High‐throughput transcriptomic profiling of mRNAs and lncRNAs in the dermatomyositis muscle by RNA sequencing
Abstract Background Dermatomyositis (DM) is an idiopathic inflammatory myopathy (IIM). In this study, we investigated the mRNAs and long noncoding RNAs (lncRNAs) in muscle biopsy specimens that are differentially expressed among patients with DM, patients with other IIM, and healthy controls (HCs)....
| Main Authors: | , , , , |
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| Format: | Article |
| Language: | English |
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Wiley
2023-09-01
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| Series: | Rheumatology & Autoimmunity |
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| Online Access: | https://doi.org/10.1002/rai2.12078 |
| _version_ | 1797672447094292480 |
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| author | Ke Li Yubao Ma Shanchun Zhang Rui Ban Qiang Shi |
| author_facet | Ke Li Yubao Ma Shanchun Zhang Rui Ban Qiang Shi |
| author_sort | Ke Li |
| collection | DOAJ |
| description | Abstract Background Dermatomyositis (DM) is an idiopathic inflammatory myopathy (IIM). In this study, we investigated the mRNAs and long noncoding RNAs (lncRNAs) in muscle biopsy specimens that are differentially expressed among patients with DM, patients with other IIM, and healthy controls (HCs). Methods In total, three patients with DM, 10 patients with other IIM, and three HCs were included. Muscle biopsy specimens were collected for RNA‐sequencing. Gene ontology and pathway analyses were employed to characterize the biological processes and signaling pathways. Results Compared with HCs, 372 differentially expressed mRNAs were identified within the DM group, including 275 upregulated and 97 downregulated ones. Moreover, 692 differentially expressed lncRNAs were identified in the DM group compared with HCs, of which 407 were upregulated and 285 were downregulated. Bioinformatic analysis indicated that the type‐I interferon signaling pathway and biological processes of innate immunity were significantly influenced by the differentially expressed mRNAs. Notably, 11 of the top 20 upregulated mRNAs were involved in the type‐I interferon signaling pathway. Reverse transcription polymerase chain reaction analysis verified the RNA‐sequencing data. Target gene prediction analysis suggested that the lncRNA NONHSAG043573.2 potentially targeting transporter associated with antigen processing 1, a key regulator of interferon signaling genes, might play an important role in the pathogenesis of DM. Conclusions Our study assessed the transcriptomic profiles of differentially expressed mRNAs and lncRNAs in the DM muscle tissue and revealed that the upregulated mRNAs are significantly involved in the innate immune response and the type‐I interferon signaling pathway, which might play important roles in the pathogenesis of DM. |
| first_indexed | 2024-03-11T21:30:11Z |
| format | Article |
| id | doaj.art-bf805dcba49040f9bf6f2200b9992c9e |
| institution | Directory Open Access Journal |
| issn | 2767-1429 |
| language | English |
| last_indexed | 2024-03-11T21:30:11Z |
| publishDate | 2023-09-01 |
| publisher | Wiley |
| record_format | Article |
| series | Rheumatology & Autoimmunity |
| spelling | doaj.art-bf805dcba49040f9bf6f2200b9992c9e2023-09-27T10:22:43ZengWileyRheumatology & Autoimmunity2767-14292023-09-013316617810.1002/rai2.12078High‐throughput transcriptomic profiling of mRNAs and lncRNAs in the dermatomyositis muscle by RNA sequencingKe Li0Yubao Ma1Shanchun Zhang2Rui Ban3Qiang Shi4Department of Neurology, The Second Medical Center Chinese PLA General Hospital Beijing ChinaDepartment of Neurology, The First Medical Center Chinese PLA General Hospital Beijing ChinaDepartment of Neurology, The Second Medical Center Chinese PLA General Hospital Beijing ChinaDepartment of Neurology The First Affiliated Hospital of Tsinghua University Beijing ChinaDepartment of National Clinical Research Center of Geriatrics Disease Chinese PLA General Hospital Beijing ChinaAbstract Background Dermatomyositis (DM) is an idiopathic inflammatory myopathy (IIM). In this study, we investigated the mRNAs and long noncoding RNAs (lncRNAs) in muscle biopsy specimens that are differentially expressed among patients with DM, patients with other IIM, and healthy controls (HCs). Methods In total, three patients with DM, 10 patients with other IIM, and three HCs were included. Muscle biopsy specimens were collected for RNA‐sequencing. Gene ontology and pathway analyses were employed to characterize the biological processes and signaling pathways. Results Compared with HCs, 372 differentially expressed mRNAs were identified within the DM group, including 275 upregulated and 97 downregulated ones. Moreover, 692 differentially expressed lncRNAs were identified in the DM group compared with HCs, of which 407 were upregulated and 285 were downregulated. Bioinformatic analysis indicated that the type‐I interferon signaling pathway and biological processes of innate immunity were significantly influenced by the differentially expressed mRNAs. Notably, 11 of the top 20 upregulated mRNAs were involved in the type‐I interferon signaling pathway. Reverse transcription polymerase chain reaction analysis verified the RNA‐sequencing data. Target gene prediction analysis suggested that the lncRNA NONHSAG043573.2 potentially targeting transporter associated with antigen processing 1, a key regulator of interferon signaling genes, might play an important role in the pathogenesis of DM. Conclusions Our study assessed the transcriptomic profiles of differentially expressed mRNAs and lncRNAs in the DM muscle tissue and revealed that the upregulated mRNAs are significantly involved in the innate immune response and the type‐I interferon signaling pathway, which might play important roles in the pathogenesis of DM.https://doi.org/10.1002/rai2.12078dermatomyositisinnate immuneISG15lncRNARNA‐sequencingtransporter associated with antigen processing 1 (TAP1) |
| spellingShingle | Ke Li Yubao Ma Shanchun Zhang Rui Ban Qiang Shi High‐throughput transcriptomic profiling of mRNAs and lncRNAs in the dermatomyositis muscle by RNA sequencing Rheumatology & Autoimmunity dermatomyositis innate immune ISG15 lncRNA RNA‐sequencing transporter associated with antigen processing 1 (TAP1) |
| title | High‐throughput transcriptomic profiling of mRNAs and lncRNAs in the dermatomyositis muscle by RNA sequencing |
| title_full | High‐throughput transcriptomic profiling of mRNAs and lncRNAs in the dermatomyositis muscle by RNA sequencing |
| title_fullStr | High‐throughput transcriptomic profiling of mRNAs and lncRNAs in the dermatomyositis muscle by RNA sequencing |
| title_full_unstemmed | High‐throughput transcriptomic profiling of mRNAs and lncRNAs in the dermatomyositis muscle by RNA sequencing |
| title_short | High‐throughput transcriptomic profiling of mRNAs and lncRNAs in the dermatomyositis muscle by RNA sequencing |
| title_sort | high throughput transcriptomic profiling of mrnas and lncrnas in the dermatomyositis muscle by rna sequencing |
| topic | dermatomyositis innate immune ISG15 lncRNA RNA‐sequencing transporter associated with antigen processing 1 (TAP1) |
| url | https://doi.org/10.1002/rai2.12078 |
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