Identification of an interactome network between lncRNAs and miRNAs in thyroid cancer reveals SPTY2D1-AS1 as a new tumor suppressor

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 importan...

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Published inScientific reports Vol. 12; no. 1; pp. 7706 - 13
Main Authors Ramírez-Moya, Julia, Wert-Lamas, León, Acuña-Ruíz, Adrián, Fletcher, Alice, Wert-Carvajal, Carlos, McCabe, Christopher J., Santisteban, Pilar, Riesco-Eizaguirre, Garcilaso
Format Journal Article
LanguageEnglish
Published London Nature Publishing Group UK 11.05.2022
Nature Publishing Group
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ISSN2045-2322
2045-2322
DOI10.1038/s41598-022-11725-4

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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.
AbstractList 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.
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.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.
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.
ArticleNumber 7706
Author Wert-Lamas, León
Santisteban, Pilar
Fletcher, Alice
McCabe, Christopher J.
Wert-Carvajal, Carlos
Ramírez-Moya, Julia
Riesco-Eizaguirre, Garcilaso
Acuña-Ruíz, Adrián
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Lim, H., Devesa, S. S., Sosa, J. A., Check, D. & Kitahara, C. M. Trends in thyroid cancer incidence and mortality in the United States, 1974–2013. JAMA317 (2017).
Ebert, M. S. & Sharp, P. A. Emerging roles for natural microRNA sponges. Curr. Biol.20 (2010).
Paraskevopoulou, M. D. et al. DIANA-LncBase v2: Indexing microRNA targets on non-coding transcripts. Nucleic Acids Res.44, (2016).
He, H. et al. Genetic predisposition to papillary thyroid carcinoma: Involvement of FOXE1, TSHR, and a novel lincRNA Gene, PTCSC2. J. Clin. Endocrinol. Metab.100, (2015).
Gutschner, T. & Diederichs, S. The hallmarks of cancer: A long non-coding RNA point of view. RNA Biol. 9 (2012).
Ma, M. et al. miRNA-221 of exosomes originating from bone marrow mesenchymal stem cells promotes oncogenic activity in gastric cancer. OncoTargets Ther.10, (2017).
Lin, S. & Gregory, R. I. MicroRNA biogenesis pathways in cancer. Nature Reviews Cancer vol. 15 (2015).
Visone, R. et al. MicroRNAs (miR)-221 and miR-222, both overexpressed in human thyroid papillary carcinomas, regulate p27Kip1 protein levels and cell cycle. Endocrine-Relat. Cancer14, (2007).
Ghafouri-Fard, S., Mohammad-Rahimi, H. & Taheri, M. The role of long non-coding RNAs in the pathogenesis of thyroid cancer. Exp. Mol. Pathol. 112 (2020).
He, H. et al. The role of microRNA genes in papillary thyroid carcinoma. Proc. Natl. Acad. Sci. USA102 (2005).
Diao, Y., Fu, H. & Wang, Q. MiR-221 exacerbate cell proliferation and invasion by targeting TIMP3 in papillary thyroid carcinoma. Am. J. Ther.24, (2017).
Wei, Z. L. et al. MicroRNA-221 promotes papillary thyroid carcinoma cell migration and invasion via targeting RECK and regulating epithelial–mesenchymal transition. OncoTargets Ther.12, (2019).
He, H. et al. A susceptibility locus for papillary thyroid carcinoma on chromosome 8q24. Cancer Res.69, (2009).
Ludvíková, M., Kalfeřt, D. & Kholová, I. Pathobiology of MicroRNAs and their emerging role in thyroid fine-needle aspiration. Acta Cytol. 59 (2015).
Song, J. et al. Potential value of miR-221/222 as diagnostic, prognostic, and therapeutic biomarkers for diseases. Front. Immunol. 8 (2017).
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Cesana, M. et al. A long noncoding RNA controls muscle differentiation by functioning as a competing endogenous RNA. Cell147, (2011).
Riesco-EizaguirreGSantistebanPAdvances in the molecular pathogenesis of thyroid cancer: Lessons from the cancer genomeEur. J. Endocrinol.2016175R203R2171:CAS:528:DC%2BC2sXhslCjt7c%3D10.1530/EJE-16-0202
Poliseno, L. et al. A coding-independent function of gene and pseudogene mRNAs regulates tumour biology. Nature465, (2010).
Statello, L., Guo, C. J., Chen, L. L. & Huarte, M. Gene regulation by long non-coding RNAs and its biological functions. Nat. Rev. Mol. Cell Biol.22 (2021).
Yoon, H. et al. Identification of a novel noncoding RNA gene, NAMA, that is downregulated in papillary thyroid carcinoma with BRAF mutation and associated with growth arrest. Int. J. Cancer121, (2007).
Ebert, M. S., Neilson, J. R. & Sharp, P. A. MicroRNA sponges: Competitive inhibitors of small RNAs in mammalian cells. Nature Methods4, (2007).
Liu, P. et al. Identification of targets of miRNA-221 and miRNA-222 in fulvestrant-resistant breast cancer. Oncol. Lett.12, (2016).
Abak, A. et al. Analysis of miRNA-221 expression level in tumors and marginal biopsies from patients with breast cancer (cross-sectional observational study). Clin. Lab.64, (2018).
Liz, J. et al. Regulation of pri-miRNA processing by a long noncoding RNA transcribed from an ultraconserved region. Mol. Cell55, (2014).
Carlberg, M., Hedendahl, L., Ahonen, M., Koppel, T. & Hardell, L. Increasing incidence of thyroid cancer in the Nordic countries with main focus on Swedish data. BMC Cancer16, (2016).
Riesco-EizaguirreGThe miR-146b-3p/PAX8/NIS regulatory circuit modulates the differentiation phenotype and function of thyroid cells during carcinogenesisCan. Res.201575411941301:CAS:528:DC%2BC2MXhsFyrtbnN10.1158/0008-5472.CAN-14-3547
Li, Q. et al. Identification of novel long non-coding RNA biomarkers for prognosis prediction of papillary thyroid cancer. Oncotarget8 (2017).
FuziwaraCSKimuraETMicroRNAs in thyroid development, function and tumorigenesisMol. Cell. Endocrinol.201745644501:CAS:528:DC%2BC2sXit1yltQ%3D%3D10.1016/j.mce.2016.12.017
Xing, M. Molecular pathogenesis and mechanisms of thyroid cancer. Nature Rev. Cancer13 (2013).
Liyanarachchi, S. et al. Genome-wide expression screening discloses long noncoding RNAs involved in thyroid carcinogenesis. J. Clin. Endocrinol. Metab.101, (2016).
Credendino, S. C. et al. A ceRNA circuitry involving the long noncoding RNA KLHL14-AS, PAX8, and BCL2 drives thyroid carcinogenesis. Cancer Res.79, (2019).
Dai, L. et al. MiR-221, a potential prognostic biomarker for recurrence in papillary thyroid cancer. World J. Surg. Oncol.15 (2017).
Qin, J. & Luo, M. MicroRNA-221 promotes colorectal cancer cell invasion and metastasis by targeting RECK. FEBS Lett.588, (2014).
Salmena, L., Poliseno, L., Tay, Y., Kats, L. & Pandolfi, P. P. A ceRNA hypothesis: The rosetta stone of a hidden RNA language? Cell146 (2011).
Ferlay, J. et al. Estimates of worldwide burden of cancer in 2008: GLOBOCAN 2008. Int. J. Cancer127, (2010).
Rosignolo, F. et al. Identification of thyroid-associated Serum microRNA profiles and their potential use in thyroid cancer follow-up. J. Endocr. Soc.1, (2017).
Zhu, J. et al. The emerging landscapes of long noncoding RNA in thyroid carcinoma: Biological functions and clinical significance. Front. Oncol. 11 (2021).
Johnson, M. et al. NCBI BLAST: A better web interface. Nucleic Acids Res.36, (2008).
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Snippet Thyroid cancer is the most common primary endocrine malignancy in adults and its incidence is rapidly increasing. Long non-coding RNAs (lncRNAs), generally...
Abstract Thyroid cancer is the most common primary endocrine malignancy in adults and its incidence is rapidly increasing. Long non-coding RNAs (lncRNAs),...
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SubjectTerms 631/67/1459
631/67/69
692/163
Gene regulation
Humanities and Social Sciences
Malignancy
miRNA
multidisciplinary
Neuroendocrine tumors
Non-coding RNA
Nucleotides
Post-transcription
Science
Science (multidisciplinary)
Therapeutic targets
Thyroid
Thyroid cancer
Tumor suppressor genes
Tumors
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Title Identification of an interactome network between lncRNAs and miRNAs in thyroid cancer reveals SPTY2D1-AS1 as a new tumor suppressor
URI https://link.springer.com/article/10.1038/s41598-022-11725-4
https://www.ncbi.nlm.nih.gov/pubmed/35562181
https://www.proquest.com/docview/2662180790
https://www.proquest.com/docview/2664799063
https://pubmed.ncbi.nlm.nih.gov/PMC9095586
https://doaj.org/article/c28b93dd23654d67a6e525026b10e771
Volume 12
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