MicroRNA - Volume 4, Issue 3, 2015

Introduction: The homeodomain-interacting protein kinase (HIPK) family consists of four evolutionarily conserved and highly related nuclear serine/threonine kinases of recent discovery. They interact with homeobox proteins and other transcription factors, as well as transcriptional coactivators or corepressors depending on the cellular context. HIPK proteins are sensors for various extracellular stimuli, which control key cellular functions such as signal transduction to downstream effectors that regulate apoptosis, embryonic development, DNA-damage response, and cellular proliferation. Thus, HIPKs are involved in proliferative diseases such as cancer and fibrosis. mRNA levels and protein stability tightly regulate expression levels of HIPKs. Methods: Here, we review recent works investigating the regulation of HIPKs expression by microRNAs (miRNAs) that are involved in the control of cell proliferation, sensitivity to chemotherapeutic drugs, epithelial-mesenchymal transition, and glucose-stimulated insulin secretion. Conclusion: It appears that HIPK family members, and their related miRNAs, may be considered as novel therapeutic targets for treating cancer, renal fibrosis and type 2 diabetes.

Background: High-altitude (HA) attracts people for its beauty and adventure. Interestingly, however, it affects the normal physiology and health due to the hypobaric hypoxic environment. Normal individuals acclimatize efficiently, but susceptible individuals encounter HA related disorders. Among these disorders, high-altitude pulmonary edema (HAPE) results into casualties. During acclimatization, body makes sequential changes in the expression of genes to counterbalance the hypobaric hypoxia induced stress. In this context, gene regulatory elements, such as transcription factors, DNA methylation and microRNAs (miRNAs) become relevant. This review, however, will primarily focus on miRNAs because of its decisive role in maintaining physiological homeostasis, both under normoxic and hypoxic conditions. Methods: Availing the literature, an in-silico study was performed to explore the anticipated role of miRNAs in HAPE pathophysiology. Results: We observed robust target based networking among the miRNAs. miR-16, 20b, 22, 206 and 17/92 were reported to have decreased expression in response to hypoxia and inhibit ion channels and increase pulmonary arterial pressure leading to vascular dysfunction and loss of cellular integrity. Whereas, miR-23b, 26a and 155 inhibit TGF signaling and contribute to increased pulmonary pressure, while miR-210 inhibits mitochondrial function. Incidentally, these physiological func- tions associate with HAPE, favoring possible role of miRNAs. Conclusion: It is concluded that the expression of individual/groups of miRNAs may change differentially under hypobaric hypoxia to modulate human physiology; however, this needs to be validated for HAPE pathophysiology.

MicroRNAs (miRNAs) are similar in importance to transcription factors and critical to confer accuracy and robustness in gene expression programs and consequently, have emerged as controllers of the immune response. On the other hand, probiotic influence over immune responses against a wide spectrum of health conditions are widely studied but the mechanism for this modulation has not yet completely elucidated. One proposed mechanism involves the receptor-mediated interaction of dendritic cells with components of the cellular membrane and/or secreted peptides of probiotics ending with the production of cytokines. However, the cytokine response elicited by dendritic cells is largely strain-dependent, and not to the same extent. The signaling pathway involved must be tightly regulated in order to be precise and effective; proteins as TNF receptor-associated factor 6 (TRAF6), Interleukin-1 receptor-associated kinase 4 (IRAK4) and Interleukin-1 receptor-associated kinase 3 (IRAK3 or IRAKM) participate in an important way in the nuclear factor kappa B (NF-ΚB) signaling pathway, which is the main cascade activated in response to probiotics. These proteins can be regulated by miRNAs and alter the immune outcome. This review discusses the current understanding on the participation of miRNAs modulating the TLR2/NF-ΚB pathway in the innate immune response mediated by probiotics.

Background: Same-nucleotide repeats (iterons) are strongly expressed in many DNA regions and RNA classes. These repeats serve importantly in association of polynucleotides and proteins, but have not been characterized in miRNAs. Methods: Iterons and nucleotide strings were quantified in currently known human miRNAs, including some comparisons with miRNAs of other species. Results: Human 5p miRNAs have significantly more G iterons than other miRNA groups. The 3p miRNAs have an inverse excess of C iterons. The miRNAs lacking functional counter-stems (which we differentiate as 5n or 3n by position in pre-miRNAs) also have a large excess of G iterons. In 5p miRNAs G and C iterons have much higher density in the seed compared to the post-seed region. This difference is lower in 5n and 3n sequences, and much lower in 3p sequences. In all groups the contiguous GC strings constitute a larger part of sequences than the AU strings. A surplus of G or C iterons and of GC strings should enable a more stable association with the target mRNAs. Conclusion: From the available evidence, the G iteron- and GC-rich miRNAs should also interact more readily with miRNA-processing and similar proteins.

Background: Heat shock factor 1 (HSF1) is the master regulator of chaperone network in mammalian cells and can protect cells from adverse effects of misfolded proteins by rapidly inducing expression of multiple heat shock proteins (HSPs) and other cytoprotective proteins. HSF1 also regulates transcription of microRNAs (miRNAs) in heat shock-dependent manner and these miRNAs are likely to regulate diverse cellular processes by acting as downstream effectors of HSF1. Methods: The study was aimed at understanding the effect of HSF1-regulated miRNAs on huntingtin expression and Huntington’s Disease (HD) pathogenesis, if any. The cumulative effect of all HSF1-regulated miRNAs on huntingtin expression was measured by quantitative real-time PCR and luciferase reporter assay and effect of miRNAs on mutant huntingtin aggregates was determined by aggregate counting assay. Results: Our study reveals that HSF1-regulated miRNAs cumulatively target huntingtin and reduce its expression in HD cell model. We also identify 4 huntingtin-targeting miRNAs viz. miR-125b, miR-146a, miR-150 and miR-214 as candidate miRNAs responsible for observed inhibitory effect of HSF1 on huntingtin expression. We further demonstrate that HSF1-regulated miRNAs together can suppress aggregates of mutant huntingtin in cell model of HD. Conclusion: We conclude that the protective effect of HSF1 in the context of HD is a consequence of synergistic induction of HSPs and HSF1-regulated huntingtin-targeting miRNAs. Moreover, the suppressive effect of HSF1-regulated miRNAs on mutant huntingtin aggregates indicates their potential as therapeutic agents for the treatment of HD.

Objective: Micro RNAs (miRNAs) are a class of non-coding regulatory RNAs. We performed a transcriptome-wide analysis of subcutaneous adipose tissue and in vitro studies to identify miRNAs and co-regulated target transcripts associated with insulin sensitivity (SI) and obesity in human. Methods: We selected 20 insulin-resistant (IR, SI=2.0±0.7) and 20 insulin-sensitive (IS, SI=7.2±2.3) subjects from a cohort of 117 metabolically characterized non-diabetic Caucasians for comparison. Results: After global profiling, 3 miRNAs had marginally different expressions between IR and IS subjects. A total of 14 miRNAs were significantly correlated with %fat mass, body mass index (BMI), or SI. The qRT-PCR validated the correlation of miR-148a-3p with BMI (r=-0.70, P=2.73X10^-6). MiRNA target filtering analysis identified DNA methyltransferase 1 (DNMT1) as one of the target genes of miR-148a-3p. DNMT1 expression in adipose tissue was positively correlated with BMI (r=0.47, p=8.42X10^-7) and was inversely correlated with miR-148a-3p (r=-0.34). Differentiation of SGBS preadipocytes showed up-regulation of miR-148a-3p and down-regulation of DNMT1 in differentiated adipocytes. After transfecting miR-148a-3p mimics into HeLa-S3 cells, DNMT1 was down-regulated, while transfection of adipose stem cells with miR-148a-3p inhibitor up-regulated DNMT1. Conclusions: Our results indicate that miR-148a-3pmediated regulation of DNMT1 expression may play a mechanistic role in obesity.

Like many other omics types, miRNomics is the topic of increased research interest. Fast accumulation of diverse biological information generates fragmented and sometimes contradictory results. There is an urgent need for development of protocols for systematic assembling, organization and integration of accumulated genomics data. In the present study we developed a protocol for connecting microRNA (miRNA) interactions into an integrative map of miRNA regulatory elements including: upstream regulators, overlapping genomic elements and downstream targets; miRNA-target interactions (MTIs). Data integration (integromics) in miRNomics enables revealing miRNA regulatory networks, obtaining new knowledge, setting more targeted hypotheses, prioritization of candidate regions, and facilitates biomarker development.

“The publishers have decided to retract the manuscript entitled “Generation of Knock Down Tools for Transcription Factor 7-Like-2 (TCF7L2) and Evaluation of its Expression Pattern in Developing Chicken Optic Tectum” published in MicroRNA, volume 4, issue 3, page numbers 209-216, 2015, for the following reasons”. • Due to conflict of interests between authors and the Principal Investigator.