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Identification of pain-related long non-coding RNAs for pulpitis prediction

Springer Nature
Clinical Oral Investigations
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Objectives We investigated the recently generated RNA-sequencing dataset of pulpitis to identify the potential pain-related lncRNAs for pulpitis prediction. Materials and methods Differential analysis was performed on the gene expression profile between normal and pulpitis samples to obtain pulpitis-related genes. The co-expressed gene modules were identified by weighted gene coexpression network analysis (WGCNA). Then the hypergeometric test was utilized to screen pain-related core modules. The functional enrichment analysis was performed on the up- and down-regulated genes in the core module of pulpitis pain to explore the underlying mechanisms. A pain-related lncRNA-based classification model was constructed using LASSO. Consensus clustering and gene set variation analysis (GSVA) on the infiltrating immunocytes was used for pulpitis subtyping. miRanda predicts miRNA-target relationship, which was filtered by expression correlation. Hallmark pathway and enrichment analysis was performed to investigate the candidate target pathways of the lncRNAs. Results A total of 1830 differential RNAs were identified in pulpitis. WGCNA explored seven co-expressed modules, among which the turquoise module is pain-related with hypergeometric test. The up-regulated genes were significantly enriched in immune response related pathways. Down-regulated genes were significantly enriched in differentiation pathways. Eight lncRNAs in the pain-related module were related to inflammation. Among them, MIR181A2HG was downregulated while other seven lncRNAs were upregulated in pulpitis. The LASSO classification model revealed that MIR181A2HG and LINC00426 achieved outstanding predictive performances with perfect ROC-AUC score (AUC = 1). We differentiated the pulpitis samples into two progression subtypes and MIR181A2HG is a progressive marker for pulpitis. The miRNA-mRNA-lncRNA regulatory network of pulpitis pain was constructed, with GATA3 as a key transcription factor. NF-kappa B signaling pathway is a candidate pathway impacted by these lncRNAs. Conclusions PCED1B-AS1, MIAT, MIR181A2HG, LINC00926, LINC00861, LINC00528, LINC00426 and ITGB2-AS1 may be potential markers of pulpitis pain. A two-lncRNA signature of LINC00426 and MIR181A2HG can accurately predict pulpitis, which could facilitate the molecular diagnosis of pulpitis. GATA3 might regulate these lncRNAs and downstream NF-kappa B signaling pathway. Clinical relevance This study identified potential pain-related lncRNAs with underlying molecular mechanism analysis for the prediction of pulpitis. The classification model based on lncRNAs will facilitate the early diagnosis of pulpitis.
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RESEARCH
Clinical Oral Investigations (2025) 29:75
https://doi.org/10.1007/s00784-025-06164-0
Yongjie Tan and Ying He contributed equally to this work.
Extended author information available on the last page of the article
Abstract
Objectives We investigated the recently generated RNA-sequencing dataset of pulpitis to identify the potential pain-related
lncRNAs for pulpitis prediction.
Materials and methods Dierential analysis was performed on the gene expression prole between normal and pulpitis
samples to obtain pulpitis-related genes. The co-expressed gene modules were identied by weighted gene coexpression
network analysis (WGCNA). Then the hypergeometric test was utilized to screen pain-related core modules. The functional
enrichment analysis was performed on the up- and down-regulated genes in the core module of pulpitis pain to explore
the underlying mechanisms. A pain-related lncRNA-based classication model was constructed using LASSO. Consensus
clustering and gene set variation analysis (GSVA) on the inltrating immunocytes was used for pulpitis subtyping. miRanda
predicts miRNA-target relationship, which was ltered by expression correlation. Hallmark pathway and enrichment analy-
sis was performed to investigate the candidate target pathways of the lncRNAs.
Results A total of 1830 dierential RNAs were identied in pulpitis. WGCNA explored seven co-expressed modules,
among which the turquoise module is pain-related with hypergeometric test. The up-regulated genes were signicantly
enriched in immune response related pathways. Down-regulated genes were signicantly enriched in dierentiation path-
ways. Eight lncRNAs in the pain-related module were related to inammation. Among them, MIR181A2HG was downregu-
lated while other seven lncRNAs were upregulated in pulpitis. The LASSO classication model revealed that MIR181A2HG
and LINC00426 achieved outstanding predictive performances with perfect ROC-AUC score (AUC = 1). We dierentiated
the pulpitis samples into two progression subtypes and MIR181A2HG is a progressive marker for pulpitis. The miRNA-
mRNA-lncRNA regulatory network of pulpitis pain was constructed, with GATA3 as a key transcription factor. NF-kappa B
signaling pathway is a candidate pathway impacted by these lncRNAs.
Conclusions PCED1B-AS1, MIAT, MIR181A2HG, LINC00926, LINC00861, LINC00528, LINC00426 and ITGB2-AS1
may be potential markers of pulpitis pain. A two-lncRNA signature of LINC00426 and MIR181A2HG can accurately predict
pulpitis, which could facilitate the molecular diagnosis of pulpitis. GATA3 might regulate these lncRNAs and downstream
NF-kappa B signaling pathway.
Clinical relevance This study identied potential pain-related lncRNAs with underlying molecular mechanism analysis for
the prediction of pulpitis. The classication model based on lncRNAs will facilitate the early diagnosis of pulpitis.
Keywords Pulpitis · Pain · lncRNA · Prediction · Bioinformatic analysis
Received: 26 June 2024 / Accepted: 15 January 2025 / Published online: 22 January 2025
© The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature 2025
Identication of pain-related long non-coding RNAs for pulpitis
prediction
YongjieTan1· YingHe2· YuexuanXu1· XilinQiu1· GuanruLiu1· LingxianLiu1· YeJiang2· MingyueLi1·
WeijunSun1,3· ZiqiangXie4· YonghuiHuang1· XinChen1· XuechaoYang2,5
1 3
Content courtesy of Springer Nature, terms of use apply. Rights reserved.
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