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Iisager L, Ahrenfeldt J, Donskov F, Ljungberg B, Bex A, Lund L, Lyskjær I, Fristrup N. Multicenter randomized trial of deferred cytoreductive nephrectomy in synchronous metastatic renal cell carcinoma receiving checkpoint inhibitors: the NORDIC-SUN-Trial. BMC Cancer 2024; 24:260. [PMID: 38402173 PMCID: PMC10893632 DOI: 10.1186/s12885-024-11987-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Accepted: 02/09/2024] [Indexed: 02/26/2024] Open
Abstract
BACKGROUND Primary tumor removal by cytoreductive nephrectomy in synchronous metastatic renal cell carcinoma patients has been investigated in the context of various treatment regimens. Two randomized controlled trials investigated the role and timing of cytoreductive nephrectomy in the era of targeted therapy and demonstrated that upfront nephrectomy should no longer be performed when patients require systemic therapy. Superiority of checkpoint immunotherapy agents has led to a paradigm change from targeted therapies to immunotherapy-based first-line treatment in patients with primary metastatic disease; thus, deferred cytoreductive nephrectomy needs to be verified in the immunotherapy setting. Furthermore, a need exists for personalizing treatment choices for the individual patient to avoid unnecessary overtreatment. METHODS/DESIGN To explore the impact of cytoreductive nephrectomy in this patient group receiving checkpoint immunotherapy, we initiated a randomized, controlled trial comparing deferred cytoreductive nephrectomy with no surgery. The trial integrates a comprehensive translational research program with specimen sampling for biomarker analysis. DISCUSSION The trial aims to show that deferred cytoreductive nephrectomy improves overall survival in patients with synchronous metastatic renal cell carcinoma, and furthermore, to identify relevant biomarkers for personalized renal cancer management. TRIAL REGISTRATION ClinicalTrials.gov NCT03977571 June 6, 2019.
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Affiliation(s)
- Laura Iisager
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Johanne Ahrenfeldt
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Frede Donskov
- Department of Oncology, Southern Denmark University Hospital, Esbjerg, Denmark
- Department of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Börje Ljungberg
- Department of Surgical and Perioperative Sciences, Umeå University, Umeå, Sweden
| | - Axel Bex
- Specialist Centre for Kidney Cancer, Royal Free Hospital London, London, England
| | - Lars Lund
- Department of Urology, Odense University Hospital, Odense, Denmark
| | - Iben Lyskjær
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Niels Fristrup
- Department of Oncology, Aarhus University Hospital, Aarhus, Denmark.
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Iisager L, Ahrenfeldt J, Keller AK, Nielsen TK, Fristrup N, Lyskjær I. KIDNEY-PAGER: analysis of circulating tumor DNA as a biomarker in renal cancer - an observational trial. Study protocol. Acta Oncol 2024; 63:51-55. [PMID: 38391290 DOI: 10.2340/1651-226x.2024.25581] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Accepted: 01/29/2024] [Indexed: 02/24/2024]
Abstract
BACKGROUND Management of localized renal cell carcinoma (RCC) is challenged by inaccurate methods to assess the risk of recurrence and deferred detection of relapse and residual disease after radical or partial nephrectomy. Circulating tumor DNA (ctDNA) has been proposed as a potential biomarker in RCC. PURPOSE Conduction of an observational study to evaluate the validity of ctDNA as a biomarker of the risk of recurrence and subclinical residual disease to improve postoperative surveillance. MATERIAL AND METHODS Urine and blood will be prospectively collected before and after surgery of the primary tumor from up to 500 patients until 5 years of follow-up. ctDNA analysis will be performed using shallow whole genome sequencing and cell-free methylated DNA immunoprecipitation sequencing. ctDNA levels in plasma and urine will be correlated to oncological outcomes. Residual blood and urine as well as tissue biopsies will be biobanked for future research. INTERPRETATION Results will pave the way for future ctDNA-guided clinical trials aiming to improve RCC management.
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Affiliation(s)
- Laura Iisager
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Johanne Ahrenfeldt
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | | | | | - Niels Fristrup
- Department of Oncology, Aarhus University Hospital, Aarhus, Denmark
| | - Iben Lyskjær
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark.
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Lyskjær I, Iisager L, Axelsen CT, Nielsen TK, Dyrskjøt L, Fristrup N. Management of Renal Cell Carcinoma: Promising Biomarkers and the Challenges to Reach the Clinic. Clin Cancer Res 2024; 30:663-672. [PMID: 37874628 PMCID: PMC10870122 DOI: 10.1158/1078-0432.ccr-23-1892] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 08/23/2023] [Accepted: 09/27/2023] [Indexed: 10/25/2023]
Abstract
The incidence of renal cell carcinoma (RCC) is increasing worldwide, yet research within this field is lagging behind other cancers. Despite increased detection of early disease as a consequence of the widespread use of diagnostic CT scans, 25% of patients have disseminated disease at diagnosis. Similarly, around 25% progress to metastatic disease following curatively intended surgery. Surgery is the cornerstone in the treatment of RCC; however, when the disease is disseminated, immunotherapy or immunotherapy in combination with a tyrosine kinase inhibitor is the patient's best option. Immunotherapy is a potent treatment, with durable treatment responses and potential to cure the patient, but only half of the patients benefit from the administered treatment, and there are currently no methods that can identify which patients will respond to immunotherapy. Moreover, there is a need to identify the patients in greatest risk of relapsing after surgery for localized disease and direct adjuvant treatment there. Even though several molecular biomarkers have been published to date, we are still lacking routinely used biomarkers to guide optimal clinical management. The purpose of this review is to highlight some of the most promising biomarkers, discuss the efforts made within this field to date, and describe the barriers needed to be overcome to have reliable and robust predictive and prognostic biomarkers in the clinic for renal cancer.
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Affiliation(s)
- Iben Lyskjær
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Laura Iisager
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | | | | | - Lars Dyrskjøt
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Niels Fristrup
- Department of Oncology, Aarhus University Hospital, Aarhus, Denmark
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Haefliger S, Chervova O, Davies C, Nottley S, Hargreaves S, Sumathi VP, Amary F, Tirabosco R, Pillay N, Beck S, Flanagan AM, Lyskjær I. Subclassification of epithelioid sarcoma with potential therapeutic impact. J Pathol 2023; 260:368-375. [PMID: 37316954 PMCID: PMC10952852 DOI: 10.1002/path.6135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2023] [Revised: 04/15/2023] [Accepted: 05/07/2023] [Indexed: 06/16/2023]
Abstract
Epithelioid sarcoma is a rare and aggressive mesenchymal tumour, the genetic hallmark of which is the loss of expression of SMARCB1, a key member of the SWItch/Sucrose Non-Fermentable (SWI/SNF) chromatin remodelling complex. Hampered by its rarity, epithelioid sarcoma has received little research attention and therapeutic options for this disease remain limited. SMARCB1-deficient tumours also include malignant rhabdoid tumour, atypical teratoid and rhabdoid tumour, epithelioid malignant peripheral nerve sheath tumour, and poorly differentiated chordoma. Histologically, it can be challenging to distinguish epithelioid sarcoma from malignant rhabdoid tumour and other SMARCB1-deficient tumours, whereas methylation profiling shows that they represent distinct entities and facilitates their classification. Methylation studies on SMARCB1-deficient tumours, although not including epithelioid sarcomas, reported methylation subgroups which resulted in new clinical stratification and therapeutic approaches. In addition, emerging evidence indicates that immunotherapy, including immune checkpoint inhibitors, represents a promising therapeutic strategy for SMARCB1-deficient tumours. Here, we show that some epithelioid sarcomas share methylation patterns of malignant rhabdoid tumours indicating that this could help to distinguish these entities and guide treatment. Using gene expression data, we also showed that the immune environment of epithelioid sarcoma is characterised by a predominance of CD8+ lymphocytes and M2 macrophages. These findings have potential implications for the management of patients with epithelioid sarcoma. © 2023 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland.
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Affiliation(s)
- Simon Haefliger
- Research Department of PathologyUniversity College London, UCL Cancer InstituteLondonUK
- Institute of Medical Genetics and PathologyUniversity Hospital BaselBaselSwitzerland
- Department of HistopathologyRoyal National Orthopaedic HospitalStanmoreUK
| | - Olga Chervova
- Medical Genomics Research GroupUniversity College London, UCL Cancer InstituteLondonUK
| | - Christopher Davies
- Research Department of PathologyUniversity College London, UCL Cancer InstituteLondonUK
- Department of HistopathologyRoyal National Orthopaedic HospitalStanmoreUK
| | - Steven Nottley
- Research Department of PathologyUniversity College London, UCL Cancer InstituteLondonUK
| | - Steven Hargreaves
- Research Department of PathologyUniversity College London, UCL Cancer InstituteLondonUK
| | | | - Fernanda Amary
- Department of HistopathologyRoyal National Orthopaedic HospitalStanmoreUK
| | - Roberto Tirabosco
- Department of HistopathologyRoyal National Orthopaedic HospitalStanmoreUK
| | - Nischalan Pillay
- Research Department of PathologyUniversity College London, UCL Cancer InstituteLondonUK
- Department of HistopathologyRoyal National Orthopaedic HospitalStanmoreUK
| | - Stephan Beck
- Medical Genomics Research GroupUniversity College London, UCL Cancer InstituteLondonUK
| | - Adrienne M Flanagan
- Research Department of PathologyUniversity College London, UCL Cancer InstituteLondonUK
- Department of HistopathologyRoyal National Orthopaedic HospitalStanmoreUK
| | - Iben Lyskjær
- Department of Molecular MedicineAarhus University HospitalAarhusDenmark
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Chen K, Kang G, Zhang Z, Lizaso A, Beck S, Lyskjær I, Chervova O, Li B, Shen H, Wang C, Li B, Zhao H, Li X, Yang F, Kanu N, Wang J. Individualized dynamic methylation-based analysis of cell-free DNA in postoperative monitoring of lung cancer. BMC Med 2023; 21:255. [PMID: 37452374 PMCID: PMC10349423 DOI: 10.1186/s12916-023-02954-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 06/20/2023] [Indexed: 07/18/2023] Open
Abstract
BACKGROUND The feasibility of DNA methylation-based assays in detecting minimal residual disease (MRD) and postoperative monitoring remains unestablished. We aim to investigate the dynamic characteristics of cancer-related methylation signals and the feasibility of methylation-based MRD detection in surgical lung cancer patients. METHODS Matched tumor, tumor-adjacent tissues, and longitudinal blood samples from a cohort (MEDAL) were analyzed by ultra-deep targeted sequencing and bisulfite sequencing. A tumor-informed methylation-based MRD (timMRD) was employed to evaluate the methylation status of each blood sample. Survival analysis was performed in the MEDAL cohort (n = 195) and validated in an independent cohort (DYNAMIC, n = 36). RESULTS Tumor-informed methylation status enabled an accurate recurrence risk assessment better than the tumor-naïve methylation approach. Baseline timMRD-scores were positively correlated with tumor burden, invasiveness, and the existence and abundance of somatic mutations. Patients with higher timMRD-scores at postoperative time-points demonstrated significantly shorter disease-free survival in the MEDAL cohort (HR: 3.08, 95% CI: 1.48-6.42; P = 0.002) and the independent DYNAMIC cohort (HR: 2.80, 95% CI: 0.96-8.20; P = 0.041). Multivariable regression analysis identified postoperative timMRD-score as an independent prognostic factor for lung cancer. Compared to tumor-informed somatic mutation status, timMRD-scores yielded better performance in identifying the relapsed patients during postoperative follow-up, including subgroups with lower tumor burden like stage I, and was more accurate among relapsed patients with baseline ctDNA-negative status. Comparing to the average lead time of ctDNA mutation, timMRD-score yielded a negative predictive value of 97.2% at 120 days prior to relapse. CONCLUSIONS The dynamic methylation-based analysis of peripheral blood provides a promising strategy for postoperative cancer surveillance. TRIAL REGISTRATION This study (MEDAL, MEthylation based Dynamic Analysis for Lung cancer) was registered on ClinicalTrials.gov on 08/05/2018 (NCT03634826). https://clinicaltrials.gov/ct2/show/NCT03634826 .
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Affiliation(s)
- Kezhong Chen
- Thoracic Oncology Institute and Department of Thoracic Surgery, Peking University People's Hospital, Beijing, 100044, China.
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, University College London, 72 Huntley St, London, WC1E 6DD, UK.
| | - Guannan Kang
- Thoracic Oncology Institute and Department of Thoracic Surgery, Peking University People's Hospital, Beijing, 100044, China
| | | | | | - Stephan Beck
- University College London Cancer Institute, University College London, 72 Huntley St, London, WC1E 6DD, UK
| | - Iben Lyskjær
- University College London Cancer Institute, University College London, 72 Huntley St, London, WC1E 6DD, UK
| | - Olga Chervova
- University College London Cancer Institute, University College London, 72 Huntley St, London, WC1E 6DD, UK
| | - Bingsi Li
- Burning Rock Biotech, Guangzhou, 510300, China
| | - Haifeng Shen
- Thoracic Oncology Institute and Department of Thoracic Surgery, Peking University People's Hospital, Beijing, 100044, China
| | | | - Bing Li
- Burning Rock Biotech, Guangzhou, 510300, China
| | - Heng Zhao
- Thoracic Oncology Institute and Department of Thoracic Surgery, Peking University People's Hospital, Beijing, 100044, China
| | - Xi Li
- Burning Rock Biotech, Guangzhou, 510300, China
| | - Fan Yang
- Thoracic Oncology Institute and Department of Thoracic Surgery, Peking University People's Hospital, Beijing, 100044, China.
| | - Nnennaya Kanu
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, University College London, 72 Huntley St, London, WC1E 6DD, UK.
| | - Jun Wang
- Thoracic Oncology Institute and Department of Thoracic Surgery, Peking University People's Hospital, Beijing, 100044, China.
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Christensen MH, Drue SO, Rasmussen MH, Frydendahl A, Lyskjær I, Demuth C, Nors J, Gotschalck KA, Iversen LH, Andersen CL, Pedersen JS. DREAMS: deep read-level error model for sequencing data applied to low-frequency variant calling and circulating tumor DNA detection. Genome Biol 2023; 24:99. [PMID: 37121998 PMCID: PMC10150536 DOI: 10.1186/s13059-023-02920-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 04/03/2023] [Indexed: 05/02/2023] Open
Abstract
Circulating tumor DNA detection using next-generation sequencing (NGS) data of plasma DNA is promising for cancer identification and characterization. However, the tumor signal in the blood is often low and difficult to distinguish from errors. We present DREAMS (Deep Read-level Modelling of Sequencing-errors) for estimating error rates of individual read positions. Using DREAMS, we develop statistical methods for variant calling (DREAMS-vc) and cancer detection (DREAMS-cc). For evaluation, we generate deep targeted NGS data of matching tumor and plasma DNA from 85 colorectal cancer patients. The DREAMS approach performs better than state-of-the-art methods for variant calling and cancer detection.
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Affiliation(s)
- Mikkel H Christensen
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
- Department of Clinical Medicine, Faculty of Health, Aarhus University, Aarhus, Denmark
| | - Simon O Drue
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Mads H Rasmussen
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
- Department of Clinical Medicine, Faculty of Health, Aarhus University, Aarhus, Denmark
| | - Amanda Frydendahl
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
- Department of Clinical Medicine, Faculty of Health, Aarhus University, Aarhus, Denmark
| | - Iben Lyskjær
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
- Department of Clinical Medicine, Faculty of Health, Aarhus University, Aarhus, Denmark
| | - Christina Demuth
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Jesper Nors
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
- Department of Clinical Medicine, Faculty of Health, Aarhus University, Aarhus, Denmark
| | - Kåre A Gotschalck
- Department of Clinical Medicine, Faculty of Health, Aarhus University, Aarhus, Denmark
- Department of Surgery, Horsens Regional Hospital, Horsens, Denmark
| | - Lene H Iversen
- Department of Clinical Medicine, Faculty of Health, Aarhus University, Aarhus, Denmark
- Department of Surgery, Aarhus University Hospital, Aarhus, Denmark
| | - Claus L Andersen
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark.
- Department of Clinical Medicine, Faculty of Health, Aarhus University, Aarhus, Denmark.
| | - Jakob Skou Pedersen
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark.
- Department of Clinical Medicine, Faculty of Health, Aarhus University, Aarhus, Denmark.
- Bioinformatics Research Center, Faculty of Science, Aarhus University, Aarhus, Denmark.
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Cross W, Lyskjær I, Lesluyes T, Hargreaves S, Strobl AC, Davies C, Waise S, Hames-Fathi S, Oukrif D, Ye H, Amary F, Tirabosco R, Gerrand C, Baker T, Barnes D, Steele C, Alexandrov L, Bond G, Cool P, Pillay N, Loo PV, Flanagan AM. A genetic model for central chondrosarcoma evolution correlates with patient outcome. Genome Med 2022; 14:99. [PMID: 36042521 PMCID: PMC9426036 DOI: 10.1186/s13073-022-01084-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 07/07/2022] [Indexed: 01/18/2023] Open
Abstract
BACKGROUND Central conventional chondrosarcoma (CS) is the most common subtype of primary malignant bone tumour in adults. Treatment options are usually limited to surgery, and prognosis is challenging. These tumours are characterised by the presence and absence of IDH1 and IDH2 mutations, and recently, TERT promoter alterations have been reported in around 20% of cases. The effect of these mutations on clinical outcome remains unclear. The purpose of this study was to determine if prognostic accuracy can be improved by the addition of genomic data, and specifically by examination of IDH1, IDH2, and TERT mutations. METHODS In this study, we combined both archival samples and data sourced from the Genomics England 100,000 Genomes Project (n = 356). Mutations in IDH1, IDH2, and TERT were profiled using digital droplet PCR (n = 346), whole genome sequencing (n=68), or both (n = 64). Complex events and other genetic features were also examined, along with methylation array data (n = 84). We correlated clinical features and patient outcomes with our genetic findings. RESULTS IDH2-mutant tumours occur in older patients and commonly present with high-grade or dedifferentiated disease. Notably, TERT mutations occur most frequently in IDH2-mutant tumours, although have no effect on survival in this group. In contrast, TERT mutations are rarer in IDH1-mutant tumours, yet they are associated with a less favourable outcome in this group. We also found that methylation profiles distinguish IDH1- from IDH2-mutant tumours. IDH wild-type tumours rarely exhibit TERT mutations and tend to be diagnosed in a younger population than those with tumours harbouring IDH1 and IDH2 mutations. A major genetic feature of this group is haploidisation and subsequent genome doubling. These tumours evolve less frequently to dedifferentiated disease and therefore constitute a lower risk group. CONCLUSIONS Tumours with IDH1 or IDH2 mutations or those that are IDHwt have significantly different genetic pathways and outcomes in relation to TERT mutation. Diagnostic testing for IDH1, IDH2, and TERT mutations could therefore help to guide clinical monitoring and prognostication.
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Affiliation(s)
- William Cross
- grid.83440.3b0000000121901201Research Department of Pathology, University College London, UCL Cancer Institute, London, UK
| | - Iben Lyskjær
- grid.83440.3b0000000121901201Research Department of Pathology, University College London, UCL Cancer Institute, London, UK ,grid.83440.3b0000000121901201Medical Genomics Research Group, University College London, UCL Cancer Institute, London, UK
| | - Tom Lesluyes
- grid.451388.30000 0004 1795 1830The Francis Crick Institute, London, UK
| | - Steven Hargreaves
- grid.83440.3b0000000121901201Research Department of Pathology, University College London, UCL Cancer Institute, London, UK
| | - Anna-Christina Strobl
- grid.416177.20000 0004 0417 7890Department of Histopathology, Royal National Orthopaedic Hospital, Stanmore, UK
| | - Christopher Davies
- grid.83440.3b0000000121901201Research Department of Pathology, University College London, UCL Cancer Institute, London, UK ,grid.416177.20000 0004 0417 7890Department of Histopathology, Royal National Orthopaedic Hospital, Stanmore, UK
| | - Sara Waise
- grid.451388.30000 0004 1795 1830The Francis Crick Institute, London, UK ,grid.5491.90000 0004 1936 9297Cancer Sciences Unit, University of Southampton, Southampton, UK
| | - Shadi Hames-Fathi
- grid.83440.3b0000000121901201Research Department of Pathology, University College London, UCL Cancer Institute, London, UK
| | - Dahmane Oukrif
- grid.83440.3b0000000121901201Research Department of Pathology, University College London, UCL Cancer Institute, London, UK
| | - Hongtao Ye
- grid.416177.20000 0004 0417 7890Department of Histopathology, Royal National Orthopaedic Hospital, Stanmore, UK
| | - Fernanda Amary
- grid.416177.20000 0004 0417 7890Department of Histopathology, Royal National Orthopaedic Hospital, Stanmore, UK
| | - Roberto Tirabosco
- grid.416177.20000 0004 0417 7890Department of Histopathology, Royal National Orthopaedic Hospital, Stanmore, UK
| | - Craig Gerrand
- grid.416177.20000 0004 0417 7890Bone Tumour Unit, Royal National Orthopaedic Hospital, Stanmore, UK
| | - Toby Baker
- grid.451388.30000 0004 1795 1830The Francis Crick Institute, London, UK
| | - David Barnes
- grid.6572.60000 0004 1936 7486Institute of Cancer and Genomic Sciences, Birmingham University, Birmingham, UK
| | - Christopher Steele
- grid.83440.3b0000000121901201Research Department of Pathology, University College London, UCL Cancer Institute, London, UK
| | - Ludmil Alexandrov
- grid.266100.30000 0001 2107 4242University of California, San Diego, USA
| | - Gareth Bond
- grid.6572.60000 0004 1936 7486Institute of Cancer and Genomic Sciences, Birmingham University, Birmingham, UK
| | | | - Paul Cool
- grid.412943.90000 0001 0507 535XRobert Jones & Agnes Hunt Orthopaedic Hospital NHS Foundation Trust, Oswestry, UK ,grid.9757.c0000 0004 0415 6205Keele University, Keele, UK
| | - Nischalan Pillay
- grid.83440.3b0000000121901201Research Department of Pathology, University College London, UCL Cancer Institute, London, UK ,grid.416177.20000 0004 0417 7890Department of Histopathology, Royal National Orthopaedic Hospital, Stanmore, UK
| | - Peter Van Loo
- grid.451388.30000 0004 1795 1830The Francis Crick Institute, London, UK
| | - Adrienne M. Flanagan
- grid.83440.3b0000000121901201Research Department of Pathology, University College London, UCL Cancer Institute, London, UK ,grid.416177.20000 0004 0417 7890Department of Histopathology, Royal National Orthopaedic Hospital, Stanmore, UK
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Lyskjær I, Kara N, De Noon S, Davies C, Rocha AM, Strobl AC, Usher I, Gerrand C, Strauss SJ, Schrimpf D, von Deimling A, Beck S, Flanagan AM. Osteosarcoma: Novel prognostic biomarkers using circulating and cell-free tumour DNA. Eur J Cancer 2022; 168:1-11. [PMID: 35421838 DOI: 10.1016/j.ejca.2022.03.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Revised: 03/02/2022] [Accepted: 03/07/2022] [Indexed: 01/21/2023]
Abstract
AIM Osteosarcoma (OS) is the most common primary bone tumour in children and adolescents. Circulating free (cfDNA) and circulating tumour DNA (ctDNA) are promising biomarkers for disease surveillance and prognostication in several cancer types; however, few such studies are reported for OS. The purpose of this study was to discover and validate methylation-based biomarkers to detect plasma ctDNA in patients with OS and explore their utility as prognostic markers. METHODS Candidate CpG markers were selected through analysis of methylation array data for OS, non-OS tumours and germline samples. Candidates were validated in two independent OS datasets (n = 162, n = 107) and the four top-performing markers were selected. Methylation-specific digital droplet PCR (ddPCR) assays were designed and experimentally validated in OS tumour samples (n = 20) and control plasma samples. Finally, ddPCR assays were applied to pre-operative plasma and where available post-operative plasma from 72 patients with OS, and findings correlated with outcome. RESULTS Custom ddPCR assays detected ctDNA in 69% and 40% of pre-operative plasma samples (n = 72), based on thresholds of one or two positive markers respectively. ctDNA was detected in 5/17 (29%) post-operative plasma samples from patients, which in four cases were associated with or preceded disease relapse. Both pre-operative cfDNA levels and ctDNA detection independently correlated with overall survival (p = 0.0015 and p = 0.0096, respectively). CONCLUSION Our findings illustrate the potential of mutation-independent methylation-based ctDNA assays for OS. This study lays the foundation for multi-institutional collaborative studies to explore the utility of plasma-derived biomarkers in the management of OS.
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Affiliation(s)
- Iben Lyskjær
- Research Department of Pathology, University College London, London, UK; Medical Genomics Research Group, University College London, London, UK
| | - Neesha Kara
- Medical Genomics Research Group, University College London, London, UK
| | - Solange De Noon
- Research Department of Pathology, University College London, London, UK; Department of Histopathology, Royal National Orthopaedic Hospital, Stanmore, HA7 4LP, UK
| | - Christopher Davies
- Research Department of Pathology, University College London, London, UK; Department of Histopathology, Royal National Orthopaedic Hospital, Stanmore, HA7 4LP, UK
| | - Ana Maia Rocha
- Research Department of Pathology, University College London, London, UK; Department of Histopathology, Royal National Orthopaedic Hospital, Stanmore, HA7 4LP, UK
| | - Anna-Christina Strobl
- Department of Histopathology, Royal National Orthopaedic Hospital, Stanmore, HA7 4LP, UK
| | - Inga Usher
- Research Department of Pathology, University College London, London, UK
| | - Craig Gerrand
- Bone Tumour Unit, Royal National Orthopaedic Hospital, Stanmore, HA7 4LP, UK
| | | | - Daniel Schrimpf
- Department of Neuropathology, Institute of Pathology, University Hospital Heidelberg, and CCU Neuropathology, German Cancer Institute, Heidelberg, Germany
| | - Andreas von Deimling
- Department of Neuropathology, Institute of Pathology, University Hospital Heidelberg, and CCU Neuropathology, German Cancer Institute, Heidelberg, Germany
| | - Stephan Beck
- Medical Genomics Research Group, University College London, London, UK
| | - Adrienne M Flanagan
- Research Department of Pathology, University College London, London, UK; Department of Histopathology, Royal National Orthopaedic Hospital, Stanmore, HA7 4LP, UK.
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Lyskjær I, Davies C, Strobl A, Hindley J, James S, Lalam RK, Cross W, Hide G, Rankin KS, Jeys L, Tirabosco R, Stevenson J, O’Donnell P, Cool P, Flanagan AM. Circulating tumour DNA is a promising biomarker for risk stratification of central chondrosarcoma with IDH1/2 and GNAS mutations. Mol Oncol 2021; 15:3679-3690. [PMID: 34528398 PMCID: PMC8637565 DOI: 10.1002/1878-0261.13102] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 08/26/2021] [Accepted: 09/14/2021] [Indexed: 11/17/2022] Open
Abstract
Chondrosarcoma (CS) is a rare tumour type and the most common primary malignant bone cancer in adults. The prognosis, currently based on tumour grade, imaging and anatomical location, is not reliable, and more objective biomarkers are required. We aimed to determine whether the level of circulating tumour DNA (ctDNA) in the blood of CS patients could be used to predict outcome. In this multi-institutional study, we recruited 145 patients with cartilaginous tumours, of which 41 were excluded. ctDNA levels were assessed in 83 of the remaining 104 patients, whose tumours harboured a hotspot mutation in IDH1/2 or GNAS. ctDNA was detected pre-operatively in 31/83 (37%) and in 12/31 (39%) patients postoperatively. We found that detection of ctDNA was more accurate than pathology for identification of high-grade tumours and was associated with a poor prognosis; ctDNA was never associated with CS grade 1/atypical cartilaginous tumours (ACT) in the long bones, in neoplasms sited in the small bones of the hands and feet or in tumours measuring less than 80 mm. Although the results are promising, they are based on a small number of patients, and therefore, introduction of this blood test into clinical practice as a complementary assay to current standard-of-care protocols would allow the assay to be assessed more stringently and developed for a more personalised approach for the treatment of patients with CS.
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Affiliation(s)
- Iben Lyskjær
- Research Department of PathologyUniversity College LondonUCL Cancer InstituteLondonUK
- Medical Genomics Research GroupUniversity College LondonUCL Cancer InstituteLondonUK
| | - Christopher Davies
- Research Department of PathologyUniversity College LondonUCL Cancer InstituteLondonUK
- Department of HistopathologyRoyal National Orthopaedic HospitalStanmoreUK
| | - Anna‐Christina Strobl
- Research Department of PathologyUniversity College LondonUCL Cancer InstituteLondonUK
- Department of HistopathologyRoyal National Orthopaedic HospitalStanmoreUK
| | - Joanna Hindley
- Department of HistopathologyRoyal National Orthopaedic HospitalStanmoreUK
| | - Steven James
- Department of Musculoskeletal ImagingRoyal Orthopaedic HospitalBirminghamUK
| | - Radhesh K. Lalam
- Department of RadiologyRoyal National Orthopaedic HospitalStanmoreUK
| | - William Cross
- Research Department of PathologyUniversity College LondonUCL Cancer InstituteLondonUK
| | - Geoff Hide
- North of England Bone and Soft Tissue Tumour ServiceFreeman HospitalNewcastleUK
| | - Kenneth S. Rankin
- North of England Bone and Soft Tissue Tumour ServiceFreeman HospitalNewcastleUK
- Newcastle Centre for CancerNewcastle UniversityUK
| | - Lee Jeys
- Orthopaedic DepartmentRoyal Orthopaedic Hospital NHS Foundation TrustBirminghamUK
| | - Roberto Tirabosco
- Department of HistopathologyRoyal National Orthopaedic HospitalStanmoreUK
| | - Jonathan Stevenson
- Department of Orthopaedic Oncology and ArthroplastyRoyal Orthopaedic Hospital NHS Foundation TrustBirminghamUK
| | | | - Paul O’Donnell
- Research Department of PathologyUniversity College LondonUCL Cancer InstituteLondonUK
- Department of RadiologyRoyal National Orthopaedic HospitalStanmoreUK
| | - Paul Cool
- Robert Jones & Agnes Hunt Orthopaedic Hospital NHS Foundation TrustOswestryUK
- Keele UniversityUK
| | - Adrienne M. Flanagan
- Research Department of PathologyUniversity College LondonUCL Cancer InstituteLondonUK
- Department of HistopathologyRoyal National Orthopaedic HospitalStanmoreUK
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10
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De Noon S, Ijaz J, Coorens THH, Amary F, Ye H, Strobl A, Lyskjær I, Flanagan AM, Behjati S. MYC amplifications are common events in childhood osteosarcoma. J Pathol Clin Res 2021; 7:425-431. [PMID: 33969640 PMCID: PMC8363928 DOI: 10.1002/cjp2.219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Revised: 03/18/2021] [Accepted: 04/06/2021] [Indexed: 12/04/2022]
Abstract
Osteosarcoma, the most common primary malignant tumour of bone, affects both children and adults. No fundamental biological differences between paediatric and adult osteosarcoma are known. Here, we apply multi-region whole-genome sequencing to an index case of a 4-year-old child whose aggressive tumour harboured high-level, focal amplifications of MYC and CCNE1 connected by translocations. We reanalysed copy number readouts of 258 cases of high-grade osteosarcoma from three different cohorts and identified a significant enrichment of focal MYC, but not CCNE1, amplifications in children. Furthermore, we identified four additional cases of MYC and CCNE1 coamplification, highlighting a rare driver event which warrants further investigation. Our findings indicate that amplification of the MYC oncogene is a major driver of childhood osteosarcoma, while CCNE1 appears recurrently amplified independent of age.
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Affiliation(s)
- Solange De Noon
- Research Department of PathologyUniversity College London (UCL) Cancer InstituteLondonUK
| | | | | | - Fernanda Amary
- Department of HistopathologyRoyal National Orthopaedic HospitalStanmoreUK
| | - Hongtao Ye
- Department of HistopathologyRoyal National Orthopaedic HospitalStanmoreUK
| | - Anna Strobl
- Department of HistopathologyRoyal National Orthopaedic HospitalStanmoreUK
| | - Iben Lyskjær
- Research Department of PathologyUniversity College London (UCL) Cancer InstituteLondonUK
- Medical Genomics Research GroupUCL Cancer InstituteLondonUK
| | - Adrienne M Flanagan
- Research Department of PathologyUniversity College London (UCL) Cancer InstituteLondonUK
- Department of HistopathologyRoyal National Orthopaedic HospitalStanmoreUK
| | - Sam Behjati
- Wellcome Sanger InstituteHinxtonUK
- Cambridge University Hospitals NHS Foundation TrustCambridgeUK
- Department of PaediatricsUniversity of CambridgeCambridgeUK
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11
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Chen K, Kang G, Zhang Z, Lizaso A, Beck S, Lyskjær I, Chervova O, Li B, Shen H, Wang C, Li B, Zhao H, Chuai S, Yang F, Kanu N, Wang J. 1159P Individualized methylation-based dynamic analysis of cell-free DNA in postoperative monitoring of resected lung cancer. Ann Oncol 2021. [DOI: 10.1016/j.annonc.2021.08.1762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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12
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Lyskjær I, De Noon S, Tirabosco R, Rocha AM, Lindsay D, Amary F, Ye H, Schrimpf D, Stichel D, Sill M, Koelsche C, Pillay N, Von Deimling A, Beck S, Flanagan AM. DNA methylation-based profiling of bone and soft tissue tumours: a validation study of the 'DKFZ Sarcoma Classifier'. J Pathol Clin Res 2021; 7:350-360. [PMID: 33949149 PMCID: PMC8185366 DOI: 10.1002/cjp2.215] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 02/26/2021] [Accepted: 03/18/2021] [Indexed: 01/01/2023]
Abstract
Diagnosing bone and soft tissue neoplasms remains challenging because of the large number of subtypes, many of which lack diagnostic biomarkers. DNA methylation profiles have proven to be a reliable basis for the classification of brain tumours and, following this success, a DNA methylation-based sarcoma classification tool from the Deutsches Krebsforschungszentrum (DKFZ) in Heidelberg has been developed. In this study, we assessed the performance of their classifier on DNA methylation profiles of an independent data set of 986 bone and soft tissue tumours and controls. We found that the 'DKFZ Sarcoma Classifier' was able to produce a diagnostic prediction for 55% of the 986 samples, with 83% of these predictions concordant with the histological diagnosis. On limiting the validation to the 820 cases with histological diagnoses for which the DKFZ Classifier was trained, 61% of cases received a prediction, and the histological diagnosis was concordant with the predicted methylation class in 88% of these cases, findings comparable to those reported in the DKFZ Classifier paper. The classifier performed best when diagnosing mesenchymal chondrosarcomas (CHSs, 88% sensitivity), chordomas (85% sensitivity), and fibrous dysplasia (83% sensitivity). Amongst the subtypes least often classified correctly were clear cell CHSs (14% sensitivity), malignant peripheral nerve sheath tumours (27% sensitivity), and pleomorphic liposarcomas (29% sensitivity). The classifier predictions resulted in revision of the histological diagnosis in six of our cases. We observed that, although a higher tumour purity resulted in a greater likelihood of a prediction being made, it did not correlate with classifier accuracy. Our results show that the DKFZ Classifier represents a powerful research tool for exploring the pathogenesis of sarcoma; with refinement, it has the potential to be a valuable diagnostic tool.
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Affiliation(s)
- Iben Lyskjær
- Research Department of PathologyUniversity College London, UCL Cancer InstituteLondonUK
- Medical Genomics Research GroupUniversity College London, UCL Cancer InstituteLondonUK
| | - Solange De Noon
- Research Department of PathologyUniversity College London, UCL Cancer InstituteLondonUK
- Department of HistopathologyRoyal National Orthopaedic HospitalStanmoreUK
| | - Roberto Tirabosco
- Department of HistopathologyRoyal National Orthopaedic HospitalStanmoreUK
| | - Ana Maia Rocha
- Research Department of PathologyUniversity College London, UCL Cancer InstituteLondonUK
- Department of HistopathologyRoyal National Orthopaedic HospitalStanmoreUK
| | - Daniel Lindsay
- Research Department of PathologyUniversity College London, UCL Cancer InstituteLondonUK
- Department of HistopathologyRoyal National Orthopaedic HospitalStanmoreUK
| | - Fernanda Amary
- Research Department of PathologyUniversity College London, UCL Cancer InstituteLondonUK
- Department of HistopathologyRoyal National Orthopaedic HospitalStanmoreUK
| | - Hongtao Ye
- Department of HistopathologyRoyal National Orthopaedic HospitalStanmoreUK
| | - Daniel Schrimpf
- Department of NeuropathologyUniversity of HeidelbergHeidelbergGermany
- Clinical Cooperation Unit Neuropathology, German Cancer Consortium (DKTK)German Cancer Research Center (DKFZ)HeidelbergGermany
| | - Damian Stichel
- Clinical Cooperation Unit Neuropathology, German Cancer Consortium (DKTK)German Cancer Research Center (DKFZ)HeidelbergGermany
| | - Martin Sill
- Hopp‐Children's Cancer Center (KiTZ)HeidelbergGermany
- Division of Pediatric Neurooncology, German Cancer Consortium (DKTK)German Cancer Research Center (DKFZ)HeidelbergGermany
| | - Christian Koelsche
- Department of NeuropathologyUniversity of HeidelbergHeidelbergGermany
- Clinical Cooperation Unit Neuropathology, German Cancer Consortium (DKTK)German Cancer Research Center (DKFZ)HeidelbergGermany
- Department of General PathologyUniversity of HeidelbergHeidelbergGermany
| | - Nischalan Pillay
- Research Department of PathologyUniversity College London, UCL Cancer InstituteLondonUK
| | - Andreas Von Deimling
- Department of NeuropathologyUniversity of HeidelbergHeidelbergGermany
- Clinical Cooperation Unit Neuropathology, German Cancer Consortium (DKTK)German Cancer Research Center (DKFZ)HeidelbergGermany
| | - Stephan Beck
- Medical Genomics Research GroupUniversity College London, UCL Cancer InstituteLondonUK
| | - Adrienne M Flanagan
- Research Department of PathologyUniversity College London, UCL Cancer InstituteLondonUK
- Department of HistopathologyRoyal National Orthopaedic HospitalStanmoreUK
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Lyskjær I, Kronborg CS, Rasmussen MH, Sørensen BS, Demuth C, Rosenkilde M, Johansen AFB, Knudsen M, Vang S, Krag SRP, Spindler KLG, Andersen CL. Correlation between early dynamics in circulating tumour DNA and outcome from FOLFIRI treatment in metastatic colorectal cancer. Sci Rep 2019; 9:11542. [PMID: 31395942 PMCID: PMC6687711 DOI: 10.1038/s41598-019-47708-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2018] [Accepted: 07/12/2019] [Indexed: 02/07/2023] Open
Abstract
Chemotherapy resistance remains a challenge in the clinical management of metastatic colorectal cancer (mCRC). Here, early changes in cell-free circulating tumour DNA (ctDNA) levels were explored as a marker of therapeutic efficacy. Twenty-four mCRC patients were enrolled and treated with FOLFIRI based first-line therapy. Blood samples collected pre-treatment, at day 7, 14, 21, 60 and at progression were analysed for cell-free DNA (cfDNA) and ctDNA levels using digital droplet PCR. A subset of samples were additionally analysed by targeted sequencing. Patients with high pre-treatment ctDNA or cfDNA levels (≥75th centile) had significantly shorter progression free survival (PFS) than patients with lower levels. Despite an overall decline in ctDNA levels from pre-treatment to first CT-scan, serial analysis identified seven patients with temporary increases in ctDNA consistent with growth of resistant cells. These patients had shorter PFS and shorter overall survival. Targeted sequencing analyses of cfDNA revealed dramatic changes in the clonal composition in response to treatment. Our study suggests that increasing ctDNA levels during the first cycles of first-line FOLFIRI treatment is a predictor of incipient progressive disease and poorer survival. Thus, we demonstrate the importance of monitoring ctDNA levels as early as one week after treatment onset to enable early detection of treatment failure.
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Affiliation(s)
- Iben Lyskjær
- Department of Molecular Medicine, Aarhus University Hospital, DK-8200, Aarhus, Denmark
| | | | | | - Boe Sandahl Sørensen
- Department of Clinical Biochemistry, Aarhus University Hospital, DK-8200, Aarhus, Denmark
| | - Christina Demuth
- Department of Clinical Biochemistry, Aarhus University Hospital, DK-8200, Aarhus, Denmark
| | - Mona Rosenkilde
- Department of Radiology, Aarhus University Hospital, DK-8200, Aarhus, Denmark
| | | | - Michael Knudsen
- Department of Molecular Medicine, Aarhus University Hospital, DK-8200, Aarhus, Denmark
| | - Søren Vang
- Department of Molecular Medicine, Aarhus University Hospital, DK-8200, Aarhus, Denmark
| | | | - Karen-Lise Garm Spindler
- Department of Experimental Clinical Oncology, Aarhus University Hospital, DK-8200, Aarhus, Denmark
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14
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Lyskjær I, Kronborg CJ, Rasmussen MH, Sørensen BS, Rosenkilde M, Knudsen M, Krag SR, Spindler KLG, Andersen CL. Abstract 3617: Prediction of irinotecan and flurouracil efficacy in metastatic colorectal cancer by early measurement of circulating tumor DNA. Cancer Res 2018. [DOI: 10.1158/1538-7445.am2018-3617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background: Chemotherapy resistance in metastatic colorectal cancer (mCRC) is a major challenge, and development of biomarkers for determining therapy efficacy is vital to ensure optimal palliative treatment. Recently, quantification of changes in circulating tumor DNA (ctDNA) levels has attracted substantial attention as a predictive marker. Here, we provide evidence that ctDNA has the potential to be used as an early marker of therapeutic efficacy of irinotecan and fluorouracil (FOLFIRI).
Experimental Procedures: Patients diagnosed with mCRC, and with indication for first-line combination chemotherapy, were prospectively enrolled in this phase II study. Blood was drawn at baseline, day 7, 14, 21, 40 and then monthly until progression. Response evaluation was done at eight-week intervals by CT scanning using RECIST criteria. Chemotherapy was administered at day one and two every two weeks. The levels of cell-free DNA (cfDNA) and ctDNA were determined using sensitive digital droplet PCR assays. ctDNA assays were designed either to mutations identified by targeted sequencing or on basis of known tumor mutations detected in primary or metastatic lesions using a panel of mutation-specific qPCR based assays (KRAS, NRAS, BRAF).
Results: Twenty-four patients were enrolled. A KRAS, NRAS or BRAF mutation was observed in tumor tissue of 16 patients. In 12 of these the mutations were confirmed in baseline samples and used for assessing ctDNA. For the remaining 12 patients, a mutation for ctDNA quantification was identified by targeted tumor sequencing. Patients with high baseline ctDNA levels (75th centile) had significantly shorter progression-free survival (PFS) than patients with low baseline ctDNA levels. After first treatment cycle all patients experienced a decline in ctDNA levels demonstrating initial response to treatment; however, the reduction in ctDNA was not associated with prolonged PFS or overall survival (OS). Conversely, change in ctDNA levels from first to second cycle of treatment (three weeks after treatment start) predicted FOLFIRI efficacy. Patients with increasing ctDNA levels at this time point had a significantly shorter PFS and a shorter OS than patients with stable or decreasing ctDNA levels.
Conclusion: In agreement with the literature, we show that baseline tumor DNA levels predicted PFS. The initial observed decline in ctDNA levels upon administration of FOLFIRI indicates that all tumors had cancer cells sensitive to treatment; however, after elimination of these, resistant clones expanded, leading to treatment resistance. Importantly, our study demonstrates that FOLFIRI efficacy can be evaluated as early as three weeks after treatment initiation by measurement of ctDNA levels. This enables early detection of treatment failure and allows for rapid adaptation of the treatment strategy.
Citation Format: Iben Lyskjær, Camilla J. Kronborg, Mads H. Rasmussen, Boe S. Sørensen, Mona Rosenkilde, Michael Knudsen, Søren R. Krag, Karen-Lise G. Spindler, Claus L. Andersen. Prediction of irinotecan and flurouracil efficacy in metastatic colorectal cancer by early measurement of circulating tumor DNA [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 3617.
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Affiliation(s)
- Iben Lyskjær
- 1Department of Molecular Medicine (MOMA), Aarhus University Hospital, Aarhus N, Denmark
| | - Camilla J. Kronborg
- 2Department of Oncology, Aarhus University Hospital, Denmark, Aarhus N, Denmark
| | - Mads H. Rasmussen
- 3Department of Molecular Medicine (MOMA), Aarhus University Hospital, Denmark, Aarhus N, Denmark
| | - Boe S. Sørensen
- 4Department of Clinical Biochemistry, Aarhus University Hospital, Denmark, Aarhus N, Denmark
| | - Mona Rosenkilde
- 5Department of Radiology, Aarhus University Hospital, Aarhus N, Denmark
| | - Michael Knudsen
- 1Department of Molecular Medicine (MOMA), Aarhus University Hospital, Aarhus N, Denmark
| | - Søren R. Krag
- 6Department of Pathology, Aarhus University Hospital, Aarhus N, Denmark
| | - Karen-Lise G. Spindler
- 7Department of Experimental Clinical Oncology, Aarhus University Hospital, Aarhus N, Denmark
| | - Claus L. Andersen
- 1Department of Molecular Medicine (MOMA), Aarhus University Hospital, Aarhus N, Denmark
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15
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Lyskjær I, Rasmussen MH, Andersen CL. Putting a brake on stress signaling: miR-625-3p as a biomarker for choice of therapy in colorectal cancer. Epigenomics 2016; 8:1449-1452. [PMID: 27779424 DOI: 10.2217/epi-2016-0128] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Affiliation(s)
- Iben Lyskjær
- Department of Molecular Medicine, Department of Clinical Medicine, Aarhus University Hospital, Palle Juul-Jensens Boulevard 99, DK-8200 Aarhus, Denmark
| | - Mads H Rasmussen
- Department of Molecular Medicine, Department of Clinical Medicine, Aarhus University Hospital, Palle Juul-Jensens Boulevard 99, DK-8200 Aarhus, Denmark
| | - Claus L Andersen
- Department of Molecular Medicine, Department of Clinical Medicine, Aarhus University Hospital, Palle Juul-Jensens Boulevard 99, DK-8200 Aarhus, Denmark
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16
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Rasmussen MH, Lyskjær I, Jersie-Christensen RR, Tarpgaard LS, Primdal-Bengtson B, Nielsen MM, Pedersen JS, Hansen TP, Hansen F, Olsen JV, Pfeiffer P, Ørntoft TF, Andersen CL. Abstract 2927: miR-625-3p regulates oxaliplatin resistance by targeting MAP2K6-p38 signalling in human colorectal adenocarcinoma cell. Cancer Res 2016. [DOI: 10.1158/1538-7445.am2016-2927] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Oxaliplatin (oxPt) resistance in colorectal cancers (CRC) is a major medical problem, and predictive markers are urgently needed. Recently, miR-625-3p was reported as a promising predictive marker. Here, we have used in vitro models to show that miR-625-3p functionally induces oxPt resistance in CRC cells, and have identified signalling networks affected by mir-625-3p. The p38 MAPK activator MAP2K6 was shown to be a direct target of miR-625-3p, and, accordingly, was downregulated in patients not responding to oxPt therapy. miR-625-3p resistance could be reversed in CRC cells by anti-miR-625-3p treatment and by ectopic expression of a miR-625-3p insensitive MAP2K6 variant. In addition, by reducing p38 MAPK signalling using either siRNA technology, chemical inhibitors to p38 or by ectopic expression of dominant negative MAP2K6 protein we induced resistance to oxPt. Transcriptome, proteome and phosphoproteome profiles revealed inactivation of MAP2K6-p38 signalling as a possible driving force behind oxPt resistance.
Our study shows that miR-625-3p induces oxPt resistance by abrogating MAP2K6-p38 regulated apoptosis and cell cycle control networks, and corroborates the predictive power of miR-625-3p.
Citation Format: Mads H. Rasmussen, Iben Lyskjær, Rosa R. Jersie-Christensen, Line S. Tarpgaard, Bjarke Primdal-Bengtson, Morten M. Nielsen, Jakob S. Pedersen, Tine P. Hansen, Flemming Hansen, Jesper V. Olsen, Per Pfeiffer, Torben F. Ørntoft, Claus L. Andersen. miR-625-3p regulates oxaliplatin resistance by targeting MAP2K6-p38 signalling in human colorectal adenocarcinoma cell. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 2927.
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