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
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

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Published Papers (25 papers)

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2015  ( 16 papers )


2014  ( 9 papers )


2015
by , , , , , , ,  and
Int. J. Mol. Sci. 2015, 16(8), 19886-19919; doi:10.3390/ijms160819886
Received: 16 July 2015 / Revised: 16 August 2015 / Accepted: 17 August 2015 / Published: 21 August 2015
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Int. J. Mol. Sci. 2015, 16(8), 18732-18740; doi:10.3390/ijms160818732
Received: 4 July 2015 / Revised: 4 July 2015 / Accepted: 4 August 2015 / Published: 11 August 2015
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Int. J. Mol. Sci. 2015, 16(8), 18077-18095; doi:10.3390/ijms160818077
Received: 12 July 2015 / Revised: 28 July 2015 / Accepted: 30 July 2015 / Published: 5 August 2015
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by ,  and
Int. J. Mol. Sci. 2015, 16(7), 16593-16621; doi:10.3390/ijms160716593
Received: 29 May 2015 / Revised: 10 July 2015 / Accepted: 15 July 2015 / Published: 22 July 2015
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by ,  and
Int. J. Mol. Sci. 2015, 16(6), 12773-12790; doi:10.3390/ijms160612773
Received: 17 May 2015 / Revised: 28 May 2015 / Accepted: 29 May 2015 / Published: 5 June 2015
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by , , ,  and
Int. J. Mol. Sci. 2015, 16(5), 10491-10506; doi:10.3390/ijms160510491
Received: 16 March 2015 / Revised: 22 April 2015 / Accepted: 4 May 2015 / Published: 7 May 2015
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Int. J. Mol. Sci. 2015, 16(5), 9635-9653; doi:10.3390/ijms16059635
Received: 8 January 2015 / Revised: 24 March 2015 / Accepted: 13 April 2015 / Published: 29 April 2015
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Int. J. Mol. Sci. 2015, 16(4), 8555-8568; doi:10.3390/ijms16048555
Received: 26 February 2015 / Revised: 24 March 2015 / Accepted: 26 March 2015 / Published: 16 April 2015
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by , , , , ,  and
Int. J. Mol. Sci. 2015, 16(4), 6855-6867; doi:10.3390/ijms16046855
Received: 6 October 2014 / Revised: 10 November 2014 / Accepted: 13 November 2014 / Published: 26 March 2015
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by ,  and
Int. J. Mol. Sci. 2015, 16(3), 5467-5496; doi:10.3390/ijms16035467
Received: 12 December 2014 / Revised: 22 February 2015 / Accepted: 3 March 2015 / Published: 10 March 2015
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by ,  and
Int. J. Mol. Sci. 2015, 16(3), 4947-4972; doi:10.3390/ijms16034947
Received: 23 December 2014 / Revised: 17 February 2015 / Accepted: 17 February 2015 / Published: 4 March 2015
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Int. J. Mol. Sci. 2015, 16(2), 3251-3266; doi:10.3390/ijms16023251
Received: 17 November 2014 / Accepted: 22 January 2015 / Published: 3 February 2015
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Int. J. Mol. Sci. 2015, 16(1), 1395-1405; doi:10.3390/ijms16011395
Received: 16 December 2014 / Accepted: 30 December 2014 / Published: 8 January 2015
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by , , ,  and
Int. J. Mol. Sci. 2015, 16(1), 1448-1465; doi:10.3390/ijms16011448
Received: 1 December 2014 / Accepted: 30 December 2014 / Published: 8 January 2015
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Int. J. Mol. Sci. 2015, 16(1), 1466-1481; doi:10.3390/ijms16011466
Received: 31 October 2014 / Accepted: 5 January 2015 / Published: 8 January 2015
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Int. J. Mol. Sci. 2015, 16(1), 1192-1208; doi:10.3390/ijms16011192
Received: 22 November 2014 / Accepted: 26 December 2014 / Published: 6 January 2015
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2014
by , ,  and
Int. J. Mol. Sci. 2014, 15(11), 21554-21586; doi:10.3390/ijms151121554
Received: 19 September 2014 / Revised: 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 / Revised: 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 / Revised: 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 / Revised: 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 / Revised: 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 / Revised: 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 / Revised: 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 / Revised: 23 July 2014 / Accepted: 5 August 2014 / Published: 12 August 2014
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Int. J. Mol. Sci. 2014, 15(8), 13494-13513; doi:10.3390/ijms150813494
Received: 14 June 2014 / Revised: 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: MiR-16-5p is the most stable-expressed housekeeping microRNA in breast cancer tissues from primary and metastatic sites
Authors: Gabriel Rinnerthaler 1,†, Hubert Hackl 2, †, Simon Peter Gampenrieder 1, Frank Hamacher 1, Clemens Hufnagl 1, Franz Zehentmayr 3, Gerd Fastner 3, Felix Sedlmayer 3, Cornelia Hauser-Kronberger 4, Brigitte Mlineritsch 1, Richard Greil 1,
Affiliations: 1 IIIrd Medical Department, Salzburg Cancer Research Institute with Laboratory of Immunological and Molecular Cancer Research and Center for Clinical Cancer and Immunology Trials, Paracelsus Medical University Salzburg; E Mails: g.rinnerthaler@salk.at (G.R.); s.gampenrieder@salk.at (SP.G.); f.hamacher@salk.at (F.H.); cl.hufnagl@salk.at (C.H.); b.mlineritsch@salk.at (B.M.); r.greil@salk.at (R.G.)
2 Division of Bioinformatics, Biocenter, Medical University of Innsbruck, Innsbruck, Austria; E mail: hubert.hackl@i-med.ac.at (H.H.)
3 Department of Radiotherapy, Paracelsus Medical University Salzburg, Austria; E Mails: f.zehentmayr@salk.at (F.Z.); g.fastner@salk.at (G.F.); f.sedlmayer@salk.at (F.S.)
4 Department of Pathology, Paracelsus Medical University Salzburg, Salzburg, Austria; E mail: c.kronberger@salk.at (C.HR.)
These authors contributed equally to this work.
* Author to whom correspondence should be addressed; E-Mail: r.greil@salk.at Tel.: +43-662-4482-2879; Fax: +43-662-4482-2898.
Abstract: Background: For quantitative microRNA analyses in formalin-fixed paraffin-embedded (FFPE) tissue, expression levels have to be normalized to endogenous controls. To investigate the most stable-expressed microRNAs in breast cancer and its surrounding tissue, we used tumor samples from the primary and from metastatic sites.
Patients and methods: MiRNA profiling using TaqMan® Array MicroRNA Cards, enabling quantification of 754 unique human miRNAs, was performed in FFPE specimen from 58 patients with metastatic breast cancer. Forty-two (72%) samples came from primary tumor and 16 (28%) from metastasis. In a cross-platform analysis of a validation cohort of 32 FFPE samples from patients with early breast cancer genome-wide microRNA expression analysis using SurePrintG3 miRNA(8x60K)® microarrays from Agilent® was performed.
Results: Eleven microRNAs could be detected in all analyzed samples. Four of these microRNAs (miR-16-5p, miR-29a-3p miR-126-3p, miR-222-3p) showed also a high correlation with the median of all measured microRNAs (Spearman rank correlation rho ≥ 0.8) and with a coefficient of variation CV from 7 to 11%. In the cross-platform validation 29 human microRNAs were strongly expressed (mean log2-intensity > 10) and 21 of these microRNAs including miR-16-5p were also stably expressed (CV < 5%).
Conclusion: In breast cancer tissues from primary tumor and metastatic sites miR-16-5p is stably expressed and might be considered as most relevant housekeeping microRNA. In a cross-platform analysis of a validation cohort miR-16-5p was confirmed to be a valid endogenous control.

Title: Long non-coding RNAs in Endometrial Carcinoma
Authors: Maria A Smolle 1, Marc D Bullock 2, Hui Ling 3, Martin Pichler 4, Johannes Haybaeck 1
Affiliations: 1 Institute of Pathology, Medical University of Graz, Auenbruggerplatz 25, A-8036 Graz, Austria; E-Mails: maria.smolle@stud.medunigraz.at (MA.S.); Johannes.haybaeck@medunigraz.at (J.H.)
2 Cancer Sciences, Faculty of Medicine, University of Southampton Southampton, UK E-Mail: bullockmd@yahoo.co.uk (MD. B.)
3 Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Centerh, Houston, USA E-Mail: hling@mdanderson.org (H.L)
4 Division of Clinical Oncology, Department of Medicine, Medical University of Graz, Auenbruggerplatz 15, A-8036 Graz, Austria; E-Mail: martin.pichler@medunigraz.at (M.P.)
Corresponding Author: Johannes Haybaeck; Johannes.haybaeck@medunigraz.at; Tel: +43-316-385-80594; Fax: +43-316-384-329
Abstract: Endometrial carcinoma (EC), the second most common form of gynaecological malignancy, can be divided into two distinct sub-types: Type I tumours arise from hyperplastic endometrium and typically effect younger women, whereas type II tumours arise in postmenopausal women from atrophic endometrium.
Long non-coding RNAs (lncRNAs) are a novel class of non-protein coding molecules which have recently been implicated in the pathogenesis of all types of cancer including gynaecological tumours. Although they play critical physiological roles in cellular metabolism, their expression and function are deregulated in EC compared with paired normal tissue, indicating that they may also participate tumour initatiation and progression. For instance, the lncRNA MALAT-1 is down-regulated in EC samples compared to normal or hyperplastic endometrium, whereas the lncRNA OVAL is down-regulated in type II disease but up-regulated in type I disease. Other notatble lncRNAs such as HOTAIR, H19 and SRA become up-regulated with increasing EC tumour grade and other poor prognosis features.
In the current review, we will examine the growing body of evidence linking deregulated lncRNAs with specific biological functions of tumor cells in EC, we will highlight associations between lncRNAs and molecular pathways implicated in EC tumorogesis and we will identify critical knowledge gaps that remain to be addressed.
Keywords: long non-coding RNAs, endometrial carcinoma, cancer

Title: MicroRNAs and their clinical relevance in Colorectal Cancer
Authors: Joe Thomas, Masahisa Ohtsuka, Martin Pichler, Hui Ling
Affiliation: Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Centerh, Houston, USA E-Mail: hling@mdanderson.org (all authors)
Abstract: Colorectal cancer is one of the most common cancer diagnoses and causes of mortality worldwide. MicroRNAs are a class of small, non-coding regulatory RNAs that have shown intensive associations with colorectal cancer. Through the repression of target messenger RNAs, microRNAs modulate many cellular pathways, such as those involved in cell proliferation, apoptosis, and differentiation. The utilization of microRNAs has shown significant promise in the diagnosis and prognosis of colorectal cancer, owing to their unique expression profiles association with cancer types and malignancies. Moreover, microRNA therapeutics with mimics or antagonists show great promise in preclinical studies, which encourages further development of microRNA therapeutics into clinical usages for colorectal cancer patients. The unique ability of microRNAs to affect multiple downstream pathways represents a novel approach for cancer therapy. Although still early in its development, we believe that microRNAs can be used in the near future as biomarkers and therapeutic targets for colorectal cancer.
Keywords: colorectal cancer; miRNA; pathophysiology; diagnosis; prognosis; treatment

Title: Combination of miR-378 and miR-210 serum levels enables sensitive detection of renal cell carcinoma
Authors: Michal Fedorko a,*, Michal Stanik b,*, Robert Iliev c,d, Martina Redova-Lojova d, Tana Machackova d, Marek Svoboda c, Dalibor Pacik a, Jan Dolezel b, Ondrej Slaby c,d,#
Affiliations: a Department of Urology, University Hospital Brno and Masaryk University Brno, Jihlavska 20, 62500 Brno, Czech Republic,
b Masaryk Memorial Cancer Institute, Department of Urologic Oncology, Zluty kopec 7, 656 53, Brno, Czech Republic,
c Masaryk Memorial Cancer Institute, Department of Comprehensive Cancer Care, Zluty kopec 7, 656 53, Brno, Czech Republic,
d Masaryk University, Central European Institute of Technology, Kamenice 5, 625 00, Brno, Czech Republic.
* Equal contributors
# Corresponding Author: Assoc. Prof. Ondrej Slaby, Ph.D., Masaryk University, Central European Institute of Technology, Kamenice 5, 625 00, Brno, Czech Republic; Email: on.slaby@gmail.com; Tel.: 00420 54949 7574; Fax.: 00420 54949 757
Abstract: Background: Serum microRNAs are emerging as a clinically useful tool for early and non-invasive detection of various cancer types including renal cell carcinoma (RCC). Based on our previous results, we performed the study to analyze circulating serum miR-378 and miR-210 in patients with various histological subtypes of RCC. Methods: RNA was purified from blood serum samples of 195 RCC patients and 100 healthy controls. The levels of miR-378 and miR-210 in serum were determined absolutely using quantitative real-time PCR. Pre- and postoperative levels of both microRNAs were compared in 20 RCC patients. Results: Significantly increased serum levels of both miR-378 and miR-210 enabled to clearly distinguish RCC patients and healthy controls with 80% sensitivity and 78% specificity if analyzed in combination (p < 0.0001), and their levels significantly decreased in the time period of three months after radical nephrectomy (p ˂ 0.0001). Increased level of miR-378 positively correlates with disease-free survival (p = 0.036) and clinical stage (p = 0.0476). Conclusion: The analysis of serum miR-378 and miR-210 proved their potential to serve as powerful non-invasive diagnostic and prognostic biomarkers in RCC.

Last update: 21 August 2015

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