Genomewide miRNA profiling of oral lichenoid disorders and oral squamous cell carcinoma

Applying Machine Learning for Enhanced MicroRNA Analysis: A Companion Risk Tool for Oral Squamous Cell Carcinoma in Standard Care Incisional Biopsy

Machine learning analyses within the realm of oral cancer outcomes are relatively underexplored compared to other cancer types. This study aimed to assess the performance of machine learning algorithms in identifying oral cancer patients, utilizing microRNA expression data. In this study, we implemented this approach using a panel of oral cancer-associated microRNAs sourced from standard incisional biopsy specimens to identify cases of oral squamous cell carcinomas (OSCC). For the model development process, we used a dataset comprising 30 OSCC and 30 histologically normal epithelium (HNE) cases. We initially trained a logistic regression prediction model using 70 percent of the dataset, while reserving the remaining 30 percent for testing. Subsequently, the model underwent hyperparameter tuning resulting in enhanced performance metrics. The hyperparameter-tuned model exhibited high accuracy (0.894) and ROC AUC (0.898) in predicting OSCC. Testing the model on cases of potentially malignant disorders (OPMDs) revealed that leukoplakia with mild dysplasia was predicted as having a high risk of progressing to OSCC, emphasizing machine learning's advantage over histopathology in detecting early molecular changes. These findings underscore the necessity for further refinement, incorporating a broader set of variables to enhance the model's predictive capabilities in assessing the risk of oral potentially malignant disorders.

Genetic linkage analysis of head and neck cancer in a Spanish family

OBJECTIVES

To describe the genetic variants that may be associated with the development of head and neck cancer (HNC) and functionally validating the molecular implications.

MATERIALS AND METHODS

A prospective observational study was carried out on a family of 3 generations in which 3 members had developed HNC. Peripheral blood sample was taken in a routine procedure for exome sequencing in one relative and genotyping in the remaining twelve relatives. For the functional analysis all-trans retinoic acid (atRA) was extracted from saliva and serum and measured using ultra-performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS). The presence of HPV-DNA.

RESULTS

None of the patients smoked or consumed alcohol. The presence of HPV DNA was not detected in any of the biopsied samples. A total amount of 6 members out of 13 (46.15%) carried out the same mutation of CYP26B1 (2p13.2; G>T). The mean plasma concentration of atRA was 3.3109 ± 1.4791 pg/mL for the study family and 4.7370 ± 1.5992 pg/mL for the controls (p = 0.042).

CONCLUSION

Lower levels of atRA were confirmed in the study family, which may open the way to the possible relationship between the polymorphism CYP26B1 (2p13.2; G>T) and HNC.

The paradigm of miRNA and siRNA influence in Oral-biome

Short nucleotide sequences like miRNA and siRNA have attracted a lot of interest in Oral-biome investigations. miRNA is a small class of non-coding RNA that regulates gene expression to provide effective regulation of post-transcription. On contrary, siRNA is 21-25 nucleotide dsRNA impairing gene function post-transcriptionally through inhibition of mRNA for homologous dependent gene silencing. This review highlights the application of miRNA in oral biome including oral cancer, dental implants, periodontal diseases, gingival fibroblasts, oral submucous fibrosis, radiation-induced oral mucositis, dental Pulp, and oral lichenoid disease. Moreover, we have also discussed the application of siRNA against the aforementioned disease along with the impact of miRNA and siRNA to the various pathways and molecular effectors pertaining to the dental diseases. The influence of upregulation and downregulation of molecular effector post-treatment with miRNA and siRNA and their impact on the clinical setting has been elucidated. Thus, the mentioned details on application of miRNA and siRNA will provide a novel gateway to the scholars to not only mitigate the long-lasting issue in dentistry but also develop new theragnostic approaches.

Mir-29a Promotes the Migration of Bone Marrow Mesenchymal Stem Cells to Oral Squamous Cell Carcinoma Cells

Oral squamous cell carcinoma (OSCC) is a tumor in the oral cavity and around oral mucosa. Mir-29a level was differentially expressed in OSCC patients. However, whether its exact role and function in OSCC remains to be further elucidated. Our study investigated the effect of Mir-29a on the migration of bone marrow mesenchymal stem cells (BMSCs) to oral squamous cell carcinoma cells (OSCCs). Mir-29a level was measured in OSCCs and BMSCs by real-time quantitative PCR and its relationship with Panc-1 was verified by dual luciferase reporter gene. After up-regulation of Mir-29a or treatment with Panc-1 siRNA, BMSCs migration to OSCCs was assessed by transwell assay and Panc-1 and Mir-29a were measure. Mir-29a level was downregualted in OSCCs and Panc-1 was upregulated in BMSCs. Panc-1 and Mir-29a was negatively correlated and Mir-29a could bind and target Panc-1. Down-regulation of Panc-1 inhibited the migration of BMSCs to OSCCs and elevated Mir-29a level promoted cell migration. After co-transfection of Mir-29a inhibitor and Panc-1 siRNA, the inhibited cell migration function can be restored. In conclusion, Mir-29a promotes the migration of BMSCs to OSCCs through targeting Panc-1.

Co-Culture of MSCs with miR-496 Prompts Epithelial-Mesenchymal Transformation of Oral Squamous Cell Carcinoma (OSCC)

This study discusses the molecular mechanism of co-culture of MSCs with miR-496 in the EMT of OSCC. miR-496 expression in OSCC tissues and cells was detected by qRT-PCR. The MSCs+si-NC, MSCs+pc-DNA-NC, MSCs+si-miR-496, MSCs+pc-DNA-miR-496 was transfected into SCC-PKUs to analyze cell apoptosis, proliferation and clone formation as well as the expression of proteins related with EMT. miR-496 in OSCC tissues was elevated and positively related with the clinical stage of OSCC patients. The cell activity and invasive ability of SCC-PKU was increased after co-culture of MSCs and pc-DNA-miR-496 along with increased expression of EMT-related proteins. However, all above changes were reversed after treatment with MSCs and si-miR-496. In conclusion, co-culture of MSCs and miR-495 prompts the occurrence and development of OSCC through regulating EMT processes, indicating that they might be novel targets for the treatment of OSCC.

miR-653 Induces Bone Marrow Mesenchymal Stem Cells Proliferation via Activating Epithelial-Mesenchymal Transition in Oral Squamous Cell Carcinoma

This study intends to assess miR-653’s expression in MSCs and OSCC and discuss molecular biological mechanism of changes of EMT in MSCs through activating miR-653 in OSCC. miR-653 expression in MSCs and OSCC was detected. si-miR-653 was transfected into MSCs followed by analysis of cell proliferation by CCK-8 and clone formation assay, cell apoptosis and cycle by FCM, and the changes of transcription factor as ZEB1 and Snail by qRT-PCR. miR-653 expression in OSCC cell was up-regulated significantly from the result of q-RT-PCR detection. The proliferation of MSCs induced by miR-653 was restrained and apoptotic rate was increased after treatment with si-miR-653 along with stagnated cycle of G1/G0 staging cell. The expression of transcription factor of EMT type as ZEB1 and Snail was elevated significantly after intervention using si-miR-653. In conclusion, the proliferation of OSCC could be induced by MSCs through activation with miR-653 which might be through regulation of EMT process.

Validation of microRNA expression profile in Oral Lichenoid Disease through cytological samples

Background

To validate oral exfoliative cytology in the analysis of the microRNA expression profile in Oral Lichenoid Disease (OLD).

Material and Methods

The expression of 13 microRNAs identified and presented by our group in a previous study was analyzed in 26 cases, 16 diagnosed as OLD and 10 controls with no oral mucosal pathology. Cytological samples from the oral mucosa obtained using an Orcellex toothbrush were analyzed using RT-qPCR and TaqMan microRNA assays.

Results

The aberrant expression was validated for 2 microRNAs (miR-146a-5p and miR-7-1-3p) of those previously recognized in the biopsy study.

Conclusions

This is the first time that oral exfoliative cytology is validated in a study of the alterations of the expression of microRNAs in OLD. The alteration of miR-146a and miR-7 compared to controls was validated. These microRNAs are associated with both inflammatory and carcinogenic phenomena that are involved in the etiopathogenesis of this potentially malignant oral disorder.

Key words:microRNAs, lichen planus, epigenetics, cytological techniques.

miRNAs expression of oral squamous cell carcinoma patients: Validation of two putative biomarkers

microRNA expression patterns have provided new directions in the search of biomarkers with prognostic value and even in the search of novel therapeutic targets for several neoplasms. Specifically, miRNAs profiling in oral squamous cell carcinoma (OSCC) represents a web of intrigue in the study of oral carcinogenesis. The objective of the present study was twofold:The first study phase comprised case-control groups: A) 8 OSCC-affected patients and 8 healthy controls. Microarray technology (Affymetrix miRNA Array Plate 4.1) was used for miRNAs expression profile. Deregulated miRNAs were studied using Diana Tools miRPath 3.0 to associate miRNA targets with molecular pathways via Kyoto Encyclopedia of Genes and Genomes (KEGG). In a second phase, 2 miRNAs chosen for the subsequent RT-qPCR validation were studied in a second OSSC cohort (n = 8).Microarray analysis identified 80 deregulated miRNAs (35 over-expressed and 45 under-expressed). Two miRNAs (miR-497-5p and miR-4417) were chosen for further validation via RT-qPCR. Prognostic analysis did not ascertain relevant relation between miR-497-5p or miR-4417 expression and clinical or pathological parameters, except high miR-4417 in the case of nodular affectation (P = .035) and diminished miR-497-5p radiotherapy-treated patients (P = .05). KEGG analysis revealed that deregulated miRNAs were implicated in several biological pathways such as Proteoglycans in cancer.Our data suggest an altered miRNAs profiling in OSCC-affected patients. We have verified the altered expression of miR-497-5p and miR-4417 in OSCC samples and related the deregulated miRNAs with the 'proteoglycans in cancer' pathway. Further longitudinal studies with large samples are warranted to confirm the present findings.

MicroRNA Microarray-Based Identification of Involvement of miR-155 and miR-19a in Development of Oral Lichen Planus (OLP) by Modulating Th1/Th2 Balance via Targeting eNOS and Toll-Like Receptor 2 (TLR2)

Background

A wide range of microRNAs (miRNAs) have been shown to play a significant role in disease regulation. The objective of this study was to explore the role of miR-155 and miR-19a in the regulation of oral lichen planus (OLP).

Material/Methods

Microarray assay, real-time PCR, Western blot assay, computational analysis, luciferase assay, ELISA, and immunohistochemistry analysis were carried out to investigate the role of miR-155 and miR-19a in OLP.

Results

According to microarray assay and real-time PCR results, the expression of miR-155 was most significantly decreased among the 16 candidate miRNAs in the OLP group, whereas the expression of miR-19a was most significantly increased. MiR-155 and miR-19a directly targeted endothelial nitric oxide synthase (eNOS) and TLR2, respectively, since only the cells co-transfected with miR-155/wild-type eNOS 3′UTR or cells co-transfected with miR-19a/wild-type TLR2 3′UTR exhibited decreased luciferase activity. In addition, the expression of TLR2 was highly upregulated in OLP, whereas the expression of eNOS was significantly downregulated. A negative correlation was found between miR-19a and TLR2 mRNA, with a coefficient value of −0.40. Similarly, a negative correlation was found between miR-155 and eNOS mRNA, with a coefficient value of −0.54. A lower level of NO, IL-4, IL-5, and IL-10 was observed in OLP, which was also accompanied by a higher level of TNF-α and IFN-γ. Finally, the upregulation in miR-155 directly decreased the expression of eNOS and further inhibited the production of NO. Downregulation of miR-19a directly increased the expression of TLR2. The inhibition of NO production and the enhancement in TLR2 expression synergistically increased the production of TNF-α and IFN-γ, while decreasing the levels of IL-4, IL-5, and IL-10.

Conclusions

In this study, the peripheral blood mononuclear cells (PBMCs) from subjects with or without OLP were collected and their gene expression profiles were compared. It was found that OLP changed the expression profile of miR-155 and miR-19a, which in turn directly affected the production of eNOS and TLR2, respectively. In addition, by synergistically inducing an imbalance between Th1 and Th2, the simultaneous deregulation of miR-155/eNOS and miR-19a/TLR2 was responsible for an elevated risk of OLP.

Predicting the Presence of Oral Squamous Cell Carcinoma Using Commonly Dysregulated MicroRNA in Oral Swirls

Oral swirls are a noninvasive, rapidly collected source of salivary microRNA (miRNA) potentially useful in the early detection of disease states, particularly oral squamous cell carcinoma (OSCC). The aim of this study was to predict the presence of OSCC using a panel of OSCC-related dysregulated miRNA found in oral swirls, identified jointly in data from formalin-fixed paraffin-embedded (FFPE) and fresh-frozen specimens. Next-generation sequencing (NGS) was used to determine miRNA fold changes in FFPE OSCC specimens relative to histologically normal epithelium. These data were placed with NGS of fresh-frozen tissue data of The Cancer Genome Atlas database to select a panel of commonly dysregulated miRNA. This panel was then analyzed by RT-qPCR in RNA extracted from oral swirls collected from 30 patients with OSCC and 30 controls. Upregulation of miR-31 and miR-21 and downregulation of miR-99a, let-7c, miR-125b, and miR-100 were found between OSCC and controls in both FFPE and fresh-frozen samples. These miRNAs were studied in a training set of 15 OSCC versus 15 control oral swirls to develop a dysregulation score [AUC, 0.95; 95% confidence interval (CI), 0.88-1.03] and classification tree. A test cohort of 15 OSCC versus 15 control oral swirls yielded a dysregulation score AUC of 0.86 (95% CI, 0.79-1.00) with the classification tree identifying 100% (15/15) of OSCC and 67% (10/15) of controls. This study debuts the use of OSCC-associated miRNA, commonly dysregulated in both FFPE and frozen specimens, in oral swirls to indicate the presence of OSCC with high accuracy. Cancer Prev Res; 11(8); 491-502. ©2018 AACR.

MicroRNAs expression profile in solid and unicystic ameloblastomas

OBJECTIVES

Odontogenic tumors (OT) represent a specific pathological category that includes some lesions with unpredictable biological behavior. Although most of these lesions are benign, some, such as the ameloblastoma, exhibit local aggressiveness and high recurrence rates. The most common types of ameloblastoma are the solid/multicystic (SA) and the unicystic ameloblastoma (UA); the latter considered a much less aggressive entity as compared to the SA. The microRNA system regulates the expression of many human genes while its deregulation has been associated with neoplastic development. The aim of the current study was to determine the expression profiles of microRNAs present in the two most common types of ameloblastomas.

MATERIAL & METHODS

MicroRNA expression profiles were assessed using TaqMan® Low Density Arrays (TLDAs) in 24 samples (8 SA, 8 UA and 8 control samples). The findings were validated using quantitative RTqPCR in an independent cohort of 19 SA, 8 UA and 19 dentigerous cysts as controls.

RESULTS

We identified 40 microRNAs differentially regulated in ameloblastomas, which are related to neoplastic development and differentiation, and with the osteogenic process. Further validation of the top ranked microRNAs revealed significant differences in the expression of 6 of them in relation to UA, 7 in relation to SA and 1 (miR-489) that was related to both types.

CONCLUSION

We identified a new microRNA signature for the ameloblastoma and for its main types, which may be useful to better understand the etiopathogenesis of this neoplasm. In addition, we identified a microRNA (miR-489) that is suggestive of differentiating among solid from unicystic ameloblastoma.

The role of microRNAs in oral lichenoid disorders. Systematic review

Background

Certain changes in the microRNA expression are considered to be associated with chronic inflammatory processes and with the malignant transformation of oral potentially malignant disorders. The purpose of this systematic review is to update the existing data on the aberrant microRNA expression profiles identified in oral lichenoid disease (OLD).

Material and Methods

A search in PubMed-Medline and Scopus was performed on the English literature published between 2010 and August 2016 using the following keywords: oral lichenoid disease, oral lichen planus and microRNA.

Results

Originally, 25 articles were considered, of which 12 case-control articles were selected according to the inclusion/exclusion criteria.

Conclusions

OLD seems to have altered microRNA expression profile. Certain altered microRNAs (146a, 155) may be useful as biomarkers for this disorder. More studies including larger number of cases are needed in order to study further on the biological processes and on the regulation pathways of these altered microRNAs.

Key words:microRNAs, oral lichenoid disease, oral lichen planus.

Integrating microRNA and messenger RNA expression profiles in a rat model of deep vein thrombosis

Deep vein thrombosis (DVT) is a disease involving multiple genes and systems. MicroRNAs (miRNAs) represent a class of non-coding small RNAs that post-transcriptionally suppress their target genes. The expression patterns of miRNA and messenger RNA (mRNA) in DVT remain poorly characterized. The aim of the present study was to evaluate miRNA and mRNA expression profiles in a stasis-induced DVT rat model. Male SD rats were randomly divided into three groups as follows: DVT, sham and control. The inferior vena cava (IVC) of rats was ligated to construct stasis-induced DVT models. Rats were sacrificed three days after ligation, and morphological changes in the vein tissues were observed by hematoxylin and eosin and Masson staining. The miRNA and mRNA expression profiles were evaluated by microarrays, followed by bioinformatics analysis. The microarray analysis identified 22 miRNAs and 487 mRNAs that were significantly differentially expressed between the experimental and control groups, and between the experimental and sham groups, but not between the control and sham groups (P≤0.05; ≥2.0-fold change). By subsequent bioinformatics analysis, a 19 miRNA-98 mRNAs network was constructed in the stasis-induced DVT rat model. Notably, the majority of these miRNAs and mRNAs are reported to be expressed by endothelial cells (ECs) and are associated with the function of ECs. The results provide evidence indicating that the regulatory association of miRNA and mRNA points to key roles played by ECs in thrombosis. These findings advance our understanding of the molecular regulatory mechanisms underlying the pathophysiology of DVT.