Prognostic potential of fusion gene analysis using plasma cell-free RNA in malignant bone and soft tissue tumours
Abstract Background Liquid biopsy, which facilitates minimally invasive analysis of body fluid samples, has considerable potential as a diagnostic and prognostic tool in various cancers. Analysis of circulating tumour cells, circulating tumour DNA, and exosomes in liquid biopsies has advantages and...
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2025-04-01
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| Online Access: | https://doi.org/10.1186/s12885-025-13950-2 |
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| author | Naoki Furukawa Nobuhiko Hasegawa Daisuke Kubota Yasuhiro Nakamura Hirokazu Tanaka Shintaro Iwata Akira Kawai Tsuyoshi Saito Tatsuya Takagi Shinji Kohsaka Muneaki Ishijima |
| author_facet | Naoki Furukawa Nobuhiko Hasegawa Daisuke Kubota Yasuhiro Nakamura Hirokazu Tanaka Shintaro Iwata Akira Kawai Tsuyoshi Saito Tatsuya Takagi Shinji Kohsaka Muneaki Ishijima |
| author_sort | Naoki Furukawa |
| collection | DOAJ |
| description | Abstract Background Liquid biopsy, which facilitates minimally invasive analysis of body fluid samples, has considerable potential as a diagnostic and prognostic tool in various cancers. Analysis of circulating tumour cells, circulating tumour DNA, and exosomes in liquid biopsies has advantages and disadvantages. However, their utility in rare cancers, such as malignant bone and soft tissue tumours, remains unknown. In this study, we examined the levels of circulating cell-free tumour RNA (cfRNA) in the blood of patients with malignant bone and soft tissue tumours harbouring specific fusion genes, to explore the relationship between fusion gene expression in the blood and therapeutic response and disease status, and to validate the clinical utility of liquid biopsy. Methods The study involved 3 cases (7 samples) of Ewing’s sarcoma, 6 cases (12 samples) of myxoid liposarcoma, and 1 case (2 samples) of synovial sarcoma with specific fusion genes. Fusion gene analysis was performed using tumour tissue samples to identify breakpoints. Primers for liquid biopsy were designed based on the fusion genes identified. cfRNA was extracted from each patient’s plasma and used for reverse transcription polymerase chain reaction (RT-PCR) with the designed primers. The RT-PCR product was subjected to Sanger sequencing. Results Fusion gene breakpoints were identified in 10 samples from 6 cases. The fusion gene detection rate in the blood was 100% at both naïve status and symptom exacerbation in patients with Stage IV disease. In patients with Stage III disease progressing to Stage IV, the fusion gene was detected in the blood prior to imaging tests. Conclusions The detection of specific fusion genes from cfRNAs shows potential for monitoring the progression of fusion-related sarcomas in the context of chemotherapy. |
| format | Article |
| id | doaj-art-61c7e39331e847b2a56018946b9010aa |
| institution | DOAJ |
| issn | 1471-2407 |
| language | English |
| publishDate | 2025-04-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Cancer |
| spelling | doaj-art-61c7e39331e847b2a56018946b9010aa2025-08-20T03:04:51ZengBMCBMC Cancer1471-24072025-04-0125111110.1186/s12885-025-13950-2Prognostic potential of fusion gene analysis using plasma cell-free RNA in malignant bone and soft tissue tumoursNaoki Furukawa0Nobuhiko Hasegawa1Daisuke Kubota2Yasuhiro Nakamura3Hirokazu Tanaka4Shintaro Iwata5Akira Kawai6Tsuyoshi Saito7Tatsuya Takagi8Shinji Kohsaka9Muneaki Ishijima10Department of Orthopaedics, Faculty of Medicine, Juntendo UniversityDepartment of Orthopaedics, Faculty of Medicine, Juntendo UniversityDepartment of Orthopaedics, Faculty of Medicine, Juntendo UniversityDepartment of Orthopaedics, Faculty of Medicine, Juntendo UniversityDepartment of Orthopaedics, Faculty of Medicine, Juntendo UniversityDepartment of Musculoskeletal Oncology and Rehabilitation Medicine, National Cancer Center HospitalDepartment of Musculoskeletal Oncology and Rehabilitation Medicine, National Cancer Center HospitalDepartment of Human Pathology, Juntendo University School of MedicineDepartment of Orthopaedics, Faculty of Medicine, Juntendo UniversityDivision of Cellular Signaling, National Cancer Center Research InstituteDepartment of Orthopaedics, Faculty of Medicine, Juntendo UniversityAbstract Background Liquid biopsy, which facilitates minimally invasive analysis of body fluid samples, has considerable potential as a diagnostic and prognostic tool in various cancers. Analysis of circulating tumour cells, circulating tumour DNA, and exosomes in liquid biopsies has advantages and disadvantages. However, their utility in rare cancers, such as malignant bone and soft tissue tumours, remains unknown. In this study, we examined the levels of circulating cell-free tumour RNA (cfRNA) in the blood of patients with malignant bone and soft tissue tumours harbouring specific fusion genes, to explore the relationship between fusion gene expression in the blood and therapeutic response and disease status, and to validate the clinical utility of liquid biopsy. Methods The study involved 3 cases (7 samples) of Ewing’s sarcoma, 6 cases (12 samples) of myxoid liposarcoma, and 1 case (2 samples) of synovial sarcoma with specific fusion genes. Fusion gene analysis was performed using tumour tissue samples to identify breakpoints. Primers for liquid biopsy were designed based on the fusion genes identified. cfRNA was extracted from each patient’s plasma and used for reverse transcription polymerase chain reaction (RT-PCR) with the designed primers. The RT-PCR product was subjected to Sanger sequencing. Results Fusion gene breakpoints were identified in 10 samples from 6 cases. The fusion gene detection rate in the blood was 100% at both naïve status and symptom exacerbation in patients with Stage IV disease. In patients with Stage III disease progressing to Stage IV, the fusion gene was detected in the blood prior to imaging tests. Conclusions The detection of specific fusion genes from cfRNAs shows potential for monitoring the progression of fusion-related sarcomas in the context of chemotherapy.https://doi.org/10.1186/s12885-025-13950-2Cell-free RNAFusion geneLiquid biopsyMalignant bone and soft tissue tumour |
| spellingShingle | Naoki Furukawa Nobuhiko Hasegawa Daisuke Kubota Yasuhiro Nakamura Hirokazu Tanaka Shintaro Iwata Akira Kawai Tsuyoshi Saito Tatsuya Takagi Shinji Kohsaka Muneaki Ishijima Prognostic potential of fusion gene analysis using plasma cell-free RNA in malignant bone and soft tissue tumours BMC Cancer Cell-free RNA Fusion gene Liquid biopsy Malignant bone and soft tissue tumour |
| title | Prognostic potential of fusion gene analysis using plasma cell-free RNA in malignant bone and soft tissue tumours |
| title_full | Prognostic potential of fusion gene analysis using plasma cell-free RNA in malignant bone and soft tissue tumours |
| title_fullStr | Prognostic potential of fusion gene analysis using plasma cell-free RNA in malignant bone and soft tissue tumours |
| title_full_unstemmed | Prognostic potential of fusion gene analysis using plasma cell-free RNA in malignant bone and soft tissue tumours |
| title_short | Prognostic potential of fusion gene analysis using plasma cell-free RNA in malignant bone and soft tissue tumours |
| title_sort | prognostic potential of fusion gene analysis using plasma cell free rna in malignant bone and soft tissue tumours |
| topic | Cell-free RNA Fusion gene Liquid biopsy Malignant bone and soft tissue tumour |
| url | https://doi.org/10.1186/s12885-025-13950-2 |
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