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Li X, Michels BE, Tosun OE, Jung J, Kappes J, Ibing S, Nataraj NB, Sahay S, Schneider M, Wörner A, Becki C, Ishaque N, Feuerbach L, Heßling B, Helm D, Will R, Yarden Y, Müller-Decker K, Wiemann S, Körner C. 5’isomiR-183-5p|+2 elicits tumor suppressor activity in a negative feedback loop with E2F1. J Exp Clin Cancer Res 2022; 41:190. [PMID: 35655310 PMCID: PMC9161486 DOI: 10.1186/s13046-022-02380-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Accepted: 05/04/2022] [Indexed: 12/24/2022] Open
Abstract
Background MicroRNAs (miRNAs) and isomiRs play important roles in tumorigenesis as essential regulators of gene expression. 5’isomiRs exhibit a shifted seed sequence compared to the canonical miRNA, resulting in different target spectra and thereby extending the phenotypic impact of the respective common pre-miRNA. However, for most miRNAs, expression and function of 5’isomiRs have not been studied in detail yet. Therefore, this study aims to investigate the functions of miRNAs and their 5’isomiRs. Methods The expression of 5’isomiRs was assessed in The Cancer Genome Atlas (TCGA) breast cancer patient dataset. Phenotypic effects of miR-183 overexpression in triple-negative breast cancer (TNBC) cell lines were investigated in vitro and in vivo by quantifying migration, proliferation, tumor growth and metastasis. Direct targeting of E2F1 by miR-183-5p|+2 was validated with a 3’UTR luciferase assay and linked to the phenotypes of isomiR overexpression. Results TCGA breast cancer patient data indicated that three variants of miR-183-5p are highly expressed and upregulated, namely miR-183-5p|0, miR-183-5p|+1 and miR-183-5p|+2. However, TNBC cell lines displayed reduced proliferation and invasion upon overexpression of pre-miR-183. While invasion was reduced individually by all three isomiRs, proliferation and cell cycle progression were specifically inhibited by overexpression of miR-183-5p|+2. Proteomic analysis revealed reduced expression of E2F target genes upon overexpression of this isomiR, which could be attributed to direct targeting of E2F1, specifically by miR-183-5p|+2. Knockdown of E2F1 partially phenocopied the effect of miR-183-5p|+2 overexpression on cell proliferation and cell cycle. Gene set enrichment analysis of TCGA and METABRIC patient data indicated that the activity of E2F strongly correlated with the expression of miR-183-5p, suggesting transcriptional regulation of the miRNA by a factor of the E2F family. Indeed, in vitro, expression of miR-183-5p was regulated by E2F1. Hence, miR-183-5p|+2 directly targeting E2F1 appears to be part of a negative feedback loop potentially fine-tuning its activity. Conclusions This study demonstrates that 5’isomiRs originating from the same arm of the same pre-miRNA (i.e. pre-miR-183-5p) may exhibit different functions and thereby collectively contribute to the same phenotype. Here, one of three isomiRs was shown to counteract expression of the pre-miRNA by negatively regulating a transcriptional activator (i.e. E2F1). We speculate that this might be part of a regulatory mechanism to prevent uncontrolled cell proliferation, which is disabled during cancer progression. Graphical Abstract ![]()
Supplementary Information The online version contains supplementary material available at 10.1186/s13046-022-02380-8.
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Berdiel-Acer M, Maia A, Hristova Z, Borgoni S, Vetter M, Burmester S, Becki C, Michels B, Abnaof K, Binenbaum I, Bethmann D, Chatziioannou A, Hasmann M, Thomssen C, Espinet E, Wiemann S. Stromal NRG1 in luminal breast cancer defines pro-fibrotic and migratory cancer-associated fibroblasts. Oncogene 2021; 40:2651-2666. [PMID: 33692466 PMCID: PMC8049869 DOI: 10.1038/s41388-021-01719-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [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: 05/10/2020] [Revised: 02/10/2021] [Accepted: 02/18/2021] [Indexed: 01/31/2023]
Abstract
HER3 is highly expressed in luminal breast cancer subtypes. Its activation by NRG1 promotes activation of AKT and ERK1/2, contributing to tumour progression and therapy resistance. HER3-targeting agents that block this activation, are currently under phase 1/2 clinical studies, and although they have shown favorable tolerability, their activity as a single agent has proven to be limited. Here we show that phosphorylation and activation of HER3 in luminal breast cancer cells occurs in a paracrine manner and is mediated by NRG1 expressed by cancer-associated fibroblasts (CAFs). Moreover, we uncover a HER3-independent NRG1 signaling in CAFs that results in the induction of a strong migratory and pro-fibrotic phenotype, describing a subtype of CAFs with elevated expression of NRG1 and an associated transcriptomic profile that determines their functional properties. Finally, we identified Hyaluronan Synthase 2 (HAS2), a targetable molecule strongly correlated with NRG1, as an attractive player supporting NRG1 signaling in CAFs.
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Affiliation(s)
- Mireia Berdiel-Acer
- grid.7497.d0000 0004 0492 0584Division of Molecular Genome Analysis, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Ana Maia
- grid.7497.d0000 0004 0492 0584Division of Molecular Genome Analysis, German Cancer Research Center (DKFZ), Heidelberg, Germany ,grid.7700.00000 0001 2190 4373Faculty of Biosciences, Ruprecht-Karls-University, Heidelberg, Germany
| | - Zhivka Hristova
- grid.7497.d0000 0004 0492 0584Division of Molecular Genome Analysis, German Cancer Research Center (DKFZ), Heidelberg, Germany ,grid.7700.00000 0001 2190 4373Faculty of Biosciences, Ruprecht-Karls-University, Heidelberg, Germany
| | - Simone Borgoni
- grid.7497.d0000 0004 0492 0584Division of Molecular Genome Analysis, German Cancer Research Center (DKFZ), Heidelberg, Germany ,grid.7700.00000 0001 2190 4373Faculty of Biosciences, Ruprecht-Karls-University, Heidelberg, Germany
| | - Martina Vetter
- grid.9018.00000 0001 0679 2801Department of Gynecology, Martin-Luther-University Halle-Wittenberg, Halle (Saale), Germany
| | - Sara Burmester
- grid.7497.d0000 0004 0492 0584Division of Molecular Genome Analysis, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Corinna Becki
- grid.7497.d0000 0004 0492 0584Division of Molecular Genome Analysis, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Birgitta Michels
- grid.7497.d0000 0004 0492 0584Division of Molecular Genome Analysis, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Khalid Abnaof
- grid.7497.d0000 0004 0492 0584Division of Molecular Genome Analysis, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Ilona Binenbaum
- grid.7497.d0000 0004 0492 0584Division of Medical Informatics for Translational Oncology, German Cancer Research Center (DKFZ), Heidelberg, Germany ,grid.11047.330000 0004 0576 5395Department of Biology, University of Patras, Patras, Greece ,grid.22459.380000 0001 2232 6894Institute of Chemical Biology, National Hellenic Research Foundation, Athens, Greece
| | - Daniel Bethmann
- grid.9018.00000 0001 0679 2801Institute of Pathology Martin-Luther-University Halle-Wittenberg, Halle (Saale), Germany
| | - Aristotelis Chatziioannou
- grid.22459.380000 0001 2232 6894Institute of Chemical Biology, National Hellenic Research Foundation, Athens, Greece ,e-NIOS PC, Kallithea-Athens, Greece
| | - Max Hasmann
- grid.424277.0Roche Diagnostics, Penzberg, Germany
| | - Christoph Thomssen
- grid.9018.00000 0001 0679 2801Department of Gynecology, Martin-Luther-University Halle-Wittenberg, Halle (Saale), Germany
| | - Elisa Espinet
- grid.7497.d0000 0004 0492 0584Divison of Stem Cells and Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany ,grid.482664.aHeidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM), Heidelberg, Germany
| | - Stefan Wiemann
- grid.7497.d0000 0004 0492 0584Division of Molecular Genome Analysis, German Cancer Research Center (DKFZ), Heidelberg, Germany
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Wahjudi LW, Bernhardt S, Abnaof K, Horak P, Kreutzfeldt S, Heining C, Borgoni S, Becki C, Berg D, Richter D, Hutter B, Uhrig S, Pfütze K, Leichsenring J, Glimm H, Brors B, von Kalle C, Stenzinger A, Korf U, Fröhling S, Wiemann S. Integrating proteomics into precision oncology. Int J Cancer 2020; 148:1438-1451. [PMID: 32949162 DOI: 10.1002/ijc.33301] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 09/03/2020] [Accepted: 09/07/2020] [Indexed: 12/13/2022]
Abstract
DNA sequencing and RNA sequencing are increasingly applied in precision oncology, where molecular tumor boards evaluate the actionability of genetic events in individual tumors to guide targeted treatment. To work toward an additional level of patient characterization, we assessed the abundance and activity of 27 proteins in 134 patients whose tumors had previously undergone whole-exome and RNA sequencing within the Molecularly Aided Stratification for Tumor Eradication Research (MASTER) program of National Center for Tumor Diseases, Heidelberg. Proteomic and phosphoproteomic targets were selected to reflect the most relevant therapeutic baskets in MASTER. Among six different therapeutic baskets, the proteomic data supported treatment recommendations that were based on DNA and RNA analyses in 10% to 57% and frequently suggested alternative treatment options. In several cases, protein activities explained the patients' clinical course and provided potential explanations for treatment failure. Our study indicates that the integrative analysis of DNA, RNA and protein data may refine therapeutic stratification of individual patients and, thus, holds potential to increase the success rate of precision cancer therapy. Prospective validation studies are needed to advance the integration of proteomic analysis into precision oncology.
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Affiliation(s)
- Leonie W Wahjudi
- Division of Molecular Genome Analysis, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Stephan Bernhardt
- Division of Molecular Genome Analysis, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Khalid Abnaof
- Division of Molecular Genome Analysis, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Peter Horak
- Division of Translational Medical Oncology, National Center for Tumor Diseases (NCT) Heidelberg and German Cancer Research Center (DKFZ), Heidelberg, Germany.,German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Simon Kreutzfeldt
- Division of Translational Medical Oncology, National Center for Tumor Diseases (NCT) Heidelberg and German Cancer Research Center (DKFZ), Heidelberg, Germany.,German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Christoph Heining
- Department of Translational Medical Oncology, National Center for Tumor Diseases (NCT) Dresden, Dresden, Germany.,German Cancer Consortium (DKTK), Dresden, Germany.,Center for Personalized Oncology, National Center for Tumour Diseases (NCT) Dresden and University Hospital Carl Gustav Carus Dresden at TU Dresden, Dresden, Germany
| | - Simone Borgoni
- Division of Molecular Genome Analysis, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Faculty of Biosciences, University Heidelberg, Heidelberg, Germany
| | - Corinna Becki
- Division of Molecular Genome Analysis, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Daniela Berg
- Division of Molecular Genome Analysis, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Daniela Richter
- Department of Translational Medical Oncology, National Center for Tumor Diseases (NCT) Dresden, Dresden, Germany.,German Cancer Consortium (DKTK), Dresden, Germany
| | - Barbara Hutter
- German Cancer Consortium (DKTK), Heidelberg, Germany.,Division of Applied Bioinformatics, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT) Heidelberg, Heidelberg, Germany
| | - Sebastian Uhrig
- German Cancer Consortium (DKTK), Heidelberg, Germany.,Faculty of Biosciences, University Heidelberg, Heidelberg, Germany.,Division of Applied Bioinformatics, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT) Heidelberg, Heidelberg, Germany
| | - Katrin Pfütze
- Division of Translational Medical Oncology, National Center for Tumor Diseases (NCT) Heidelberg and German Cancer Research Center (DKFZ), Heidelberg, Germany.,German Cancer Consortium (DKTK), Heidelberg, Germany
| | | | - Hanno Glimm
- Department of Translational Medical Oncology, National Center for Tumor Diseases (NCT) Dresden, Dresden, Germany.,Translational Functional Cancer Genomics, National Center for Tumor Diseases (NCT) and German Cancer Research Center (DKFZ), Heidelberg, Germany.,German Cancer Consortium (DKTK), Dresden, Germany.,Center for Personalized Oncology, National Center for Tumour Diseases (NCT) Dresden and University Hospital Carl Gustav Carus Dresden at TU Dresden, Dresden, Germany
| | - Benedikt Brors
- German Cancer Consortium (DKTK), Heidelberg, Germany.,Division of Applied Bioinformatics, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT) Heidelberg, Heidelberg, Germany
| | - Christof von Kalle
- Division of Translational Medical Oncology, National Center for Tumor Diseases (NCT) Heidelberg and German Cancer Research Center (DKFZ), Heidelberg, Germany.,Translational Functional Cancer Genomics, National Center for Tumor Diseases (NCT) and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Albrecht Stenzinger
- German Cancer Consortium (DKTK), Heidelberg, Germany.,Institute of Pathology, University Heidelberg, Heidelberg, Germany
| | - Ulrike Korf
- Division of Molecular Genome Analysis, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Stefan Fröhling
- Division of Translational Medical Oncology, National Center for Tumor Diseases (NCT) Heidelberg and German Cancer Research Center (DKFZ), Heidelberg, Germany.,German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Stefan Wiemann
- Division of Molecular Genome Analysis, German Cancer Research Center (DKFZ), Heidelberg, Germany.,German Cancer Consortium (DKTK), Heidelberg, Germany
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