Vitamin D and the RNA transcriptome: more than mRNA regulation

The GRCh37.p13 primary assembly of the human genome contains 20805 protein coding mRNA, and 37147 non-protein coding genes and pseudogenes that as a result of RNA processing and editing generate 196501 gene transcripts. Given the size and diversity of the human transcriptome, it is timely to revisit what is known of VDR function in the regulation and targeting of transcription.Early transcriptomic studies using microarray approaches focused on the protein coding mRNA that were regulated by the VDR, usually following treatment with ligand. These studies quickly established the approxamte size, and surprising diversity of the VDR transcriptome, revealing it to be highly heterogenous and cell type and time dependent. With the discovery of microRNA, investigators also considered VDR regulation of these non-protein coding RNA. Again, cell and time dependency has emerged. Attempts to integrate mRNA and miRNA regulation patterns are beginning to reveal patterns of co-regulation and interaction that allow for greater control of mRNA expression, and the capacity to govern more complex cellular events. As the awareness of the diversity of non-coding RNA increases, it is evident that VDR actions are mediated through these molecules also. Key knowledge gaps remain over the VDR transcriptome. The causes for the cell and type dependent transcriptional heterogenetiy remain enigmatic. ChIP-Seq approaches have confirmed that VDR binding choices differ very significantly by cell type, but as yet the underlying causes distilling VDR binding choices are unclear. Similarly, it is clear that many of the VDR binding sites are non-canonical in nature but again the mechanisms underlying these interactions are unclear. Finally, although alternative splicing is clearly a very significant process in cellular transcriptional control, the lack of RNA-Seq data centered on VDR function are currently limiting the global assessment of the VDR transcriptome. VDR focused research that complement

A Role for the PPARγ in Cancer Therapy

In 1997, the first published reports highlighted PPARγ as a novel cancer therapeutic target regulating differentiation of cancer cells. A subsequent flurry of papers described these activities more widely and fuelled further enthusiasm for differentiation therapy, as the ligands for the PPARγ were seen as well tolerated and in several cases well-established in other therapeutic contexts. This initial enthusiasm and promise was somewhat tempered by contradictory findings in several murine cancer models and equivocal trial findings. As more understanding has emerged in recent years, a renaissance has occurred in targeting PPARγ within the context of either chemoprevention or chemotherapy. This clarity has arisen in part through a clearer understanding of PPARγ biology, how the receptor interacts with other proteins and signaling events, and the mechanisms that modulate its transcriptional actions. Equally greater translational understanding of this target has arisen from a clearer understanding of in vivo murine cancer models. Clinical exploitation will most likely require precise and quantifiable description of PPARγ actions, and resolution of which targets are the most beneficial to target combined with an understanding of the mechanisms that limits its anticancer effectiveness

Regulation of the human p21((waf1/cip1)) gene promoter via multiple binding sites for p53 and the vitamin D(3) receptor

The main regulator of the human tumor suppresser gene p21((waf1/cip1)) is the transcription factor p53, but more recently it has been suggested to be a primary anti-proliferative target for the nuclear receptor VDR in the presence of its ligand 1α,25-dihydroxyvitamin D(3) (1α,25(OH)(2)D(3)). To identify VDR responding regions, we analyzed 20 overlapping regions covering the first 7.1 kb of the p21((waf1/cip1)) promoter in MCF-7 human breast cancer cells using chromatin immuno-precipitation assays (ChIP) with antibodies against p53 and VDR. We confirmed two known p53 binding regions at approximate positions −1400 and −2300 and identified a novel site at position −4500. In addition, we found three VDR-associated promoter regions at positions −2300, −4500 and −6900, i.e. two regions showed binding for both p53 and VDR. In silico screening and in vitro binding assays using recombinant and in vitro translated proteins identified five p53 binding sites within the three p53-positive promoter regions and also five 1α,25(OH)(2)D(3) response elements within the three VDR-positive regions. Reporter gene assays confirmed the expected responsiveness of the respective promoter regions to the p53 inducer 5-fluorouracil and 1α,25(OH)(2)D(3). Moreover, re-ChIP assays confirmed the functionality of the three 1α,25(OH)(2)D(3)-reponsive promoter regions by monitoring simultaneous occupancy of VDR with the co-activator proteins CBP, SRC-1 and TRAP220. Taken together, we demonstrated that the human p21((waf1/cip1)) gene is a primary 1α,25(OH)(2)D(3)-responding gene with at least three VDR binding promoter regions, in two of which also p53 co-localizes

PseudoFuN: Deriving functional potentials of pseudogenes from integrative relationships with genes and microRNAs across 32 cancers

BACKGROUND: Long thought "relics" of evolution, not until recently have pseudogenes been of medical interest regarding regulation in cancer. Often, these regulatory roles are a direct by-product of their close sequence homology to protein-coding genes. Novel pseudogene-gene (PGG) functional associations can be identified through the integration of biomedical data, such as sequence homology, functional pathways, gene expression, pseudogene expression, and microRNA expression. However, not all of the information has been integrated, and almost all previous pseudogene studies relied on 1:1 pseudogene-parent gene relationships without leveraging other homologous genes/pseudogenes. RESULTS: We produce PGG families that expand beyond the current 1:1 paradigm. First, we construct expansive PGG databases by (i) CUDAlign graphics processing unit (GPU) accelerated local alignment of all pseudogenes to gene families (totaling 1.6 billion individual local alignments and >40,000 GPU hours) and (ii) BLAST-based assignment of pseudogenes to gene families. Second, we create an open-source web application (PseudoFuN [Pseudogene Functional Networks]) to search for integrative functional relationships of sequence homology, microRNA expression, gene expression, pseudogene expression, and gene ontology. We produce four "flavors" of CUDAlign-based databases (>462,000,000 PGG pairwise alignments and 133,770 PGG families) that can be queried and downloaded using PseudoFuN. These databases are consistent with previous 1:1 PGG annotation and also are much more powerful including millions of de novo PGG associations. For example, we find multiple known (e.g., miR-20a-PTEN-PTENP1) and novel (e.g., miR-375-SOX15-PPP4R1L) microRNA-gene-pseudogene associations in prostate cancer. PseudoFuN provides a "one stop shop" for identifying and visualizing thousands of potential regulatory relationships related to pseudogenes in The Cancer Genome Atlas cancers. CONCLUSIONS: Thousands of new PGG associations can be explored in the context of microRNA-gene-pseudogene co-expression and differential expression with a simple-to-use online tool by bioinformaticians and oncologists alike

Non-coding and Coding Transcriptional Profiles Are Significantly Altered in Pediatric Retinoblastoma Tumors.

Retinoblastoma is a rare pediatric tumor of the retina, caused by the homozygous loss of the Retinoblastoma 1 (RB1) tumor suppressor gene. Previous microarray studies have identified changes in the expression profiles of coding genes; however, our understanding of how non-coding genes change in this tumor is absent. This is an important area of research, as in many adult malignancies, non-coding genes including LNC-RNAs are used as biomarkers to predict outcome and/or relapse. To establish a complete and in-depth RNA profile, of both coding and non-coding genes, in Retinoblastoma tumors, we conducted RNA-seq from a cohort of tumors and normal retina controls. This analysis identified widespread transcriptional changes in the levels of both coding and non-coding genes. Unexpectedly, we also found rare RNA fusion products resulting from genomic alterations, specific to Retinoblastoma tumor samples. We then determined whether these gene expression changes, of both coding and non-coding genes, were also found in a completely independent Retinoblastoma cohort. Using our dataset, we then profiled the potential effects of deregulated LNC-RNAs on the expression of neighboring genes, the entire genome, and on mRNAs that contain a putative area of homology. This analysis showed that most deregulated LNC-RNAs do not act locally to change the transcriptional environment, but potentially function to modulate genes at distant sites. From this analysis, we selected a strongly down-regulated LNC-RNA in Retinoblastoma, DRAIC, and found that restoring DRAIC RNA levels significantly slowed the growth of the Y79 Retinoblastoma cell line. Collectively, our work has generated the first non-coding RNA profile of Retinoblastoma tumors and has found that these tumors show widespread transcriptional deregulation

Актуальные вопросы совершенствования медико-психологической помощи детям с пороками грудной клетки

Врожденные деформации грудной клетки в виде воронкообразной и килевидной встречаются более чем у 0,3% населения. Воронкообразная деформация грудной клетки (ВДГК) встречается в 5-7 раз чаще, чем килевидная деформация грудной клетки (КДГК). Общепризнанным методом лечения деформации грудной клетки является исключительно хирургическая коррекция

Сучасний погляд на проблему бронхолегеневої дисплазії та відкритої артеріальної протоки у недоношених новонароджених

У статті відображені сучасні аспекти патогенезу та клініки бронхолегеневої дисплазії у недоношених новонароджених. Надано аналіз впливу різних антенатальних та інтранатальних факторів на формування та перебіг бронхолегеневої дисплазії. Окремо розглянуто проблему відкритої артеріальної протоки, патогенез, механізми впливу на розвиток бронхолегеневої дисплазії та обтяження її стану. Розглянуто клінічні та патогенетичні апекти функціонування відкритої артеріальної протоки у недоношених новонароджених. . The article reflects the modern aspects of the pathogenesis and clinic of bronchopulmonary dysplasia in premature infants. An analysis of the impact of various antenatal and intranatal factors on the development and course of bronchopulmonary dysplasia. Separately the problem of patent ductus arteriosus. Pathogenesis, mechanisms of influence on the development of bronchopulmonary dysplasia and encumbrance of her condition. Discussed the clinical and pathogenetic apects functioning of patent ductus arteriosus in preterm infants

Epigenetic distortion to VDR transcriptional regulation in prostate cancer cells

AbstractThe current study aimed to examine the gene specific mechanisms by which the actions of the vitamin D receptor (VDR) are distorted in prostate cancer. Transcriptional responses toward the VDR ligand, 1α,25(OH)2D3, were examined in non-malignant prostate epithelial cells (RWPE-1) and compared to the 1α,25(OH)2D3-recalcitrant prostate cancer cells (PC-3). Time resolved transcriptional studies for two VDR target genes revealed selective attenuation and repression of VDR transcriptional responses in PC-3 cells. For example, responses in PC-3 cells revealed suppressed responsiveness of IGFBP3 and G0S2. Furthermore, Chromatin Immunoprecipitation (ChIP) assays revealed that suppressed transcriptional responses in PC-3 cells of IGFBP3 and G0S2 were associated with selective VDR-induced NCOR1 enrichment at VDR-binding regions on target-gene promoter regions. We propose that VDR inappropriately recruits co-repressors in prostate cancer cells. Subsequent direct and indirect mechanisms may induce local DNA methylation and stable transcriptional silencing. Thus a transient epigenetic process mediated by co-repressor binding, namely, the control of H3K9 acetylation, is distorted to favor a more stable epigenetic event, namely DNA methylation.This article is part of a Special Issue entitled ‘Vitamin D Workshop’

Design principles of nuclear receptor signaling: how complex networking improves signal transduction

Nuclear receptors often function in the cytoplasm.A triple conveyor belt pumps ligand (signal) into the nucleus and onto the DNA.The active export of importins enhances signaling to the nucleus.Sharing a single nuclear pore may reduce rather than increase crosstalk