Identification of microRNA-mRNA-TF regulatory networks in periodontitis by bioinformatics analysis

ONECUT3 activates the TRIM46-NF-κB pathway to promote the development of pancreatic cancer

Pancreatic cancer (PC) remains one of the deadliest cancers, characterized by its high aggressiveness and low overall survival, with chemotherapy and immunotherapy showing limited efficacy. It is essential to investigate the molecular mechanisms driving the PC progression. In this study, we showed that One Cut homeobox 3 (ONECUT3) acted as an oncogene promoting PC progression and observed a significant increase of ONECUT3 levels in PC tissues and cells. The reduced ONECUT3 expression was positively correlated with decreased tumor volumes and weight, and the depressed proliferation, migration and invasion abilities. Mechanistically, ONECUT3 directly bound to the promoter of tripartite motif-containing 46 (TRIM46) and transcriptionally upregulated its expression. Tripartite motif (TRIM)-containing proteins have been identified as closely linked to the advancement of tumors. However, the role of TRIM46 in PC remains largely unexplored. The expression of ONECUT3 was found to be positively linked with TRIM46 in human PC tissues. The upregulation of TRIM46 rescued ONECUT3 knockdown-induced suppression of cell proliferation, migration and invasion abilities, and tumor growth in PC. TRIM46 overexpression also activated NF-κB signaling in PC cells. To sum up, ONECUT3 has been identified as a promising prognostic indicator in PC, and targeting this cancer-promoting pathway could offer an effective therapeutic approach to combat the PC progression.

The investigation of apoptosis-related genes in periodontitis

OBJECTIVES

This study aims at determination of the roles of five apoptosis-related genes, namely CASP2, CASP8, BCL2, HULC and PVT1 in the pathoetiology of periodontitis via measurement of their expressions in both peripheral blood and tissues of affected persons.

RESULTS

CASP2 was over-expressed in gingiva of patients compared with healthy subjects (RME = 24.56, P < 0.001), and in both affected females and males (RME = 30.53, P = 0.03 and RME = 20.59, P = 0.01, respectively). BCL2 was higher in affected tissues compared with controls (RME = 32.28, P < 0.001) and in affected tissues of males versus controls (RME = 69.03, P < 0.001). Finally, HULC had lower level in the blood of patients (RME = 0.21, P = 0.01) and in the blood of female patients compared with normal females (RME = 0.15, P = 0.01). Other comparisons yielded no significant results. BCL2 and CASP2 had the highest diagnostic values for separation of diseased gingival tissues from normal ones. HULC has the best values in the distinction of blood samples of affected persons from control persons. Combination of transcript levels of CASP2, CASP8, BCL2, HULC and PVT1 changed AUC to 0.84 and 0.72 in tissues and blood samples, respectively. To conclude, these genes might be regarded as putative contributors in the pathophysiology of periodontitis.

A Regulatory Circuits Analysis Tool, "miRCuit," Helps Reveal Breast Cancer Pathways: Toward Systems Medicine in Oncology

A systems medicine understanding of the regulatory molecular circuits that underpin breast cancer is essential for early cancer detection and precision/personalized medicine in clinical oncology. Transcription factors (TFs), microRNAs (miRNAs), and long non-coding RNAs (lncRNAs) control gene expression and cell biology, and by extension, serve as pillars of the regulatory circuits that determine human health and disease. We report here the development of a regulatory circuit analysis program, miRCuit, constructing 10 different types of regulatory elements involving messenger RNA, miRNA, lncRNA, and TFs. Using the miRCuit, we analyzed expression profiling data from 179 invasive ductal breast carcinoma and 51 normal tissue samples from the Gene Expression Omnibus database. We identified eight circuit types along with two special types of circuits, one of which highlighted the significant roles of lncRNA CASC15, miR-130b-3p, and TF KLF5 in breast cancer development and progression. These findings advance our understanding of the regulatory molecules associated with breast cancer. Moreover, miRCuit offers a new avenue for users to construct circuits from regulatory molecules for potential applications to decipher disease pathogenesis.

Porphyromonas gingivalis infection alters microRNA composition in extracellular vesicles

OBJECTIVES

Periodontitis, commonly associated with Porphyromonas gingivalis (Pg), involves intricate alterations of oral intercellular interactions, in which extracellular vesicles (EVs) play a pivotal role. The understanding of the miRNA profiles in the EVs derived from Pg-infected cells (Pg-EVs) remains incomplete despite acknowledging their importance in intercellular communication during periodontitis. Therefore, our objective was to identify and characterize the miRNAs enriched in Pg-EVs.

METHODS

Microarray analysis was conducted to examine the miRNA profiles in the EVs derived from Pg-infected THP-1 cells. We compared the identified miRNAs with those upregulated in the EVs after stimulation with LPS. Additionally, we explored how inhibiting TLR signaling during Pg infection affects the transcription of specific miRNAs. We investigated the unique sequence motifs specific to the miRNAs concentrated in Pg-EVs.

RESULTS

The levels of eleven miRNAs, including miR-155, were increased in Pg-EVs compared with those elevated after LPS stimulation. The Pg-induced miR-155 upregulation via TLR2 but not TLR4 signaling suggests the influence of TLR signaling on the miRNA composition of EVs. Furthermore, the miRNAs upregulated in Pg-EVs contained AGAGGG and GRGGSGC sequence motifs.

CONCLUSIONS

Our findings demonstrate that Pg-induced alterations in EV-containing miRNA composition occur in a TLR4-independent manner. Notably, the concentrated miRNAs in Pg-EVs harbor specific motifs with a high G + C content within their sequences. The upregulation of specific miRNAs in EVs under infectious conditions suggests the influence of both innate immune receptor signals and miRNA sequence characteristics.

Role of ONECUT family transcription factors in cancer and other diseases

Members of ONECUT transcription factor play an essential role in several developmental processes, however, the atypical expression of ONECUT proteins lead to numerous diseases, including cancer. ONECUT family proteins promote cell proliferation, progression, invasion, metastasis, angiogenesis, and stemness. This family of proteins interacts with other proteins such as KLF4, TGF-β, VEGFA, PRC2, SMAD3 and alters their expression involved in the regulation of various signaling pathways including Jak/Stat3, Akt/Erk, TGF-β, Smad2/3, and HIF-1α. Furthermore, ONECUT proteins are proposed as predictive biomarkers for pancreatic and gastric cancers. The present review summarizes the involvement of ONECUT family proteins in the development and progression of various human cancers and other diseases.

Identifying genes for regulating osteogenic differentiation of human periodontal ligament stem cells in inflammatory environments by bioinformatics analysis

BACKGROUND AND OBJECTIVES

Periodontitis is an immuno-inflammatory disease caused by dental plaque biofilms and inflammations. The regeneration of bone tissue in inflammatory environment is of great significance for the treatment of periodontal disease, but the specific molecular mechanism of bone formation in periodontitis still needs further exploration. The objective of this study was to identify key osteogenesis-related genes (ORGs) in periodontitis.

METHODS

We used two datasets from the Gene Expression Omnibus (GEO) database to find differentially expressed mRNAs and miRNAs, further performed Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis. Then we predicted the downstream genes of the differentially expressed miRNAs (DEMs) by the TargetScan database and established a miRNA-mRNA regulatory network. Finally, the osteogenic mechanism of periodontitis was explored through quantitative real-time PCR (qRT-PCR) by inducing inflammatory environment and osteogenic differentiation of hPDLSCs.

RESULTS

Through differential expression analysis and prediction of downstream target genes of DEMs, we created a miRNA-mRNA regulatory network consisting of 29 DEMs and 11 differentially expressed osteogenesis-related genes (DEORGs). In addition, the qRT-PCR results demonstrated that BTBD3, PLAT, AKAP12, SGK1, and GLCE expression levels were significantly upregulated, while those of TIMP3, ZCCHC14, LIN7A, DNAH6, NNT, and ITGA6 were downregulated under the dual effects of inflammatory stimulation and osteogenic induction.

CONCLUSION

DEORGs might be important factors in the osteogenic phase of periodontitis, and the miRNA-mRNA network may shed light on the clarification of the role and mechanism of osteogenesis in periodontitis and contribute to the development of novel therapeutic strategies.

MicroRNA-223 negatively regulates the osteogenic differentiation of periodontal ligament derived cells by directly targeting growth factor receptors

Background

MicroRNA (miRNA) is accepted as a critical regulator of cell differentiation. However, whether microRNA-223 (miR-223) could affect the osteogenic differentiation of periodontal ligament (PDL)-derived cells is still unknown. The aim of this study was to explore the mechanisms underlying the roles of miR-223 in the osteogenesis of PDL-derived cells in periodontitis.

Methods

Microarray analysis and real-time polymerase chain reaction (RT-PCR) were used to identify difference in miR-223 expression pattern between healthy and inflamed gingival tissue. The target genes of miR-223 were predicted based on Targetscan and selected for enrichment analyses based on Metascape database. The gain-and loss-of-function experiments were performed to discuss roles of miR-223 and growth factor receptor genes in osteogenic differentiation of PDL-derived cells. The target relationship between miR-223 and growth factor receptor genes was confirmed by a dual luciferase assay. Osteogenic differentiation of PDL-derived cells was assessed by Alizarin red staining, RT-PCR and western blot detection of osteogenic markers, including osteocalcin (OCN), osteopontin (OPN) and runt-related transcription factor 2 (Runx2).

Results

MiR-223 was significantly increased in inflamed gingival tissues and down-regulated in PDL-derived cells during osteogenesis. The expression of miR-223 in gingival tissues was positively correlated with the clinical parameters in periodontitis patients. Overexpression of miR-223 markedly inhibited PDL-derived cells osteogenesis, which was evidenced by reduced Alizarin red staining and osteogenic markers expressions. Furthermore, two growth factor receptor genes, including fibroblast growth factor receptor 2 (FGFR2) and transforming growth factor beta receptor 2 (TGFβR2), were revealed to be direct targets of miR-223 and shown to undergo up-regulation in PDL-derived cells during osteogenesis. Moreover, suppression of FGFR2 or TGFβR2 dramatically blocked PDL-derived cells osteogenic differentiation.

Conclusions

Our study provides novel evidence that miR-223 can be induced by periodontitis and acts as a negative regulator of PDL-derived cells osteogenesis by targeting two growth factor receptors (TGFβR2 and FGFR2).

Supplementary Information

The online version contains supplementary material available at 10.1186/s12967-022-03676-1.