MicroRNA-27a-3p targets FoxO signalling to induce tumour-like phenotypes in bile duct cells
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MicroRNA-27a-3p targets FoxO signalling to induce tumour-like phenotypes in bile duct cells. / Duwe, Lea; Munoz-Garrido, Patricia; Lewinska, Monika; Lafuente-Barquero, Juan; Satriano, Letizia; Høgdall, Dan; Taranta, Andrzej; Nielsen, Boye S.; Ghazal, Awaisa; Matter, Matthias S.; Banales, Jesus M.; Aldana, Blanca I.; Gao, Yu-Tang; Marquardt, Jens U.; Roberts, Lewis R.; Oliveira, Rui C.; Koshiol, Jill; O'Rourke, Colm J.; Andersen, Jesper B.
I: Journal of Hepatology, Bind 78, 2023.Publikation: Bidrag til tidsskrift › Tidsskriftartikel › Forskning › fagfællebedømt
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T1 - MicroRNA-27a-3p targets FoxO signalling to induce tumour-like phenotypes in bile duct cells
AU - Duwe, Lea
AU - Munoz-Garrido, Patricia
AU - Lewinska, Monika
AU - Lafuente-Barquero, Juan
AU - Satriano, Letizia
AU - Høgdall, Dan
AU - Taranta, Andrzej
AU - Nielsen, Boye S.
AU - Ghazal, Awaisa
AU - Matter, Matthias S.
AU - Banales, Jesus M.
AU - Aldana, Blanca I.
AU - Gao, Yu-Tang
AU - Marquardt, Jens U.
AU - Roberts, Lewis R.
AU - Oliveira, Rui C.
AU - Koshiol, Jill
AU - O'Rourke, Colm J.
AU - Andersen, Jesper B.
N1 - Publisher Copyright: © 2022 The Author(s)
PY - 2023
Y1 - 2023
N2 - 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.
AB - 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.
KW - Cholangiocarcinoma
KW - cholangiocytes
KW - FoxO1
KW - microRNAs
KW - proliferation
U2 - 10.1016/j.jhep.2022.10.012
DO - 10.1016/j.jhep.2022.10.012
M3 - Journal article
C2 - 36848245
AN - SCOPUS:85142754397
VL - 78
JO - Journal of Hepatology, Supplement
JF - Journal of Hepatology, Supplement
SN - 0169-5185
ER -
ID: 327789292