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Early Circulating Tumour DNA Kinetics Measured by Ultra-Deep Next-Generation Sequencing During Radical Radiotherapy for Non-Smal

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Early Circulating Tumour DNA Kinetics Measured by Ultra-Deep Next-Generation Sequencing During Radical Radiotherapy for Non-Smal Walls et al. Radiation Oncology (2020) 15:132 https://doi.org/10.1186/s13014-020-01583-7 RESEARCH Open Access Early circulating tumour DNA kinetics measured by ultra-deep next-generation sequencing during radical radiotherapy for non-small cell lung cancer: a feasibility study G. M. Walls1,2* , L. McConnell1, J. McAleese2, P. Murray3, T. B. Lynch2, K. Savage1, G. G. Hanna4 and D. Gonzalez de Castro1 Abstract Background: The evaluation of circulating tumour DNA (ctDNA) from clinical blood samples, liquid biopsy, offers several diagnostic advantages compared with traditional tissue biopsy, such as shorter processing time, reduced patient risk and the opportunity to assess tumour heterogeneity. The historically poor sensitivity of ctDNA testing, has restricted its integration into routine clinical practice for non-metastatic disease. The early kinetics of ctDNA during radical radiotherapy for localised NSCLC have not been described with ultra-deep next generation sequencing previously. Materials and methods: Patients with CT/PET-staged locally advanced, NSCLC prospectively consented to undergo serial venepuncture during the first week of radical radiotherapy alone. All patients received 55Gy in 20 fractions. Plasma samples were processed using the commercially available Roche AVENIO Expanded kit (Roche Sequencing Solutions, Pleasanton, CA, US) which targets 77 genes. Results: Tumour-specific mutations were found in all patients (1 in 3 patients; 2 in 1 patient, and 3 in 1 patient). The variant allele frequency of these mutations ranged from 0.05–3.35%. In 2 patients there was a transient increase in ctDNA levels at the 72 h timepoint compared to baseline. In all patients there was a non-significant decrease in ctDNA levels at the 7-day timepoint in comparison to baseline (p = 0.4627). Conclusion: This study demonstrates the feasibility of applying ctDNA-optimised NGS protocols through specified time-points in a small homogenous cohort of patients with localised lung cancer treated with radiotherapy. Studies are required to assess ctDNA kinetics as a predictive biomarker in radiotherapy. Priming tumours for liquid biopsy using radiation warrants further exploration. Keywords: ctDNA, Ultra-deep NGS, Radical radiotherapy, Lung cancer * Correspondence: [email protected] 1Centre for Cancer Research & Cell Biology, Queen’s University Belfast, 97 Lisburn Road, Belfast BT9 7AE, Northern Ireland 2Cancer Centre Belfast City Hospital, Belfast Health & Social Care Trust, 51 Lisburn Road, Belfast BT9 7AB, Northern Ireland Full list of author information is available at the end of the article © The Author(s). 2020 Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data. Walls et al. Radiation Oncology (2020) 15:132 Page 2 of 9 Introduction consent for serial venepuncture during the first week of Circulating tumour DNA (ctDNA) describes tumour- treatment. All patients were deemed unsuitable for derived DNA fragments released into peripheral blood concurrent chemoradiation. Routine diagnostic investi- through necrosis, apoptosis and spontaneous release [1]. gations included an 18-FDG-PET-CT for all patients, The term ‘liquid biopsy’ has been used to describe the and TNM8 staging was applied [27]. Patients were evaluation of total cell-free DNA (cfDNA) from clinical approached at the radiotherapy consent clinic regarding blood samples, and compared with traditional tissue bi- study participation. Routine clinical assessments were re- opsy, liquid biopsy can be faster, less invasive and more corded including ECOG PS and smoking history. Re- comprehensive in terms of reflecting tumour heterogen- sponse assessments were carried out by a Consultant eity. The ctDNA must be identified amongst the cfDNA Radiologist with expertise in lung cancer. produced by non-malignant cells from around the body [2]. There are conflicting data for total cell-free circulat- Radiotherapy ing DNA trends during treatment, and cfDNA is less All patients received 55Gy in 20 fractions over 4 weeks useful as a prognostic biomarker [3]. planned with the intensity modulated radiotherapy The half-life of ctDNA is estimated to be up to 2 technique and delivered as 6MV arc therapy, with daily hours, and is dependent on factors including cell turn- online cone beam-CT image guidance, treating Monday over, tumour size, excretion in bodily fluids and degrad- to Friday for 4 weeks. All target volumes were subject to ation rate by circulating nucleases [4]. Therefore, in peer review [28]. Patients were routinely clinically non-metastatic cancer, concentration ranges of ctDNA, assessed once per week by an Oncologist or considered as fractions of total cell-free DNA, vary be- Radiographer. tween tumour types, ranging from undetectable in pros- tate cancer [5] to 0.02–3.2% in non-small cell lung Sample Collection & Processing cancer (NSCLC) [6]. The historically poor sensitivity of The time, date and location of blood draws were agreed ctDNA testing, has restricted its integration into routine with each patient in consideration with their radiother- clinical practice in non-metastatic disease [7]. apy appointments and no additional hospital visits were The emerging potential clinical utilities of ctDNA in lung required as part of the study. Patients provided 20 mL of cancer management include screening [8], histological and blood at 3 different time periods i) immediately prior to molecular subtyping [9, 10], disease burden assessment fraction 1, ii) 72 h after fraction 1 and iii) 7 days after [11], overall prognosis [12, 13], systemic treatment response fraction 1, as illustrated in the study schema in Fig. 1. assessment [14] (oncogenic-driven cases included [15, 16]), Samples were transferred to the local Biobank where all identification of resistance mechanisms [17] and response blood samples were processed within a 2-h time period. to local consolidative radiotherapy [18]. Each blood sample was initially collected via a vacutainer Although approximately 45% stage I-III NSCLC cases system into 2 × 10 mL EDTA tubes and transported in receive radical radiotherapy as multi- or single modality ambient temperature to the dedicated Biobank labora- treatment [19], there is only one published series on the tory. The EDTA tubes were centrifuged at 2000 g for 10 impact of radiotherapy on cfDNA in NSCLC [20]. Fur- min producing 10 mL of plasma and a 1 mL buffy coat thermore, the paucity of data on ctDNA dynamics during sample (which was not available for processing). The radiotherapy across other tumour sites means there are plasma was then decanted into a 15 mL conical tube and few transferable lessons about any possible interplay in centrifuged again at 2000 g for 10 min to produce cell NSCLC [20–26] As the anti-tumour activity of radiother- free plasma and frozen at − 80 °C. apy is achieved through DNA damage-mediated cell death, it is expected that an interaction will be observed. Library Generation & Next-Generation Sequencing Additional evidence for transient ctDNA increases on Plasma samples were processed using the commercially commencing treatment may support the evaluation of available Roche AVENIO Expanded kit (Roche Sequen- radiotherapy as a preparatory procedure for liquid biopsy. cing Solutions, Pleasanton, CA, US) as per the manufac- This prospective pilot study aimed to demonstrate the turer’s protocol. Briefly, DNA was extracted using the suitability of ultra-deep NGS ctDNA quantitation for AVENIO cfDNA Isolation Kit. Libraries were prepared, examination of the relationship between radiotherapy de- hybridised and analysed according to the AVENIO livery and ctDNA dynamics in non-metastatic NSCLC. ctDNA Analysis Kits Reagent Workflow User Guide (Version 1.1; Software Version 1.0.0). Following extrac- Methods and materials tion, DNA was washed using the AVENIO cfDNA Isola- Patient selection tion Kit and quantified using the Qubit High Sensitivity Patients receiving radical radiotherapy alone for locally assay kit and Qubit 2.0 Fluorometer (Thermo Fisher Sci- advanced, histologically confirmed NSCLC provided entific, Massachusetts, USA). In order to assess average Walls et al. Radiation Oncology (2020) 15:132 Page 3 of 9 Fig. 1 Schema of plasma collection time-points. (blue arrows = venepuncture time-points) fragment size, the 4200 TapeStation System using the Ethics & Governance D1000 ScreenTape with D1000 Reagents (Agilent Samples in this study were acquired from the local Technologies, California, USA) was used. Library Biobank who have ethical approval (REC reference preparation involved
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