1
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He G, Wang W, Zhou Y, Zhao G, Liao J. Ampholytic ion-exchange magnetic beads: a promising tool for selecting short fragments in circulating cell-free DNA analysis. Front Oncol 2024; 14:1397680. [PMID: 38779084 PMCID: PMC11109406 DOI: 10.3389/fonc.2024.1397680] [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: 03/08/2024] [Accepted: 04/23/2024] [Indexed: 05/25/2024] Open
Abstract
Objective For liquid biopsy of cancer, the extraction of circulating cell-free DNA (cfDNA) from plasma is required. We evaluated the efficacy of use of magnetic submicron particles coated with abundant small zwitterions (MSP-ZEWBs) for extracting short fragments of cfDNA. Methods We developed and optimized an MSP-ZEWB-based cfDNA extraction method using ampholytic ion-exchange materials and compared its results with those using a control kit. We measured the cfDNA concentration by quantitative polymerase-chain-reaction and using the Qubit method and analyzed cfDNA fragmentation patterns using a bioanalyzer. Results The fragment size of cfDNA isolated from glycine hydrochloric acid at a pH of 2.2 exhibited a better alignment with the DNA marker. The highest DNA intensity was observed at the final concentration of 0.8% polyethylene glycol 8000. The intensity of cfDNA decreased significantly when isolated from plasma with DNA marker using MSP-ZEWBs with an adsorption buffer containing guanidine hydrochloride or isothiocyanoguanidine. All fragments were successfully extracted using MSP-ZEWBs from both plasma and phosphate-buffered saline. Notably, the intensity of short cfDNA fragments isolated using MSP-ZEWBs remained consistent for recovery of long DNA fragments. indicating a potential selective of small fragments. Conclusion The extraction of plasma cfDNA with MSP-ZEWBs requires no protein denaturation, shows resistance to cells remaining in plasma, and demonstrates higher overall efficiency and better reproducibility than other extraction methods. Use of MSP-ZEWBs may greatly enhance liquid biopsy of cancers through the analysis of plasma cfDNA in clinical practice.
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Affiliation(s)
- Gan He
- Gastrointestinal Surgery, Yongchuan Hospital of Chongqing Medical University, Chongqing, China
| | - Weixuan Wang
- Institute of Life Sciences, Chongqing Medical University, Chongqing, China
| | - Yongxia Zhou
- Department of Radiology, Yongchuan Hospital of Chongqing Medical University, Chongqing, China
- Center Laboratory, Yongchuan Hospital of Chongqing Medical University, Chongqing, China
| | - Guowei Zhao
- Gastrointestinal Surgery, Yongchuan Hospital of Chongqing Medical University, Chongqing, China
| | - Juan Liao
- Center Laboratory, Yongchuan Hospital of Chongqing Medical University, Chongqing, China
- Chongqing Geriatric Disease Clinical Research Center, Chongqing, China
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2
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Fardella E, Zanirato G, Magni M, Caldarelli N, Chiappella A, Dodero A, Ljevar S, Orsucci L, Re A, Usai SV, Stefoni V, Castellino C, Rossi FG, Pinto A, Carniti C, Corradini P. Prognostic impact of pretreatment cell-free DNA concentration in newly diagnosed peripheral T-cell lymphomas. Br J Haematol 2024; 204:1752-1756. [PMID: 38176400 DOI: 10.1111/bjh.19280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 12/14/2023] [Accepted: 12/19/2023] [Indexed: 01/06/2024]
Abstract
Peripheral T-cell lymphomas (PTCLs) have a poor prognosis and, to date, there are no reliable predictive biomarkers of response. In this work we explored the prognostic impact of cell-free DNA (cfDNA) concentration in 75 newly diagnosed patients enrolled in a prospective multicenter study. Pre-treatment cfDNA was strongly associated with clinical risk factors and was identified as a superior predictor for shorter progression-free survival in multivariable analysis, outweighing canonical risk parameters. Furthermore, we identified a cfDNA value above which survival worsens. In conclusion, pre-treatment cfDNA concentration represents an easily usable predictive biomarker that is highly associated with survival of PTCL patients.
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MESH Headings
- Humans
- Lymphoma, T-Cell, Peripheral/mortality
- Lymphoma, T-Cell, Peripheral/diagnosis
- Lymphoma, T-Cell, Peripheral/blood
- Lymphoma, T-Cell, Peripheral/genetics
- Male
- Female
- Middle Aged
- Aged
- Cell-Free Nucleic Acids/blood
- Prognosis
- Adult
- Biomarkers, Tumor/blood
- Prospective Studies
- Aged, 80 and over
- Antineoplastic Combined Chemotherapy Protocols/therapeutic use
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Affiliation(s)
| | - G Zanirato
- Division of Hematology and Stem Cell Transplantation, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - M Magni
- Division of Hematology and Stem Cell Transplantation, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | | | - A Chiappella
- Division of Hematology and Stem Cell Transplantation, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - A Dodero
- Division of Hematology and Stem Cell Transplantation, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - S Ljevar
- Unit of Biostatistics for Clinical Research, Fondazione IRCCS Istituto Nazionale dei Tumori, Milano, Italy
| | - L Orsucci
- Division of Hematology, Azienda Ospedaliera e Universitaria Città della Salute e della Scienza, Turin, Italy
| | - A Re
- Hematology Division, ASST Spedali Civili di Brescia, Brescia, Italy
| | - S V Usai
- Hematology Unit, Ospedale Oncologico Armando Businco, Cagliari, Italy
| | - V Stefoni
- Institute of Hematology Seràgnoli, University of Bologna, Bologna, Italy
| | - C Castellino
- Division of Hematology, Azienda Ospedaliera S. Croce e Carle, Cuneo, Italy
| | - F G Rossi
- Division of Hematology, Fondazione IRCCS Cà Granda, Ospedale Maggiore Policlinico, Milan, Italy
| | - A Pinto
- Hematology-Oncology & Stem Cell Transplantation Unit, IRCCS Istituto Nazionale Tumori, Fondazione G. Pascale, Napoli, Italy
| | - C Carniti
- Division of Hematology and Stem Cell Transplantation, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - P Corradini
- University of Milan, Milan, Italy
- Division of Hematology and Stem Cell Transplantation, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
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3
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Huang Q, Ji M, Li F, Li Y, Zhou X, Hsueh CY, Zhou L. Diagnostic and prognostic value of plasma cell-free DNA combined with VEGF-C in laryngeal squamous cell carcinoma. Mol Cell Probes 2023; 67:101895. [PMID: 36682577 DOI: 10.1016/j.mcp.2023.101895] [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: 09/12/2022] [Revised: 01/18/2023] [Accepted: 01/18/2023] [Indexed: 01/20/2023]
Abstract
BACKGROUND Circulating cell-free DNA (cfDNA) and vascular endothelial growth factor-C (VEGF-C) can be utilized to detect cancer and predict its prognosis. However, their potential application in laryngeal squamous cell carcinoma (LSCC) is unclear. PURPOSE This study aimed to identify the diagnostic and prognostic value of cfDNA and VEGF-C in LSCC patients. METHODS The plasma cfDNA of 148 LSCC patients and 43 non-tumor patients were isolated. Quantitative real-time PCR (qRT-PCR) was performed to assess long and short DNA fragments in plasma by amplifying the ALU repeats. ALU-qPCR results (ALU247/ALU115) were used to calculate cfDNA integrity index. Vascular endothelial growth factor-C (VEGF-C) level was detected by ELISA assay. Correlation between cfDNA and clinical features was analyzed. For detecting the sensitivity and specificity of cfDNA and VEGF-C alone or in combination for diagnosing LSCC, receiver operator characteristic (ROC) was established. For evaluating the overall survival (OS) of LSCC, Kaplan-Meier curves were established. RESULTS LSCC patients had significantly higher levels of plasma cfDNA (ALU115, ALU247, and cfDNA integrity index) and VEGF-C than those without cancer (p < 0.05), showing area under the curve (AUC) values of 0.79, 0.74, 0.62 and 0.80, when cutoff value was correspondingly defined at 2.14 ng/mL, 1.39 ng/mL, 0.73 and 412.90 pg/mL, respectively. The AUC for distinguishing LSCC patients from non-tumor patients by plasma cfDNA combined with VEGF-C was 0.89 (95% CI: 0.83-0.94). A significant correlation was found between plasma cfDNA levels and Ki-67, tumor size, pT stage, and smoking history (p < 0.05). Based on survival analysis, low VEGF-C concentration groups had longer OS than those with high VEGF-C concentration (p = 0.02). CONCLUSION Indicators such as plasma cfDNA and VEGF-C may be used to diagnose and monitor LSCC for its noninvasiveness and rapid accessibility.
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Affiliation(s)
- Qiang Huang
- Department of Otorhinolaryngology, Eye & ENT Hospital, Fudan University, Shanghai, 200031, China
| | - Mengyou Ji
- Department of Otorhinolaryngology, Eye & ENT Hospital, Fudan University, Shanghai, 200031, China
| | - Feiran Li
- Department of Otorhinolaryngology, Eye & ENT Hospital, Fudan University, Shanghai, 200031, China
| | - Yufeng Li
- Department of Anesthesiology, Eye & ENT Hospital, Fudan University, Shanghai, 200031, China
| | - Xuehua Zhou
- Department of Anesthesiology, Eye & ENT Hospital, Fudan University, Shanghai, 200031, China
| | - Chi-Yao Hsueh
- Department of Otorhinolaryngology, Eye & ENT Hospital, Fudan University, Shanghai, 200031, China.
| | - Liang Zhou
- Department of Otorhinolaryngology, Eye & ENT Hospital, Fudan University, Shanghai, 200031, China.
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4
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Fernández-Miranda I, Pedrosa L, Llanos M, Franco FF, Gómez S, Martín-Acosta P, García-Arroyo FR, Gumá J, Horcajo B, Ballesteros AK, Gálvez L, Martínez N, Marín M, Sequero S, Navarro M, Yanguas-Casás N, Calvo V, Rueda-Domínguez A, Provencio M, Sánchez-Beato M. Monitoring of Circulating Tumor DNA Predicts Response to Treatment and Early Progression in Follicular Lymphoma: Results of a Prospective Pilot Study. Clin Cancer Res 2023; 29:209-220. [PMID: 36269794 PMCID: PMC9811164 DOI: 10.1158/1078-0432.ccr-22-1654] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 07/26/2022] [Accepted: 10/19/2022] [Indexed: 02/07/2023]
Abstract
PURPOSE Follicular lymphoma (FL) is the most frequent indolent non-Hodgkin lymphoma. Around 20% of patients suffer early disease progression within 24 months (POD24) of diagnosis. This study examined the significance of circulating tumor DNA (ctDNA) in predicting response to therapy and POD24 in patients with FL. EXPERIMENTAL DESIGN We collected 100 plasma samples, before and during the treatment, from 36 patients with FL prospectively enrolled in 8 Spanish hospitals. They were treated with a chemotherapy-rituximab regimen and followed up for a median of 3.43 years. We performed targeted deep sequencing in cell-free DNA (cfDNA) and tumor genomic DNA from 31 diagnostic biopsy samples. RESULTS Of the alterations detected in the diagnostic tissue samples, 73% (300/411) were also identified in basal cfDNA. The mean numbers of alterations per basal cfDNA sample in patients who suffered progression of disease within 24 months (POD24-pos) or did not achieve complete response (non-CR) were significantly higher than in POD24-neg or CR patients (unpaired samples t test, P = 0.0001 and 0.001, respectively). Pretreatment ctDNA levels, as haploid genome equivalents per milliliter of plasma, were higher in patients without CR (P = 0.02) and in POD24-pos patients compared with POD24-neg patients (P < 0.001). Dynamic analysis showed that ctDNA levels decreased dramatically after treatment, although the reduction was more significant in patients with CR and POD24-neg patients. CONCLUSIONS Basal ctDNA levels are associated with the risk of early progression and response to treatment in FL. cfDNA monitoring and genotyping during treatment and follow-up predict response to treatment and early progression.
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Affiliation(s)
- Ismael Fernández-Miranda
- Department of Medical Oncology, Lymphoma Research Group, Hospital Universitario Puerta de Hierro-Majadahonda, IDIPHISA, Madrid, Spain.,PhD Program in Molecular Biosciences, Doctoral School, Universidad Autónoma de Madrid, Madrid, Spain
| | - Lucía Pedrosa
- Department of Medical Oncology, Lymphoma Research Group, Hospital Universitario Puerta de Hierro-Majadahonda, IDIPHISA, Madrid, Spain.,PhD Program in Molecular Biosciences, Doctoral School, Universidad Autónoma de Madrid, Madrid, Spain
| | - Marta Llanos
- Department of Medical Oncology, Hospital Universitario de Canarias, Tenerife, Spain.,Grupo Oncológico para el Tratamiento y Estudio de los Linfomas (GOTEL), Madrid, Spain
| | - Fernando F. Franco
- Department of Medical Oncology, Hospital Universitario Puerta de Hierro-Majadahonda, Madrid, Spain
| | - Sagrario Gómez
- Department of Medical Oncology, Lymphoma Research Group, Hospital Universitario Puerta de Hierro-Majadahonda, IDIPHISA, Madrid, Spain
| | - Paloma Martín-Acosta
- Department of Pathology, Cancer Molecular Pathology Group, Hospital Universitario Puerta de Hierro-Majadahonda, IDIPHISA, CIBERONC, Madrid, Spain
| | - Francisco R. García-Arroyo
- Grupo Oncológico para el Tratamiento y Estudio de los Linfomas (GOTEL), Madrid, Spain.,Department of Medical Oncology, Complejo Hospitalario de Pontevedra, Spain
| | - Josep Gumá
- Grupo Oncológico para el Tratamiento y Estudio de los Linfomas (GOTEL), Madrid, Spain.,Department of Medical Oncology, IISPV-URV, Hospital Universitari Sant Joan de Reus, Reus, Spain
| | - Beatriz Horcajo
- Department of Medical Oncology, Lymphoma Research Group, Hospital Universitario Puerta de Hierro-Majadahonda, IDIPHISA, Madrid, Spain
| | - Ana K. Ballesteros
- Department of Medical Oncology, Lymphoma Research Group, Hospital Universitario Puerta de Hierro-Majadahonda, IDIPHISA, Madrid, Spain
| | - Laura Gálvez
- Grupo Oncológico para el Tratamiento y Estudio de los Linfomas (GOTEL), Madrid, Spain.,Department of Medical Oncology, Hospitales Universitarios Regional y Virgen de la Victoria de Málaga, Spain
| | - Natividad Martínez
- Grupo Oncológico para el Tratamiento y Estudio de los Linfomas (GOTEL), Madrid, Spain.,Department of Medical Oncology, Dr. Balmis General University Hospital, Alicante Institute for Health and Biomedical Research (ISABIAL), Alicante, Spain
| | - Miguel Marín
- Grupo Oncológico para el Tratamiento y Estudio de los Linfomas (GOTEL), Madrid, Spain.,Department of Medical Oncology, Hospital Clínico Universitario Virgen de la Arrixaca, Murcia, Spain
| | - Silvia Sequero
- Grupo Oncológico para el Tratamiento y Estudio de los Linfomas (GOTEL), Madrid, Spain.,Department of Medical Oncology, Hospital Universitario San Cecilio, Granada, Spain
| | - Marta Navarro
- Department of Medical Oncology, Lymphoma Research Group, Hospital Universitario Puerta de Hierro-Majadahonda, IDIPHISA, Madrid, Spain
| | - Natalia Yanguas-Casás
- Department of Medical Oncology, Lymphoma Research Group, Hospital Universitario Puerta de Hierro-Majadahonda, IDIPHISA, Madrid, Spain.,Centro de Investigación Biomédica en Red Fragilidad y Envejecimiento Saludable (CIBERFES), Madrid, Spain
| | - Virginia Calvo
- Grupo Oncológico para el Tratamiento y Estudio de los Linfomas (GOTEL), Madrid, Spain.,Department of Medical Oncology, Hospital Universitario Puerta de Hierro-Majadahonda, Madrid, Spain
| | - Antonio Rueda-Domínguez
- Grupo Oncológico para el Tratamiento y Estudio de los Linfomas (GOTEL), Madrid, Spain.,Department of Medical Oncology, Hospitales Universitarios Regional y Virgen de la Victoria de Málaga, Spain
| | - Mariano Provencio
- Grupo Oncológico para el Tratamiento y Estudio de los Linfomas (GOTEL), Madrid, Spain.,Department of Medical Oncology, Hospital Universitario Puerta de Hierro-Majadahonda, Facultad de Medicina, Universidad Autónoma de Madrid, IDIPHISA, Madrid, Spain
| | - Margarita Sánchez-Beato
- Department of Medical Oncology, Lymphoma Research Group, Hospital Universitario Puerta de Hierro-Majadahonda, IDIPHISA, Madrid, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain.,Corresponding Author: Margarita Sánchez-Beato, Joaquín Rodrigo 2, Majadahonda, Madrid 28222, Spain. Phone: 349-1191-6095; E-mail:
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5
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Ma J, Teng Y, Youming H, Tao X, Fan Y. The Value of Cell-Free Circulating DNA Profiling in Patients with Skin Diseases. Methods Mol Biol 2023; 2695:247-262. [PMID: 37450124 DOI: 10.1007/978-1-0716-3346-5_17] [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
Liquid biopsy, also known as fluid biopsy or fluid-phase biopsy, is the sampling and analysis of the blood, cerebrospinal fluid, saliva, pleural fluid, ascites, and urine. Compared with tissue biopsy, liquid biopsy technology has the advantages of being noninvasive, having strong repeatability, enabling early diagnosis, dynamic monitoring, and overcoming tumor heterogeneity. However, interest in cfDNA and skin diseases has not expanded until recently. In this review, we present an overview of the literature related to the basic biology of cfDNA in the field of dermatology as a biomarker for early diagnosis, monitoring disease activity, predicting progression, and treatment response.
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Affiliation(s)
- Jingwen Ma
- Medical Cosmetic Center, Shanghai Skin Disease Hospital, Tongji University, Shanghai, People's Republic of China
| | - Yan Teng
- Health Management Center, Department of Dermatology, Zhejiang Provincial People's Hospital, Affiliated People's Hospital, Hangzhou Medical College, Hangzhou, People's Republic of China
| | - Huang Youming
- Health Management Center, Department of Dermatology, Zhejiang Provincial People's Hospital, Affiliated People's Hospital, Hangzhou Medical College, Hangzhou, People's Republic of China
| | - Xiaohua Tao
- Health Management Center, Department of Dermatology, Zhejiang Provincial People's Hospital, Affiliated People's Hospital, Hangzhou Medical College, Hangzhou, People's Republic of China
| | - Yibin Fan
- Health Management Center, Department of Dermatology, Zhejiang Provincial People's Hospital, Affiliated People's Hospital, Hangzhou Medical College, Hangzhou, People's Republic of China.
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6
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Yuwono NL, Warton K, Ford CE. The influence of biological and lifestyle factors on circulating cell-free DNA in blood plasma. eLife 2021; 10:e69679. [PMID: 34752217 PMCID: PMC8577835 DOI: 10.7554/elife.69679] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 10/23/2021] [Indexed: 01/02/2023] Open
Abstract
Research and clinical use of circulating cell-free DNA (cirDNA) is expanding rapidly; however, there remain large gaps in our understanding of the influence of lifestyle and biological factors on the amount of cirDNA present in blood. Here, we review 66 individual studies of cirDNA levels and lifestyle and biological factors, including exercise (acute and chronic), alcohol consumption, occupational hazard exposure, smoking, body mass index, menstruation, hypertension, circadian rhythm, stress, biological sex and age. Despite technical and methodological inconsistences across studies, we identify acute exercise as a significant influence on cirDNA levels. Given the large increase in cirDNA induced by acute exercise, we recommend that controlling for physical activity prior to blood collection is routinely incorporated into study design when total cirDNA levels are of interest. We also highlight appropriate selection and complete reporting of laboratory protocols as important for improving the reproducibility cirDNA studies and ability to critically evaluate the results.
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Affiliation(s)
- Nicole Laurencia Yuwono
- Gynaecological Cancer Research Group, Adult Cancer Program, Lowy Cancer Research Centre, Department of Obstetrics & Gynaecology, School of Women's and Children's Health, Faculty of Medicine & Health, University of New South WalesSydneyAustralia
| | - Kristina Warton
- Gynaecological Cancer Research Group, Adult Cancer Program, Lowy Cancer Research Centre, Department of Obstetrics & Gynaecology, School of Women's and Children's Health, Faculty of Medicine & Health, University of New South WalesSydneyAustralia
| | - Caroline Elizabeth Ford
- Gynaecological Cancer Research Group, Adult Cancer Program, Lowy Cancer Research Centre, Department of Obstetrics & Gynaecology, School of Women's and Children's Health, Faculty of Medicine & Health, University of New South WalesSydneyAustralia
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7
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Zhang Y, Liu Z, Ji K, Li X, Wang C, Ren Z, Liu Y, Chen X, Han X, Meng L, Li L, Li Z. Clinical Application Value of Circulating Cell-free DNA in Hepatocellular Carcinoma. Front Mol Biosci 2021; 8:736330. [PMID: 34660697 PMCID: PMC8511426 DOI: 10.3389/fmolb.2021.736330] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Accepted: 09/14/2021] [Indexed: 01/08/2023] Open
Abstract
Hepatocellular carcinoma (HCC) is one of the most common cancers worldwide and a leading cause of cancer-related deaths. Due to late diagnosis, early intrahepatic metastasis and nonresponse to systemic treatments, surgical resection and/or biopsy specimens remain the gold standard for disease staging, grading and clinical decision-making. Since only a small amount of tissue was obtained in a needle biopsy, the conventional tissue biopsy is unable to represent tumor heterogeneity in HCC. For this reason, it is imperative to find a new non-invasive and easily available diagnostic tool to detect HCC at an early stage and to monitor HCC recurrence. The past decade has witnessed considerable evolution in the development of liquid biopsy technologies with the emergence of next-generation sequencing. As a liquid biopsy approach, molecular analysis of cell-free DNA (cfDNA), characterized by noninvasiveness and real-time analysis, may accurately represent the tumor burden and comprehensively reflect genetic profile of HCC. Therefore, cfDNA may be used clinically as a predictive biomarker in early diagnosis, outcome assessment, and even molecular typing. In this review, we provide an update on the recent advances made in clinical applications of cfDNA in HCC.
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Affiliation(s)
- Yuyuan Zhang
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Interventional Institute of Zhengzhou University, Zhengzhou, China.,Interventional Treatment and Clinical Research Center of Henan Province, Zhengzhou, China
| | - Zaoqu Liu
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Interventional Institute of Zhengzhou University, Zhengzhou, China.,Interventional Treatment and Clinical Research Center of Henan Province, Zhengzhou, China
| | - Kun Ji
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Interventional Institute of Zhengzhou University, Zhengzhou, China.,Interventional Treatment and Clinical Research Center of Henan Province, Zhengzhou, China
| | - Xin Li
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Interventional Institute of Zhengzhou University, Zhengzhou, China.,Interventional Treatment and Clinical Research Center of Henan Province, Zhengzhou, China
| | - Caihong Wang
- Department of Magnetic Resonance, The First Affiliated Hospital, Zhengzhou University, Zhengzhou, China
| | - Zhigang Ren
- Department of Infections Disease, The First Affiliated Hospital, Zhengzhou University, Zhengzhou, China
| | - Yang Liu
- Department of Radiation Oncology, The Affiliated Cancer Hospital of Zhengzhou University, Zhengzhou, China
| | - Xinju Chen
- First Ward of Spleen, Stomach, Liver and Gall, The First Affiliated Hospital of Henan University of TCM, Zhengzhou, China
| | - Xinwei Han
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Interventional Institute of Zhengzhou University, Zhengzhou, China.,Interventional Treatment and Clinical Research Center of Henan Province, Zhengzhou, China
| | - Lingfang Meng
- Department of Ultrasound, Zhengzhou Sixth People's Hospital, Henan Infectious Disease Hospital, Zhengzhou, China
| | - Lifeng Li
- Internet Medical and System Applications of National Engineering Laboratory, Zhengzhou, China.,Cancer Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Zhen Li
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Interventional Institute of Zhengzhou University, Zhengzhou, China.,Interventional Treatment and Clinical Research Center of Henan Province, Zhengzhou, China
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8
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Ogawa M, Yokoyama K, Imoto S, Tojo A. Role of Circulating Tumor DNA in Hematological Malignancy. Cancers (Basel) 2021; 13:2078. [PMID: 33923024 PMCID: PMC8123338 DOI: 10.3390/cancers13092078] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 04/23/2021] [Indexed: 02/07/2023] Open
Abstract
With the recent advances in noninvasive approaches for cancer diagnosis and surveillance, the term "liquid biopsy" has become more familiar to clinicians, including hematologists. Liquid biopsy provides a variety of clinically useful genetic data. In this era of personalized medicine, genetic information is critical to early diagnosis, aiding risk stratification, directing therapeutic options, and monitoring disease relapse. The validity of circulating tumor DNA (ctDNA)-mediated liquid biopsies has received increasing attention. This review summarizes the current knowledge of liquid biopsy ctDNA in hematological malignancies, focusing on the feasibility, limitations, and key areas of clinical application. We also highlight recent advances in the minimal residual disease monitoring of leukemia using ctDNA. This article will be useful to those involved in the clinical practice of hematopoietic oncology.
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Affiliation(s)
- Miho Ogawa
- Division of Molecular Therapy, Advanced Clinical Research Center, The Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan; (M.O.); (A.T.)
| | - Kazuaki Yokoyama
- Department of Hematology/Oncology, Research Hospital, The Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan
| | - Seiya Imoto
- Division of Health Medical Intelligence, Human Genome Center, The Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan;
| | - Arinobu Tojo
- Division of Molecular Therapy, Advanced Clinical Research Center, The Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan; (M.O.); (A.T.)
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9
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Somatic Mutation Profiling in the Liquid Biopsy and Clinical Analysis of Hereditary and Familial Pancreatic Cancer Cases Reveals KRAS Negativity and a Longer Overall Survival. Cancers (Basel) 2021; 13:cancers13071612. [PMID: 33807330 PMCID: PMC8038004 DOI: 10.3390/cancers13071612] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 03/27/2021] [Indexed: 12/21/2022] Open
Abstract
Simple Summary Pancreatic ductal adenocarcinoma (PDAC) has a poor prognosis. KRAS mutations occur in up to 95% of cases and render the tumor resistant to many types of therapy. Therefore, these patients are treated with traditional cytotoxic agents, according to guidelines. The familial or hereditary form of the disease accounts for up to 10–15% of cases. We hypothesized that hereditary and Familial Pancreatic Cancer cases (H/FPC) have a distinct tumor specific mutation profile due to the presence of pathogenic germline mutations and we used circulating free DNA (cfDNA) in plasma to assess this hypothesis. H/FPC cases were mainly KRAS mutation negative and harbored tumor specific mutations that are potential treatment targets in the clinic. Thus, we conclude that cases with a hereditary or familial background can be treated with newer and more effective agents that may ultimately improve their overall survival. Abstract Pancreatic ductal adenocarcinoma (PDAC) presents many challenges in the clinic and there are many areas for improvement in diagnostics and patient management. The five-year survival rate is around 7.2% as the majority of patients present with advanced disease at diagnosis that is treatment resistant. Approximately 10–15% of PDAC cases have a hereditary basis or Familial Pancreatic Cancer (FPC). Here we demonstrate the use of circulating free DNA (cfDNA) in plasma as a prognostic biomarker in PDAC. The levels of cfDNA correlated with disease status, disease stage, and overall survival. Furthermore, we show for the first time via BEAMing that the majority of hereditary or familial PDAC cases (around 84%) are negative for a KRAS somatic mutation. In addition, KRAS mutation negative cases harbor somatic mutations in potentially druggable genes such as KIT, PDGFR, MET, BRAF, and PIK3CA that could be exploited in the clinic. Finally, familial or hereditary cases have a longer overall survival compared to sporadic cases (10.2 vs. 21.7 months, respectively). Currently, all patients are treated the same in the clinic with cytotoxic agents, although here we demonstrate that there are different subtypes of tumors at the genetic level that could pave the way to personalized treatment.
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Lv L, Liu Y. Clinical Application of Liquid Biopsy in Non-Hodgkin Lymphoma. Front Oncol 2021; 11:658234. [PMID: 33816315 PMCID: PMC8013700 DOI: 10.3389/fonc.2021.658234] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 03/02/2021] [Indexed: 12/14/2022] Open
Abstract
Non-Hodgkin lymphoma (NHL) is a common type of hematological malignant tumor, composed of multiple subtypes that originate from B lymphocytes, T lymphocytes, and natural killer cells. A diagnosis of NHL depends on the results of a pathology examination, which requires an invasive tissue biopsy. However, due to their invasive nature, tissue biopsies have many limitations in clinical applications, especially in terms of evaluating the therapeutic response and monitoring tumor progression. To overcome these limitations of traditional tissue biopsies, a technique known as "liquid biopsies" (LBs) was proposed. LBs refer to noninvasive examinations that can provide biological tumor data for analysis. Many studies have shown that LBs can be broadly applied to the diagnosis, treatment, prognosis, and monitoring of NHL. This article will briefly review various LB methods that aim to improve NHL management, including the evaluation of cell-free DNA/circulating tumor DNA, microRNA, and tumor-derived exosomes extracted from peripheral blood in NHL.
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Affiliation(s)
- Liwei Lv
- Department of Hematology, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Yuanbo Liu
- Department of Hematology, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
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Diffuse large B-cell lymphoma: Time to focus on circulating blood nucleic acids? Blood Rev 2020; 47:100776. [PMID: 33229139 DOI: 10.1016/j.blre.2020.100776] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 10/05/2020] [Accepted: 10/28/2020] [Indexed: 01/10/2023]
Abstract
Diffuse large B-cell lymphoma (DLBCL) is a heterogeneous neoplasm with diverse genetic abnormalities and outcomes. To date, DLBCL is invasively diagnosed by tissue biopsy and few biomarkers are available to predict patient outcome, treatment response and progression. The identification of patient-specific biomarkers would allow a "personalized medicine" approach for DLBCL patients. In this regard, "liquid biopsies" hold great promise, capturing the entire genetic landscape of the tumour and allowing a rapid and dynamic management of cancer. Liquid biopsy studies particularly focus on cell-free nucleic acids, such as cell-free DNA (cfDNA) and microRNAs, which are easy to collect and analyse. In accordance with the PRISMA criteria, we performed a systematic review on circulating nucleic acids as potential biomarkers for DLBCL management. The results suggest that combining information from the genetic (cfDNA) and epigenetic (microRNAs) landscape of the disease could lead to developing an integrated network of non-invasive biomarkers for the better management of DLBCL.
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Lefèvre AC, Kronborg C, Sørensen BS, Krag SRP, Serup-Hansen E, Spindler KLG. Measurement of circulating free DNA in squamous cell carcinoma of the anus and relation to risk factors and recurrence. Radiother Oncol 2020; 150:211-216. [PMID: 32622778 DOI: 10.1016/j.radonc.2020.06.045] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 06/26/2020] [Accepted: 06/27/2020] [Indexed: 12/18/2022]
Abstract
BACKGROUND Measuring circulating-free-deoxyribonucleic-acid (cfDNA) has created a new framework for personalized treatment in oncology. The aim of this study was to analyze the relation between cfDNA and risk factors and outcome in squamous cell carcinoma of the anus (SCCA). METHODS Patients treated with radiotherapy for localized SCCA were included in Aarhus, Denmark from 2016 to 2019. Serum samples from baseline, during and after therapy, were measured for the level of cfDNA in copies per mL by a direct fluorescent assay. RESULTS Eighty patients were included. Samples were available at baseline (n = 73) mid-therapy (n = 74), end-therapy (n = 67) and one-year follow-up (1Y) (n = 29). P16-positivity was found in 89% (n = 55). The median level of cfDNA was higher for P16 negative tumors (1.48) compared with the P16 positive tumors (0.90, P = 0.04). Data showed a correlation between baseline cfDNA levels and Gross Tumor Volume (R2 = 0.13, P < 0.01), and increasing levels with increasing T-stage (T1 = 0.80, T2 = 0.94, T3 = 1.11, T4 = 1.3). Higher cfDNA levels were observed in patients with poor performance status (P < 0.01). The cfDNA level decreased from baseline to mid-therapy (0.92-0.78, P < 0.01) and from baseline to 1Y (0.92-0.71, P < 0.01). Baseline levels for patients with treatment failure (n = 8) were above the 25th percentile (p = 0.05) which translates into difference in disease free survival. CONCLUSION Results indicate an association between baseline cfDNA levels and risk factors in SCCA and a low baseline level correlates to lower risk of treatment failure. Findings contribute with new knowledge of the biological role of cfDNA in SCCA and holds potential knowledge for personalized treatment of SCCA.
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Affiliation(s)
| | - Camilla Kronborg
- Department of Oncology, Aarhus University Hospital, Denmark; Danish Centre for Particle Therapy, Denmark
| | | | | | | | - Karen-Lise Garm Spindler
- Experimental Clinical Oncology, Aarhus University Hospital, Denmark; Department of Oncology, Aarhus University Hospital, Denmark
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Thakur S, Tobey A, Daley B, Auh S, Walter M, Patel D, Nilubol N, Kebebew E, Patel A, Jensen K, Vasko V, Klubo-Gwiezdzinska J. Limited Utility of Circulating Cell-Free DNA Integrity as a Diagnostic Tool for Differentiating Between Malignant and Benign Thyroid Nodules With Indeterminate Cytology (Bethesda Category III). Front Oncol 2019; 9:905. [PMID: 31620364 PMCID: PMC6759775 DOI: 10.3389/fonc.2019.00905] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Accepted: 08/30/2019] [Indexed: 12/17/2022] Open
Abstract
Background: Analysis of plasma circulating cell-free DNA integrity (cfDI) has emerged as a promising tool in the diagnosis of malignant vs. benign tumors. There is limited data on the role of cfDI in thyroid cancer. The goal of this study was to analyze cfDI as a biomarker of malignancy in patients with cytologically indeterminate thyroid nodules. Methods: The cfDI was measured in the plasma of patients with cytologically indeterminate thyroid nodules. All patients underwent plasma collection within 24–72 h before surgical treatment for thyroid nodules. Additionally, samples were collected from seven patients via the vein draining the thyroid and peripheral vein during surgery. Quantitative real-time PCR was performed on the isolated cell-free DNA using two different primer sets (115 and 247 bp) to amplify consensus ALU sequences. The cfDI was calculated as the ratio of ALU247 to ALU115. Results: All data are given as median [25th−75th percentile]. The study group consisted of 67 patients with 100 nodules, 80.6% (54/67) women, aged 43 [33-60] years. There was no difference in cfDI between 29 patients with benign nodules (0.49 [0.41–0.59]) and 38 patients with malignant lesions (0.45 [0.36–0.57], p = 0.19). There was no difference in cfDI in the vein draining the thyroid (0.47 [0.24–1.05]) and peripheral vein (0.48 [0.36–0.56], p = 0.44). In comparison to thyroid cancer patients, patients with benign nodules were characterized by significantly higher concentrations of ALU115 (1,064 [529–2,960] vs. 411 [27–1,049] ng/ml; p = 0.002) and ALU247 (548 [276–1,894] vs. 170 [17-540] ng/ml; p = 0.0005), most likely because benign tumors were larger (3, [1.8–4.1 cm]) than malignant lesions (0.7 [0.23–1.45], p < 0.0001). Women had significantly lower cfDI (0.45 [0.27–0.54]) than men (0.56 [0.44–0.8], p = 0.011). Conclusion: The cfDI measured in the vein draining the thyroid is similar to the cfDI measured in the antecubital vein, validating cfDI measurements by peripheral liquid biopsy. Analysis of cfDI needs to be stratified by patients gender. In contrast to its diagnostic utility in aggressive cancers, cfDI has limited utility as a biomarker of malignancy in cytologically indeterminate thyroid nodules.
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Affiliation(s)
- Shilpa Thakur
- Metabolic Disease Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Andrew Tobey
- Metabolic Disease Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Brianna Daley
- Metabolic Disease Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Sungyoung Auh
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Mary Walter
- Core for Clinical Laboratory Services, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Dhaval Patel
- Cancer Center - Froedtert Hospital, Milwaukee, WI, United States
| | - Naris Nilubol
- Endocrine Oncology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, United States
| | - Electron Kebebew
- Division of General Surgery, Endocrine Oncology Research Laboratory, Department of Surgery, Stanford Medicine, School of Medicine, Stanford, CA, United States
| | - Aneeta Patel
- Department of Pediatric Endocrinology, Uniformed Services University of the Health Sciences, Bethesda, MD, United States
| | - Kirk Jensen
- Department of Pediatric Endocrinology, Uniformed Services University of the Health Sciences, Bethesda, MD, United States
| | - Vasyl Vasko
- Department of Pediatric Endocrinology, Uniformed Services University of the Health Sciences, Bethesda, MD, United States
| | - Joanna Klubo-Gwiezdzinska
- Metabolic Disease Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, United States
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Liu L, Kuang Y, Yang H, Chen Y. An amplification strategy using DNA-Peptide dendrimer probe and mass spectrometry for sensitive MicroRNA detection in breast cancer. Anal Chim Acta 2019; 1069:73-81. [DOI: 10.1016/j.aca.2019.04.009] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Revised: 04/01/2019] [Accepted: 04/07/2019] [Indexed: 01/12/2023]
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Arzuaga-Mendez J, Prieto-Fernández E, Lopez-Lopez E, Martin-Guerrero I, García-Ruiz JC, García-Orad A. Cell-free DNA as a biomarker in diffuse large B-cell lymphoma: A systematic review. Crit Rev Oncol Hematol 2019; 139:7-15. [DOI: 10.1016/j.critrevonc.2019.04.013] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Revised: 04/12/2019] [Accepted: 04/13/2019] [Indexed: 02/08/2023] Open
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