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Hayashi Y, Millen JC, Ramos RI, Linehan JA, Wilson TG, Hoon DSB, Bustos MA. Cell-free and extracellular vesicle microRNAs with clinical utility for solid tumors. Mol Oncol 2024. [PMID: 39129372 DOI: 10.1002/1878-0261.13709] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Revised: 05/28/2024] [Accepted: 07/23/2024] [Indexed: 08/13/2024] Open
Abstract
As cutting-edge technologies applied for the study of body fluid molecular biomarkers are continuously evolving, clinical applications of these biomarkers improve. Diverse forms of circulating molecular biomarkers have been described, including cell-free DNA (cfDNA), circulating tumor cells (CTCs), and cell-free microRNAs (cfmiRs), although unresolved issues remain in their applicability, specificity, sensitivity, and reproducibility. Translational studies demonstrating the clinical utility and importance of cfmiRs in multiple cancers have significantly increased. This review aims to summarize the last 5 years of translational cancer research in the field of cfmiRs and their potential clinical applications to diagnosis, prognosis, and monitoring disease recurrence or treatment responses with a focus on solid tumors. PubMed was utilized for the literature search, following rigorous exclusion criteria for studies based on tumor types, patient sample size, and clinical applications. A total of 136 studies on cfmiRs in different solid tumors were identified and divided based on tumor types, organ sites, number of cfmiRs found, methodology, and types of biofluids analyzed. This comprehensive review emphasizes clinical applications of cfmiRs and summarizes underserved areas where more research and validations are needed.
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Affiliation(s)
- Yoshinori Hayashi
- Department of Translational Molecular Medicine, Saint John's Cancer Institute at Providence Saint John's Health Center, Santa Monica, CA, USA
| | - Janelle-Cheri Millen
- Department of Surgical Oncology, Saint John's Cancer Institute at Providence Saint John's Health Center, Santa Monica, CA, USA
| | - Romela Irene Ramos
- Department of Translational Molecular Medicine, Saint John's Cancer Institute at Providence Saint John's Health Center, Santa Monica, CA, USA
| | - Jennifer A Linehan
- Department of Urology and Urologic Oncology, Saint John's Cancer Institute at Providence Saint John's Health Center, Santa Monica, CA, USA
| | - Timothy G Wilson
- Department of Urology and Urologic Oncology, Saint John's Cancer Institute at Providence Saint John's Health Center, Santa Monica, CA, USA
| | - Dave S B Hoon
- Department of Translational Molecular Medicine, Saint John's Cancer Institute at Providence Saint John's Health Center, Santa Monica, CA, USA
- Department of Genome Sequencing Center, Saint John's Cancer Institute at Providence Saint John's Health Center, Santa Monica, CA, USA
| | - Matias A Bustos
- Department of Translational Molecular Medicine, Saint John's Cancer Institute at Providence Saint John's Health Center, Santa Monica, CA, USA
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Yan X, Zhang W, Yang J. Self-signal electrochemical identification of circulating tumor DNA employing poly-xanthurenic acid assembled on black phosphorus nanosheets. Anal Biochem 2024; 690:115512. [PMID: 38527608 DOI: 10.1016/j.ab.2024.115512] [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: 12/29/2023] [Revised: 03/14/2024] [Accepted: 03/20/2024] [Indexed: 03/27/2024]
Abstract
A self-signal electrochemical identification interface was prepared for the determination of circulating tumor DNA (ctDNA) in peripheral blood based on poly-xanthurenic acid (PXTA) assembled on black phosphorus nanosheets (BPNSs) acquired through simple ultrasonication method. The BPNSs with large surface area could be integrated with the xanthurenic acid (XTA) monomers by right of physisorption, and hence improved the electropolymerization efficiency and was beneficial to the enlargement of the signal response of PXTA. The assembled PXTA/BPNSs composite with attractive electrochemical activity was adopted as a platform for the recognition of DNA immobilization and hybridization. The probe ssDNA was covalently fixed onto the PXTA/BPNSs composite with plentiful carboxyl groups through the terminate free amines of DNA probes by use of the 1-ethyl-3-(3-dimethylaminopropyl) carbodiimide and N-hydrosulfosuccinimide cross-linking reaction, accompanied with the decline of the self-signal response. When the hybridization between the probe ssDNA and the target DNA was accomplished, the self-signal response of the composite interface reproduced by virtue of the shaping of helix construction. The determination limit of the assembled DNA identification interface was 2.1 × 10-19 mol/L, and the complementary target DNA concentrations varied from 1.0 × 10-18 mol/L to 1.0 × 10-12 mol/L. The DNA identification platform displayed magnificent sensitivity, specificity and stability, and was efficaciously implemented to the mensuration of ctDNA derived from colorectal cancer.
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Affiliation(s)
- Xinyu Yan
- School of Chemistry and Chemical Engineering, Linyi University, Linyi, 276000, China
| | - Wei Zhang
- School of Chemistry and Chemical Engineering, Linyi University, Linyi, 276000, China.
| | - Jimin Yang
- School of Chemistry and Chemical Engineering, Linyi University, Linyi, 276000, China
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Marinello A, Tagliamento M, Pagliaro A, Conci N, Cella E, Vasseur D, Remon J, Levy A, Dall'Olio FG, Besse B. Circulating tumor DNA to guide diagnosis and treatment of localized and locally advanced non-small cell lung cancer. Cancer Treat Rev 2024; 129:102791. [PMID: 38963991 DOI: 10.1016/j.ctrv.2024.102791] [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: 04/23/2024] [Revised: 06/15/2024] [Accepted: 06/22/2024] [Indexed: 07/06/2024]
Abstract
Liquid biopsy is a minimally invasive method for biomarkers detection in body fluids, particularly in blood, which offers an elevated and growing number of clinical applications in oncology. As a result of the improvement in the techniques for DNA analysis, above all next-generation sequencing (NGS) assays, circulating tumor DNA (ctDNA) has become the most informing tumor-derived material for most types of cancer, including non-small cell lung cancer (NSCLC). Although ctDNA concentration is higher in patients with advanced tumors, it can be detected even in patients with early-stage disease. Therefore, numerous clinical applications of ctDNA in the management of early-stage lung cancer are emerging, such as lung cancer screening, the identification of minimal residual disease (MRD), and the prediction of relapse before radiologic progression. Moreover, a high number of clinical trials are ongoing to better define the impact of ctDNA evaluation in this setting. Aim of this review is to offer a comprehensive overview of the most relevant implementations in using ctDNA for the management of early-stage lung cancer, addressing available data, technical aspects, limitations, and future perspectives.
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Affiliation(s)
- Arianna Marinello
- Department of Cancer Medicine, Gustave Roussy, Villejuif, France; INSERM Unit 1030 - Molecular Radiotherapy and Therapeutic Innovation, Gustave Roussy, Villejuif, France
| | - Marco Tagliamento
- Department of Cancer Medicine, Gustave Roussy, Villejuif, France; Department of Internal Medicine and Medical Specialties, University of Genova, Genova, Italy.
| | - Arianna Pagliaro
- Department of Cancer Medicine, Gustave Roussy, Villejuif, France; Department of Medical Oncology, IRCCS Istituto Clinico Humanitas, Rozzano, Italy
| | - Nicole Conci
- Department of Medical Oncology, IRCCS Sant'Orsola-Malpighi, Bologna, Italy
| | - Eugenia Cella
- Department of Internal Medicine and Medical Specialties, University of Genova, Genova, Italy
| | - Damien Vasseur
- Department of Medical Biology and Pathology, Gustave Roussy, Villejuif, France
| | - Jordi Remon
- Department of Cancer Medicine, Gustave Roussy, Villejuif, France
| | - Antonin Levy
- Department of Radiotherapy, Gustave Roussy, Villejuif, France
| | | | - Benjamin Besse
- Department of Cancer Medicine, Gustave Roussy, Villejuif, France
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Ma Z, Xu J, Hou W, Lei Z, Li T, Shen W, Yu H, Liu C, Zhang J, Tang S. Detection of Single Nucleotide Polymorphisms of Circulating Tumor DNA by Strand Displacement Amplification Coupled with Liquid Chromatography. Anal Chem 2024; 96:5195-5204. [PMID: 38520334 DOI: 10.1021/acs.analchem.3c05500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/25/2024]
Abstract
The detection of multiple single nucleotide polymorphisms (SNPs) of circulating tumor DNA (ctDNA) is still a great challenge. In this study, we designed enzyme-assisted nucleic acid strand displacement amplification combined with high-performance liquid chromatography (HPLC) for the simultaneous detection of three ctDNA SNPs. First, the trace ctDNA could be hybridized to the specially designed template strand, which initiated the strand displacement nucleic acid amplification process under the synergistic action of DNA polymerase and restriction endonuclease. Then, the targets would be replaced with G-quadruplex fluorescent probes with different tail lengths. Finally, the HPLC-fluorescence assay enabled the separation and quantification of multiple signals. Notably, this method can simultaneously detect both the wild type (WT) and mutant type (MT) of multiple ctDNA SNPs. Within a linear range of 0.1 fM-0.1 nM, the detection limits of BRAF V600E-WT, EGFR T790M-WT, and KRAS 134A-WT and BRAF V600E-MT, EGFR T790M-MT, and KRAS 134A-MT were 29, 31, and 11 aM and 22, 29, and 33 aM, respectively. By using this method, the mutation rates of multiple ctDNA SNPs in blood samples from patients with lung or breast cancer can be obtained in a simple way, providing a convenient and highly sensitive analytical assay for the early screening and monitoring of lung cancer.
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Affiliation(s)
- Ziyu Ma
- School of Environmental and Chemical Engineering, Jiangsu University of Science and Technology, Zhenjiang 212003, Jiangsu, P. R. China
| | - Junjie Xu
- School of Environmental and Chemical Engineering, Jiangsu University of Science and Technology, Zhenjiang 212003, Jiangsu, P. R. China
| | - Weilin Hou
- School of Environmental and Chemical Engineering, Jiangsu University of Science and Technology, Zhenjiang 212003, Jiangsu, P. R. China
| | - Zi Lei
- School of Environmental and Chemical Engineering, Jiangsu University of Science and Technology, Zhenjiang 212003, Jiangsu, P. R. China
| | - Tingting Li
- School of Environmental and Chemical Engineering, Jiangsu University of Science and Technology, Zhenjiang 212003, Jiangsu, P. R. China
| | - Wei Shen
- School of Environmental and Chemical Engineering, Jiangsu University of Science and Technology, Zhenjiang 212003, Jiangsu, P. R. China
| | - Hui Yu
- Department of Thoracic Surgery, Affiliated Hospital of Jiangsu University, No. 438, Jiefang Road, Zhenjiang 212000, Jiangsu, P. R. China
| | - Chang Liu
- School of Grain Science and Technology, Jiangsu University of Science and Technology, Zhenjiang 212003, Jiangsu, P. R. China
| | - Jinghui Zhang
- School of Environmental and Chemical Engineering, Jiangsu University of Science and Technology, Zhenjiang 212003, Jiangsu, P. R. China
| | - Sheng Tang
- School of Environmental and Chemical Engineering, Jiangsu University of Science and Technology, Zhenjiang 212003, Jiangsu, P. R. China
- College of Chemistry, Chemical Engineering and Materials Science, Soochow University, Suzhou 215123, P. R. China
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Kus T, Cicin I. A perspective: the integration of ctDNA into Response Evaluation Criteria in Solid Tumours 1.1 for phase II immunotherapy clinical trials. Immunotherapy 2024; 16:319-329. [PMID: 38197142 DOI: 10.2217/imt-2023-0184] [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: 01/11/2024] Open
Abstract
A consensus guideline, iRECIST, was developed by the Response Evaluation Criteria in Solid Tumours (RECIST) working group for the use of the modified RECIST version 1.1 in cancer immunotherapy trials. iRECIST was designed to separate pseudoprogression from real progression. However, this is not the only ambiguous situation. In clinical immunotherapy trials, stable disease may reflect three tumor responses, including real stable disease, progressive disease and responsive disease. The prediction of a "true complete/partial response" is also important. Much data has accumulated showing that ctDNA can guide decisions at this point; thus, integrating ctDNA into the RECIST 1.1 criteria may help to distinguish a true tumor response type earlier in patients treated with immunotherapy; however, prospectively designed validation studies are needed.
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Affiliation(s)
- Tulay Kus
- School of Medicine, Department of Medical Oncology, Gaziantep University, Gaziantep, 27310, Turkey
| | - Irfan Cicin
- Department of Medical Oncology, Istinye University Topkapı Health Sciences Campus, Istanbul, 34295, Turkey
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Gimeno-Valiente F, Martín-Arana J, Tébar-Martínez R, Gambardella V, Martínez-Ciarpaglini C, García-Micó B, Martínez-Castedo B, Palomar B, García-Bartolomé M, Seguí V, Huerta M, Moro-Valdezate D, Pla-Martí V, Pérez-Santiago L, Roselló S, Roda D, Cervantes A, Tarazona N. Sequencing paired tumor DNA and white blood cells improves circulating tumor DNA tracking and detects pathogenic germline variants in localized colon cancer. ESMO Open 2023; 8:102051. [PMID: 37951129 PMCID: PMC10774972 DOI: 10.1016/j.esmoop.2023.102051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 09/22/2023] [Indexed: 11/13/2023] Open
Abstract
BACKGROUND In the setting of localized colon cancer (CC), circulating tumor DNA (ctDNA) monitoring in plasma has shown potential for detecting minimal residual disease (MRD) and predicting a higher risk of recurrence. With the tumor-only sequencing approach, however, germline variants may be misidentified as somatic variations, precluding the possibility of tracking in up to 11% of patients due to a lack of known somatic mutations. In this study, we assess the potential value of adding white blood cells (WBCs) to tumor tissue sequencing to enhance the accuracy of sequencing results. PATIENTS AND METHODS A total of 148 patients diagnosed with localized CC were prospectively recruited at the Hospital Clínico Universitario in Valencia (Spain). Employing a custom 29-gene panel, sequencing was conducted on tumor tissue, plasma and corresponding WBCs. Droplet digital PCR and amplicon-based NGS were performed on plasma samples post-surgery to track MRD. Oncogenic somatic variants were identified by annotating with COSMIC, OncoKB and an internal repository of pathogenic mutations database. A variant prioritization analysis, mainly characterized by the match of oncogenic mutations with the evidence levels defined in OncoKB, was carried out to select specific targeted therapies. RESULTS Utilizing paired tumor and WBCs sequencing, we identified somatic mutations in all patients (100%) within our cohort, compared to 89% using only tumor tissue. Consequently, the top 10 most frequently mutated genes for plasma monitoring were altered. The sequencing of WBCs identified 9% of patients with pathogenic mutations in the germline, with APC and TP53 being the most frequently mutated genes. Additionally, mutations in genes related to clonal hematopoiesis of indeterminate potential were detected in 27% of the cohort, with TP53, KRAS, and KMT2C being the most frequently altered genes. There were no observed differences in the sensitivity of monitoring MRD using ddPCR or amplicon-based NGS (p = 1). Ultimately, 41% of the patients harbored potentially targetable alterations at diagnosis. CONCLUSION The germline testing method not only enhanced sequencing results and raised the proportion of patients eligible for plasma monitoring, but also uncovered the existence of pathogenic germline variations, thereby aiding in the identification of patients at a higher risk of hereditary cancer syndromes.
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Affiliation(s)
- F Gimeno-Valiente
- Cancer Evolution and Genome Instability Laboratory, University College London Cancer Institute, London, UK
| | - J Martín-Arana
- Department of Medical Oncology, INCLIVA Biomedical Research Institute, University of Valencia, Valencia; CIBERONC, Instituto de Salud Carlos III, Madrid
| | - R Tébar-Martínez
- Department of Medical Oncology, INCLIVA Biomedical Research Institute, University of Valencia, Valencia
| | - V Gambardella
- Department of Medical Oncology, INCLIVA Biomedical Research Institute, University of Valencia, Valencia
| | - C Martínez-Ciarpaglini
- CIBERONC, Instituto de Salud Carlos III, Madrid; Department of Pathology, INCLIVA Biomedical Research Institute, University of Valencia, Valencia
| | - B García-Micó
- Department of Medical Oncology, INCLIVA Biomedical Research Institute, University of Valencia, Valencia; CIBERONC, Instituto de Salud Carlos III, Madrid
| | - B Martínez-Castedo
- Department of Medical Oncology, INCLIVA Biomedical Research Institute, University of Valencia, Valencia; CIBERONC, Instituto de Salud Carlos III, Madrid
| | - B Palomar
- Department of Pathology, INCLIVA Biomedical Research Institute, University of Valencia, Valencia
| | - M García-Bartolomé
- Department of Medical Oncology, INCLIVA Biomedical Research Institute, University of Valencia, Valencia
| | - V Seguí
- Department of Medical Oncology, INCLIVA Biomedical Research Institute, University of Valencia, Valencia
| | - M Huerta
- Department of Medical Oncology, INCLIVA Biomedical Research Institute, University of Valencia, Valencia
| | - D Moro-Valdezate
- Colorectal Surgery Unit, INCLIVA Biomedical Research Institute, Hospital Clínico Universitario de Valencia, Department of Surgery, University of Valencia, Valencia, Spain
| | - V Pla-Martí
- Colorectal Surgery Unit, INCLIVA Biomedical Research Institute, Hospital Clínico Universitario de Valencia, Department of Surgery, University of Valencia, Valencia, Spain
| | - L Pérez-Santiago
- Colorectal Surgery Unit, INCLIVA Biomedical Research Institute, Hospital Clínico Universitario de Valencia, Department of Surgery, University of Valencia, Valencia, Spain
| | - S Roselló
- Department of Medical Oncology, INCLIVA Biomedical Research Institute, University of Valencia, Valencia; CIBERONC, Instituto de Salud Carlos III, Madrid
| | - D Roda
- Department of Medical Oncology, INCLIVA Biomedical Research Institute, University of Valencia, Valencia; CIBERONC, Instituto de Salud Carlos III, Madrid
| | - A Cervantes
- Department of Medical Oncology, INCLIVA Biomedical Research Institute, University of Valencia, Valencia; CIBERONC, Instituto de Salud Carlos III, Madrid.
| | - N Tarazona
- Department of Medical Oncology, INCLIVA Biomedical Research Institute, University of Valencia, Valencia; CIBERONC, Instituto de Salud Carlos III, Madrid.
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