MicroRNA - Volume 5, Issue 3, 2016

Breast cancer among women is one of the most common carcinomas worldwide. Compared to developed countries, the breast cancer cases reported in India have boosted rapidly. At the same time, alarming statistics show that ratio of mortality cases over the total incidences is significantly high in comparison to developed world (Global Heath Estimates, WHO 2015). In recent times, several oncogenic signaling pathways have shown convergent effects on various types of cancer cell metabolism including breast cancer leading to tumor development. In 1931, German biochemist Otto Warburg revealed that cancer cells burn sugar (glycolysis) differently than normal cells. Cancer cells prefer to burn sugar over energy rich fats even when cellular oxygen conditions favor mitochondrial fat burning. Further, Warburg hypothesized that cancer is caused by mitochondrial dysfunction forcing the cells to use aerobic glycolysis instead of oxidative phosphorylation (OXPHOS). MicroRNAs (miRNAs) are critical classes of small ~22 nt non-coding endogenous RNAs implicated in gene expression regulation. To date, miRNAs have shown to regulate many cellular metabolic pathways critical for breast carcinoma patho-physiology. There is common consent that miRNAs dedicated to mitochondria and cellular metabolism have profound positive effects on breast carcinoma survival and metastasis. Therefore, in future there is huge scope for identification of miRNA types playing as a driver in mitochondria for breast tumor development. Further, several strategies to taming as well as knocking down these miRNA in breast tumor would be one of the fascinating approaches in medical sciences and cancer therapy. Here, we review updated scientific findings and possible therapeutic interventions with reference to miRNAs, mitochondria, cellular metabolism and breast carcinoma.

MicroRNAs (miRNAs) are short 19-25 nucleotide RNA molecules that impact on most biological processes by regulating the efficiency of messenger RNA (mRNA) translation. To date, most research activities have been focused on the control of miRNA expression and its functional consequences. Nonetheless, much remains unknown about the mechanisms affecting the level of specific miRNAs in the cell, a critical feature impacting their regulatory activity. This review focuses on the factors that regulate the abundance of miRNAs, including synthesis, post-transcriptional modifications, nucleases, target binding, and secretion.

The vast majority of cancer epigenetic research is now focused on micro RNA (miRNA). Though thousands of miRNA have been identified, the validation of their role is a continuous process. Aim: the aim of this paper is to comprehensively review the role of miRNA 21 in Oral cancer as a marker for diagnosis, prognosis and therapeutic target. Method: The data was collected from major search engines like PubMed, Science Direct, Cochrane library and Google Patents with the key words miRNA 21, miRNA and Oral Cancer, miRNA 21 prognostic role, miRNA therapeutic target etc. The articles published in the period of 2001 to 2016 in English language only were considered for this review. Articles in other language and focusing cancer other than oral cancer were beyond the scope of review and were excluded. Articles pertaining to Oral squamous cell carcinoma only were included in this review. The data synthesized was comprehensively categorized in to diagnostic, prognostic and therapeutic role along with targets of miRNA 21. Conclusion: miRNA 21 mainly targets the tumour suppressor genes and thus affects the process of carcinogenesis. The identification of expression of various markers associated with carcinogenesis will help in diagnosis of lesion. miRNA 21 expression is negatively correlated with prognosis of Oral cancer. The addition of nucleic acid constructer along with vector carrying anticancer agents in the promoter sequence of miRNA 21 has lot of therapeutic potential.

Cell cycle is a complex process and regulated at transcriptional, post-transcriptional and posttranslational levels. Large numbers of genes are implicated in the process. Abnormality at any stage of cell cycle may lead to diseases including cancer. To gain global view of genes associated with cell cycle, their regulation by transcription factors and microRNAs, we collected genes related to cell cycle from different databases. Experimentally validated targets of microRNAs are collected from miRTarbase. Transcription factors that bind to upstream sequences of cell cycle associated genes and microRNA genes were collected from published papers. We collected 3028 genes associated with cell cycle. These proteins belong to different protein classes like nucleic acid binding (594 proteins), transcription factors (305 proteins), cytoskeletal (232 proteins), kinases (174 proteins), phosphatase (111 proteins) and chaperones (84 proteins). Among 3028 cell cycle associated genes, 2125 genes are validated targets of 424 microRNAs; CDKN1A is a target of 46 miRNAs and miR-335 targets 301 genes. About 100 transcription factors had binding sites at potential promoter regions of 2722 genes and 329 microRNAs that target cell cycle associated genes. We presented the largest numbers of cell cycle associated genes. Many transcription factors regulate both cell cycle associated genes and the miRNAs that target cell cycle associated genes. These resources will be utilized to identify the co-regulation of cell cycle associated genes by transcription factors and miRNAs and to test specific hypothesis for cell cycle regulation and its alteration in different diseases.

Objective: microRNA assessments in biological samples can be performed by different methods that mainly rely on hybridization process, qPCR or RNA sequencing. With the aim to detect and validate microRNA biomarkers in tumor samples, we challenged the consistency of the quantitative results obtained with the different methods. Methods: We measured microRNA concentrations in several biological samples such as cultured tumor cells or tumor tissues (frozen tissues or FFPE samples) using different microRNA assay methods, in particular hybridization to AffymetrixTM arrays, qPCR and digital droplet qPCR (BioradTM) based on Taqman microRNA assays (Life TechnologiesTM). We also compared our results to other data that have been obtained with different technical approaches and available in the literature. Results: We found poor consistency for the microRNA amounts measured in the samples assayed by the different methods. Both technical platforms and microRNA assays protocols may be responsible for the observed inconsistencies. Conclusion: When assaying microRNAs for clinical purpose or fundamental researches it seems necessary to keep in mind the specific pitfalls of all the microRNA detection methods such as those we disclose here. Obviously, valid inter sample comparisons and meaningful multicenter studies can only be obtained when microRNA assessments are strictly performed with identical technical approaches and reagents.

Background: Canonical hydrogen-bonding multi-nucleotide matches of microRNAs (miRs) with mRNAs are considered as important in mRNA regulation. MiR "seed" positions 2-8 are frequently viewed as mRNA partners, but there is ample evidence for use of other (and even non-contiguous) miR parts. No detailed information is available about canonical matching, and the GC content of the matches is rarely considered, although it should have a major regulatory potential. Methods: Sequences of 2586 human miRs and of 5'utr, cds and 3'utr in 18810 human mRNAs were examined for number and GC content of contiguous Watson-Crick antisense matches of six or more nucleotides (nt) in successive windows shifted by 1 nt. Results: Frequency of the antisense matches is within all sectors similar for segments of up to 10 nt starting at positions 1-10 of miR sequences, with decrease of 3.5 to 4-fold for each 1-nt increment. Adenine and uracil rich elements (ARE-like) are very frequent in cds and 3'utr. All mRNAs have matches of up to 10 nt, and most also those of 11-15 nt. The match density is largest in 5'utr, and the match number in cds. The 5'utr and cds matches average much higher GC content than those of 3'utr. The GC content of matches is above that for the whole sector in 5'utr and cds, but lower in 3'utr. Conclusion: Human mRNA matches across miR sequences constitute a positionally similar matrix of canonical hydrogen-bonding reactivity. This presents ample opportunities for contiguous binding independent of miR position. The ubiquitous 10 to 15-nt matches could serve as binding foci. Interaction of miRs with the abundant GC-rich 5'utr and cds counterparts could be important in the regulation of mRNA-ribosome interaction as well as in mRNA disposal. The lower density and GC content of a majority of 3'utr matches could mainly support a dynamic regulation by miRs.

Background: The diagnosis of ulcerative colitis (UC) or Crohn disease (CD) can be challenging given the overlapping features. Knowledge of microRNAs in IBD has expanded recently and supports that microRNAs play an important role. This study aimed to identify novel microRNA biomarkers through comprehensive genome-wide sequencing to distinguish UC from CD. Design: Illumina next generation sequencing was performed on nondysplastic fresh-frozen colonic mucosa of the distal-most colectomy from 19 patients (10 UC and 9 CD) and 18 patients with diverticular disease serving as controls. Results: USeq software package identified 44 microRNAs with altered expression (fold change ≥2 and false discovery rate ≤0.10) compared to controls. Among them, a panel of 11 microRNAs was aberrantly expressed between UC and CD. qRT-PCR validation assays performed on frozen tissue from additional samples of UC (n=20) and CD (n=10) confirmed specific differential expression of miR-147b, miR-194-2, miR-383, miR-615 and miR-1826 (P<0.05). In addition, pathway analysis identified target genes of epithelial adhesion junction, integrin, glycolysis and cell cycle that involve in signaling pathways of TGF-β, STAT3, IL-8 and PI3L/AKT/mTOR. Conclusion: Identification of differentially expressed microRNAs in UC and CD supports the hypothesis that UC and CD are regulated by distinct pathophysiologic mechanisms. MicroRNA panels show promise as diagnostic biomarkers for the subtyping of inflammatory bowel disease.