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Runkel A, Braig D, Bogner B, Schmid A, Lausch U, Boneberg A, Brugger Z, Eisenhardt A, Kiefer J, Pauli T, Boerries M, Fuellgraf H, Kurowski K, Bronsert P, Scholber J, Grosu AL, Rovedo P, Bamberg F, Eisenhardt SU, Jung M. Non-invasive monitoring of neoadjuvant radiation therapy response in soft tissue sarcomas by multiparametric MRI and quantification of circulating tumor DNA-A study protocol. PLoS One 2023; 18:e0285580. [PMID: 37910565 PMCID: PMC10619790 DOI: 10.1371/journal.pone.0285580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 04/03/2023] [Indexed: 11/03/2023] Open
Abstract
BACKGROUND Wide resection remains the cornerstone of localized soft-tissue sarcomas (STS) treatment. Neoadjuvant radiation therapy (NRT) may decrease the risk of local recurrences; however, its effectiveness for different histological STS subtypes has not been systematically investigated. The proposed prospective study evaluates the NRT response in STS using liquid biopsies and the correlation of multiparametric magnetic resonance imaging (mpMRI) with histopathology and immunohistochemistry. METHODS Patients with localized high-grade STS, who qualify for NRT, are included in this study. LIQUID BIOPSIES Quantification of circulating tumor DNA (ctDNA) in patient blood samples is performed by targeted next-generation sequencing. Soft-tissue sarcoma subtype-specific panel sequencing in combination with patient-specific exome sequencing allows the detection of individual structural variants and point mutations. Circulating free DNA is isolated from peritherapeutically collected patient plasma samples and ctDNA quantified therein. Identification of breakpoints is carried out using FACTERA. Bioinformatic analysis is performed using samtools, picard, fgbio, and the MIRACUM Pipeline. MPMRI Combination of conventional MRI sequences with diffusion-weighted imaging, intravoxel-incoherent motion, and dynamic contrast enhancement. Multiparametric MRI is performed before, during, and after NRT. We aim to correlate mpMRI data with the resected specimen's macroscopical, histological, and immunohistochemical findings. RESULTS Preliminary data support the notion that quantification of ctDNA in combination with tumor mass characterization through co-registration of mpMRI and histopathology can predict NRT response of STS. CLINICAL RELEVANCE The methods presented in this prospective study are necessary to assess therapy response in heterogeneous tumors and lay the foundation of future patient- and tumor-specific therapy concepts. These methods can be applied to various tumor entities. Thus, the participation and support of a wider group of oncologic surgeons are needed to validate these findings on a larger patient cohort.
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Affiliation(s)
- Alexander Runkel
- Faculty of Medicine, Department of Plastic and Hand Surgery, Medical Center—University of Freiburg, Freiburg, Germany
- Faculty of Medicine, Berta-Ottenstein-Programme, University of Freiburg, Freiburg, Germany
| | - David Braig
- Faculty of Medicine, Department of Plastic and Hand Surgery, Medical Center—University of Freiburg, Freiburg, Germany
- Division of Hand, Plastic and Aesthetic Surgery, University Hospital, Ludwig Maximilian University of Munich, Munich, Germany
| | - Balazs Bogner
- Faculty of Medicine, Department of Radiology, Medical Center—University of Freiburg, Freiburg, Germany
| | - Adrian Schmid
- Faculty of Medicine, Department of Plastic and Hand Surgery, Medical Center—University of Freiburg, Freiburg, Germany
| | - Ute Lausch
- Faculty of Medicine, Department of Plastic and Hand Surgery, Medical Center—University of Freiburg, Freiburg, Germany
| | - Anika Boneberg
- Faculty of Medicine, Department of Plastic and Hand Surgery, Medical Center—University of Freiburg, Freiburg, Germany
| | - Zacharias Brugger
- Faculty of Medicine, Department of Medicine I, Medical Center—University of Freiburg, Freiburg, Germany
| | - Anja Eisenhardt
- Faculty of Medicine, Department of Plastic and Hand Surgery, Medical Center—University of Freiburg, Freiburg, Germany
| | - Jurij Kiefer
- Faculty of Medicine, Department of Plastic and Hand Surgery, Medical Center—University of Freiburg, Freiburg, Germany
| | - Thomas Pauli
- Faculty of Medicine, Institute of Medical Bioinformatics, Medical Center—University of Freiburg, Freiburg, Germany
| | - Melanie Boerries
- Faculty of Medicine, Institute of Medical Bioinformatics, Medical Center—University of Freiburg, Freiburg, Germany
| | - Hannah Fuellgraf
- Faculty of Medicine, Institute of Surgical Pathology, Medical Center—University of Freiburg, Freiburg, Germany
| | - Konrad Kurowski
- Faculty of Medicine, Institute of Surgical Pathology, Medical Center—University of Freiburg, Freiburg, Germany
| | - Peter Bronsert
- Faculty of Medicine, Institute of Surgical Pathology, Medical Center—University of Freiburg, Freiburg, Germany
- Tumorbank Comprehensive Cancer Center Freiburg, Medical Center—University of Freiburg, Freiburg, Germany
- Core Facility for Histopathology and Digital Pathology, Medical Center—University of Freiburg, Freiburg, Germany
| | - Jutta Scholber
- Faculty of Medicine, Department of Radiation Oncology, Medical Center—University of Freiburg, Freiburg, Germany
| | - Anca-Ligia Grosu
- Faculty of Medicine, Department of Radiation Oncology, Medical Center—University of Freiburg, Freiburg, Germany
| | - Philipp Rovedo
- Faculty of Medicine, Department of Radiology, Medical Physics, Medical Center-University of Freiburg, Freiburg, Germany
| | - Fabian Bamberg
- Faculty of Medicine, Department of Radiology, Medical Center—University of Freiburg, Freiburg, Germany
| | - Steffen Ulrich Eisenhardt
- Faculty of Medicine, Department of Plastic and Hand Surgery, Medical Center—University of Freiburg, Freiburg, Germany
| | - Matthias Jung
- Faculty of Medicine, Berta-Ottenstein-Programme, University of Freiburg, Freiburg, Germany
- Faculty of Medicine, Department of Radiology, Medical Center—University of Freiburg, Freiburg, Germany
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Chellini L, Palombo R, Riccioni V, Paronetto MP. Oncogenic Dysregulation of Circulating Noncoding RNAs: Novel Challenges and Opportunities in Sarcoma Diagnosis and Treatment. Cancers (Basel) 2022; 14:cancers14194677. [PMID: 36230599 PMCID: PMC9562196 DOI: 10.3390/cancers14194677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 09/07/2022] [Accepted: 09/17/2022] [Indexed: 12/03/2022] Open
Abstract
Simple Summary Body fluids contain different classes of RNA molecules such as protein-coding messenger RNAs (mRNA) and noncoding RNAs, including microRNAs (miRNAs), long noncoding RNAs (lncRNAs) and circular RNAs (circRNAs). These circulating RNAs can travel naked or packed into extracellular vesicles and display valuable potential as non-invasive biomarkers of sarcoma malignancy. In this review, we summarize current knowledge on the possible functions of these circulating RNAs and discuss their possible exploitation as novel markers to improve sarcoma diagnosis and prognosis. Despite the recent advance in technological tools have improved protocols for the extraction and detection of circulating RNA, many aspects related to the biology of these molecules remain to be elucidated. In particular, the lack of standardization in the assessment of these markers makes difficult their adoption into clinical practice. Abstract Sarcomas comprise a heterogeneous group of rare mesenchymal malignancies. Sarcomas can be grouped into two categories characterized by different prognosis and treatment approaches: soft tissue sarcoma and primary bone sarcoma. In the last years, research on novel diagnostic, prognostic or predictive biomarkers in sarcoma management has been focused on circulating tumor-derived molecules as valuable tools. Liquid biopsies that measure various tumor components, including circulating cell-free DNA and RNA, circulating tumor cells, tumor extracellular vesicles and exosomes, are gaining attention as methods for molecular screening and early diagnosis. Compared with traditional tissue biopsies, liquid biopsies are minimally invasive and blood samples can be collected serially over time to monitor cancer progression. This review will focus on circulating noncoding RNA molecules from liquid biopsies that are dysregulated in sarcoma malignancies and discuss advantages and current limitations of their employment as biomarkers in the management of sarcomas. It will also explore their utility in the evaluation of the clinical response to treatments and of disease relapse. Moreover, it will explore state-of-the-art techniques that allow for the early detection of these circulating biomarkers. Despite the huge potential, current reports highlight poor sensitivity, specificity, and survival benefit of these methods, that are therefore still insufficient for routine screening purposes.
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Affiliation(s)
- Lidia Chellini
- Laboratory of Molecular and Cellular Neurobiology, IRCCS Fondazione Santa Lucia, 00143 Rome, Italy
| | - Ramona Palombo
- Laboratory of Molecular and Cellular Neurobiology, IRCCS Fondazione Santa Lucia, 00143 Rome, Italy
- Department of Movement, Human and Health Sciences, Università degli Studi di Roma “Foro Italico”, Piazza Lauro de Bosis, 15, 00135 Rome, Italy
| | - Veronica Riccioni
- Laboratory of Molecular and Cellular Neurobiology, IRCCS Fondazione Santa Lucia, 00143 Rome, Italy
| | - Maria Paola Paronetto
- Laboratory of Molecular and Cellular Neurobiology, IRCCS Fondazione Santa Lucia, 00143 Rome, Italy
- Department of Movement, Human and Health Sciences, Università degli Studi di Roma “Foro Italico”, Piazza Lauro de Bosis, 15, 00135 Rome, Italy
- Correspondence:
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Sharma SR, Paonessa NE, Casadei L, Costas De Faria F, Pollock RE, Grignol V. Clinical biomarkers in soft tissue sarcoma A comprehensive review of current soft tissue sarcoma biomarkers. J Surg Oncol 2021; 125:239-245. [PMID: 34586640 DOI: 10.1002/jso.26680] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Accepted: 09/04/2021] [Indexed: 12/13/2022]
Abstract
Soft tissue sarcomas (STS) are a heterogeneous group of tumors that arise from mesenchymal tissue. Investigation at the molecular level has been challenging due to the rarity of STS and the number of histologic subtypes. However, recent research has provided new insight into potential genomic, proteomic, and immunological biomarkers of STS. The identification of biomarkers can improve diagnosis, prognosis, and prediction of recurrence and treatment response. This review provides an understanding of biomarkers, discussing the current status of biomarker research in STS.
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Affiliation(s)
- Soumya R Sharma
- James Cancer Hospital Solove Research Institute, The Ohio State University, Columbus, Ohio, USA
| | - Nadia E Paonessa
- James Cancer Hospital Solove Research Institute, The Ohio State University, Columbus, Ohio, USA
| | - Lucia Casadei
- James Cancer Hospital Solove Research Institute, The Ohio State University, Columbus, Ohio, USA
| | | | - Raphael E Pollock
- Department of Surgery, Division of Surgical Oncology, The Ohio State University, Columbus, Ohio, USA
| | - Valerie Grignol
- Department of Surgery, Division of Surgical Oncology, The Ohio State University, Columbus, Ohio, USA
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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: 0] [Impact Index Per Article: 0] [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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Gómez-Peregrina D, García-Valverde A, Pilco-Janeta D, Serrano C. Liquid Biopsy in Gastrointestinal Stromal Tumors: Ready for Prime Time? Curr Treat Options Oncol 2021; 22:32. [PMID: 33641024 DOI: 10.1007/s11864-021-00832-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/18/2021] [Indexed: 02/07/2023]
Abstract
OPINION STATEMENT Gastrointestinal stromal tumor (GIST) constitutes a paradigm for clinically effective targeted inhibition of oncogenic driver mutations. Therefore, GIST has emerged as a compelling clinical and biological model to study oncogene addiction and to validate preclinical concepts for drug response and drug resistance. Oncogenic activation of KIT or PDGFRA receptor tyrosine kinases is the essential drivers of GIST progression throughout all stages of the disease. Interestingly, KIT/PDGFRA genotype predicts the response to first-line imatinib and to all tyrosine kinase inhibitors (TKIs) approved or in investigation after imatinib failure. Considering that TKIs are effective only against a subset of KIT or PDGFRA resistance mutations, close monitoring of tumor dynamics with non-invasive methods such as liquid biopsy emerges as a necessary step forward in the field. Liquid biopsy, in contrast to solid tumor biopsy, aims to characterize tumors irrespective of heterogeneity. Although there are several components in the peripheral blood, most recent studies have been focused on circulating tumor (ct)DNA, due to the technological feasibility, the stability of DNA itself and DNA alterations, and the therapeutic development in precision oncology largely based on the identification of genetic driver mutations. In the present review, we systematically dissect the current wealth of data of ctDNA in GIST. To do so, a critical understanding of the promises and limitations of the current technologies will be followed by an exposition of the knowledge gathered with such studies in GIST. Collectively, our goal is to establish clear premises that can be used as the foundations to build future studies towards the clinical implementation of ctDNA evaluation in GIST patients.
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Affiliation(s)
- David Gómez-Peregrina
- Sarcoma Translational Research Laboratory, Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron Hospital Campus, C/ Natzaret 115-117, 08035, Barcelona, Spain
| | - Alfonso García-Valverde
- Sarcoma Translational Research Laboratory, Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron Hospital Campus, C/ Natzaret 115-117, 08035, Barcelona, Spain
| | - Daniel Pilco-Janeta
- Sarcoma Translational Research Laboratory, Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron Hospital Campus, C/ Natzaret 115-117, 08035, Barcelona, Spain
| | - César Serrano
- Sarcoma Translational Research Laboratory, Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron Hospital Campus, C/ Natzaret 115-117, 08035, Barcelona, Spain. .,Department of Medical Oncology, Vall d'Hebron University Hospital, P/Vall d'Hebron 119, 08035, Barcelona, Spain.
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Wainsztein VE, Chen TW. When Molecular-Targeted Agents Meet Immunotherapy: The Opportunities for Soft Tissue Sarcoma. JOURNAL OF IMMUNOTHERAPY AND PRECISION ONCOLOGY 2020; 3:69-82. [PMID: 36751522 PMCID: PMC9179404 DOI: 10.36401/jipo-19-37] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Accepted: 03/25/2020] [Indexed: 01/02/2023]
Abstract
Soft tissue sarcomas (STS) account for less than 1% of adult cancers with a median overall survival of 12 months in the metastatic setting. Although chemotherapy remains the standard of treatment for advanced disease, molecular targeted agents (MTAs) and immunotherapies are under intensive investigation in STS. The success of MTAs comes mainly from antiangiogenic agents in various STS subtypes, from colony-stimulating factor-1 receptor inhibitor in tenosynovial giant cell tumor and neurotrophic tropomyocin receptor kinase (NTRK) inhibitors while others, such as cyclin-dependent kinase (CDK)-4 inhibitors, remain under evaluation. In advanced STS the activity of single-agent immunotherapy was not paradigm-changing as in other tumor types. A better understanding of tumor microenvironment, the immunogenic properties of MTAs, and finding an optimal treatment combination to improve patients outcomes became a central topic of research and discussion. Furthermore, the development and incorporation of transcriptomic profiling-based classification will allow identification, refined patient selection, and guided-treatment assignment. This article reviewed recent advances in STS treatment in MTAs and immunotherapy, strategies to overcome resistance, and outcomes of combination treatments in different STS subtypes. Promising preliminary results from combination strategies have shed light on STS treatment. The increasing understanding of this heterogeneous group of tumors and its microenvironment biology may help develop and guide treatment strategies with MTA and immunotherapies, alone or in combination, in a tailored way based on predictive and validated biomarkers and tumor molecular profiling in this new coming era.
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Affiliation(s)
| | - Tom W. Chen
- Department of Oncology, National Taiwan University Hospital, Taipei, Taiwan
,National Taiwan University Cancer Center, Taipei, Taiwan
,Graduate Institute of Oncology, National Taiwan University College of Medicine, Taipei, Taiwan
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