Identification and characterization of the ferroptosis-related ceRNA network in irreversible pulpitis
BackgroundThe role of ferroptosis in irreversible pulpitis (IP) remains unclear. The competing endogenous RNA (ceRNA) theory that has been widely investigated is rarely used studied in IP. Hub lncRNAs selected from a ceRNA network may provide a novel hypothesis for the interaction of ferroptosis and...
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Frontiers Media S.A.
2023-05-01
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| Series: | Frontiers in Immunology |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fimmu.2023.1198053/full |
| _version_ | 1797823740002697216 |
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| author | Qiuyan Xie Qiuyan Xie Hongwen Yu Hongwen Yu Zining Liu Zining Liu Bangyi Zhou Fuchun Fang Wei Qiu Hongle Wu |
| author_facet | Qiuyan Xie Qiuyan Xie Hongwen Yu Hongwen Yu Zining Liu Zining Liu Bangyi Zhou Fuchun Fang Wei Qiu Hongle Wu |
| author_sort | Qiuyan Xie |
| collection | DOAJ |
| description | BackgroundThe role of ferroptosis in irreversible pulpitis (IP) remains unclear. The competing endogenous RNA (ceRNA) theory that has been widely investigated is rarely used studied in IP. Hub lncRNAs selected from a ceRNA network may provide a novel hypothesis for the interaction of ferroptosis and IP.MethodsDifferentially expressed genes (DEGs) were intersected with 484 ferroptosis markers to identify differentially expressed ferroptosis-related genes (DE-FRGs). Functional analysis and protein−protein interaction (PPI) networks were constructed to reveal the functions of DE-FRGs. Then, coexpression analyses were conducted between DE-FRGs and DElncRNAs to define ferroptosis-related DElncRNAs (FR-DElncRNAs). Predictions of DE-FRG- and FR-DElncRNA-related miRNAs were obtained, and members of both groups were selected. Additionally, two ceRNA networks consisting of FR-DElncRNAs, miRNAs and DE-FRGs from upregulated and downregulated groups were built. Finally, the hub lncRNAs of the ceRNA networks were used for immuno-infiltration analysis and qPCR verification.ResultsAccording to the results of PCA and clustering analysis, 5 inflamed and 5 healthy pulp tissue samples were selected for analysis. The intersection of DEGs with 484 ferroptosis marker genes identified 72 DE-FRGs. The response to stimulus, cellular process, signaling, localization, and biological regulation pathways related to DE-FRGs were enriched. In total, 161 downregulated and 40 upregulated FR-DElncRNAs were chosen by coexpression analysis for further investigation. The MultimiR package and starBase were used to predict miRNAs of DE-FRGs and FR-DElncRNAs, respectively. The upregulated ceRNA network contained 2 FR-DElncRNAs (↑), 19 miRNAs (↓) and 22 DE-FRGs (↑). The downregulated network contained 44 FR-DElncRNAs (↓), 251 miRNAs (↑) and 10 DE-FRGs (↓). Six hub lncRNAs were identified based on the MCC method (LUCAT1 and AC106897.1 ↑; LINC00943, AL583810.1, AC068888.1, and AC125257.1↓). In addition, strong relationships between hub lncRNAs and immune cells were shown by immune infiltration analysis. Finally, validated by qPCR assays of the pulp tissue of IP patients, the expression levels in clinical samples were consistent with the microarray data.ConclusionTwo ceRNA networks were comprehensively constructed, and 6 hub lncRNAs were identified. These genes provide novel insights into the relationship between ferroptosis and IP. Intriguingly, the LINC00943/hsa-miR-29a-3p/PDK4 axis was deemed to be the key node in this network. |
| first_indexed | 2024-03-13T10:28:26Z |
| format | Article |
| id | doaj.art-f286fc6e99fc415d915de71d810d2d6f |
| institution | Directory Open Access Journal |
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| language | English |
| last_indexed | 2024-03-13T10:28:26Z |
| publishDate | 2023-05-01 |
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| spelling | doaj.art-f286fc6e99fc415d915de71d810d2d6f2023-05-19T05:00:08ZengFrontiers Media S.A.Frontiers in Immunology1664-32242023-05-011410.3389/fimmu.2023.11980531198053Identification and characterization of the ferroptosis-related ceRNA network in irreversible pulpitisQiuyan Xie0Qiuyan Xie1Hongwen Yu2Hongwen Yu3Zining Liu4Zining Liu5Bangyi Zhou6Fuchun Fang7Wei Qiu8Hongle Wu9Department of Endodontics, Stomatological Hospital, School of Stomatology, Southern Medical University, Guangzhou, ChinaDepartment of Stomatology, Nanfang Hospital, Southern Medical University, Guangzhou, ChinaDepartment of Endodontics, Stomatological Hospital, School of Stomatology, Southern Medical University, Guangzhou, ChinaDepartment of Stomatology, Nanfang Hospital, Southern Medical University, Guangzhou, ChinaDepartment of Endodontics, Stomatological Hospital, School of Stomatology, Southern Medical University, Guangzhou, ChinaDepartment of Stomatology, Nanfang Hospital, Southern Medical University, Guangzhou, ChinaDepartment of Stomatology, Nanfang Hospital, Southern Medical University, Guangzhou, ChinaDepartment of Stomatology, Nanfang Hospital, Southern Medical University, Guangzhou, ChinaDepartment of Stomatology, Nanfang Hospital, Southern Medical University, Guangzhou, ChinaDepartment of Endodontics, Stomatological Hospital, School of Stomatology, Southern Medical University, Guangzhou, ChinaBackgroundThe role of ferroptosis in irreversible pulpitis (IP) remains unclear. The competing endogenous RNA (ceRNA) theory that has been widely investigated is rarely used studied in IP. Hub lncRNAs selected from a ceRNA network may provide a novel hypothesis for the interaction of ferroptosis and IP.MethodsDifferentially expressed genes (DEGs) were intersected with 484 ferroptosis markers to identify differentially expressed ferroptosis-related genes (DE-FRGs). Functional analysis and protein−protein interaction (PPI) networks were constructed to reveal the functions of DE-FRGs. Then, coexpression analyses were conducted between DE-FRGs and DElncRNAs to define ferroptosis-related DElncRNAs (FR-DElncRNAs). Predictions of DE-FRG- and FR-DElncRNA-related miRNAs were obtained, and members of both groups were selected. Additionally, two ceRNA networks consisting of FR-DElncRNAs, miRNAs and DE-FRGs from upregulated and downregulated groups were built. Finally, the hub lncRNAs of the ceRNA networks were used for immuno-infiltration analysis and qPCR verification.ResultsAccording to the results of PCA and clustering analysis, 5 inflamed and 5 healthy pulp tissue samples were selected for analysis. The intersection of DEGs with 484 ferroptosis marker genes identified 72 DE-FRGs. The response to stimulus, cellular process, signaling, localization, and biological regulation pathways related to DE-FRGs were enriched. In total, 161 downregulated and 40 upregulated FR-DElncRNAs were chosen by coexpression analysis for further investigation. The MultimiR package and starBase were used to predict miRNAs of DE-FRGs and FR-DElncRNAs, respectively. The upregulated ceRNA network contained 2 FR-DElncRNAs (↑), 19 miRNAs (↓) and 22 DE-FRGs (↑). The downregulated network contained 44 FR-DElncRNAs (↓), 251 miRNAs (↑) and 10 DE-FRGs (↓). Six hub lncRNAs were identified based on the MCC method (LUCAT1 and AC106897.1 ↑; LINC00943, AL583810.1, AC068888.1, and AC125257.1↓). In addition, strong relationships between hub lncRNAs and immune cells were shown by immune infiltration analysis. Finally, validated by qPCR assays of the pulp tissue of IP patients, the expression levels in clinical samples were consistent with the microarray data.ConclusionTwo ceRNA networks were comprehensively constructed, and 6 hub lncRNAs were identified. These genes provide novel insights into the relationship between ferroptosis and IP. Intriguingly, the LINC00943/hsa-miR-29a-3p/PDK4 axis was deemed to be the key node in this network.https://www.frontiersin.org/articles/10.3389/fimmu.2023.1198053/fullirreversible pulpitisferroptosisceRNAlncRNAbioinformatics |
| spellingShingle | Qiuyan Xie Qiuyan Xie Hongwen Yu Hongwen Yu Zining Liu Zining Liu Bangyi Zhou Fuchun Fang Wei Qiu Hongle Wu Identification and characterization of the ferroptosis-related ceRNA network in irreversible pulpitis Frontiers in Immunology irreversible pulpitis ferroptosis ceRNA lncRNA bioinformatics |
| title | Identification and characterization of the ferroptosis-related ceRNA network in irreversible pulpitis |
| title_full | Identification and characterization of the ferroptosis-related ceRNA network in irreversible pulpitis |
| title_fullStr | Identification and characterization of the ferroptosis-related ceRNA network in irreversible pulpitis |
| title_full_unstemmed | Identification and characterization of the ferroptosis-related ceRNA network in irreversible pulpitis |
| title_short | Identification and characterization of the ferroptosis-related ceRNA network in irreversible pulpitis |
| title_sort | identification and characterization of the ferroptosis related cerna network in irreversible pulpitis |
| topic | irreversible pulpitis ferroptosis ceRNA lncRNA bioinformatics |
| url | https://www.frontiersin.org/articles/10.3389/fimmu.2023.1198053/full |
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