Genomes and Genes
Experts and Doctors on micrornas in Denmark
- Coskun M, Bjerrum J, Seidelin J, Troelsen J, Olsen J, Nielsen O. miR-20b, miR-98, miR-125b-1*, and let-7e* as new potential diagnostic biomarkers in ulcerative colitis. World J Gastroenterol. 2013;19:4289-99 pubmed publisher..The present study provides the first evidence that miR-20b, miR-98, miR-125b-1*, and let-7e* are deregulated in patients with UC. The level of these miRNAs may serve as new potential biomarkers for this chronic disease. ..
- Willenbrock H, Salomon J, Søkilde R, Barken K, Hansen T, Nielsen F, et al. Quantitative miRNA expression analysis: comparing microarrays with next-generation sequencing. RNA. 2009;15:2028-34 pubmed publisher..In addition, microarrays appear highly sensitive and perform equivalently to next-generation sequencing in terms of reproducibility and relative ratio quantification. ..
- Wen J, Parker B, Jacobsen A, Krogh A. MicroRNA transfection and AGO-bound CLIP-seq data sets reveal distinct determinants of miRNA action. RNA. 2011;17:820-34 pubmed publisher..Predictive models and results are available at http://servers.binf.ku.dk/antar/. ..
- Jørgensen S, Baker A, Møller S, Nielsen B. Robust one-day in situ hybridization protocol for detection of microRNAs in paraffin samples using LNA probes. Methods. 2010;52:375-81 pubmed publisher..The well established localization of these microRNAs makes them ideal for use as reference microRNAs when optimizing the microRNA in situ hybridization assay for a particular tissue and miRNA. ..
- Parker B, Wen J. Predicting microRNA targets in time-series microarray experiments via functional data analysis. BMC Bioinformatics. 2009;10 Suppl 1:S32 pubmed publisher..This approach would be applicable to the investigation of other miRNAs and suggests that dynamic microarray studies at a higher time resolution could reveal further details on miRNA regulation. ..
- Brameier M, Wiuf C. Ab initio identification of human microRNAs based on structure motifs. BMC Bioinformatics. 2007;8:478 pubmed..In doing so, it requires less previous knowledge about miRNA precursor structures while programs and motifs allow a more straightforward interpretation and extraction of the acquired knowledge. ..
- Nielsen B, Jørgensen S, Fog J, Søkilde R, Christensen I, Hansen U, et al. High levels of microRNA-21 in the stroma of colorectal cancers predict short disease-free survival in stage II colon cancer patients. Clin Exp Metastasis. 2011;28:27-38 pubmed publisher..We conclude that miR-21 is primarily a stromal microRNA, which when measured by image analysis identifies a subgroup of stage II colon cancer patients with short disease-free survival. ..
- ..Importantly, microRNA molecules are already entering the clinic as diagnostic and prognostic biomarkers for patient stratification and also as therapeutic targets and agents. ..
- Aure M, Vitelli V, Jernström S, Kumar S, Krohn M, Due E, et al. Integrative clustering reveals a novel split in the luminal A subtype of breast cancer with impact on outcome. Breast Cancer Res. 2017;19:44 pubmed publisher..Increasing knowledge of the heterogeneity of the luminal A subtype may add pivotal information to guide therapeutic choices, evidently bringing us closer to improved treatment for this largest subgroup of breast cancer. ..
- Aslan D, Garde C, Nygaard M, Helbo A, Dimopoulos K, Hansen J, et al. Tumor suppressor microRNAs are downregulated in myelodysplastic syndrome with spliceosome mutations. Oncotarget. 2016;7:9951-63 pubmed publisher..Our data indicate that spliceosome mutations may play an important role in MDS pathophysiology by affecting the expression of tumor suppressor miRNA genes involved in the development and progression of MDS. ..
- Coskun M, Bjerrum J, Seidelin J, Nielsen O. MicroRNAs in inflammatory bowel disease--pathogenesis, diagnostics and therapeutics. World J Gastroenterol. 2012;18:4629-34 pubmed..Here, we provide a short review of the current state-of-the-art of miRNAs in IBD pathogenesis, diagnostics and therapeutics. ..
- Jensen S, Lamy P, Rasmussen M, Ostenfeld M, Dyrskjøt L, Orntoft T, et al. Evaluation of two commercial global miRNA expression profiling platforms for detection of less abundant miRNAs. BMC Genomics. 2011;12:435 pubmed publisher..For profiling clinical samples with low miRNA abundance, such as plasma samples, the miRCURY platform with its better sensitivity and linearity would probably be superior. ..
- Blondal T, Jensby Nielsen S, Baker A, Andreasen D, Mouritzen P, Wrang Teilum M, et al. Assessing sample and miRNA profile quality in serum and plasma or other biofluids. Methods. 2013;59:S1-6 pubmed publisher..Specifically we have developed normal reference ranges for circulating miRNAs in serum and plasma as well as a hemolysis indicator based on microRNA expression. ..
- Lajer C, Garnæs E, Friis Hansen L, Norrild B, Therkildsen M, Glud M, et al. The role of miRNAs in human papilloma virus (HPV)-associated cancers: bridging between HPV-related head and neck cancer and cervical cancer. Br J Cancer. 2012;106:1526-34 pubmed publisher..This study adds new knowledge to the known pathogenic pathways of HPV and substantiates the oncogenic role of HPV in subsets of HNSCCs. ..
- Hansen T, Kjems J, Damgaard C. Circular RNA and miR-7 in cancer. Cancer Res. 2013;73:5609-12 pubmed publisher..Here, we review the current knowledge about the ciRS-7/miR-7 axis in cancer-related pathways and discuss possible models explaining the relevance of coexpressing miR-7 along with a circRNA inhibitor. ..
- Silahtaroglu A, Nolting D, Dyrskjøt L, Berezikov E, Møller M, Tommerup N, et al. Detection of microRNAs in frozen tissue sections by fluorescence in situ hybridization using locked nucleic acid probes and tyramide signal amplification. Nat Protoc. 2007;2:2520-8 pubmed
- Glud M, Rossing M, Hother C, Holst L, Hastrup N, Nielsen F, et al. Downregulation of miR-125b in metastatic cutaneous malignant melanoma. Melanoma Res. 2010;20:479-84 pubmed publisher..MiR-125b has earlier been found to be downregulated in other tumor types and in atypic naevi compared with the common acquired naevi. In conclusion, miR-125b may be involved in an early progression of cutaneous MM. ..
- Glud M, Manfé V, Biskup E, Holst L, Dirksen A, Hastrup N, et al. MicroRNA miR-125b induces senescence in human melanoma cells. Melanoma Res. 2011;21:253-6 pubmed publisher..We propose that downregulation of miR-125b in an early cutaneous malignant melanoma can contribute to the increased metastatic capability of this tumor. ..
- Nielsen S, Scheele C, Yfanti C, Akerstrom T, Nielsen A, Pedersen B, et al. Muscle specific microRNAs are regulated by endurance exercise in human skeletal muscle. J Physiol. 2010;588:4029-37 pubmed publisher..In conclusion, our data suggest myomiRs respond to physiological stimuli, but their role in regulating human skeletal muscle adaptation remains unknown. ..
- Lindow M, Krogh A. Computational evidence for hundreds of non-conserved plant microRNAs. BMC Genomics. 2005;6:119 pubmed..Furthermore it suggests that the number of plant miRNAs have been underestimated and points to the existence of recently evolved miRNAs in Arabidopsis. ..
- Luu H, Lin H, Sørensen K, Ogunwobi O, Kumar N, Chornokur G, et al. miRNAs associated with prostate cancer risk and progression. BMC Urol. 2017;17:18 pubmed publisher..Nevertheless, the findings from previous studies suggest miRNAs may play an important role in the risk and progression of prostate cancer as promising biomarkers. ..
- Hansen T, Jensen T, Clausen B, Bramsen J, Finsen B, Damgaard C, et al. Natural RNA circles function as efficient microRNA sponges. Nature. 2013;495:384-8 pubmed publisher..This study serves as the first, to our knowledge, functional analysis of a naturally expressed circRNA. ..
- Lindow M, Kauppinen S. Discovering the first microRNA-targeted drug. J Cell Biol. 2012;199:407-12 pubmed publisher..Here, we describe the discovery of miravirsen, which is currently in phase 2 clinical trials for treatment of hepatitis C virus (HCV) infection. ..
- Krintel S, Dehlendorff C, Hetland M, Hørslev Petersen K, Andersen K, Junker P, et al. Prediction of treatment response to adalimumab: a double-blind placebo-controlled study of circulating microRNA in patients with early rheumatoid arthritis. Pharmacogenomics J. 2016;16:141-6 pubmed publisher..3p was associated with EULAR good response. Future studies to assess the utility of these miRNAs as predictive biomarkers are needed. ..
- Wenzel A, Akbasli E, Gorodkin J. RIsearch: fast RNA-RNA interaction search using a simplified nearest-neighbor energy model. Bioinformatics. 2012;28:2738-46 pubmed publisher..Likewise, substantial filtering was performed on bacterial RNA-RNA interaction data. The source code for RIsearch is available at: http://rth.dk/resources/risearch. ..
- Min A, Zhu C, Peng S, Shuai C, Sun L, Han Y, et al. Downregulation of Microrna-148a in Cancer-Associated Fibroblasts from Oral Cancer Promotes Cancer Cell Migration and Invasion by Targeting Wnt10b. J Biochem Mol Toxicol. 2016;30:186-91 pubmed publisher..Taken together, these data suggested that miR-148a might be a novel candidate target for the treatment of OSCC. ..
- Zibert J, Løvendorf M, Litman T, Olsen J, Kaczkowski B, Skov L. MicroRNAs and potential target interactions in psoriasis. J Dermatol Sci. 2010;58:177-85 pubmed publisher..Our data indicate several novel important associations for miRNAs in psoriasis and in particular the miR-221/2-TIMP3 target interaction could among others play a role in the psoriasis pathogenesis. ..
- Nielsen L, Wang C, Sørensen K, Bang Berthelsen C, Hansen L, Andersen M, et al. Circulating levels of microRNA from children with newly diagnosed type 1 diabetes and healthy controls: evidence that miR-25 associates to residual beta-cell function and glycaemic control during disease progression. Exp Diabetes Res. 2012;2012:896362 pubmed publisher
- Eichenlaub T, Cohen S, Herranz H. Cell Competition Drives the Formation of Metastatic Tumors in a Drosophila Model of Epithelial Tumor Formation. Curr Biol. 2016;26:419-27 pubmed publisher..Analogous mechanisms for cytokinesis failure may lead to polyploid intermediates in tumorigenesis in mammalian cancer models. ..
- Frankel L, Christoffersen N, Jacobsen A, Lindow M, Krogh A, Lund A. Programmed cell death 4 (PDCD4) is an important functional target of the microRNA miR-21 in breast cancer cells. J Biol Chem. 2008;283:1026-33 pubmed..We furthermore found that the tumor suppressor protein Programmed Cell Death 4 (PDCD4) is regulated by miR-21 and demonstrated that PDCD4 is a functionally important target for miR-21 in breast cancer cells. ..
- Rasmussen M, Jensen N, Tarpgaard L, Qvortrup C, Rømer M, Stenvang J, et al. High expression of microRNA-625-3p is associated with poor response to first-line oxaliplatin based treatment of metastatic colorectal cancer. Mol Oncol. 2013;7:637-46 pubmed publisher..Altogether, our results suggest an association between miR-625-3p and response to first-line oxaliplatin based chemotherapy of mCRC. ..
- Frankel L, Wen J, Lees M, Høyer Hansen M, Farkas T, Krogh A, et al. microRNA-101 is a potent inhibitor of autophagy. EMBO J. 2011;30:4628-41 pubmed publisher..Collectively, these data establish a novel link between two highly important and rapidly growing research fields and present a new role for miR-101 as a key regulator of autophagy. ..
- Dyrskjøt L, Ostenfeld M, Bramsen J, Silahtaroglu A, Lamy P, Ramanathan R, et al. Genomic profiling of microRNAs in bladder cancer: miR-129 is associated with poor outcome and promotes cell death in vitro. Cancer Res. 2009;69:4851-60 pubmed publisher..The findings reported here indicate that several miRNAs are differentially regulated in bladder cancer and may form a basis for clinical development of new biomarkers for bladder cancer. ..
- Daugaard I, Hansen T. Biogenesis and Function of Ago-Associated RNAs. Trends Genet. 2017;33:208-219 pubmed publisher..We review here the current knowledge and most recent discoveries relating to alternative functions and biogenesis strategies for Ago-associated RNAs in mammals. ..
- Rajman M, Metge F, Fiore R, Khudayberdiev S, Aksoy Aksel A, Bicker S, et al. A microRNA-129-5p/Rbfox crosstalk coordinates homeostatic downscaling of excitatory synapses. EMBO J. 2017;36:1770-1787 pubmed publisher..We therefore identified a novel activity-dependent miRNA/RBP crosstalk during synaptic scaling, with potential implications for neural network homeostasis and epileptogenesis. ..
- Eskildsen T, Taipaleenmaki H, Stenvang J, Abdallah B, Ditzel N, Nossent A, et al. MicroRNA-138 regulates osteogenic differentiation of human stromal (mesenchymal) stem cells in vivo. Proc Natl Acad Sci U S A. 2011;108:6139-44 pubmed publisher..Our findings suggest that pharmacological inhibition of miR-138 by antimiR-138 could represent a therapeutic strategy for enhancing bone formation in vivo. ..
- Jacobsen A, Krogh A, Kauppinen S, Lindow M. miRMaid: a unified programming interface for microRNA data resources. BMC Bioinformatics. 2010;11:29 pubmed publisher..Furthermore, miRMaid constitutes a basic framework for further programming in which microRNA-interested bioinformaticians can readily develop their own tools and data sources. ..
- Crone S, Jacobsen A, Federspiel B, Bardram L, Krogh A, Lund A, et al. microRNA-146a inhibits G protein-coupled receptor-mediated activation of NF-?B by targeting CARD10 and COPS8 in gastric cancer. Mol Cancer. 2012;11:71 pubmed publisher..By targeting components of several NF-kappaB-activating pathways, miR-146a is a key component in the regulation of NF-kappaB activity. ..
- Primo M, Bak R, Schibler B, Mikkelsen J. Regulation of pro-inflammatory cytokines TNF? and IL24 by microRNA-203 in primary keratinocytes. Cytokine. 2012;60:741-8 pubmed publisher..Our findings suggest that miR-203 serves to fine-tune cytokine signaling and may dampen skin immune responses by repressing key pro-inflammatory cytokines...
- Nairismägi M, Vislovukh A, Meng Q, Kratassiouk G, Beldiman C, Petretich M, et al. Translational control of TWIST1 expression in MCF-10A cell lines recapitulating breast cancer progression. Oncogene. 2012;31:4960-6 pubmed publisher..We found that miR-580, CPEB1, and CPEB2 act as negative regulators of TWIST1 expression in a sequence-specific and additive/cooperative manner. ..
- Nygren M, Tekle C, Ingebrigtsen V, Mäkelä R, Krohn M, Aure M, et al. Identifying microRNAs regulating B7-H3 in breast cancer: the clinical impact of microRNA-29c. Br J Cancer. 2014;110:2072-80 pubmed publisher..We identified miRNAs efficiently downregulating B7-H3 expression. The expression of miR-29c correlated with survival in breast cancer patients, suggesting a tumour suppressive role for this miRNA. ..
- Wen L, Andersen P, Husum D, Nørregaard R, Zhao Z, Liu Z, et al. MicroRNA-148b regulates megalin expression and is associated with receptor downregulation in mice with unilateral ureteral obstruction. Am J Physiol Renal Physiol. 2017;313:F210-F217 pubmed publisher..Furthermore, the identification of a miRNA regulating megalin expression may allow for targeted interventions to modulate megalin function and proximal tubule uptake of proteins, as well as other ligands. ..
- Bache S, Rasmussen R, Rossing M, Laigaard F, Nielsen F, MÃ¸ller K. MicroRNA Changes in Cerebrospinal Fluid After Subarachnoid Hemorrhage. Stroke. 2017;48:2391-2398 pubmed publisher..SAH is associated with marked changes in the cerebrospinal fluid miRNA profile. These changes could be associated to the development of DCI. URL: http://www.clinicaltrials.gov. Unique identifier: NCT01791257. ..
- Ostenfeld M, Bramsen J, Lamy P, Villadsen S, Fristrup N, Sørensen K, et al. miR-145 induces caspase-dependent and -independent cell death in urothelial cancer cell lines with targeting of an expression signature present in Ta bladder tumors. Oncogene. 2010;29:1073-84 pubmed publisher..Our data indicate that reduction in miR-145 expression may provide bladder cancer cells with a selective advantage by inhibition of cell death otherwise triggered in malignant cells. ..
- Dabrowska M, Dybkaer K, Johnsen H, Wang B, Wabl M, Pedersen F. Loss of MicroRNA targets in the 3' untranslated region as a mechanism of retroviral insertional activation of growth factor independence 1. J Virol. 2009;83:8051-61 pubmed publisher..Here we provide data in support of a mechanism by which retroviral insertions in the Gfi1 3'UTR decouple microRNA-mediated posttranscriptional regulation. ..
- Hansen T, Christensen R, Andersen R, Sørensen F, Johnsson A, Jakobsen A. MicroRNA-126 and epidermal growth factor-like domain 7-an angiogenic couple of importance in metastatic colorectal cancer. Results from the Nordic ACT trial. Br J Cancer. 2013;109:1243-51 pubmed publisher..As miRNA-126 may target VEGF-A as well as EGFL7, the results may provide predictive information in relation to next-generation anti-angiogenetics. ..
- Øster B, Linnet L, Christensen L, Thorsen K, Ongen H, Dermitzakis E, et al. Non-CpG island promoter hypomethylation and miR-149 regulate the expression of SRPX2 in colorectal cancer. Int J Cancer. 2013;132:2303-15 pubmed publisher..The hypomethylation of SRPX2 is focal and not part of a large block. Furthermore, it often translates to an increased expression level, which may be modulated by miR-149. ..
- Gregersen L, Jacobsen A, Frankel L, Wen J, Krogh A, Lund A. MicroRNA-143 down-regulates Hexokinase 2 in colon cancer cells. BMC Cancer. 2012;12:232 pubmed publisher..We hypothesize that loss of miR-143-mediated repression of HK2 can promote glucose metabolism in cancer cells, contributing to the shift towards aerobic glycolysis observed in many tumors. ..
- Wiklund E, Bramsen J, Hulf T, Dyrskjøt L, Ramanathan R, Hansen T, et al. Coordinated epigenetic repression of the miR-200 family and miR-205 in invasive bladder cancer. Int J Cancer. 2011;128:1327-34 pubmed publisher..TWIST1 associates directly with the miR-200 and miR-205 promoters, and may act as a repressor of miR-200 and miR-205 expression. ..
- Rask L, Fregil M, Høgdall E, Mitchelmore C, Eriksen J. Development of a metastatic fluorescent Lewis Lung carcinoma mouse model: identification of mRNAs and microRNAs involved in tumor invasion. Gene. 2013;517:72-81 pubmed publisher..Our results suggest that increases in metalloproteinase expression and impairment of microRNA processing are involved in the acquirement of metastatic ability. ..
- Sørensen A, Udesen P, Wissing M, Englund A, Dalgaard L. MicroRNAs related to androgen metabolism and polycystic ovary syndrome. Chem Biol Interact. 2016;259:8-16 pubmed publisher..Our understanding of miRNAs, particularly in relation to PCOS, is currently at a very early stage, and additional studies will yield important insight into the molecular mechanisms behind this complex and heterogenic syndrome. ..
- Andersen D, Jensen C, Schneider M, Nossent A, Eskildsen T, Hansen J, et al. MicroRNA-15a fine-tunes the level of Delta-like 1 homolog (DLK1) in proliferating 3T3-L1 preadipocytes. Exp Cell Res. 2010;316:1681-91 pubmed publisher..Our data thus imply that miR-15a regulates cell size and proliferation by fine-tuning Dlk1 among others, and further emphasize miR-15a and DLK1 levels to play important roles in growth signaling networks. ..
- Cirera S, Birck M, Busk P, Fredholm M. Expression profiles of miRNA-122 and its target CAT1 in minipigs (Sus scrofa) fed a high-cholesterol diet. Comp Med. 2010;60:136-41 pubmed..Gene expression levels of CAT1 did not differ between groups...
- Hansen T, Bramsen J, Kjems J. Re-inspection of small RNA sequence datasets reveals several novel human miRNA genes. PLoS ONE. 2010;5:e10961 pubmed publisher..Our analysis highlights that existing datasets are not yet exhaustedly studied and continuous re-analysis of the available data is important to uncover all features of small RNA sequencing. ..
- Li Y, Gottwein J, Scheel T, Jensen T, Bukh J. MicroRNA-122 antagonism against hepatitis C virus genotypes 1-6 and reduced efficacy by host RNA insertion or mutations in the HCV 5' UTR. Proc Natl Acad Sci U S A. 2011;108:4991-6 pubmed publisher..5 cells. These mutations reduced the efficacy of SPC3649 treatment, indicating that escape variants to miR-122 antagonism-based HCV therapy could potentially occur. ..
- Hansen T, Sørensen F, Lindebjerg J, Jakobsen A. The predictive value of microRNA-126 in relation to first line treatment with capecitabine and oxaliplatin in patients with metastatic colorectal cancer. BMC Cancer. 2012;12:83 pubmed publisher..The predictive value of miRNA-126 remains to be further elucidated in prospective studies. ..
- Daugaard I, Knudsen A, Kjeldsen T, Hager H, Hansen L. The association between miR-34 dysregulation and distant metastases formation in lung adenocarcinoma. Exp Mol Pathol. 2017;102:484-491 pubmed publisher..7% and 35.3% of tested cases (n=51), respectively. Low miR-34b and miR-34c expression was associated with distant metastases formation in LAC. These changes can be targeted as novel biomarkers in LAC. ..
- Hansen T, Wiklund E, Bramsen J, Villadsen S, Statham A, Clark S, et al. miRNA-dependent gene silencing involving Ago2-mediated cleavage of a circular antisense RNA. EMBO J. 2011;30:4414-22 pubmed publisher..This study provides the first evidence for non-coding antisense transcripts as functional miRNA targets, and a novel regulatory mechanism involving a positive correlation between mRNA and antisense circular RNA levels. ..