1
|
Yu F, Ahmed F, Smilkou S, Yasmin-Karim S, Darbeheshti F, Markou A, Bullock M, Boukovinas I, Adalsteinsson VA, Lianidou E, Makrigiorgos GM. Pyrimidine-Dependent UV-Mediated Cross-Linking Magnifies Minor Genetic or Epigenetic Changes in Clinical Samples. Clin Chem 2024:hvae086. [PMID: 39039866 DOI: 10.1093/clinchem/hvae086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Accepted: 05/20/2024] [Indexed: 07/24/2024]
Abstract
BACKGROUND Detection of minor DNA allele alterations is becoming increasingly important for early detection and monitoring of cancer. We describe a new method that uses ultraviolet light to eliminate wild-type DNA alleles and enables improved detection of minor genetic or epigenetic changes. METHODS Pyrimidine-dependent UV-based minor-allele enrichment (PD-UVME) employed oligonucleotide probes that incorporated a UVA-sensitive 3-cyanovinylcarbazole (CNVK), placed directly opposite interrogated pyrimidines, such as thymine (T) or cytosine (C) in wild-type (WT) DNA. Upon UVA-illumination, CNVK cross-linked with T/C, preventing subsequent amplification. Mutations that removed the T/C escaped cross-linking and were amplified and detected. Similarly, CNVK discriminated between methylated and unmethylated cytosine in CpG dinucleotides, enabling direct enrichment of unmethylated DNA targets. PD-UVME was combined with digital droplet PCR (ddPCR) to detect serine/threonine-protein kinase B-Raf (BRAF) V600E mutations in model systems, thyroid patient cancer tissue samples, and circulating DNA of tumor origin (ctDNA) from melanoma patients. RESULTS One thyroid cancer sample out of 9, and 6 circulating-DNA samples out of 7 were found to be BRAF V600E-positive via PD-UVME while classified as negative by conventional ddPCR. Positive samples via conventional ddPCR were also found positive via PD-UVME. All 10 circulating cell-free DNA (cfDNA) samples obtained from normal volunteers were negative via both approaches. Furthermore, preferential enrichment of unmethylated alleles in MAGEA1 promoters using PD-UVME was demonstrated. CONCLUSIONS PD-UVME mutation/methylation enrichment performed prior to ddPCR magnifies low-level mutations or epigenetic changes and increases sensitivity and confidence in the results. It can assist with clinical decisions that hinge on the presence of trace alterations like BRAF V600E.
Collapse
Affiliation(s)
- Fangyan Yu
- Department of Radiation Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA, United States
| | - Farzana Ahmed
- Department of Radiation Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA, United States
| | - Stavroula Smilkou
- Laboratory of Analytical Chemistry, Department of Chemistry, University of Athens, Athens, Greece
| | - Sayeda Yasmin-Karim
- Department of Radiation Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA, United States
| | - Farzaneh Darbeheshti
- Department of Radiation Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA, United States
| | - Athina Markou
- Laboratory of Analytical Chemistry, Department of Chemistry, University of Athens, Athens, Greece
| | - Martyn Bullock
- Cancer Genetics Laboratory, Kolling Institute, Northern Clinical School, Faculty of Medicine and Health, The University of Sydney & Northern Sydney Local Health District, St Leonards, NSW, Australia
| | - Ioannis Boukovinas
- Bioclinic Thessaloniki Medical Oncology Unit, Department of Medical Oncology, Thessaloniki, Greece
| | - Viktor A Adalsteinsson
- Gerstner Center for Cancer Diagnostics, Broad Institute of MIT and Harvard, Cambridge, MA, United States
| | - Evi Lianidou
- Laboratory of Analytical Chemistry, Department of Chemistry, University of Athens, Athens, Greece
| | - G Mike Makrigiorgos
- Department of Radiation Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA, United States
| |
Collapse
|
2
|
Ding H, Xu Y, Fang F, Wang H, Chen A. Functionalized primer initiated signal cycles and personal glucose meter for sensitive and portable miRNA analysis. Biotechniques 2024; 76:333-341. [PMID: 39185784 DOI: 10.1080/07366205.2024.2348347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2023] [Accepted: 04/18/2024] [Indexed: 08/27/2024] Open
Abstract
MicroRNA (miRNA) has garnered considerable attention due to its diagnostic capabilities, such as in hypoxic cognitive impairment and cancers. However, the existing miRNA detection methods are commonly criticized for the drawbacks of low sensitivity and false-positive detection derived from interfering molecules. Here, we provide a novel, sensitive and portable method for miRNA detection by combining target identification based cyclization of padlocks, immobilized primer-based signal amplification and a personal glucose meter. The proposed method exhibits several advantages, including precise identification of specific sites, exceptional sensitivity and instrument-free feature. These attributes hold great promise for the diagnosis and clinical investigation of various diseases, such as cancer and hypoxic cognitive impairment, enabling a deeper understanding of their pathological and physiological aspects.
Collapse
Affiliation(s)
- Heguo Ding
- Geriatrics Department, Huzhou Third Municipal Hospital, the Affiliated Hospital of Huzhou University, Zhejiang province, Huzhou 313000, China
| | - Yue Xu
- Department of Psychiatry, Huzhou Third Municipal Hospital, the Affiliated Hospital of Huzhou University, Zhejiang province, Huzhou 313000, China
| | - Fei Fang
- Geriatrics Department, Huzhou Third Municipal Hospital, the Affiliated Hospital of Huzhou University, Zhejiang province, Huzhou 313000, China
| | - Hong Wang
- Department of Psychiatry, Huzhou Third Municipal Hospital, the Affiliated Hospital of Huzhou University, Zhejiang province, Huzhou 313000, China
| | - Anqi Chen
- The Research Institute of Advanced Technologies, Ningbo University, Zhejiang province, Ningbo 315211, China
| |
Collapse
|
3
|
Ma J, Teng Y, Youming H, Tao X, Fan Y. The Value of Cell-Free Circulating DNA Profiling in Patients with Skin Diseases. Methods Mol Biol 2023; 2695:247-262. [PMID: 37450124 DOI: 10.1007/978-1-0716-3346-5_17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/18/2023]
Abstract
Liquid biopsy, also known as fluid biopsy or fluid-phase biopsy, is the sampling and analysis of the blood, cerebrospinal fluid, saliva, pleural fluid, ascites, and urine. Compared with tissue biopsy, liquid biopsy technology has the advantages of being noninvasive, having strong repeatability, enabling early diagnosis, dynamic monitoring, and overcoming tumor heterogeneity. However, interest in cfDNA and skin diseases has not expanded until recently. In this review, we present an overview of the literature related to the basic biology of cfDNA in the field of dermatology as a biomarker for early diagnosis, monitoring disease activity, predicting progression, and treatment response.
Collapse
Affiliation(s)
- Jingwen Ma
- Medical Cosmetic Center, Shanghai Skin Disease Hospital, Tongji University, Shanghai, People's Republic of China
| | - Yan Teng
- Health Management Center, Department of Dermatology, Zhejiang Provincial People's Hospital, Affiliated People's Hospital, Hangzhou Medical College, Hangzhou, People's Republic of China
| | - Huang Youming
- Health Management Center, Department of Dermatology, Zhejiang Provincial People's Hospital, Affiliated People's Hospital, Hangzhou Medical College, Hangzhou, People's Republic of China
| | - Xiaohua Tao
- Health Management Center, Department of Dermatology, Zhejiang Provincial People's Hospital, Affiliated People's Hospital, Hangzhou Medical College, Hangzhou, People's Republic of China
| | - Yibin Fan
- Health Management Center, Department of Dermatology, Zhejiang Provincial People's Hospital, Affiliated People's Hospital, Hangzhou Medical College, Hangzhou, People's Republic of China.
| |
Collapse
|
4
|
Hedtke M, Pessoa Rejas R, Froelich MF, Ast V, Duda A, Mirbach L, Costina V, Martens UM, Hofheinz R, Neumaier M, Haselmann V. Liquid profiling of circulating tumor DNA in colorectal cancer: steps needed to achieve its full clinical value as standard care. Mol Oncol 2022; 16:2042-2056. [PMID: 34873826 PMCID: PMC9120900 DOI: 10.1002/1878-0261.13156] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 10/27/2021] [Accepted: 12/06/2021] [Indexed: 12/23/2022] Open
Abstract
The analysis of circulating tumor DNA (ctDNA) is at the threshold of implementation into standard care for colorectal cancer (CRC) patients. However, data about the clinical utility of liquid profiling (LP), its acceptance by clinicians, and its integration into clinical workflows in real-world settings remain limited. Here, LP tests requested as part of routine care since 2016 were retrospectively evaluated. Results show restrained request behavior that improved moderately over time, as well as reliable diagnostic performance comparable to translational studies, with an overall agreement of 91.7%. Extremely low ctDNA levels at < 0.1% in over 20% of cases, a high frequency of concomitant driver mutations (in up to 14% of cases), and ctDNA levels reflecting the clinical course of disease were revealed. However, certain limitations hampering successful translation of ctDNA into clinical practice were uncovered, including the lack of clinically relevant ctDNA thresholds, appropriate time points of LP requests, and integrative evaluation of ctDNA, imaging, and clinical findings. In conclusion, these results highlight the potential clinical value of LP for CRC patient management and demonstrate issues that need to be addressed for successful long-term implementation in clinical workflows.
Collapse
Affiliation(s)
- Maren Hedtke
- Institute of Clinical ChemistryMedical Faculty Mannheim of the University of HeidelbergUniversity Hospital MannheimGermany
| | - Rodrigo Pessoa Rejas
- Institute of Clinical ChemistryMedical Faculty Mannheim of the University of HeidelbergUniversity Hospital MannheimGermany
| | - Matthias F. Froelich
- Department of Radiology and Nuclear MedicineUniversity Medicine MannheimMedical Faculty Mannheim of the University of HeidelbergGermany
| | - Volker Ast
- Institute of Clinical ChemistryMedical Faculty Mannheim of the University of HeidelbergUniversity Hospital MannheimGermany
| | - Angelika Duda
- Institute of Clinical ChemistryMedical Faculty Mannheim of the University of HeidelbergUniversity Hospital MannheimGermany
| | - Laura Mirbach
- Institute of Clinical ChemistryMedical Faculty Mannheim of the University of HeidelbergUniversity Hospital MannheimGermany
| | - Victor Costina
- Institute of Clinical ChemistryMedical Faculty Mannheim of the University of HeidelbergUniversity Hospital MannheimGermany
| | - Uwe M. Martens
- Cancer Center Heilbronn‐FrankenSLK‐ClinicsMOLIT Institute for Personalized MedicineHeilbronnGermany
| | - Ralf‐Dieter Hofheinz
- Day Treatment Center (TTZ)Interdisciplinary Tumor Center Mannheim (ITM)III Medical ClinicMedical Faculty Mannheim of the University of HeidelbergUniversity Hospital MannheimGermany
| | - Michael Neumaier
- Institute of Clinical ChemistryMedical Faculty Mannheim of the University of HeidelbergUniversity Hospital MannheimGermany
| | - Verena Haselmann
- Institute of Clinical ChemistryMedical Faculty Mannheim of the University of HeidelbergUniversity Hospital MannheimGermany
| |
Collapse
|
5
|
Liu S, Yang Y, Shi M, Shi H, Mao D, Mao X, Zhang Y. Smartphone-Based Pure DNAzyme Hydrogel Platform for Visible and Portable Colorimetric Detection of Cell-Free DNA. ACS Sens 2022; 7:658-665. [PMID: 35107259 DOI: 10.1021/acssensors.1c02662] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Cell-free DNA (cfDNA), as a tumor marker, is of great importance for the diagnosis of cancer and targeted therapy. However, the need for huge analytical instruments for cfDNA analysis has restricted its practical applications, especially in rural areas and third-world countries. Herein, a portable and visual smartphone-based DNAzyme hydrogel platform is developed for cfDNA detection. The target cfDNA triggers rolling circle amplification to produce a G-quadruplex-comprised DNA hydrogel with an horseradish peroxidase (HRP)-like catalytic function, which further catalyzes the chromogenic substrate to generate a visible output signal. Notably, the naked-eye detection of cfDNA can be realized by the macroscale visibility and catalytic ability of the DNA hydrogel. The linear range of the DNAzyme hydrogel platform for cfDNA detection is 0.1 pM-1500 nM with a detection limit of 0.042 pM. Moreover, this platform is exploited for the detection of cfDNA in spiked human serum with favorable sensitivity and recovery. Therefore, the DNAzyme hydrogel platform provides highly promising potential for testing other nucleic acid biomarkers.
Collapse
Affiliation(s)
- Shaowei Liu
- Key Laboratory of Aqueous Environment Protection and Pollution Control of Yangtze River in Anhui of Anhui Provincial Education Department, College of Resources and Environment, Anqing Normal University, Anqing 246011, China
| | - Yumeng Yang
- College of Chemistry and Chemical Engineering, Anqing Normal University, Anqing 246011, China
| | - Mengqin Shi
- Key Laboratory of Aqueous Environment Protection and Pollution Control of Yangtze River in Anhui of Anhui Provincial Education Department, College of Resources and Environment, Anqing Normal University, Anqing 246011, China
| | - Hai Shi
- The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China
| | - Dongsheng Mao
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai 200444, China
| | - Xiaoxia Mao
- Key Laboratory of Aqueous Environment Protection and Pollution Control of Yangtze River in Anhui of Anhui Provincial Education Department, College of Resources and Environment, Anqing Normal University, Anqing 246011, China
| | - Yuanguang Zhang
- Key Laboratory of Aqueous Environment Protection and Pollution Control of Yangtze River in Anhui of Anhui Provincial Education Department, College of Resources and Environment, Anqing Normal University, Anqing 246011, China
| |
Collapse
|
6
|
Ye P, Cai P, Xie J, Zhang J. Reliability of BRAF mutation detection using plasma sample: A systematic review and meta-analysis. Medicine (Baltimore) 2021; 100:e28382. [PMID: 34941166 PMCID: PMC8701458 DOI: 10.1097/md.0000000000028382] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/04/2020] [Revised: 11/10/2021] [Accepted: 12/01/2021] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND Testing of B-Raf proto-oncogene (BRAF) mutation in tumor is necessary before targeted therapies are given. When tumor samples are not available, plasma samples are commonly used for the testing of BRAF mutation. The aim of this study was to investigate the diagnostic accuracy of BRAF mutation testing using plasma sample of cancer patients. METHODS Databases of Pubmed, Embase, and Cochrane Library were searched for eligible studies investigating BRAF mutation in paired tissue and plasma samples of cancer patients. A total of 798 publications were identified after database searching. After removing 229 duplicated publications, 569 studies were screened using the following exclusion criteria: (1) BRAF mutation not measured in plasma or in tumor sample; (2) lacking BRAF-wildtype or BRAF-mutated samples; (3) tissue and plasma samples not paired; (4) lacking tumor or plasma samples; (5) not plasma sample; (6) not cancer; (7) un-interpretable data. Accuracy data and relevant information were extracted from each eligible study by 2 independent researchers and analyzed using statistical software. RESULTS After pooling the accuracy data from 3943 patients of the 53 eligible studies, the pooled sensitivity, specificity, and diagnostic odds ratio of BRAF mutation testing using plasma sample were 69%, 98%, and 55.78, respectively. Area under curve of summary receiver operating characteristic curve was 0.9435. Subgroup analysis indicated that BRAF mutation testing using plasma had overall higher accuracy (diagnostic odds ratio of 89.17) in colorectal cancer, compared to melanoma and thyroid carcinoma. In addition, next-generation sequencing had an overall higher accuracy in detecting BRAF mutation using plasma sample (diagnostic odds ratio of 63.90), compared to digital polymerase chain reaction (PCR) and conventional PCR, while digital PCR showed the highest sensitivity (74%) among the 3 techniques. CONCLUSION BRAF testing using plasma sample showed an overall high accuracy compared to paired tumor tissue sample, which could be used for cancer genotyping when tissue sample is not available. Large prospective studies are needed to further investigate the accuracy of BRAF mutation testing in plasma sample.
Collapse
Affiliation(s)
- Peng Ye
- Department of Anatomy and Histology, School of Preclinical Medicine, Chengdu University, Chengdu, P.R. China
| | - Peiling Cai
- Department of Anatomy and Histology, School of Preclinical Medicine, Chengdu University, Chengdu, P.R. China
| | - Jing Xie
- Department of Pathology and Clinical Laboratory, Sichuan Provincial Fourth People's Hospital, Chengdu, P.R. China
| | - Jie Zhang
- Adverse Drug Reaction Monitoring Center, Chengdu, P.R. China
| |
Collapse
|
7
|
The BRAF V600E Mutation Detection by quasa Sensitive Real-Time PCR Assay in Northeast Romania Melanoma Patients. APPLIED SCIENCES-BASEL 2021. [DOI: 10.3390/app11209511] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Background: The prevalence of melanoma in Romanian patients is underestimated. There is a need to identify the BRAF V600E mutation to accurately treat patients with the newest approved BRAF inhibitor therapy. This is a pilot study in which we first aimed to choose the optimal DNA purification method from formalin fixation and paraffin embedding (FFPE) malignant melanoma skin samples to assess the BRAF mutation prevalence and correlate it with clinical pathological parameters. Methods: 30 FFPE samples were purified in parallel with two DNA extraction kits, a manual and a semi-automated kit. The extracted DNA in pure and optimum quantity was tested for the BRAF V600E mutation using the quantitative allele-specific amplification (quasa) method. quasa is a method for the sensitive detection of mutations that may be present in clinical samples at low levels. Results: The BRAF V600E mutation was detected in 60% (18/30) samples in patients with primary cutaneous melanoma of the skin. BRAFV600E mutation was equally distributed by gender and was associated with age >60, nodular melanoma, and trunk localization. Conclusions: The high prevalence of BRAF V600E mutations in our study group raises awareness for improvements to the national reporting system and initiation of the target therapy for patients with malignant melanoma of the skin.
Collapse
|
8
|
de Miranda FS, Barauna VG, dos Santos L, Costa G, Vassallo PF, Campos LCG. Properties and Application of Cell-Free DNA as a Clinical Biomarker. Int J Mol Sci 2021; 22:9110. [PMID: 34502023 PMCID: PMC8431421 DOI: 10.3390/ijms22179110] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 04/18/2021] [Accepted: 04/20/2021] [Indexed: 12/17/2022] Open
Abstract
Biomarkers are valuable tools in clinical practice. In 2001, the National Institutes of Health (NIH) standardized the definition of a biomarker as a characteristic that is objectively measured and evaluated as an indicator of normal biological processes, pathogenic processes, or pharmacological responses to a therapeutic intervention. A biomarker has clinical relevance when it presents precision, standardization and reproducibility, suitability to the patient, straightforward interpretation by clinicians, and high sensitivity and/or specificity by the parameter it proposes to identify. Thus, serum biomarkers should have advantages related to the simplicity of the procedures and to the fact that venous blood collection is commonplace in clinical practice. We described the potentiality of cfDNA as a general clinical biomarker and focused on endothelial dysfunction. Circulating cell-free DNA (cfDNA) refers to extracellular DNA present in body fluid that may be derived from both normal and diseased cells. An increasing number of studies demonstrate the potential use of cfDNA as a noninvasive biomarker to determine physiologic and pathologic conditions. However, although still scarce, increasing evidence has been reported regarding using cfDNA in cardiovascular diseases. Here, we have reviewed the history of cfDNA, its source, molecular features, and release mechanism. We also show recent studies that have investigated cfDNA as a possible marker of endothelial damage in clinical settings. In the cardiovascular system, the studies are quite new, and although interesting, stronger evidence is still needed. However, some drawbacks in cfDNA methodologies should be overcome before its recommendation as a biomarker in the clinical setting.
Collapse
Affiliation(s)
- Felipe Silva de Miranda
- Post Graduation Program in Biology and Biotechnology of Microorganisms, State University of Santa Cruz, Ilhéus 45662-900, Bahia, Brazil;
- Department of Biological Science, State University of Santa Cruz, Ilhéus 45662-900, Bahia, Brazil
- Laboratory of Applied Pathology and Genetics, State University of Santa Cruz, Ilhéus 45662-900, Bahia, Brazil
| | - Valério Garrone Barauna
- Post Graduation Program in Health Sciences, State University of Santa Cruz, Ilhéus 45662-900, Bahia, Brazil;
- Molecular Physiology Laboratory of Exercise Science, Federal University of Espírito Santo, Vitória 29075-910, Espírito Santo, Brazil
- Post Graduation Program in Physiological Sciences, Federal University of Espírito Santo, Vitória 29075-910, Espírito Santo, Brazil; (G.C.); (P.F.V.)
| | - Leandro dos Santos
- Academic Unit of Serra Talhada, Rural Federal University of Pernambuco, Serra Talhada 56909-535, Pernambuco, Brazil;
| | - Gustavo Costa
- Post Graduation Program in Physiological Sciences, Federal University of Espírito Santo, Vitória 29075-910, Espírito Santo, Brazil; (G.C.); (P.F.V.)
| | - Paula Frizera Vassallo
- Post Graduation Program in Physiological Sciences, Federal University of Espírito Santo, Vitória 29075-910, Espírito Santo, Brazil; (G.C.); (P.F.V.)
- Clinical Hospital, Federal University of Minas Gerais, Belo Horizonte 30130-100, Minas Gerais, Brazil
| | - Luciene Cristina Gastalho Campos
- Post Graduation Program in Biology and Biotechnology of Microorganisms, State University of Santa Cruz, Ilhéus 45662-900, Bahia, Brazil;
- Department of Biological Science, State University of Santa Cruz, Ilhéus 45662-900, Bahia, Brazil
- Laboratory of Applied Pathology and Genetics, State University of Santa Cruz, Ilhéus 45662-900, Bahia, Brazil
- Post Graduation Program in Health Sciences, State University of Santa Cruz, Ilhéus 45662-900, Bahia, Brazil;
| |
Collapse
|
9
|
Herbreteau G, Vallée A, Knol AC, Théoleyre S, Quéreux G, Varey E, Khammari A, Dréno B, Denis MG. Circulating Tumor DNA Early Kinetics Predict Response of Metastatic Melanoma to Anti-PD1 Immunotherapy: Validation Study. Cancers (Basel) 2021; 13:1826. [PMID: 33920470 PMCID: PMC8069589 DOI: 10.3390/cancers13081826] [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: 03/06/2021] [Revised: 04/06/2021] [Accepted: 04/09/2021] [Indexed: 12/16/2022] Open
Abstract
The ability of early (first weeks of treatment) ctDNA kinetics to identify primary resistance to anti-PD1 immunotherapies was evaluated with a validation cohort of 49 patients treated with anti-PD1 for metastatic BRAF or NRAS-mutated melanoma, alone and pooled with the 53 patients from a previously described derivation cohort. BRAF or NRAS mutations were quantified on plasma DNA by digital PCR at baseline and after two or four weeks of treatment. ctDNA kinetics were interpreted according to pre-established biological response criteria. A biological progression (bP, i.e., a significant increase in ctDNA levels) at week two or week four was associated with a lack of benefit from anti-PD1 (4-month PFS = 0%; 1-year OS = 13%; n = 12/102). Patients without initial bP had significantly better PFS and OS (4-month PFS = 78%; 1-year OS = 73%; n = 26/102), as did patients whose ctDNA kinetics were not evaluable, due to low/undetectable baseline ctDNA (4-month PFS = 80%; 1-year OS = 81%; n = 64/102). ctDNA detection at first-line anti-PD1 initiation was an independent prognostic factor for OS and PFS in multivariate analysis. Overall, early ctDNA quantitative monitoring may allow the detection of primary resistances of metastatic melanoma to anti-PD1 immunotherapies.
Collapse
Affiliation(s)
- Guillaume Herbreteau
- Laboratoire de Biochimie et Plateforme de Génétique Moléculaire des Cancers, Centre Hospitalier Universitaire (CHU) Nantes, 44093 Nantes, France; (G.H.); (A.V.); (S.T.)
- Centre de Recherche en Cancérologie et Immunologie (CRCINA), Institut National de la Santé et de la Recherche Médicale (INSERM) U1232, 44007 Nantes, France; (A.-C.K.); (G.Q.); (E.V.); (A.K.); (B.D.)
| | - Audrey Vallée
- Laboratoire de Biochimie et Plateforme de Génétique Moléculaire des Cancers, Centre Hospitalier Universitaire (CHU) Nantes, 44093 Nantes, France; (G.H.); (A.V.); (S.T.)
- Centre de Recherche en Cancérologie et Immunologie (CRCINA), Institut National de la Santé et de la Recherche Médicale (INSERM) U1232, 44007 Nantes, France; (A.-C.K.); (G.Q.); (E.V.); (A.K.); (B.D.)
| | - Anne-Chantal Knol
- Centre de Recherche en Cancérologie et Immunologie (CRCINA), Institut National de la Santé et de la Recherche Médicale (INSERM) U1232, 44007 Nantes, France; (A.-C.K.); (G.Q.); (E.V.); (A.K.); (B.D.)
| | - Sandrine Théoleyre
- Laboratoire de Biochimie et Plateforme de Génétique Moléculaire des Cancers, Centre Hospitalier Universitaire (CHU) Nantes, 44093 Nantes, France; (G.H.); (A.V.); (S.T.)
- Centre de Recherche en Cancérologie et Immunologie (CRCINA), Institut National de la Santé et de la Recherche Médicale (INSERM) U1232, 44007 Nantes, France; (A.-C.K.); (G.Q.); (E.V.); (A.K.); (B.D.)
| | - Gaëlle Quéreux
- Centre de Recherche en Cancérologie et Immunologie (CRCINA), Institut National de la Santé et de la Recherche Médicale (INSERM) U1232, 44007 Nantes, France; (A.-C.K.); (G.Q.); (E.V.); (A.K.); (B.D.)
- Service de Dermatologie, Centre Hospitalier Universitaire (CHU) Nantes, 44000 Nantes, France
- Centre d′Investigation Clinique (CIC) 1413, Institut National de la Santé et de la Recherche Médicale (INSERM), Centre Hospitalier Universitaire (CHU) Nantes, 44021 Nantes, France
| | - Emilie Varey
- Centre de Recherche en Cancérologie et Immunologie (CRCINA), Institut National de la Santé et de la Recherche Médicale (INSERM) U1232, 44007 Nantes, France; (A.-C.K.); (G.Q.); (E.V.); (A.K.); (B.D.)
- Centre d′Investigation Clinique (CIC) 1413, Institut National de la Santé et de la Recherche Médicale (INSERM), Centre Hospitalier Universitaire (CHU) Nantes, 44021 Nantes, France
| | - Amir Khammari
- Centre de Recherche en Cancérologie et Immunologie (CRCINA), Institut National de la Santé et de la Recherche Médicale (INSERM) U1232, 44007 Nantes, France; (A.-C.K.); (G.Q.); (E.V.); (A.K.); (B.D.)
- Service de Dermatologie, Centre Hospitalier Universitaire (CHU) Nantes, 44000 Nantes, France
- Centre d′Investigation Clinique (CIC) 1413, Institut National de la Santé et de la Recherche Médicale (INSERM), Centre Hospitalier Universitaire (CHU) Nantes, 44021 Nantes, France
| | - Brigitte Dréno
- Centre de Recherche en Cancérologie et Immunologie (CRCINA), Institut National de la Santé et de la Recherche Médicale (INSERM) U1232, 44007 Nantes, France; (A.-C.K.); (G.Q.); (E.V.); (A.K.); (B.D.)
- Service de Dermatologie, Centre Hospitalier Universitaire (CHU) Nantes, 44000 Nantes, France
- Centre d′Investigation Clinique (CIC) 1413, Institut National de la Santé et de la Recherche Médicale (INSERM), Centre Hospitalier Universitaire (CHU) Nantes, 44021 Nantes, France
| | - Marc G. Denis
- Laboratoire de Biochimie et Plateforme de Génétique Moléculaire des Cancers, Centre Hospitalier Universitaire (CHU) Nantes, 44093 Nantes, France; (G.H.); (A.V.); (S.T.)
- Centre de Recherche en Cancérologie et Immunologie (CRCINA), Institut National de la Santé et de la Recherche Médicale (INSERM) U1232, 44007 Nantes, France; (A.-C.K.); (G.Q.); (E.V.); (A.K.); (B.D.)
| |
Collapse
|
10
|
Strati A, Zavridou M, Economopoulou P, Gkolfinopoulos S, Psyrri A, Lianidou E. Development and Analytical Validation of a Reverse Transcription Droplet Digital PCR (RT-ddPCR) Assay for PD-L1 Transcripts in Circulating Tumor Cells. Clin Chem 2021; 67:642-652. [PMID: 33421061 DOI: 10.1093/clinchem/hvaa321] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Accepted: 11/09/2020] [Indexed: 01/03/2023]
Abstract
BACKGROUND PD-L1, an immune checkpoint protein, is an important biomarker for monitoring cancer patients during the administration of cancer immunotherapy. Droplet digital PCR (ddPCR), is a highly sensitive and accurate tool for the quantification of cancer biomarkers in liquid biopsy. We report the development and analytical validation of a novel duplex RT-ddPCR assay for the simultaneous quantification of PD-L1 and hypoxanthine phosphoribosyltransferase (HPRT) (used as reference gene) transcripts in circulating tumor cells (CTCs). METHODS RT-ddPCR experimental conditions were first optimized and the assay was analytically validated using synthetic standards and the BB49 and SCC47 cancer cell lines. The developed assay was further applied in 71 peripheral blood (PB) samples from head and neck squamous cell carcinoma (HNSCC) patients and 20 PB samples from healthy donors. PD-L1 and HPRT transcripts were quantified in cDNAs derived from CTCs isolated by a size-dependent microfluidic device. The developed RT-ddPCR assay was directly compared to RT-qPCR using 71 identical patient cDNA samples. RESULTS Analytical sensitivity was 0.64 copies/μL, while estimation of intra- and interassay variation revealed a high reproducibility (within-run CV%:4.7-23%; between-run CV%:13%). Using the developed RT-ddPCR assay 33/71(46.5%) HNSCC patients' samples were found positive for PD-L1 expression in CTCs, while by using RT-qPCR fewer samples (23/71, 32.4%) were positive (concordance: 55/71, 77.5%). CONCLUSIONS The developed RT-ddPCR assay for PD-L1 in CTCs is highly sensitive, specific, and reproducible; additionally, it offers improved diagnostic sensitivity over RT-qPCR. The clinical utility of the assay should be prospectively evaluated for the real-time monitoring of CTCs of cancer patients under immunotherapy.
Collapse
Affiliation(s)
- Areti Strati
- Department of Chemistry, Analysis of Circulating Tumor Cells Lab, National and Kapodistrian University of Athens, Athens, Greece
| | - Martha Zavridou
- Department of Chemistry, Analysis of Circulating Tumor Cells Lab, National and Kapodistrian University of Athens, Athens, Greece
| | - Panagiota Economopoulou
- Oncology Unit, 2nd Department of Internal Medicine-Propaedeutic, Attikon University Hospital, National and Kapodistrian University of Athens, Athens, Greece
| | - Stavros Gkolfinopoulos
- Oncology Unit, 2nd Department of Internal Medicine-Propaedeutic, Attikon University Hospital, National and Kapodistrian University of Athens, Athens, Greece
| | - Amanda Psyrri
- Oncology Unit, 2nd Department of Internal Medicine-Propaedeutic, Attikon University Hospital, National and Kapodistrian University of Athens, Athens, Greece
| | - Evi Lianidou
- Department of Chemistry, Analysis of Circulating Tumor Cells Lab, National and Kapodistrian University of Athens, Athens, Greece
| |
Collapse
|
11
|
Forschner A, Weißgraeber S, Hadaschik D, Schulze M, Kopp M, Kelkenberg S, Sinnberg T, Garbe C, Biskup S, Battke F. Circulating Tumor DNA Correlates with Outcome in Metastatic Melanoma Treated by BRAF and MEK Inhibitors - Results of a Prospective Biomarker Study. Onco Targets Ther 2020; 13:5017-5032. [PMID: 32581559 PMCID: PMC7280255 DOI: 10.2147/ott.s248237] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Accepted: 04/09/2020] [Indexed: 12/14/2022] Open
Abstract
Purpose BRAF and MEK inhibitors significantly improved the prognosis of metastatic melanoma. Nevertheless, initial treatment response may be only temporary. Liquid biopsies (LB) offer a possibility to monitor patients by measuring circulating tumor DNA (ctDNA). We sought to find out whether ctDNA can be used to reliably determine progressive disease under targeted therapy. In addition, we wanted to check whether ctDNA may represent a possible prognostic marker for survival. Patients and Methods We included 19 melanoma patients with BRAF and MEK inhibitor therapy. For each patient, a 710 gene panel was analyzed on the latest available tumor tissue before the start of therapy. Repetitive LB were collected in which BRAF V600E/K mutations were monitored using digital droplet PCR (ddPCR). We correlated radiological staging results and overall survival with ctDNA results. Results In 13 patients, ctDNA was detectable when starting targeted therapy, whereas in six patients, ddPCR was always negative, which we confirmed with ultra-deep sequencing. All patients with initially detectable ctDNA had ctDNA values declining to zero during follow-up, increasing again at the time of extracerebral progression or even slightly before detection by imaging. Survival was significantly worse for patients with elevated LDH (p=0.034) or detectable ctDNA (p=0.008) at the start of targeted therapy. Conclusion Therapy monitoring by ctDNA seems to be a reliable method for detecting extracranial progression, even more sensitive and specific than LDH or S100B. However, due to the small number of cases in our study, further studies are necessary.
Collapse
Affiliation(s)
- Andrea Forschner
- Center for Dermatooncology, Department of Dermatology, University Hospital Tuebingen, Tuebingen, Germany
| | | | - Dirk Hadaschik
- Center for Genomics and Transcriptomics (CeGaT) GmbH, Tuebingen, Germany
| | | | - Maria Kopp
- Center for Genomics and Transcriptomics (CeGaT) GmbH, Tuebingen, Germany
| | - Sabine Kelkenberg
- Center for Genomics and Transcriptomics (CeGaT) GmbH, Tuebingen, Germany
| | - Tobias Sinnberg
- Center for Dermatooncology, Department of Dermatology, University Hospital Tuebingen, Tuebingen, Germany
| | - Claus Garbe
- Center for Dermatooncology, Department of Dermatology, University Hospital Tuebingen, Tuebingen, Germany
| | - Saskia Biskup
- Center for Genomics and Transcriptomics (CeGaT) GmbH, Tuebingen, Germany.,Practice for Human Genetics, Tuebingen, Germany
| | - Florian Battke
- Center for Genomics and Transcriptomics (CeGaT) GmbH, Tuebingen, Germany
| |
Collapse
|