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Witz A, Dardare J, Betz M, Gilson P, Merlin JL, Harlé A. Tumor-derived cell-free DNA and circulating tumor cells: partners or rivals in metastasis formation? Clin Exp Med 2024; 24:2. [PMID: 38231464 PMCID: PMC10794481 DOI: 10.1007/s10238-023-01278-9] [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: 09/25/2023] [Accepted: 11/20/2023] [Indexed: 01/18/2024]
Abstract
The origin of metastases is a topic that has sparked controversy. Despite recent advancements, metastatic disease continues to pose challenges. The first admitted model of how metastases develop revolves around cells breaking away from the primary tumor, known as circulating tumor cells (CTCs). These cells survive while circulating through the bloodstream and subsequently establish themselves in secondary organs, a process often referred to as the "metastatic cascade". This intricate and dynamic process involves various steps, but all the mechanisms behind metastatic dissemination are not yet comprehensively elucidated. The "seed and soil" theory has shed light on the phenomenon of metastatic organotropism and the existence of pre-metastatic niches. It is now established that these niches can be primed by factors secreted by the primary tumor before the arrival of CTCs. In particular, exosomes have been identified as important contributors to this priming. Another concept then emerged, i.e. the "genometastasis" theory, which challenged all other postulates. It emphasizes the intriguing but promising role of cell-free DNA (cfDNA) in metastasis formation through oncogenic formation of recipient cells. However, it cannot be ruled out that all these theories are intertwined. This review outlines the primary theories regarding the metastases formation that involve CTCs, and depicts cfDNA, a potential second player in the metastasis formation. We discuss the potential interrelationships between CTCs and cfDNA, and propose both in vitro and in vivo experimental strategies to explore all plausible theories.
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Affiliation(s)
- Andréa Witz
- Département de Biopathologie, Institut de Cancérologie de Lorraine, CNRS UMR 7039 CRAN-Université de Lorraine, 6 avenue de Bourgogne, 54519, Vandœuvre-lès-Nancy Cedex, France.
| | - Julie Dardare
- Département de Biopathologie, Institut de Cancérologie de Lorraine, CNRS UMR 7039 CRAN-Université de Lorraine, 6 avenue de Bourgogne, 54519, Vandœuvre-lès-Nancy Cedex, France
| | - Margaux Betz
- Département de Biopathologie, Institut de Cancérologie de Lorraine, CNRS UMR 7039 CRAN-Université de Lorraine, 6 avenue de Bourgogne, 54519, Vandœuvre-lès-Nancy Cedex, France
| | - Pauline Gilson
- Département de Biopathologie, Institut de Cancérologie de Lorraine, CNRS UMR 7039 CRAN-Université de Lorraine, 6 avenue de Bourgogne, 54519, Vandœuvre-lès-Nancy Cedex, France
| | - Jean-Louis Merlin
- Département de Biopathologie, Institut de Cancérologie de Lorraine, CNRS UMR 7039 CRAN-Université de Lorraine, 6 avenue de Bourgogne, 54519, Vandœuvre-lès-Nancy Cedex, France
| | - Alexandre Harlé
- Département de Biopathologie, Institut de Cancérologie de Lorraine, CNRS UMR 7039 CRAN-Université de Lorraine, 6 avenue de Bourgogne, 54519, Vandœuvre-lès-Nancy Cedex, France
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2
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Zhao J, Reuther J, Scozzaro K, Hawley M, Metzger E, Emery M, Chen I, Barbosa M, Johnson L, O'Connor A, Washburn M, Hartje L, Reckase E, Johnson V, Zhang Y, Westheimer E, O'Callaghan W, Malani N, Chesh A, Moreau M, Daber R. Personalized Cancer Monitoring Assay for the Detection of ctDNA in Patients with Solid Tumors. Mol Diagn Ther 2023; 27:753-768. [PMID: 37632661 PMCID: PMC10590345 DOI: 10.1007/s40291-023-00670-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/27/2023] [Indexed: 08/28/2023]
Abstract
BACKGROUND Highly sensitive molecular assays have been developed to detect plasma-based circulating tumor DNA (ctDNA), and emerging evidence suggests their clinical utility for monitoring minimal residual disease and recurrent disease, providing prognostic information, and monitoring therapy responses in patients with solid tumors. The Invitae Personalized Cancer Monitoring™ assay uses a patient-specific, tumor-informed variant signature identified through whole exome sequencing to detect ctDNA in peripheral blood of patients with solid tumors. METHODS The assay's tumor whole exome sequencing and ctDNA detection components were analytically validated using 250 unique human specimens and nine commercial reference samples that generated 1349 whole exome sequencing and cell-free DNA (cfDNA)-derived libraries. A comparison of tumor and germline whole exome sequencing was used to identify patient-specific tumor variant signatures and generate patient-specific panels, followed by targeted next-generation sequencing of plasma-derived cfDNA using the patient-specific panels with anchored multiplex polymerase chain reaction chemistry leveraging unique molecular identifiers. RESULTS Whole exome sequencing resulted in overall sensitivity of 99.8% and specificity of > 99.9%. Patient-specific panels were successfully designed for all 63 samples (100%) with ≥ 20% tumor content and 24 (80%) of 30 samples with ≥ 10% tumor content. Limit of blank studies using 30 histologically normal, formalin-fixed paraffin-embedded specimens resulted in 100% expected panel design failure. The ctDNA detection component demonstrated specificity of > 99.9% and sensitivity of 96.3% for a combination of 10 ng of cfDNA input, 0.008% allele frequency, 50 variants on the patient-specific panels, and a baseline threshold. Limit of detection ranged from 0.008% allele frequency when utilizing 60 ng of cfDNA input with 18-50 variants in the patient-specific panels (> 99.9% sensitivity) with a baseline threshold, to 0.05% allele frequency when using 10 ng of cfDNA input with an 18-variant panel with a monitoring threshold (> 99.9% sensitivity). CONCLUSIONS The Invitae Personalized Cancer Monitoring assay, featuring a flexible patient-specific panel design with 18-50 variants, demonstrated high sensitivity and specificity for detecting ctDNA at variant allele frequencies as low as 0.008%. This assay may support patient prognostic stratification, provide real-time data on therapy responses, and enable early detection of residual/recurrent disease.
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Affiliation(s)
- Jianhua Zhao
- Invitae Corp., 1400 16th Street, San Francisco, CA, 94103, USA.
| | | | - Kaylee Scozzaro
- Invitae Corp., 1400 16th Street, San Francisco, CA, 94103, USA
| | - Megan Hawley
- Invitae Corp., 1400 16th Street, San Francisco, CA, 94103, USA
| | - Emily Metzger
- Invitae Corp., 1400 16th Street, San Francisco, CA, 94103, USA
| | - Matthew Emery
- Invitae Corp., 1400 16th Street, San Francisco, CA, 94103, USA
| | - Ingrid Chen
- Invitae Corp., 1400 16th Street, San Francisco, CA, 94103, USA
| | | | - Laura Johnson
- Invitae Corp., 1400 16th Street, San Francisco, CA, 94103, USA
- Affiliated with Invitae Corp. at the time of the study, currently employees at Integrated DNA Technologies, 1710 Commercial Park, Coralville, IA, 52241, USA
| | - Alijah O'Connor
- Invitae Corp., 1400 16th Street, San Francisco, CA, 94103, USA
| | - Mike Washburn
- Invitae Corp., 1400 16th Street, San Francisco, CA, 94103, USA
- Affiliated with Invitae Corp. at the time of the study, currently employees at Integrated DNA Technologies, 1710 Commercial Park, Coralville, IA, 52241, USA
| | - Luke Hartje
- Invitae Corp., 1400 16th Street, San Francisco, CA, 94103, USA
- Affiliated with Invitae Corp. at the time of the study, currently employees at Integrated DNA Technologies, 1710 Commercial Park, Coralville, IA, 52241, USA
| | - Erik Reckase
- Invitae Corp., 1400 16th Street, San Francisco, CA, 94103, USA
- Affiliated with Invitae Corp. at the time of the study, currently employees at Integrated DNA Technologies, 1710 Commercial Park, Coralville, IA, 52241, USA
| | - Verity Johnson
- Invitae Corp., 1400 16th Street, San Francisco, CA, 94103, USA
- Affiliated with Invitae Corp. at the time of the study, currently employees at Integrated DNA Technologies, 1710 Commercial Park, Coralville, IA, 52241, USA
| | - Yuhua Zhang
- Invitae Corp., 1400 16th Street, San Francisco, CA, 94103, USA
| | | | | | - Nirav Malani
- Invitae Corp., 1400 16th Street, San Francisco, CA, 94103, USA
| | - Adrian Chesh
- Invitae Corp., 1400 16th Street, San Francisco, CA, 94103, USA
| | - Michael Moreau
- Invitae Corp., 1400 16th Street, San Francisco, CA, 94103, USA
| | - Robert Daber
- Invitae Corp., 1400 16th Street, San Francisco, CA, 94103, USA
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3
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Oberoi S, Choy E, Chen YL, Scharschmidt T, Weiss AR. Trimodality Treatment of Extremity Soft Tissue Sarcoma: Where Do We Go Now? Curr Treat Options Oncol 2023; 24:300-326. [PMID: 36877374 DOI: 10.1007/s11864-023-01059-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/23/2023] [Indexed: 03/07/2023]
Abstract
OPINION STATEMENT Extremity soft tissue sarcoma (ESTS) constitutes the majority of patients with soft tissue sarcoma (STS). Patients with localized high-grade ESTS > 5 cm in size carry a substantial risk of developing distant metastasis on follow-up. A neoadjuvant chemoradiotherapy approach can enhance local control by facilitating resection of the large and deep locally advanced tumors while trying to address distant spread by treating the micrometastasis for these high-risk ESTS. Preoperative chemoradiotherapy and adjuvant chemotherapy are often used for children with intermediate- or high-risk non-rhabdomyosarcoma soft tissue tumors in North America and Europe. In adults, the cumulative evidence supporting preoperative chemoradiotherapy or adjuvant chemotherapy remains controversial. However, some studies support a possible benefit of 10% in overall survival (OS) for high-risk localized ESTS, especially for those with a probability of 10-year OS < 60% using validated nomograms. Opponents of neoadjuvant chemotherapy argue that it delays curative surgery, compromises local control, and increases the rate of wound complications and treatment-related mortality; however, the published trials do not support these arguments. Most treatment-related side effects can be managed with adequate supportive care. A coordinated multidisciplinary approach involving sarcoma expertise in surgery, radiation, and chemotherapy is required to achieve better outcomes for ESTS. The next generation of clinical trials will shed light on how comprehensive molecular characterization, targeted agents and/or immunotherapy can be integrated into the upfront trimodality treatment to improve outcomes. To that end, every effort should be made to enroll these patients on clinical trials, when available.
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Affiliation(s)
- Sapna Oberoi
- Department of Pediatric Hematology Oncology, CancerCare Manitoba, Winnipeg, MB, Canada
| | - Edwin Choy
- Division of Medical Oncology, Massachusetts General Hospital, Boston, MA, USA
| | - Yen-Lin Chen
- Department of Orthopedics, Division of Musculoskeletal Oncology, The Ohio State University, Columbus, OH, USA
| | - Thomas Scharschmidt
- Department of Radiation Oncology, Massachusetts General Hospital, Boston, MA, USA
| | - Aaron R Weiss
- Department of Pediatric Hematology Oncology, Maine Medical Center, 100 Campus Drive, Suite 107 Scarborough, Portland, ME, USA.
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4
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Seidel MG, Kashofer K, Moser T, Thueringer A, Liegl-Atzwanger B, Leithner A, Szkandera J, Benesch M, El-Heliebi A, Heitzer E. Clinical implementation of plasma cell-free circulating tumor DNA quantification by digital droplet PCR for the monitoring of Ewing sarcoma in children and adolescents. Front Pediatr 2022; 10:926405. [PMID: 36046479 PMCID: PMC9420963 DOI: 10.3389/fped.2022.926405] [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] [Received: 04/22/2022] [Accepted: 07/15/2022] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND Treatment stratification and response assessment in pediatric sarcomas has relied on imaging studies and surgical/histopathological evidence of vital tumor cells. Such studies and evidence collection processes often involve radiation and/or general anesthesia in children. Cell-free circulating tumor DNA (ctDNA) detection in blood plasma is one available method of so-called liquid biopsies that has been shown to correlate qualitatively and quantitatively with the existence of vital tumor cells in the body. Our clinical observational study focused on the utility and feasibility of ctDNA detection in pediatric Ewing sarcoma (EWS) as a marker of minimal residual disease (MRD). PATIENTS AND METHODS We performed whole genome sequencing (WGS) to identify the exact breakpoints in tumors known to carry the EWS-FLI1 fusion gene. Patient-specific fusion breakpoints were tracked in peripheral blood plasma using digital droplet PCR (ddPCR) before, during, and after therapy in six children and young adults with EWS. Presence and levels of fusion breakpoints were correlated with clinical disease courses. RESULTS We show that the detection of ctDNA in the peripheral blood of EWS patients (i) is feasible in the clinical routine and (ii) allows for the longitudinal real-time monitoring of MRD activity in children and young adults. Although changing ctDNA levels correlated well with clinical outcome within patients, between patients, a high variability was observed (inter-individually). CONCLUSION ctDNA detection by ddPCR is a highly sensitive, specific, feasible, and highly accurate method that can be applied in EWS for follow-up assessments as an additional surrogate parameter for clinical MRD monitoring and, potentially, also for treatment stratification in the near future.
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Affiliation(s)
- Markus G Seidel
- Division for Pediatric Hematology-Oncology, Department of Pediatrics and Adolescent Medicine, Medical University of Graz, Graz, Austria
| | - Karl Kashofer
- Diagnostic and Research Center for Molecular BioMedicine, Diagnostic and Research Institute of Pathology, Medical University of Graz, Graz, Austria.,BioTechMed-Graz, Graz, Austria
| | - Tina Moser
- Diagnostic and Research Center for Molecular BioMedicine, Diagnostic and Research Institute of Human Genetics, Medical University of Graz, Graz, Austria.,Christian Doppler Laboratory for Liquid Biopsies for Early Detection of Cancer, Medical University of Graz, Graz, Austria
| | - Andrea Thueringer
- Diagnostic and Research Center for Molecular BioMedicine, Diagnostic and Research Institute of Pathology, Medical University of Graz, Graz, Austria
| | - Bernadette Liegl-Atzwanger
- Diagnostic and Research Center for Molecular BioMedicine, Diagnostic and Research Institute of Pathology, Medical University of Graz, Graz, Austria
| | - Andreas Leithner
- Department of Orthopedics and Trauma, Medical University of Graz, Graz, Austria
| | - Joanna Szkandera
- Division of Oncology, Department of Internal Medicine, Medical University of Graz, Graz, Austria
| | - Martin Benesch
- Division for Pediatric Hematology-Oncology, Department of Pediatrics and Adolescent Medicine, Medical University of Graz, Graz, Austria
| | - Amin El-Heliebi
- BioTechMed-Graz, Graz, Austria.,Division of Cell Biology, Histology and Embryology, Gottfried Schatz Research Center, Medical University of Graz, Graz, Austria.,Center for Biomarker Research in Medicine (CBmed), Graz, Austria
| | - Ellen Heitzer
- Diagnostic and Research Center for Molecular BioMedicine, Diagnostic and Research Institute of Human Genetics, Medical University of Graz, Graz, Austria.,Christian Doppler Laboratory for Liquid Biopsies for Early Detection of Cancer, Medical University of Graz, Graz, Austria
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Zhang J, Alexandrou G, Toumazou C, Kalofonou M. Automating the Design of Cancer Specific DNA Probes Using Computational Algorithms. ANNUAL INTERNATIONAL CONFERENCE OF THE IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. ANNUAL INTERNATIONAL CONFERENCE 2021; 2021:1852-1856. [PMID: 34891648 DOI: 10.1109/embc46164.2021.9630589] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
This paper introduces a novel Python script which automates the design process of cancer variant-specific DNA probes, based on the amplification method LAMP (Loop-Mediated Isothermal Amplification). With just an input of the DNA sequence and the mutation base location, the script outputs suggestions of two best fitting primer sets for a given target, together with an estimated working efficiency. The script also implements a feature of 'script training', using experimentally-validated primers as a benchmark for primer design optimisation. The proposed script has been tested using the gene sequences of ESR1 p.E380Q and ESR1 p.Y537S cancer specific mutations, with the results to closely resemble the experimentally validated primer sets. Creating a rapid LAMP primer design utility allows LAMP to be more easily used as a molecular method for assay development in Lab-on-Chip (LoC) systems to track mutational profiles of variant-specific assays.
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6
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van der Laan P, van Houdt WJ, van den Broek D, Steeghs N, van der Graaf WTA. Liquid Biopsies in Sarcoma Clinical Practice: Where Do We Stand? Biomedicines 2021; 9:1315. [PMID: 34680432 PMCID: PMC8533081 DOI: 10.3390/biomedicines9101315] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 09/17/2021] [Accepted: 09/22/2021] [Indexed: 12/17/2022] Open
Abstract
Sarcomas are rare tumors of bone and soft tissue with a mesenchymal origin. This uncommon type of cancer is marked by a high heterogeneity, consisting of over 70 subtypes. Because of this broad spectrum, their treatment requires a subtype-specific therapeutic approach. Tissue biopsy is currently the golden standard for sarcoma diagnosis, but it has its limitations. Over the recent years, methods to detect, characterize, and monitor cancer through liquid biopsy have evolved rapidly. The analysis of circulating biomarkers in peripheral blood, such as circulating tumor cells (CTC) or circulating tumor DNA (ctDNA), could provide real-time information on tumor genetics, disease state, and resistance mechanisms. Furthermore, it traces tumor evolution and can assess tumor heterogeneity. Although the first results in sarcomas are encouraging, there are technical challenges that need to be addressed for implementation in clinical practice. Here, we summarize current knowledge about liquid biopsies in sarcomas and elaborate on different strategies to integrate liquid biopsy into sarcoma clinical care.
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Affiliation(s)
- Pia van der Laan
- Department of Surgical Oncology, Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands; (P.v.d.L.); (W.J.v.H.)
- Department of Medical Oncology, Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands;
| | - Winan J. van Houdt
- Department of Surgical Oncology, Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands; (P.v.d.L.); (W.J.v.H.)
| | - Daan van den Broek
- Department of Laboratory Medicine, Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands;
| | - Neeltje Steeghs
- Department of Medical Oncology, Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands;
| | - Winette T. A. van der Graaf
- Department of Medical Oncology, Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands;
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus MC, 3015 GD Rotterdam, The Netherlands
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7
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Jones J, Cain S, Pesic-Smith J, Choong PFM, Morokoff AP, Drummond KJ, Dabscheck G. Circulating tumor DNA for malignant peripheral nerve sheath tumors in neurofibromatosis type 1. J Neurooncol 2021; 154:265-274. [PMID: 34529228 DOI: 10.1007/s11060-021-03846-z] [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: 07/21/2021] [Accepted: 09/14/2021] [Indexed: 10/20/2022]
Abstract
PURPOSE The leading cause of early death in patients with neurofibromatosis type 1 (NF1) is malignant peripheral nerve sheath tumor (MPNST). The principles of management include early diagnosis, surgical clearance and close monitoring for tumor recurrence. Current methods for diagnosis, detection of residual disease and monitoring tumor burden are inadequate, as clinical and radiological features are non-specific for malignancy in patients with multiple tumors and lack the sensitivity to identify early evidence of malignant transformation or tumor recurrence. Circulating tumor DNA (ctDNA) is a promising tool in cancer management and has the potential to improve the care of patients with NF1. In the following article we summarise the current understanding of the genomic landscape of MPNST, report on the previous literature of ctDNA in MPNST and outline the potential clinical applications for ctDNA in NF1 associated MPNST. Finally, we describe our prospective cohort study protocol investigating the utility of using ctDNA as an early diagnostic tool for MPNSTs in NF1 patients.
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Affiliation(s)
- Jordan Jones
- Department of Surgery, University of Melbourne, Melbourne, VIC, Australia. .,Department of Neurosurgery, Royal Melbourne Hospital, Melbourne, VIC, 3050, Australia.
| | - Sarah Cain
- Department of Neurosurgery, Royal Melbourne Hospital, Melbourne, VIC, 3050, Australia
| | - Jonathan Pesic-Smith
- Department of Neurosurgery, Royal Melbourne Hospital, Melbourne, VIC, 3050, Australia
| | - Peter F M Choong
- Department of Surgery, University of Melbourne, Melbourne, VIC, Australia.,Department of Orthopaedics, St Vincent's Hospital, Melbourne, VIC, Australia.,Bone and Soft Tissue Sarcoma Service, Perter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | - Andrew P Morokoff
- Department of Surgery, University of Melbourne, Melbourne, VIC, Australia.,Department of Neurosurgery, Royal Melbourne Hospital, Melbourne, VIC, 3050, Australia
| | - Kate J Drummond
- Department of Surgery, University of Melbourne, Melbourne, VIC, Australia.,Department of Neurosurgery, Royal Melbourne Hospital, Melbourne, VIC, 3050, Australia
| | - Gabriel Dabscheck
- Department of Neurology, Royal Children's Hospital, Melbourne, VIC, Australia.,Murdoch Children's Research Institute, Melbourne, VIC, Australia
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8
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Scheipl S, Brcic I, Moser T, Fischerauer S, Riedl J, Bergovec M, Smolle M, Posch F, Gerger A, Pichler M, Stoeger H, Leithner A, Heitzer E, Liegl-Atzwanger B, Szkandera J. Molecular profiling of soft-tissue sarcomas with FoundationOne ® Heme identifies potential targets for sarcoma therapy: a single-centre experience. Ther Adv Med Oncol 2021; 13:17588359211029125. [PMID: 34367342 PMCID: PMC8317253 DOI: 10.1177/17588359211029125] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2021] [Accepted: 06/11/2021] [Indexed: 11/25/2022] Open
Abstract
Background: Molecular diagnosis has become an established tool in the characterisation of adult soft-tissue sarcomas (STS). FoundationOne® Heme analyses somatic gene alterations in sarcomas via DNA and RNA-hotspot sequencing of tumour-associated genes. Methods: We evaluated FoundationOne® Heme testing in 81 localised STS including 35 translocation-associated and 46 complex-karyotyped cases from a single institution. Results: Although FoundationOne® Heme achieved broad patient coverage and identified at least five genetic alterations in each sample, the sensitivity for fusion detection was rather low, at 42.4%. Nevertheless, potential targets for STS treatment were detected using the FoundationOne® Heme assay: complex-karyotyped sarcomas frequently displayed copy-number alterations of common tumour-suppressor genes, particularly deletions in TP53, NF1, ATRX, and CDKN2A. A subset of myxofibrosarcomas (MFS) was amplified for HGF (n = 3) and MET (n = 1). PIK3CA was mutated in 7/15 cases of myxoid liposarcoma (MLS; 46.7%). Epigenetic regulators (e.g. MLL2 and MLL3) were frequently mutated. Conclusions: In summary, FoundationOne® Heme detected a broad range of genetic alterations and potential therapeutic targets in STS (e.g. HGF/MET in a subset of MFS, or PIK3CA in MLS). The assay’s sensitivity for fusion detection was low in our sample and needs to be re-evaluated in a larger cohort.
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Affiliation(s)
- Susanne Scheipl
- Department of Orthopaedics and Trauma, Medical University of Graz, Graz, Austria
| | - Iva Brcic
- Diagnostic and Research Institute of Pathology, Medical University of Graz, Graz, Austria
| | - Tina Moser
- Institute of Human Genetics, Diagnostic and Research Center for Molecular BioMedicine, Medical University of Graz, Graz, Austria
| | - Stefan Fischerauer
- Department of Orthopaedics and Trauma, Medical University of Graz, Graz, Austria
| | - Jakob Riedl
- Division of Clinical Oncology, Medical University of Graz, Graz, Austria
| | - Marko Bergovec
- Department of Orthopaedics and Trauma, Medical University of Graz, Graz, Austria
| | - Maria Smolle
- Department of Orthopaedics and Trauma, Medical University of Graz, Graz, Austria
| | - Florian Posch
- Division of Clinical Oncology, Medical University of Graz, Graz, Austria
| | - Armin Gerger
- Division of Clinical Oncology, Medical University of Graz, Graz, Austria
| | - Martin Pichler
- Division of Clinical Oncology, Medical University of Graz, Graz, Austria
| | - Herbert Stoeger
- Division of Clinical Oncology, Medical University of Graz, Graz, Austria
| | - Andreas Leithner
- Department of Orthopaedics and Trauma, Medical University of Graz, Graz, Austria
| | - Ellen Heitzer
- Institute of Human Genetics, Diagnostic and Research Center for Molecular BioMedicine, Medical University of Graz, Graz, Austria
| | - Bernadette Liegl-Atzwanger
- Diagnostic and Research Institute of Pathology, Diagnostic and Research Centre for Molecular BioMedicine, Medical University of Graz, Neue Stiftingtalstraße 10, Graz 8010 Austria
| | - Joanna Szkandera
- Division of Clinical Oncology, Medical University of Graz, Graz, Austria
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