MicroRNA expression profiling with a droplet digital PCR assay enables molecular diagnosis and prognosis of cancers of unknown primary
Metastasis is responsible for the majority of cancer‐related deaths. Particularly, challenging is the management of metastatic cancer of unknown primary site (CUP), whose tissue of origin (TOO) remains undetermined even after extensive investigations and whose therapy is rather unspecific and poorly...
| Main Authors: | , , , , , , , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
Wiley
2021-10-01
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| Series: | Molecular Oncology |
| Subjects: | |
| Online Access: | https://doi.org/10.1002/1878-0261.13026 |
| _version_ | 1828915758706458624 |
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| author | Noemi Laprovitera Mattia Riefolo Elisa Porcellini Giorgio Durante Ingrid Garajova Francesco Vasuri Ariane Aigelsreiter Nadia Dandachi Giuseppe Benvenuto Federico Agostinis Silvia Sabbioni Ioana Berindan Neagoe Chiara Romualdi Andrea Ardizzoni Davide Trerè Martin Pichler Antonietta D'Errico Manuela Ferracin |
| author_facet | Noemi Laprovitera Mattia Riefolo Elisa Porcellini Giorgio Durante Ingrid Garajova Francesco Vasuri Ariane Aigelsreiter Nadia Dandachi Giuseppe Benvenuto Federico Agostinis Silvia Sabbioni Ioana Berindan Neagoe Chiara Romualdi Andrea Ardizzoni Davide Trerè Martin Pichler Antonietta D'Errico Manuela Ferracin |
| author_sort | Noemi Laprovitera |
| collection | DOAJ |
| description | Metastasis is responsible for the majority of cancer‐related deaths. Particularly, challenging is the management of metastatic cancer of unknown primary site (CUP), whose tissue of origin (TOO) remains undetermined even after extensive investigations and whose therapy is rather unspecific and poorly effective. Molecular approaches to identify the most probable TOO of CUPs can overcome some of these issues. In this study, we applied a predetermined set of 89 microRNAs (miRNAs) to infer the TOO of 53 metastatic cancers of unknown or uncertain origin. The miRNA expression was assessed with droplet digital PCR in 159 samples, including primary tumors from 17 tumor classes (reference set) and metastases of known and unknown origin (test set). We combined two different statistical models for class prediction to obtain the most probable TOOs: the nearest shrunken centroids approach of Prediction Analysis of Microarrays (PAMR) and the least absolute shrinkage and selection operator (LASSO) models. The molecular test was successful for all formalin‐fixed paraffin‐embedded samples and provided a TOO identification within 1 week from the biopsy procedure. The most frequently predicted origins were gastrointestinal, pancreas, breast, lung, and bile duct. The assay was applied also to multiple metastases from the same CUP, collected from different metastatic sites: The predictions showed a strong agreement, intrinsically validating our assay. The final CUPs' TOO prediction was compared with the clinicopathological hypothesis of primary site. Moreover, a panel of 13 miRNAs proved to have prognostic value and be associated with overall survival in CUP patients. Our study demonstrated that miRNA expression profiling in CUP samples could be employed as diagnostic and prognostic test. Our molecular analysis can be performed on request, concomitantly with standard diagnostic workup and in association with genetic profiling, to offer valuable indications about the possible primary site, thereby supporting treatment decisions. |
| first_indexed | 2024-12-13T20:20:01Z |
| format | Article |
| id | doaj.art-424ff11210464919aa307fab5d15bc99 |
| institution | Directory Open Access Journal |
| issn | 1574-7891 1878-0261 |
| language | English |
| last_indexed | 2024-12-13T20:20:01Z |
| publishDate | 2021-10-01 |
| publisher | Wiley |
| record_format | Article |
| series | Molecular Oncology |
| spelling | doaj.art-424ff11210464919aa307fab5d15bc992022-12-21T23:32:43ZengWileyMolecular Oncology1574-78911878-02612021-10-0115102732275110.1002/1878-0261.13026MicroRNA expression profiling with a droplet digital PCR assay enables molecular diagnosis and prognosis of cancers of unknown primaryNoemi Laprovitera0Mattia Riefolo1Elisa Porcellini2Giorgio Durante3Ingrid Garajova4Francesco Vasuri5Ariane Aigelsreiter6Nadia Dandachi7Giuseppe Benvenuto8Federico Agostinis9Silvia Sabbioni10Ioana Berindan Neagoe11Chiara Romualdi12Andrea Ardizzoni13Davide Trerè14Martin Pichler15Antonietta D'Errico16Manuela Ferracin17Department of Experimental, Diagnostic and Specialty Medicine (DIMES) University of Bologna ItalyDepartment of Experimental, Diagnostic and Specialty Medicine (DIMES) University of Bologna ItalyDepartment of Experimental, Diagnostic and Specialty Medicine (DIMES) University of Bologna ItalyDepartment of Experimental, Diagnostic and Specialty Medicine (DIMES) University of Bologna ItalyMedical Oncology Unit University Hospital of Parma ItalyPathology Unit IRCCS Azienda Ospedaliero‐Universitaria di Bologna ItalyDiagnostic and Research Institute of Pathology Medical University of Graz AustriaDivision of Oncology Medical University of Graz AustriaDepartment of Biology University of Padua ItalyDepartment of Biology University of Padua ItalyDepartment of Life Sciences and Biotechnologies University of Ferrara ItalyResearch Center for Functional Genomics, Biomedicine and Translational Medicine “Iuliu Hatieganu” University of Medicine and Pharmacy Cluj‐Napoca RomaniaDepartment of Biology University of Padua ItalyDepartment of Experimental, Diagnostic and Specialty Medicine (DIMES) University of Bologna ItalyDepartment of Experimental, Diagnostic and Specialty Medicine (DIMES) University of Bologna ItalyDivision of Oncology Medical University of Graz AustriaDepartment of Experimental, Diagnostic and Specialty Medicine (DIMES) University of Bologna ItalyDepartment of Experimental, Diagnostic and Specialty Medicine (DIMES) University of Bologna ItalyMetastasis is responsible for the majority of cancer‐related deaths. Particularly, challenging is the management of metastatic cancer of unknown primary site (CUP), whose tissue of origin (TOO) remains undetermined even after extensive investigations and whose therapy is rather unspecific and poorly effective. Molecular approaches to identify the most probable TOO of CUPs can overcome some of these issues. In this study, we applied a predetermined set of 89 microRNAs (miRNAs) to infer the TOO of 53 metastatic cancers of unknown or uncertain origin. The miRNA expression was assessed with droplet digital PCR in 159 samples, including primary tumors from 17 tumor classes (reference set) and metastases of known and unknown origin (test set). We combined two different statistical models for class prediction to obtain the most probable TOOs: the nearest shrunken centroids approach of Prediction Analysis of Microarrays (PAMR) and the least absolute shrinkage and selection operator (LASSO) models. The molecular test was successful for all formalin‐fixed paraffin‐embedded samples and provided a TOO identification within 1 week from the biopsy procedure. The most frequently predicted origins were gastrointestinal, pancreas, breast, lung, and bile duct. The assay was applied also to multiple metastases from the same CUP, collected from different metastatic sites: The predictions showed a strong agreement, intrinsically validating our assay. The final CUPs' TOO prediction was compared with the clinicopathological hypothesis of primary site. Moreover, a panel of 13 miRNAs proved to have prognostic value and be associated with overall survival in CUP patients. Our study demonstrated that miRNA expression profiling in CUP samples could be employed as diagnostic and prognostic test. Our molecular analysis can be performed on request, concomitantly with standard diagnostic workup and in association with genetic profiling, to offer valuable indications about the possible primary site, thereby supporting treatment decisions.https://doi.org/10.1002/1878-0261.13026cancer of unknown primarydroplet digital PCRmetastasismicroRNAsmolecular diagnostics |
| spellingShingle | Noemi Laprovitera Mattia Riefolo Elisa Porcellini Giorgio Durante Ingrid Garajova Francesco Vasuri Ariane Aigelsreiter Nadia Dandachi Giuseppe Benvenuto Federico Agostinis Silvia Sabbioni Ioana Berindan Neagoe Chiara Romualdi Andrea Ardizzoni Davide Trerè Martin Pichler Antonietta D'Errico Manuela Ferracin MicroRNA expression profiling with a droplet digital PCR assay enables molecular diagnosis and prognosis of cancers of unknown primary Molecular Oncology cancer of unknown primary droplet digital PCR metastasis microRNAs molecular diagnostics |
| title | MicroRNA expression profiling with a droplet digital PCR assay enables molecular diagnosis and prognosis of cancers of unknown primary |
| title_full | MicroRNA expression profiling with a droplet digital PCR assay enables molecular diagnosis and prognosis of cancers of unknown primary |
| title_fullStr | MicroRNA expression profiling with a droplet digital PCR assay enables molecular diagnosis and prognosis of cancers of unknown primary |
| title_full_unstemmed | MicroRNA expression profiling with a droplet digital PCR assay enables molecular diagnosis and prognosis of cancers of unknown primary |
| title_short | MicroRNA expression profiling with a droplet digital PCR assay enables molecular diagnosis and prognosis of cancers of unknown primary |
| title_sort | microrna expression profiling with a droplet digital pcr assay enables molecular diagnosis and prognosis of cancers of unknown primary |
| topic | cancer of unknown primary droplet digital PCR metastasis microRNAs molecular diagnostics |
| url | https://doi.org/10.1002/1878-0261.13026 |
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