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Søkilde R, Persson H, Ehinger A, Pirona AC, Fernö M, Hegardt C, Larsson C, Loman N, Malmberg M, Rydén L, Saal L, Borg Å, Vallon-Christerson J, Rovira C. Refinement of breast cancer molecular classification by miRNA expression profiles. BMC Genomics 2019; 20:503. [PMID: 31208318 PMCID: PMC6580620 DOI: 10.1186/s12864-019-5887-7] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [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: 03/14/2019] [Accepted: 06/06/2019] [Indexed: 02/06/2023] Open
Abstract
Background Accurate classification of breast cancer using gene expression profiles has contributed to a better understanding of the biological mechanisms behind the disease and has paved the way for better prognostication and treatment prediction. Results We found that miRNA profiles largely recapitulate intrinsic subtypes. In the case of HER2-enriched tumors a small set of miRNAs including the HER2-encoded mir-4728 identifies the group with very high specificity. We also identified differential expression of the miR-99a/let-7c/miR-125b miRNA cluster as a marker for separation of the Luminal A and B subtypes. High expression of this miRNA cluster is linked to better overall survival among patients with Luminal A tumors. Correlation between the miRNA cluster and their precursor LINC00478 is highly significant suggesting that its expression could help improve the accuracy of present day’s signatures. Conclusions We show here that miRNA expression can be translated into mRNA profiles and that the inclusion of miRNA information facilitates the molecular diagnosis of specific subtypes, in particular the clinically relevant sub-classification of luminal tumors. Electronic supplementary material The online version of this article (10.1186/s12864-019-5887-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Rolf Søkilde
- Division of Oncology, Department of Clinical Sciences Lund, Lund University, Medicon Village, Scheelevägen 2, 223 81, Lund, Sweden
| | - Helena Persson
- Division of Oncology, Department of Clinical Sciences Lund, Lund University, Medicon Village, Scheelevägen 2, 223 81, Lund, Sweden
| | - Anna Ehinger
- Clinical Pathology, Laboratory Medicine, Skåne University Hospital, Lund, Sweden
| | - Anna Chiara Pirona
- Division of Oncology, Department of Clinical Sciences Lund, Lund University, Medicon Village, Scheelevägen 2, 223 81, Lund, Sweden.,German Cancer Research Center DKFZ, Division of Functional Genome Analysis, Heidelberg, Germany
| | - Mårten Fernö
- Division of Oncology, Department of Clinical Sciences Lund, Lund University, Medicon Village, Scheelevägen 2, 223 81, Lund, Sweden
| | - Cecilia Hegardt
- Division of Oncology, Department of Clinical Sciences Lund, Lund University, Medicon Village, Scheelevägen 2, 223 81, Lund, Sweden
| | - Christer Larsson
- Division of Translational Cancer Research, Lund University, Lund, Sweden.,BioCARE, Strategic Cancer Research Program, Lund, Sweden
| | - Niklas Loman
- Division of Oncology, Skåne University Hospital, Lund, Sweden
| | - Martin Malmberg
- Division of Oncology, Skåne University Hospital, Lund, Sweden
| | - Lisa Rydén
- Department of Surgery, Skåne University Hospital, Lund, Sweden
| | - Lao Saal
- Division of Oncology, Department of Clinical Sciences Lund, Lund University, Medicon Village, Scheelevägen 2, 223 81, Lund, Sweden.,BioCARE, Strategic Cancer Research Program, Lund, Sweden
| | - Åke Borg
- Division of Oncology, Department of Clinical Sciences Lund, Lund University, Medicon Village, Scheelevägen 2, 223 81, Lund, Sweden.,BioCARE, Strategic Cancer Research Program, Lund, Sweden
| | - Johan Vallon-Christerson
- Division of Oncology, Department of Clinical Sciences Lund, Lund University, Medicon Village, Scheelevägen 2, 223 81, Lund, Sweden
| | - Carlos Rovira
- Division of Oncology, Department of Clinical Sciences Lund, Lund University, Medicon Village, Scheelevägen 2, 223 81, Lund, Sweden. .,BioCARE, Strategic Cancer Research Program, Lund, Sweden.
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