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Merlini A, Centomo ML, Ferrero G, Chiabotto G, Miglio U, Berrino E, Giordano G, Brusco S, Pisacane A, Maldi E, Sarotto I, Capozzi F, Lano C, Isella C, Crisafulli G, Aglietta M, Dei Tos AP, Sbaraglia M, Sangiolo D, D’Ambrosio L, Bardelli A, Pignochino Y, Grignani G. DNA damage response and repair genes in advanced bone and soft tissue sarcomas: An 8-gene signature as a candidate predictive biomarker of response to trabectedin and olaparib combination. Front Oncol 2022; 12:844250. [PMID: 36110934 PMCID: PMC9469659 DOI: 10.3389/fonc.2022.844250] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Accepted: 07/26/2022] [Indexed: 11/21/2022] Open
Abstract
Background Advanced and unresectable bone and soft tissue sarcomas (BSTS) still represent an unmet medical need. We demonstrated that the alkylating agent trabectedin and the PARP1-inhibitor olaparib display antitumor activity in BSTS preclinical models. Moreover, in a phase Ib clinical trial (NCT02398058), feasibility, tolerability and encouraging results have been observed and the treatment combination is currently under study in a phase II trial (NCT03838744). Methods Differential expression of genes involved in DNA Damage Response and Repair was evaluated by Nanostring® technology, extracting RNA from pre-treatment tumor samples of 16 responder (≥6-month progression free survival) and 16 non-responder patients. Data validation was performed by quantitative real-time PCR, RNA in situ hybridization, and immunohistochemistry. The correlation between the identified candidate genes and both progression-free survival and overall survival was investigated in the publicly available dataset “Sarcoma (TCGA, The Cancer Genome Atlas)”. Results Differential RNA expression analysis revealed an 8-gene signature (CDKN2A, PIK3R1, SLFN11, ATM, APEX2, BLM, XRCC2, MAD2L2) defining patients with better outcome upon trabectedin+olaparib treatment. In responder vs. non-responder patients, a significant differential expression of these genes was further confirmed by RNA in situ hybridization and by qRT-PCR and immunohistochemistry in selected experiments. Correlation between survival outcomes and genetic alterations in the identified genes was shown in the TCGA sarcoma dataset. Conclusions This work identified an 8-gene expression signature to improve prediction of response to trabectedin+olaparib combination in BSTS. The predictive role of these potential biomarkers warrants further investigation.
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Affiliation(s)
- Alessandra Merlini
- Candiolo Cancer Institute, FPO-IRCCS, Turin, Italy
- Department of Oncology, University of Torino, Turin, Italy
| | - Maria Laura Centomo
- Candiolo Cancer Institute, FPO-IRCCS, Turin, Italy
- Department of Oncology, University of Torino, Turin, Italy
| | - Giulio Ferrero
- Department of Clinical and Biological Sciences, University of Torino, Turin, Italy
- Department of Computer Science, University of Torino, Turin, Italy
| | - Giulia Chiabotto
- Department of Medical Sciences, University of Torino, Turin, Italy
| | | | - Enrico Berrino
- Candiolo Cancer Institute, FPO-IRCCS, Turin, Italy
- Department of Medical Sciences, University of Torino, Turin, Italy
| | - Giorgia Giordano
- Candiolo Cancer Institute, FPO-IRCCS, Turin, Italy
- Department of Oncology, University of Torino, Turin, Italy
| | - Silvia Brusco
- Candiolo Cancer Institute, FPO-IRCCS, Turin, Italy
- Department of Oncology, University of Torino, Turin, Italy
| | | | - Elena Maldi
- Candiolo Cancer Institute, FPO-IRCCS, Turin, Italy
| | | | | | - Cristina Lano
- Candiolo Cancer Institute, FPO-IRCCS, Turin, Italy
- Department of Oncology, University of Torino, Turin, Italy
| | - Claudio Isella
- Candiolo Cancer Institute, FPO-IRCCS, Turin, Italy
- Department of Oncology, University of Torino, Turin, Italy
| | - Giovanni Crisafulli
- Candiolo Cancer Institute, FPO-IRCCS, Turin, Italy
- Department of Oncology, University of Torino, Turin, Italy
| | - Massimo Aglietta
- Candiolo Cancer Institute, FPO-IRCCS, Turin, Italy
- Department of Oncology, University of Torino, Turin, Italy
| | - Angelo Paolo Dei Tos
- Department of Pathology, Azienda Ospedale-Università Padova, Padua, Italy
- Department of Medicine (DIMED), University of Padua School of Medicine, Padua, Italy
| | - Marta Sbaraglia
- Department of Pathology, Azienda Ospedale-Università Padova, Padua, Italy
| | - Dario Sangiolo
- Candiolo Cancer Institute, FPO-IRCCS, Turin, Italy
- Department of Oncology, University of Torino, Turin, Italy
| | - Lorenzo D’Ambrosio
- Candiolo Cancer Institute, FPO-IRCCS, Turin, Italy
- Department of Oncology, University of Torino, Turin, Italy
- Medical Oncology, AOU San Luigi Gonzaga, Orbassano (TO), Italy
| | - Alberto Bardelli
- Candiolo Cancer Institute, FPO-IRCCS, Turin, Italy
- Department of Oncology, University of Torino, Turin, Italy
| | - Ymera Pignochino
- Candiolo Cancer Institute, FPO-IRCCS, Turin, Italy
- Department of Clinical and Biological Sciences, University of Torino, Turin, Italy
- *Correspondence: Ymera Pignochino, ; Giovanni Grignani,
| | - Giovanni Grignani
- Candiolo Cancer Institute, FPO-IRCCS, Turin, Italy
- *Correspondence: Ymera Pignochino, ; Giovanni Grignani,
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Pasqui A, Boddi A, Campanacci DA, Scoccianti G, Bernini A, Grasso D, Gambale E, Scolari F, Palchetti I, Palomba A, Fancelli S, Caliman E, Antonuzzo L, Pillozzi S. Alteration of the Nucleotide Excision Repair (NER) Pathway in Soft Tissue Sarcoma. Int J Mol Sci 2022; 23:ijms23158360. [PMID: 35955506 PMCID: PMC9369086 DOI: 10.3390/ijms23158360] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 07/23/2022] [Accepted: 07/25/2022] [Indexed: 02/02/2023] Open
Abstract
Clinical responses to anticancer therapies in advanced soft tissue sarcoma (STS) are unluckily restricted to a small subgroup of patients. Much of the inter-individual variability in treatment efficacy is as result of polymorphisms in genes encoding proteins involved in drug pharmacokinetics and pharmacodynamics. The nucleotide excision repair (NER) system is the main defense mechanism for repairing DNA damage caused by carcinogens and chemotherapy drugs. Single nucleotide polymorphisms (SNPs) of NER pathway key genes, altering mRNA expression or protein activity, can be significantly associated with response to chemotherapy, toxicities, tumor relapse or risk of developing cancer. In the present study, in a cohort of STS patients, we performed DNA extraction and genotyping by SNP assay, RNA extraction and quantitative real-time reverse transcription PCR (qPCR), a molecular dynamics simulation in order to characterize the NER pathway in STS. We observed a severe deregulation of the NER pathway and we describe for the first time the effect of SNP rs1047768 in the ERCC5 structure, suggesting a role in modulating single-stranded DNA (ssDNA) binding. Our results evidenced, for the first time, the correlation between a specific genotype profile of ERCC genes and proficiency of the NER pathway in STS.
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Affiliation(s)
- Adriano Pasqui
- Medical Oncology Unit, Careggi University Hospital, 50134 Florence, Italy; (A.P.); (L.A.); (S.P.)
| | - Anna Boddi
- Orthopaedic Oncology Unit, Careggi University Hospital, 50134 Florence, Italy; (A.B.); (D.A.C.); (G.S.); (F.S.)
| | - Domenico Andrea Campanacci
- Orthopaedic Oncology Unit, Careggi University Hospital, 50134 Florence, Italy; (A.B.); (D.A.C.); (G.S.); (F.S.)
- Orthopaedic Oncology Unit, Careggi University Hospital, Department of Health Sciences, University of Florence, 50134 Florence, Italy
| | - Guido Scoccianti
- Orthopaedic Oncology Unit, Careggi University Hospital, 50134 Florence, Italy; (A.B.); (D.A.C.); (G.S.); (F.S.)
| | - Andrea Bernini
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, 53100 Siena, Italy;
- Correspondence:
| | - Daniela Grasso
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, 53100 Siena, Italy;
| | - Elisabetta Gambale
- Clinical Oncology Unit, Careggi University Hospital, 50134 Florence, Italy;
| | - Federico Scolari
- Orthopaedic Oncology Unit, Careggi University Hospital, 50134 Florence, Italy; (A.B.); (D.A.C.); (G.S.); (F.S.)
| | - Ilaria Palchetti
- Department of Chemistry Ugo Schiff, University of Florence, 50019 Sesto Fiorentino, Italy;
| | - Annarita Palomba
- Histopathology and Molecular Diagnostic Unit, Careggi University Hospital, 50134 Florence, Italy;
| | - Sara Fancelli
- Department of Experimental and Clinical Medicine, University of Florence, 50134 Florence, Italy; (S.F.); (E.C.)
| | - Enrico Caliman
- Department of Experimental and Clinical Medicine, University of Florence, 50134 Florence, Italy; (S.F.); (E.C.)
| | - Lorenzo Antonuzzo
- Medical Oncology Unit, Careggi University Hospital, 50134 Florence, Italy; (A.P.); (L.A.); (S.P.)
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, 53100 Siena, Italy;
- Department of Experimental and Clinical Medicine, University of Florence, 50134 Florence, Italy; (S.F.); (E.C.)
| | - Serena Pillozzi
- Medical Oncology Unit, Careggi University Hospital, 50134 Florence, Italy; (A.P.); (L.A.); (S.P.)
- Department of Experimental and Clinical Medicine, University of Florence, 50134 Florence, Italy; (S.F.); (E.C.)
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Nakamura T, Sudo A. The Role of Trabectedin in Soft Tissue Sarcoma. Front Pharmacol 2022; 13:777872. [PMID: 35281940 PMCID: PMC8904719 DOI: 10.3389/fphar.2022.777872] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Accepted: 02/08/2022] [Indexed: 11/13/2022] Open
Abstract
Background: Systemic chemotherapy for advanced disease is another therapeutic option in the management of metastases in soft tissue sarcoma (STS). Doxorubicin either alone or in combination with ifosfamide has been used as first-line chemotherapy. Furthermore, in the past decade, new drugs have been shown to be effective in the treatment of advanced STS after the failure of first-line anthracycline-based chemotherapy: trabectedin, pazopanib and eribulin. However, the appropriate usage of these agents has not been established. Methods: We summarized clinical trials of trabectedin focusing on the efficacy and toxicity of trabectedin in the treatment of STS. Results: Trabectedin can be administered safely and effectively to the patients with advanced STS at second line setting or later. Although trabectedin may be effective as first-line treatment in selected patients, anthracycline-based chemotherapy should be recommended because no regimen in addition to trabectedin has proved to be unequivocally superior to doxorubicin as the first-line treatment for locally advanced or metastatic STS. Nucleotide excision repair (NER) and homologous recombination (HRe) repair may be of particular importance as efficacy of trabectedin. Conclusion: Trabectedin has shown a favorable toxicity profile and is an alternative therapeutic option in patients with advanced STS.
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Affiliation(s)
- Tomoki Nakamura
- Departmemt of Orthopaedic Surgery, Mie University Graduate School of Medicine, Tsu, Japan
| | - Akihiro Sudo
- Departmemt of Orthopaedic Surgery, Mie University Graduate School of Medicine, Tsu, Japan
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Moura DS, Peña‐Chilet M, Cordero Varela JA, Alvarez‐Alegret R, Agra‐Pujol C, Izquierdo F, Ramos R, Ortega‐Medina L, Martin‐Davila F, Castilla‐Ramirez C, Hernandez‐Leon CN, Romagosa C, Vaz Salgado MA, Lavernia J, Bagué S, Mayodormo‐Aranda E, Vicioso L, Hernández Barceló JE, Rubio‐Casadevall J, de Juan A, Fiaño‐Valverde MC, Hindi N, Lopez‐Alvarez M, Lacerenza S, Dopazo J, Gutierrez A, Alvarez R, Valverde C, Martinez‐Trufero J, Martín‐Broto J. A DNA damage repair gene-associated signature predicts responses of patients with advanced soft-tissue sarcoma to treatment with trabectedin. Mol Oncol 2021; 15:3691-3705. [PMID: 33983674 PMCID: PMC8637557 DOI: 10.1002/1878-0261.12996] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 04/13/2021] [Accepted: 05/10/2021] [Indexed: 11/29/2022] Open
Abstract
Predictive biomarkers of trabectedin represent an unmet need in advanced soft‐tissue sarcomas (STS). DNA damage repair (DDR) genes, involved in homologous recombination or nucleotide excision repair, had been previously described as biomarkers of trabectedin resistance or sensitivity, respectively. The majority of these studies only focused on specific factors (ERCC1, ERCC5, and BRCA1) and did not evaluate several other DDR‐related genes that could have a relevant role for trabectedin efficacy. In this retrospective translational study, 118 genes involved in DDR were evaluated to determine, by transcriptomics, a predictive gene signature of trabectedin efficacy. A six‐gene predictive signature of trabectedin efficacy was built in a series of 139 tumor samples from patients with advanced STS. Patients in the high‐risk gene signature group showed a significantly worse progression‐free survival compared with patients in the low‐risk group (2.1 vs 6.0 months, respectively). Differential gene expression analysis defined new potential predictive biomarkers of trabectedin sensitivity (PARP3 and CCNH) or resistance (DNAJB11 and PARP1). Our study identified a new gene signature that significantly predicts patients with higher probability to respond to treatment with trabectedin. Targeting some genes of this signature emerges as a potential strategy to enhance trabectedin efficacy.
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Affiliation(s)
- David S. Moura
- Institute of Biomedicine of Seville (IBIS, HUVR, CSIC, Universidad de Sevilla)Spain
| | - Maria Peña‐Chilet
- Institute of Biomedicine of Seville (IBIS, HUVR, CSIC, Universidad de Sevilla)Spain
- Clinical Bioinformatics AreaFundación Progreso y Salud (FPS)CDCAHospital Virgen del RocioSevilleSpain
- Bioinformatics in Rare Diseases (BiER)Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER)FPSHospital Virgen del RocioSevilleSpain
| | | | | | | | | | - Rafael Ramos
- Pathology DepartmentSon Espases University HospitalMallorcaSpain
| | | | | | | | | | - Cleofe Romagosa
- Pathology DepartmentVall d'Hebron University HospitalBarcelonaSpain
| | | | - Javier Lavernia
- Medical Oncology DepartmentInstituto Valenciano de OncologiaValenciaSpain
| | - Silvia Bagué
- Pathology ServiceHospital de la Santa Creu i Sant PauBarcelonaSpain
| | | | - Luis Vicioso
- Pathology DepartmentVirgen de la Victoria University HospitalMalagaSpain
| | | | - Jordi Rubio‐Casadevall
- Medical Oncology DepartmentHospital Josep TruetaCatalan Institute of OncologyGironaSpain
| | - Ana de Juan
- Medical Oncology DepartmentMarqués de Valdecilla University HospitalSantanderSpain
| | | | - Nadia Hindi
- Institute of Biomedicine of Seville (IBIS, HUVR, CSIC, Universidad de Sevilla)Spain
- Medical Oncology DepartmentUniversity Hospital Fundación Jimenez DiazMadridSpain
- University Hospital General de VillalbaMadridSpain
- Instituto de Investigacion Sanitaria Fundacion Jimenez Diaz (IIS/FJD)MadridSpain
| | - Maria Lopez‐Alvarez
- Institute of Biomedicine of Seville (IBIS, HUVR, CSIC, Universidad de Sevilla)Spain
| | - Serena Lacerenza
- Institute of Biomedicine of Seville (IBIS, HUVR, CSIC, Universidad de Sevilla)Spain
| | - Joaquin Dopazo
- Institute of Biomedicine of Seville (IBIS, HUVR, CSIC, Universidad de Sevilla)Spain
- Clinical Bioinformatics AreaFundación Progreso y Salud (FPS)CDCAHospital Virgen del RocioSevilleSpain
- Bioinformatics in Rare Diseases (BiER)Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER)FPSHospital Virgen del RocioSevilleSpain
- INB‐ELIXIR‐esFPSHospital Virgen del RocíoSevilleSpain
| | | | - Rosa Alvarez
- Medical Oncology DepartmentGregorio Marañon University HospitalMadridSpain
| | - Claudia Valverde
- Medical Oncology DepartmentVall d'Hebron University HospitalBarcelonaSpain
| | | | - Javier Martín‐Broto
- Institute of Biomedicine of Seville (IBIS, HUVR, CSIC, Universidad de Sevilla)Spain
- Medical Oncology DepartmentUniversity Hospital Fundación Jimenez DiazMadridSpain
- University Hospital General de VillalbaMadridSpain
- Instituto de Investigacion Sanitaria Fundacion Jimenez Diaz (IIS/FJD)MadridSpain
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Miolo G, Di Gregorio E, Saorin A, Lombardi D, Scalone S, Buonadonna A, Steffan A, Corona G. Integration of Serum Metabolomics into Clinical Assessment to Improve Outcome Prediction of Metastatic Soft Tissue Sarcoma Patients Treated with Trabectedin. Cancers (Basel) 2020; 12:E1983. [PMID: 32708128 DOI: 10.3390/cancers12071983] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 07/15/2020] [Accepted: 07/17/2020] [Indexed: 12/13/2022] Open
Abstract
Soft tissue sarcomas (STS) are a group of rare and heterogeneous cancers with few diagnostic or prognostic biomarkers. This metabolomics study aimed to identify new serum prognostic biomarkers to improve the prediction of overall survival in patients with metastatic STS. The study enrolled 24 patients treated with the same trabectedin regimen. The baseline serum metabolomics profile, targeted to 68 metabolites encompassing amino acids and bile acids pathways, was quantified by liquid chromatography-tandem mass spectrometry. Correlations between individual metabolomics profiles and overall survival were examined and a risk model to predict survival was built by Cox multivariate regression. The median overall survival of the studied patients was 13.0 months (95% CI, 5.6–23.5). Among all the metabolites investigated, only citrulline and histidine correlated significantly with overall survival. The best Cox risk prediction model obtained integrating metabolomics and clinical data, included citrulline, hemoglobin and patients’ performance status score. It allowed to distinguish patients into a high-risk group with a low median overall survival of 2.1 months and a low- to moderate-risk group with a median overall survival of 19.1 months (p < 0.0001). The results of this metabolomics translation study indicate that citrulline, an amino acid belonging to the arginine metabolism, represents an important metabolic signature that may contribute to explain the high inter-patients overall survival variability of STS patients. The risk prediction model based on baseline serum citrulline, hemoglobin and performance status may represent a new prognostic tool for the early classification of patients with metastatic STS, according to their overall survival expectancy.
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