Differential lncRNA/mRNA Expression Profiling and Functional Network Analyses in Bmp2 Deletion of Mouse Dental Papilla Cells

Abstract

Bmp2 is essential for dentin development and formation. Bmp2 conditional knock-out (KO) mice display a similar tooth phenotype of dentinogenesis imperfecta (DGI). To elucidate a foundation for subsequent functional studies of cross talk between mRNAs and lncRNAs in Bmp2-mediated dentinogenesis, we investigated the profiling of lncRNAs and mRNAs using immortalized mouse dental Bmp2 flox/flox (iBmp2fx/fx) and Bmp2 knock-out (iBmp2ko/ko) papilla cells. RNA sequencing was implemented to study the expression of the lncRNAs and mRNAs. Quantitative real-time PCR (RT-qPCR) was used to validate expressions of lncRNAs and mRNAs. The Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases were used to predict functions of differentially expressed genes (DEGs). Protein–protein interaction (PPI) and lncRNA–mRNA co-expression network were analyzed by using bioinformatics methods. As a result, a total of 22 differentially expressed lncRNAs (16 downregulated vs 6 upregulated) and 227 differentially expressed mRNAs (133 downregulated vs. 94 upregulated) were identified in the iBmp2ko/ko cells compared with those of the iBmp2fx/fx cells. RT-qPCR results showed significantly differential expressions of several lncRNAs and mRNAs which were consistent with the RNA-seq data. GO and KEGG analyses showed differentially expressed genes were closely related to cell differentiation, transcriptional regulation, and developmentally relevant signaling pathways. Moreover, network-based bioinformatics analysis depicted the co-expression network between lncRNAs and mRNAs regulated by Bmp2 in mouse dental papilla cells and symmetrically analyzed the effect of Bmp2 during dentinogenesis via coding and non-coding RNA signaling.

Correlation analysis of human papillomavirus E6/E7 mRNA detection with diagnosis, prognosis and recurrence risk in patients with cervical epithelioma

“…Both CIN and cervical cancer are known to be associated with HPV infection, which can be considered as the early lesion of cervical cancer[ 23 , 24 ]. The transformation of CIN to cervical cancer requires a process, but not all CIN will transition to high-risk areas; some CIN patients can return to normal state[ 25 , 26 ] through autoimmune regulation without surgical treatment. The clinical morphological evaluation method is commonly used for the clinical morphological evaluation method of cervical lesions[ 27 , 28 ].…”

Expression profiling of mRNA and functional network analyses of genes regulated by human papilloma virus E6 and E7 proteins in HaCaT cells

“…The expression of E6 and E7 resulted in the detection of many DEGs using RNA-seq and RT-qPCR. Fourteen of these hub genes were linked to cell adhesion ( Chute, 2006 ; Teicher and Fricker, 2010 ; Paolillo and Schinelli, 2019 ; Marotta et al, 2021 ), leukocyte–endothelial migration ( Yakovlev et al, 2019 ; Morein et al, 2020 ; Yan et al, 2021 ), stem cell signaling ( Davidson et al, 2007 ; Bijlmakers, 2009 ), and epithelial–mesenchymal transition ( Pastushenko et al, 2021 ; Wang et al, 2021 ). Based on these experimental and bioinformatics analyses, we hypothesized that HPV16 E6 and E7 signaling causes differential mRNA expression through direct or indirect mRNA pathways that regulate cell adhesion and chemokine secretion.…”

“…With the increasing prevalence of Illumina technology in recent years, RNA-sequencing (RNA-Seq) technology has been effectively used in biomedical research ( Tao et al, 2021 ; Wang et al, 2021 ). The carcinogenetic effect of E6 and E7 is apparent, but molecules that are induced by these proteins in HaCaT cells still need to be researched, and high-throughput sequencing would contribute vastly to this question.…”

BMP Signaling Pathway in Dentin Development and Diseases

“…Loss of Bmp-2, Bmp-4, Bmp-7, and Bmp-9 causes severe impairment of dentinogenesis, enlarged dental pulp cavity, wide predentin, thin dentin, tooth attrition, delayed root eruption, and impairment of odontoblast differentiation [ 33 , 34 , 36 , 37 , 38 , 43 , 44 , 46 , 47 , 299 , 300 , 301 , 302 ]. Using bioinformatics software, this study showed that the Bmp-2 signal regulates cell differentiation, transcriptional regulation, and developmentally relevant signaling pathways [ 303 ]. Teeth in mice lacking Bmp-2, Bmp-4, and Bmp-9 showed reduced tooth-related gene expression, including phosphorylated Smad1/5/8, Alp, Collα1, Dlx3, Dmp1, Dspp, Osx, and Runx2 [ 32 , 36 , 37 , 38 , 39 , 46 , 47 , 302 ].…”