Single nucleotide polymorphisms in microRNAs action as biomarkers for breast cancer

BreVamiR3': A comprehensive database for breast cancer-associated genetic variations in miRNA and 3' UTR of their target genes

Breast cancer (BC) is a multifactorial disease where microRNA (miRNA)-mediated dysregulated gene expression plays a pivotal role in tumorigenesis, progression, and clinical outcomes. Genetic variation, particularly SNPs in miRNA sequences and the 3' untranslated regions (3'UTRs) of their target genes, can disrupt miRNA-mRNA interactions, leading to altered gene expression. Despite several existing databases providing insights into various aspects of miRNAs and their target genes in association with the development of the disease. Still, there remains a critical gap in a unified, BC-specific repository that integrates SNPs in miRNAs, their target genes, and associated molecular mechanisms. To address this, we developed BreVamiR3' (Breast cancer-associated genetic Variations in miRNA and 3'UTR of their target genes), a novel, freely accessible database (https://brevamir3.web.app/index.html). BreVamiR3' features comprehensive and curated data on 500 miRNAs and 828 target genes associated with BC, including experimentally validated SNPs, chromosomal loci, expression profiles, BC subtypes, signaling pathways, and classifications of genes i.e. oncogene, tumor suppressor, or both. Unique features of BreVamiR3' include detailed annotations of SNPs disrupting miRNA-target interactions, subtype-specific miRNA expression, visualization of miRNA-chromosomal distributions and their experimental validation. Chromosome 19 harbours the highest number of BC-associated miRNAs, while target genes such as CCND1, KRAS, and ERBB2 demonstrate extensive miRNA regulation. By integrating genetic variations with functional and clinical relevance, BreVamiR3' provides a single platform to explore miRNA-mediated regulatory networks, their genetic variation, and downstream signaling pathways in BC. This database serves as a powerful resource for researchers, enabling exploration of miRNA-gene interactions, genetic variation, and their role in pathogenesis of BC and diverse clinical outcomes.

mirSNPs as Potential Colorectal Cancer Biomarkers: A Systematic Review

Colorectal cancer (CRC) is the third most common neoplasm in the world and the second with the highest mortality rate. Single nucleotide polymorphisms (SNPs) in microRNA (miRNA) genes known as mirSNPs may be related to dysregulated miRNA expression in several neoplasms. This systematic review aims to investigate studies that investigate SNPs located in regions of miRNA genes that influence their expression and are associated with CRC, as well as their potential as biomarkers for the disease, based on the available literature. For this, searches were performed in public databases, including MEDLINE/PubMed, Embase, Web of Science, and Scopus. The rigorous review of the PRISMA 2020 guidelines and the methodological quality of these studies was assessed using the Newcastle-Ottawa scale and the Mixed Methods Assessment Tool. Of the 175 studies identified, 26 were considered eligible: 18 of them highlighted mirSNPs as potential biomarkers of risk and prognosis for CRC; 4 studies suggested a protective role; 1 study linked mirSNPs to treatment; 3 studies found no relevant evidence. These results highlight the importance of conducting further research on the topic, given the potential of these biomarkers to contribute to risk assessment, prognosis, and the development of therapeutic strategies for patients with CRC.

MicroRNAs: Potential prognostic and theranostic biomarkers in chronic lymphocytic leukemia

Small noncoding ribonucleic acids called microRNAs coordinate numerous critical physiological and biological processes such as cell division, proliferation, and death. These regulatory molecules interfere with the function of many genes by binding the 3'-UTR region of target mRNAs to inhibit their translation or even degrade them. Given that a large proportion of miRNAs behave as either tumor suppressors or oncogenes, any genetic or epigenetic aberration changeing their structure and/or function could initiate tumor formation and development. An example of such cancers is chronic lymphocytic leukemia (CLL), the most prevalent adult leukemia in Western nations, which is caused by unregulated growth and buildup of defective cells in the peripheral blood and lymphoid organs. Genetic alterations at cellular and molecular levels play an important role in the occurrence and development of CLL. In this vein, it was noted that the development of this disease is noticeably affected by changes in the expression and function of miRNAs. Many studies on miRNAs have shown that these molecules are pivotal in the prognosis of different cancers, including CLL, and their epigenetic alterations (e.g., methylation) can predict disease progression and response to treatment. Furthermore, miRNAs are involved in the development of drug resistance in CLL, and targeting these molecules can be considered a new therapeutic approach for the treatment of this disease. MiRNA screening can offer important information on the etiology and development of CLL. Considering the importance of miRNAs in gene expression regulation, their application in the diagnosis, prognosis, and treatment of CLL is reviewed in this paper.

In silico Analysis of Single Nucleotide Polymorphisms Associated with MicroRNA Regulating 5-fluorouracil Resistance in Colorectal Cancer

Background:

Due to the broad influence and reversible nature of microRNA (miRNA) on the expression and regulation of target genes, researchers suggest that miRNAs and single nucleotide polymorphisms (SNPs) in miRNA genes interfere with 5-fluorouracil (5-FU) drug resistance in colorectal cancer chemotherapy.

Methods:

Computational assessment and cataloging of miRNA gene polymorphisms that target mRNA transcripts directly or indirectly through regulation of 5-FU chemoresistance in CRC were screened out by applying various universally accessible datasets such as miRNA SNP3.0 software.

Results:

1255 SNPs in 85 miRNAs affecting 5-FU resistance (retrieved from literature) were detected. Computational analysis showed that 167 from 1255 SNPs alter microRNA expression levels leading to inadequate response to 5-FU resistance in CRC. Among these 167 SNPs, 39 were located in the seed region of 25/85 miRNA and were more critical than other SNPs. Has-miR-320a-5p with 4 SNP in seed region was miRNA with the most number of SNPs. On the other hand, it has been identified that proteoglycan in cancer, adherents junction, ECM-receptor interaction, Hippo signaling pathway, TGF-beta signaling cascade, biosynthesis of fatty acid, and fatty acid metabolism were the most important pathways targeted by these 85 predicted miRNAs.

Conclusion:

Our data suggest 39 SNPs in the seed region of 25 miRNAs as catalog in miRNA genes that control the 5-FU resistance in CRC. These data also identify the most important pathways regulated by miRNA.