Topical Collection "Regulation by Non-Coding RNAs"

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A topical collection in International Journal of Molecular Sciences (ISSN 1422-0067). This collection belongs to the section "Biochemistry, Molecular Biology and Biophysics".

Editor

Collection Editor
Dr. Martin Pichler
Division of Clinical Oncology, Department of Medicine, Medical University of Graz, Auenbruggerplatz 15, Austria
Website: https://forschung.medunigraz.at/fodok/suchen.person_uebersicht?sprache_in=en&ansicht_in=&menue_id_in=101&id_in=2001296
E-Mail: martin.pichler@medunigraz.at
Interests: Non-coding RNAs; MicroRNAs; cancer; Inflammation; Metabolism; Gene expression; cancer stem cells; epithelial-mesenchymal transition

Topical Collection Information

Dear Colleagues,

Non-Coding RNAs are currently a hot research topic in many fields of biology, medicine, and chemistry. It is increasingly clear that non-coding RNAs are involved in fundamentally physiological and pathological processes. These processes touch on many important disciplines, from metabolism to cancer. Non-coding RNAs are regulative: they mainly influence biological processes by regulating other (protein-)coding gene expression. By doing this, the cellular properties of development and growth, stem cell regeneration, apoptosis, authophagy, etc., are strictly controlled by non-coding RNAs. This collection is dedicated to summarizing and highlighting the current research concerning the role of non-coding RNAs in regulating the aforementioned functions. The underlying mechanisms of action, the target molecules, the interactor pairs, and the pertinent cellular functions should all be presented. All relevant fields in medicine (with a special focus on metabolism, cancer, and inflammation) are of interest. The classes of non-coding RNAs should include microRNAs, other small non-coding RNAs, and long non-coding RNAs. Original research articles, review articles, and research letters are welcomed.

Dr. Martin Pichler
Collection Editor

Manuscript Submission Information

Manuscripts for the topical collection can be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. All papers will be peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on this website. The topical collection considers regular research articles, short communications and review articles. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 1600 CHF (Swiss Francs).

Keywords

  • Regulatory RNA
  • sRNA
  • ncRNA
  • lncRNA
  • miRNA
  • siRNA
  • piRNA
  • CRISPR RNA
  • regulatory small RNA fragments

Related Special Issues

Published Papers (9 papers)

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2014  ( 9 papers )


2014
by , ,  and
Int. J. Mol. Sci. 2014, 15(11), 21554-21586; doi:10.3390/ijms151121554
Received: 19 September 2014; in revised form: 7 November 2014 / Accepted: 8 November 2014 / Published: 24 November 2014
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by , , ,  and
Int. J. Mol. Sci. 2014, 15(11), 20434-20448; doi:10.3390/ijms151120434
Received: 17 September 2014; in revised form: 30 October 2014 / Accepted: 30 October 2014 / Published: 7 November 2014
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by ,  and
Int. J. Mol. Sci. 2014, 15(11), 20266-20289; doi:10.3390/ijms151120266
Received: 11 August 2014; in revised form: 22 October 2014 / Accepted: 27 October 2014 / Published: 6 November 2014
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by , , , , , , ,  and
Int. J. Mol. Sci. 2014, 15(11), 20134-20157; doi:10.3390/ijms151120134
Received: 29 May 2014; in revised form: 27 August 2014 / Accepted: 27 October 2014 / Published: 5 November 2014
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by , ,  and
Int. J. Mol. Sci. 2014, 15(9), 15891-15911; doi:10.3390/ijms150915891
Received: 11 July 2014; in revised form: 27 August 2014 / Accepted: 27 August 2014 / Published: 9 September 2014
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by  and
Int. J. Mol. Sci. 2014, 15(9), 15700-15733; doi:10.3390/ijms150915700
Received: 20 June 2014; in revised form: 5 August 2014 / Accepted: 13 August 2014 / Published: 4 September 2014
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by , ,  and
Int. J. Mol. Sci. 2014, 15(8), 14475-14491; doi:10.3390/ijms150814475
Received: 2 July 2014; in revised form: 7 August 2014 / Accepted: 12 August 2014 / Published: 20 August 2014
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by , , ,  and
Int. J. Mol. Sci. 2014, 15(8), 13993-14013; doi:10.3390/ijms150813993
Received: 30 June 2014; in revised form: 23 July 2014 / Accepted: 5 August 2014 / Published: 12 August 2014
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by  and
Int. J. Mol. Sci. 2014, 15(8), 13494-13513; doi:10.3390/ijms150813494
Received: 14 June 2014; in revised form: 14 July 2014 / Accepted: 28 July 2014 / Published: 4 August 2014
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Planned Papers

The below list represents only planned manuscripts. Some of these manuscripts have not been received by the Editorial Office yet. Papers submitted to MDPI journals are subject to peer-review.

Title: MicroRNAs Associated with the Efficacy of Photodynamic Therapy in Biliary Tract Cancer Cell Lines
Authors: Andrej Wagner1*, Christian Mayr1, Doris Bach1, Romana Illig2, Kristjan Plaetzer3, Frieder Berr1, Martin Pichler4, 5, Daniel Neureiter2 and Tobias Kiesslich1,6

Affiliations: 1 Department of Internal Medicine I, Paracelsus Medical University / Salzburger Landeskliniken (SALK), Salzburg, Austria
2 Institute of Pathology, Paracelsus Medical University / Salzburger Landeskliniken (SALK), Salzburg, Austria
3
Laboratory of Photodynamic Inactivation of Microorganisms, Department of Materials Science and Physics, University of Salzburg, Salzburg, Austria
4
Division of Oncology, Medical University Graz, Graz, Austria
5 Department of Experimental Therapeutics, The University of Texas MD Anderson
Cancer Center, Houston, USA
6
Institute of Physiology and Pathophysiology, Paracelsus Medical University, Salzburg, Austria
Abstract
: Photodynamic therapy (PDT) is a palliative treatment option for unresectable hilar biliary tract cancer (hilar BTC) showing a considerable benefit for survival and quality of life with few side effects. Currently, factors determining the cellular response of BTC cells towards PDT are unknown. Due to their multifaceted nature, microRNAs (miRs) are a promising analyte to investigate the cellular mechanisms following PDT. For two photosensitizers, Photofrin® and Foscan®, the phototoxicity was investigated in eight BTC cell lines. Each cell line (untreated) was profiled for expression of n=754 miRs using TaqMan® Array Human MicroRNA Cards. Statistical analysis and bioinformatic tools were used to identify miRs associated with PDT efficiency and their putative targets, respectively. Nineteen miRs correlated significantly with either high or low PDT efficiency. PDT was particularly effective in cells with high levels of clustered miRs 25-106b and (in case of miR106b) a phenotype characterized by high expression of the mesenchymal marker vimentin and high proliferation (cyclinD1 and Ki67 expression). Insensitivity towards PDT was associated with high miR-200 family expression and (for miR-cluster 200a/b-429) expression of differentiation markers Ck19 and Ck8/18. Predicted and validated downstream targets indicate plausible involvement of miRs 130a, 25, 141, 200a, 200c and 203 in response mechanisms to PDT, suggesting that targeting these miRs could improve susceptibility to PDT in insensitive cell lines. Taken together, the miRNome pattern may provide a novel tool for predicting the efficiency of PDT and may subsequently allow for optimization of the PDT protocol.
Keywords: MicroRNAs; Bile Duct Cancer; Photodynamic Therapy; Cytotoxicity; Sensitivity

Type of Paper: Review
Title: Long non-coding RNA in Cancer and Development: Where do we go from here?
Authors
: Monika Haemmerle1,2 & Tony Gutschner3
1
Department of Gynecologic Oncology and Reproductive Medicine, Division of Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX
2
Institute of Pathology, University Hospital Heidelberg, Germany
3
Department of Genomic Medicine, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX
Abstract
: Recent genome-wide expression profiling studies have uncovered a huge amount of novel, long non-protein-coding RNA transcripts (lncRNA). In general, these transcripts possess a low, but tissue-specific expression, and their nucleotide sequences are often poorly conserved. However, several studies showed that lncRNAs can have important roles for normal tissue development and regulate cellular pluripotency as well as differentiation.  Moreover, lncRNAs are implicated in the control of multiple molecular pathways leading to gene expression changes and thus, ultimately modulate cell proliferation, migration and apoptosis. Consequently, deregulation of lncRNA expression contributes to carcinogenesis and is associated with human diseases, e.g. Alzheimer Disease. Here, we will focus on some major challenges of lncRNA research, e.g. gain- and loss-of-function studies, and we will discuss what can be learnt from previous pitfalls of in vivo animal models. Finally, we will highlight future opportunities for lncRNAs as disease biomarkers and potential therapeutic targets.
Keywords
: LincRNA; Functional Genomics; Cancer Therapy; Metastasis; MALAT1; HOTAIR; HULC

Type of Paper: review
Title
: Identification and validation methods of microRNA targets
Authors
: Karbiener M, Glantschnig C, Scheideler M
Affiliations
: RNA Biology Group, Institute of Molecular Biotechnology, Graz University of Technology, Petersgasse 14, 8010 Graz, Austria
Abstract
: MicroRNAs are natural, single-stranded, small RNA molecules that regulate gene expression by binding to target mRNAs and suppress its translation or initiate its degradation. In contrast to the identification and validation of many miRNA genes is the lack of experimental evidence identifying their corresponding mRNA targets. The most fundamental challenge in miRNA biology is to define the rules of miRNA target recognition. This is critical since the biological role of individual miRNAs will be dictated by the mRNAs that they regulate. Therefore, only as target mRNAs are validated will it be possible to establish commonalities that will enable more precise predictions of miRNA/mRNA interactions. Currently there is no clear agreement as to what experimental procedures should be followed to demonstrate that a given mRNA is a target of a specific miRNA. Therefore, this review outlines several methods by which to validate miRNA targets. Additionally, we propose that multiple criteria should be met before miRNA target validation should be considered "confirmed".
Keywords
: obesity, adipogenesis, microRNA, regulatory network,

Last update: 8 August 2014

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