Integrating extracellular vesicle and circulating cell‐free DNA analysis using a single plasma aliquot improves the detection of HER2 positivity in breast cancer patients
Abstract Multi‐analyte liquid biopsies represent an emerging opportunity for non‐invasive cancer assessment. We developed ONCE (One Aliquot for Circulating Elements), an approach for the isolation of extracellular vesicles (EV) and cell‐free DNA (cfDNA) from a single aliquot of blood. We assessed ON...
| Main Authors: | , , , , , , , , , , , , , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Wiley
2023-09-01
|
| Series: | Journal of Extracellular Biology |
| Subjects: | |
| Online Access: | https://doi.org/10.1002/jex2.108 |
| _version_ | 1797674125586595840 |
|---|---|
| author | Vera Mugoni Yari Ciani Orsetta Quaini Simone Tomasini Michela Notarangelo Federico Vannuccini Alessia Marinelli Elena Leonardi Stefano Pontalti Angela Martinelli Daniele Rossetto Isabella Pesce Sheref S. Mansy Mattia Barbareschi Antonella Ferro Orazio Caffo Gerhardt Attard Dolores Di Vizio Vito Giuseppe D'Agostino Caterina Nardella Francesca Demichelis |
| author_facet | Vera Mugoni Yari Ciani Orsetta Quaini Simone Tomasini Michela Notarangelo Federico Vannuccini Alessia Marinelli Elena Leonardi Stefano Pontalti Angela Martinelli Daniele Rossetto Isabella Pesce Sheref S. Mansy Mattia Barbareschi Antonella Ferro Orazio Caffo Gerhardt Attard Dolores Di Vizio Vito Giuseppe D'Agostino Caterina Nardella Francesca Demichelis |
| author_sort | Vera Mugoni |
| collection | DOAJ |
| description | Abstract Multi‐analyte liquid biopsies represent an emerging opportunity for non‐invasive cancer assessment. We developed ONCE (One Aliquot for Circulating Elements), an approach for the isolation of extracellular vesicles (EV) and cell‐free DNA (cfDNA) from a single aliquot of blood. We assessed ONCE performance to classify HER2‐positive early‐stage breast cancer (BrCa) patients by combining EV‐associated RNA (EV‐RNA) and cfDNA signals on n = 64 healthy donors (HD) and non–metastatic BrCa patients. Specifically, we isolated EV‐enriched samples by a charge‐based (CB) method and investigated EV‐RNA and cfDNA by next‐generation sequencing (NGS) and by digital droplet PCR (ddPCR). Sequencing of cfDNA and EV‐RNA from HER2‐ and HER2+ patients demonstrated concordance with in situ molecular analyses of matched tissues. Combined analysis of the two circulating analytes by ddPCR showed increased sensitivity in ERBB2/HER2 detection compared to single nucleic acid components. Multi‐analyte liquid biopsy prediction performance was comparable to tissue‐based sequencing results from TCGA. Also, imaging flow cytometry analysis revealed HER2 protein on the surface of EV isolated from the HER2+ BrCa plasma, thus corroborating the potential relevance of studying EV as companion analyte to cfDNA. This data confirms the relevance of combining cfDNA and EV‐RNA for HER2 cancer assessment and supports ONCE as a valuable tool for multi‐analytes liquid biopsies’ clinical implementation. |
| first_indexed | 2024-03-11T21:55:37Z |
| format | Article |
| id | doaj.art-4ec0396d0d6d4b53b34bf42dcddc3061 |
| institution | Directory Open Access Journal |
| issn | 2768-2811 |
| language | English |
| last_indexed | 2024-03-11T21:55:37Z |
| publishDate | 2023-09-01 |
| publisher | Wiley |
| record_format | Article |
| series | Journal of Extracellular Biology |
| spelling | doaj.art-4ec0396d0d6d4b53b34bf42dcddc30612023-09-26T03:15:40ZengWileyJournal of Extracellular Biology2768-28112023-09-0129n/an/a10.1002/jex2.108Integrating extracellular vesicle and circulating cell‐free DNA analysis using a single plasma aliquot improves the detection of HER2 positivity in breast cancer patientsVera Mugoni0Yari Ciani1Orsetta Quaini2Simone Tomasini3Michela Notarangelo4Federico Vannuccini5Alessia Marinelli6Elena Leonardi7Stefano Pontalti8Angela Martinelli9Daniele Rossetto10Isabella Pesce11Sheref S. Mansy12Mattia Barbareschi13Antonella Ferro14Orazio Caffo15Gerhardt Attard16Dolores Di Vizio17Vito Giuseppe D'Agostino18Caterina Nardella19Francesca Demichelis20Department of Cellular, Computational and Integrative Biology University of Trento Trento ItalyDepartment of Cellular, Computational and Integrative Biology University of Trento Trento ItalyDepartment of Cellular, Computational and Integrative Biology University of Trento Trento ItalyDepartment of Cellular, Computational and Integrative Biology University of Trento Trento ItalyDepartment of Cellular, Computational and Integrative Biology University of Trento Trento ItalyDepartment of Cellular, Computational and Integrative Biology University of Trento Trento ItalyDepartment of Cellular, Computational and Integrative Biology University of Trento Trento ItalyUnit of Surgical Pathology, Santa Chiara Hospital, APSS Trento ItalyDepartment of Medical Oncology Santa Chiara Hospital, APSS Trento ItalyDepartment of Cellular, Computational and Integrative Biology University of Trento Trento ItalyDepartment of Cellular, Computational and Integrative Biology University of Trento Trento ItalyDepartment of Cellular, Computational and Integrative Biology University of Trento Trento ItalyDepartment of Cellular, Computational and Integrative Biology University of Trento Trento ItalyUnit of Surgical Pathology, Santa Chiara Hospital, APSS Trento ItalyDepartment of Medical Oncology Santa Chiara Hospital, APSS Trento ItalyDepartment of Medical Oncology Santa Chiara Hospital, APSS Trento ItalyUniversity College London Cancer Institute London UKDepartment of Surgery, Division of Cancer Biology and Therapeutics Cedars‐Sinai Medical Center Los Angeles California USADepartment of Cellular, Computational and Integrative Biology University of Trento Trento ItalyDepartment of Cellular, Computational and Integrative Biology University of Trento Trento ItalyDepartment of Cellular, Computational and Integrative Biology University of Trento Trento ItalyAbstract Multi‐analyte liquid biopsies represent an emerging opportunity for non‐invasive cancer assessment. We developed ONCE (One Aliquot for Circulating Elements), an approach for the isolation of extracellular vesicles (EV) and cell‐free DNA (cfDNA) from a single aliquot of blood. We assessed ONCE performance to classify HER2‐positive early‐stage breast cancer (BrCa) patients by combining EV‐associated RNA (EV‐RNA) and cfDNA signals on n = 64 healthy donors (HD) and non–metastatic BrCa patients. Specifically, we isolated EV‐enriched samples by a charge‐based (CB) method and investigated EV‐RNA and cfDNA by next‐generation sequencing (NGS) and by digital droplet PCR (ddPCR). Sequencing of cfDNA and EV‐RNA from HER2‐ and HER2+ patients demonstrated concordance with in situ molecular analyses of matched tissues. Combined analysis of the two circulating analytes by ddPCR showed increased sensitivity in ERBB2/HER2 detection compared to single nucleic acid components. Multi‐analyte liquid biopsy prediction performance was comparable to tissue‐based sequencing results from TCGA. Also, imaging flow cytometry analysis revealed HER2 protein on the surface of EV isolated from the HER2+ BrCa plasma, thus corroborating the potential relevance of studying EV as companion analyte to cfDNA. This data confirms the relevance of combining cfDNA and EV‐RNA for HER2 cancer assessment and supports ONCE as a valuable tool for multi‐analytes liquid biopsies’ clinical implementation.https://doi.org/10.1002/jex2.108breast cancercell‐free DNA (cfDNA)ddPCREV‐RNAextracellular vesicles (EV)HER2 |
| spellingShingle | Vera Mugoni Yari Ciani Orsetta Quaini Simone Tomasini Michela Notarangelo Federico Vannuccini Alessia Marinelli Elena Leonardi Stefano Pontalti Angela Martinelli Daniele Rossetto Isabella Pesce Sheref S. Mansy Mattia Barbareschi Antonella Ferro Orazio Caffo Gerhardt Attard Dolores Di Vizio Vito Giuseppe D'Agostino Caterina Nardella Francesca Demichelis Integrating extracellular vesicle and circulating cell‐free DNA analysis using a single plasma aliquot improves the detection of HER2 positivity in breast cancer patients Journal of Extracellular Biology breast cancer cell‐free DNA (cfDNA) ddPCR EV‐RNA extracellular vesicles (EV) HER2 |
| title | Integrating extracellular vesicle and circulating cell‐free DNA analysis using a single plasma aliquot improves the detection of HER2 positivity in breast cancer patients |
| title_full | Integrating extracellular vesicle and circulating cell‐free DNA analysis using a single plasma aliquot improves the detection of HER2 positivity in breast cancer patients |
| title_fullStr | Integrating extracellular vesicle and circulating cell‐free DNA analysis using a single plasma aliquot improves the detection of HER2 positivity in breast cancer patients |
| title_full_unstemmed | Integrating extracellular vesicle and circulating cell‐free DNA analysis using a single plasma aliquot improves the detection of HER2 positivity in breast cancer patients |
| title_short | Integrating extracellular vesicle and circulating cell‐free DNA analysis using a single plasma aliquot improves the detection of HER2 positivity in breast cancer patients |
| title_sort | integrating extracellular vesicle and circulating cell free dna analysis using a single plasma aliquot improves the detection of her2 positivity in breast cancer patients |
| topic | breast cancer cell‐free DNA (cfDNA) ddPCR EV‐RNA extracellular vesicles (EV) HER2 |
| url | https://doi.org/10.1002/jex2.108 |
| work_keys_str_mv | AT veramugoni integratingextracellularvesicleandcirculatingcellfreednaanalysisusingasingleplasmaaliquotimprovesthedetectionofher2positivityinbreastcancerpatients AT yariciani integratingextracellularvesicleandcirculatingcellfreednaanalysisusingasingleplasmaaliquotimprovesthedetectionofher2positivityinbreastcancerpatients AT orsettaquaini integratingextracellularvesicleandcirculatingcellfreednaanalysisusingasingleplasmaaliquotimprovesthedetectionofher2positivityinbreastcancerpatients AT simonetomasini integratingextracellularvesicleandcirculatingcellfreednaanalysisusingasingleplasmaaliquotimprovesthedetectionofher2positivityinbreastcancerpatients AT michelanotarangelo integratingextracellularvesicleandcirculatingcellfreednaanalysisusingasingleplasmaaliquotimprovesthedetectionofher2positivityinbreastcancerpatients AT federicovannuccini integratingextracellularvesicleandcirculatingcellfreednaanalysisusingasingleplasmaaliquotimprovesthedetectionofher2positivityinbreastcancerpatients AT alessiamarinelli integratingextracellularvesicleandcirculatingcellfreednaanalysisusingasingleplasmaaliquotimprovesthedetectionofher2positivityinbreastcancerpatients AT elenaleonardi integratingextracellularvesicleandcirculatingcellfreednaanalysisusingasingleplasmaaliquotimprovesthedetectionofher2positivityinbreastcancerpatients AT stefanopontalti integratingextracellularvesicleandcirculatingcellfreednaanalysisusingasingleplasmaaliquotimprovesthedetectionofher2positivityinbreastcancerpatients AT angelamartinelli integratingextracellularvesicleandcirculatingcellfreednaanalysisusingasingleplasmaaliquotimprovesthedetectionofher2positivityinbreastcancerpatients AT danielerossetto integratingextracellularvesicleandcirculatingcellfreednaanalysisusingasingleplasmaaliquotimprovesthedetectionofher2positivityinbreastcancerpatients AT isabellapesce integratingextracellularvesicleandcirculatingcellfreednaanalysisusingasingleplasmaaliquotimprovesthedetectionofher2positivityinbreastcancerpatients AT sherefsmansy integratingextracellularvesicleandcirculatingcellfreednaanalysisusingasingleplasmaaliquotimprovesthedetectionofher2positivityinbreastcancerpatients AT mattiabarbareschi integratingextracellularvesicleandcirculatingcellfreednaanalysisusingasingleplasmaaliquotimprovesthedetectionofher2positivityinbreastcancerpatients AT antonellaferro integratingextracellularvesicleandcirculatingcellfreednaanalysisusingasingleplasmaaliquotimprovesthedetectionofher2positivityinbreastcancerpatients AT oraziocaffo integratingextracellularvesicleandcirculatingcellfreednaanalysisusingasingleplasmaaliquotimprovesthedetectionofher2positivityinbreastcancerpatients AT gerhardtattard integratingextracellularvesicleandcirculatingcellfreednaanalysisusingasingleplasmaaliquotimprovesthedetectionofher2positivityinbreastcancerpatients AT doloresdivizio integratingextracellularvesicleandcirculatingcellfreednaanalysisusingasingleplasmaaliquotimprovesthedetectionofher2positivityinbreastcancerpatients AT vitogiuseppedagostino integratingextracellularvesicleandcirculatingcellfreednaanalysisusingasingleplasmaaliquotimprovesthedetectionofher2positivityinbreastcancerpatients AT caterinanardella integratingextracellularvesicleandcirculatingcellfreednaanalysisusingasingleplasmaaliquotimprovesthedetectionofher2positivityinbreastcancerpatients AT francescademichelis integratingextracellularvesicleandcirculatingcellfreednaanalysisusingasingleplasmaaliquotimprovesthedetectionofher2positivityinbreastcancerpatients |