MicroRNA-27a-3p targets FoxO signalling to induce tumour-like phenotypes in bile duct cells
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Background & Aims: Cholangiocarcinoma (CCA) is a heterogeneous and lethal malignancy, the molecular origins of which remain poorly understood. MicroRNAs (miRs) target diverse signalling pathways, functioning as potent epigenetic regulators of transcriptional output. We aimed to characterise miRNome dysregulation in CCA, including its impact on transcriptome homeostasis and cell behaviour. Methods: Small RNA sequencing was performed on 119 resected CCAs, 63 surrounding liver tissues, and 22 normal livers. High-throughput miR mimic screens were performed in three primary human cholangiocyte cultures. Integration of patient transcriptomes and miRseq together with miR screening data identified an oncogenic miR for characterization. MiR-mRNA interactions were investigated by a luciferase assay. MiR-CRISPR knockout cells were generated and phenotypically characterized in vitro (proliferation, migration, colony, mitochondrial function, glycolysis) and in vivo using subcutaneous xenografts. Results: In total, 13% (140/1,049) of detected miRs were differentially expressed between CCA and surrounding liver tissues, including 135 that were upregulated in tumours. CCA tissues were characterised by higher miRNome heterogeneity and miR biogenesis pathway expression. Unsupervised hierarchical clustering of tumour miRNomes identified three subgroups, including distal CCA-enriched and IDH1 mutant-enriched subgroups. High-throughput screening of miR mimics uncovered 71 miRs that consistently increased proliferation of three primary cholangiocyte models and were upregulated in CCA tissues regardless of anatomical location, among which only miR-27a-3p had consistently increased expression and activity in several cohorts. FoxO signalling was predominantly downregulated by miR-27a-3p in CCA, partially through targeting of FOXO1. MiR-27a knockout increased FOXO1 levels in vitro and in vivo, impeding tumour behaviour and growth. Conclusions: The miRNomes of CCA tissues are highly remodelled, impacting transcriptome homeostasis in part through regulation of transcription factors like FOXO1. MiR-27a-3p arises as an oncogenic vulnerability in CCA. Impact and implications: Cholangiocarcinogenesis entails extensive cellular reprogramming driven by genetic and non-genetic alterations, but the functional roles of these non-genetic events remain poorly understood. By unveiling global miRNA upregulation in patient tumours and their functional ability to increase proliferation of cholangiocytes, these small non-coding RNAs are implicated as critical non-genetic alterations promoting biliary tumour initiation. These findings identify possible mechanisms for transcriptome rewiring during transformation, with potential implications for patient stratification.
| Originalsprog | Engelsk |
|---|---|
| Tidsskrift | Journal of Hepatology |
| Vol/bind | 78 |
| Antal sider | 13 |
| ISSN | 0168-8278 |
| DOI | |
| Status | Udgivet - 2023 |
Bibliografisk note
Funding Information:
The authors would like to thank members of the Biotech Research and Innovation Centre (BRIC) Histocore, Microscopy and High Throughput robotics screening facilities. The project described was supported in parts by Award Number P50 CA210964 ( Mayo Clinic Hepatobiliary SPORE) from the National Cancer Institute (NCI), USA. The content is solely the responsibility of the authors and does not necessarily represent the official views of the NIH, USA. Furthermore , the results are in part supported by data generated by the TCGA Research Network: https://www.cancer.gov/tcga .
Funding Information:
JBA is a member of the scientific advisory board at SEALD, Norway and reports scientific consultancies for QED Therapeutics and Flagship Pioneering. JBA has received funding from Incyte. MSM has served as a consultant for Novartis and GSK, and received speaker honoraria from ThermoFisher and Merck, all outside the current work.
Funding Information:
The Laboratory of JBA is funded by a competitive grant from the Novo Nordisk Foundation (#14040). PMG, CJO, JFLB were awarded postdoc fellowships from the European Union Marie Curie program – MiRCHOL, EpiTarget and EpiCC, respectively. PMG was awarded a Sheila Sherlock postdoc fellowship from the European Association for the Study of the Liver (EASL). AT was awarded an individual postdoc fellowship from the Lundbeck Foundation. LD was awarded a PhD project grant from the Danish Cancer Research Foundation. This project was supported by the European Union's Horizon 2020 research and innovation program under the Marie Skłodowska-Curie grant agreement no. 801481. JMB is supported by Spanish Carlos III Health Institute (ISCIII) [(FIS PI18/01075, PI21/00922, and Miguel Servet Programme CPII19/00008) cofinanced by “Fondo Europeo de Desarrollo Regional” (FEDER)] and CIBERehd (ISCIII); La Caixa Scientific Foundation (HR17-00601); AMMF-The Cholangiocarcinoma Charity (EU/2019/AMMFt/001); PSC Partners US and PSC Supports UK (06119JB); European Union's Horizon 2020 Research and Innovation Program [grant number 825510, ESCALON]. MSM is supported by the National Science Foundation (SNSF; Grant No. 320030_189275)The authors would like to thank members of the Biotech Research and Innovation Centre (BRIC) Histocore, Microscopy and High Throughput robotics screening facilities. The project described was supported in parts by Award Number P50 CA210964 (Mayo Clinic Hepatobiliary SPORE) from the National Cancer Institute (NCI), USA. The content is solely the responsibility of the authors and does not necessarily represent the official views of the NIH, USA. Furthermore, the results are in part supported by data generated by the TCGA Research Network: https://www.cancer.gov/tcga.
Funding Information:
The Laboratory of JBA is funded by a competitive grant from the Novo Nordisk Foundation (#14040). PMG, CJO, JFLB were awarded postdoc fellowships from the European Union Marie Curie program – MiRCHOL, EpiTarget and EpiCC, respectively. PMG was awarded a Sheila Sherlock postdoc fellowship from the European Association for the Study of the Liver (EASL). AT was awarded an individual postdoc fellowship from the Lundbeck Foundation. LD was awarded a PhD project grant from the Danish Cancer Research Foundation. This project was supported by the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie grant agreement no. 801481. JMB is supported by Spanish Carlos III Health Institute (ISCIII) [(FIS PI18/01075, PI21/00922, and Miguel Servet Programme CPII19/00008) cofinanced by “Fondo Europeo de Desarrollo Regional” (FEDER)] and CIBERehd (ISCIII); La Caixa Scientific Foundation (HR17-00601); AMMF-The Cholangiocarcinoma Charity (EU/2019/AMMFt/001); PSC Partners US and PSC Supports UK (06119JB); European Union’s Horizon 2020 Research and Innovation Program [grant number 825510, ESCALON]. MSM is supported by the National Science Foundation (SNSF; Grant No. 320030_189275)
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© 2022 The Author(s)
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