1
|
Ramírez-Moya J, Wert-Lamas L, Acuña-Ruíz A, Fletcher A, Wert-Carvajal C, McCabe CJ, Santisteban P, Riesco-Eizaguirre G. Identification of an interactome network between lncRNAs and miRNAs in thyroid cancer reveals SPTY2D1-AS1 as a new tumor suppressor. Sci Rep 2022; 12:7706. [PMID: 35562181 PMCID: PMC9095586 DOI: 10.1038/s41598-022-11725-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Accepted: 04/19/2022] [Indexed: 11/26/2022] Open
Abstract
Thyroid cancer is the most common primary endocrine malignancy in adults and its incidence is rapidly increasing. Long non-coding RNAs (lncRNAs), generally defined as RNA molecules longer than 200 nucleotides with no protein-encoding capacity, are highly tissue-specific molecules that serve important roles in gene regulation through a variety of different mechanisms, including acting as competing endogenous RNAs (ceRNAs) that ‘sponge’ microRNAs (miRNAs). In the present study, using an integrated approach through RNA-sequencing of paired thyroid tumor and non-tumor samples, we have identified an interactome network between lncRNAs and miRNAs and examined the functional consequences in vitro and in vivo of one of such interactions. We have identified a likely operative post-transcriptional regulatory network in which the downregulated lncRNA, SPTY2D1-AS1, is predicted to target the most abundant and upregulated miRNAs in thyroid cancer, particularly miR-221, a well-known oncomiRNA in cancer. Indeed, SPTY2D1-AS1 functions as a potent tumor suppressor in vitro and in vivo, it is downregulated in the most advanced stages of human thyroid cancer, and it seems to block the processing of the primary form of miR-221. Overall, our results link SPTY2D1-AS1 to thyroid cancer progression and highlight the potential use of this lncRNA as a therapeutic target of thyroid cancer.
Collapse
Affiliation(s)
- Julia Ramírez-Moya
- Instituto de Investigaciones Biomédicas "Alberto Sols", Consejo Superior Investigaciones Científicas, Universidad Autónoma de Madrid (CSIC-UAM), 28029, Madrid, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Instituto de Salud Carlos III (ISCIII), 28029, Madrid, Spain
| | - León Wert-Lamas
- Instituto de Investigaciones Biomédicas "Alberto Sols", Consejo Superior Investigaciones Científicas, Universidad Autónoma de Madrid (CSIC-UAM), 28029, Madrid, Spain
| | - Adrián Acuña-Ruíz
- Instituto de Investigaciones Biomédicas "Alberto Sols", Consejo Superior Investigaciones Científicas, Universidad Autónoma de Madrid (CSIC-UAM), 28029, Madrid, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Instituto de Salud Carlos III (ISCIII), 28029, Madrid, Spain
| | - Alice Fletcher
- Instituto de Investigaciones Biomédicas "Alberto Sols", Consejo Superior Investigaciones Científicas, Universidad Autónoma de Madrid (CSIC-UAM), 28029, Madrid, Spain.,Institute of Metabolism and Systems Research, University of Birmingham, Birmingham, B152TT, UK
| | - Carlos Wert-Carvajal
- Instituto de Investigaciones Biomédicas "Alberto Sols", Consejo Superior Investigaciones Científicas, Universidad Autónoma de Madrid (CSIC-UAM), 28029, Madrid, Spain.,Department of Bioengineering and Aerospace Engineering, Universidad Carlos III, 28911, Madrid, Spain
| | - Christopher J McCabe
- Institute of Metabolism and Systems Research, University of Birmingham, Birmingham, B152TT, UK
| | - Pilar Santisteban
- Instituto de Investigaciones Biomédicas "Alberto Sols", Consejo Superior Investigaciones Científicas, Universidad Autónoma de Madrid (CSIC-UAM), 28029, Madrid, Spain. .,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Instituto de Salud Carlos III (ISCIII), 28029, Madrid, Spain.
| | - Garcilaso Riesco-Eizaguirre
- Instituto de Investigaciones Biomédicas "Alberto Sols", Consejo Superior Investigaciones Científicas, Universidad Autónoma de Madrid (CSIC-UAM), 28029, Madrid, Spain. .,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Instituto de Salud Carlos III (ISCIII), 28029, Madrid, Spain. .,Hospital Universitario de Móstoles, 28223, Madrid, Spain. .,Endocrinology Molecular Group, Faculty of Medicine, Universidad Francisco de Vitoria, Madrid, Spain.
| |
Collapse
|
2
|
Baker AR, Miliotis C, Ramírez-Moya J, Marc T, Vlachos IS, Santisteban P, Slack FJ. Transcriptome profiling of ADAR1 targets in triple-negative breast cancer cells reveals mechanisms for regulating growth and invasion. Mol Cancer Res 2022; 20:960-971. [PMID: 35247916 DOI: 10.1158/1541-7786.mcr-21-0604] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 12/23/2021] [Accepted: 02/28/2022] [Indexed: 11/16/2022]
Abstract
ADARs catalyze Adenosine-to-Inosine (A-to-I) editing of double-stranded RNA and regulate global gene expression output through interactions with RNA and other proteins. ADARs play important roles in development and disease, and previous work has shown that ADAR1 is oncogenic in a growing list of cancer types. Here we show that ADAR1 is a critical gene for triple-negative breast cancer cells, as ADAR1 loss results in reduced growth (viability and cell cycle progression), invasion, and mammosphere formation. Whole transcriptome sequencing analyses demonstrate that ADAR1 regulates both coding and non-coding targets by altering gene expression level, A-to-I editing, and splicing. We determine that a recoding edit in filamin B (FLNB chr3:58156064) reduces the tumor suppressive activities of the protein to promote growth and invasion. We also show that several tumor suppressor microRNAs are upregulated upon ADAR1 loss and suppress cell cycle progression and invasion. Implications: This work describes several novel mechanisms of ADAR1-mediated oncogenesis in triple-negative breast cancer, providing support to strategies targeting ADAR1 in this aggressive cancer type that has few treatment options.
Collapse
Affiliation(s)
| | | | - Julia Ramírez-Moya
- Boston Children's Hospital / Harvard Medical School, Boston, MA, United States
| | | | | | - Pilar Santisteban
- Instituto de Investigaciones Biomedicas CSIC/UAM, Madrid, Madrid, Spain
| | | |
Collapse
|
3
|
Ramírez-Moya J, Miliotis C, Baker AR, Gregory RI, Slack FJ, Santisteban P. An ADAR1-dependent RNA editing event in the cyclin-dependent kinase CDK13 promotes thyroid cancer hallmarks. Mol Cancer 2021; 20:115. [PMID: 34496885 PMCID: PMC8424981 DOI: 10.1186/s12943-021-01401-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [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: 03/04/2021] [Accepted: 08/03/2021] [Indexed: 11/10/2022] Open
Abstract
Background Adenosine deaminases acting on RNA (ADARs) modify many cellular RNAs by catalyzing the conversion of adenosine to inosine (A-to-I), and their deregulation is associated with several cancers. We recently showed that A-to-I editing is elevated in thyroid tumors and that ADAR1 is functionally important for thyroid cancer cell progression. The downstream effectors regulated or edited by ADAR1 and the significance of ADAR1 deregulation in thyroid cancer remain, however, poorly defined. Methods We performed whole transcriptome sequencing to determine the consequences of ADAR1 deregulation for global gene expression, RNA splicing and editing. The effects of gene silencing or RNA editing were investigated by analyzing cell viability, proliferation, invasion and subnuclear localization, and by protein and gene expression analysis. Results We report an oncogenic function for CDK13 in thyroid cancer and identify a new ADAR1-dependent RNA editing event that occurs in the coding region of its transcript. CDK13 was significantly over-edited (c.308A > G) in tumor samples and functional analysis revealed that this editing event promoted cancer cell hallmarks. Finally, we show that CDK13 editing increases the nucleolar abundance of the protein, and that this event might explain, at least partly, the global change in splicing produced by ADAR1 deregulation. Conclusions Overall, our data support A-to-I editing as an important pathway in cancer progression and highlight novel mechanisms that might be used therapeutically in thyroid and other cancers. Supplementary Information The online version contains supplementary material available at 10.1186/s12943-021-01401-y.
Collapse
Affiliation(s)
- Julia Ramírez-Moya
- Instituto, de Investigaciones Biomédicas "Alberto Sols"; Consejo Superior de Investigaciones Científicas (CSIC), Universidad Autónoma de Madrid (UAM), Madrid, Spain.,Department of Pathology, Harvard Medical School Initiative for RNA Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA.,Stem Cell Program, Division of Hematology/Oncology, Boston Children's Hospital, Departments of Biological Chemistry and Molecular Pharmacology, and Pediatrics, Harvard Medical School, Harvard Medical School Initiative for RNA Medicine, Boston, MA, USA.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC) Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| | - Christos Miliotis
- Department of Pathology, Harvard Medical School Initiative for RNA Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Allison R Baker
- Department of Pathology, Harvard Medical School Initiative for RNA Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Richard I Gregory
- Stem Cell Program, Division of Hematology/Oncology, Boston Children's Hospital, Departments of Biological Chemistry and Molecular Pharmacology, and Pediatrics, Harvard Medical School, Harvard Medical School Initiative for RNA Medicine, Boston, MA, USA
| | - Frank J Slack
- Department of Pathology, Harvard Medical School Initiative for RNA Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA.
| | - Pilar Santisteban
- Instituto, de Investigaciones Biomédicas "Alberto Sols"; Consejo Superior de Investigaciones Científicas (CSIC), Universidad Autónoma de Madrid (UAM), Madrid, Spain. .,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC) Instituto de Salud Carlos III (ISCIII), Madrid, Spain.
| |
Collapse
|
4
|
Abstract
Background: DICER1 plays a central role in microRNA biogenesis and functions as a tumor suppressor in thyroid cancer, which is the most frequent endocrine malignancy with a rapidly increasing incidence. Thyroid cancer progression is associated with loss of cell differentiation and reduced expression of thyroid differentiation genes and response to thyrotropin (TSH). Here we investigated whether a molecular link exists between DICER1 and thyroid differentiation pathways. Methods: We used bioinformatic tools to search for transcription factor binding sites in the DICER1 promoter. DICER1, NKX2-1, PAX8, and CREB expression levels were evaluated by gene and protein expression in vitro and by interrogation of The Cancer Genome Atlas (TCGA) thyroid cancer data. Transcription factor binding and activity were assayed by chromatin immunoprecipitation, band-shift analysis, and promoter-reporter gene activity. Gene-silencing and overexpression approaches were used to elucidate the functional link between DICER1 and differentiation. Results: We identified binding sites for NKX2-1 and CREB within the DICER1 promoter and found that both transcription factors are functional in thyroid cells. TSH induced DICER1 expression in differentiated thyroid cells, at least in part, through the cAMP/PKA/CREB pathway. TCGA analysis revealed a significant positive correlation between CREB and DICER1 expression in human thyroid tumors. NKX2-1 overexpression increased DICER1 promoter activity and expression in vitro, and this was significantly greater in the presence of CREB and/or PAX8. Gain- and loss-of-function assays revealed that DICER1 regulates NKX2-1 expression in thyroid tumor cells and vice versa, thus establishing a positive feedback loop between both proteins. We also found a positive correlation between NKX2-1 and DICER1 expression in human thyroid tumors. DICER1 silencing decreased PAX8 expression and, importantly, the expression and activity of the sodium iodide symporter, which is essential for the diagnostic and therapeutic use of radioiodine in thyroid cancer. Conclusions: The differentiation transcription factors NKX2.1, PAX8, and CREB act in a positive feedback loop with DICER1. As the expression of these transcription factors is markedly diminished in thyroid cancer, our findings suggest that DICER1 downregulation in this cancer is mediated, at least partly, through impairment of its transcription.
Collapse
Affiliation(s)
- Julia Ramírez-Moya
- Instituto de Investigaciones Biomédicas “Alberto Sols,” Consejo Superior Investigaciones Científicas, and Universidad Autónoma de Madrid (CSIC-UAM), Madrid, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| | - Pilar Santisteban
- Instituto de Investigaciones Biomédicas “Alberto Sols,” Consejo Superior Investigaciones Científicas, and Universidad Autónoma de Madrid (CSIC-UAM), Madrid, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Instituto de Salud Carlos III (ISCIII), Madrid, Spain
- Address correspondence to: Pilar Santisteban, PhD, Instituto de Investigaciones Biomédicas “Alberto Sols”, Consejo Superior Investigaciones Científicas, Universidad Autónoma de Madrid (CSIC-UAM), C/Arturo Duperier 4, Madrid 28029, Spain
| |
Collapse
|
5
|
Abstract
In the last two decades, great strides have been made in the study of microRNAs in development and in diseases such as cancer, as reflected in the exponential increase in the number of reviews on this topic including those on undifferentiated and well-differentiated thyroid cancer. Nevertheless, few reviews have focused on understanding the functional significance of the most up- or down-regulated miRNAs in thyroid cancer for the main signaling pathways hyperactivated in this tumor type. The aim of this review is to discuss the major miRNAs targeting proteins of the MAPK, PI3K, and TGFβ pathways, to define their mechanisms of action through the 3'UTR regions of their target genes, and to describe how they affect thyroid tumorigenesis through their actions on cell proliferation, migration, and invasion. Given the importance of miRNAs in cancer as diagnostic, prognostic and therapeutic candidates, a better understanding of this cross-talk might shed new light on the biomedical treatment of thyroid cancer.
Collapse
Affiliation(s)
- Julia Ramírez-Moya
- Instituto de Investigaciones Biomédicas “Alberto Sols”, Consejo Superior Investigaciones Científicas and Universidad Autónoma de Madrid (CSIC-UAM), Madrid, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| | - Pilar Santisteban
- Instituto de Investigaciones Biomédicas “Alberto Sols”, Consejo Superior Investigaciones Científicas and Universidad Autónoma de Madrid (CSIC-UAM), Madrid, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Instituto de Salud Carlos III (ISCIII), Madrid, Spain
- *Correspondence: Pilar Santisteban
| |
Collapse
|
6
|
Ramírez-Moya J, Santisteban P. An oncogenic role for microRNA-146b in the thyroid. Oncoscience 2018; 5:155-156. [PMID: 30035174 PMCID: PMC6049317 DOI: 10.18632/oncoscience.432] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2018] [Accepted: 05/04/2018] [Indexed: 11/28/2022] Open
Affiliation(s)
- Julia Ramírez-Moya
- Instituto de Investigaciones Biomédicas, CSIC-UAM, Ciberonc, Madrid, Spain
| | - Pilar Santisteban
- Instituto de Investigaciones Biomédicas, CSIC-UAM, Ciberonc, Madrid, Spain
| |
Collapse
|