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Huebner A, Black JRM, Sarno F, Pazo R, Juez I, Medina L, Garcia-Carbonero R, Guillén C, Feliú J, Alonso C, Arenillas C, Moreno-Cárdenas AB, Verdaguer H, Macarulla T, Hidalgo M, McGranahan N, Toledo RA. ACT-Discover: identifying karyotype heterogeneity in pancreatic cancer evolution using ctDNA. Genome Med 2023; 15:27. [PMID: 37081523 PMCID: PMC10120117 DOI: 10.1186/s13073-023-01171-w] [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: 08/08/2022] [Accepted: 03/10/2023] [Indexed: 04/22/2023] Open
Abstract
BACKGROUND Liquid biopsies and the dynamic tracking of somatic mutations within circulating tumour DNA (ctDNA) can provide insight into the dynamics of cancer evolution and the intra-tumour heterogeneity that fuels treatment resistance. However, identifying and tracking dynamic changes in somatic copy number alterations (SCNAs), which have been associated with poor outcome and metastasis, using ctDNA is challenging. Pancreatic adenocarcinoma is a disease which has been considered to harbour early punctuated events in its evolution, leading to an early fitness peak, with minimal further subclonal evolution. METHODS To interrogate the role of SCNAs in pancreatic adenocarcinoma cancer evolution, we applied whole-exome sequencing of 55 longitudinal cell-free DNA (cfDNA) samples taken from 24 patients (including 8 from whom a patient-derived xenograft (PDX) was derived) with metastatic disease prospectively recruited into a clinical trial. We developed a method, Aneuploidy in Circulating Tumour DNA (ACT-Discover), that leverages haplotype phasing of paired tumour biopsies or PDXs to identify SCNAs in cfDNA with greater sensitivity. RESULTS SCNAs were observed within 28 of 47 evaluable cfDNA samples. Of these events, 30% could only be identified by harnessing the haplotype-aware approach leveraged in ACT-Discover. The exceptional purity of PDX tumours enabled near-complete phasing of genomic regions in allelic imbalance, highlighting an important auxiliary function of PDXs. Finally, although the classical model of pancreatic cancer evolution emphasises the importance of early, homogenous somatic events as a key requirement for cancer development, ACT-Discover identified substantial heterogeneity of SCNAs, including parallel focal and arm-level events, affecting different parental alleles within individual tumours. Indeed, ongoing acquisition of SCNAs was identified within tumours throughout the disease course, including within an untreated metastatic tumour. CONCLUSIONS This work demonstrates the power of haplotype phasing to study genomic variation in cfDNA samples and reveals undiscovered intra-tumour heterogeneity with important scientific and clinical implications. Implementation of ACT-Discover could lead to important insights from existing cohorts or underpin future prospective studies seeking to characterise the landscape of tumour evolution through liquid biopsy.
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Affiliation(s)
- Ariana Huebner
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Genome Evolution Research Group, Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - James R M Black
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Genome Evolution Research Group, Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | | | - Roberto Pazo
- Hospital Universitario Miguel Servet, Zaragoza, Spain
| | - Ignacio Juez
- Hospital Universitario de Fuenlabrada, Madrid, Spain
| | | | | | | | - Jaime Feliú
- Hospital Universitario La Paz, Madrid, Spain
| | | | - Carlota Arenillas
- Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | | | - Helena Verdaguer
- Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
- Vall d'Hebron University Hospital, Barcelona, Spain
| | - Teresa Macarulla
- Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
- Vall d'Hebron University Hospital, Barcelona, Spain
| | | | - Nicholas McGranahan
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK.
- Cancer Genome Evolution Research Group, Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK.
| | - Rodrigo A Toledo
- Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain.
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain.
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Elez E, Ros J, Fernández J, Villacampa G, Moreno-Cárdenas AB, Arenillas C, Bernatowicz K, Comas R, Li S, Kodack DP, Fasani R, Garcia A, Gonzalo-Ruiz J, Piris-Gimenez A, Nuciforo P, Kerr G, Intini R, Montagna A, Germani MM, Randon G, Vivancos A, Smits R, Graus D, Perez-Lopez R, Cremolini C, Lonardi S, Pietrantonio F, Dienstmann R, Tabernero J, Toledo RA. RNF43 mutations predict response to anti-BRAF/EGFR combinatory therapies in BRAF V600E metastatic colorectal cancer. Nat Med 2022; 28:2162-2170. [PMID: 36097219 PMCID: PMC9556333 DOI: 10.1038/s41591-022-01976-z] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 07/26/2022] [Indexed: 11/22/2022]
Abstract
Anti-BRAF/EGFR therapy was recently approved for the treatment of metastatic BRAFV600E colorectal cancer (mCRCBRAF-V600E). However, a large fraction of patients do not respond, underscoring the need to identify molecular determinants of treatment response. Using whole-exome sequencing in a discovery cohort of patients with mCRCBRAF-V600E treated with anti-BRAF/EGFR therapy, we found that inactivating mutations in RNF43, a negative regulator of WNT, predict improved response rates and survival outcomes in patients with microsatellite-stable (MSS) tumors. Analysis of an independent validation cohort confirmed the relevance of RNF43 mutations to predicting clinical benefit (72.7% versus 30.8%; P = 0.03), as well as longer progression-free survival (hazard ratio (HR), 0.30; 95% confidence interval (CI), 0.12–0.75; P = 0.01) and overall survival (HR, 0.26; 95% CI, 0.10–0.71; P = 0.008), in patients with MSS-RNF43mutated versus MSS-RNF43wild-type tumors. Microsatellite-instable tumors invariably carried a wild-type-like RNF43 genotype encoding p.G659fs and presented an intermediate response profile. We found no association of RNF43 mutations with patient outcomes in a control cohort of patients with MSS-mCRCBRAF-V600E tumors not exposed to anti-BRAF targeted therapies. Overall, our findings suggest a cross-talk between the MAPK and WNT pathways that may modulate the antitumor activity of anti-BRAF/EGFR therapy and uncover predictive biomarkers to optimize the clinical management of these patients. The presence of inactivating mutations in RNF43, a negative regulator of WNT, in tumor cells predicts improved response rates and survival outcomes in patients with metastatic BRAFV600E colorectal cancer treated with anti-BRAF/EGFR therapy.
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Affiliation(s)
- Elena Elez
- Medical Oncology Department, Vall d'Hebron University Hospital, Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain. .,Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain.
| | - Javier Ros
- Medical Oncology Department, Vall d'Hebron University Hospital, Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain.,Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain.,Oncologia Medica, Dipartimento di Medicina di Precisione, Università degli Studi della Campania Luigi Vanvitelli, Naples, Italy
| | - Jose Fernández
- Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
| | - Guillermo Villacampa
- Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
| | - Ana Belén Moreno-Cárdenas
- Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
| | - Carlota Arenillas
- Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Institute of Health Carlos III (ISCIII), Madrid, Spain
| | - Kinga Bernatowicz
- Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
| | - Raquel Comas
- Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
| | - Shanshan Li
- Department of Gastroenterology and Hepatology, Erasmus MC-University Medical Center, Rotterdam, the Netherlands
| | | | - Roberta Fasani
- Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
| | - Ariadna Garcia
- Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
| | - Javier Gonzalo-Ruiz
- Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
| | - Alejandro Piris-Gimenez
- Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
| | - Paolo Nuciforo
- Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
| | - Grainne Kerr
- Oncology Department, Novartis Institutes for Biomedical Research, Novartis, Basel, Switzerland
| | - Rossana Intini
- Department of Oncology, Veneto Institute of Oncology IRCCS, Padova, Italy
| | - Aldo Montagna
- Department of Oncology, Veneto Institute of Oncology IRCCS, Padova, Italy
| | - Marco Maria Germani
- Unit of Medical Oncology, Azienda Ospedaliero-Universitaria Pisana, Department of Trans-lational Research and New Technologies in Medicine, University of Pisa, Pisa, Italy
| | - Giovanni Randon
- Department of Medical Oncology, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Ana Vivancos
- Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
| | - Ron Smits
- Department of Gastroenterology and Hepatology, Erasmus MC-University Medical Center, Rotterdam, the Netherlands
| | - Diana Graus
- Oncology Department, Novartis Institutes for Biomedical Research, Novartis, Basel, Switzerland.,Ridgeline Discovery, Basel, Switzerland
| | - Raquel Perez-Lopez
- Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain.,Radiology Department, Vall d'Hebron University Hospital, Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
| | - Chiara Cremolini
- Unit of Medical Oncology, Azienda Ospedaliero-Universitaria Pisana, Department of Trans-lational Research and New Technologies in Medicine, University of Pisa, Pisa, Italy
| | - Sara Lonardi
- Department of Oncology, Veneto Institute of Oncology IRCCS, Padova, Italy
| | - Filippo Pietrantonio
- Department of Medical Oncology, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Rodrigo Dienstmann
- Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
| | - Josep Tabernero
- Medical Oncology Department, Vall d'Hebron University Hospital, Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain.,Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Institute of Health Carlos III (ISCIII), Madrid, Spain.,UVic-UCC, IOB-Quirón, Barcelona, Spain
| | - Rodrigo A Toledo
- Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain. .,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Institute of Health Carlos III (ISCIII), Madrid, Spain.
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Tsoi KM, Gokgoz N, Darville-O'Quinn P, Prochazka P, Malekoltojari A, Griffin AM, Ferguson PC, Wunder JS, Andrulis IL. Detection and utility of cell-free and circulating tumour DNA in bone and soft-tissue sarcomas. Bone Joint Res 2021; 10:602-610. [PMID: 34558310 PMCID: PMC8479566 DOI: 10.1302/2046-3758.109.bjr-2021-0014.r1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Aims Cell-free DNA (cfDNA) and circulating tumour DNA (ctDNA) are used for prognostication and monitoring in patients with carcinomas, but their utility is unclear in sarcomas. The objectives of this pilot study were to explore the prognostic significance of cfDNA and investigate whether tumour-specific alterations can be detected in the circulation of sarcoma patients. Methods Matched tumour and blood were collected from 64 sarcoma patients (n = 70 samples) prior to resection of the primary tumour (n = 57) or disease recurrence (n = 7). DNA was isolated from plasma, quantified, and analyzed for cfDNA. A subset of cases (n = 6) underwent whole exome sequencing to identify tumour-specific alterations used to detect ctDNA using digital droplet polymerase chain reaction (ddPCR). Results Cell-free was present in 69 of 70 samples above 0.5 ng/ml. Improved disease-free survival was found for patients with lower cfDNA levels (90% vs 48% at one-year for ≤ 6 ng/ml and > 6 ng/ml, respectively; p = 0.005). Digital droplet PCR was performed as a pilot study and mutant alleles were detectable at 0.5% to 2.5% of the wild type genome, and at a level of 0.25 ng tumour DNA. Tumour-specific alterations (ctDNA) were found in five of six cases. Conclusion This work demonstrates the feasibility and potential utility of cfDNA and ctDNA as biomarkers for bone and soft-tissue sarcomas, despite the lack of recurrent genomic alterations. A larger study is required to validate these findings. Cite this article: Bone Joint Res 2021;10(9):602–610.
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Affiliation(s)
- Kim M Tsoi
- University of Toronto Musculoskeletal Oncology Unit, Sinai Health System, Toronto, Canada.,Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Canada.,Department of Surgery, University of Toronto, Toronto, Canada
| | - Nalan Gokgoz
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Canada
| | | | - Patrick Prochazka
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Canada
| | - Ainaz Malekoltojari
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Canada
| | - Anthony M Griffin
- University of Toronto Musculoskeletal Oncology Unit, Sinai Health System, Toronto, Canada
| | - Peter C Ferguson
- University of Toronto Musculoskeletal Oncology Unit, Sinai Health System, Toronto, Canada.,Department of Surgery, University of Toronto, Toronto, Canada
| | - Jay S Wunder
- University of Toronto Musculoskeletal Oncology Unit, Sinai Health System, Toronto, Canada.,Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Canada.,Department of Surgery, University of Toronto, Toronto, Canada
| | - Irene L Andrulis
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
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