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.

Integrating extracellular vesicle and circulating cell-free DNA analysis on a single plasma aliquot improves the detection of HER2 positivity in breast cancer patients / Mugoni, Vera; Ciani, Yari; Quaini, Orsetta; Tomasini, Simone; Notarangelo, Michela; Vannuccini, Federico; Marinelli, Alessia; Leonardi, Elena; Pontalti, Stefano; Martinelli, Angela; Rossetto, Daniele; Pesce, Isabella; Mansy, Sheref S.; Barbareschi, Mattia; Ferro, Antonella; Caffo, Orazio; Attard, Gerhardt; Di Vizio, Dolores; D'Agostino, Vito Giuseppe; Nardella, Caterina; Demichelis, Francesca. - In: JOURNAL OF EXTRACELLULAR BIOLOGY. - ISSN 2768-2811. - 2023, 2:(2023), pp. 1-15. [10.1002/jex2.108]

Integrating extracellular vesicle and circulating cell-free DNA analysis on a single plasma aliquot improves the detection of HER2 positivity in breast cancer patients

Mugoni, Vera;Ciani, Yari;Quaini, Orsetta;Tomasini, Simone;Notarangelo, Michela;Vannuccini, Federico;Marinelli, Alessia;Pontalti, Stefano;Martinelli, Angela;Rossetto, Daniele;Pesce, Isabella;Mansy, Sheref S.;Barbareschi, Mattia;Ferro, Antonella;Caffo, Orazio;Di Vizio, Dolores;D'Agostino, Vito Giuseppe;Nardella, Caterina;Demichelis, Francesca
2023-01-01

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.
2023
Mugoni, Vera; Ciani, Yari; Quaini, Orsetta; Tomasini, Simone; Notarangelo, Michela; Vannuccini, Federico; Marinelli, Alessia; Leonardi, Elena; Pontalt...espandi
Integrating extracellular vesicle and circulating cell-free DNA analysis on a single plasma aliquot improves the detection of HER2 positivity in breast cancer patients / Mugoni, Vera; Ciani, Yari; Quaini, Orsetta; Tomasini, Simone; Notarangelo, Michela; Vannuccini, Federico; Marinelli, Alessia; Leonardi, Elena; Pontalti, Stefano; Martinelli, Angela; Rossetto, Daniele; Pesce, Isabella; Mansy, Sheref S.; Barbareschi, Mattia; Ferro, Antonella; Caffo, Orazio; Attard, Gerhardt; Di Vizio, Dolores; D'Agostino, Vito Giuseppe; Nardella, Caterina; Demichelis, Francesca. - In: JOURNAL OF EXTRACELLULAR BIOLOGY. - ISSN 2768-2811. - 2023, 2:(2023), pp. 1-15. [10.1002/jex2.108]
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Utilizza questo identificativo per citare o creare un link a questo documento: https://hdl.handle.net/11572/427311
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