Genome-wide analysis of dysregulated RNA-binding proteins and alternative splicing genes in keloid
Introduction: The pathogenesis of keloids remains unclear.Methods: In this study, we analyzed RNA-Seq data (GSE113619) of the local skin tissue of 8 keloid-prone individuals (KPI) and 6 healthy controls (HC) before and 42 days after trauma from the gene expression omnibus (GEO) database. The differe...
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Frontiers Media S.A.
2023-01-01
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| Series: | Frontiers in Genetics |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fgene.2023.1118999/full |
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| author | Zhen Zhu Shuangying Ni Shuangying Ni Jiali Zhang Jiali Zhang Ying Yuan Ying Yuan Yun Bai Xueli Yin Zhengwei Zhu Zhengwei Zhu |
| author_facet | Zhen Zhu Shuangying Ni Shuangying Ni Jiali Zhang Jiali Zhang Ying Yuan Ying Yuan Yun Bai Xueli Yin Zhengwei Zhu Zhengwei Zhu |
| author_sort | Zhen Zhu |
| collection | DOAJ |
| description | Introduction: The pathogenesis of keloids remains unclear.Methods: In this study, we analyzed RNA-Seq data (GSE113619) of the local skin tissue of 8 keloid-prone individuals (KPI) and 6 healthy controls (HC) before and 42 days after trauma from the gene expression omnibus (GEO) database. The differential alternative splicing (AS) events associated with trauma healing between KPIs and HCs were identifified, and their functional differences were analyzed by gene ontology (GO) and kyoto encyclopedia of genes and genomes (KEGG) pathways. The co-expression relationship of differentially alternative splicing genes and differentially expressed RNA binding proteins (RBPs) was established subsequently.Results: A total of 674 differential AS events between the KD42 and the KD0 and 378 differential AS events between the HD42 and the HD0 were discovered. Notably, most of the differential genes related to keloids are enriched in actin, microtubule cells, and cortical actin cytoskeletal tissue pathway. We observed a signifificant association between AS genes (EPB41, TPM1, NF2, PARD3) and trauma healing in KPIs and HCs. We also found that the differential expression of healthy controls-specifific trauma healing-related RBPs (TKT, FDPS, SAMHD1) may affect the response of HCs to trauma healing by regulating the AS of downstream trauma healing-related genes such as DCN and DST. In contrast, KPIs also has specifific differential expression of trauma healing related RBPs (S100A9, HspB1, LIMA1, FBL), which may affect the healing response of KPIs to trauma by regulating the AS of downstream trauma healing-related genes such as FN1 and TPM1.Discussion: Our results were innovative in revealing early wound healing-related genes (EPB41, TPM1, NF2, PARD3) in KPI from the perspective of AS regulated by RBPs. |
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| issn | 1664-8021 |
| language | English |
| last_indexed | 2024-04-10T20:15:19Z |
| publishDate | 2023-01-01 |
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| spelling | doaj.art-2784128af54f4ecb88a3b71c9a916b862023-01-26T05:35:01ZengFrontiers Media S.A.Frontiers in Genetics1664-80212023-01-011410.3389/fgene.2023.11189991118999Genome-wide analysis of dysregulated RNA-binding proteins and alternative splicing genes in keloidZhen Zhu0Shuangying Ni1Shuangying Ni2Jiali Zhang3Jiali Zhang4Ying Yuan5Ying Yuan6Yun Bai7Xueli Yin8Zhengwei Zhu9Zhengwei Zhu10Hangzhou Plastic Surgery Hospital, Hangzhou, ChinaDepartment of Dermatology, The First Affiliated Hospital, Institute of Dermatology, Anhui Medical University, Hefei, ChinaThe Key Laboratory of Dermatology, Ministry of Education, Anhui Medical University, Hefei, ChinaDepartment of Dermatology, The First Affiliated Hospital, Institute of Dermatology, Anhui Medical University, Hefei, ChinaThe Key Laboratory of Dermatology, Ministry of Education, Anhui Medical University, Hefei, ChinaDepartment of Dermatology, The First Affiliated Hospital, Institute of Dermatology, Anhui Medical University, Hefei, ChinaThe Key Laboratory of Dermatology, Ministry of Education, Anhui Medical University, Hefei, ChinaDepartment of Plastic Surgery, The First Affiliated Hospital, Anhui Medical University, Hefei, ChinaFunctional Experiment Center, School of Basic Medical Sciences, Anhui Medical University, Hefei, ChinaDepartment of Dermatology, The First Affiliated Hospital, Institute of Dermatology, Anhui Medical University, Hefei, ChinaThe Key Laboratory of Dermatology, Ministry of Education, Anhui Medical University, Hefei, ChinaIntroduction: The pathogenesis of keloids remains unclear.Methods: In this study, we analyzed RNA-Seq data (GSE113619) of the local skin tissue of 8 keloid-prone individuals (KPI) and 6 healthy controls (HC) before and 42 days after trauma from the gene expression omnibus (GEO) database. The differential alternative splicing (AS) events associated with trauma healing between KPIs and HCs were identifified, and their functional differences were analyzed by gene ontology (GO) and kyoto encyclopedia of genes and genomes (KEGG) pathways. The co-expression relationship of differentially alternative splicing genes and differentially expressed RNA binding proteins (RBPs) was established subsequently.Results: A total of 674 differential AS events between the KD42 and the KD0 and 378 differential AS events between the HD42 and the HD0 were discovered. Notably, most of the differential genes related to keloids are enriched in actin, microtubule cells, and cortical actin cytoskeletal tissue pathway. We observed a signifificant association between AS genes (EPB41, TPM1, NF2, PARD3) and trauma healing in KPIs and HCs. We also found that the differential expression of healthy controls-specifific trauma healing-related RBPs (TKT, FDPS, SAMHD1) may affect the response of HCs to trauma healing by regulating the AS of downstream trauma healing-related genes such as DCN and DST. In contrast, KPIs also has specifific differential expression of trauma healing related RBPs (S100A9, HspB1, LIMA1, FBL), which may affect the healing response of KPIs to trauma by regulating the AS of downstream trauma healing-related genes such as FN1 and TPM1.Discussion: Our results were innovative in revealing early wound healing-related genes (EPB41, TPM1, NF2, PARD3) in KPI from the perspective of AS regulated by RBPs.https://www.frontiersin.org/articles/10.3389/fgene.2023.1118999/fullkeloidalternative splicingtrauma healingRNA-bindig proteinsRNA-sequencing (RNA-seq) |
| spellingShingle | Zhen Zhu Shuangying Ni Shuangying Ni Jiali Zhang Jiali Zhang Ying Yuan Ying Yuan Yun Bai Xueli Yin Zhengwei Zhu Zhengwei Zhu Genome-wide analysis of dysregulated RNA-binding proteins and alternative splicing genes in keloid Frontiers in Genetics keloid alternative splicing trauma healing RNA-bindig proteins RNA-sequencing (RNA-seq) |
| title | Genome-wide analysis of dysregulated RNA-binding proteins and alternative splicing genes in keloid |
| title_full | Genome-wide analysis of dysregulated RNA-binding proteins and alternative splicing genes in keloid |
| title_fullStr | Genome-wide analysis of dysregulated RNA-binding proteins and alternative splicing genes in keloid |
| title_full_unstemmed | Genome-wide analysis of dysregulated RNA-binding proteins and alternative splicing genes in keloid |
| title_short | Genome-wide analysis of dysregulated RNA-binding proteins and alternative splicing genes in keloid |
| title_sort | genome wide analysis of dysregulated rna binding proteins and alternative splicing genes in keloid |
| topic | keloid alternative splicing trauma healing RNA-bindig proteins RNA-sequencing (RNA-seq) |
| url | https://www.frontiersin.org/articles/10.3389/fgene.2023.1118999/full |
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