from human matrices like breath, perspiration, and urine has received increasing attention from academic and medical researchers worldwide. These biological-borne VOCs molecules have characteristics that can be directly related to physiologic and pathophysiologic metabolic processes. In this work, gathers a total of 292 analytes that have been identified as potential biomarkers for the diagnosis of various non-carcinogenic diseases. Herein we review the advances in VOCs with a focus on breath biomarkers and their potential role as minimally invasive tools to improve diagnosis prognosis and therapeutic monitoring.
Collapse
Affiliation(s)
- Pedro Catalão Moura
- Laboratory for Instrumentation, Biomedical Engineering and Radiation Physics (LIBPhys-UNL), Department of Physics, NOVA School of Science and Technology, NOVA University of Lisbon, Campus FCT-UNL, 2829-516, Caparica, Portugal.
| | - Maria Raposo
- Laboratory for Instrumentation, Biomedical Engineering and Radiation Physics (LIBPhys-UNL), Department of Physics, NOVA School of Science and Technology, NOVA University of Lisbon, Campus FCT-UNL, 2829-516, Caparica, Portugal.
| | - Valentina Vassilenko
- Laboratory for Instrumentation, Biomedical Engineering and Radiation Physics (LIBPhys-UNL), Department of Physics, NOVA School of Science and Technology, NOVA University of Lisbon, Campus FCT-UNL, 2829-516, Caparica, Portugal.
| |
Collapse
|
8
|
Venetis K, Pepe F, Pescia C, Cursano G, Criscitiello C, Frascarelli C, Mane E, Russo G, Taurelli Salimbeni B, Troncone G, Guerini Rocco E, Curigliano G, Fusco N, Malapelle U. ESR1 mutations in HR+/HER2-metastatic breast cancer: Enhancing the accuracy of ctDNA testing. Cancer Treat Rev 2023; 121:102642. [PMID: 37864956 DOI: 10.1016/j.ctrv.2023.102642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2023] [Revised: 10/08/2023] [Accepted: 10/11/2023] [Indexed: 10/23/2023]
Abstract
Activating mutations of the estrogen receptor alpha gene (ESR1) are common mechanisms of endocrine therapy (ET) resistance in hormone receptor-positive (HR + )/Human Epidermal Growth Factor Receptor 2 (HER2)-negative metastatic breast cancer (MBC). Recent clinical findings emphasize that both old and new generations of selective ER degraders (SERDs) demonstrate enhanced clinical effectiveness in patients with MBC who have detectable ESR1 mutations via liquid biopsy. This stands in contrast to individuals with MBC carrying these mutations and undergoing conventional endocrine monotherapies like aromatase inhibitors (AIs). Liquid biopsy, particularly the analysis of circulating tumor DNA (ctDNA), has emerged as a promising, minimally invasive alternative to conventional tissue-based testing for identifying ESR1 mutations. Within the context of the PADA-1 and EMERALD trials, distinct molecular methodologies and assays, specifically digital droplet PCR (ddPCR) and next-generation sequencing (NGS), have been employed to evaluate the mutational status of ESR1 within ctDNA. This manuscript critically examines the advantages and indications of various ctDNA testing methods on liquid biopsy for HR+/HER2-negative MBC. Specifically, we delve into the capabilities of ddPCR and NGS in identifying ESR1 mutations. Each methodology boasts unique strengths and limitations: ddPCR excels in its analytical sensitivity for pinpointing hotspot mutations, while NGS offers comprehensive coverage of the spectrum of ESR1 mutations. The significance of meticulous sample handling and timely analysis is emphasized, acknowledging the transient nature of cfDNA. Furthermore, we underscore the importance of detecting sub-clonal ESR1 mutations, as these variants can exert a pivotal influence on predicting both endocrine therapy resistance and responsiveness to SERDs. In essence, this work discusses the role of ctDNA analysis for detecting ESR1 mutations and their implications in tailoring effective therapeutic strategies for HR+/HER2- MBC.
Collapse
Affiliation(s)
| | - Francesco Pepe
- Department of Public Health, Federico II University of Naples, Naples, Italy
| | - Carlo Pescia
- Division of Pathology, IEO, European Institute of Oncology IRCCS, Milan, Italy; School of Pathology, University of Milan, Milan, Italy
| | - Giulia Cursano
- Division of Pathology, IEO, European Institute of Oncology IRCCS, Milan, Italy
| | - Carmen Criscitiello
- Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy; Division of New Drugs and Early Drug Development for Innovative Therapies, IEO, European Institute of Oncology IRCCS, Milan, Italy
| | - Chiara Frascarelli
- Division of Pathology, IEO, European Institute of Oncology IRCCS, Milan, Italy; Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
| | - Eltjona Mane
- Division of Pathology, IEO, European Institute of Oncology IRCCS, Milan, Italy
| | - Gianluca Russo
- Department of Public Health, Federico II University of Naples, Naples, Italy
| | | | - Giancarlo Troncone
- Department of Public Health, Federico II University of Naples, Naples, Italy
| | - Elena Guerini Rocco
- Division of Pathology, IEO, European Institute of Oncology IRCCS, Milan, Italy; Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
| | - Giuseppe Curigliano
- Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy; Division of New Drugs and Early Drug Development for Innovative Therapies, IEO, European Institute of Oncology IRCCS, Milan, Italy.
| | - Nicola Fusco
- Division of Pathology, IEO, European Institute of Oncology IRCCS, Milan, Italy; Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
| | - Umberto Malapelle
- Department of Public Health, Federico II University of Naples, Naples, Italy
| |
Collapse
|
9
|
Roisman LC, Kian W, Anoze A, Fuchs V, Spector M, Steiner R, Kassel L, Rechnitzer G, Fried I, Peled N, Bogot NR. Radiological artificial intelligence - predicting personalized immunotherapy outcomes in lung cancer. NPJ Precis Oncol 2023; 7:125. [PMID: 37990050 PMCID: PMC10663598 DOI: 10.1038/s41698-023-00473-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 10/24/2023] [Indexed: 11/23/2023] Open
Abstract
Personalized medicine has revolutionized approaches to treatment in the field of lung cancer by enabling therapies to be specific to each patient. However, physicians encounter an immense number of challenges in providing the optimal treatment regimen for the individual given the sheer complexity of clinical aspects such as tumor molecular profile, tumor microenvironment, expected adverse events, acquired or inherent resistance mechanisms, the development of brain metastases, the limited availability of biomarkers and the choice of combination therapy. The integration of innovative next-generation technologies such as deep learning-a subset of machine learning-and radiomics has the potential to transform the field by supporting clinical decision making in cancer treatment and the delivery of precision therapies while integrating numerous clinical considerations. In this review, we present a brief explanation of the available technologies, the benefits of using these technologies in predicting immunotherapy response in lung cancer, and the expected future challenges in the context of precision medicine.
Collapse
Affiliation(s)
- Laila C Roisman
- The Hebrew University, Helmsley Cancer Center, Shaare Zedek Medical Center, Jerusalem, Israel.
- Ben-Gurion University of the Negev, Be'er Sheva, Israel.
| | - Waleed Kian
- The Hebrew University, Helmsley Cancer Center, Shaare Zedek Medical Center, Jerusalem, Israel
- The Institute of Oncology, Assuta Ashdod, Ashdod, Israel
| | - Alaa Anoze
- The Hebrew University, Helmsley Cancer Center, Shaare Zedek Medical Center, Jerusalem, Israel
| | - Vered Fuchs
- Ben-Gurion University of the Negev, Be'er Sheva, Israel
| | - Maria Spector
- The Department of Radiology, Shaare Zedek Medical Center, Jerusalem, Israel
| | - Roee Steiner
- The Institute for Nuclear Medicine, Shaare Zedek Medical Center, Jerusalem, Israel
| | - Levi Kassel
- The Hebrew University, Helmsley Cancer Center, Shaare Zedek Medical Center, Jerusalem, Israel
| | - Gilad Rechnitzer
- The Hebrew University, Helmsley Cancer Center, Shaare Zedek Medical Center, Jerusalem, Israel
| | - Iris Fried
- The Hebrew University, Helmsley Cancer Center, Shaare Zedek Medical Center, Jerusalem, Israel
| | - Nir Peled
- The Hebrew University, Helmsley Cancer Center, Shaare Zedek Medical Center, Jerusalem, Israel.
| | - Naama R Bogot
- The Department of Radiology, Shaare Zedek Medical Center, Jerusalem, Israel
| |
Collapse
|
10
|
Ogura R, Ito S, Ueda T, Gabata Y, Sako S, Inoue Y, Yamada T, Konishi H, Fujihara A, Ukimura O. Screening for a practical method to monitor the status of patients with metastatic bladder cancer at the circulating cell-gene level. Sci Rep 2023; 13:19517. [PMID: 37945655 PMCID: PMC10636091 DOI: 10.1038/s41598-023-46977-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Accepted: 11/07/2023] [Indexed: 11/12/2023] Open
Abstract
Identifying a novel method to monitor metastatic bladder cancer status at the cell-gene level could lead to earlier appropriate therapeutic intervention and better outcomes. In this study, we evaluated a practical method to monitor the cancer status at the circulating cell-gene level before and after treatment in fourteen patients with metastatic bladder cancer who were indicated for systemic drug therapy. Patients were assessed via imaging before and after drug treatment, and cell-free DNA (cfDNA) analysis was performed to detect three parameters: cfDNA level, ERRB2 gene copy numbers, and telomerase reverse transcriptase (TERT) gene mutations. We hypothesized that decreased cfDNA levels, a normal copy number of ERB-B2 receptor tyrosine kinase 2 (ERBB2), and the absence of the TERT C228T mutation indicate cancer suppression. We found that a > 1.8-fold increase in cfDNA levels, increased copy number of ERBB2, or the existence of the TERT C228T mutation indicated disease progression. Stable cfDNA levels, normal ERBB2 copy number, and the absence of TERT C228T mutations indicate a stable cancer status. Collectively, our results show that the combination of cfDNA concentration, TERT mutation, and ERBB2 copy number may be useful for determining the efficacy of drug therapy in patients with metastatic bladder cancer.
Collapse
Affiliation(s)
- Ryota Ogura
- Department of Urology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Kyoto, 602-8566, Japan
| | - Saya Ito
- Department of Urology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Kyoto, 602-8566, Japan
| | - Takashi Ueda
- Department of Urology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Kyoto, 602-8566, Japan.
| | - Yusuke Gabata
- Department of Urology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Kyoto, 602-8566, Japan
| | - Satoshi Sako
- Department of Urology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Kyoto, 602-8566, Japan
| | - Yuta Inoue
- Department of Urology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Kyoto, 602-8566, Japan
| | - Takeshi Yamada
- Department of Urology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Kyoto, 602-8566, Japan
| | - Hirotaka Konishi
- Division of Digestive Surgery, Department of Surgery, Kyoto Prefectural University of Medicine, Kyoto, Kyoto, Japan
| | - Atsuko Fujihara
- Department of Urology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Kyoto, 602-8566, Japan
| | - Osamu Ukimura
- Department of Urology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Kyoto, 602-8566, Japan
| |
Collapse
|
11
|
Ranghiero A, Frascarelli C, Cursano G, Pescia C, Ivanova M, Vacirca D, Rappa A, Taormina SV, Barberis M, Fusco N, Rocco EG, Venetis K. Circulating tumour DNA testing in metastatic breast cancer: Integration with tissue testing. Cytopathology 2023; 34:519-529. [PMID: 37640801 DOI: 10.1111/cyt.13295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 07/26/2023] [Accepted: 08/14/2023] [Indexed: 08/31/2023]
Abstract
Breast cancer biomarker profiling predominantly relies on tissue testing (surgical and/or biopsy samples). However, the field of liquid biopsy, particularly the analysis of circulating tumour DNA (ctDNA), has witnessed remarkable progress and continues to evolve rapidly. The incorporation of ctDNA-based testing into clinical practice is creating new opportunities for patients with metastatic breast cancer (MBC). ctDNA offers advantages over conventional tissue analyses, as it reflects tumour heterogeneity and enables multiple serial biopsies in a minimally invasive manner. Thus, it serves as a valuable complement to standard tumour tissues and, in certain instances, may even present a potential alternative approach. In the context of MBC, ctDNA testing proves highly informative in the detection of disease progression, monitoring treatment response, assessing actionable biomarkers, and identifying mechanisms of resistance. Nevertheless, ctDNA does exhibit inherent limitations, including its generally low abundance, necessitating timely blood samplings and rigorous management of the pre-analytical phase. The development of highly sensitive assays and robust bioinformatic tools has paved the way for reliable ctDNA analyses. The time has now come to establish how ctDNA and tissue analyses can be effectively integrated into the diagnostic workflow of MBC to provide patients with the most comprehensive and accurate profiling. In this manuscript, we comprehensively analyse the current methodologies employed in ctDNA analysis and explore the potential benefits arising from the integration of tissue and ctDNA testing for patients diagnosed with MBC.
Collapse
Affiliation(s)
- Alberto Ranghiero
- Division of Pathology, IEO, European Institute of Oncology IRCCS, Milan, Italy
| | - Chiara Frascarelli
- Division of Pathology, IEO, European Institute of Oncology IRCCS, Milan, Italy
- Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
| | - Giulia Cursano
- Division of Pathology, IEO, European Institute of Oncology IRCCS, Milan, Italy
| | - Carlo Pescia
- Division of Pathology, IEO, European Institute of Oncology IRCCS, Milan, Italy
- School of Pathology, University of Milan, Milan, Italy
| | - Mariia Ivanova
- Division of Pathology, IEO, European Institute of Oncology IRCCS, Milan, Italy
| | - Davide Vacirca
- Division of Pathology, IEO, European Institute of Oncology IRCCS, Milan, Italy
| | - Alessandra Rappa
- Division of Pathology, IEO, European Institute of Oncology IRCCS, Milan, Italy
| | | | - Massimo Barberis
- Division of Pathology, IEO, European Institute of Oncology IRCCS, Milan, Italy
| | - Nicola Fusco
- Division of Pathology, IEO, European Institute of Oncology IRCCS, Milan, Italy
- Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
| | - Elena Guerini Rocco
- Division of Pathology, IEO, European Institute of Oncology IRCCS, Milan, Italy
- Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
| | | |
Collapse
|
12
|
Ren F, Jin Q, Liu T, Ren X, Zhan Y. Proteome-wide mendelian randomization study implicates therapeutic targets in common cancers. J Transl Med 2023; 21:646. [PMID: 37735436 PMCID: PMC10512580 DOI: 10.1186/s12967-023-04525-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 09/13/2023] [Indexed: 09/23/2023] Open
Abstract
BACKGROUND The interest in targeted cancer therapies has been growing rapidly. While numerous cancer biomarkers and targeted treatment strategies have been developed and employed, there are still significant limitations and challenges in the early diagnosis and targeted treatment of cancers. Accordingly, there is an urgent need to identify novel targets and develop new targeted drugs. METHODS The study was conducted using combined cis-Mendelian randomization (cis-MR) and colocalization analysis. We analyzed data from 732 plasma proteins to identify potential drug targets associated with eight site-specific cancers. These findings were further validated using the UK Biobank dataset. Then, a protein-protein interaction network was also constructed to examine the interplay between the identified proteins and the targets of existing cancer medications. RESULTS This MR analysis revealed associations between five plasma proteins and prostate cancer, five with breast cancer, and three with lung cancer. Subsequently, these proteins were classified into four distinct target groups, with a focus on tier 1 and 2 targets due to their higher potential to become drug targets. Our study indicatied that genetically predicted KDELC2 (OR: 0.89, 95% CI 0.86-0.93) and TNFRSF10B (OR: 0.74, 95% CI 0.65-0.83) are inversely associated with prostate cancer. Furthermore, we observed an inverse association between CPNE1 (OR: 0.96, 95% CI 0.94-0.98) and breast cancer, while PDIA3 (OR: 1.19, 95% CI 1.10-1.30) were found to be associated with the risk of breast cancer. In addition, we also propose that SPINT2 (OR: 1.05, 95% CI 1.03-1.06), GSTP1 (OR: 0.82, 95% CI 0.74-0.90), and CTSS (OR: 0.91, 95% CI 0.88-0.95) may serve as potential therapeutic targets in prostate cancer. Similarly, GDI2 (OR: 0.85, 95% CI 0.80-0.91), ISLR2 (OR: 0.87, 95% CI 0.82-0.93), and CTSF (OR: 1.14, 95% CI 1.08-1.21) could potentially be targets for breast cancer. Additionally, we identified SFTPB (OR: 0.93, 95% CI 0.91-0.95), ICAM5 (OR: 0.95, 95% CI 0.93-0.97), and FLRT3 (OR: 1.10, 95% CI 1.05-1.15) as potential targets for lung cancer. Notably, TNFRSF10B, GSTP1, and PDIA3 were found to interact with the target proteins of current medications used in prostate or breast cancer treatment. CONCLUSIONS This comprehensive analysis has highlighted thirteen plasma proteins with potential roles in three site-specific cancers. Continued research in this area may reveal their therapeutic potential, particularly KDELC2, TNFRSF10B, CPNE1, and PDIA3, paving the way for more effective cancer treatments.
Collapse
Affiliation(s)
- Feihong Ren
- Guang'anmen Hospital, China Academy of Chinese Medical Sciences, Beijing, 100053, China
- Graduate School, Beijing University of Chinese Medicine, Beijing, 100029, China
| | - Qiubai Jin
- Guang'anmen Hospital, China Academy of Chinese Medical Sciences, Beijing, 100053, China
| | - Tongtong Liu
- Guang'anmen Hospital, China Academy of Chinese Medical Sciences, Beijing, 100053, China
| | - Xuelei Ren
- Guang'anmen Hospital, China Academy of Chinese Medical Sciences, Beijing, 100053, China
| | - Yongli Zhan
- Guang'anmen Hospital, China Academy of Chinese Medical Sciences, Beijing, 100053, China.
| |
Collapse
|
13
|
Wu S, Li R, Jiang Y, Yu J, Zheng J, Li Z, Li M, Xin K, Wang Y, Xu Z, Li S, Chen X. Liquid biopsy in urothelial carcinoma: Detection techniques and clinical applications. Biomed Pharmacother 2023; 165:115027. [PMID: 37354812 DOI: 10.1016/j.biopha.2023.115027] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 06/13/2023] [Accepted: 06/14/2023] [Indexed: 06/26/2023] Open
Abstract
The types of urothelial carcinoma (UC) include urothelial bladder cancer and upper tract urothelial carcinoma. Current diagnostic techniques cannot meet the needs of patients. Liquid biopsy is an accurate method of determining the molecular profile of UC and is a cutting-edge and popular technique that is expected to complement existing detection techniques and benefit patients with UC. Circulating tumor cells, cell-free DNA, cell-free RNA, extracellular vesicles, proteins, and metabolites can be found in the blood, urine, or other bodily fluids and are examined during liquid biopsies. This article focuses on the components of liquid biopsies and their clinical applications in UC. Liquid biopsies have tremendous potential in multiple aspects of precision oncology, from early diagnosis and treatment monitoring to predicting prognoses. They may therefore play an important role in the management of UC and precision medicine.
Collapse
Affiliation(s)
- Siyu Wu
- Department of Urology, Shengjing Hospital of China Medical University, Shenyang, Liaoning 110004, China
| | - Rong Li
- Department of Urology, Shengjing Hospital of China Medical University, Shenyang, Liaoning 110004, China
| | - Yuanhong Jiang
- Department of Urology, Shengjing Hospital of China Medical University, Shenyang, Liaoning 110004, China
| | - Jiazheng Yu
- Department of Urology, Shengjing Hospital of China Medical University, Shenyang, Liaoning 110004, China
| | - Jianyi Zheng
- Department of Urology, Shengjing Hospital of China Medical University, Shenyang, Liaoning 110004, China
| | - Zeyu Li
- Department of Urology, Shengjing Hospital of China Medical University, Shenyang, Liaoning 110004, China
| | - Mingyang Li
- Department of Urology, Shengjing Hospital of China Medical University, Shenyang, Liaoning 110004, China
| | - Kerong Xin
- Department of Urology, Shengjing Hospital of China Medical University, Shenyang, Liaoning 110004, China
| | - Yang Wang
- Department of Gynecology, Cancer Hospital of China Medical University, Liaoning Cancer Hospital & Institute, Shenyang, Liaoning 110042, China.
| | - Zhenqun Xu
- Department of Urology, Shengjing Hospital of China Medical University, Shenyang, Liaoning 110004, China.
| | - Shijie Li
- Department of Urology, Shengjing Hospital of China Medical University, Shenyang, Liaoning 110004, China.
| | - Xiaonan Chen
- Department of Urology, Shengjing Hospital of China Medical University, Shenyang, Liaoning 110004, China.
| |
Collapse
|
14
|
Lo N, He HH, Chen S. Genome-wide studies in prostate cancer poised liquid biopsy as a molecular discovery tool. Front Oncol 2023; 13:1185013. [PMID: 37692852 PMCID: PMC10484097 DOI: 10.3389/fonc.2023.1185013] [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: 03/13/2023] [Accepted: 08/10/2023] [Indexed: 09/12/2023] Open
Abstract
Liquid biopsy is emerging as an intriguing tool in clinical disease detection and monitoring. Compared to a standard tissue biopsy, performing a liquid biopsy incurs minimal invasiveness, captures comprehensive disease representation, and can be more sensitive at an early stage. Recent genome-wide liquid biopsy studies in prostate cancer analyzing plasma samples have provided insights into the genome and epigenome dynamics during disease progression. In-depth genomic sequencing can offer a comprehensive understanding of cancer evolution, enabling more accurate clinical decision-making. Furthermore, exploring beyond the DNA sequence itself provides opportunities to investigate the regulatory mechanisms underlying various disease phenotypes. Here, we summarize these advances and offer prospects for their future application.
Collapse
Affiliation(s)
- Nicholas Lo
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Housheng Hansen He
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
| | - Sujun Chen
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
- West China School of Public Health, West China Fourth Hospital, and State Key Laboratory of Biotherapy, Sichuan University, Chengdu, China
| |
Collapse
|
15
|
Duquesne I, Abou Chakra M, Hage L, Pinar U, Loriot Y. Liquid biopsies for detection, surveillance, and prognosis of urothelial cancer: a future standard? Expert Rev Anticancer Ther 2023; 23:995-1007. [PMID: 37542214 DOI: 10.1080/14737140.2023.2245144] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Accepted: 08/02/2023] [Indexed: 08/06/2023]
Abstract
INTRODUCTION Liquid biopsies are used for the detection of tumor-specific elements in body fluid. Their application in prognosis and diagnosis of muscle/non-muscle invasive bladder cancer (MIBC/NMIBC) or upper tract urothelial cancer (UTUC) remains poorly known and rarely mentioned in clinical guidelines. AREAS COVERED Herein, we provide an overview of current data regarding the use of liquid biopsies in urothelial tumors. EXPERT OPINION Studies that were included analyzed liquid biopsies using the detection of circulating tumor cells (CTCs), deoxyribonucleic acid (DNA), ribonucleic acid (RNA), exosomes, or metabolomics. The sensitivity of blood CTC detection in patients with localized cancer was 35% and raised to 50% in patients with metastatic cancer. In NMIBC patients, blood CTC was associated with poor prognosis, whereas discrepancies were seen in MIBC patients. Circulating plasma DNA presented a superior sensitivity to urine and was a good indicator for diagnosis, follow-up, and oncological outcome. In urine, specific bladder cancer (BC) microRNA had an overall sensitivity of 85% and a specificity of 86% in the diagnosis of urothelial cancer. These results are in favor of the use of liquid biopsies as biomarkers for in urothelial cancer management.
Collapse
Affiliation(s)
- Igor Duquesne
- Department of Urology, Cochin Hospital, Assistance Publique-Hopitaux de Paris, Universite Paris Cite, Paris, France
| | - Mohamad Abou Chakra
- Department of Urology, Cochin Hospital, Assistance Publique-Hopitaux de Paris, Universite Paris Cite, Paris, France
| | - Lory Hage
- Department of Urology, Cochin Hospital, Assistance Publique-Hopitaux de Paris, Universite Paris Cite, Paris, France
| | - Ugo Pinar
- Department of Urology, Pitie Salpetriere Hospital, Assistance Publique-Hopitaux de Paris, Universite Paris Sorbonne, Paris, France
| | - Yohann Loriot
- Department of Cancer Medicine, Gustave Roussy Institute, Cancer Campus, Grand Paris, Universite Paris-Sud, Villejuif, France
| |
Collapse
|
16
|
Kolb T, Benckendorff J, Möller P, Barth TFE, Marienfeld RB. Heterogeneous expression of predictive biomarkers PD-L1 and TIGIT in non-mucinous lung adenocarcinoma and corresponding lymph node metastasis: A challenge for clinical biomarker testing. Neoplasia 2023; 38:100884. [PMID: 36812781 PMCID: PMC9976464 DOI: 10.1016/j.neo.2023.100884] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 01/27/2023] [Indexed: 02/22/2023]
Abstract
The use of immune checkpoint inhibitors (ICI) targeting the PD-L1:PD1 interaction revolutionized tumor treatment by re-activating the anti-tumoral capacity of the immune system. Assessment of tumor mutational burden, microsatellite instability, or expression of the surface marker PD-L1 have been used to predict individual response to ICI therapy. However, the predicted response does not always correspond to the actual therapy outcome. We hypothesize that tumor heterogeneity might be a major cause of this inconsistency. In this respect we recently demonstrated that PD-L1 shows heterogenous expression in the different growth patterns of non-small cell lung cancer (NSCLC) - lepidic, acinar, papillary, micropapillary and solid. Furthermore, additional inhibitory receptors, like T cell immunoglobulin and ITIM domain (TIGIT), appear to be heterogeneously expressed and affect the outcome of anti-PD-L1 treatment. Given this heterogeneity in the primary tumor, we set out to analyze the situation in corresponding lymph node metastases, since these are often used to obtain biopsy material for tumor diagnosis, staging and molecular analysis. Again, we observed heterogeneous expression of PD-1, PD-L1, TIGIT, Nectin-2 and PVR in relation to different regions and growth pattern distribution that varied between the primary tumor and their metastases. Together, our study underscores the complex situation regarding the heterogeneity of NSCLC samples and suggest that the analysis of a small biopsy from lymph node metastases may not be sufficient to ensure a reliable prediction of ICI therapy success.
Collapse
Affiliation(s)
- Tobias Kolb
- From the Institute of Pathology, Ulm University, Albert-Einstein-Allee 23, Ulm D-89070, Germany
| | - Julian Benckendorff
- From the Institute of Pathology, Ulm University, Albert-Einstein-Allee 23, Ulm D-89070, Germany
| | - Peter Möller
- From the Institute of Pathology, Ulm University, Albert-Einstein-Allee 23, Ulm D-89070, Germany
| | - Thomas F E Barth
- From the Institute of Pathology, Ulm University, Albert-Einstein-Allee 23, Ulm D-89070, Germany.
| | - Ralf B Marienfeld
- From the Institute of Pathology, Ulm University, Albert-Einstein-Allee 23, Ulm D-89070, Germany.
| |
Collapse
|
17
|
Watanabe F, Suzuki K, Aizawa H, Endo Y, Takayama Y, Kakizawa N, Kato T, Noda H, Rikiyama T. Circulating tumor DNA in molecular assessment feasibly predicts early progression of pancreatic cancer that cannot be identified via initial imaging. Sci Rep 2023; 13:4809. [PMID: 36959222 PMCID: PMC10036464 DOI: 10.1038/s41598-023-31051-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2022] [Accepted: 03/06/2023] [Indexed: 03/25/2023] Open
Abstract
Molecular assessment using circulating tumor DNA (ctDNA) has not been well-defined. We recruited 61 pancreatic cancer (PC) patients who underwent initial computed tomography (CT) imaging study during first-line chemotherapy. Initial molecular assessment was performed using droplet digital PCR and defined as the change in KRAS-mutated ctDNA before and after treatments, which was classified into five categories: mNT, molecular negative; mCR, complete response; mPR, partial response; mSD, stable disease; mPD, progressive disease. Of 61 patients, 14 diagnosed with PD after initial CT imaging showed significantly worse therapeutic outcomes than 47 patients with disease control. In these 47 patients, initial molecular assessment exhibited significant differences in therapeutic outcomes between patients with and without ctDNA (mPD + mSD vs. mCR + mNT; 13.2 M vs. 21.7 M, P = 0.0029) but no difference between those with mPD and mSD + mCR + mNT, suggesting that the presence of ctDNA had more impact on the therapeutic outcomes than change in its number. Multivariate analysis revealed that it was the only independent prognostic factor (P = 0.0405). The presence of ctDNA in initial molecular assessment predicted early tumor progression and identified PC patients more likely to benefit from chemotherapy.
Collapse
Affiliation(s)
- Fumiaki Watanabe
- Department of Surgery, Saitama Medical Center, Jichi Medical University, 1-847, Amanuma-cho, Omiya-ku, Saitama, 330-8503, Japan
| | - Koichi Suzuki
- Department of Surgery, Saitama Medical Center, Jichi Medical University, 1-847, Amanuma-cho, Omiya-ku, Saitama, 330-8503, Japan.
| | - Hidetoshi Aizawa
- Department of Surgery, Saitama Medical Center, Jichi Medical University, 1-847, Amanuma-cho, Omiya-ku, Saitama, 330-8503, Japan
| | - Yuhei Endo
- Department of Surgery, Saitama Medical Center, Jichi Medical University, 1-847, Amanuma-cho, Omiya-ku, Saitama, 330-8503, Japan
| | - Yuji Takayama
- Department of Surgery, Saitama Medical Center, Jichi Medical University, 1-847, Amanuma-cho, Omiya-ku, Saitama, 330-8503, Japan
| | - Nao Kakizawa
- Department of Surgery, Saitama Medical Center, Jichi Medical University, 1-847, Amanuma-cho, Omiya-ku, Saitama, 330-8503, Japan
| | - Takaharu Kato
- Department of Surgery, Saitama Medical Center, Jichi Medical University, 1-847, Amanuma-cho, Omiya-ku, Saitama, 330-8503, Japan
| | - Hiroshi Noda
- Department of Surgery, Saitama Medical Center, Jichi Medical University, 1-847, Amanuma-cho, Omiya-ku, Saitama, 330-8503, Japan
| | - Toshiki Rikiyama
- Department of Surgery, Saitama Medical Center, Jichi Medical University, 1-847, Amanuma-cho, Omiya-ku, Saitama, 330-8503, Japan
| |
Collapse
|
18
|
Pourmadadi M, Mahdi Eshaghi M, Ostovar S, Mohammadi Z, K. Sharma R, Paiva-Santos AC, Rahmani E, Rahdar A, Pandey S. Innovative nanomaterials for cancer diagnosis, imaging, and therapy: Drug deliveryapplications. J Drug Deliv Sci Technol 2023. [DOI: 10.1016/j.jddst.2023.104357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/14/2023]
|
19
|
Clinical utility of liquid biopsy and integrative genomic profiling in early-stage and oligometastatic cancer patients treated with radiotherapy. Br J Cancer 2023; 128:857-876. [PMID: 36550207 PMCID: PMC9977775 DOI: 10.1038/s41416-022-02102-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 11/29/2022] [Accepted: 12/02/2022] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Liquid biopsy and Integrative Genomic Profiling (IGP) are yet to be implemented into routine Radiation Oncology. Here we assess the utility of germline, tumour and circulating cell-free DNA-based genomic analyses for the clinical management of early-stage and oligometastatic cancer patients treated by precision radiotherapy. METHODS We performed germline, tissue- and liquid biopsy NGS panels on 50 early-stage/oligometastatic cancer patients undergoing radiotherapy. We also monitored ctDNA variants in serial liquid biopsies collected during radiotherapy and follow-up and evaluated the clinical utility of such comprehensive approach. RESULTS The integration of different genomic studies revealed that only 1/3 of the liquid biopsy variants are of tumour origin. Altogether, 55 tumour variants (affecting 3/4 of the patients) were considered potentially actionable (for treatment and prognosis), whereas potential follow-up biomarkers were identified in all cases. Germline cancer-predisposing variants were present in three patients, which would have not been eligible for hereditary cancer testing according to clinical guidelines. The presence of detectable ctDNA variants before radiotherapy was associated with progression-free survival both in oligometastatic patients and in those with early-stage. CONCLUSIONS IGP provides both valuable and actionable information for personalised decision-making in Radiation Oncology.
Collapse
|
20
|
Udagawa S, Ooki A, Shinozaki E, Fukuda K, Yamaguchi K, Osumi H. Circulating Tumor DNA: The Dawn of a New Era in the Optimization of Chemotherapeutic Strategies for Metastatic Colo-Rectal Cancer Focusing on RAS Mutation. Cancers (Basel) 2023; 15:cancers15051473. [PMID: 36900264 PMCID: PMC10001242 DOI: 10.3390/cancers15051473] [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: 01/03/2023] [Revised: 02/10/2023] [Accepted: 02/22/2023] [Indexed: 03/02/2023] Open
Abstract
Genotyping of tumor tissues to assess RAS and BRAF V600E mutations enables us to select optimal molecularly targeted therapies when considering treatment strategies for patients with metastatic colorectal cancer. Tissue-based genetic testing is limited by the difficulty of performing repeated tests, due to the invasive nature of tissue biopsy, and by tumor heterogeneity, which can limit the usefulness of the information it yields. Liquid biopsy, represented by circulating tumor DNA (ctDNA), has attracted attention as a novel method for detecting genetic alterations. Liquid biopsies are more convenient and much less invasive than tissue biopsies and are useful for obtaining comprehensive genomic information on primary and metastatic tumors. Assessing ctDNA can help track genomic evolution and the status of alterations in genes such as RAS, which are sometimes altered following chemotherapy. In this review, we discuss the potential clinical applications of ctDNA, summarize clinical trials focusing on RAS, and present the future prospects of ctDNA analysis that could change daily clinical practice.
Collapse
Affiliation(s)
| | | | | | | | | | - Hiroki Osumi
- Correspondence: ; Tel.: +81-3-3520-0111 or +81-3-3570-0515
| |
Collapse
|
21
|
Molecular MRI-Based Monitoring of Cancer Immunotherapy Treatment Response. Int J Mol Sci 2023; 24:ijms24043151. [PMID: 36834563 PMCID: PMC9959624 DOI: 10.3390/ijms24043151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2023] [Revised: 01/29/2023] [Accepted: 02/02/2023] [Indexed: 02/09/2023] Open
Abstract
Immunotherapy constitutes a paradigm shift in cancer treatment. Its FDA approval for several indications has yielded improved prognosis for cases where traditional therapy has shown limited efficiency. However, many patients still fail to benefit from this treatment modality, and the exact mechanisms responsible for tumor response are unknown. Noninvasive treatment monitoring is crucial for longitudinal tumor characterization and the early detection of non-responders. While various medical imaging techniques can provide a morphological picture of the lesion and its surrounding tissue, a molecular-oriented imaging approach holds the key to unraveling biological effects that occur much earlier in the immunotherapy timeline. Magnetic resonance imaging (MRI) is a highly versatile imaging modality, where the image contrast can be tailored to emphasize a particular biophysical property of interest using advanced engineering of the imaging pipeline. In this review, recent advances in molecular-MRI based cancer immunotherapy monitoring are described. Next, the presentation of the underlying physics, computational, and biological features are complemented by a critical analysis of the results obtained in preclinical and clinical studies. Finally, emerging artificial intelligence (AI)-based strategies to further distill, quantify, and interpret the image-based molecular MRI information are discussed in terms of perspectives for the future.
Collapse
|
22
|
Luo ZD, Wang YF, Zhao YX, Yu LC, Li T, Fan YJ, Zeng SJ, Zhang YL, Zhang Y, Zhang X. Emerging roles of non-coding RNAs in colorectal cancer oxaliplatin resistance and liquid biopsy potential. World J Gastroenterol 2023; 29:1-18. [PMID: 36683709 PMCID: PMC9850945 DOI: 10.3748/wjg.v29.i1.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/10/2022] [Revised: 10/11/2022] [Accepted: 11/04/2022] [Indexed: 01/04/2023] Open
Abstract
Colorectal cancer (CRC) is one of the most common malignancies of the digestive tract, with the annual incidence and mortality increasing consistently. Oxaliplatin-based chemotherapy is a preferred therapeutic regimen for patients with advanced CRC. However, most patients will inevitably develop resistance to oxaliplatin. Many studies have reported that non-coding RNAs (ncRNAs), such as microRNAs, long non-coding RNAs, and circular RNAs, are extensively involved in cancer progression. Moreover, emerging evidence has revealed that ncRNAs mediate chemoresistance to oxaliplatin by transcriptional and post-transcriptional regulation, and by epigenetic modification. In this review, we summarize the mechanisms by which ncRNAs regulate the initiation and development of CRC chemoresistance to oxaliplatin. Furthermore, we investigate the clinical application of ncRNAs as promising biomarkers for liquid CRC biopsy. This review provides new insights into overcoming oxaliplatin resistance in CRC by targeting ncRNAs.
Collapse
Affiliation(s)
- Zheng-Dong Luo
- Department of Clinical Laboratory, Qilu Hospital of Shandong University, Shandong Engineering Research Center of Biomarker and Artificial Intelligence Application, Jinan 250012, Shandong Province, China
| | - Yi-Feng Wang
- Department of Clinical Laboratory, Qilu Hospital of Shandong University, Shandong Engineering Research Center of Biomarker and Artificial Intelligence Application, Jinan 250012, Shandong Province, China
| | - Yu-Xiao Zhao
- Department of Clinical Laboratory, Qilu Hospital of Shandong University, Shandong Engineering Research Center of Biomarker and Artificial Intelligence Application, Jinan 250012, Shandong Province, China
| | - Long-Chen Yu
- Department of Clinical Laboratory, Qilu Hospital of Shandong University, Shandong Engineering Research Center of Biomarker and Artificial Intelligence Application, Jinan 250012, Shandong Province, China
| | - Tian Li
- Department of Clinical Laboratory, Qilu Hospital of Shandong University, Shandong Engineering Research Center of Biomarker and Artificial Intelligence Application, Jinan 250012, Shandong Province, China
| | - Ying-Jing Fan
- Department of Clinical Laboratory, Qilu Hospital of Shandong University, Shandong Engineering Research Center of Biomarker and Artificial Intelligence Application, Jinan 250012, Shandong Province, China
| | - Shun-Jie Zeng
- Department of Clinical Laboratory, Qilu Hospital of Shandong University, Shandong Engineering Research Center of Biomarker and Artificial Intelligence Application, Jinan 250012, Shandong Province, China
| | - Yan-Li Zhang
- Department of Clinical Laboratory, Shandong Provincial Third Hospital, Jinan 250012, Shandong Province, China
| | - Yi Zhang
- Department of Clinical Laboratory, Qilu Hospital of Shandong University, Shandong Engineering Research Center of Biomarker and Artificial Intelligence Application, Jinan 250012, Shandong Province, China
| | - Xin Zhang
- Department of Clinical Laboratory, Qilu Hospital of Shandong University, Shandong Engineering Research Center of Biomarker and Artificial Intelligence Application, Jinan 250012, Shandong Province, China
| |
Collapse
|
23
|
Kwon HS, Shin DH, Kim SY, Hwang CS, Kim A, Lee HJ, Na J, Lee JH, Kim JY. DNA Extracted from Cytologic Slides Is a Valuable Source for PCR-Based Molecular Tests. Acta Cytol 2023; 67:92-99. [PMID: 36455541 PMCID: PMC9872841 DOI: 10.1159/000526634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Accepted: 08/16/2022] [Indexed: 12/03/2022]
Abstract
INTRODUCTION DNA extracted from cytologic samples is occasionally used for various molecular tests. The aim of this study was to evaluate DNA extracted from differently prepared cytologic slides that can be used for PCR-based molecular tests. METHODS For each 23 cases of papillary thyroid carcinoma or colorectal adenocarcinoma tissues, six touch-imprinted cytological slides were prepared (group 1∼3), and remnant tissues were blocked for FFPE tissue (group 4). Cytologic slides were grouped by preparation methods: air-dried slides (group 1), fixed slides (group 2), and stained slides (group 3). Fixed slides were classified as 95% ethanol fixed (group 2A) and CytoRich Red Preservative solution fixed (group 2B). Stained slides were divided in 3 ways: Giemsa, Pap, and H&E stained (group 3A, 3B, and 3C, respectively). DNA extracted from each group was evaluated for concentration, 260/280 ratio, DNA Integrity Number (DIN) value, and mutation. RESULTS DNA concentration was highest in group 1 and lowest in group 2B. DIN value was highest in group 2A and lowest in group 2B. A mutation of BRAF or KRAS genes was detected in 18 FFPE tissue samples. Matched DNA extracts from groups 1, 2A, and 3 produced results consistent with FFPE tissue results, while mutation testing was successful for only four samples of DNA from group 2B. CONCLUSION The mutation tests worked well for most samples except CytoRich Red Preservative-fixed slides. This study indicates that stained and unstained cytologic slides are a suitable source of PCR-based molecular tests as long as they are fixed in ethanol or stored for a short time in an air-dried condition.
Collapse
|
24
|
Ren J, Liu R. The Implication of Liquid Biopsy in the Non-small Cell Lung Cancer: Potential and Expectation. Methods Mol Biol 2023; 2695:145-163. [PMID: 37450117 DOI: 10.1007/978-1-0716-3346-5_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/18/2023]
Abstract
Nowadays, lung cancer has remained the most lethal cancer, despite great advances in diagnosis and treatment. However, a large proportion of patients were diagnosed with locally advanced or metastatic disease and have poor prognosis. Immunotherapy and targeted drugs have greatly improved the survival and prognosis of patients with advanced lung cancer. However, how to identify the optimal patients to accept those therapies and how to monitor therapeutic efficacy are still in dispute. In the past few decades, tissue biopsy, including percutaneous fine needle biopsy and surgical excision, has still been the gold standard for examining the gene mutation such as EGFR, ALK, ROS, and PD-1/PD/L1, which can indicate the follow-up treatment. Nevertheless, the biopsy techniques mentioned above were invasive and unrepeatable, which were not suitable for advanced patients. Liquid biopsy, accounting for heterogeneity compared with tissue biopsy, is an alternative technique for monitoring the mutation, and a large quantity of research has demonstrated its feasibility to detect the circulating tumor cell, cell-free DNA, circulating tumor DNA, and extracellular vesicles from peripheral venous blood. The proposal of the concept of precision medicine brings a novel medical model developed with the rapid progress of genome sequencing technology and the cross-application of bioinformation, which was based on personalized medicine. The emerging method of liquid biopsy might contribute to promoting the development of precision medicine. In this review, we intend to describe the liquid biopsy in non-small cell lung cancer in detail in the aspect of screening, diagnosis, monitoring, treatment, and drug resistance.
Collapse
Affiliation(s)
- Jianghao Ren
- Shanghai Lung Tumor Clinical Medicine Center, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, P.R. China
| | - Ruijun Liu
- Shanghai Lung Tumor Clinical Medicine Center, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, P.R. China
| |
Collapse
|
25
|
Palmieri M, Zulato E, Wahl SGF, Guibert N, Frullanti E. Diagnostic accuracy of circulating free DNA testing for the detection of KRAS mutations in non-small cell lung cancer: A systematic review and meta-analysis. Front Genet 2022; 13:1015161. [PMID: 36386815 PMCID: PMC9640997 DOI: 10.3389/fgene.2022.1015161] [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: 08/09/2022] [Accepted: 10/11/2022] [Indexed: 11/25/2022] Open
Abstract
Kirsten rat sarcoma viral oncogene homolog (KRAS) gene encodes a GTPase that acts as a molecular switch for intracellular signal transduction, promoting cell growth and proliferation. Mutations in the KRAS gene represent important biomarkers for NSCLC targeted therapy. However, detection of KRAS mutations in tissues has shown some limitations. During the last years, analyses of circulating free DNA (cfDNA) has emerged as an alternative and minimally invasive, approach to investigate tumor molecular changes. Here, we assessed the diagnostic performance of cfDNA analysis, compared to tissues through a meta-analysis and systematic review of existing literature. From 561 candidate papers, we finally identified 40 studies, including 2,805 NSCLC patients. We extracted values relating to the number of true-positive, false-positive, false-negative, and true-negative. Pooled sensitivity, specificity, positive likelihood ratio, negative likelihood ratio, and diagnostic odds ratio, each with 95% CI, were calculated. A summary receiver operating characteristic curve and the area under curve (AUC) were used to evaluate the overall diagnostic performance. The pooled sensitivity was 0.71 (95% CI 0.68–0.74) and the specificity was 0.93 (95% CI 0.92–0.94). The diagnostic odds ratio was 35.24 (95% CI 24.88–49.91) and the area under the curve was 0.92 (SE = 0.094). These results provide evidence that detection of KRAS mutation using cfDNA testing is of adequate diagnostic accuracy thus offering to the clinicians a new promising screening test for NSCLC patients.
Collapse
Affiliation(s)
- Maria Palmieri
- Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Elisabetta Zulato
- Basic and Translational Oncology Unit, Istituto Oncologico Veneto IOV—IRCCS, Padova, Italy
| | - Sissel Gyrid Freim Wahl
- Department of Pathology, St. Olavs Hospital, Trondheim University Hospital, Trondheim, Norway
- Department of Clinical and Molecular Medicine, NTNU, Norwegian University of Technology and Science, Trondheim, Norway
| | - Nicolas Guibert
- Thoracic Oncology Department, Larrey Hospital, University Hospital of Toulouse, Toulouse, France
- Inserm, Centre de Recherche en Cancérologie de Toulouse, CRCT UMR-1037, Toulouse, France
- University of Toulouse III (Paul Sabatier), Toulouse, France
| | - Elisa Frullanti
- Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Siena, Italy
- *Correspondence: Elisa Frullanti,
| |
Collapse
|
26
|
Yuan K, Wu J, Zhao Y, Lyu S, Zhou Q, Shi F, Li Y, Song Q. Consistent expression of PD-L1 in tumor microenvironment with peripheral PD-1/PD-L1 in circulating T lymphocytes of operable breast cancer: a diagnostic test. Diagn Pathol 2022; 17:68. [PMID: 36088412 PMCID: PMC9464389 DOI: 10.1186/s13000-022-01249-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 08/19/2022] [Indexed: 12/24/2022] Open
Abstract
Background The expression of PD-L1 in the immune microenvironment can guide the application of immunosuppressants. In order to monitor the immune status of the body, repeated biopsies have to be taken. Our research aims to find new and convenient means to evaluate this indicator. Methods Eighty-three cases of newly diagnosed operable breast cancer without receiving preoperative treatment, were recruited from Beijing Shijitan Hospital between November 2018 and November 2019. The expression of PD-1/PD-L1 on circulating T lymphocytes was detected by flow cytometry and the expression of PD-L1 on immune cells in tumor microenvironment was detected by immunohistochemistry. Results The median percentage of positive PD-1 and PD-L1 expression on circulating T lymphocytes was 15.2% and 0.7%, respectively. The peripheral PD-1 had no relationship with clinicopathological characteristics, but the peripheral PD-L1 expression had a correlation with lymph node metastasis (p = 0.005) and Her-2 expression (p = 0.034) (p < 0.05). The positive rate of PD-L1 expression was 32.9% in tumor microenvironment. PD-L1 expression in tumor microenvironment had a significant correlation with PD-1/PD-L1 expression on circulating T lymphocytes, the correlation coefficients being 0.24 (p < 0.05) and 0.26 (p < 0.05), respectively. To predict the PD-L1 expression in tumor microenvironment, the area under the receiver operating characteristic curve was 0.65 and 0.66 for peripheral PD-1 and PD-L1, respectively. High level of peripheral PD-1/PD-L1 expression was associated with the odds ratios of 5.42 and 4.76 for positive PD-L1 expression in tumor microenvironment. Conclusion Peripheral PD-1/PD-L1 expression had a significant consistency with PD-L1 expression in tumor microenvironment and could act as an alternative choice of tissue detection, for the patients intolerable of biopsy.
Collapse
|
27
|
Introduction of Nanomaterials to Biosensors for Exosome Detection: Case Study for Cancer Analysis. BIOSENSORS 2022; 12:bios12080648. [PMID: 36005042 PMCID: PMC9405681 DOI: 10.3390/bios12080648] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 08/04/2022] [Accepted: 08/15/2022] [Indexed: 11/17/2022]
Abstract
Exosomes have been gaining attention for early cancer diagnosis owing to their biological functions in cells. Several studies have reported the relevance of exosomes in various diseases, including pancreatic cancer, retroperitoneal fibrosis, obesity, neurodegenerative diseases, and atherosclerosis. Particularly, exosomes are regarded as biomarkers for cancer diagnosis and can be detected in biofluids, such as saliva, urine, peritoneal fluid, and blood. Thus, exosomes are advantageous for cancer liquid biopsies as they overcome the current limitations of cancer tissue biopsies. Several studies have reported methods for exosome isolation, and analysis for cancer diagnosis. However, further clinical trials are still required to determine accurate exosome concentration quantification methods. Recently, various biosensors have been developed to detect exosomal biomarkers, including tumor-derived exosomes, nucleic acids, and proteins. Among these, the exact quantification of tumor-derived exosomes is a serious obstacle to the clinical use of liquid biopsies. Precise detection of exosome concentration is difficult because it requires clinical sample pretreatment. To solve this problem, the use of the nanobiohybrid material-based biosensor provides improved sensitivity and selectivity. The present review will discuss recent progress in exosome biosensors consisting of nanomaterials and biomaterial hybrids for electrochemical, electrical, and optical-based biosensors.
Collapse
|
28
|
Luo Z, Wang L, Shang Z, Guo Q, Liu Q, Zhang M, Li T, Wang Y, Zhang Y, Zhang Y, Zhang X. A panel of necroptosis-related genes predicts the prognosis of pancreatic adenocarcinoma. Transl Oncol 2022; 22:101462. [PMID: 35635957 PMCID: PMC9157256 DOI: 10.1016/j.tranon.2022.101462] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 05/20/2022] [Accepted: 05/22/2022] [Indexed: 12/27/2022] Open
Abstract
The 5-NRGs signature can predict the prognosis of pancreatic adenocarcinoma. The 5-NRGs signature reflects the immune landscape of pancreatic adenocarcinoma. The 5-NRGs can be detected in exosomes of serum using RT-qPCR method.
Pancreatic adenocarcinoma (PAAD) has become one of the deadliest malignancies in the world. Since necroptosis plays a crucial role in regulating the immune system, it is necessary to develop novel prognostic biomarkers associated with necroptosis and explore its potential role in PAAD. The transcriptome RNA-seq data of PAAD were downloaded from the TCGA and GTEx databases. A prognostic signature was constructed by the least absolute shrinkage and selection operator (LASSO) Cox regression, and its prognostic value was evaluated by nomogram and validated in an independent GEO cohort. We identified a total of 24 differentially expressed NRGs in PAAD, and constructed a prognostic signature with 5 NRGs, which showed good performance in predicting the prognosis of PAAD patients. The ROC curves for 1-, 3-, and 5-year survival rate were 0.652, 0.778, and 0.817, respectively. This prognostic signature showed consistent prognosis prediction in an independent patient cohort. Furthermore, the correlations between 5-NRGs signature and TMB, MSI, histopathological classification, immune infiltration, immune types, and immunomodulators were all significant. Notably, the expression profiles of the five NRGs in exosomes of serum were consistent with their expression in tumor tissues. These data suggested that the 5-NRGs signature is a promising biomarker for predicting the prognosis of PAAD.
Collapse
|
29
|
Malla M, Loree JM, Kasi PM, Parikh AR. Using Circulating Tumor DNA in Colorectal Cancer: Current and Evolving Practices. J Clin Oncol 2022; 40:2846-2857. [PMID: 35839443 PMCID: PMC9390824 DOI: 10.1200/jco.21.02615] [Citation(s) in RCA: 78] [Impact Index Per Article: 39.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
There exists a tremendous opportunity in identifying and determining the appropriate predictive and prognostic biomarker(s) for risk stratification of patients with colorectal cancers (CRCs). Circulating tumor DNA (ctDNA) has emerged as a promising prognostic and possibly predictive biomarker in the personalized management of patients with CRCs. The disease is particularly suited to a liquid biopsy–based approach since there is a great deal of shedding of circulating tumor fragments (cells, DNA, methylation markers, etc). ctDNA has been shown to have several potential applications, including detecting minimal residual disease (MRD), monitoring for early recurrence, molecular profiling, and therapeutic response prediction. The utility of ctDNA has broadened from its initial use in the advanced/metastatic setting for molecular profiling and detection of acquired resistance mechanisms, toward identifying MRD, as well as early detection. Prospective studies such as CIRCULATE, COBRA, Dynamic II/III, and ACT3 are underway in the MRD setting to further understand how ctDNA may be used to inform clinical decision making using both tumor-informed and tumor-agnostic platforms. These prospective studies use ctDNA to guide management of patients with CRC and will be critical to help guide how and where ctDNA should or should not be used in clinical decision making. It is also important to understand that there are different types of ctDNA liquid biopsy platforms, each with advantages and disadvantages in different clinical indications. This review provides an overview of the current and evolving use of ctDNA in CRC.
Collapse
Affiliation(s)
- Midhun Malla
- West Virginia University School of Medicine, Section of Hematology/Oncology, Morgantown, WV
| | - Jonathan M Loree
- BC Cancer/The University of British Columbia, Division of Medical Oncology, Vancouver, BC, Canada
| | - Pashtoon Murtaza Kasi
- Weill Cornell Medicine, Meyer Cancer Center, Englander Institute of Precision Medicine, New York, NY
| | - Aparna Raj Parikh
- Harvard Medical School, Massachusetts General Hospital Cancer Center, Tucker Gosnell Center for Gastrointestinal Malignancies, Termeer Center for Targeted Therapies, Boston, MA
| |
Collapse
|
30
|
Corvigno S, Johnson AM, Wong KK, Cho MS, Afshar-Kharghan V, Menter DG, Sood AK. Novel Markers for Liquid Biopsies in Cancer Management: Circulating Platelets and Extracellular Vesicles. Mol Cancer Ther 2022; 21:1067-1075. [PMID: 35545008 DOI: 10.1158/1535-7163.mct-22-0087] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 04/05/2022] [Accepted: 05/05/2022] [Indexed: 02/03/2023]
Abstract
Although radiologic imaging and histologic assessment of tumor tissues are classic approaches for diagnosis and monitoring of treatment response, they have many limitations. These include challenges in distinguishing benign from malignant masses, difficult access to the tumor, high cost of the procedures, and tumor heterogeneity. In this setting, liquid biopsy has emerged as a potential alternative for both diagnostic and monitoring purposes. The approaches to liquid biopsy include cell-free DNA/circulating tumor DNA, long and micro noncoding RNAs, proteins/peptides, carbohydrates/lectins, lipids, and metabolites. Other approaches include detection and analysis of circulating tumor cells, extracellular vesicles, and tumor-activated platelets. Ultimately, reliable use of liquid biopsies requires bioinformatics and statistical integration of multiple datasets to achieve approval in a Clinical Laboratory Improvement Amendments setting. This review provides a balanced and critical assessment of recent discoveries regarding tumor-derived biomarkers in liquid biopsies along with the potential and pitfalls for cancer detection and longitudinal monitoring.
Collapse
Affiliation(s)
- Sara Corvigno
- Department of Gynecologic Oncology & Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Anna Maria Johnson
- Department of Gynecologic Oncology & Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Kwong-Kwok Wong
- Department of Gynecologic Oncology & Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas.,The University of Texas Graduate School of Biomedical Sciences at Houston, Houston, Texas
| | - Min Soon Cho
- Division of Internal Medicine, Benign Hematology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Vahid Afshar-Kharghan
- Division of Internal Medicine, Benign Hematology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - David G Menter
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Anil K Sood
- Department of Gynecologic Oncology & Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas.,Center for RNA Interference and Non-Coding RNA, The University of Texas MD Anderson Cancer Center, Houston, Texas
| |
Collapse
|
31
|
Chan HT, Chin YM, Low SK. Circulating Tumor DNA-Based Genomic Profiling Assays in Adult Solid Tumors for Precision Oncology: Recent Advancements and Future Challenges. Cancers (Basel) 2022; 14:3275. [PMID: 35805046 PMCID: PMC9265547 DOI: 10.3390/cancers14133275] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2022] [Revised: 06/30/2022] [Accepted: 07/02/2022] [Indexed: 12/04/2022] Open
Abstract
Genomic profiling using tumor biopsies remains the standard approach for the selection of approved molecular targeted therapies. However, this is often limited by its invasiveness, feasibility, and poor sample quality. Liquid biopsies provide a less invasive approach while capturing a contemporaneous and comprehensive tumor genomic profile. Recent advancements in the detection of circulating tumor DNA (ctDNA) from plasma samples at satisfactory sensitivity, specificity, and detection concordance to tumor tissues have facilitated the approval of ctDNA-based genomic profiling to be integrated into regular clinical practice. The recent approval of both single-gene and multigene assays to detect genetic biomarkers from plasma cell-free DNA (cfDNA) as companion diagnostic tools for molecular targeted therapies has transformed the therapeutic decision-making procedure for advanced solid tumors. Despite the increasing use of cfDNA-based molecular profiling, there is an ongoing debate about a 'plasma first' or 'tissue first' approach toward genomic testing for advanced solid malignancies. Both approaches present possible advantages and disadvantages, and these factors should be carefully considered to personalize and select the most appropriate genomic assay. This review focuses on the recent advancements of cfDNA-based genomic profiling assays in advanced solid tumors while highlighting the major challenges that should be tackled to formulate evidence-based guidelines in recommending the 'right assay for the right patient at the right time'.
Collapse
Affiliation(s)
- Hiu Ting Chan
- Project for Development of Liquid Biopsy Diagnosis, Cancer Precision Medicine Center, Japanese Foundation for Cancer Research, Tokyo 135-8550, Japan; (Y.M.C.); (S.-K.L.)
| | - Yoon Ming Chin
- Project for Development of Liquid Biopsy Diagnosis, Cancer Precision Medicine Center, Japanese Foundation for Cancer Research, Tokyo 135-8550, Japan; (Y.M.C.); (S.-K.L.)
- Cancer Precision Medicine, Inc., Kawasaki 213-0012, Japan
| | - Siew-Kee Low
- Project for Development of Liquid Biopsy Diagnosis, Cancer Precision Medicine Center, Japanese Foundation for Cancer Research, Tokyo 135-8550, Japan; (Y.M.C.); (S.-K.L.)
| |
Collapse
|
32
|
Wang F, Huang YS, Wu HX, Wang ZX, Jin Y, Yao YC, Chen YX, Zhao Q, Chen S, He MM, Luo HY, Qiu MZ, Wang DS, Wang FH, Xu M, Li YH, Xu RH. Genomic temporal heterogeneity of circulating tumour DNA in unresectable metastatic colorectal cancer under first-line treatment. Gut 2022; 71:1340-1349. [PMID: 34489309 PMCID: PMC9185813 DOI: 10.1136/gutjnl-2021-324852] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Accepted: 08/23/2021] [Indexed: 02/07/2023]
Abstract
OBJECTIVE Circulating tumour DNA (ctDNA) sequencing is increasingly used in the clinical management of patients with colorectal cancer. However, the genomic heterogeneity in ctDNA during treatments and its impact on clinical outcomes remain largely unknown. DESIGN We conducted a prospective cohort study (NCT04228614) of 171 patients with unresectable metastatic colorectal cancer (mCRC) who underwent first-line treatment and prospectively collected blood samples with or without tumour samples from patients at baseline and sequentially until disease progression or last follow-up. RESULTS The RAS/BRAF alterations in paired baseline tissue and plasma samples from 63 patients displayed a favourable concordance (81.0%, 51/63). After a period of first-line treatment (median time between baseline and last liquid biopsy, 4.67 months), 42.6% (26/61) of RAS-mutant patients showed RAS clearance and 50.0% (5/10) of BRAF-mutant patients showed BRAF clearance, while 3.6% (3/84) and 0.7% (1/135) of patients showed new RAS or BRAF mutations in ctDNA. Patients with plasma RAS/BRAF clearance showed similar progression-free survival (PFS) and overall survival (OS) with patients who remained RAS/BRAF wild-type, while much better outcomes than those who remained RAS/BRAF mutant. Patients who gained new RAS/BRAF mutations showed similar prognosis as those who maintained RAS/BRAF mutations, and shorter PFS and OS than those who remained RAS/BRAF wild-type. CONCLUSION This prospective, serial and large-scale ctDNA profiling study reveals the temporal heterogeneity of mCRC-related somatic variants, which should be given special attention in clinical practice, as evidenced by the finding that the shift in plasma RAS/BRAF mutational status can yield a drastic change in survival outcomes.
Collapse
Affiliation(s)
- Feng Wang
- Department of Medical Oncology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University, Guangzhou, Guangdong, People's Republic of China .,Research Unit of Precision Diagnosis and Treatment for Gastrointestinal Cancer, Chinese Academy of Medical Sciences, Guangzhou, Guangdong, People's Republic of China
| | - You-Sheng Huang
- Department of Medical Oncology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University, Guangzhou, Guangdong, People's Republic of China,Research Unit of Precision Diagnosis and Treatment for Gastrointestinal Cancer, Chinese Academy of Medical Sciences, Guangzhou, Guangdong, People's Republic of China,Bioinformatics Platform, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, People's Republic of China
| | - Hao-Xiang Wu
- Department of Medical Oncology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University, Guangzhou, Guangdong, People's Republic of China,Research Unit of Precision Diagnosis and Treatment for Gastrointestinal Cancer, Chinese Academy of Medical Sciences, Guangzhou, Guangdong, People's Republic of China
| | - Zi-Xian Wang
- Department of Medical Oncology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University, Guangzhou, Guangdong, People's Republic of China,Research Unit of Precision Diagnosis and Treatment for Gastrointestinal Cancer, Chinese Academy of Medical Sciences, Guangzhou, Guangdong, People's Republic of China
| | - Ying Jin
- Department of Medical Oncology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University, Guangzhou, Guangdong, People's Republic of China,Research Unit of Precision Diagnosis and Treatment for Gastrointestinal Cancer, Chinese Academy of Medical Sciences, Guangzhou, Guangdong, People's Republic of China
| | - Yi-Chen Yao
- Department of Medical Oncology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University, Guangzhou, Guangdong, People's Republic of China,Research Unit of Precision Diagnosis and Treatment for Gastrointestinal Cancer, Chinese Academy of Medical Sciences, Guangzhou, Guangdong, People's Republic of China
| | - Yan-Xing Chen
- Department of Medical Oncology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University, Guangzhou, Guangdong, People's Republic of China,Research Unit of Precision Diagnosis and Treatment for Gastrointestinal Cancer, Chinese Academy of Medical Sciences, Guangzhou, Guangdong, People's Republic of China,Bioinformatics Platform, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, People's Republic of China
| | - Qi Zhao
- Department of Medical Oncology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University, Guangzhou, Guangdong, People's Republic of China,Research Unit of Precision Diagnosis and Treatment for Gastrointestinal Cancer, Chinese Academy of Medical Sciences, Guangzhou, Guangdong, People's Republic of China,Bioinformatics Platform, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, People's Republic of China
| | - Shifu Chen
- Research and Development Division, HaploX Biotechnology, Shenzhen, Guangdong, People's Republic of China
| | - Ming-Ming He
- Department of Medical Oncology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University, Guangzhou, Guangdong, People's Republic of China,Research Unit of Precision Diagnosis and Treatment for Gastrointestinal Cancer, Chinese Academy of Medical Sciences, Guangzhou, Guangdong, People's Republic of China
| | - Hui-Yan Luo
- Department of Medical Oncology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University, Guangzhou, Guangdong, People's Republic of China,Research Unit of Precision Diagnosis and Treatment for Gastrointestinal Cancer, Chinese Academy of Medical Sciences, Guangzhou, Guangdong, People's Republic of China
| | - Miao-Zhen Qiu
- Department of Medical Oncology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University, Guangzhou, Guangdong, People's Republic of China,Research Unit of Precision Diagnosis and Treatment for Gastrointestinal Cancer, Chinese Academy of Medical Sciences, Guangzhou, Guangdong, People's Republic of China
| | - De-shen Wang
- Department of Medical Oncology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University, Guangzhou, Guangdong, People's Republic of China,Research Unit of Precision Diagnosis and Treatment for Gastrointestinal Cancer, Chinese Academy of Medical Sciences, Guangzhou, Guangdong, People's Republic of China
| | - Feng-Hua Wang
- Department of Medical Oncology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University, Guangzhou, Guangdong, People's Republic of China,Research Unit of Precision Diagnosis and Treatment for Gastrointestinal Cancer, Chinese Academy of Medical Sciences, Guangzhou, Guangdong, People's Republic of China
| | - Mingyan Xu
- Research and Development Division, HaploX Biotechnology, Shenzhen, Guangdong, People's Republic of China
| | - Yu-Hong Li
- Department of Medical Oncology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University, Guangzhou, Guangdong, People's Republic of China,Research Unit of Precision Diagnosis and Treatment for Gastrointestinal Cancer, Chinese Academy of Medical Sciences, Guangzhou, Guangdong, People's Republic of China
| | - Rui-Hua Xu
- Department of Medical Oncology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University, Guangzhou, Guangdong, People's Republic of China .,Research Unit of Precision Diagnosis and Treatment for Gastrointestinal Cancer, Chinese Academy of Medical Sciences, Guangzhou, Guangdong, People's Republic of China
| |
Collapse
|
33
|
Igari F, Tanaka H, Giuliano AE. The applications of plasma cell-free DNA in cancer detection: Implications in the management of breast cancer patients. Crit Rev Oncol Hematol 2022; 175:103725. [PMID: 35618229 DOI: 10.1016/j.critrevonc.2022.103725] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 04/28/2022] [Accepted: 05/19/2022] [Indexed: 11/27/2022] Open
Abstract
Liquid biopsy probes DNA, RNA, and proteins in body fluids for cancer detection and is one of the most rapidly developing areas in oncology. Tumor-derived DNA (circulating tumor DNA, ctDNA) in the context of cell-free DNA (cfDNA) in blood has been the main target for its potential utilities in cancer detection. Liquid biopsy can report tumor burden in real-time without invasive interventions, and would be feasible for screening tumor types that lack standard-of-care screening approaches. Two major approaches to interrogating ctDNA are genetic mutation and DNA methylation profiling. Mutation profiling can identify tumor driver mutations and guide precision therapy. Targeted genomic profiling of DNA methylation has become the main approach for cancer screening in the general population. Here we review the recent technological development and ongoing efforts in clinical applications. For clinical applications, we focus on breast cancer, in which subtype-specific biology demarcates the applications of ctDNA.
Collapse
Affiliation(s)
- Fumie Igari
- Department of Surgery, Cedars-Sinai Medical Center, West Hollywood, CA 90048, USA; Department of Breast Oncology, Juntendo University, Tokyo, Japan
| | - Hisashi Tanaka
- Department of Surgery, Cedars-Sinai Medical Center, West Hollywood, CA 90048, USA; Samuel Oschin Comprehensive Cancer Institute and Cedars-Sinai Medical Center, West Hollywood, CA 90048, USA; Biomedical Sciences, Cedars-Sinai Medical Center, West Hollywood, CA 90048, USA.
| | - Armando E Giuliano
- Department of Surgery, Cedars-Sinai Medical Center, West Hollywood, CA 90048, USA; Samuel Oschin Comprehensive Cancer Institute and Cedars-Sinai Medical Center, West Hollywood, CA 90048, USA; Biomedical Sciences, Cedars-Sinai Medical Center, West Hollywood, CA 90048, USA
| |
Collapse
|
34
|
Gouda MA, Huang HJ, Piha-Paul SA, Call SG, Karp DD, Fu S, Naing A, Subbiah V, Pant S, Dustin DJ, Tsimberidou AM, Hong DS, Rodon J, Meric-Bernstam F, Janku F. Longitudinal Monitoring of Circulating Tumor DNA to Predict Treatment Outcomes in Advanced Cancers. JCO Precis Oncol 2022; 6:e2100512. [PMID: 35834760 PMCID: PMC9307306 DOI: 10.1200/po.21.00512] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
PURPOSE The response to cancer therapies is typically assessed with radiologic imaging 6-10 weeks after treatment initiation. Circulating tumor DNA (ctDNA), however, has a short half-life, and dynamic changes in ctDNA quantity may allow for earlier assessment of the therapeutic response. METHODS Patients with advanced solid tumors referred to the Department of Investigational Cancer Therapeutics at The University of Texas MD Anderson Cancer Center were invited to participate in a liquid biopsy protocol for which serial blood samples were collected before, during, and after systemic therapy. We isolated ctDNA from serially collected plasma samples at baseline, mid-treatment, and first restaging. Genomically informed droplet digital polymerase chain reaction (ddPCR) was performed, and ctDNA quantities were reported as aggregate variant allele frequencies for all detected molecular aberrations. RESULTS We included 204 patients receiving 260 systemic therapies. The ctDNA detection rate was higher in progressors (patients with progressive disease) compared with nonprogressors (patients with stable disease, partial responses, or complete responses) at all time points (P < .009). Moreover, ctDNA detection was associated with a shorter median time-to-treatment failure (P ≤ .001). Positive delta and slope values for changes in ctDNA quantity were more frequent in progressors (P ≤ .03 and P < .001, respectively) and were associated with a shorter median time-to-treatment failure (P ≤ .014 and P < .001, respectively). Increasing ctDNA quantity was predictive of clinical and/or radiologic progressive disease in 73% of patients (median lead time, 23 days). CONCLUSION Detection of ctDNA and early dynamic changes in its quantity can predict the clinical outcomes of systemic therapies in patients with advanced solid tumors.
Collapse
Affiliation(s)
- Mohamed A Gouda
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX.,Department of Clinical Oncology, Faculty of Medicine, Menoufia University. Shebin Al-Kom, Egypt
| | - Helen J Huang
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Sarina A Piha-Paul
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - S Greg Call
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Daniel D Karp
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Siqing Fu
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Aung Naing
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Vivek Subbiah
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Shubham Pant
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Derek J Dustin
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Apostolia M Tsimberidou
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - David S Hong
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Jordi Rodon
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Funda Meric-Bernstam
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Filip Janku
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX
| |
Collapse
|
35
|
Liu S, Wang J. Current and Future Perspectives of Cell-Free DNA in Liquid Biopsy. Curr Issues Mol Biol 2022; 44:2695-2709. [PMID: 35735625 PMCID: PMC9222159 DOI: 10.3390/cimb44060184] [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] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 06/01/2022] [Accepted: 06/09/2022] [Indexed: 11/16/2022] Open
Abstract
A liquid biopsy is a minimally invasive or non-invasive method to analyze a range of tumor material in blood or other body fluids, including circulating tumor cells (CTCs), cell-free DNA (cfDNA), messenger RNA (mRNA), microRNA (miRNA), and exosomes, which is a very promising technology. Among these cancer biomarkers, plasma cfDNA is the most widely used in clinical practice. Compared with a tissue biopsy of traditional cancer diagnosis, in assessing tumor heterogeneity, a liquid biopsy is more reliable because all tumor sites release cfDNA into the blood. Therefore, a cfDNA liquid biopsy is less invasive and comprehensive. Moreover, the development of next-generation sequencing technology makes cfDNA sequencing more sensitive than a tissue biopsy, with higher clinical applicability and wider application. In this publication, we aim to review the latest perspectives of cfDNA liquid biopsy clinical significance and application in cancer diagnosis, treatment, and prognosis. We introduce the sequencing techniques and challenges of cfDNA detection, analysis, and clinical applications, and discuss future research directions.
Collapse
|
36
|
A Novel Brain Tumor Detection and Coloring Technique from 2D MRI Images. APPLIED SCIENCES-BASEL 2022. [DOI: 10.3390/app12115744] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The early automated identification of brain tumors is a difficult task in MRI images. For a long time, continuous research efforts have floated a new idea of replacing different grayscale anatomic regions of diagnostic images with appropriate colors that could overcome the problems being faced by radiologists. The colorization of grayscale images is challenging for enhancing various regions’ contrasts by transforming grayscale images into high-contrast color images. This study investigates standard solutions in discriminating between normal and abnormal regions by assigning colors to grayscale human brain MR images to differentiate different kinds of tissues. The proposed approach is influenced by connected component and index-based colorization methods for applying colors to different regions and abnormal areas. It is an automated approach that varies its inputs using luminance and pixel matrix values and provides the possible outcome. After segmentation, a specific algorithm is devised to colorize the region-of-interest (ROI) areas, which distinguishes and applies colors to differentiate the regions. Results show that implementing the watershed-based area segmentation method and ROI selection method based on the morphological operation helps identify tissues during processing. Moreover, the colorization approach based on luminance and pixel matrix after segmentation and ROI selection is beneficial due to better PSNR and SSIM values and visible contrast improvement. Our proposed algorithm works with less processing overhead and uses less time than those of the industry’s previously used color transfer method.
Collapse
|
37
|
Liu MC, MacKay M, Kase M, Piwowarczyk A, Lo C, Schaeffer J, Finkle JD, Mason CE, Beaubier N, Blackwell KL, Park BH. Longitudinal Shifts of Solid Tumor and Liquid Biopsy Sequencing Concordance in Metastatic Breast Cancer. JCO Precis Oncol 2022; 6:e2100321. [PMID: 35721584 PMCID: PMC9200387 DOI: 10.1200/po.21.00321] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 11/17/2021] [Accepted: 03/24/2022] [Indexed: 11/21/2022] Open
Abstract
Tissue-based next-generation sequencing (NGS) in metastatic breast cancer (mBC) is limited by the inability to noninvasively track tumor evolution. Cell-free DNA (cfDNA) NGS has made sequential testing feasible; however, the relationship between cfDNA and tissue-based testing in mBC is not well understood. Here, we evaluate concordance between tissue and cfDNA NGS relative to cfDNA sampling frequency in a large, clinically annotated mBC data set. METHODS Tempus LENS was used to analyze deidentified records of mBC cases with Tempus xT (tissue) and xF (cfDNA) sequencing results. Then, various metrics of concordance were assessed within overlapping probe regions of the tissue and cfDNA assays (104 genes), focusing on pathogenic variants. Variant allele frequencies of discordant and concordant pathogenic variants were also compared. Analyses were stratified by mBC subtype and time between tests. RESULTS Records from 300 paired tissue and liquid biopsies were analyzed. Median time between tissue and blood collection was 78.5 days (standard deviation = 642.99). The median number of pathogenic variants/patient was one for cfDNA and two for tissue. Across the cohort, 77.8% of pathogenic tissue variants were found in cfDNA and 75.7% of pathogenic cfDNA variants were found in tissue when tests were ≤ 7 days apart, which decreased to 50.3% and 51.8%, respectively, for > 365 days. Furthermore, the median patient-level variant concordance was 67% when tests were ≤7 days apart and 30%-37% when > 30 days. The median variant allele frequencies of discordant variants were generally lower than those of concordant variants within the same time frame. CONCLUSION We observed high concordances between tissue and cfDNA results that generally decreased with longer durations between tests. Thus, cfDNA NGS reliably measures tissue genomics and is likely beneficial for longitudinal monitoring of molecular changes in mBC.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Ben Ho Park
- Vanderbilt University Medical Center, Nashville, TN
| |
Collapse
|
38
|
Chen Z, Liu L, Zhu F, Cai X, Zhao Y, Liang P, Ou L, Zhong R, Yu Z, Li C, Li J, Xiong S, Feng Y, Cheng B, Liang H, Xie Z, Liang W, He J. Dynamic monitoring serum tumor markers to predict molecular features of EGFR-mutated lung cancer during targeted therapy. Cancer Med 2022; 11:3115-3125. [PMID: 35543090 PMCID: PMC9385589 DOI: 10.1002/cam4.4676] [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: 11/19/2021] [Revised: 01/21/2022] [Accepted: 02/11/2022] [Indexed: 12/24/2022] Open
Abstract
To reveal the correlation of dynamic serum tumor markers (STMs) and molecular features of epidermal growth factor receptor‐mutated (EGFR‐mutated) lung cancer during targeted therapy, we retrospectively reviewed 303 lung cancer patients who underwent dynamic STM tests [neuron‐specific enolase (NSE), carcinoembryonic antigen (CEA), carbohydrate antigen 125 (CA125), carbohydrate antigen 153 (CA153), the soluble fragment of cytokeratin 19 (CYFRA21‐1), and squamous cell carcinoma antigen (SCC)] and circulating tumor DNA (ctDNA) testing with a panel covering 168 genes. At baseline, patients with EGFR mutation trended to have abnormal CEA, abnormal CA153, and normal SCC levels. Additionally, patients with Thr790Met (T790M) mutation were more likely to have abnormal CEA levels than patients without T790M mutation. Among patients with secondary resistance to EGFR tyrosine kinase inhibitors (TKI), the dynamic STMs showed a descending trend in the responsive stage and a rising trend in the resistant stage. However, the changing slopes differed between T790M subgroup and the non‐T790M subgroup in individual STMs. Our study demonstrated that the combination of baseline levels and variations of STMs (including the responsive stage and resistant stage) can be suggestive of secondary EGFR‐T790M mutation [area under the curve (AUC) = 0.897] and that changing trends of STMs (within 8 weeks after initiating the TKI therapy) can be potential predictors for the clearance of EGFR ctDNA [AUC = 0.871]. In conclusion, dynamic monitoring STMs can help to predict the molecular features of EGFR‐mutated lung cancer during targeted therapy.
Collapse
Affiliation(s)
- Zhuxing Chen
- Department of Thoracic Surgery/Oncology, China State Key Laboratory of Respiratory Disease & National Clinical Research Center for Respiratory Disease, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Liping Liu
- Department of Thoracic Surgery/Oncology, China State Key Laboratory of Respiratory Disease & National Clinical Research Center for Respiratory Disease, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Feng Zhu
- Department of Thoracic Surgery/Oncology, China State Key Laboratory of Respiratory Disease & National Clinical Research Center for Respiratory Disease, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Xiuyu Cai
- Department of General Internal Medicine, Sun Yat-sen University Cancer Centre, State Key Laboratory of Oncology in South China, Collaborative Innovation Centre for Cancer Medicine, Guangzhou, China
| | - Yi Zhao
- Department of Thoracic Surgery/Oncology, China State Key Laboratory of Respiratory Disease & National Clinical Research Center for Respiratory Disease, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Peng Liang
- Department of Thoracic Surgery/Oncology, China State Key Laboratory of Respiratory Disease & National Clinical Research Center for Respiratory Disease, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Limin Ou
- Department of Thoracic Surgery/Oncology, China State Key Laboratory of Respiratory Disease & National Clinical Research Center for Respiratory Disease, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Ran Zhong
- Department of Thoracic Surgery/Oncology, China State Key Laboratory of Respiratory Disease & National Clinical Research Center for Respiratory Disease, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Ziwen Yu
- Department of Thoracic Surgery/Oncology, China State Key Laboratory of Respiratory Disease & National Clinical Research Center for Respiratory Disease, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Caichen Li
- Department of Thoracic Surgery/Oncology, China State Key Laboratory of Respiratory Disease & National Clinical Research Center for Respiratory Disease, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Jianfu Li
- Department of Thoracic Surgery/Oncology, China State Key Laboratory of Respiratory Disease & National Clinical Research Center for Respiratory Disease, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Shan Xiong
- Department of Thoracic Surgery/Oncology, China State Key Laboratory of Respiratory Disease & National Clinical Research Center for Respiratory Disease, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Yi Feng
- Department of Thoracic Surgery/Oncology, China State Key Laboratory of Respiratory Disease & National Clinical Research Center for Respiratory Disease, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Bo Cheng
- Department of Thoracic Surgery/Oncology, China State Key Laboratory of Respiratory Disease & National Clinical Research Center for Respiratory Disease, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Hengrui Liang
- Department of Thoracic Surgery/Oncology, China State Key Laboratory of Respiratory Disease & National Clinical Research Center for Respiratory Disease, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Zhanhong Xie
- Department of Respiratory Disease, China State Key Laboratory of Respiratory Disease & National Clinical Research Center for Respiratory Disease, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Wenhua Liang
- Department of Thoracic Surgery/Oncology, China State Key Laboratory of Respiratory Disease & National Clinical Research Center for Respiratory Disease, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Jianxing He
- Department of Thoracic Surgery/Oncology, China State Key Laboratory of Respiratory Disease & National Clinical Research Center for Respiratory Disease, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| |
Collapse
|
39
|
Malla M, Parikh AR. Evolving Role of Circulating Tumor DNA and Emerging Targeted Therapy in Colorectal Cancer. Hematol Oncol Clin North Am 2022; 36:583-601. [DOI: 10.1016/j.hoc.2022.02.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
40
|
Behel V, Choughule A, Noronha V, Patil V, Menon N, Singh A, Kumar S, Kumar R, Shah S, More S, Banavali S, Chandrani P, Prabhash K. Clinical utility of liquid biopsy (cell-free DNA) based EGFR mutation detection post treatment initiation as a disease monitoring tool in patients with advanced EGFR-mutant NSCLC. Clin Lung Cancer 2022; 23:410-418. [DOI: 10.1016/j.cllc.2022.04.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 04/07/2022] [Accepted: 04/10/2022] [Indexed: 12/15/2022]
|
41
|
Haselmann V, Hedtke M, Neumaier M. Liquid Profiling for Cancer Patient Stratification in Precision Medicine—Current Status and Challenges for Successful Implementation in Standard Care. Diagnostics (Basel) 2022; 12:diagnostics12030748. [PMID: 35328301 PMCID: PMC8947441 DOI: 10.3390/diagnostics12030748] [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: 02/21/2022] [Revised: 03/09/2022] [Accepted: 03/11/2022] [Indexed: 12/13/2022] Open
Abstract
Circulating tumor DNA (ctDNA), accurately described by the term liquid profiling (LP), enables real-time assessment of the tumor mutational profile as a minimally invasive test and has therefore rapidly gained traction, particular for the management of cancer patients. By LP, tumor-specific genetic alterations can be determined as part of companion diagnostics to guide selection of appropriate targeted therapeutics. Because LP facilitates longitudinal monitoring of cancer patients, it can be used to detect acquired resistant mechanisms or as a personalized biomarker for earlier detection of disease recurrence, among other applications. However, LP is not yet integrated into routine care to the extent that might be expected. This is due to the lack of harmonization and standardization of preanalytical and analytical workflows, the lack of proper quality controls, limited evidence of its clinical utility, heterogeneous study results, the uncertainty of clinicians regarding the value and appropriate indications for LP and its interpretation, and finally, the lack of reimbursement for most LP tests. In this review, the value proposition of LP for cancer patient management and treatment optimization, the current status of implementation in standard care, and the main challenges that need to be overcome are discussed in detail.
Collapse
|
42
|
Bittlinger M, Bicer S, Peppercorn J, Kimmelman J. Ethical Considerations for Phase I Trials in Oncology. J Clin Oncol 2022; 40:3474-3488. [PMID: 35275736 DOI: 10.1200/jco.21.02125] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Phase I trials often represent the first occasion where new cancer strategies are tested in patients. Various developments in cancer biology, methodology, regulation, and medical ethics have altered the ethical landscape of such trials. We provide a narrative review of contemporary ethical challenges in design, conduct, and reporting of phase I cancer trials and outline recommendations for addressing each. We organized our review around four topics, supplementing the first three with scoping reviews: (1) benefit/risk, (2) research biopsies, (3) therapeutic misconception and misestimation, and (4) reporting. The main ethical challenges of conducting phase I trials stem from three issues. First, phase I trials often involve higher research burden and scientific uncertainty compared with other cancer trials. Second, many patients arrive at phase I trials at a transitional point in their illness trajectory where they have exhausted standard survival-extending options. Third, phase I trial results play a major role in informing downstream drug development and regulatory decisions. Together, these issues create distinct pressures for study design, ethical review, informed consent, and reporting. Developments in methodology, regulation, cancer biology, and ethical awareness have helped mitigate some of these challenges, while introducing others. We conclude our review with a series of recommendations regarding trial design, ethical review, consent, and reporting. We also outline several unresolved questions that, if addressed, would strengthen the ethical foundation of phase I cancer trials.
Collapse
Affiliation(s)
- Merlin Bittlinger
- Studies of Translation, Ethics and Medicine (STREAM), Department of Equity, Ethics and Policy, McGill University, Montreal, Quebec, Canada
| | - Selin Bicer
- Studies of Translation, Ethics and Medicine (STREAM), Department of Equity, Ethics and Policy, McGill University, Montreal, Quebec, Canada
| | | | - Jonathan Kimmelman
- Studies of Translation, Ethics and Medicine (STREAM), Department of Equity, Ethics and Policy, McGill University, Montreal, Quebec, Canada
| |
Collapse
|
43
|
Petranovic M, Raoof S, Digumarthy SR, Sharma A, Shepard JAO, Gainor JF, Pandharipande PV. Liquid Biopsy, Diagnostic Imaging, and Future Synergies. J Am Coll Radiol 2022; 19:336-343. [DOI: 10.1016/j.jacr.2021.11.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 11/04/2021] [Accepted: 11/05/2021] [Indexed: 12/16/2022]
|
44
|
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: 29] [Impact Index Per Article: 14.5] [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.
Collapse
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
| |
Collapse
|
45
|
Danyi A, Jager M, de Ridder J. Cancer Type Classification in Liquid Biopsies Based on Sparse Mutational Profiles Enabled through Data Augmentation and Integration. Life (Basel) 2021; 12:1. [PMID: 35054395 PMCID: PMC8780455 DOI: 10.3390/life12010001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2021] [Revised: 12/14/2021] [Accepted: 12/17/2021] [Indexed: 01/21/2023] Open
Abstract
Identifying the cell of origin of cancer is important to guide treatment decisions. Machine learning approaches have been proposed to classify the cell of origin based on somatic mutation profiles from solid biopsies. However, solid biopsies can cause complications and certain tumors are not accessible. Liquid biopsies are promising alternatives but their somatic mutation profile is sparse and current machine learning models fail to perform in this setting. We propose an improved method to deal with sparsity in liquid biopsy data. Firstly, data augmentation is performed on sparse data to enhance model robustness. Secondly, we employ data integration to merge information from: (i) SNV density; (ii) SNVs in driver genes and (iii) trinucleotide motifs. Our adapted method achieves an average accuracy of 0.88 and 0.65 on data where only 70% and 2% of SNVs are retained, compared to 0.83 and 0.41 with the original model, respectively. The method and results presented here open the way for application of machine learning in the detection of the cell of origin of cancer from liquid biopsy data.
Collapse
Affiliation(s)
- Alexandra Danyi
- Center for Molecular Medicine, University Medical Center Utrecht, 3584 CX Utrecht, The Netherlands; (A.D.); (M.J.)
| | - Myrthe Jager
- Center for Molecular Medicine, University Medical Center Utrecht, 3584 CX Utrecht, The Netherlands; (A.D.); (M.J.)
- Oncode Institute, 3521 AL Utrecht, The Netherlands
| | - Jeroen de Ridder
- Center for Molecular Medicine, University Medical Center Utrecht, 3584 CX Utrecht, The Netherlands; (A.D.); (M.J.)
- Oncode Institute, 3521 AL Utrecht, The Netherlands
| |
Collapse
|
46
|
Chen W, Hua Y, Mao D, Wu H, Tan M, Ma W, Huang X, Lu J, Li C, Li M. A Computed Tomography-Derived Radiomics Approach for Predicting Uncommon EGFR Mutation in Patients With NSCLC. Front Oncol 2021; 11:722106. [PMID: 34976788 PMCID: PMC8716946 DOI: 10.3389/fonc.2021.722106] [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: 06/08/2021] [Accepted: 11/29/2021] [Indexed: 11/13/2022] Open
Abstract
PURPOSE This study aims to develop a CT-based radiomics approach for identifying the uncommon epidermal growth factor receptor (EGFR) mutation in patients with non-small cell lung cancer (NSCLC). METHODS This study involved 223 NSCLC patients (107 with uncommon EGFR mutation-positive and 116 with uncommon EGFR mutation-negative). A total of 1,269 radiomics features were extracted from the non-contrast-enhanced CT images after image segmentation and preprocessing. Support vector machine algorithm was used for feature selection and model construction. Receiver operating characteristic curve analysis was applied to evaluate the performance of the radiomics signature, the clinicopathological model, and the integrated model. A nomogram was developed and evaluated by using the calibration curve and decision curve analysis. RESULTS The radiomics signature demonstrated a good performance for predicting the uncommon EGFR mutation in the training cohort (area under the curve, AUC = 0.802; 95% confidence interval, CI: 0.736-0.858) and was verified in the validation cohort (AUC = 0.791, 95% CI: 0.642-0.899). The integrated model combined radiomics signature with clinicopathological independent predictors exhibited an incremental performance compared with the radiomics signature or the clinicopathological model. A nomogram based on the integrated model was developed and showed good calibration (Hosmer-Lemeshow test, P = 0.92 in the training cohort and 0.608 in the validation cohort) and discrimination capacity (AUC of 0.816 in the training cohort and 0.795 in the validation cohort). CONCLUSION Radiomics signature combined with the clinicopathological features can predict uncommon EGFR mutation in NSCLC patients.
Collapse
Affiliation(s)
| | - Yanqing Hua
- Department of Radiology, Huadong Hospital, Fudan University, Shanghai, China
| | | | | | | | | | | | | | | | - Ming Li
- Department of Radiology, Huadong Hospital, Fudan University, Shanghai, China
| |
Collapse
|
47
|
Hedtke M, Pessoa Rejas R, Froelich MF, Ast V, Duda A, Mirbach L, Costina V, Martens UM, Hofheinz RD, Neumaier M, Haselmann V. Liquid profiling of circulating tumor DNA in colorectal cancer: steps needed to achieve its full clinical value as standard care. Mol Oncol 2021; 16:2042-2056. [PMID: 34873826 PMCID: PMC9120900 DOI: 10.1002/1878-0261.13156] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 10/27/2021] [Accepted: 12/06/2021] [Indexed: 12/23/2022] Open
Abstract
The analysis of circulating tumor DNA (ctDNA) is at the threshold of implementation into standard care for colorectal cancer (CRC) patients. However, data about the clinical utility of liquid profiling (LP), its acceptance by clinicians, and its integration into clinical workflows in real‐world settings remain limited. Here, LP tests requested as part of routine care since 2016 were retrospectively evaluated. Results show restrained request behavior that improved moderately over time, as well as reliable diagnostic performance comparable to translational studies, with an overall agreement of 91.7%. Extremely low ctDNA levels at < 0.1% in over 20% of cases, a high frequency of concomitant driver mutations (in up to 14% of cases), and ctDNA levels reflecting the clinical course of disease were revealed. However, certain limitations hampering successful translation of ctDNA into clinical practice were uncovered, including the lack of clinically relevant ctDNA thresholds, appropriate time points of LP requests, and integrative evaluation of ctDNA, imaging, and clinical findings. In conclusion, these results highlight the potential clinical value of LP for CRC patient management and demonstrate issues that need to be addressed for successful long‐term implementation in clinical workflows.
Collapse
Affiliation(s)
- Maren Hedtke
- Institute of Clinical Chemistry, Medical Faculty Mannheim of the University of Heidelberg, University Hospital Mannheim, Germany
| | - Rodrigo Pessoa Rejas
- Institute of Clinical Chemistry, Medical Faculty Mannheim of the University of Heidelberg, University Hospital Mannheim, Germany
| | - Matthias F Froelich
- Department of Radiology and Nuclear Medicine, University Medicine Mannheim, Medical Faculty Mannheim of the University of Heidelberg, Germany
| | - Volker Ast
- Institute of Clinical Chemistry, Medical Faculty Mannheim of the University of Heidelberg, University Hospital Mannheim, Germany
| | - Angelika Duda
- Institute of Clinical Chemistry, Medical Faculty Mannheim of the University of Heidelberg, University Hospital Mannheim, Germany
| | - Laura Mirbach
- Institute of Clinical Chemistry, Medical Faculty Mannheim of the University of Heidelberg, University Hospital Mannheim, Germany
| | - Victor Costina
- Institute of Clinical Chemistry, Medical Faculty Mannheim of the University of Heidelberg, University Hospital Mannheim, Germany
| | - Uwe M Martens
- Cancer Center Heilbronn-Franken, SLK-Clinics, MOLIT Institute for Personalized Medicine, Heilbronn, Germany
| | - Ralf-Dieter Hofheinz
- Day Treatment Center (TTZ), Interdisciplinary Tumor Center Mannheim (ITM), III Medical Clinic, Medical Faculty Mannheim of the University of Heidelberg, University Hospital Mannheim, Germany
| | - Michael Neumaier
- Institute of Clinical Chemistry, Medical Faculty Mannheim of the University of Heidelberg, University Hospital Mannheim, Germany
| | - Verena Haselmann
- Institute of Clinical Chemistry, Medical Faculty Mannheim of the University of Heidelberg, University Hospital Mannheim, Germany
| |
Collapse
|
48
|
Circulating Tumor DNA in Oncology. Processes (Basel) 2021. [DOI: 10.3390/pr9122198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
When somatic cells in the human body undergo apoptosis or necrosis, the released DNA enters the bloodstream. This type of DNA is called cell-free DNA (cfDNA). In patients with cancer, DNA released from tumor cells is called circulating tumor DNA (ctDNA), which carries genetic alterations specific to tumor cells. In recent years, ctDNA has attracted particular attention in terms of the concept of liquid biopsy in cancer care. Conventionally, tissue biopsy is required for the definitive diagnosis of cancer, and imaging examinations, such as CT, are performed for evaluating recurrence and residual lesions. Although the treatment burden on cancer patients is being slightly reduced due to advances in medicine, invasive examinations and medical exposure are still unavoidable. In addition, the prognosis of cancer varies considerably depending on the degree of progression at the time of detection. Therefore, the early detection of cancer is of utmost importance. With the increase in health consciousness, more people undergo regular health checkups, and it becomes necessary to diagnose cancer in a larger number of patients at an earlier stage. Although the accuracy of early detection has been improved by new imaging tests and examination techniques, each organ must be examined separately, and some organs are more difficult to examine than others in a regular health checkup. The process of cancer screening, diagnosis, and detection of recurrence after treatment is extensive. It can also be expensive, and some of the examinations may be invasive. If all of these processes can be replaced by the analysis of ctDNA in liquid biopsy, only a single blood sample is required. Under these circumstances, various studies are currently in progress on the use of ctDNA in clinical practice as an approach that may greatly reduce such burden. We present an overview of the current situation of ctDNA, as well as its future issues and prospects.
Collapse
|
49
|
Olympios N, Collet L, Paesmans M, Jungels C, Kotecki N, Awada A, Aftimos P. Analyses of the Rationale and Implementation of Research Biopsies in Oncology Clinical Trials at a Tertiary Cancer Center. Oncologist 2021; 26:1062-1070. [PMID: 34286890 PMCID: PMC8649004 DOI: 10.1002/onco.13906] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Accepted: 07/09/2021] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND Biomarkers in clinical trials have led to massive incorporation of research biopsies, with potentially risks and no direct benefit for patients. In 2018, the American Society of Clinical Oncology (ASCO) released an ethical framework to provide guidance on incorporating research biopsies in cancer clinical trials. MATERIALS AND METHODS We collected biopsy requirements of cancer clinical trials conducted at Institut Jules Bordet (IJB) between 2015 and 2019 to examine adherence with the ASCO Ethical Framework. We used logistic regression models to test the association between the request for biopsy, the request for tissue, and the adherence to the ASCO framework as well as some trial characteristics. RESULTS Between January 2015 and December 2019, 178 oncological studies were conducted at IJB. Of these, 138 (78%) were sponsored by industry, 132 (74%) were phase II and III studies, and 141 (79%) concerned metastatic disease. Tissue was required for inclusion for 119 (67%) studies, among which 59 required at least one new biopsy. Adherence to ASCO's Ethical Framework was 67% for studies requiring tissue and went down to 39% for studies requiring at least one new biopsy. In multivariate analysis, requests for tissue or new biopsies increased in early-phase studies (p < .001, p < .001, respectively) and in studies investigating innovative treatments (immunotherapy or targeted therapies; p < .01, p = .02). Compliance to the ASCO framework significantly decreased with time (p < .001) and in early-phase studies (p < .001). CONCLUSION Numerous studies required tissue or new biopsies for exploratory objectives of unknown clinical utility. Requests for tissue increased over the years, whereas compliance to ASCO's Ethical Framework decreased. IMPLICATIONS FOR PRACTICE In 2019, the American Society of Clinical Oncology (ASCO) developed an ethical framework to provide guidance on incorporating research biopsies in clinical trials. This study underlines the growing request for tissue in clinical trials with potentially no impact on drug development and no benefit to actual or future patients. Adherence to ASCO's Ethical Framework decreases through time. These results highlight the importance of improving the ethics of research biopsies. ASCO's Ethical Framework offers an opportunity to improve quality of care in clinical research by maximizing scientific utility and allowing for clinically meaningful correlative science and safe access to innovative treatments for a maximum number of patients.
Collapse
Affiliation(s)
- Nathalie Olympios
- Medical Oncology Clinic, Institut Jules Bordet, Université Libre de BruxellesBrusselsBelgium
| | - Laetitia Collet
- Medical Oncology Clinic, Institut Jules Bordet, Université Libre de BruxellesBrusselsBelgium
| | - Marianne Paesmans
- Data Centre, Institut Jules Bordet, Université Libre de BruxellesBrusselsBelgium
| | - Christiane Jungels
- Medical Oncology Clinic, Institut Jules Bordet, Université Libre de BruxellesBrusselsBelgium
- Clinical Trials Conduct Unit (CTCU), Institut Jules Bordet, Université Libre de BruxellesBrusselsBelgium
| | - Nuria Kotecki
- Medical Oncology Clinic, Institut Jules Bordet, Université Libre de BruxellesBrusselsBelgium
- Clinical Trials Conduct Unit (CTCU), Institut Jules Bordet, Université Libre de BruxellesBrusselsBelgium
| | - Ahmad Awada
- Medical Oncology Clinic, Institut Jules Bordet, Université Libre de BruxellesBrusselsBelgium
| | - Philippe Aftimos
- Medical Oncology Clinic, Institut Jules Bordet, Université Libre de BruxellesBrusselsBelgium
- Clinical Trials Conduct Unit (CTCU), Institut Jules Bordet, Université Libre de BruxellesBrusselsBelgium
| |
Collapse
|
50
|
Madariaga A, Bhat G, Wilson MK, Li X, Cyriac S, Bowering V, Hunt W, Gutierrez D, Bonilla L, Kasherman L, McMullen M, Wang L, Ghai S, Dhani NC, Oza AM, Lheureux S. Research biopsies in patients with gynecologic cancers: patient-reported outcomes, perceptions, and preferences. Am J Obstet Gynecol 2021; 225:658.e1-658.e9. [PMID: 34174204 DOI: 10.1016/j.ajog.2021.06.071] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 06/09/2021] [Accepted: 06/17/2021] [Indexed: 12/31/2022]
Abstract
BACKGROUND Despite the growing integration of mandatory biopsies for correlative endpoints within oncology clinical trials, there are sparse data on patient-reported outcomes, perceptions, and preferences. OBJECTIVE This study aimed to prospectively assess the impact of research biopsies on the quality of life in patients with gynecologic cancer, evaluate patient-reported outcomes, and determine factors associated with patients' willingness to undergo sequential biopsies. STUDY DESIGN We conducted a prospective study in patients with gynecologic malignancies undergoing research biopsies between 2015 and 2019 at Princess Margaret Cancer Centre (ClinicalTrials.gov Identifier: NCT02334761). Here, we report the results of the paper-based surveys performed before and 1 week after biopsy. Although the questionnaires each assessed the impact of anxiety using a modified version of the Hospital Anxiety and Depression Scale, the postbiopsy questionnaire specifically assessed the likelihood of future biopsies, postbiopsy symptoms, complications, and perceptions. RESULTS A total of 129 patients were enrolled, of which 91 (70.5%) completed at least 1 questionnaire. These patients had either ovarian (89%; 81 of 91) or endometrial cancer (11%; 10 of 91). Of all biopsies taken, 75% were from the abdomen or pelvis (67 of 89). There was 1 clinician-reported complication, a perihepatic hematoma (1%). Pain during the biopsy and physical discomfort were experienced by 60.3% (41 of 68) and 61.8% (42 of 68), respectively. Embarrassment and loss of dignity were experienced by 13.2% (9 of 68) and 11.8% (8 of 68), respectively. Although the mean Hospital Anxiety and Depression Scale score was in the normal range before and after biopsy, there was a significant decline in the total score after the biopsy (prebiopsy, 5.3 [standard deviation, 4.7] vs postbiopsy, 3.7 [standard deviation, 4.5]; P=.005); 84% of subjects (58 of 69) stated that they would definitely or likely consent to another biopsy. There was no impact on patients' willingness for future biopsies based on Eastern Cooperative Oncology Group status, biopsy site, age, number of cores, and pain during the biopsy; however, subjects who reported feeling physically uncomfortable (odds ratio, 0.14; P=.005), embarrassed (odds ratio, 0.03; P=.004) or experienced loss of dignity (odds ratio, 0.05; P=.01) during the biopsy and those who experienced flu-like symptoms (odds ratio, 0.2; P=.018) or felt feverish (odds ratio, 0.2; P=.035) 1 week after biopsy, were less likely to undergo a sequential biopsy. Similarly, those with higher Hospital Anxiety and Depression Scale scores before biopsy (odds ratio, 0.83; P=.008) and after biopsy (odds ratio, 0.8; P=.003) were less likely to consent for another biopsy. CONCLUSION Research biopsies were generally well accepted. Most patients (83%) were willing to undergo serial biopsies if necessary. Addressing the potentially modifiable psychosocial aspects of the procedure may improve the experience with research biopsies for patients with gynecologic cancers.
Collapse
Affiliation(s)
- Ainhoa Madariaga
- Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada; University of Toronto, Toronto, Ontario, Canada; Autonomous University of Barcelona, Barcelona, Spain
| | - Gita Bhat
- Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada; University of Toronto, Toronto, Ontario, Canada
| | - Michelle K Wilson
- Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada; University of Toronto, Toronto, Ontario, Canada
| | - Xuan Li
- Department of Biostatistics, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Sunu Cyriac
- Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada; University of Toronto, Toronto, Ontario, Canada
| | - Valerie Bowering
- Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Wendy Hunt
- Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - David Gutierrez
- Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Luisa Bonilla
- Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada; University of Toronto, Toronto, Ontario, Canada
| | - Lawrence Kasherman
- Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada; University of Toronto, Toronto, Ontario, Canada
| | - Michelle McMullen
- Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada; University of Toronto, Toronto, Ontario, Canada
| | - Lisa Wang
- University of Toronto, Toronto, Ontario, Canada; Department of Biostatistics, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Sangeet Ghai
- University of Toronto, Toronto, Ontario, Canada; Department of Medical Imaging, University Health Network, Toronto, Ontario, Canada
| | - Neesha C Dhani
- Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada; University of Toronto, Toronto, Ontario, Canada
| | - Amit M Oza
- Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada; University of Toronto, Toronto, Ontario, Canada
| | - Stephanie Lheureux
- Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada; University of Toronto, Toronto, Ontario, Canada.
| |
Collapse
|