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Kim S, Choi BH, Shin H, Kwon K, Lee SY, Yoon HB, Kim HK, Choi Y. Plasma Exosome Analysis for Protein Mutation Identification Using a Combination of Raman Spectroscopy and Deep Learning. ACS Sens 2023; 8:2391-2400. [PMID: 37279515 DOI: 10.1021/acssensors.3c00681] [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] [Indexed: 06/08/2023]
Abstract
Protein mutation detection using liquid biopsy can be simply performed periodically, making it easy to detect the occurrence of newly emerging mutations rapidly. However, it has low diagnostic accuracy since there are more normal proteins than mutated proteins in body fluids. To increase the diagnostic accuracy, we analyzed plasma exosomes using nanoplasmonic spectra and deep learning. Exosomes, a promising biomarker, are abundant in plasma and stably carry intact proteins originating from mother cells. However, the mutated exosomal proteins cannot be detected sensitively because of the subtle changes in their structure. Therefore, we obtained Raman spectra that provide molecular information about structural changes in mutated proteins. To extract the unique features of the protein from complex Raman spectra, we developed a deep-learning classification algorithm with two deep-learning models. Consequently, controls with wild-type proteins and patients with mutated proteins were classified with high accuracy. As a proof of concept, we discriminated the lung cancer patients with mutations in the epidermal growth factor receptor (EGFR), L858R, E19del, L858R + T790M, and E19del + T790M, from controls with an accuracy of 0.93. Moreover, the protein mutation status of the patients with primary (E19del, L858R) and secondary (+T790M) mutations was clearly monitored. Overall, our technique is expected to be applied as a novel method for companion diagnostic and treatment monitoring.
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Affiliation(s)
- Seungmin Kim
- Department of Biomedical Engineering, Korea University, Seoul 02841, Republic of Korea
- Interdisciplinary Program in Precision Public Health, Korea University, Seoul 02841, Republic of Korea
| | - Byeong Hyeon Choi
- Korea Artificial Organ Center, Korea University, Seoul 02841, Republic of Korea
- Department of Thoracic and Cardiovascular Surgery, College of Medicine, Korea University Guro Hospital, Korea University, Seoul 08308, Republic of Korea
| | - Hyunku Shin
- Exopert Corporation, Seoul 02580, Republic of Korea
| | - Kihun Kwon
- Exopert Corporation, Seoul 02580, Republic of Korea
| | - Sung Yong Lee
- Division of Respiratory and Critical Care, Department of Internal Medicine, Guro Hospital, Korea University, Seoul 08308, Republic of Korea
| | - Hyun Bin Yoon
- Department of Chemical Engineering, Kyonggi University, Suwon 16227, Republic of Korea
| | - Hyun Koo Kim
- Korea Artificial Organ Center, Korea University, Seoul 02841, Republic of Korea
- Department of Thoracic and Cardiovascular Surgery, College of Medicine, Korea University Guro Hospital, Korea University, Seoul 08308, Republic of Korea
| | - Yeonho Choi
- Department of Biomedical Engineering, Korea University, Seoul 02841, Republic of Korea
- Interdisciplinary Program in Precision Public Health, Korea University, Seoul 02841, Republic of Korea
- Exopert Corporation, Seoul 02580, Republic of Korea
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2
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Černe K, Kelhar N, Resnik N, Herzog M, Vodnik L, Veranič P, Kobal B. Characteristics of Extracellular Vesicles from a High-Grade Serous Ovarian Cancer Cell Line Derived from a Platinum-Resistant Patient as a Potential Tool for Aiding the Prediction of Responses to Chemotherapy. Pharmaceuticals (Basel) 2023; 16:907. [PMID: 37375854 DOI: 10.3390/ph16060907] [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: 05/02/2023] [Revised: 06/02/2023] [Accepted: 06/15/2023] [Indexed: 06/29/2023] Open
Abstract
Platinum-resistant high-grade serous ovarian cancer (HGSOC) is invariably a fatal disease. A central goal of ovarian cancer research is therefore to develop new strategies to overcome platinum resistance. Treatment is thus moving towards personalized therapy. However, validated molecular biomarkers that predict patients' risk of developing platinum resistance are still lacking. Extracellular vesicles (EVs) are promising candidate biomarkers. EpCAM-specific EVs are largely unexplored biomarkers for predicting chemoresistance. Using transmission electron microscopy, nanoparticle tracking analysis and flow cytometry, we compared the characteristics of EVs released from a cell line derived from a clinically confirmed cisplatin-resistant patient (OAW28) and EVs released from two cell lines from tumors sensitive to platinum-based chemotherapy (PEO1 and OAW42). We demonstrated that EVs released from the HGSOC cell line of chemoresistant patients exhibited greater size heterogeneity, a larger proportion of medium/large (>200 nm) Evs and a higher number of released EpCAM-positive EVs of different sizes, although the expression of EpCAM was predominant in EVs larger than 400 nm. We also found a strong positive correlation between the concentration of EpCAM-positive EVs and the expression of cellular EpCAM. These results may contribute to the prediction of platinum resistance in the future, although they should first be validated in clinical samples.
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Affiliation(s)
- Katarina Černe
- Institute of Pharmacology and Experimental Toxicology, Faculty of Medicine, University of Ljubljana, SI-1000 Ljubljana, Slovenia
| | - Nuša Kelhar
- Institute of Pharmacology and Experimental Toxicology, Faculty of Medicine, University of Ljubljana, SI-1000 Ljubljana, Slovenia
| | - Nataša Resnik
- Institute of Cell Biology, Faculty of Medicine, University of Ljubljana, SI-1000 Ljubljana, Slovenia
| | - Maruša Herzog
- Division of Gynecology and Obstetrics, University Medical Centre Ljubljana, SI-1000 Ljubljana, Slovenia
- Department of Gynecology and Obstetrics, Faculty of Medicine, University Ljubljana, SI-1000 Ljubljana, Slovenia
| | - Lana Vodnik
- Institute of Pharmacology and Experimental Toxicology, Faculty of Medicine, University of Ljubljana, SI-1000 Ljubljana, Slovenia
| | - Peter Veranič
- Institute of Cell Biology, Faculty of Medicine, University of Ljubljana, SI-1000 Ljubljana, Slovenia
| | - Borut Kobal
- Division of Gynecology and Obstetrics, University Medical Centre Ljubljana, SI-1000 Ljubljana, Slovenia
- Department of Gynecology and Obstetrics, Faculty of Medicine, University Ljubljana, SI-1000 Ljubljana, Slovenia
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Paramanantham A, Asfiya R, Das S, McCully G, Srivastava A. Extracellular Vesicle (EVs) Associated Non-Coding RNAs in Lung Cancer and Therapeutics. Int J Mol Sci 2022; 23:13637. [PMID: 36362424 PMCID: PMC9655370 DOI: 10.3390/ijms232113637] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 10/26/2022] [Indexed: 08/13/2023] Open
Abstract
Lung cancer is one of the most lethal forms of cancer, with a very high mortality rate. The precise pathophysiology of lung cancer is not well understood, and pertinent information regarding the initiation and progression of lung cancer is currently a crucial area of scientific investigation. Enhanced knowledge about the disease will lead to the development of potent therapeutic interventions. Extracellular vesicles (EVs) are membrane-bound heterogeneous populations of cellular entities that are abundantly produced by all cells in the human body, including the tumor cells. A defined class of EVs called small Extracellular Vesicles (sEVs or exosomes) carries key biomolecules such as RNA, DNA, Proteins and Lipids. Exosomes, therefore, mediate physiological activities and intracellular communication between various cells, including constituent cells of the tumor microenvironment, namely stromal cells, immunological cells, and tumor cells. In recent years, a surge in studying tumor-associated non-coding RNAs (ncRNAs) has been observed. Subsequently, studies have also reported that exosomes abundantly carry different species of ncRNAs and these exosomal ncRNAs are functionally involved in cancer initiation and progression. Here, we discuss the function of exosomal ncRNAs, such as miRNAs and long non-coding RNAs, in the pathophysiology of lung tumors. Further, the future application of exosomal-ncRNAs in clinics as biomarkers and therapeutic targets in lung cancer is also discussed due to the multifaceted influence of exosomes on cellular physiology.
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Affiliation(s)
- Anjugam Paramanantham
- Department of Pathology and Anatomical Sciences, University of Missouri School of Medicine, Columbia, MO 65212, USA
| | - Rahmat Asfiya
- Department of Pathology and Anatomical Sciences, University of Missouri School of Medicine, Columbia, MO 65212, USA
| | - Siddharth Das
- Department of Pathology and Anatomical Sciences, University of Missouri School of Medicine, Columbia, MO 65212, USA
| | - Grace McCully
- Department of Pathology and Anatomical Sciences, University of Missouri School of Medicine, Columbia, MO 65212, USA
| | - Akhil Srivastava
- Department of Pathology and Anatomical Sciences, University of Missouri School of Medicine, Columbia, MO 65212, USA
- Ellis Fischel Cancer Center, University of Missouri School of Medicine, Columbia, MO 65212, USA
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Recent Developments of Circulating Tumor Cell Analysis for Monitoring Cutaneous Melanoma Patients. Cancers (Basel) 2022; 14:cancers14040859. [PMID: 35205608 PMCID: PMC8870206 DOI: 10.3390/cancers14040859] [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] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 02/04/2022] [Accepted: 02/06/2022] [Indexed: 02/04/2023] Open
Abstract
Simple Summary Circulating tumor cells (CTCs) originating from cutaneous melanoma patients have been studied for several decades as surrogates for real-time clinical status and disease outcomes. Here, we will review clinical studies from the last 15 years that assessed CTCs and disease outcomes for melanoma patients. Assessment of multiple molecular melanoma-associated antigen (MAA) markers by quantitative reverse transcriptase-polymerase chain reaction (RT-PCR) was the most common assay allowing for the improvement of assay sensitivity, to address tumor heterogeneity, and to predict patient outcomes. Multicenter studies demonstrate the utility of CTC assays reducing the bias observed in single-center trials. Recent development of CTC enrichment platforms has provided reproducible methods. CTC assessment enables both multiple mRNAs and DNAs genomic profiling. CTC provides specific important translational information on tumor progression, prediction of treatment response, and survival outcomes for cutaneous melanoma patients. Abstract Circulating tumor cells (CTCs) have been studied using multiple technical approaches for interrogating various cancers, as they allow for the real-time assessment of tumor progression, disease recurrence, treatment response, and tumor molecular profiling without the need for a tumor tissue biopsy. Here, we will review studies from the last 15 years on the assessment of CTCs in cutaneous melanoma patients in relation to different clinical outcomes. The focus will be on CTC detection in blood samples obtained from cutaneous melanoma patients of different clinical stages and treatments utilizing multiple platforms. Assessment of multiple molecular melanoma-associated antigen (MAA) markers by quantitative reverse transcriptase-polymerase chain reaction (RT-PCR) was the most common assay allowing for the improvement of assay sensitivity, tumor heterogeneity, and to predict patient outcomes. Multicenter studies demonstrate the utility of CTC assays reducing the bias observed in single- center trials. The recent development of CTC enrichment platforms has provided reproducible methods. CTC assessment enables both multiple mRNAs and DNAs genomic aberration profiling. CTC provides specific important translational information on tumor progression, prediction of treatment response, and survival outcomes for cutaneous melanoma patients. The molecular studies on melanoma CTCs have provided and may set standards for other solid tumor CTC analyses.
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Marvaso G, Volpe S, Pepa M, Zaffaroni M, Corrao G, Augugliaro M, Nolè F, De Cobelli O, Jereczek-Fossa BA. Recent Advances in the Management of Hormone-Sensitive Oligometastatic Prostate Cancer. Cancer Manag Res 2022; 14:89-101. [PMID: 35023972 PMCID: PMC8747627 DOI: 10.2147/cmar.s321136] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Accepted: 12/08/2021] [Indexed: 12/11/2022] Open
Abstract
After primary treatment for prostate cancer with either radical prostatectomy or radiotherapy, a significant proportion of patients are at risk of developing metastases. In recent years, a deeper understanding of the underlying biology together with improved imaging techniques and the advent of new therapeutic options including metastases-directed therapies and new drugs have revolutionized the management of low-burden metastatic disease, also known as oligometastatic state. The purpose of this narrative review is to report the recent developments in the management of hormone-sensitive oligometastatic prostate cancer patients.
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Affiliation(s)
- Giulia Marvaso
- Division of Radiation Oncology, IEO European Institute of Oncology IRCCS, Milan, Italy.,Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
| | - Stefania Volpe
- Division of Radiation Oncology, IEO European Institute of Oncology IRCCS, Milan, Italy.,Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
| | - Matteo Pepa
- Division of Radiation Oncology, IEO European Institute of Oncology IRCCS, Milan, Italy
| | - Mattia Zaffaroni
- Division of Radiation Oncology, IEO European Institute of Oncology IRCCS, Milan, Italy
| | - Giulia Corrao
- Division of Radiation Oncology, IEO European Institute of Oncology IRCCS, Milan, Italy.,Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
| | - Matteo Augugliaro
- Division of Radiation Oncology, IEO European Institute of Oncology IRCCS, Milan, Italy
| | - Franco Nolè
- Medical Oncology Division of Urogenital & Head & Neck Tumors, IEO European Institute of Oncology IRCCS, Milan, Italy
| | - Ottavio De Cobelli
- Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy.,Department of Urology, IEO, European Institute of Oncology IRCCS, Milan, Italy
| | - Barbara Alicja Jereczek-Fossa
- Division of Radiation Oncology, IEO European Institute of Oncology IRCCS, Milan, Italy.,Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
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6
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Corrao G, Zaffaroni M, Bergamaschi L, Augugliaro M, Volpe S, Pepa M, Bonizzi G, Pece S, Amodio N, Mistretta FA, Luzzago S, Musi G, Alessi S, La Fauci FM, Tordonato C, Tosoni D, Cattani F, Gandini S, Petralia G, Pravettoni G, De Cobelli O, Viale G, Orecchia R, Marvaso G, Jereczek-Fossa BA. Exploring miRNA Signature and Other Potential Biomarkers for Oligometastatic Prostate Cancer Characterization: The Biological Challenge behind Clinical Practice. A Narrative Review. Cancers (Basel) 2021; 13:cancers13133278. [PMID: 34208918 PMCID: PMC8267686 DOI: 10.3390/cancers13133278] [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: 04/29/2021] [Revised: 06/16/2021] [Accepted: 06/24/2021] [Indexed: 02/07/2023] Open
Abstract
Simple Summary The oligometastatic prostate cancer state is defined as the presence of a number of lesions ≤ 5 and has been significantly correlated with better survival if compared to a number of metastases > 5. In particular, patients in an oligometastatic setting could benefit from a metastates directed therapy, which could control the disease delaying the start of systemic therapies. For this reason, the selection of true-oligometastatic patients who could benefit from such approach is particularly important in this setting. The aim of the present narrative review is to report the current state of the art on the liquid biopsy-derived analytes and their reliability as biomarkers in the clinics for the identification of true-oligometastatic patients. This kind of molecular profiling could refine current developments in the era of precision oncology allowing patients’ stratification and leading to more refined therapeutic strategies. Abstract In recent years, a growing interest has been directed towards oligometastatic prostate cancer (OMPC), as patients with three to five metastatic lesions have shown a significantly better survival as compared with those harboring a higher number of lesions. The efficacy of local ablative treatments directed on metastatic lesions (metastases-directed treatments) was extensively investigated, with the aim of preventing further disease progression and delaying the start of systemic androgen deprivation therapies. Definitive diagnosis of prostate cancer is traditionally based on histopathological analysis. Nevertheless, a bioptic sample—static in nature—inevitably fails to reflect the dynamics of the tumor and its biological response due to the dynamic selective pressure of cancer therapies, which can profoundly influence spatio-temporal heterogeneity. Furthermore, even with new imaging technologies allowing an increasingly early detection, the diagnosis of oligometastasis is currently based exclusively on radiological investigations. Given these premises, the development of minimally-invasive liquid biopsies was recently promoted and implemented as predictive biomarkers both for clinical decision-making at pre-treatment (baseline assessment) and for monitoring treatment response during the clinical course of the disease. Through liquid biopsy, different biomarkers, commonly extracted from blood, urine or saliva, can be characterized and implemented in clinical routine to select targeted therapies and assess treatment response. Moreover, this approach has the potential to act as a tissue substitute and to accelerate the identification of novel and consistent predictive analytes cost-efficiently. However, the utility of tumor profiling is currently limited in OMPC due to the lack of clinically validated predictive biomarkers. In this scenario, different ongoing trials, such as the RADIOSA trial, might provide additional insights into the biology of the oligometastatic state and on the identification of novel biomarkers for the outlining of true oligometastatic patients, paving the way towards a wider ideal approach of personalized medicine. The aim of the present narrative review is to report the current state of the art on the solidity of liquid biopsy-related analytes such as CTCs, cfDNA, miRNA and epi-miRNA, and to provide a benchmark for their further clinical implementation. Arguably, this kind of molecular profiling could refine current developments in the era of precision oncology and lead to more refined therapeutic strategies in this subset of oligometastatic patients.
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Affiliation(s)
- Giulia Corrao
- Division of Radiation Oncology, IEO, European Institute of Oncology IRCCS, Via Ripamonti 435, 20141 Milan, Italy; (G.C.); (M.Z.); (L.B.); (S.V.); (M.P.); (G.M.); (B.A.J.-F.)
- Department of Oncology and Hemato-Oncology, University of Milan, 20141 Milan, Italy; (S.P.); (G.M.); (C.T.); (G.P.); (G.P.); (O.D.C.); (G.V.)
| | - Mattia Zaffaroni
- Division of Radiation Oncology, IEO, European Institute of Oncology IRCCS, Via Ripamonti 435, 20141 Milan, Italy; (G.C.); (M.Z.); (L.B.); (S.V.); (M.P.); (G.M.); (B.A.J.-F.)
| | - Luca Bergamaschi
- Division of Radiation Oncology, IEO, European Institute of Oncology IRCCS, Via Ripamonti 435, 20141 Milan, Italy; (G.C.); (M.Z.); (L.B.); (S.V.); (M.P.); (G.M.); (B.A.J.-F.)
- Department of Oncology and Hemato-Oncology, University of Milan, 20141 Milan, Italy; (S.P.); (G.M.); (C.T.); (G.P.); (G.P.); (O.D.C.); (G.V.)
| | - Matteo Augugliaro
- Division of Radiation Oncology, IEO, European Institute of Oncology IRCCS, Via Ripamonti 435, 20141 Milan, Italy; (G.C.); (M.Z.); (L.B.); (S.V.); (M.P.); (G.M.); (B.A.J.-F.)
- Correspondence:
| | - Stefania Volpe
- Division of Radiation Oncology, IEO, European Institute of Oncology IRCCS, Via Ripamonti 435, 20141 Milan, Italy; (G.C.); (M.Z.); (L.B.); (S.V.); (M.P.); (G.M.); (B.A.J.-F.)
- Department of Oncology and Hemato-Oncology, University of Milan, 20141 Milan, Italy; (S.P.); (G.M.); (C.T.); (G.P.); (G.P.); (O.D.C.); (G.V.)
| | - Matteo Pepa
- Division of Radiation Oncology, IEO, European Institute of Oncology IRCCS, Via Ripamonti 435, 20141 Milan, Italy; (G.C.); (M.Z.); (L.B.); (S.V.); (M.P.); (G.M.); (B.A.J.-F.)
| | - Giuseppina Bonizzi
- Department of Pathology, IEO, European Institute of Oncology IRCCS, 20141 Milan, Italy;
| | - Salvatore Pece
- Department of Oncology and Hemato-Oncology, University of Milan, 20141 Milan, Italy; (S.P.); (G.M.); (C.T.); (G.P.); (G.P.); (O.D.C.); (G.V.)
- Novel Diagnostics Program, IEO, European Institute of Oncology IRCCS, 20141 Milan, Italy;
| | - Nicola Amodio
- Department of Experimental and Clinical Medicine, Magna Graecia University of Catanzaro, 88100 Catanzaro, Italy;
| | | | - Stefano Luzzago
- Department of Urology, IEO, European Institute of Oncology IRCCS, 20141 Milan, Italy; (F.A.M.); (S.L.)
| | - Gennaro Musi
- Department of Oncology and Hemato-Oncology, University of Milan, 20141 Milan, Italy; (S.P.); (G.M.); (C.T.); (G.P.); (G.P.); (O.D.C.); (G.V.)
- Department of Urology, IEO, European Institute of Oncology IRCCS, 20141 Milan, Italy; (F.A.M.); (S.L.)
| | - Sarah Alessi
- Division of Radiology, IEO, European Institute of Oncology IRCCS, 20141 Milan, Italy;
| | - Francesco Maria La Fauci
- Unit of Medical Physics IEO, European Institute of Oncology IRCCS, 20141 Milan, Italy; (F.M.L.F.); (F.C.)
| | - Chiara Tordonato
- Department of Oncology and Hemato-Oncology, University of Milan, 20141 Milan, Italy; (S.P.); (G.M.); (C.T.); (G.P.); (G.P.); (O.D.C.); (G.V.)
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, 20141 Milan, Italy;
| | - Daniela Tosoni
- Novel Diagnostics Program, IEO, European Institute of Oncology IRCCS, 20141 Milan, Italy;
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, 20141 Milan, Italy;
| | - Federica Cattani
- Unit of Medical Physics IEO, European Institute of Oncology IRCCS, 20141 Milan, Italy; (F.M.L.F.); (F.C.)
| | - Sara Gandini
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, 20141 Milan, Italy;
| | - Giuseppe Petralia
- Department of Oncology and Hemato-Oncology, University of Milan, 20141 Milan, Italy; (S.P.); (G.M.); (C.T.); (G.P.); (G.P.); (O.D.C.); (G.V.)
- Division of Radiology, IEO, European Institute of Oncology IRCCS, 20141 Milan, Italy;
| | - Gabriella Pravettoni
- Department of Oncology and Hemato-Oncology, University of Milan, 20141 Milan, Italy; (S.P.); (G.M.); (C.T.); (G.P.); (G.P.); (O.D.C.); (G.V.)
- Applied Research Division for Cognitive and Psychological Science, IEO, European Institute of Oncology IRCCS, 20141 Milan, Italy
| | - Ottavio De Cobelli
- Department of Oncology and Hemato-Oncology, University of Milan, 20141 Milan, Italy; (S.P.); (G.M.); (C.T.); (G.P.); (G.P.); (O.D.C.); (G.V.)
- Department of Urology, IEO, European Institute of Oncology IRCCS, 20141 Milan, Italy; (F.A.M.); (S.L.)
| | - Giuseppe Viale
- Department of Oncology and Hemato-Oncology, University of Milan, 20141 Milan, Italy; (S.P.); (G.M.); (C.T.); (G.P.); (G.P.); (O.D.C.); (G.V.)
- Department of Pathology, IEO, European Institute of Oncology IRCCS, 20141 Milan, Italy;
| | - Roberto Orecchia
- Scientific Direction, IEO, European Institute of Oncology IRCCS, 20141 Milan, Italy;
| | - Giulia Marvaso
- Division of Radiation Oncology, IEO, European Institute of Oncology IRCCS, Via Ripamonti 435, 20141 Milan, Italy; (G.C.); (M.Z.); (L.B.); (S.V.); (M.P.); (G.M.); (B.A.J.-F.)
- Department of Oncology and Hemato-Oncology, University of Milan, 20141 Milan, Italy; (S.P.); (G.M.); (C.T.); (G.P.); (G.P.); (O.D.C.); (G.V.)
| | - Barbara Alicja Jereczek-Fossa
- Division of Radiation Oncology, IEO, European Institute of Oncology IRCCS, Via Ripamonti 435, 20141 Milan, Italy; (G.C.); (M.Z.); (L.B.); (S.V.); (M.P.); (G.M.); (B.A.J.-F.)
- Department of Oncology and Hemato-Oncology, University of Milan, 20141 Milan, Italy; (S.P.); (G.M.); (C.T.); (G.P.); (G.P.); (O.D.C.); (G.V.)
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Jensen SG, Epistolio S, Madsen CL, Kyneb MH, Riva A, Paganotti A, Barizzi J, Petersen RK, Børgesen M, Molinari F, Boldorini R, Lorenzen J, Sørensen E, Christensen UB, Høgdall E, Frattini M. A new sensitive and fast assay for the detection of EGFR mutations in liquid biopsies. PLoS One 2021; 16:e0253687. [PMID: 34166445 PMCID: PMC8224962 DOI: 10.1371/journal.pone.0253687] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Accepted: 06/10/2021] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND A major perspective for the use of circulating tumor DNA (ctDNA) in the clinical setting of non-small cell lung cancer (NSCLC) is expected as predictive factor for resistance and response to EGFR TKI therapy and, especially, as a non-invasive alternative to tissue biopsy. However, ctDNA is both highly fragmented and mostly low concentrated in plasma and serum. On this basis, it is important to use a platform characterized by high sensitivity and linear performance in the low concentration range. This motivated us to evaluate the newly developed and commercially available SensiScreen® EGFR Liquid assay platform (PentaBase) with regard to sensitivity, linearity, repeatability and accuracy and finally to compare it to our already implemented methods. The validation was made in three independent European laboratories using two cohorts on a total of 68 unique liquid biopsies. RESULTS Using artificial samples containing 1600 copies of WT DNA spiked with 50% - 0.1% of mutant copies across a seven-log dilution scale, we assessed the sensitivity, linearity, repeatability and accuracy for the p.T790M, p.L858R and exon 19 deletion assays of the SensiScreen® EGFR Liquid assay platform. The lowest value detectable ranged from 0.5% to 0.1% with R2≥0,97 indicating good linearity. High PCR efficiency was shown for all three assays. In 102 single PCRs each containing theoretical one copy of the mutant at initiating, assays showed repeatable positivity in 75.5% - 80.4% of reactions. At low ctDNA levels, as in plasma, the SensiScreen® EGFR Liquid assay platform showed better sensitivity than the Therascreen® EGFR platform (Qiagen) and equal performance to the ctEGFR Mutation Detection Kit (EntroGen) and the IOT® Oncomine cell-free nucleic acids assay (Thermo Fisher Scientific) with 100% concordance at the sequence level. CONCLUSION For profiling clinical plasma samples, characterized by low ctDNA abundance, the SensiScreen® EGFR Liquid assay is able to identify down to 1 copy of mutant alleles and with its high sensitivity, linearity and accuracy it may be a competitive platform of choice.
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Affiliation(s)
| | | | | | | | - Alice Riva
- Institute of Pathology, Locarno, Switzerland
| | - Alessia Paganotti
- Department of Pathology, ’Maggiore della Carità’ Hospital, Novara, Italy
| | | | | | | | | | - Renzo Boldorini
- Department of Pathology, ’Maggiore della Carità’ Hospital, Novara, Italy
- Department of Health Sciences, Universitá degli Studi del Piemonte Orientale "A. Avogadro", Novara, Italy
| | - Jan Lorenzen
- Life Science Division, Danish Technological Institute, Aarhus, Denmark
| | - Erik Sørensen
- Department of Clinical Immunology, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | | | - Estrid Høgdall
- Department of Pathology, Herlev—Gentofte University Hospital, Herlev, Denmark
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Zhang X, He Y, Gu H, Liu Z, Li B, Yang Y, Hao J, Hua R. Construction of a Nine-MicroRNA-Based Signature to Predict the Overall Survival of Esophageal Cancer Patients. Front Genet 2021; 12:670405. [PMID: 34093662 PMCID: PMC8170160 DOI: 10.3389/fgene.2021.670405] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Accepted: 03/22/2021] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Esophageal cancer (EC) is a common malignant tumor. MicroRNAs (miRNAs) play a key role in the occurrence and metastasis and are closely related to the prognosis of EC. Therefore, it will provide a powerful tool to predict the overall survival (OS) of EC patients based on miRNAs expression in EC tissues and blood samples. METHODS Five independent databases, TCGA, GSE106817, GSE113486, GSE122497, and GSE112264, were used to construct nine-miRna signature and nomograms for prognosis. The bioinformatics analysis was used to predict the enrichment pathways of targets. RESULTS A total of 132 overexpressed miRNAs and 23 suppressed miRNAs showed significant differential expression in both EC serum and tissue samples compared with normal samples. We also showed that nine miRNAs were related to the prognosis of EC. Higher levels of miR-15a-5p, miR-92a-3p, miR-92a-1-5p, miR-590-5p, miR-324-5p, miR-25-3p, miR-181b-5p, miR-421, and miR-93-5p were correlated to the shorter survival time in patients with EC. In addition, we constructed a risk prediction model based on the levels of nine differentially expressed miRNAs (DEMs) and found that the OS time of EC patients with high-risk score was shorter than that of EC patients with low-risk score. Furthermore, our results showed that the risk prediction scores of EC samples were higher than those of normal samples. Finally, the area under the curve (AUC) was used to analyze the risk characteristics of EC and normal controls. By calculating the AUC and the calibration curve, the RNA signature showed a good performance. Bioinformatics analysis showed that nine DEMs were associated with several crucial signaling, including p53, FoxO, PI3K-Akt, HIF-1, and TORC1 signaling. Finally, 14 messenger RNAs (mRNAs) were identified as hub targets of nine miRNAs, including BTRC, SIAH1, RNF138, CDC27, NEDD4L, MKRN1, RLIM, FBXO11, RNF34, MYLIP, FBXW7, RNF4, UBE3C, and RNF111. TCGA dataset validation showed that these hub targets were significantly differently expressed in EC tissues compared with normal samples. CONCLUSION We have constructed maps and nomograms of nine-miRna risk signals associated with EC prognosis. Bioinformatics analysis revealed that nine DEMs were associated with several crucial signaling, including p53, FoxO, PI3K-Akt, HIF-1, and TORC1 signaling, in EC. We think that this study will provide clinicians with an effective decision-making tool.
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Affiliation(s)
- Xiaobin Zhang
- Department of Thoracic Surgery, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China
- Department of Cardiovascular Surgery, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Yi He
- Department of Thoracic Surgery, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Haiyong Gu
- Department of Thoracic Surgery, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Zhichao Liu
- Department of Thoracic Surgery, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Bin Li
- Department of Thoracic Surgery, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Yang Yang
- Department of Thoracic Surgery, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Jie Hao
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, China
| | - Rong Hua
- Department of Thoracic Surgery, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China
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9
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Chatfield-Reed K, Roche VP, Pan Q. cfDNA detection for HPV+ squamous cell carcinomas. Oral Oncol 2021; 115:104958. [PMID: 33582486 PMCID: PMC8331111 DOI: 10.1016/j.oraloncology.2020.104958] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2020] [Revised: 08/03/2020] [Accepted: 08/04/2020] [Indexed: 12/13/2022]
Abstract
High-risk human papillomavirus (HPV) is an etiologic factor in a spectrum of squamous cell carcinomas including anal, cervical, and oropharyngeal. HPV cell free DNA (cfDNA) is shed from the primary tumor into systemic circulation and can be detected using several platforms including quantitative PCR, digital droplet PCR, or next generation sequencing. Levels of HPV cfDNA at time of initial presentation is associated with known poor prognostic clinicopathologic variables, such as advanced stage and, locoregional and distant metastases. Moreover, longitudinal sampling revealed that persistent or increasing HPV cfDNA levels are indicative of treatment relapse and, in some studies, HPV cfDNA detection predicted treatment failures prior to routine post-treatment clinical imaging. A liquid biopsy platform using HPV cfDNA offers unique advantages over traditional approaches and may have clinical utility for detection of minimum residual disease, treatment response, and disease progression in patients with HPV+ cancers.
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Affiliation(s)
- Kate Chatfield-Reed
- University Hospitals Seidman Cancer Center, Cleveland, OH 44106, United States; Department of Otolaryngology-Head and Neck Surgery, University Hospitals Cleveland Medical Center, Case Western Reserve University, School of Medicine, Cleveland, OH 44106, United States
| | - Veronique P Roche
- Department of Otolaryngology-Head and Neck Surgery, University Hospitals Cleveland Medical Center, Case Western Reserve University, School of Medicine, Cleveland, OH 44106, United States; Case Comprehensive Cancer Center, Case Western Reserve University, School of Medicine, Cleveland, OH 44106, United States
| | - Quintin Pan
- University Hospitals Seidman Cancer Center, Cleveland, OH 44106, United States; Department of Otolaryngology-Head and Neck Surgery, University Hospitals Cleveland Medical Center, Case Western Reserve University, School of Medicine, Cleveland, OH 44106, United States; Case Comprehensive Cancer Center, Case Western Reserve University, School of Medicine, Cleveland, OH 44106, United States.
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10
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Camus V, Jardin F. Cell-Free DNA for the Management of Classical Hodgkin Lymphoma. Pharmaceuticals (Basel) 2021; 14:ph14030207. [PMID: 33801462 PMCID: PMC7998645 DOI: 10.3390/ph14030207] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2021] [Revised: 02/25/2021] [Accepted: 02/26/2021] [Indexed: 12/12/2022] Open
Abstract
Cell-free DNA (cfDNA) testing, is an emerging “liquid biopsy” tool for noninvasive lymphoma detection, and an increased amount of data are now available to use this technique with accuracy, especially in classical Hodgkin lymphoma (cHL). The advantages of cfDNA include simplicity of repeated blood sample acquisition over time; dynamic, noninvasive, and quantitative analysis; fast turnover time; reasonable cost; and established consistency with results from tumor genomic DNA. cfDNA analysis offers an easy method for genotyping the overall molecular landscape of pediatric and adult cHL and may help in cases of diagnostic difficulties between cHL and other lymphomas. cfDNA levels are correlated with clinical, prognostic, and metabolic features, and may serve as a therapeutic response evaluation tool and as a minimal residual disease (MRD) biomarker in complement to positron emission tomography (PET). Indeed, cfDNA real-time monitoring by fast high-throughput techniques enables the prompt detection of refractory disease or may help to address PET residual hypermetabolic situations during or at the end of treatment. The major recent works presented and described here demonstrated the clinically meaningful applicability of cfDNA testing in diagnostic and theranostic settings, but also in disease risk assessment, therapeutic molecular response, and monitoring of cHL treatments.
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Affiliation(s)
- Vincent Camus
- Correspondence: ; Tel.: +33(0)-2-32-08-29-47; Fax: +33-(0)-2-32-08-22-83
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11
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DeCastro J, Littig J, Chou PP, Mack-Onyeike J, Srinivasan A, Conboy MJ, Conboy IM, Aran K. The Microfluidic Toolbox for Analyzing Exosome Biomarkers of Aging. Molecules 2021; 26:535. [PMID: 33498573 PMCID: PMC7864353 DOI: 10.3390/molecules26030535] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 01/04/2021] [Accepted: 01/14/2021] [Indexed: 12/30/2022] Open
Abstract
As the fields of aging and neurological disease expand to liquid biopsies, there is a need to identify informative biomarkers for the diagnosis of neurodegeneration and other age-related disorders such as cancers. A means of high-throughput screening of biomolecules relevant to aging can facilitate this discovery in complex biofluids, such as blood. Exosomes, the smallest of extracellular vesicles, are found in many biofluids and, in recent years, have been found to be excellent candidates as liquid biopsy biomarkers due to their participation in intercellular communication and various pathologies such as cancer metastasis. Recently, exosomes have emerged as novel biomarkers for age-related diseases. Hence, the study of exosomes, their protein and genetic cargo can serve as early biomarkers for age-associated pathologies, especially neurodegenerative diseases. However, a disadvantage of exosome studies includes a lack in standardization of isolating, detecting, and profiling exosomes for downstream analysis. In this review, we will address current techniques for high-throughput isolation and detection of exosomes through various microfluidic and biosensing strategies and how they may be adapted for the detection of biomarkers of age-associated disorders.
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Affiliation(s)
- Jonalyn DeCastro
- Keck Graduate Institute, The Claremont Colleges, Claremont, CA 91711, USA; (J.D.); (J.L.); (J.M.-O.)
| | - Joshua Littig
- Keck Graduate Institute, The Claremont Colleges, Claremont, CA 91711, USA; (J.D.); (J.L.); (J.M.-O.)
| | | | - Jada Mack-Onyeike
- Keck Graduate Institute, The Claremont Colleges, Claremont, CA 91711, USA; (J.D.); (J.L.); (J.M.-O.)
| | - Amrita Srinivasan
- Claremont McKenna College, The Claremont Colleges, Claremont, CA 91711, USA;
| | - Michael J. Conboy
- Department of Bioengineering, University of California, Berkeley, CA 94720, USA; (M.J.C.); (I.M.C.)
| | - Irina M. Conboy
- Department of Bioengineering, University of California, Berkeley, CA 94720, USA; (M.J.C.); (I.M.C.)
| | - Kiana Aran
- Keck Graduate Institute, The Claremont Colleges, Claremont, CA 91711, USA; (J.D.); (J.L.); (J.M.-O.)
- Department of Bioengineering, University of California, Berkeley, CA 94720, USA; (M.J.C.); (I.M.C.)
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12
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Ray SK, Mukherjee S. Cell free DNA as an evolving liquid biopsy biomarker for initial diagnosis and therapeutic nursing in Cancer- An evolving aspect in Medical Biotechnology. Curr Pharm Biotechnol 2020; 23:112-122. [PMID: 33308128 DOI: 10.2174/1389201021666201211102710] [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: 08/03/2020] [Revised: 09/26/2020] [Accepted: 10/20/2020] [Indexed: 11/22/2022]
Abstract
Cell-free DNA (cfDNA) is present in numerous body fluids in addition to initiates generally from blood cells. It is undoubtedly the utmost promising tool among all components of liquid biopsy. Liquid biopsy is a specialized method investigating the nonsolid biological tissue by revealing of circulating cells, cell free DNA etc. that enter body fluids. Since, cancer cells disengage from compact tumors circulate in peripheral blood, evaluating blood of cancer patients holds the opportunities for capture and molecular level analysis of various tumor-derived constituents. Cell free DNA samples can deliver a significant perceptions into oncology, for instance tumor heterogeneity, instantaneous tumor development, response to therapy and treatment, comprising immunotherapy and mechanisms of cancer metastasis. Malignant growth at any phase can outhouse tumor cells in addition to fragments of neoplasticity causing DNA into circulatory system giving noble sign of mutation in the tumor at sampling time. Liquid biopsy distinguishes diverse blood based evolving biomarkers comprising circulating tumor cells (CTCs), circulating tumor DNA (ctDNA) or cfDNA, circulating RNA (cfRNA) and exosomes. Cell free DNA are little DNA fragments found circulating in plasma or serum, just as other fluids present in our body. Cell free DNA involves primarily double stranded nuclear DNA and mitochondrial DNA, present both on a surface level and in the lumen of vesicles. The probable origins of the tumor-inferred portion of cfDNA are apoptosis or tumor necrosis, lysis of CTCs or release of DNA from the tumor cells into circulation. The evolution of innovations, refinement and improvement in therapeutics for determination of cfDNA fragment size and its distribution provide significant information related with pathological conditions of the cell, thus emerging as promising indicator for clinical output in medical biotechnology.
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Affiliation(s)
| | - Sukhes Mukherjee
- Department of Biochemistry. All India Institute of Medical Sciences. Bhopal, Madhya pradesh-462020. India
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13
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Freitas MO, Gartner J, Rangel-Pozzo A, Mai S. Genomic Instability in Circulating Tumor Cells. Cancers (Basel) 2020; 12:cancers12103001. [PMID: 33081135 PMCID: PMC7602879 DOI: 10.3390/cancers12103001] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 10/09/2020] [Accepted: 10/13/2020] [Indexed: 12/21/2022] Open
Abstract
Simple Summary In this review, we focus on recent advances in the detection and quantification of tumor cell heterogeneity and genomic instability of CTCs and the contribution of chromosome instability studies to genetic heterogeneity in CTCs at the single-CTC level. Abstract Circulating tumor cells (CTCs) can promote distant metastases and can be obtained through minimally invasive liquid biopsy for clinical assessment in cancer patients. Having both genomic heterogeneity and instability as common features, the genetic characterization of CTCs can serve as a powerful tool for a better understanding of the molecular changes occurring at tumor initiation and during tumor progression/metastasis. In this review, we will highlight recent advances in the detection and quantification of tumor cell heterogeneity and genomic instability in CTCs. We will focus on the contribution of chromosome instability studies to genetic heterogeneity in CTCs at the single-CTC level by discussing data from different cancer subtypes and their impact on diagnosis and precision medicine.
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Affiliation(s)
- Monique Oliveira Freitas
- Cell Biology, Research Institute of Oncology and Hematology, University of Manitoba, Cancer Care Manitoba, Winnipeg, MB R3C 2B7, Canada;
- Genetic Service, Institute of Paediatrics and Puericulture Martagão Gesteira (IPPMG), Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro 21941-912, Brazil
- Clinical Medicine Postgraduate Programme, College of Medicine, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro 21941-913, Brazil
| | - John Gartner
- Departments of Pathology and Immunology, Faculty of Health Sciences, University of Manitoba, Winnipeg, MB R3E 3P5, Canada;
| | - Aline Rangel-Pozzo
- Cell Biology, Research Institute of Oncology and Hematology, University of Manitoba, Cancer Care Manitoba, Winnipeg, MB R3C 2B7, Canada;
- Correspondence: (A.R.-P.); (S.M.); Tel.: +1-204-787-4125 (S.M.)
| | - Sabine Mai
- Cell Biology, Research Institute of Oncology and Hematology, University of Manitoba, Cancer Care Manitoba, Winnipeg, MB R3C 2B7, Canada;
- Correspondence: (A.R.-P.); (S.M.); Tel.: +1-204-787-4125 (S.M.)
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Ungerer V, Bronkhorst AJ, Holdenrieder S. Preanalytical variables that affect the outcome of cell-free DNA measurements. Crit Rev Clin Lab Sci 2020; 57:484-507. [DOI: 10.1080/10408363.2020.1750558] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Vida Ungerer
- Institute for Laboratory Medicine, German Heart Centre, Technical University Munich, Munich, Germany
| | - Abel J. Bronkhorst
- Institute for Laboratory Medicine, German Heart Centre, Technical University Munich, Munich, Germany
| | - Stefan Holdenrieder
- Institute for Laboratory Medicine, German Heart Centre, Technical University Munich, Munich, Germany
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15
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Bronkhorst AJ, Ungerer V, Holdenrieder S. Comparison of methods for the isolation of cell-free DNA from cell culture supernatant. Tumour Biol 2020; 42:1010428320916314. [PMID: 32338581 DOI: 10.1177/1010428320916314] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
In vitro characterization of cell-free DNA using two-dimensional cell culture models is emerging as an important step toward an improved understanding of the physical and biological characteristics of cell-free DNA in human biology. However, precise measurement of the cell-free DNA in cell culture medium is highly dependent on the efficacy of the method used for DNA purification, and is often a juncture of experimental confusion. Therefore, in this study, we compared six commercially available cell-free DNA isolation kits for the recovery of cell-free DNA from the cell culture supernatant of a human bone cancer cell line (143B), including two magnetic bead-based manual kits, one automated magnetic bead-based extraction method, and three manual spin-column kits. Based on cell-free DNA quantitation and sizing, using the Qubit dsDNA HS assay and Bioanalyzer HS DNA assay, respectively, the different methods showed significant variability concerning recovery, reproducibility, and size discrimination. These findings highlight the importance of selecting a cell-free DNA extraction method that is appropriate for the aims of a study. For example, mutational analysis of cell-free DNA may be enhanced by a method that favors a high yield or is biased toward the isolation of short cell-free DNA fragments. In contrast, quantitative analysis of cell-free DNA in a comparative setting (e.g. measuring the fluctuation of cell-free DNA levels over time) may require the selection of a cell-free DNA isolation method that forgoes a high recovery for high reproducibility and minimal size bias.
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Affiliation(s)
- Abel Jacobus Bronkhorst
- Institute for Laboratory Medicine, German Heart Centre, Technical University Munich, Munich, Germany
| | - Vida Ungerer
- Institute for Laboratory Medicine, German Heart Centre, Technical University Munich, Munich, Germany
| | - Stefan Holdenrieder
- Institute for Laboratory Medicine, German Heart Centre, Technical University Munich, Munich, Germany
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16
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de Melo-Silva AJ, Lucena JP, Hueneburg T. The evolution of molecular diagnosis using digital polymerase chain reaction to detect cancer via cell-free DNA and circulating tumor cells. Cell Biol Int 2019; 44:735-743. [PMID: 31829466 DOI: 10.1002/cbin.11286] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Accepted: 12/10/2019] [Indexed: 01/05/2023]
Abstract
Cancer is one of the most important causes of death worldwide. The onset of cancer may be initiated due to a variety of factors such as environment, genetics or even due to personal lifestyle choices. To counteract this tremendous increase, the demand for a new technology has risen. By this means, the use of digital polymerase chain reaction (dPCR) has been shown to be a promising methodology in the early detection of many types of cancers. Furthermore, several researchers confirmed that the use of tumor cell-free DNA (cfDNA) and circulating tumor cells (CTC) in peripheral blood is essential in revealing an early prognosis of such diseases. Besides this, it was established that dPCR might be used in a much more efficient, accurate, and reliable manner to amplify a variety of genetic material up to the identification of mutations in hematological diseases. Therefore, this article demonstrates the differences between conventional PCR and dPCR as a molecular technique to detect the early onset of cancer. Furthermore, CTC and cfDNA were officially approved by the Food and Drug Administration as new biological biomarkers in cancer development and monitoring.
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Affiliation(s)
- Alex José de Melo-Silva
- Department of Immunology, Aggeu Magalhães Institute, IAM/FIOCRUZ-PE, Recife-PE, 50670-420, Brazil
| | - Jessica Paula Lucena
- Department of Immunology, Aggeu Magalhães Institute, IAM/FIOCRUZ-PE, Recife-PE, 50670-420, Brazil
| | - Thomas Hueneburg
- University of Technology Sydney, Sydney, 2007, Australia.,Department of Microbiology and Immunology, University of Melbourne, Melbourne-Vic, 3010 Parkeville VIC, Australia
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Abstract
The technique of cell-free DNA (cfDNA) analysis, also called liquid biopsy, has been developed over the past several years to serve as a minimal residual disease tool, as has already been done with reliability and robustness in acute leukemias. This technique has important theoretical advantages, including the simplicity of acquiring blood samples, which can easily be repeated over time, its noninvasive and quantitative nature, which provides results consistent with the results obtained from tumor genomic DNA, and its speed and low cost. cfDNA analysis, as the leading tool to quantify somatic mutations, is a major technological leap in the noninvasive management of lymphomas. This technology may empower monitoring and treatment adjustment in real time and enable the quick detection of refractory lymphomas and resistance to routine therapies. Here, we summarize the results that have established the clinical relevance of cfDNA in diagnostic and prognostic stratification and the monitoring of lymphoma treatments.
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Affiliation(s)
- Vincent Camus
- Department of Hematology, Centre Henri Becquerel, 1 Rue D'Amiens, 76038 Rouen Cedex, France
| | - Fabrice Jardin
- Department of Hematology, Centre Henri Becquerel, 1 Rue D'Amiens, 76038 Rouen Cedex, France
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18
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Ciruelos E, Pérez-García JM, Gavilá J, Rodríguez A, de la Haba-Rodriguez J. Maintenance Therapy in HER2-Negative Metastatic Breast Cancer: A New Approach for an Old Concept. Clin Drug Investig 2019; 39:595-606. [PMID: 31054086 DOI: 10.1007/s40261-019-00790-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The aim of this article is to discuss the role of maintenance therapy with chemotherapy, endocrine therapy, or bevacizumab-based combination therapy in patients with human epidermal growth factor receptor 2 (HER2)-negative metastatic breast cancer. The optimization of maintenance therapy in patients with HER2-negative metastatic breast cancer must be based on disease profile (tumor subtype and endocrine-sensitive status), the prior use of bevacizumab-containing regimens, and the number of prognostic risk factors. Chemotherapy should be used in patients with triple-negative breast cancer and endocrine-resistant hormone receptor-positive metastatic breast cancer, whereas endocrine therapy is the preferred option for patients with endocrine-sensitive hormone receptor-positive metastatic breast cancer. After first-line bevacizumab plus chemotherapy, bevacizumab may be continued until disease progression or unacceptable toxicity, and endocrine therapy or capecitabine may be added. The goals of maintenance therapy in patients with HER2-negative metastatic breast cancer are to improve and maintain clinical response, increase time to progression, extend overall survival, relieve tumor-related symptoms, and delay the use of aggressive therapies, without compromising quality of life. Maintenance therapy, using chemotherapy, endocrine therapy, and combined therapy with bevacizumab, is a reasonable strategy to achieve these goals in patients with either triple-negative breast cancer or hormone receptor-positive and HER2-negative metastatic breast cancer. Ongoing clinical studies of new molecular-targeted therapies may provide additional pharmacological options for future maintenance strategies in these patients.
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Affiliation(s)
- Eva Ciruelos
- Medical Oncology Department, Hospital Universitario 12 de Octubre, Madrid, Spain
| | - José Manuel Pérez-García
- IOB Institute of Oncology, Quiron University Hospital, Plaza Alfonso Comin 5-7, 08023, Barcelona, Spain.
| | | | | | - Juan de la Haba-Rodriguez
- Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBIC), Hospital Universitario Reina Sofía, Centro de Investigación Biomédica en Red de Oncología, CIBERONC-ISCIII, Universidad de Córdoba, Córdoba, Spain
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19
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Ahn SB, Sharma S, Mohamedali A, Mahboob S, Redmond WJ, Pascovici D, Wu JX, Zaw T, Adhikari S, Vaibhav V, Nice EC, Baker MS. Potential early clinical stage colorectal cancer diagnosis using a proteomics blood test panel. Clin Proteomics 2019; 16:34. [PMID: 31467500 PMCID: PMC6712843 DOI: 10.1186/s12014-019-9255-z] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Accepted: 08/14/2019] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND One of the most significant challenges in colorectal cancer (CRC) management is the use of compliant early stage population-based diagnostic tests as adjuncts to confirmatory colonoscopy. Despite the near curative nature of early clinical stage surgical resection, mortality remains unacceptably high-as the majority of patients diagnosed by faecal haemoglobin followed by colonoscopy occur at latter stages. Additionally, current population-based screens reliant on fecal occult blood test (FOBT) have low compliance (~ 40%) and tests suffer low sensitivities. Therefore, blood-based diagnostic tests offer survival benefits from their higher compliance (≥ 97%), if they can at least match the sensitivity and specificity of FOBTs. However, discovery of low abundance plasma biomarkers is difficult due to occupancy of a high percentage of proteomic discovery space by many high abundance plasma proteins (e.g., human serum albumin). METHODS A combination of high abundance protein ultradepletion (e.g., MARS-14 and an in-house IgY depletion columns) strategies, extensive peptide fractionation methods (SCX, SAX, High pH and SEC) and SWATH-MS were utilized to uncover protein biomarkers from a cohort of 100 plasma samples (i.e., pools of 20 healthy and 20 stages I-IV CRC plasmas). The differentially expressed proteins were analyzed using ANOVA and pairwise t-tests (p < 0.05; fold-change > 1.5), and further examined with a neural network classification method using in silico augmented 5000 patient datasets. RESULTS Ultradepletion combined with peptide fractionation allowed for the identification of a total of 513 plasma proteins, 8 of which had not been previously reported in human plasma (based on PeptideAtlas database). SWATH-MS analysis revealed 37 protein biomarker candidates that exhibited differential expression across CRC stages compared to healthy controls. Of those, 7 candidates (CST3, GPX3, CFD, MRC1, COMP, PON1 and ADAMDEC1) were validated using Western blotting and/or ELISA. The neural network classification narrowed down candidate biomarkers to 5 proteins (SAA2, APCS, APOA4, F2 and AMBP) that had maintained accuracy which could discern early (I/II) from late (III/IV) stage CRC. CONCLUSION MS-based proteomics in combination with ultradepletion strategies have an immense potential of identifying diagnostic protein biosignature.
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Affiliation(s)
- Seong Beom Ahn
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, Level 1, 75 Talavera Road, Sydney, NSW 2109 Australia
| | - Samridhi Sharma
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, Level 1, 75 Talavera Road, Sydney, NSW 2109 Australia
| | - Abidali Mohamedali
- Department of Molecular Sciences, Faculty of Science and Engineering, Macquarie University, Sydney, NSW 2109 Australia
| | - Sadia Mahboob
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, Level 1, 75 Talavera Road, Sydney, NSW 2109 Australia
| | - William J. Redmond
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, Level 1, 75 Talavera Road, Sydney, NSW 2109 Australia
| | - Dana Pascovici
- Australian Proteome Analysis Facility (APAF), Department of Molecular Sciences, Faculty of Science and Engineering, Macquarie University, Sydney, NSW 2109 Australia
| | - Jemma X. Wu
- Australian Proteome Analysis Facility (APAF), Department of Molecular Sciences, Faculty of Science and Engineering, Macquarie University, Sydney, NSW 2109 Australia
| | - Thiri Zaw
- Australian Proteome Analysis Facility (APAF), Department of Molecular Sciences, Faculty of Science and Engineering, Macquarie University, Sydney, NSW 2109 Australia
| | - Subash Adhikari
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, Level 1, 75 Talavera Road, Sydney, NSW 2109 Australia
| | - Vineet Vaibhav
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, Level 1, 75 Talavera Road, Sydney, NSW 2109 Australia
| | - Edouard C. Nice
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, VIC 3800 Australia
| | - Mark S. Baker
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, Level 1, 75 Talavera Road, Sydney, NSW 2109 Australia
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Stelcer E, Konkol M, Głȩboka A, Suchorska WM. Liquid Biopsy in Oligometastatic Prostate Cancer-A Biologist's Point of View. Front Oncol 2019; 9:775. [PMID: 31475117 PMCID: PMC6702517 DOI: 10.3389/fonc.2019.00775] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Accepted: 07/31/2019] [Indexed: 12/13/2022] Open
Abstract
Prostate cancer (PCa) is the main cause of cancer-related mortality in males and the diagnosis, treatment, and care of these patients places a great burden on healthcare systems globally. Clinically, PCa is highly heterogeneous, ranging from indolent tumors to highly aggressive disease. In many cases treatment-generally either radiotherapy (RT) or surgery-can be curative. Several key genetic and demographic factors such as age, family history, genetic susceptibility, and race are associated with a high incidence of PCa. While our understanding of PCa, which is mainly based on the tools of molecular biology-has improved dramatically in recent years, efforts to better understand this complex disease have led to the identification of a new type of PCa-oligometastatic PCa. Oligometastatic disease should be considered an individual, heterogeneous entity with distinct metastatic phenotypes and, consequently, wide prognostic variability. In general, patients with oligometastatic disease typically present less biologically aggressive tumors whose metastatic potential is more limited and which are slow-growing. These patients are good candidates for more aggressive treatment approaches. The main aim of the presented review was to evaluate the utility of liquid biopsy for diagnostic purposes in PCa and for use in monitoring disease progression and treatment response, particularly in patients with oligometastatic PCa. Liquid biopsies offer a rapid, non-invasive approach whose use t is expected to play an important role in routine clinical practice to benefit patients. However, more research is needed to resolve the many existing discrepancies with regard to the definition and isolation method for specific biomarkers, as well as the need to determine the most appropriate markers. Consequently, the current priority in this field is to standardize liquid biopsy-based techniques. This review will help to improve understanding of the biology of PCa, particularly the recently defined condition known as "oligometastatic PCa". The presented review of the body of evidence suggests that additional research in molecular biology may help to establish novel treatments for oligometastatic PCa. In the near future, the treatment of PCa will require an interdisciplinary approach involving active cooperation among clinicians, physicians, and biologists.
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Affiliation(s)
- Ewelina Stelcer
- Radiobiology Laboratory, Greater Poland Cancer Centre, Poznan, Poland
- Department of Electroradiology, Poznan University of Medical Sciences, Poznan, Poland
- Department of Histology and Embryology, Poznan University of Medical Sciences, Poznan, Poland
| | - Marek Konkol
- Department of Electroradiology, Poznan University of Medical Sciences, Poznan, Poland
- Radiation Oncology Department, Greater Poland Cancer Centre, Poznan, Poland
| | | | - Wiktoria Maria Suchorska
- Radiobiology Laboratory, Greater Poland Cancer Centre, Poznan, Poland
- Department of Electroradiology, Poznan University of Medical Sciences, Poznan, Poland
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21
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Medeiros B, Allan AL. Molecular Mechanisms of Breast Cancer Metastasis to the Lung: Clinical and Experimental Perspectives. Int J Mol Sci 2019; 20:E2272. [PMID: 31071959 PMCID: PMC6540248 DOI: 10.3390/ijms20092272] [Citation(s) in RCA: 132] [Impact Index Per Article: 26.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2019] [Revised: 05/01/2019] [Accepted: 05/06/2019] [Indexed: 12/24/2022] Open
Abstract
Breast cancer is the most commonly diagnosed cancer in women worldwide, and >90% of breast cancer-related deaths are associated with metastasis. Breast cancer spreads preferentially to the lung, brain, bone and liver; termed organ tropism. Current treatment methods for metastatic breast cancer have been ineffective, compounded by the lack of early prognostic/predictive methods to determine which organs are most susceptible to developing metastases. A better understanding of the mechanisms that drive breast cancer metastasis is crucial for identifying novel biomarkers and therapeutic targets. Lung metastasis is of particular concern as it is associated with significant patient morbidity and a mortality rate of 60-70%. This review highlights the current understanding of breast cancer metastasis to the lung, including discussion of potential new treatment approaches for development.
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Affiliation(s)
- Braeden Medeiros
- London Regional Cancer Program, London Health Sciences Centre, Department of Anatomy & Cell Biology, Western University, London, ON N6A 5W9, Canada.
| | - Alison L Allan
- London Regional Cancer Program, London Health Sciences Centre, Departments of Anatomy & Cell Biology and Oncology, Western University, London, ON N6A 5W9, Canada.
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22
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Kulasinghe A, Kapeleris J, Cooper C, Warkiani ME, O'Byrne K, Punyadeera C. Phenotypic Characterization of Circulating Lung Cancer Cells for Clinically Actionable Targets. Cancers (Basel) 2019; 11:cancers11030380. [PMID: 30889898 PMCID: PMC6468795 DOI: 10.3390/cancers11030380] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Revised: 03/14/2019] [Accepted: 03/14/2019] [Indexed: 12/26/2022] Open
Abstract
Objectives: In non-small cell lung cancers (NSCLC), tumour biopsy can often be an invasive procedure. The development of a non-invasive methodology to study genetic changes via circulating tumour cells (CTCs) is an appealing concept. Whilst CTCs typically remain as rare cells, improvements in epitope-independent CTC isolation techniques has given rise to a greater capture of CTCs. In this cross sectional study, we demonstrate the capture and characterization of NSCLC CTCs for the clinically actionable markers epidermal growth factor receptor (EGFR) alterations, anaplastic lymphoma kinase (ALK) rearrangements and programmed death ligand-1 (PD-L1) expression. The study identified CTCs/CTC clusters in 26/35 Stage IV NSCLC patients, and subsequently characterized the CTCs for EGFR mutation, ALK status and PD-L1 status. This pilot study demonstrates the potential of a non-invasive fluid biopsy to determine clinically relevant biomarkers in NSCLC.
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Affiliation(s)
- Arutha Kulasinghe
- The School of Biomedical Sciences, Room 603D, Institute of Health and Biomedical Innovation, Queensland University of Technology, 60 Musk Avenue, Kelvin Grove, QLD 4059, Australia.
- Translational Research Institute, Brisbane, QLD 4102, Australia.
| | - Joanna Kapeleris
- The School of Biomedical Sciences, Room 603D, Institute of Health and Biomedical Innovation, Queensland University of Technology, 60 Musk Avenue, Kelvin Grove, QLD 4059, Australia.
- Translational Research Institute, Brisbane, QLD 4102, Australia.
| | - Carolina Cooper
- Department of Anatomical Pathology, Pathology Queensland, QLD 4006, Australia.
- Princess Alexandra Hospital, Woolloongabba, QLD 4102, Australia.
| | - Majid Ebrahimi Warkiani
- The School of Biomedical Engineering, University of Technology Sydney, Ultimo, NSW 2007, Australia.
- Department of Biomedical Engineering, Institute of Molecular Medicine, Sechenov First Moscow State Medical University, Moscow 119991, Russia.
| | - Kenneth O'Byrne
- Translational Research Institute, Brisbane, QLD 4102, Australia.
- Princess Alexandra Hospital, Woolloongabba, QLD 4102, Australia.
| | - Chamindie Punyadeera
- The School of Biomedical Sciences, Room 603D, Institute of Health and Biomedical Innovation, Queensland University of Technology, 60 Musk Avenue, Kelvin Grove, QLD 4059, Australia.
- Translational Research Institute, Brisbane, QLD 4102, Australia.
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23
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Anderson RL, Balasas T, Callaghan J, Coombes RC, Evans J, Hall JA, Kinrade S, Jones D, Jones PS, Jones R, Marshall JF, Panico MB, Shaw JA, Steeg PS, Sullivan M, Tong W, Westwell AD, Ritchie JWA. A framework for the development of effective anti-metastatic agents. Nat Rev Clin Oncol 2019; 16:185-204. [PMID: 30514977 PMCID: PMC7136167 DOI: 10.1038/s41571-018-0134-8] [Citation(s) in RCA: 196] [Impact Index Per Article: 39.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Most cancer-related deaths are a result of metastasis, and thus the importance of this process as a target of therapy cannot be understated. By asking 'how can we effectively treat cancer?', we do not capture the complexity of a disease encompassing >200 different cancer types - many consisting of multiple subtypes - with considerable intratumoural heterogeneity, which can result in variable responses to a specific therapy. Moreover, we have much less information on the pathophysiological characteristics of metastases than is available for the primary tumour. Most disseminated tumour cells that arrive in distant tissues, surrounded by unfamiliar cells and a foreign microenvironment, are likely to die; however, those that survive can generate metastatic tumours with a markedly different biology from that of the primary tumour. To treat metastasis effectively, we must inhibit fundamental metastatic processes and develop specific preclinical and clinical strategies that do not rely on primary tumour responses. To address this crucial issue, Cancer Research UK and Cancer Therapeutics CRC Australia formed a Metastasis Working Group with representatives from not-for-profit, academic, government, industry and regulatory bodies in order to develop recommendations on how to tackle the challenges associated with treating (micro)metastatic disease. Herein, we describe the challenges identified as well as the proposed approaches for discovering and developing anticancer agents designed specifically to prevent or delay the metastatic outgrowth of cancer.
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Affiliation(s)
- Robin L Anderson
- Translational Breast Cancer Program, Olivia Newton-John Cancer Research Institute, Heidelberg, Victoria, Australia
- School of Cancer Medicine, La Trobe University, Bundoora, Victoria, Australia
- Cancer Therapeutics Cooperative Research Centre (CTx), Melbourne, Victoria, Australia
| | - Theo Balasas
- Commercial Partnerships, Cancer Research UK (CRUK), London, UK
| | - Juliana Callaghan
- Research and Innovation Services, University of Portsmouth, Portsmouth, Hampshire, UK
| | - R Charles Coombes
- Department of Surgery and Cancer, Imperial College London, Hammersmith Hospital, London, UK
| | - Jeff Evans
- Institute of Cancer Sciences, University of Glasgow, Glasgow, Scotland, UK
| | - Jacqueline A Hall
- Research and Development, Vivacitv Ltd, Chesham, Buckinghamshire, UK
| | - Sally Kinrade
- Cancer Therapeutics Cooperative Research Centre (CTx), Melbourne, Victoria, Australia
- Medicines Development for Global Health, Southbank, Victoria, Australia
| | - David Jones
- Medicines and Healthcare Products Regulatory Agency, London, UK
| | | | - Rob Jones
- Institute of Cancer Sciences, University of Glasgow, Glasgow, Scotland, UK
| | - John F Marshall
- Queen Mary University of London, Barts Cancer Institute, London, UK
| | | | - Jacqui A Shaw
- Leicester Cancer Research Centre, University of Leicester, Leicester, Leicestershire, UK
| | - Patricia S Steeg
- Women's Malignancies Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Mark Sullivan
- Cancer Therapeutics Cooperative Research Centre (CTx), Melbourne, Victoria, Australia
- Medicines Development for Global Health, Southbank, Victoria, Australia
| | - Warwick Tong
- Cancer Therapeutics Cooperative Research Centre (CTx), Melbourne, Victoria, Australia
| | - Andrew D Westwell
- School of Pharmacy and Pharmaceutical Sciences, Cardiff University, Cardiff, Wales, UK
| | - James W A Ritchie
- Commercial Partnerships, Cancer Research UK (CRUK), London, UK.
- Centre for Drug Development, CRUK, London, UK.
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24
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Bronkhorst AJ, Ungerer V, Holdenrieder S. The emerging role of cell-free DNA as a molecular marker for cancer management. BIOMOLECULAR DETECTION AND QUANTIFICATION 2019; 17:100087. [PMID: 30923679 PMCID: PMC6425120 DOI: 10.1016/j.bdq.2019.100087] [Citation(s) in RCA: 317] [Impact Index Per Article: 63.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Revised: 02/26/2019] [Accepted: 03/11/2019] [Indexed: 02/07/2023]
Abstract
An increasing number of studies demonstrate the potential use of cell-free DNA (cfDNA) as a surrogate marker for multiple indications in cancer, including diagnosis, prognosis, and monitoring. However, harnessing the full potential of cfDNA requires (i) the optimization and standardization of preanalytical steps, (ii) refinement of current analysis strategies, and, perhaps most importantly, (iii) significant improvements in our understanding of its origin, physical properties, and dynamics in circulation. The latter knowledge is crucial for interpreting the associations between changes in the baseline characteristics of cfDNA and the clinical manifestations of cancer. In this review we explore recent advancements and highlight the current gaps in our knowledge concerning each point of contact between cfDNA analysis and the different stages of cancer management.
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Affiliation(s)
| | | | - Stefan Holdenrieder
- Institute for Laboratory Medicine, German Heart Centre, Technical University Munich, Lazarettstraße. 36, D-80636, Munich, Germany
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25
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Lee KH, Shin TJ, Kim WH, Cho JY. Methylation of LINE-1 in cell-free DNA serves as a liquid biopsy biomarker for human breast cancers and dog mammary tumors. Sci Rep 2019; 9:175. [PMID: 30655558 PMCID: PMC6336845 DOI: 10.1038/s41598-018-36470-5] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Accepted: 11/21/2018] [Indexed: 12/15/2022] Open
Abstract
Breast cancer (BC) is one of the most common cancers in both women and female dogs. Methylation changes of LINE-1 have been reported in human cancers. The aim of this study was to determine the hypomethylation of canine LINE-1 in liquid biopsies for canine mammary tumors (CMT) and to assess its diagnostic performance in human plasma. BC associated LINE-1 methylation was measured by methylation sensitive (HpaII) and insensitive (MspI) restriction enzyme digestion followed by real-time PCR using the cfDNA isolated from 300 µl of plasma. The relative level of methylated canine LINE-1 was less than 0.4 in the benign and malignant CMTs (0.29 ± 0.061 and 0.39 ± 0.066, respectively) when it was 0.92 ± 0.067 in the healthy controls. The area under the ROC curve (AUC) was significantly high in both benign and malignant tumors (0.97 and 0.93). Furthermore, this approach was also successfully implemented in a set of 26 human BCs with 10 healthy controls (AUC = 0.78). Altogether, our data suggest that the comparative approach using a dog model might be helpful to rapidly develop a new diagnostic biomarker and that the methylation of LINE-1 in cfDNA may be a good target as a diagnostic marker of both human BC and CMT.
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Affiliation(s)
- Kang-Hoon Lee
- Department of Biochemistry, BK21 Plus and Research Institute for Veterinary Science, School of Veterinary Medicine, Seoul National University, Seoul, South Korea
| | - Tae-Jin Shin
- Department of Biochemistry, BK21 Plus and Research Institute for Veterinary Science, School of Veterinary Medicine, Seoul National University, Seoul, South Korea
| | - Wan-Hee Kim
- Department of Veterinary Clinical Sciences, College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul, Republic of Korea
| | - Je-Yoel Cho
- Department of Biochemistry, BK21 Plus and Research Institute for Veterinary Science, School of Veterinary Medicine, Seoul National University, Seoul, South Korea.
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26
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Nagahashi M, Shimada Y, Ichikawa H, Kameyama H, Takabe K, Okuda S, Wakai T. Next generation sequencing-based gene panel tests for the management of solid tumors. Cancer Sci 2019; 110:6-15. [PMID: 30338623 PMCID: PMC6317963 DOI: 10.1111/cas.13837] [Citation(s) in RCA: 90] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2018] [Revised: 10/13/2018] [Accepted: 10/16/2018] [Indexed: 12/16/2022] Open
Abstract
Next generation sequencing (NGS) has been an invaluable tool to put genomic sequencing into clinical practice. The incorporation of clinically relevant target sequences into NGS-based gene panel tests has generated practical diagnostic tools that enable individualized cancer-patient care. The clinical utility of gene panel testing includes investigation of the genetic basis for an individual's response to therapy, such as signaling pathways associated with a response to specific therapies, microsatellite instability and a hypermutated phenotype, and deficiency in the DNA double-strand break repair pathway. In this review, we describe the concept of precision cancer medicine using target sequences in gene panel tests as well as the importance of the control of sample quality in routine NGS-based genomic testing. We describe geographic and ethnic differences in cancer genomes, and discuss issues that need to be addressed in the future based on our experiences in Japan.
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Affiliation(s)
- Masayuki Nagahashi
- Division of Digestive and General SurgeryGraduate School of Medical and Dental SciencesNiigata UniversityNiigataJapan
| | - Yoshifumi Shimada
- Division of Digestive and General SurgeryGraduate School of Medical and Dental SciencesNiigata UniversityNiigataJapan
| | - Hiroshi Ichikawa
- Division of Digestive and General SurgeryGraduate School of Medical and Dental SciencesNiigata UniversityNiigataJapan
| | - Hitoshi Kameyama
- Division of Digestive and General SurgeryGraduate School of Medical and Dental SciencesNiigata UniversityNiigataJapan
| | - Kazuaki Takabe
- Division of Digestive and General SurgeryGraduate School of Medical and Dental SciencesNiigata UniversityNiigataJapan
- Breast SurgeryRoswell Park Cancer InstituteBuffaloNew York
- Department of SurgeryThe State University of New York Jacobs School of Medicine and Biomedical SciencesUniversity at BuffaloBuffaloNew York
| | - Shujiro Okuda
- Division of BioinformaticsGraduate School of Medical and Dental SciencesNiigata UniversityNiigataJapan
| | - Toshifumi Wakai
- Division of Digestive and General SurgeryGraduate School of Medical and Dental SciencesNiigata UniversityNiigataJapan
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27
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Bonner ER, Bornhorst M, Packer RJ, Nazarian J. Liquid biopsy for pediatric central nervous system tumors. NPJ Precis Oncol 2018; 2:29. [PMID: 30588509 PMCID: PMC6297139 DOI: 10.1038/s41698-018-0072-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Accepted: 11/19/2018] [Indexed: 02/07/2023] Open
Abstract
Central nervous system (CNS) tumors are the most common solid tumors in children, and the leading cause of cancer-related death. Over the past decade, molecular profiling has been incorporated into treatment for pediatric CNS tumors, allowing for a more personalized approach to therapy. Through the identification of tumor-specific changes, it is now possible to diagnose, assign a prognostic subgroup, and develop targeted chemotherapeutic treatment plans for many cancer types. The successful incorporation of informative liquid biopsies, where the liquid biome is interrogated for tumor-associated molecular clues, has the potential to greatly complement the precision-based approach to treatment, and ultimately, to improve clinical outcomes for children with CNS tumors. In this article, the current application of liquid biopsy in cancer therapy will be reviewed, as will its potential for the diagnosis and therapeutic monitoring of pediatric CNS tumors.
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Affiliation(s)
- Erin R Bonner
- 1Center for Genetic Medicine, Children's National Health System, Washington, DC 20010 USA.,2Institute for Biomedical Sciences, The George Washington University School of Medicine and Health Sciences, Washington, DC 20052 USA
| | - Miriam Bornhorst
- 1Center for Genetic Medicine, Children's National Health System, Washington, DC 20010 USA.,3Brain Tumor Institute, Children's National Health System, Washington, DC 20010 USA
| | - Roger J Packer
- 3Brain Tumor Institute, Children's National Health System, Washington, DC 20010 USA
| | - Javad Nazarian
- 1Center for Genetic Medicine, Children's National Health System, Washington, DC 20010 USA.,3Brain Tumor Institute, Children's National Health System, Washington, DC 20010 USA.,4Department of Genomics and Precision Medicine, The George Washington University School of Medicine and Health Sciences, Washington, DC 20052 USA
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28
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Wang XM, Zhang Z, Pan LH, Cao XC, Xiao C. KRT19 and CEACAM5 mRNA-marked circulated tumor cells indicate unfavorable prognosis of breast cancer patients. Breast Cancer Res Treat 2018; 174:375-385. [PMID: 30535933 DOI: 10.1007/s10549-018-05069-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Accepted: 11/23/2018] [Indexed: 02/06/2023]
Abstract
AIM To investigate the clinical and prognostic significance of circulated tumor cells (CTC) marked by cytokeratin 19 coding gene KRT19 mRNA and carcinoembryonic antigen coding gene CEACAM5 mRNA in preoperative peripheral blood of breast cancer patients and provide molecular markers for breast cancer metastasis risk. METHODS The mRNA levels of KRT19 and CEACAM5 in preoperative peripheral blood of breast cancer patients without (n = 603) and with (n = 76) distant metastases at the time of initial diagnosis were detected by reverse transcription-quantitative polymerase chain reaction (RT-qPCR). The relationship between CTCKRT19, CTCCEACAM5 and clinicopathological features, local recurrence-free survival (LRFS), distant metastasis-free survival (DMFS), or overall survival (OS) was statistically analyzed. RESULTS In different pathological stages of breast cancer, the rates of CTCKRT19-pos and CTCCEACAM5-pos increased with the increase of the stages (P = 0.077 and P = 0.004). Preoperative CTCKRT19-pos in breast cancer patients was closely related to the lymph node metastasis statues (P < 0.0001), and had no significant correlation with other clinicopathological features. There was no significant correlation between CTCCEACAM5 and the clinicopathological features. Patients with high levels of CTC double-marked by KRT19 and CEACAM5 mRNA had shorter DMFS (P < 0.0001) and OS (P = 0.016) for patients with breast cancer. The 7-year DMFS rates for the low-, intermediate-, and high-risk groups were 90.7%, 67.5%, and 59.1%, respectively (P < 0.0001). The prognosis of patients with decreased KRT19 and CEACAM5 mRNA after treatment is better than that of patients who have not decreased, and the combination of the two indicators is better than the single one for predicting PFS (P = 0.002 compare with P = 0.036 or P = 0.047). CONCLUSION Double-marked CTC by KRT19 and CEACAM5 mRNA is a prognostic index of breast cancer patients before surgery and after chemotherapy. Single-marked CTC by KRT19 mRNA indicates lymph node statues of preoperative patients. Therefore, the RT-qPCR-based molecular diagnosis of CTC could be used for prognostic prediction of breast cancer patients and guiding clinical treatment.
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Affiliation(s)
- Xi-Mei Wang
- First Department of Breast Cancer, National Clinical Research Center of Cancer, Tianjin Medical University Cancer Institute and Hospital, 1 Huan-Hu Xi Road, Ti-Yuan Bei, He Xi, Tianjin, 300060, People's Republic of China.,Key Laboratory of Cancer Prevention and Therapy, Tianjin, People's Republic of China.,Key Laboratory of Breast Cancer Prevention and Therapy, Ministry of Education, Tianjin Medical University, Tianjin, 300060, People's Republic of China
| | - Zhen Zhang
- First Department of Breast Cancer, National Clinical Research Center of Cancer, Tianjin Medical University Cancer Institute and Hospital, 1 Huan-Hu Xi Road, Ti-Yuan Bei, He Xi, Tianjin, 300060, People's Republic of China.,Key Laboratory of Cancer Prevention and Therapy, Tianjin, People's Republic of China.,Key Laboratory of Breast Cancer Prevention and Therapy, Ministry of Education, Tianjin Medical University, Tianjin, 300060, People's Republic of China
| | - Li-Hui Pan
- First Department of Breast Cancer, National Clinical Research Center of Cancer, Tianjin Medical University Cancer Institute and Hospital, 1 Huan-Hu Xi Road, Ti-Yuan Bei, He Xi, Tianjin, 300060, People's Republic of China.,Key Laboratory of Cancer Prevention and Therapy, Tianjin, People's Republic of China.,Key Laboratory of Breast Cancer Prevention and Therapy, Ministry of Education, Tianjin Medical University, Tianjin, 300060, People's Republic of China
| | - Xu-Chen Cao
- First Department of Breast Cancer, National Clinical Research Center of Cancer, Tianjin Medical University Cancer Institute and Hospital, 1 Huan-Hu Xi Road, Ti-Yuan Bei, He Xi, Tianjin, 300060, People's Republic of China.,Key Laboratory of Cancer Prevention and Therapy, Tianjin, People's Republic of China.,Key Laboratory of Breast Cancer Prevention and Therapy, Ministry of Education, Tianjin Medical University, Tianjin, 300060, People's Republic of China
| | - Chunhua Xiao
- First Department of Breast Cancer, National Clinical Research Center of Cancer, Tianjin Medical University Cancer Institute and Hospital, 1 Huan-Hu Xi Road, Ti-Yuan Bei, He Xi, Tianjin, 300060, People's Republic of China. .,Key Laboratory of Cancer Prevention and Therapy, Tianjin, People's Republic of China. .,Key Laboratory of Breast Cancer Prevention and Therapy, Ministry of Education, Tianjin Medical University, Tianjin, 300060, People's Republic of China.
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29
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Wakai T, Prasoon P, Hirose Y, Shimada Y, Ichikawa H, Nagahashi M. Next-generation sequencing-based clinical sequencing: toward precision medicine in solid tumors. Int J Clin Oncol 2018; 24:115-122. [PMID: 30515675 DOI: 10.1007/s10147-018-1375-3] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Accepted: 11/26/2018] [Indexed: 12/14/2022]
Abstract
Numerous technical and functional advances in next-generation sequencing (NGS) have led to the adoption of this technique in conventional clinical practice. Recently, large-scale genomic research and NGS technological innovation have revealed many more details of somatic and germline mutations in solid tumors. This development is allowing for the classification of tumor type sub-categories based on genetic alterations in solid tumors, and based on this information, new drugs and targeted therapies are being administered to patients. This has largely been facilitated by gene panel testing, which allows for a better understanding of the genetic basis for an individual's response to therapy. NGS-based comprehensive gene panel testing is a clinically useful approach to investigate genomic mechanisms, including therapy-related signaling pathways, microsatellite instability, hypermutated phenotypes, and tumor mutation burden. In this review, we describe the concept of precision medicine in solid tumors using NGS-based comprehensive gene panel testing, as well as the importance of quality control of tissue sample handling in routine NGS-based genomic testing, and we discuss issues for the future adoption of this technique in Japan.
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Affiliation(s)
- Toshifumi Wakai
- Division of Digestive and General Surgery, Niigata University Graduate School of Medical and Dental Sciences, 1-757 Asahimachi-dori, Chuo-ku, Niigata, Niigata, 951-8510, Japan.
| | - Pankaj Prasoon
- Division of Digestive and General Surgery, Niigata University Graduate School of Medical and Dental Sciences, 1-757 Asahimachi-dori, Chuo-ku, Niigata, Niigata, 951-8510, Japan
| | - Yuki Hirose
- Division of Digestive and General Surgery, Niigata University Graduate School of Medical and Dental Sciences, 1-757 Asahimachi-dori, Chuo-ku, Niigata, Niigata, 951-8510, Japan
| | - Yoshifumi Shimada
- Division of Digestive and General Surgery, Niigata University Graduate School of Medical and Dental Sciences, 1-757 Asahimachi-dori, Chuo-ku, Niigata, Niigata, 951-8510, Japan
| | - Hiroshi Ichikawa
- Division of Digestive and General Surgery, Niigata University Graduate School of Medical and Dental Sciences, 1-757 Asahimachi-dori, Chuo-ku, Niigata, Niigata, 951-8510, Japan
| | - Masayuki Nagahashi
- Division of Digestive and General Surgery, Niigata University Graduate School of Medical and Dental Sciences, 1-757 Asahimachi-dori, Chuo-ku, Niigata, Niigata, 951-8510, Japan
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30
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Zhang Y, Zheng H, Zhan Y, Long M, Liu S, Lu J, Zang H, Fan S. Detection and application of circulating tumor cell and circulating tumor DNA in the non-small cell lung cancer. Am J Cancer Res 2018; 8:2377-2386. [PMID: 30662798 PMCID: PMC6325475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Accepted: 11/02/2018] [Indexed: 06/09/2023] Open
Abstract
Non-small cell lung cancer (NSCLC) is the leading cause of cancer-related death in both men and women. The ability of cancer cells to break-off from the primary tumor and spread to distant organs is the main cause of death of cancer patients. The detection of circulating tumor cells (CTCs) and circulating tumor DNA (ctDNA) is a considerable part of liquid biopsy, which contributes to the diagnosis, treatment and prognosis, and especially to identify the targetable mutations of NSCLC. This review is to discuss the detection and application of CTC and ctDNA in the diagnosis, prognostic evaluation and guiding targeted therapy of NSCLC.
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Affiliation(s)
- Yuting Zhang
- Department of Pathology, The Second Xiangya Hospital, Central South University Changsha, Hunan, China
| | - Hongmei Zheng
- Department of Pathology, The Second Xiangya Hospital, Central South University Changsha, Hunan, China
| | - Yuting Zhan
- Department of Pathology, The Second Xiangya Hospital, Central South University Changsha, Hunan, China
| | - Mengping Long
- Department of Pathology, The Second Xiangya Hospital, Central South University Changsha, Hunan, China
| | - Sile Liu
- Department of Pathology, The Second Xiangya Hospital, Central South University Changsha, Hunan, China
| | - Junmi Lu
- Department of Pathology, The Second Xiangya Hospital, Central South University Changsha, Hunan, China
| | - Hongjing Zang
- Department of Pathology, The Second Xiangya Hospital, Central South University Changsha, Hunan, China
| | - Songqing Fan
- Department of Pathology, The Second Xiangya Hospital, Central South University Changsha, Hunan, China
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Complexity of genome sequencing and reporting: Next generation sequencing (NGS) technologies and implementation of precision medicine in real life. Crit Rev Oncol Hematol 2018; 133:171-182. [PMID: 30661654 DOI: 10.1016/j.critrevonc.2018.11.008] [Citation(s) in RCA: 72] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Accepted: 11/23/2018] [Indexed: 12/17/2022] Open
Abstract
The finalization of the Human Genome Project in 2003 paved the way for a deeper understanding of cancer, favouring a faster progression towards "personalized" medicine. Research in oncology has progressively focused on the sequencing of cancer genomes, to better understand the genetic basis of tumorigenesis and identify actionable alterations to guide cancer therapy. Thanks to the development of next-generation-sequencing (NGS) techniques, sequencing of tumoral DNA is today technically easier, faster and cheaper. Commercially available NGS panels enable the detection of single or global genomic alterations, namely gene mutation and mutagenic burden, both on germline and somatic DNA, potentially predicting the response or resistance to cancer treatments. Profiling of tumor DNA is nowadays a standard in cancer research and treatment. In this review we discuss the history, techniques and applications of NGS in cancer care, under a "personalized tailored therapy" perspective.
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Tan W, Yang M, Yang H, Zhou F, Shen W. Predicting the response to neoadjuvant therapy for early-stage breast cancer: tumor-, blood-, and imaging-related biomarkers. Cancer Manag Res 2018; 10:4333-4347. [PMID: 30349367 PMCID: PMC6188192 DOI: 10.2147/cmar.s174435] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Neoadjuvant therapy (NAT) has been used increasingly in patients with locally advanced or early-stage breast cancer. However, the accurate evaluation and prediction of response to NAT remain the great challenge. Biomarkers could prove useful to identify responders or nonresponders, or even to distinguish between early and delayed responses. These biomarkers could include markers from the tumor itself, such as versatile proteins, genes, and ribonucleic acids, various biological factors or peripheral blood cells, and clinical and pathological features. Possible predictive markers could also include multiple features from functional imaging, such as standard uptake values in positron emission tomography, apparent diffusion coefficient in magnetic resonance, or radiomics imaging biomarkers. In addition, cells that indirectly present the immune status of tumor cells and/or their host could also potentially be used as biomarkers, eg, tumor-infiltrating lymphocytes, tumor-associated macrophages, and myeloid-derived suppressor cells. Though numerous biomarkers have been widely investigated, only estrogen and/or progesterone receptors and human epidermal growth factor receptor have been proven to be reliable biomarkers to predict the response to NAT. They are the only biomarkers recommended in several international guidelines. The other aforementioned biomarkers warrant further validation studies. Some multigene profiling assays that are commercially available, eg, Oncotype DX and MammaPrint, should be used with caution when extrapolated to NAT settings. A panel of combined multilevel biomarkers might be able to predict the response to NAT more robustly than individual biomarkers. To establish such a panel and its prediction model, reliable methods and extensive clinical validation are warranted.
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Affiliation(s)
- Wenyong Tan
- Department of Oncology, Shenzhen Hospital of Southern Medical University, Shenzhen, People's Republic of China, ;
- Clinical Medical Research Center, The Second Clinical Medical College (Shenzhen People Hospital), Jinan University, Shenzhen, People's Republic of China,
| | - Ming Yang
- Shenzhen Jingmai Medical Scientific and Technique Company, Shenzhen, People's Republic of China
| | - Hongli Yang
- Clinical Medical Research Center, The Second Clinical Medical College (Shenzhen People Hospital), Jinan University, Shenzhen, People's Republic of China,
| | - Fangbin Zhou
- Clinical Medical Research Center, The Second Clinical Medical College (Shenzhen People Hospital), Jinan University, Shenzhen, People's Republic of China,
| | - Weixi Shen
- Department of Oncology, Shenzhen Hospital of Southern Medical University, Shenzhen, People's Republic of China, ;
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Bohers E, Viailly PJ, Becker S, Marchand V, Ruminy P, Maingonnat C, Bertrand P, Etancelin P, Picquenot JM, Camus V, Menard AL, Lemasle E, Contentin N, Leprêtre S, Lenain P, Stamatoullas A, Lanic H, Libraire J, Vaudaux S, Pepin LF, Vera P, Tilly H, Jardin F. Non-invasive monitoring of diffuse large B-cell lymphoma by cell-free DNA high-throughput targeted sequencing: analysis of a prospective cohort. Blood Cancer J 2018; 8:74. [PMID: 30069017 PMCID: PMC6070497 DOI: 10.1038/s41408-018-0111-6] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Revised: 05/28/2018] [Accepted: 06/08/2018] [Indexed: 12/15/2022] Open
Abstract
From a liquid biopsy, cell-free DNA (cfDNA) can provide information regarding basal tumoral genetic patterns and changes upon treatment. In a prospective cohort of 30 diffuse large B-cell lymphomas (DLBCL), we determined the clinical relevance of cfDNA using targeted next-generation sequencing and its correlation with PET scan imaging at the time of diagnosis and during treatment. Using a dedicated DLBCL panel, mutations were identified at baseline for 19 cfDNAs and profiles were consistent with expected DLBCL patterns. Tumor burden-related clinical and PET scan features (LDH, IPI, and metabolic tumor volume) were significantly correlated with the quantity of tumoral cfDNA. Among the four patients presenting additional mutations in their cfDNAs, three had high metabolic tumor volumes, suggesting that cfDNA more accurately reflects tumor heterogeneity than tissues biopsy itself. Mid-treatment, four patients still had basal mutations in their cfDNAs, including three in partial response according to their Deauville scores. Our study highlights the major interests in liquid biopsy, in particular in the context of bulky tumors where cfDNA allows capturing the entire tumoral mutation profile. Therefore, cfDNA analysis in DLBCL represents a complementary approach to PET scan imaging.
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Affiliation(s)
- Elodie Bohers
- INSERM U1245, Centre Henri Becquerel, University of Rouen, Rouen, France
| | | | - Stéphanie Becker
- Department of Nuclear Medicine, Centre Henri Becquerel, University of Rouen, Rouen, France
- QuantIF-LITIS (EA 4108-FR CNRS 3638), Faculty of Medicine, University of Rouen, Rouen, France
| | - Vinciane Marchand
- INSERM U1245, Centre Henri Becquerel, University of Rouen, Rouen, France
| | - Philippe Ruminy
- INSERM U1245, Centre Henri Becquerel, University of Rouen, Rouen, France
| | | | - Philippe Bertrand
- INSERM U1245, Centre Henri Becquerel, University of Rouen, Rouen, France
| | | | | | - Vincent Camus
- Department of Clinical Haematology, Centre Henri Becquerel, Rouen, France
| | - Anne-Lise Menard
- Department of Clinical Haematology, Centre Henri Becquerel, Rouen, France
| | - Emilie Lemasle
- Department of Clinical Haematology, Centre Henri Becquerel, Rouen, France
| | - Nathalie Contentin
- Department of Clinical Haematology, Centre Henri Becquerel, Rouen, France
| | - Stéphane Leprêtre
- Department of Clinical Haematology, Centre Henri Becquerel, Rouen, France
| | - Pascal Lenain
- Department of Clinical Haematology, Centre Henri Becquerel, Rouen, France
| | | | - Hélène Lanic
- Department of Clinical Haematology, Centre Henri Becquerel, Rouen, France
| | - Julie Libraire
- Clinical Research Unit, Centre Henri Becquerel, Rouen, France
| | | | | | - Pierre Vera
- Department of Nuclear Medicine, Centre Henri Becquerel, University of Rouen, Rouen, France
- QuantIF-LITIS (EA 4108-FR CNRS 3638), Faculty of Medicine, University of Rouen, Rouen, France
| | - Hervé Tilly
- INSERM U1245, Centre Henri Becquerel, University of Rouen, Rouen, France
- Department of Clinical Haematology, Centre Henri Becquerel, Rouen, France
- Clinical Research Unit, Centre Henri Becquerel, Rouen, France
| | - Fabrice Jardin
- INSERM U1245, Centre Henri Becquerel, University of Rouen, Rouen, France.
- Department of Clinical Haematology, Centre Henri Becquerel, Rouen, France.
- Clinical Research Unit, Centre Henri Becquerel, Rouen, France.
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Park ES, Yan JP, Ang RA, Lee JH, Deng X, Duffy SP, Beja K, Annala M, Black PC, Chi KN, Wyatt AW, Ma H. Isolation and genome sequencing of individual circulating tumor cells using hydrogel encapsulation and laser capture microdissection. LAB ON A CHIP 2018; 18:1736-1749. [PMID: 29762619 DOI: 10.1039/c8lc00184g] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Circulating tumor cells (CTCs) are malignant cells released into the bloodstream with the potential to form metastases in secondary sites. These cells, acquired non-invasively, represent a sample of highly relevant tumor tissue that is an alternative to difficult and low-yield tumor biopsies. In recent years, there has been growing interest in genomic profiling of CTCs to enable longitudinal monitoring of the tumor's adaptive response to therapy. However, due to their extreme rarity, genotyping CTCs has proved challenging. Relevant mutations can be masked by leukocyte contamination in isolates. Heterogeneity between subpopulations of tumor cells poses an additional obstacle. Recent advances in single-cell sequencing can overcome these limitations but isolation of single CTCs is prone to cell loss and is prohibitively difficult and time consuming. To address these limitations, we developed a single cell sample preparation and genome sequencing pipeline that combines biophysical enrichment and single cell isolation using laser capture microdissection (LCM). A key component of this process is the encapsulation of enriched CTC sample in a hydrogel matrix, which enhances the efficiency of single-cell isolation by LCM, and is compatible with downstream sequencing. We validated this process by sequencing of single CTCs and cell free DNA (cfDNA) from a single patient with castration resistant prostate cancer. Identical mutations were observed in prostate cancer driver genes (TP53, PTEN, FOXA1) in both single CTCs and cfDNA. However, two independently isolated CTCs also had identical missense mutations in the genes for ATR serine/threonine kinase, KMT2C histone methyltransferase, and FANCC DNA damage repair gene. These mutations may be missed by bulk sequencing libraries, whereas single cell sequencing could potentially enable the characterization of key CTC subpopulations that arise during metastasis.
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Affiliation(s)
- Emily S Park
- Department of Mechanical Engineering, University of British Columbia, Canada.
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Gallaher JA, Enriquez-Navas PM, Luddy KA, Gatenby RA, Anderson ARA. Spatial Heterogeneity and Evolutionary Dynamics Modulate Time to Recurrence in Continuous and Adaptive Cancer Therapies. Cancer Res 2018; 78:2127-2139. [PMID: 29382708 PMCID: PMC5899666 DOI: 10.1158/0008-5472.can-17-2649] [Citation(s) in RCA: 134] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Revised: 12/05/2017] [Accepted: 01/24/2018] [Indexed: 12/31/2022]
Abstract
Treatment of advanced cancers has benefited from new agents that supplement or bypass conventional therapies. However, even effective therapies fail as cancer cells deploy a wide range of resistance strategies. We propose that evolutionary dynamics ultimately determine survival and proliferation of resistant cells. Therefore, evolutionary strategies should be used with conventional therapies to delay or prevent resistance. Using an agent-based framework to model spatial competition among sensitive and resistant populations, we applied antiproliferative drug treatments to varying ratios of sensitive and resistant cells. We compared a continuous maximum-tolerated dose schedule with an adaptive schedule aimed at tumor control via competition between sensitive and resistant cells. Continuous treatment cured mostly sensitive tumors, but with any resistant cells, recurrence was inevitable. We identified two adaptive strategies that control heterogeneous tumors: dose modulation controls most tumors with less drug, while a more vacation-oriented schedule can control more invasive tumors. These findings offer potential modifications to treatment regimens that may improve outcomes and reduce resistance and recurrence.Significance: By using drug dose modulation or treatment vacations, adaptive therapy strategies control the emergence of tumor drug resistance by spatially suppressing less fit resistant populations in favor of treatment sensitive ones. Cancer Res; 78(8); 2127-39. ©2018 AACR.
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Affiliation(s)
- Jill A Gallaher
- H. Lee Moffitt Cancer Center, Integrated Mathematical Oncology, Tampa, Florida
| | | | - Kimberly A Luddy
- H. Lee Moffitt Cancer Center, Cancer Imaging and Metabolism, Tampa, Florida
| | - Robert A Gatenby
- H. Lee Moffitt Cancer Center, Integrated Mathematical Oncology, Tampa, Florida
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Aucamp J, Bronkhorst AJ, Badenhorst CPS, Pretorius PJ. The diverse origins of circulating cell-free DNA in the human body: a critical re-evaluation of the literature. Biol Rev Camb Philos Soc 2018; 93:1649-1683. [PMID: 29654714 DOI: 10.1111/brv.12413] [Citation(s) in RCA: 184] [Impact Index Per Article: 30.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Revised: 03/06/2018] [Accepted: 03/09/2018] [Indexed: 12/13/2022]
Abstract
Since the detection of cell-free DNA (cfDNA) in human plasma in 1948, it has been investigated as a non-invasive screening tool for many diseases, especially solid tumours and foetal genetic abnormalities. However, to date our lack of knowledge regarding the origin and purpose of cfDNA in a physiological environment has limited its use to more obvious diagnostics, neglecting, for example, its potential utility in the identification of predisposition to disease, earlier detection of cancers, and lifestyle-induced epigenetic changes. Moreover, the concept or mechanism of cfDNA could also have potential therapeutic uses such as in immuno- or gene therapy. This review presents an extensive compilation of the putative origins of cfDNA and then contrasts the contributions of cellular breakdown processes with active mechanisms for the release of cfDNA into the extracellular environment. The involvement of cfDNA derived from both cellular breakdown and active release in lateral information transfer is also discussed. We hope to encourage researchers to adopt a more holistic view of cfDNA research, taking into account all the biological pathways in which cfDNA is involved, and to give serious consideration to the integration of in vitro and in vivo research. We also wish to encourage researchers not to limit their focus to the apoptotic or necrotic fraction of cfDNA, but to investigate the intercellular messaging capabilities of the actively released fraction of cfDNA and to study the role of cfDNA in pathogenesis.
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Affiliation(s)
- Janine Aucamp
- Human Metabolomics, Biochemistry Division, Hoffman Street, North-West University, Private bag X6001 Potchefstroom, 2520, South Africa
| | - Abel J Bronkhorst
- Human Metabolomics, Biochemistry Division, Hoffman Street, North-West University, Private bag X6001 Potchefstroom, 2520, South Africa
| | - Christoffel P S Badenhorst
- Department of Biotechnology and Enzyme Catalysis, Institute of Biochemistry, Greifswald University, Felix-Hausdorff-Straße 4, 17487, Greifswald, Germany
| | - Piet J Pretorius
- Human Metabolomics, Biochemistry Division, Hoffman Street, North-West University, Private bag X6001 Potchefstroom, 2520, South Africa
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Abstract
BACKGROUND Circulating cell-free DNA (cfDNA) isolated from plasma or serum by noninvasive procedures can serve as a "liquid biopsy" and has potential as a biomarker for the tumor burden and survival prediction of breast cancer (BC). However, its prognostic value in patients with BC is currently under debate. The aim of this meta-analysis was to investigate the relationship between cfDNA and survival outcome. METHODS We systematically searched PubMed, Embase, and Science Citation Index electronic databases for studies about the prognostic utility of cfDNA in patients with BC. The clinical characteristics, relapse/disease-free survival (RFS/DFS), and overall survival (OS) data were extracted from the eligible studies. The hazard ratios (HR) and 95% confidence intervals (CI) were calculated and pooled with a fixed-effects model using the Stata12.0 software. Subgroup and sensitivity analyses were also performed. RESULTS This meta-analysis included a total of 10 eligible studies and 1127 patients with BC. The pooled HR with 95% CI showed strong associations between cfDNA and OS (HR = 2.41, 95% CI, 1.83-3.16) along with DFS/RFS (HR = 2.73, 95% CI, 2.04-3.67) in patients with BC. Although publication bias was found in the studies regarding RFS/DFS, further trim and fill analysis revealed that the adjusted HR would be 2.53 (95% CI, 1.83-3.51), which is close to the original HR. Subgroup analyses confirmed the role of cfDNA as a strong prognostic marker in patients with BC, regardless of cfDNA analysis, sampling time, sample source, detection method, tumor stage, sample size, or area. CONCLUSIONS Our meta-analysis indicates that cfDNA is a strong predictive and prognostic marker in patients with BC.
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Affiliation(s)
| | - Chang Chu
- Department of Nephrology, The First Affiliated Hospital of Jinan University, Guangzhou, Guangdong Province, People's Republic of China
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Abstract
The majority of cancer-related deaths result from metastasis, the process by which cancer cells escape the primary tumor site and enter into the blood circulation in order to disseminate to secondary locations throughout the body. Tumor cells found within the circulation are referred to as circulating tumor cells (CTCs), and their detection and enumeration correlate with poor prognosis. The epithelial-to-mesenchymal transition (EMT) is a dynamic process that imparts epithelial cells with mesenchymal-like properties, thus facilitating tumor cell dissemination and contributing to metastasis. However, EMT also results in the downregulation of various epithelial proteins typically utilized by CTC technologies for enrichment and detection of these rare cells, resulting in reduced detection of some CTCs, potentially those with a more metastatic phenotype. In addition to the current clinical role of CTCs as a prognostic biomarker, they also have potential as a predictive biomarker via CTC characterization. However, CTC characterization is complicated by the unknown biological significance of CTCs possessing an EMT-like phenotype, and the ability to capture and understand this CTC subpopulation is an essential step in the utilization of CTCs for patient management. This chapter will review the process of EMT and its contribution to metastasis; discusses current and future clinical applications of CTCs; and describes both traditional and novel methods for CTC enrichment, detection, and characterization with a specific focus on CTCs with an EMT phenotype.
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Camus V, Bohers E, Dubois S, Tilly H, Jardin F. Circulating tumor DNA: an important tool in precision medicine for lymphoma. EXPERT REVIEW OF PRECISION MEDICINE AND DRUG DEVELOPMENT 2017. [DOI: 10.1080/23808993.2018.1412798] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Vincent Camus
- UMR INSERM U1245 and Department of Clinical Hematology, Centre Henri Becquerel, Rouen, France
| | - Elodie Bohers
- UMR INSERM U1245 and Department of Clinical Hematology, Centre Henri Becquerel, Rouen, France
| | - Sydney Dubois
- UMR INSERM U1245 and Department of Clinical Hematology, Centre Henri Becquerel, Rouen, France
| | - Hervé Tilly
- UMR INSERM U1245 and Department of Clinical Hematology, Centre Henri Becquerel, Rouen, France
| | - Fabrice Jardin
- UMR INSERM U1245 and Department of Clinical Hematology, Centre Henri Becquerel, Rouen, France
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Riethdorf S, Soave A, Rink M. The current status and clinical value of circulating tumor cells and circulating cell-free tumor DNA in bladder cancer. Transl Androl Urol 2017; 6:1090-1110. [PMID: 29354496 PMCID: PMC5760371 DOI: 10.21037/tau.2017.09.16] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Urothelial carcinoma of the bladder (UCB) is a complex disease, which is associated with highly aggressive tumor biologic behavior, especially in patients with muscle-invasive and advanced tumors. Despite multimodal therapy options including surgery, radiotherapy and chemotherapy, UCB patients frequently suffer from poor clinical outcome. Indeed, the potential of diverse opportunities for modern targeted therapies is not sufficiently elucidated in UCB yet. To improve the suboptimal treatment situation in UCB, biomarkers are urgently needed that help detecting minimal residual disease (MRD), predicting therapy response and subsequently prognosis as well as enabling patient stratification for further therapies and therapy monitoring, respectively. To date, decision making regarding treatment planning is mainly based on histopathologic evaluation of biopsies predominantly derived from the primary tumors and on clinical staging. However, both methods are imperfect for sufficient outcome prediction. During disease progression, individual disseminated tumor cells and consecutively metastases can acquire characteristics that do not match those of the corresponding primary tumors, and often are only hardly assessable for further evaluation. Therefore, during recent years, strong efforts were directed to establish non-invasive biomarkers from liquid biopsies. Urine cytology and serum tumor markers have been established for diagnostic purposes, but are still insufficient as universal biomarkers for decision-making and treatment of UCB patients. To date, the clinical relevance of various newly established blood-based biomarkers comprising circulating tumor cells (CTCs), circulating cell-free nucleic acids or tumor-educated platelets is being tested in cancer patients. In this review we summarize the current state and clinical application of CTCs and circulating cell-free tumor DNA originating from blood as biomarkers in patients with different UCB stages.
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Affiliation(s)
- Sabine Riethdorf
- Department of Tumor Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Armin Soave
- Department of Urology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Michael Rink
- Department of Urology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
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Mason J, Blyth B, MacManus MP, Martin OA. Treatment for non-small-cell lung cancer and circulating tumor cells. Lung Cancer Manag 2017; 6:129-139. [PMID: 30643579 PMCID: PMC6310303 DOI: 10.2217/lmt-2017-0019] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2017] [Accepted: 03/02/2018] [Indexed: 12/25/2022] Open
Abstract
Surgery is the main curative therapy for patients with localized non-small-cell lung cancer while radiotherapy (RT), alone or with concurrent platinum-based chemotherapy, remains the primary curative modality for locoregionally advanced non-small-cell lung cancer. The risk of distant metastasis is high after curative-intent treatment, largely attributable to the presence of undetected micrometastases, but which could also be related to treatment-related increases in circulating tumor cells (CTCs). CTC mobilization by RT or systemic therapies might either reflect efficient tumor destruction with improved prognosis, or might promote metastasis and thus represent a potential therapeutic target. RT may induce prometastatic biological alterations in CTC at the cellular level, which are detectable by 'liquid biopsies', though their rarity represents a major challenge. Improved methods of isolation and ex vivo propagation will be essential for the future of CTC research.
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Affiliation(s)
- Joel Mason
- Division of Radiation Oncology, Peter MacCallum Cancer Centre, Melbourne, Australia
- Research Division, Peter MacCallum Cancer Center, Melbourne, Australia
- Department of Pathology, The University of Melbourne, Melbourne, Australia
| | - Benjamin Blyth
- Division of Radiation Oncology, Peter MacCallum Cancer Centre, Melbourne, Australia
- Research Division, Peter MacCallum Cancer Center, Melbourne, Australia
| | - Michael P MacManus
- Division of Radiation Oncology, Peter MacCallum Cancer Centre, Melbourne, Australia
- Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, Australia
| | - Olga A Martin
- Division of Radiation Oncology, Peter MacCallum Cancer Centre, Melbourne, Australia
- Research Division, Peter MacCallum Cancer Center, Melbourne, Australia
- Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, Australia
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Salvianti F, Pinzani P. The diagnostic potential of mutation detection from single circulating tumor cells in cancer patients. Expert Rev Mol Diagn 2017; 17:975-981. [PMID: 28931314 DOI: 10.1080/14737159.2017.1381561] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
INTRODUCTION Circulating tumor cells (CTCs) have gained importance in the oncology field as biomarkers of tumor development. The most relevant observation that emerged from the recent studies on CTCs is their heterogeneity, which can be investigated by new technologies for single cell analysis. Areas covered: This review considers the most recent advances (limited to the last two years) in the mutational analysis of single CTCs with a critical point of view on the technical challenges still to be faced and the steps needed to reach a standardization of the procedures able to translate these new approaches into clinical practice. Expert commentary: CTCs represent a surrogate tumor sample obtained by a minimally invasive procedure allowing the serial monitoring of the patient during the follow-up period or after treatment. Notwithstanding that, the analysis of CTCs is not so widespread; in fact, a limited number of centers can be equipped and possess the expertise for the development of workflows able to identify, enrich and isolate CTCs from blood. Moreover, the lack of standardized procedures and guidelines limits the study of CTCs to 'research use only' approaches.
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Affiliation(s)
- Francesca Salvianti
- a Department of Clinical and Experimental Biomedical Sciences 'Mario Serio' , University of Florence , Florence , Italy
| | - Pamela Pinzani
- a Department of Clinical and Experimental Biomedical Sciences 'Mario Serio' , University of Florence , Florence , Italy
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Velcheti V, Pennell NA. Non-invasive diagnostic platforms in management of non-small cell lung cancer: opportunities and challenges. ANNALS OF TRANSLATIONAL MEDICINE 2017; 5:378. [PMID: 29057238 DOI: 10.21037/atm.2017.08.24] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Several non-invasive diagnostic platforms are already being incorporated in routine clinical practice in the work up and monitoring of patients with lung cancer. These approaches have great potential to improve patient selection and monitor patients while on therapy, however several challenges exist in clinical validation and standardization of such platforms. In this review, we summarize the current technologies available for non-invasive diagnostic evaluation from the blood of patients with non-small cell lung cancer (NSCLC), and discuss the technical and logistical challenges associated incorporating such testing in clinical practice.
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Affiliation(s)
- Vamsidhar Velcheti
- Department of Hematology and Medical Oncology, Cleveland Clinic Taussig Cancer Institute, Cleveland, OH, USA
| | - Nathan A Pennell
- Department of Hematology and Medical Oncology, Cleveland Clinic Taussig Cancer Institute, Cleveland, OH, USA
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Li Y, Xu H, Su S, Ye J, Chen J, Jin X, Lin Q, Zhang D, Ye C, Chen C. Clinical validation of a highly sensitive assay to detect EGFR mutations in plasma cell-free DNA from patients with advanced lung adenocarcinoma. PLoS One 2017; 12:e0183331. [PMID: 28829813 PMCID: PMC5568724 DOI: 10.1371/journal.pone.0183331] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Accepted: 08/02/2017] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Circulating tumor DNA (ctDNA) is a promising biomarker for noninvasive epidermal growth factor receptor (EGFR) mutations detection in lung cancer patients, but the existing methods have limitations in sensitivity or in availability. In this study, we evaluated the performance of a novel assay called ADx-SuperARMS in detecting EGFR mutations in plasma cell-free DNA from patients with advanced lung adenocarcinoma. METHODS A total of 109 patients with metastatic advanced adenocarcinoma were recruited who provided both blood samples and matched tumor tissue samples. EGFR mutation status in plasma samples were tested with ADx-SuperARMS EGFR assay and tumor tissue samples were tested with ADx-ARMS EGFR assay. The clinical sensitivity, specificity, positive prediction value (PPV), and negative prediction value (NPV) of ADx-SuperARMS EGFR assay were calculated by using EGFR mutation status in tumor tissue as standard reference. A receiver operating characteristic (ROC) analysis was implemented and an area under the curve (AUC) was calculated to evaluate sensitivity and specificity of exon 19 deletion (E19Del) and L858R mutation detection. The objective response rate (ORR) were calculated according to the EGFR mutation status determined by ADx-superARMS as well. RESULTS 0.2% analytical sensitivity and 100% specificity of the ADx-SuperARMS EGFR assays for EGFR E19Del, L858R, and T790M mutants were confirmed by using a series of diluted cell line DNA. In the clinical study, EGFR mutations were detected in 45.9% (50/109) of the plasma samples and in 56.9% (62/109) of the matched tumor tissue samples. The sensitivity, specificity, PPV and NPV of the ADx-SuperARMS EGFR assay for plasma EGFR mutation detection were 82.0% (50/61), 100% (48/48), 100% (50/50), and 81.4% (48/59), respectively. In ROC analysis, ADx-SuperARMS achieved sensitivity and specificity of 88% and 99% in E19Dels as well as sensitivity and specificity of 89% and 100% in L858R, respectively. Among the 35 patients who were plasma EGFR mutation positive and treated with first generation of EGFR-tyrosine kinase inhibitors (TKIs), 23 (65.7%) achieved partial response, 11 (31.4%) sustained disease, and 1 (2.9%) progressive disease. The ORR and disease control rate (DCR) were 65.7% and 97.1%, respectively. CONCLUSIONS ADx-SuperARMS EGFR assay is likely to be a highly sensitive and specific method to noninvasively detect plasma EGFR mutations of patients with advanced lung adenocarcinoma. The EGFR mutations detected by ADx-SuperARMS EGFR assay could predict the efficacy of the treatment with first generation of EGFR-TKIs. Hence, EGFR blood testing with ADx-SuperARMS could address the unmet clinical needs.
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Affiliation(s)
- Yuping Li
- Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Hanyan Xu
- Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Shanshan Su
- Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Junru Ye
- Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Junjie Chen
- Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Xuru Jin
- Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Quan Lin
- Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Dongqing Zhang
- Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Caier Ye
- Department of Radiology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Chengshui Chen
- Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
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45
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Aucamp J, Bronkhorst AJ, Peters DL, Van Dyk HC, Van der Westhuizen FH, Pretorius PJ. Kinetic analysis, size profiling, and bioenergetic association of DNA released by selected cell lines in vitro. Cell Mol Life Sci 2017; 74:2689-2707. [PMID: 28315952 PMCID: PMC11107759 DOI: 10.1007/s00018-017-2495-z] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Revised: 02/19/2017] [Accepted: 02/22/2017] [Indexed: 01/09/2023]
Abstract
Although circulating DNA (cirDNA) analysis shows great promise as a screening tool for a wide range of pathologies, numerous stumbling blocks hinder the rapid translation of research to clinical practice. This is related directly to the inherent complexity of the in vivo setting, wherein the influence of complex systems of interconnected cellular responses and putative DNA sources creates a seemingly arbitrary representation of the quantitative and qualitative properties of the cirDNA in the blood of any individual. Therefore, to evaluate the potential of in vitro cell cultures to circumvent the difficulties encountered in in vivo investigations, the purpose of this work was to elucidate the characteristics of the DNA released [cell-free DNA (cfDNA)] by eight different cell lines. This revealed three different forms of cfDNA release patterns and the presence of nucleosomal fragments as well as actively released forms of DNA, which are not only consistently observed in every tested cell line, but also in plasma samples. Correlations between cfDNA release and cellular origin, growth rate, and cancer status were also investigated by screening and comparing bioenergetics flux parameters. These results show statistically significant correlations between cfDNA levels and glycolysis, while no correlations between cfDNA levels and oxidative phosphorylation were observed. Furthermore, several correlations between growth rate, cancer status, and dependency on aerobic glycolysis were observed. Cell cultures can, therefore, successfully serve as closed-circuit models to either replace or be used in conjunction with biofluid samples, which will enable sharper focus on specific cell types or DNA origins.
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Affiliation(s)
- Janine Aucamp
- Human Metabolomics, North-West University, Hoffman Street, Potchefstroom, 2520, South Africa.
| | - Abel J Bronkhorst
- Human Metabolomics, North-West University, Hoffman Street, Potchefstroom, 2520, South Africa
| | - Dimetrie L Peters
- Human Metabolomics, North-West University, Hoffman Street, Potchefstroom, 2520, South Africa
| | - Hayley C Van Dyk
- Human Metabolomics, North-West University, Hoffman Street, Potchefstroom, 2520, South Africa
| | | | - Piet J Pretorius
- Human Metabolomics, North-West University, Hoffman Street, Potchefstroom, 2520, South Africa
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46
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Petrylak DP, Crawford ED. Biomarkers for the Management of Castration-Resistant Prostate Cancer: We Are Not There Yet. Target Oncol 2017; 12:401-412. [DOI: 10.1007/s11523-017-0500-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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47
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Camus V, Jardin F, Tilly H. The value of liquid biopsy in diagnosis and monitoring of diffuse large b-cell lymphoma: recent developments and future potential. Expert Rev Mol Diagn 2017; 17:557-566. [DOI: 10.1080/14737159.2017.1319765] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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48
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Beffagna G, Sammarco A, Bedin C, Romualdi C, Mainenti M, Mollo A, Cavicchioli L, Ferro S, Trez D, De Maria R, Nitti D, Saccani A, Campanella M, Agostini M, Zappulli V. Circulating Cell-Free DNA in Dogs with Mammary Tumors: Short and Long Fragments and Integrity Index. PLoS One 2017; 12:e0169454. [PMID: 28081183 PMCID: PMC5231265 DOI: 10.1371/journal.pone.0169454] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Accepted: 12/16/2016] [Indexed: 02/06/2023] Open
Abstract
Circulating cell-free DNA (cfDNA) has been considered an interesting diagnostic/prognostic plasma biomarker in tumor-bearing subjects. In cancer patients, cfDNA can hypothetically derive from tumor necrosis/apoptosis, lysed circulating cells, and some yet unrevealed mechanisms of active release. This study aimed to preliminarily analyze cfDNA in dogs with canine mammary tumors (CMTs). Forty-four neoplastic, 17 non-neoplastic disease-bearing, and 15 healthy dogs were recruited. Necrosis and apoptosis were also assessed as potential source of cfDNA on 78 CMTs diagnosed from the 44 dogs. The cfDNA fragments and integrity index significantly differentiated neoplastic versus non-neoplastic dogs (P<0.05), and allowed the distinction between benign and malignant lesions (P<0.05). Even if without statistical significance, the amount of cfDNA was also affected by tumor necrosis and correlated with tumor size and apoptotic markers expression. A significant (P<0.01) increase of Bcl-2 in malignant tumors was observed, and in metastatic CMTs the evasion of apoptosis was also suggested. This study, therefore, provides evidence that cfDNA could be a diagnostic marker in dogs carrying mammary nodules suggesting that its potential application in early diagnostic procedures should be further investigated.
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Affiliation(s)
- Giorgia Beffagna
- Department of Comparative Biomedicine and Food Science, University of Padua, Legnaro, Padua, Italy
| | - Alessandro Sammarco
- Department of Comparative Biomedicine and Food Science, University of Padua, Legnaro, Padua, Italy
| | - Chiara Bedin
- Department of Surgical, Oncological and Gastroenterological Sciences, University of Padua, Padua, Italy
- Istituto di Ricerca Pediatrica – Città della Speranza, Padua, Italy
| | | | - Marta Mainenti
- Department of Comparative Biomedicine and Food Science, University of Padua, Legnaro, Padua, Italy
| | - Antonio Mollo
- Department of Animal Medicine, Productions and Health, University of Padua, Legnaro, Padua, Italy
| | - Laura Cavicchioli
- Department of Comparative Biomedicine and Food Science, University of Padua, Legnaro, Padua, Italy
| | - Silvia Ferro
- Department of Comparative Biomedicine and Food Science, University of Padua, Legnaro, Padua, Italy
| | - Davide Trez
- Department of Comparative Biomedicine and Food Science, University of Padua, Legnaro, Padua, Italy
| | - Raffaella De Maria
- Department of Veterinary Sciences, University of Turin, Grugliasco, Turin, Italy
| | - Donato Nitti
- Department of Surgical, Oncological and Gastroenterological Sciences, University of Padua, Padua, Italy
| | | | - Michelangelo Campanella
- Department of Comparative Biomedical Sciences, The Royal Veterinary College, London, United Kingdom
- UCL Consortium for Mitochondrial Research, London, United Kingdom
| | - Marco Agostini
- Department of Surgical, Oncological and Gastroenterological Sciences, University of Padua, Padua, Italy
- Istituto di Ricerca Pediatrica – Città della Speranza, Padua, Italy
| | - Valentina Zappulli
- Department of Comparative Biomedicine and Food Science, University of Padua, Legnaro, Padua, Italy
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