Abstract 1824: The non-coding RNA landscape of lung, liver and breast cancer reveals novel tumor-associated ncRNAs, concerted regulation and unexpected tissue specificity

Non-coding RNA profiles in cancer are largely unknown which greatly impedes the discovery of functionally important ncRNAs in tumorigenesis as well as the generation of genome-wide libraries.

Here, we define the ncRNA expression landscape of lung, breast and liver cancer as well as normal tissue from the respective organs in a large set of primary patient samples (N=150). These samples were carefully selected to have a long patient follow-up and complete clinical datasets to allow an in-depth analysis. We provide the first comprehensive map of 17000+ long ncRNAs in a broad range of human tumor and normal tissues and discovered hundreds of new ncRNAs associated with three major tumor entities. Importantly, we uncovered that ncRNA profiles are significantly more specific to the tissue of origin than patterns of protein-coding mRNAs. Also, the significant ncRNA signatures in this study demonstrate specific ncRNA patterns that are unlikely to be transcriptional background but rather the result of concerted regulation.

To mimic the response to cytotoxic chemotherapy, we have also treated lung and liver cancer cells with the DNA damaging agents Cisplatin and

Etoposide and found significant deregulation of long ncRNAs - reversing in part the differences seen between normal and malignant lung tissue. Importantly, one of the Cisplatin-regulated ncRNAs interacts with DNA repair factors linking it immediately to the DNA damage response.

To elucidate the molecular functions of the novel ncRNAs, we used RNA affinity purification to identify the protein interaction partners. In addition, we create human knockout cells for lncRNAs using ZFN and TALEN technology to integrate RNA destabilizing elements into the human genome which yields more than 1000-fold lncRNA silencing. Our so far largest ncRNA expression map is also exploited in another way: We generate an siRNA library specifically targeting over 600 tumor-associated ncRNAs based on our profiling landscape. This comprehensive but focused library will elucidate the role of ncRNAs in tumorigenesis, viability, apoptosis and the DNA damage response.

In summary, we provide the first global comprehensive map of long ncRNA expression in a broad range of human tumor and normal tissue samples and discovered many new lncRNAs associated with cancer as well as tissue-, histology- and prognosis-specific ncRNA signatures.

Citation Format: Maria Polycarpou-Schwarz, Tony Gutschner, Monika Hämmerle, Anna Roth, Ashish Goyal, Stefanie Grund, Catherina Hildenbrand, Arne Warth, Thomas Longerich, Sebastian Aulmann, Joachim Rom, Michael Meister, Thomas Muley, Heike Zabeck, Sabine Schmidt, Tomi Ivacevic, Vladimir Benes, Kai Breuhahn, Philipp Schnabel, Peter Sinn, Hans Hoffmann, Peter Schirmacher, Sven Diederichs. The non-coding RNA landscape of lung, liver and breast cancer reveals novel tumor-associated ncRNAs, concerted regulation and unexpected tissue specificity. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 1824. doi:10.1158/1538-7445.AM2013-1824

The digital MIQE guidelines: Minimum Information for Publication of Quantitative Digital PCR Experiments

There is growing interest in digital PCR (dPCR) because technological progress makes it a practical and increasingly affordable technology. dPCR allows the precise quantification of nucleic acids, facilitating the measurement of small percentage differences and quantification of rare variants. dPCR may also be more reproducible and less susceptible to inhibition than quantitative real-time PCR (qPCR). Consequently, dPCR has the potential to have a substantial impact on research as well as diagnostic applications. However, as with qPCR, the ability to perform robust meaningful experiments requires careful design and adequate controls. To assist independent evaluation of experimental data, comprehensive disclosure of all relevant experimental details is required. To facilitate this process we present the Minimum Information for Publication of Quantitative Digital PCR Experiments guidelines. This report addresses known requirements for dPCR that have already been identified during this early stage of its development and commercial implementation. Adoption of these guidelines by the scientific community will help to standardize experimental protocols, maximize efficient utilization of resources, and enhance the impact of this promising new technology.

Integrative genomic analyses reveal an androgen-driven somatic alteration landscape in early-onset prostate cancer

Early-onset prostate cancer (EO-PCA) represents the earliest clinical manifestation of prostate cancer. To compare the genomic alteration landscapes of EO-PCA with "classical" (elderly-onset) PCA, we performed deep sequencing-based genomics analyses in 11 tumors diagnosed at young age, and pursued comparative assessments with seven elderly-onset PCA genomes. Remarkable age-related differences in structural rearrangement (SR) formation became evident, suggesting distinct disease pathomechanisms. Whereas EO-PCAs harbored a prevalence of balanced SRs, with a specific abundance of androgen-regulated ETS gene fusions including TMPRSS2:ERG, elderly-onset PCAs displayed primarily non-androgen-associated SRs. Data from a validation cohort of > 10,000 patients showed age-dependent androgen receptor levels and a prevalence of SRs affecting androgen-regulated genes, further substantiating the activity of a characteristic "androgen-type" pathomechanism in EO-PCA.

Treatment for brain arteriovenous malformation in the 1998-2011 period and review of the literature

PURPOSE

The results of the treatment of pial AVM provided at our neurosurgical centre are presented. Based on these results and on an overview of literary data on the efficacy and complications of each therapeutic modality, the algorithm of indications, as used at our institution, is presented. COHORT OF PATIENTS: The series comprises 195 patients, aged 9 to 87 years and treated in the years 1998-2011. The surgical group consists of 76 patients; of these, 49 patients solely received endovascular treatment, 25 were consulted and referred directly to the radiosurgical unit, and the remaining 45 were recommended to abide by the strategy of "watch and wait".

RESULTS

In the surgical group, serious complications were 3.9 %, at a 96.1 % therapeutic efficacy. As for AVM treated with purely endovascular methods, serious procedural complications were seen in 4.1 % of patients, with efficacy totalling 32.7 %. One observed patient suffered bleeding, resulting in death. For comparison with literary data for each modality, a survival analysis without haemorrhage following monotherapy for AVM with each particular modality was carried out.

CONCLUSIONS

Based on our analysis, we have devised the following algorithm of treatment: 1. We regard surgical treatment as the treatment of choice for AVM of Spetzler-Martin (S-M) grades I and II, and only for those grade III cases that are surgically accessible. 2. Endovascular intervention should mainly be used for preoperative embolisation, as a curative procedure for lower-grade AVM in patients with comorbidities, and as palliation only for higher-grade cases. 3. Stereotactic irradiation with Leksell Gamma Knife (LGK) is advisable, mainly for poorly accessible, deep-seated grade-III AV malformations. In the case of lower grades, the final decision is left to the properly informed patient. 4. Observation should be used as the method of choice in AVM of grades IV and V, where active therapy carries greater risk than the natural course of the disease.

An efficient method for genome-wide polyadenylation site mapping and RNA quantification

The use of alternative poly(A) sites is common and affects the post-transcriptional fate of mRNA, including its stability, subcellular localization and translation. Here, we present a method to identify poly(A) sites in a genome-wide and strand-specific manner. This method, termed 3′T-fill, initially fills in the poly(A) stretch with unlabeled dTTPs, allowing sequencing to start directly after the poly(A) tail into the 3′-untranslated regions (UTR). Our comparative analysis demonstrates that it outperforms existing protocols in quality and throughput and accurately quantifies RNA levels as only one read is produced from each transcript. We use this method to characterize the diversity of polyadenylation in Saccharomyces cerevisiae, showing that alternative RNA molecules are present even in a genetically identical cell population. Finally, we observe that overlap of convergent 3′-UTRs is frequent but sharply limited by coding regions, suggesting factors that restrict compression of the yeast genome.

Df31 protein and snoRNAs maintain accessible higher-order structures of chromatin

Packaging of DNA into nucleosomes and the formation of higher-order chromatin structures determine DNA accessibility and activity of genome domains. We identified an RNA-dependent mechanism maintaining the open chromatin structure within euchromatic regions in Drosophila cells. The mechanism of reversible chromatin opening, reconstituted in vitro, depends on the Drosophila decondensation factor 31 (Df31) that specifically binds to RNA and localizes to euchromatic regions. Df31 is capable to tether a heterogeneous pool of short, single-stranded RNAs to chromatin. This class of chromatin-associated RNA (caRNA) is stably linked to chromatin and is largely composed of snoRNAs, which are preferentially bound by Df31. We suggest that the Df31-mediated linkage of snoRNAs and chromatin, forms a RNA-chromatin network resulting in the establishment of open chromatin domains. Analysis of caRNAs in human cells also reveals a strong enrichment of snoRNAs, implying a conserved role for these molecules in higher-order structures of chromatin.

DELLY: structural variant discovery by integrated paired-end and split-read analysis

MOTIVATION

The discovery of genomic structural variants (SVs) at high sensitivity and specificity is an essential requirement for characterizing naturally occurring variation and for understanding pathological somatic rearrangements in personal genome sequencing data. Of particular interest are integrated methods that accurately identify simple and complex rearrangements in heterogeneous sequencing datasets at single-nucleotide resolution, as an optimal basis for investigating the formation mechanisms and functional consequences of SVs.

RESULTS

We have developed an SV discovery method, called DELLY, that integrates short insert paired-ends, long-range mate-pairs and split-read alignments to accurately delineate genomic rearrangements at single-nucleotide resolution. DELLY is suitable for detecting copy-number variable deletion and tandem duplication events as well as balanced rearrangements such as inversions or reciprocal translocations. DELLY, thus, enables to ascertain the full spectrum of genomic rearrangements, including complex events. On simulated data, DELLY compares favorably to other SV prediction methods across a wide range of sequencing parameters. On real data, DELLY reliably uncovers SVs from the 1000 Genomes Project and cancer genomes, and validation experiments of randomly selected deletion loci show a high specificity.

AVAILABILITY

DELLY is available at www.korbel.embl.de/software.html

CONTACT

tobias.rausch@embl.de.

Dissecting the genomic complexity underlying medulloblastoma

Medulloblastoma is an aggressively growing tumour, arising in the cerebellum or medulla/brain stem. It is the most common malignant brain tumour in children, and shows tremendous biological and clinical heterogeneity. Despite recent treatment advances, approximately 40% of children experience tumour recurrence, and 30% will die from their disease. Those who survive often have a significantly reduced quality of life. Four tumour subgroups with distinct clinical, biological and genetic profiles are currently identified. WNT tumours, showing activated wingless pathway signalling, carry a favourable prognosis under current treatment regimens. SHH tumours show hedgehog pathway activation, and have an intermediate prognosis. Group 3 and 4 tumours are molecularly less well characterized, and also present the greatest clinical challenges. The full repertoire of genetic events driving this distinction, however, remains unclear. Here we describe an integrative deep-sequencing analysis of 125 tumour-normal pairs, conducted as part of the International Cancer Genome Consortium (ICGC) PedBrain Tumor Project. Tetraploidy was identified as a frequent early event in Group 3 and 4 tumours, and a positive correlation between patient age and mutation rate was observed. Several recurrent mutations were identified, both in known medulloblastoma-related genes (CTNNB1, PTCH1, MLL2, SMARCA4) and in genes not previously linked to this tumour (DDX3X, CTDNEP1, KDM6A, TBR1), often in subgroup-specific patterns. RNA sequencing confirmed these alterations, and revealed the expression of what are, to our knowledge, the first medulloblastoma fusion genes identified. Chromatin modifiers were frequently altered across all subgroups. These findings enhance our understanding of the genomic complexity and heterogeneity underlying medulloblastoma, and provide several potential targets for new therapeutics, especially for Group 3 and 4 patients.

Comparison of 3 fusion techniques in the treatment of the degenerative cervical spine disease. Is stand-alone autograft really the "gold standard?": prospective study with 2-year follow-up

STUDY DESIGN

A prospective study.

OBJECTIVE

The aim of this study was to compare the 3 different methods of interbody fusion of the cervical spine-autograft in stand-alone technique, autograft with anterior plate, and polyetheretherketone cage supported by anterior plate. The clinical and radiological data obtained were analyzed and discussed.

SUMMARY OF BACKGROUND DATA

Although degenerative cervical spine disease has been treated by an anterior approach for more than 50 years, there is not one generally accepted operative approach. There is a very low-quality evidence of little or no difference in pain relief between each of the techniques. Iliac crest autograft still seems to be the "gold standard" for interbody fusion.

METHODS

Prospective study collecting clinical and radiological data of 81 patients undergoing anterior cervical interbody fusion, in which the interbody fusion of 1 or 2 motion segments from C3 to C7 was done by any of the 3 techniques--stand-alone insertion of autograft (group 1: 28 patients), autograft and anterior plate (group 2: 18 patients), and polyetheretherketone cage filled with beta-tricalcium phosphate and plate (group 3: 29 patients). Patients were followed for 2 years after surgery.

RESULTS

Significant interaction of relative height in the segment and time was found (P < 0.001). The values of the relative height of stand-alone autograft dropped below 95% of initial height and the values of the other 2 groups remained above 105%. Significant interaction of time and group was found for Cobb S angles (P < 0.001). Values of group 1 decreased substantially and remained significantly lower than values of other 2 groups. Fusion rate was 100% in all groups. Neck Disability Index group and time interaction was found (P = 0.023). During postoperative follow-up, group 1 scored in all controls higher than the other 2 groups, but differences were not significant. Visual analogue scale showed effect of time (P < 0.001). This was due to a smaller improvement of patients in group 1 during the whole follow-up in comparison with the other 2 groups. Highest proportion of unsatisfied patients was in group 1 compared with the other 2 groups after 2 years (P = 0.034).

CONCLUSION

Significantly worse radiological and clinical results after 2 years of follow-up were achieved using stand-alone autograft technique in comparison with autograft supported by anterior plating similarly as in comparison with cage implant and anterior plating. Using artificial fusion substrate together with plate and cage can offer the same clinical and radiological results such as iliac autograft and plating. Anterior plating seems to be an important factor influencing the postoperative cervical spine alignment and also the clinical outcome.

A role for Fkbp6 and the chaperone machinery in piRNA amplification and transposon silencing

Epigenetic silencing of transposons by Piwi-interacting RNAs (piRNAs) constitutes an RNA-based genome defense mechanism. Piwi endonuclease action amplifies the piRNA pool by generating new piRNAs from target transcripts by a poorly understood mechanism. Here, we identified mouse Fkbp6 as a factor in this biogenesis pathway delivering piRNAs to the Piwi protein Miwi2. Mice lacking Fkbp6 derepress LINE1 (L1) retrotransposon and display reduced DNA methylation due to deficient nuclear accumulation of Miwi2. Like other cochaperones, Fkbp6 associates with the molecular chaperone Hsp90 via its tetratricopeptide repeat (TPR) domain. Inhibition of the ATP-dependent Hsp90 activity in an insect cell culture model results in the accumulation of short antisense RNAs in Piwi complexes. We identify these to be byproducts of piRNA amplification that accumulate only in nuage-localized Piwi proteins. We propose that the chaperone machinery normally ejects these inhibitory RNAs, allowing turnover of Piwi complexes for their continued participation in piRNA amplification.

Genomics of DNA cytosine methylation in Escherichia coli reveals its role in stationary phase transcription

DNA cytosine methylation regulates gene expression in mammals. In bacteria, its role in gene expression and genome architecture is less understood. Here we perform high-throughput sequencing of bisulfite-treated genomic DNA from Escherichia coli K12 to describe, for the first time, the extent of cytosine methylation of bacterial DNA at single-base resolution. Whereas most target sites (C(m)CWGG) are fully methylated in stationary phase cells, many sites with an extended CC(m)CWGG motif are only partially methylated in exponentially growing cells. We speculate that these partially methylated sites may be selected, as these are slightly correlated with the risk of spontaneous, non-synonymous conversion of methylated cytosines to thymines. Microarray analysis in a cytosine methylation-deficient mutant of E. coli shows increased expression of the stress response sigma factor RpoS and many of its targets in stationary phase. Thus, DNA cytosine methylation is a regulator of stationary phase gene expression in E. coli.

Aneurysm treatment in Europe 2010: an internet survey

BACKGROUND

Aneurysm (AN) treatment appears to differ from country to country and even from centre to centre. Therefore we decided to conduct a survey in order to better understand the "state of the art" in aneurysm treatment in Europe. The primary aim was to understand the roles of clipping and coiling in aneurysm treatment.

METHODS

An interactive form was sent to major European neurosurgical centres. The responses relating to AN location, status (ruptured/unruptured) and treatment modality were divided with regard to the volume of cases and the centre's geographical location.

RESULTS

Responses were received from 96 European centres. The main finding was that clipping was used significantly more often in Eastern Europe than in the rest of Europe to treat ruptured ANs of the anterior circulation. Almost all ruptured ANs across all locations are treated actively. The treatment of unruptured aneurysms of the anterior circulation is similar. The median relating to observed unruptured ANs across the Europe was 10 %. Posterior circulation ANs are treated predominantly by coiling, regardless of aneurysm status or geographical location. The average number of coilers versus surgeons per centre was 2.5:3.0 in Western, 1.9:3.6 in Southern, 1.9:4.3 in Eastern and 2.7:3.1 in Northern Europe.

CONCLUSIONS

The way in which intracranial aneurysms are treated appears to correlate with the economic development of European countries. It is probably also affected by the lack of experienced coilers in Eastern Europe.

Genome sequencing of pediatric medulloblastoma links catastrophic DNA rearrangements with TP53 mutations

Genomic rearrangements are thought to occur progressively during tumor development. Recent findings, however, suggest an alternative mechanism, involving massive chromosome rearrangements in a one-step catastrophic event termed chromothripsis. We report the whole-genome sequencing-based analysis of a Sonic-Hedgehog medulloblastoma (SHH-MB) brain tumor from a patient with a germline TP53 mutation (Li-Fraumeni syndrome), uncovering massive, complex chromosome rearrangements. Integrating TP53 status with microarray and deep sequencing-based DNA rearrangement data in additional patients reveals a striking association between TP53 mutation and chromothripsis in SHH-MBs. Analysis of additional tumor entities substantiates a link between TP53 mutation and chromothripsis, and indicates a context-specific role for p53 in catastrophic DNA rearrangements. Among these, we observed a strong association between somatic TP53 mutations and chromothripsis in acute myeloid leukemia. These findings connect p53 status and chromothripsis in specific tumor types, providing a genetic basis for understanding particularly aggressive subtypes of cancer.

HnRNP L and L-like cooperate in multiple-exon regulation of CD45 alternative splicing

CD45 encodes a trans-membrane protein-tyrosine phosphatase expressed in diverse cells of the immune system. By combinatorial use of three variable exons 4–6, isoforms are generated that differ in their extracellular domain, thereby modulating phosphatase activity and immune response. Alternative splicing of these CD45 exons involves two heterogeneous ribonucleoproteins, hnRNP L and its cell-type specific paralog hnRNP L-like (LL). To address the complex combinatorial splicing of exons 4–6, we investigated hnRNP L/LL protein expression in human B-cells in relation to CD45 splicing patterns, applying RNA-Seq. In addition, mutational and RNA-binding analyses were carried out in HeLa cells. We conclude that hnRNP LL functions as the major CD45 splicing repressor, with two CA elements in exon 6 as its primary target. In exon 4, one element is targeted by both hnRNP L and LL. In contrast, exon 5 was never repressed on its own and only co-regulated with exons 4 and 6. Stable L/LL interaction requires CD45 RNA, specifically exons 4 and 6. We propose a novel model of combinatorial alternative splicing: HnRNP L and LL cooperate on the CD45 pre-mRNA, bridging exons 4 and 6 and looping out exon 5, thereby achieving full repression of the three variable exons.

Direct regulation of microRNA biogenesis and expression by estrogen receptor beta in hormone-responsive breast cancer

Estrogen effects on mammary epithelial and breast cancer (BC) cells are mediated by the nuclear receptors ERα and ERβ, transcription factors that display functional antagonism with each other, with ERβ acting as oncosuppressor and interfering with the effects of ERα on cell proliferation, tumor promotion and progression. Indeed, hormone-responsive, ERα+ BC cells often lack ERβ, which when present associates with a less aggressive clinical phenotype of the disease. Recent evidences point to a significant role of microRNAs (miRNAs) in BC, where specific miRNA expression profiles associate with distinct clinical and biological phenotypes of the lesion. Considering the possibility that ERβ might influence BC cell behavior via miRNAs, we compared miRNome expression in ERβ+ vs ERβ- hormone-responsive BC cells and found a widespread effect of this ER subtype on the expression pattern of these non-coding RNAs. More importantly, the expression pattern of 67 miRNAs, including 10 regulated by ERβ in BC cells, clearly distinguishes ERβ+, node-negative, from ERβ-, metastatic, mammary tumors. Molecular dissection of miRNA biogenesis revealed multiple mechanisms for direct regulation of this process by ERβ+ in BC cell nuclei. In particular, ERβ downregulates miR-30a by binding to two specific sites proximal to the gene and thereby inhibiting pri-miR synthesis. On the other hand, the receptor promotes miR-23b, -27b and 24-1 accumulation in the cell by binding in close proximity of the corresponding gene cluster and preventing in situ the inhibitory effects of ERα on pri-miR maturation by the p68/DDX5-Drosha microprocessor complex. These results indicate that cell autonomous regulation of miRNA expression is part of the mechanism of action of ERβ in BC cells and could contribute to establishment or maintenance of a less aggressive tumor phenotype mediated by this nuclear receptor.

Kaposi's sarcoma herpesvirus microRNAs target caspase 3 and regulate apoptosis

Kaposi's sarcoma herpesvirus (KSHV) encodes a cluster of twelve micro (mi)RNAs, which are abundantly expressed during both latent and lytic infection. Previous studies reported that KSHV is able to inhibit apoptosis during latent infection; we thus tested the involvement of viral miRNAs in this process. We found that both HEK293 epithelial cells and DG75 cells stably expressing KSHV miRNAs were protected from apoptosis. Potential cellular targets that were significantly down-regulated upon KSHV miRNAs expression were identified by microarray profiling. Among them, we validated by luciferase reporter assays, quantitative PCR and western blotting caspase 3 (Casp3), a critical factor for the control of apoptosis. Using site-directed mutagenesis, we found that three KSHV miRNAs, miR-K12-1, 3 and 4-3p, were responsible for the targeting of Casp3. Specific inhibition of these miRNAs in KSHV-infected cells resulted in increased expression levels of endogenous Casp3 and enhanced apoptosis. Altogether, our results suggest that KSHV miRNAs directly participate in the previously reported inhibition of apoptosis by the virus, and are thus likely to play a role in KSHV-induced oncogenesis.

Role of CXCL13 in asthma: novel therapeutic target

BACKGROUND

B cells play an important role in allergic asthma. However, the mechanisms by which these cells are activated in the airways remain poorly understood.

METHODS

We used a mouse model of ovalbumin (OVA)-induced allergic inflammation to study CXCL13 and to investigate the concentration of this chemokine in the BAL fluid derived from asthmatic and normal control subjects.

RESULTS

We found that OVA-challenged mice upregulate the CXCL13/CXCR5 axis, which is associated with several changes in their airways, including recruitment of B and CD4(+) cells, development of bronchial-associated lymphoid tissue, and airway inflammation. Treating sensitized mice with an anti-CXCL13 antibody reduced cell recruitment, bronchial-associated lymphoid tissue formation, and airways inflammation. Interestingly, measurements of CXCL13 using enzyme-linked immunosorbent assay showed that levels of this cytokine were significantly elevated in BAL fluid from subjects with asthma compared with control subjects (median, 162 [range, 120-296] vs 31 [range, 120-156] pg/mL; P = .005).

CONCLUSIONS

All together, these findings suggest that CXCL13 is involved in the allergic airway inflammatory process, and targeting this chemokine may constitute a novel approach in asthma.

Nuclear hormone 1α,25-dihydroxyvitamin D3 elicits a genome-wide shift in the locations of VDR chromatin occupancy

A global understanding of the actions of the nuclear hormone 1α,25-dihydroxyvitamin D₃ (1α,25(OH)₂D₃) and its vitamin D receptor (VDR) requires a genome-wide analysis of VDR binding sites. In THP-1 human monocytic leukemia cells we identified by ChIP-seq 2340 VDR binding locations, of which 1171 and 520 occurred uniquely with and without 1α,25(OH)₂D₃ treatment, respectively, while 649 were common. De novo identified direct repeat spaced by 3 nucleotides (DR3)-type response elements (REs) were strongly associated with the ligand-responsiveness of VDR occupation. Only 20% of the VDR peaks diminishing most after ligand treatment have a DR3-type RE, in contrast to 90% for the most growing peaks. Ligand treatment revealed 638 1α,25(OH)₂D₃ target genes enriched in gene ontology categories associated with immunity and signaling. From the 408 upregulated genes, 72% showed VDR binding within 400 kb of their transcription start sites (TSSs), while this applied only for 43% of the 230 downregulated genes. The VDR loci showed considerable variation in gene regulatory scenarios ranging from a single VDR location near the target gene TSS to very complex clusters of multiple VDR locations and target genes. In conclusion, ligand binding shifts the locations of VDR occupation to DR3-type REs that surround its target genes and occur in a large variety of regulatory constellations.

The liver-specific microRNA miR-122 controls systemic iron homeostasis in mice

Systemic iron homeostasis is mainly controlled by the liver through synthesis of the peptide hormone hepcidin (encoded by Hamp), the key regulator of duodenal iron absorption and macrophage iron release. Here we show that the liver-specific microRNA miR-122 is important for regulating Hamp mRNA expression and tissue iron levels. Efficient and specific depletion of miR-122 by injection of a locked-nucleic-acid-modified (LNA-modified) anti-miR into WT mice caused systemic iron deficiency, characterized by reduced plasma and liver iron levels, mildly impaired hematopoiesis, and increased extramedullary erythropoiesis in the spleen. Moreover, miR-122 inhibition increased the amount of mRNA transcribed by genes that control systemic iron levels, such as hemochromatosis (Hfe), hemojuvelin (Hjv), bone morphogenetic protein receptor type 1A (Bmpr1a), and Hamp. Importantly, miR-122 directly targeted the 3′ untranslated region of 2 mRNAs that encode activators of hepcidin expression, Hfe and Hjv. These data help to explain the increased Hamp mRNA levels and subsequent iron deficiency in mice with reduced miR-122 levels and establish a direct mechanistic link between miR-122 and the regulation of systemic iron metabolism.