Comparative Analysis of Published Database Predicting MicroRNA Binding in 3'UTR of mRNA in Diverse Species

BACKGROUND

Micro-RNAs are endogenous non-coding RNA moieties of 22-27 nucleotides that play a crucial role in the regulation of various biological processes and make them useful prognostic and diagnostic biomarkers. Discovery and experimental validation of miRNA is a laborious and time-consuming process. For early prediction, multiple bioinformatics databases are available for miRNA target prediction; however, their utility can confuse amateur researchers in selecting the most appropriate tools for their study.

OBJECTIVE

This descriptive review aimed to analyse the usability of the existing database based on the following criteria: accessibility, efficiency, interpretability, updatability, and flexibility for miRNA target prediction of 3'UTR of mRNA in diverse species so that the researchers can utilize the database most appropriate to their research.

METHODS

A systematic literature search was performed in PubMed, Google Scholar and Scopus databases up to November 2022. ≥10,000 articles found online, including ⁓130 miRNA tools, which contain various information on miRNA. Out of them, 31 databases that provide information on validated 3'UTR miRNAs target databases were included and analysed in this review.

RESULTS

These miRNA database tools are being used in varied areas of biological research to select the most suitable miRNA for their experimental validation. These databases, updated until the year 2021, consist of miRNA-related data from humans, animals, mice, plants, viruses etc. They contain 525-29806351 data entries, and information from most databases is freely available on the online platform.

CONCLUSION

Reviewed databases provide significant information, but not all information is accurate or up-to-date. Therefore, Diana-TarBase and miRWalk are the most comprehensive and up-to-date databases.

Overexpression of XRCC1 is Associated with Poor Survival in Patients with Head and Neck Squamous Carcinoma and Has Potential to Be Used as Targeted Therapy by Synthetic Lethality

Background: Head neck squamous cell carcinoma (HNSC) is globally prevalent cancer attributed to tobacco habit. Despite the significant advances in early diagnosis and treatment of HNSC chemo-radio resistance are routinely observed in patients. Aberrant DNA repair mechanisms mainly microhomology mediated DNA end joining (MMEJ) pathway causing deleterious mutations and is implicated in treatment resistance. X-ray cross complimenting group 1 (XRCC1) has recently been shown to play an essential role in MMEJ making XRCC1 a potential therapeutic target to render tumors chemo-radiosensitive. This study analyzes the correlation between the expression level of XRCC1 gene with survival, regulation by miRNA and synthetic lethality partners in HNSCC. Materials and Methods: XRCC1 gene expression was evaluated in 520 HNSC patients and 44 of normal tissues using the UALCAN (TCGA) database and its correlation with survival outcome of HNSC patients was analyzed by Kaplan-Meier plot. Infiltration of immune cells in tumors was analyzed by “Tumor-Infiltrating Immune Estimation Resource (TIMER) and promoter methylation status of XRCC1 in samples was analysed by UALCAN. STRING was used to find gene interacting partners of XRCC1.  Results: XRCC1 was significantly overexpressed in primary tumor of HNSCC and significantly increased with tumor stages and grade and associated with poor survival rate. High XRCC1 expression in HNSC was positively correlated with infiltration level of B cells naïsve, CD4+ and macrophages. Conclusion: These results indicate that XRCC1 is a prognostic marker for predicting survival in HNSC patients. Understanding how XRCC1 leads to treatment resistance and modulate immune response can lead to development of targeted therapy.

Distribution and molecular characterisation of Lactobacilli in the oral cavity of children

Background

Dental caries is a chronic and multifactorial disease mainly caused by microorganisms that are accumulated on soft and hard tissues of oral cavity. Lactobacillus is one of that kind, produces acid after metabolic breakdown of dietary sugar and reduces the pH of oral environment, resulting in teeth demineralisation or dental caries.

Aim

The present study focuses on the distribution and characterisation of lactobacilli in the oral cavity of children which are associated with dental caries formation.

Methods

Total 116 swab samples were collected from different age groups of children by swabbing the caries surface of teeth. Physiological, morphological and biochemical characteristics of Lactobacillus were analysed. Whole cell protein profiling using SDS-PAGE was also performed for their characterisation. Molecular characterisation of selected isolates was done using 16S-rRNA sequencing for identification.

Results

Total 269 isolates were successfully isolated and identified by physiological and biochemical tests according to Bergey's Manual Systematic Bacteriology, which belongs to the seven species of Lactobacillus i.e., L. acidophilus, L. casei, L. delbrueckii, L. helveticus, L. plantarum, L. rhamnosus, L. salivarius. All the isolates were further differentiated by whole cell proteins profiling and species level identification was done by 16S-rRNA gene sequencing method.

Conclusions

The present study, suggested that the occurrence of the species of Lactobacillus changes with the age of the individual, but L. rhamnosus (20.54%) and L. acidophilus (18.21%) were abundantly found in age group of 3-12 yr which could be the possible causative agent of dental caries formation in the children of Central India.