Identification and bioinformatics analysis of lncRNAs in serum of patients with ankylosing spondylitis
Abstract Objectives The aim of this study was to explore the long non-coding RNA (lncRNA) expression profiles in serum of patients with ankylosing spondylitis (AS). The role of these lncRNAs in this complex autoimmune situation needs to be evaluated. Methods We used high-throughput whole-transcripto...
| Main Authors: | , , , , , , |
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| Format: | Article |
| Language: | English |
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BMC
2024-04-01
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| Series: | BMC Musculoskeletal Disorders |
| Subjects: | |
| Online Access: | https://doi.org/10.1186/s12891-024-07396-z |
| _version_ | 1797199777245429760 |
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| author | Jianqiang Kou Yongchen Bie Mingquan Liu Liqin Wang Xiangyun Liu Yuanliang Sun Xiujun Zheng |
| author_facet | Jianqiang Kou Yongchen Bie Mingquan Liu Liqin Wang Xiangyun Liu Yuanliang Sun Xiujun Zheng |
| author_sort | Jianqiang Kou |
| collection | DOAJ |
| description | Abstract Objectives The aim of this study was to explore the long non-coding RNA (lncRNA) expression profiles in serum of patients with ankylosing spondylitis (AS). The role of these lncRNAs in this complex autoimmune situation needs to be evaluated. Methods We used high-throughput whole-transcriptome sequencing to generate sequencing data from three patients with AS and three normal controls (NC). Then, we performed bioinformatics analyses to identify the functional and biological processes associated with differentially expressed lncRNAs (DElncRNAs). We confirmed the validity of our RNA-seq data by assessing the expression of eight lncRNAs via quantitative reverse transcription polymerase chain reaction (qRT-PCR) in 20 AS and 20 NC samples. We measured the correlation between the expression levels of lncRNAs and patient clinical index values using the Spearman correlation test. Results We identified 72 significantly upregulated and 73 significantly downregulated lncRNAs in AS patients compared to NC. qRT-PCR was performed to validate the expression of selected DElncRNAs; the results demonstrated that the expression levels of MALAT1:24, NBR2:9, lnc-DLK1-35:13, lnc-LARP1-1:1, lnc-AIPL1-1:7, and lnc-SLC12A7-1:16 were consistent with the sequencing analysis results. Enrichment analysis showed that DElncRNAs mainly participated in the immune and inflammatory responses pathways, such as regulation of protein ubiquitination, major histocompatibility complex class I-mediated antigen processing and presentation, MAPkinase activation, and interleukin-17 signaling pathways. In addition, a competing endogenous RNA network was constructed to determine the interaction among the lncRNAs, microRNAs, and mRNAs based on the confirmed lncRNAs (MALAT1:24 and NBR2:9). We further found the expression of MALAT1:24 and NBR2:9 to be positively correlated with disease severity. Conclusion Taken together, our study presents a comprehensive overview of lncRNAs in the serum of AS patients, thereby contributing novel perspectives on the underlying pathogenic mechanisms of this condition. In addition, our study predicted MALAT1 has the potential to be deeply involved in the pathogenesis of AS. |
| first_indexed | 2024-04-24T07:21:08Z |
| format | Article |
| id | doaj.art-9e217485dec942a9b396c9b19146a7ba |
| institution | Directory Open Access Journal |
| issn | 1471-2474 |
| language | English |
| last_indexed | 2024-04-24T07:21:08Z |
| publishDate | 2024-04-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Musculoskeletal Disorders |
| spelling | doaj.art-9e217485dec942a9b396c9b19146a7ba2024-04-21T11:03:34ZengBMCBMC Musculoskeletal Disorders1471-24742024-04-0125111010.1186/s12891-024-07396-zIdentification and bioinformatics analysis of lncRNAs in serum of patients with ankylosing spondylitisJianqiang Kou0Yongchen Bie1Mingquan Liu2Liqin Wang3Xiangyun Liu4Yuanliang Sun5Xiujun Zheng6Department of Spinal Surgery, The Affiliated Hospital of Qingdao UniversityDepartment of Spinal Surgery, The Affiliated Hospital of Qingdao UniversityDepartment of Operating Room, The Affiliated Hospital of Qingdao UniversityDepartment of Rheumatology, The Affiliated Hospital of Qingdao UniversityDepartment of Spinal Surgery, The Affiliated Hospital of Qingdao UniversityDepartment of Spinal Surgery, The Affiliated Hospital of Qingdao UniversityDepartment of Spinal Surgery, The Affiliated Hospital of Qingdao UniversityAbstract Objectives The aim of this study was to explore the long non-coding RNA (lncRNA) expression profiles in serum of patients with ankylosing spondylitis (AS). The role of these lncRNAs in this complex autoimmune situation needs to be evaluated. Methods We used high-throughput whole-transcriptome sequencing to generate sequencing data from three patients with AS and three normal controls (NC). Then, we performed bioinformatics analyses to identify the functional and biological processes associated with differentially expressed lncRNAs (DElncRNAs). We confirmed the validity of our RNA-seq data by assessing the expression of eight lncRNAs via quantitative reverse transcription polymerase chain reaction (qRT-PCR) in 20 AS and 20 NC samples. We measured the correlation between the expression levels of lncRNAs and patient clinical index values using the Spearman correlation test. Results We identified 72 significantly upregulated and 73 significantly downregulated lncRNAs in AS patients compared to NC. qRT-PCR was performed to validate the expression of selected DElncRNAs; the results demonstrated that the expression levels of MALAT1:24, NBR2:9, lnc-DLK1-35:13, lnc-LARP1-1:1, lnc-AIPL1-1:7, and lnc-SLC12A7-1:16 were consistent with the sequencing analysis results. Enrichment analysis showed that DElncRNAs mainly participated in the immune and inflammatory responses pathways, such as regulation of protein ubiquitination, major histocompatibility complex class I-mediated antigen processing and presentation, MAPkinase activation, and interleukin-17 signaling pathways. In addition, a competing endogenous RNA network was constructed to determine the interaction among the lncRNAs, microRNAs, and mRNAs based on the confirmed lncRNAs (MALAT1:24 and NBR2:9). We further found the expression of MALAT1:24 and NBR2:9 to be positively correlated with disease severity. Conclusion Taken together, our study presents a comprehensive overview of lncRNAs in the serum of AS patients, thereby contributing novel perspectives on the underlying pathogenic mechanisms of this condition. In addition, our study predicted MALAT1 has the potential to be deeply involved in the pathogenesis of AS.https://doi.org/10.1186/s12891-024-07396-zDifferentially expressed lncRNARNA sequencingSerumAnkylosing spondylitis |
| spellingShingle | Jianqiang Kou Yongchen Bie Mingquan Liu Liqin Wang Xiangyun Liu Yuanliang Sun Xiujun Zheng Identification and bioinformatics analysis of lncRNAs in serum of patients with ankylosing spondylitis BMC Musculoskeletal Disorders Differentially expressed lncRNA RNA sequencing Serum Ankylosing spondylitis |
| title | Identification and bioinformatics analysis of lncRNAs in serum of patients with ankylosing spondylitis |
| title_full | Identification and bioinformatics analysis of lncRNAs in serum of patients with ankylosing spondylitis |
| title_fullStr | Identification and bioinformatics analysis of lncRNAs in serum of patients with ankylosing spondylitis |
| title_full_unstemmed | Identification and bioinformatics analysis of lncRNAs in serum of patients with ankylosing spondylitis |
| title_short | Identification and bioinformatics analysis of lncRNAs in serum of patients with ankylosing spondylitis |
| title_sort | identification and bioinformatics analysis of lncrnas in serum of patients with ankylosing spondylitis |
| topic | Differentially expressed lncRNA RNA sequencing Serum Ankylosing spondylitis |
| url | https://doi.org/10.1186/s12891-024-07396-z |
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