Identification of non-coding RNA related prognosis biomarkers based on ceRNA network in thyroid cancer
Introduction: Thyroid cancer (THCA) has become a serious malignant tumor worldwide. Identification of non-coding RNA related regulators is very necessary to improve the knowledge of THCA treatment. The aim of this study was to identify novel therapeutic targets and prognosis biomarkers for predictin...
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2023-04-01
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| Series: | Frontiers in Genetics |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fgene.2023.1157438/full |
| _version_ | 1797822388804517888 |
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| author | Xin Fang Xin Fang Xiliang Chen Jingquan Gao Liquan Tong |
| author_facet | Xin Fang Xin Fang Xiliang Chen Jingquan Gao Liquan Tong |
| author_sort | Xin Fang |
| collection | DOAJ |
| description | Introduction: Thyroid cancer (THCA) has become a serious malignant tumor worldwide. Identification of non-coding RNA related regulators is very necessary to improve the knowledge of THCA treatment. The aim of this study was to identify novel therapeutic targets and prognosis biomarkers for predicting pathological characteristics and subsequently treating THCA.Methods: We investigated the alterations of miRNAs, mRNAs and lncRNAs in THCA. Functional enrichment and clustering analysis were conducted for these aberrantly expressed RNAs. Multiple interaction networks among miRNAs, mRNAs and lncRNAs were constructed and the functional modules associated with THCA patients’ prognosis were identified. Furthermore, we evaluated the prognostic roles of the important miRNAs, mRNAs and lncRNAs in THCA and investigated the regulatory potential of non-coding RNAs on immune cell infiltration.Results: We firstly identified that miR-4709-3p and miR-146b-3p could significantly classify patients into high/low risk groups, which may be potential prognosis biomarkers of THCA. Secondly, we constructed a THCA-related miRNA-mRNA network, which displayed small world network topological characters. Two THCA-related functional modules were identified from the miRNA-mRNA network by MCODE. Results showed that two modules could implicate in known cancer pathways, such as apoptosis and focal adhesion. Thirdly, a THCA-related miRNA-lncRNA network was constructed. A subnetwork of miRNA-lncRNA network showed strong prognosis effect in THCA. Fourthly, we constructed a THCA-related mRNA-lncRNA network and detected several typical lncRNA-miRNA-mRNA crosstalk, such as AC068138, BCL2, miR-21 and miR-146b, which had good prognosis effect in THCA. Immune infiltration results showed that lncRNAs LA16c−329F2, RP11−395N3, RP11−423H2, RP11−399B17 and RP11–1036E20 were high related to neutrophil and dendritic cell infiltration.Discussion: Non-coding RNA-mediated gene regulatory network has the strong regulatory potential in pathological processes of THCA. All these results could help us uncover the non-coding RNA-mediated regulatory mechanism in THCA. |
| first_indexed | 2024-03-13T10:08:18Z |
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| id | doaj.art-39c25c2b5341401f9a1b809580750996 |
| institution | Directory Open Access Journal |
| issn | 1664-8021 |
| language | English |
| last_indexed | 2024-03-13T10:08:18Z |
| publishDate | 2023-04-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Genetics |
| spelling | doaj.art-39c25c2b5341401f9a1b8095807509962023-05-22T08:10:37ZengFrontiers Media S.A.Frontiers in Genetics1664-80212023-04-011410.3389/fgene.2023.11574381157438Identification of non-coding RNA related prognosis biomarkers based on ceRNA network in thyroid cancerXin Fang0Xin Fang1Xiliang Chen2Jingquan Gao3Liquan Tong4Department of General Surgery II, Daqing Oilfield General Hospital, Daqing, ChinaDepartment of Rehabilitation, Beijing Rehabilitation Hospital of Capital Medical University, Beijing, ChinaDepartment of Rehabilitation, Beijing Rehabilitation Hospital of Capital Medical University, Beijing, ChinaDepartment of Nursing Sciences, Faculty of Medicine and Health, Lishui University, Lishui, ChinaDepartment of General Surgery, The Fifth Affiliated Hospital of Harbin Medical University, Daqing, ChinaIntroduction: Thyroid cancer (THCA) has become a serious malignant tumor worldwide. Identification of non-coding RNA related regulators is very necessary to improve the knowledge of THCA treatment. The aim of this study was to identify novel therapeutic targets and prognosis biomarkers for predicting pathological characteristics and subsequently treating THCA.Methods: We investigated the alterations of miRNAs, mRNAs and lncRNAs in THCA. Functional enrichment and clustering analysis were conducted for these aberrantly expressed RNAs. Multiple interaction networks among miRNAs, mRNAs and lncRNAs were constructed and the functional modules associated with THCA patients’ prognosis were identified. Furthermore, we evaluated the prognostic roles of the important miRNAs, mRNAs and lncRNAs in THCA and investigated the regulatory potential of non-coding RNAs on immune cell infiltration.Results: We firstly identified that miR-4709-3p and miR-146b-3p could significantly classify patients into high/low risk groups, which may be potential prognosis biomarkers of THCA. Secondly, we constructed a THCA-related miRNA-mRNA network, which displayed small world network topological characters. Two THCA-related functional modules were identified from the miRNA-mRNA network by MCODE. Results showed that two modules could implicate in known cancer pathways, such as apoptosis and focal adhesion. Thirdly, a THCA-related miRNA-lncRNA network was constructed. A subnetwork of miRNA-lncRNA network showed strong prognosis effect in THCA. Fourthly, we constructed a THCA-related mRNA-lncRNA network and detected several typical lncRNA-miRNA-mRNA crosstalk, such as AC068138, BCL2, miR-21 and miR-146b, which had good prognosis effect in THCA. Immune infiltration results showed that lncRNAs LA16c−329F2, RP11−395N3, RP11−423H2, RP11−399B17 and RP11–1036E20 were high related to neutrophil and dendritic cell infiltration.Discussion: Non-coding RNA-mediated gene regulatory network has the strong regulatory potential in pathological processes of THCA. All these results could help us uncover the non-coding RNA-mediated regulatory mechanism in THCA.https://www.frontiersin.org/articles/10.3389/fgene.2023.1157438/fullthyroid cancerprognosis markermiRNAslncRNAnetwork |
| spellingShingle | Xin Fang Xin Fang Xiliang Chen Jingquan Gao Liquan Tong Identification of non-coding RNA related prognosis biomarkers based on ceRNA network in thyroid cancer Frontiers in Genetics thyroid cancer prognosis marker miRNAs lncRNA network |
| title | Identification of non-coding RNA related prognosis biomarkers based on ceRNA network in thyroid cancer |
| title_full | Identification of non-coding RNA related prognosis biomarkers based on ceRNA network in thyroid cancer |
| title_fullStr | Identification of non-coding RNA related prognosis biomarkers based on ceRNA network in thyroid cancer |
| title_full_unstemmed | Identification of non-coding RNA related prognosis biomarkers based on ceRNA network in thyroid cancer |
| title_short | Identification of non-coding RNA related prognosis biomarkers based on ceRNA network in thyroid cancer |
| title_sort | identification of non coding rna related prognosis biomarkers based on cerna network in thyroid cancer |
| topic | thyroid cancer prognosis marker miRNAs lncRNA network |
| url | https://www.frontiersin.org/articles/10.3389/fgene.2023.1157438/full |
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