1
|
Huang P, Xia L, Guo Q, Huang C, Wang Z, Huang Y, Qin S, Leng W, Li D. Genome-wide association studies identify miRNA-194 as a prognostic biomarker for gastrointestinal cancer by targeting ATP6V1F, PPP1R14B, BTF3L4 and SLC7A5. Front Oncol 2022; 12:1025594. [PMID: 36620589 PMCID: PMC9815773 DOI: 10.3389/fonc.2022.1025594] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Accepted: 12/06/2022] [Indexed: 12/24/2022] Open
Abstract
Background The dysregulated genes and miRNAs in tumor progression can be used as biomarkers for tumor diagnosis and prognosis. However, the biomarkers for predicting the clinical outcome of gastrointestinal cancer (GIC) are still scarce. Methods Genome-wide association studies were performed to screen optimal prognostic miRNA biomarkers. RNA-seq, Ago-HITS-CLIP-seq, western blotting and qRT-PCR assays were conducted to identify target genes of miR-194. Genome-wide CRISPR-cas9 proliferation screening analysis were conducted to distinguish passenger gene and driver gene. Results A total of 9 prognostic miRNAs for GIC were identified by global microRNA expression analysis. Among them, miR-194 was the only one miRNA that significantly associated with overall survival, disease-specific survival and progress-free interval in both gastric, colorectal and liver cancers, indicating miR-194 was an optimal prognostic biomarker for GIC. RNA-seq analysis confirmed 18 conservative target genes of miR-194. Four of them, including ATP6V1F, PPP1R14B, BTF3L4 and SLC7A5, were directly targeted by miR-194 and required for cell proliferation. Cell proliferation assay validated that miR-194 inhibits cell proliferation by targeting ATP6V1F, PPP1R14B, BTF3L4 and SLC7A5 in GIC. Conclusion In summary, miR-194 is an optimal biomarker for predicting the outcome of GIC. Our finding highlights that miR-194 exerts a tumor-suppressive role in digestive system cancers by targeting ATP6V1F, PPP1R14B, BTF3L4 and SLC7A5.
Collapse
Affiliation(s)
- Pan Huang
- Department of Stomatology, Taihe Hospital and Hubei Key Laboratory of Embryonic Stem Cell Research, School of Basic Medical Sciences, Hubei University of Medicine, Shiyan, Hubei, China,Laboratory of Tumor Biology, Academy of Bio-Medicine Research, Hubei University of Medicine, Shiyan, Hubei, China
| | - Lingyun Xia
- Department of Stomatology, Taihe Hospital and Hubei Key Laboratory of Embryonic Stem Cell Research, School of Basic Medical Sciences, Hubei University of Medicine, Shiyan, Hubei, China
| | - Qiwei Guo
- Laboratory of Tumor Biology, Academy of Bio-Medicine Research, Hubei University of Medicine, Shiyan, Hubei, China
| | - Congcong Huang
- Laboratory of Tumor Biology, Academy of Bio-Medicine Research, Hubei University of Medicine, Shiyan, Hubei, China
| | - Zidi Wang
- Laboratory of Tumor Biology, Academy of Bio-Medicine Research, Hubei University of Medicine, Shiyan, Hubei, China
| | - Yinxuan Huang
- Laboratory of Tumor Biology, Academy of Bio-Medicine Research, Hubei University of Medicine, Shiyan, Hubei, China
| | - Shanshan Qin
- Department of Stomatology, Taihe Hospital and Hubei Key Laboratory of Embryonic Stem Cell Research, School of Basic Medical Sciences, Hubei University of Medicine, Shiyan, Hubei, China,Laboratory of Tumor Biology, Academy of Bio-Medicine Research, Hubei University of Medicine, Shiyan, Hubei, China,*Correspondence: Shanshan Qin, ; Weidong Leng, ; Dandan Li,
| | - Weidong Leng
- Department of Stomatology, Taihe Hospital and Hubei Key Laboratory of Embryonic Stem Cell Research, School of Basic Medical Sciences, Hubei University of Medicine, Shiyan, Hubei, China,*Correspondence: Shanshan Qin, ; Weidong Leng, ; Dandan Li,
| | - Dandan Li
- Department of Stomatology, Taihe Hospital and Hubei Key Laboratory of Embryonic Stem Cell Research, School of Basic Medical Sciences, Hubei University of Medicine, Shiyan, Hubei, China,Laboratory of Tumor Biology, Academy of Bio-Medicine Research, Hubei University of Medicine, Shiyan, Hubei, China,*Correspondence: Shanshan Qin, ; Weidong Leng, ; Dandan Li,
| |
Collapse
|
2
|
Makler A, Narayanan R, Asghar W. An Exosomal miRNA Biomarker for the Detection of Pancreatic Ductal Adenocarcinoma. BIOSENSORS 2022; 12:831. [PMID: 36290970 PMCID: PMC9599289 DOI: 10.3390/bios12100831] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 09/25/2022] [Accepted: 09/29/2022] [Indexed: 06/16/2023]
Abstract
Pancreatic ductal adenocarcinoma (PDAC) remains a difficult tumor to diagnose and treat. To date, PDAC lacks routine screening with no markers available for early detection. Exosomes are 40-150 nm-sized extracellular vesicles that contain DNA, RNA, and proteins. These exosomes are released by all cell types into circulation and thus can be harvested from patient body fluids, thereby facilitating a non-invasive method for PDAC detection. A bioinformatics analysis was conducted utilizing publicly available miRNA pancreatic cancer expression and genome databases. Through this analysis, we identified 18 miRNA with strong potential for PDAC detection. From this analysis, 10 (MIR31, MIR93, MIR133A1, MIR210, MIR330, MIR339, MIR425, MIR429, MIR1208, and MIR3620) were chosen due to high copy number variation as well as their potential to differentiate patients with chronic pancreatitis, neoplasms, and PDAC. These 10 were examined for their mature miRNA expression patterns, giving rise to 18 mature miRs for further analysis. Exosomal RNA from cell culture media was analyzed via RTqPCR and seven mature miRs exhibited statistical significance (miR-31-5p, miR-31-3p, miR-210-3p, miR-339-5p, miR-425-5p, miR-425-3p, and miR-429). These identified biomarkers can potentially be used for early detection of PDAC.
Collapse
Affiliation(s)
- Amy Makler
- Micro and Nanotechnology in Medicine, College of Engineering and Computer Science, Boca Raton, FL 33431, USA
- Department of Biomedical Science, Charles E. Schmidt College of Medicine, Florida Atlantic University, Boca Raton, FL 33431, USA
- Department of Biological Sciences, Florida Atlantic University, Boca Raton, FL 33431, USA
| | - Ramaswamy Narayanan
- Department of Biological Sciences, Florida Atlantic University, Boca Raton, FL 33431, USA
- Department of Biology, University of North Florida, Jacksonville, FL 32224, USA
| | - Waseem Asghar
- Micro and Nanotechnology in Medicine, College of Engineering and Computer Science, Boca Raton, FL 33431, USA
- Department of Computer & Electrical Engineering and Computer Science, Florida Atlantic University, Boca Raton, FL 33431, USA
| |
Collapse
|
3
|
Du X, He X, Liu Q, Liu Q, Di R, Chu M. Identification of photoperiod-induced specific miRNAs in the adrenal glands of Sunite sheep (Ovis aries). Front Vet Sci 2022; 9:888207. [PMID: 35937294 PMCID: PMC9354845 DOI: 10.3389/fvets.2022.888207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 07/05/2022] [Indexed: 11/18/2022] Open
Abstract
In seasonal estrus, it is well known that melatonin-regulated biorhythm plays a key role. Some studies indicate that the adrenal gland plays an important role in reproduction in mammals, but the molecular mechanism is not clear. This study used an artificially controlled light photoperiod model, combined with RNA-seq technology and bioinformatics analysis, to analyze the messenger RNA (mRNA) and microRNA (miRNA) of ewe (Sunite) adrenal glands under different photoperiod treatments. After identification, the key candidate genes GRHL2, CENPF, FGF16 and SLC25A30 that photoperiod affects reproduction were confirmed. The miRNAs (oar-miR-544-3p, oar-miR-411b-5p, oar-miR-376e-3p, oar-miR-376d, oar-miR-376b-3p, oar-miR-376a-3p) were specifically expressed in the adrenal gland. The candidate mRNA-miRNA pairs (e.g., SLC25A30 coagulated by novel miRNA554, novel miRNA555 and novel miRNA559) may affect seasonal estrus. In summary, we constructed relation network of the mRNAs and miRNAs of sheep adrenal glands using RNA sequencing and bioinformatics analysis, thereby, providing a valuable genetic variation resource for sheep genome research, which will contribute to the study of complex traits in sheep.
Collapse
Affiliation(s)
- Xiaolong Du
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences of Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xiaoyun He
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences of Chinese Academy of Agricultural Sciences, Beijing, China
| | - Qingqing Liu
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, China
| | - Qiuyue Liu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences of Chinese Academy of Agricultural Sciences, Beijing, China
| | - Ran Di
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences of Chinese Academy of Agricultural Sciences, Beijing, China
| | - Mingxing Chu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences of Chinese Academy of Agricultural Sciences, Beijing, China
- *Correspondence: Mingxing Chu
| |
Collapse
|
4
|
Kuo Y, Falk BW. Artificial microRNA guide strand selection from duplexes with no mismatches shows a purine-rich preference for virus- and non-virus-based expression vectors in plants. PLANT BIOTECHNOLOGY JOURNAL 2022; 20:1069-1084. [PMID: 35113475 PMCID: PMC9129084 DOI: 10.1111/pbi.13786] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/08/2020] [Revised: 01/18/2022] [Accepted: 01/24/2022] [Indexed: 06/14/2023]
Abstract
Artificial microRNA (amiRNA) technology has allowed researchers to direct efficient silencing of specific transcripts using as few as 21 nucleotides (nt). However, not all the artificially designed amiRNA constructs result in selection of the intended ~21-nt guide strand amiRNA. Selection of the miRNA guide strand from the mature miRNA duplex has been studied in detail in human and insect systems, but not so much for plants. Here, we compared a nuclear-replicating DNA viral vector (tomato mottle virus, ToMoV, based), a cytoplasmic-replicating RNA viral vector (tobacco mosaic virus, TMV, based), and a non-viral binary vector to express amiRNAs in plants. We then used deep sequencing and mutational analysis and show that when the structural factors caused by base mismatches in the mature amiRNA duplex were excluded, the nucleotide composition of the mature amiRNA region determined the guide strand selection. We found that the strand with excess purines was preferentially selected as the guide strand and the artificial miRNAs that had no mismatches in the amiRNA duplex were predominantly loaded into AGO2 instead of loading into AGO1 like the majority of the plant endogenous miRNAs. By performing assays for target effects, we also showed that only when the intended strand was selected as the guide strand and showed AGO loading, the amiRNA could provide the expected RNAi effects. Thus, by removing mismatches in the mature amiRNA duplex and designing the intended guide strand to contain excess purines provide better control of the guide strand selection of amiRNAs for functional RNAi effects.
Collapse
Affiliation(s)
- Yen‐Wen Kuo
- Department of Plant PathologyUniversity of California DavisDavisCAUSA
| | - Bryce W. Falk
- Department of Plant PathologyUniversity of California DavisDavisCAUSA
| |
Collapse
|
5
|
Medhi R, Price J, Furlan G, Gorges B, Sapetschnig A, Miska EA. RNA uridyl transferases TUT4/7 differentially regulate miRNA variants depending on the cancer cell type. RNA (NEW YORK, N.Y.) 2022; 28:353-370. [PMID: 34949722 PMCID: PMC8848932 DOI: 10.1261/rna.078976.121] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Accepted: 12/02/2021] [Indexed: 06/14/2023]
Abstract
The human terminal uridyl transferases TUT4 and TUT7 (TUT4/7) catalyze the additions of uridines at the 3' end of RNAs, including the precursors of the tumor suppressor miRNA let-7 upon recruitment by the oncoprotein LIN28A. As a consequence, let-7 family miRNAs are down-regulated. Disruption of this TUT4/7 activity inhibits tumorigenesis. Hence, targeting TUT4/7 could be a potential anticancer therapy. In this study, we investigate TUT4/7-mediated RNA regulation in two cancer cell lines by establishing catalytic knockout models. Upon TUT4/7 mutation, we observe a significant reduction in miRNA uridylation, which results in defects in cancer cell properties such as cell proliferation and migration. With the loss of TUT4/7-mediated miRNA uridylation, the uridylated miRNA variants are replaced by adenylated isomiRs. Changes in miRNA modification profiles are accompanied by deregulation of expression levels in specific cases. Unlike let-7s, most miRNAs do not depend on LIN28A for TUT4/7-mediated regulation. Additionally, we identify TUT4/7-regulated cell-type-specific miRNA clusters and deregulation in their corresponding mRNA targets. Expression levels of miR-200c-3p and miR-141-3p are regulated by TUT4/7 in a cancer cell-type-specific manner. Subsequently, BCL2, which is a well-established target of miR-200c is up-regulated. Therefore, TUT4/7 loss causes deregulation of miRNA-mRNA networks in a cell-type-specific manner. Understanding of the underlying biology of such cell-type-specific deregulation will be an important aspect of targeting TUT4/7 for potential cancer therapies.
Collapse
Affiliation(s)
- Ragini Medhi
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, United Kingdom
- Wellcome Trust Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge CB2 1QN, United Kingdom
| | - Jonathan Price
- Wellcome Trust Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge CB2 1QN, United Kingdom
| | - Giulia Furlan
- Wellcome Trust Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge CB2 1QN, United Kingdom
| | - Beronia Gorges
- STORM Therapeutics Limited, Moneta Building, Babraham Research Campus, Cambridge CB22 3AT, United Kingdom
| | - Alexandra Sapetschnig
- STORM Therapeutics Limited, Moneta Building, Babraham Research Campus, Cambridge CB22 3AT, United Kingdom
| | - Eric A Miska
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, United Kingdom
- Wellcome Trust Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge CB2 1QN, United Kingdom
| |
Collapse
|
6
|
Bryzgunova O, Konoshenko M, Zaporozhchenko I, Yakovlev A, Laktionov P. Isolation of Cell-Free miRNA from Biological Fluids: Influencing Factors and Methods. Diagnostics (Basel) 2021; 11:865. [PMID: 34064927 PMCID: PMC8151063 DOI: 10.3390/diagnostics11050865] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 04/29/2021] [Accepted: 05/04/2021] [Indexed: 12/11/2022] Open
Abstract
A vast wealth of recent research has seen attempts of using microRNA (miRNA) found in biological fluids in clinical research and medicine. One of the reasons behind this trend is the apparent their high stability of cell-free miRNA conferred by small size and packaging in supramolecular complexes. However, researchers in both basic and clinical settings often face the problem of selecting adequate methods to extract appropriate quality miRNA preparations for use in specific downstream analysis pipelines. This review outlines the variety of different methods of miRNA isolation from biofluids and examines the key determinants of their efficiency, including, but not limited to, the structural properties of miRNA and factors defining their stability in the extracellular environment.
Collapse
Affiliation(s)
- Olga Bryzgunova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch, Russian Academy of Sciences, 630090 Novosibirsk, Russia; (M.K.); (A.Y.); (P.L.)
- Meshalkin Siberian Federal Biomedical Research Center, Ministry of Public Health of the Russian Federation, 630055 Novosibirsk, Russia
| | - Maria Konoshenko
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch, Russian Academy of Sciences, 630090 Novosibirsk, Russia; (M.K.); (A.Y.); (P.L.)
- Meshalkin Siberian Federal Biomedical Research Center, Ministry of Public Health of the Russian Federation, 630055 Novosibirsk, Russia
| | - Ivan Zaporozhchenko
- Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus, Denmark;
| | - Alexey Yakovlev
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch, Russian Academy of Sciences, 630090 Novosibirsk, Russia; (M.K.); (A.Y.); (P.L.)
- Meshalkin Siberian Federal Biomedical Research Center, Ministry of Public Health of the Russian Federation, 630055 Novosibirsk, Russia
| | - Pavel Laktionov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch, Russian Academy of Sciences, 630090 Novosibirsk, Russia; (M.K.); (A.Y.); (P.L.)
- Meshalkin Siberian Federal Biomedical Research Center, Ministry of Public Health of the Russian Federation, 630055 Novosibirsk, Russia
| |
Collapse
|
7
|
Heydarzadeh S, Ranjbar M, Karimi F, Seif F, Alivand MR. Overview of host miRNA properties and their association with epigenetics, long non-coding RNAs, and Xeno-infectious factors. Cell Biosci 2021; 11:43. [PMID: 33632341 PMCID: PMC7905430 DOI: 10.1186/s13578-021-00552-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 02/06/2021] [Indexed: 12/19/2022] Open
Abstract
MicroRNA-derived structures play impressive roles in various biological processes. So dysregulation of miRNAs can lead to different human diseases. Recent studies have extended our comprehension of the control of miRNA function and features. Here, we overview some remarkable miRNA properties that have potential implications for the miRNA functions, including different variants of a miRNA called isomiRs, miRNA arm selection/arm switching, and the effect of these factors on miRNA target selection. Besides, we review some aspects of miRNA interactions such as the interaction between epigenetics and miRNA (different miRNAs and their related processing enzymes are epigenetically regulated by multiple DNA methylation enzymes. moreover, DNA methylation could be controlled by diverse mechanisms related to miRNAs), direct and indirect crosstalk between miRNA and lnc (Long Non-Coding) RNAs as a further approach to conduct intercellular regulation called "competing endogenous RNA" (ceRNA) that is involved in the pathogenesis of different diseases, and the interaction of miRNA activities and some Xeno-infectious (virus/bacteria/parasite) factors, which result in modulation of the pathogenesis of infections. This review provides some related studies to a better understanding of miRNA involvement mechanisms and overcoming the complexity of related diseases that may be applicable and useful to prognostic, diagnostic, therapeutic purposes and personalized medicine in the future.
Collapse
Affiliation(s)
- Samaneh Heydarzadeh
- Department of Medical Genetics, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Maryam Ranjbar
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Farokh Karimi
- Department of Biotechnology, Faculty of Science, University of Maragheh, Maragheh, Iran
| | - Farhad Seif
- Department of Immunology and Allergy, Academic Center for Education, Culture, and Research (ACECR), Tehran, Iran
- Neuroscience Research Center, Iran University of Medical Sciences, Tehran, Iran
| | - Mohammad Reza Alivand
- Department of Medical Genetics, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran.
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.
| |
Collapse
|
8
|
Boubaker G, Strempel S, Hemphill A, Müller N, Wang J, Gottstein B, Spiliotis M. Regulation of hepatic microRNAs in response to early stage Echinococcus multilocularis egg infection in C57BL/6 mice. PLoS Negl Trop Dis 2020; 14:e0007640. [PMID: 32442168 PMCID: PMC7244097 DOI: 10.1371/journal.pntd.0007640] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Accepted: 03/05/2020] [Indexed: 12/15/2022] Open
Abstract
We present a comprehensive analysis of the hepatic miRNA transcriptome at one month post-infection of experimental primary alveolar echinococcosis (AE), a parasitic infection caused upon ingestion of E. multilocularis eggs. Liver tissues were collected from infected and non-infected C57BL/6 mice, then small RNA libraries were prepared for next-generation sequencing (NGS). We conducted a Stem-loop RT-qPCR for validation of most dysregulated miRNAs. In infected mice, the expression levels of 28 miRNAs were significantly altered. Of these, 9 were up-regulated (fold change (FC) ≥ 1.5) and 19 were down-regulated (FC ≤ 0.66) as compared to the non-infected controls. In infected livers, mmu-miR-148a-3p and mmu-miR-101b-3p were 8- and 6-fold down-regulated, respectively, and the expression of mmu-miR-22-3p was reduced by 50%, compared to non-infected liver tissue. Conversely, significantly higher hepatic levels were noted for Mus musculus (mmu)-miR-21a-5p (FC = 2.3) and mmu-miR-122-5p (FC = 1.8). In addition, the relative mRNA expression levels of five genes (vegfa, mtor, hif1-α, fasn and acsl1) that were identified as targets of down-regulated miRNAs were significantly enhanced. All the five genes exhibited a higher expression level in livers of E. multilocularis infected mice compared to non-infected mice. Finally, we studied the issue related to functionally mature arm selection preference (5p and/or 3p) from the miRNA precursor and showed that 9 pre-miRNAs exhibited different arm selection preferences in normal versus infected liver tissues. In conclusion, this study provides first evidence that miRNAs are regulated early in primary murine AE. Our findings raise intriguing questions such as (i) how E. multilocularis affects hepatic miRNA expression;(ii) what are the alterations in miRNA expression patterns in more advanced AE-stages; and (iii) which hepatic cellular, metabolic and/or immunologic processes are modulated through altered miRNAs in AE. Thus, further research on the regulation of miRNAs during AE is needed, since miRNAs constitute an attractive potential option for development of novel therapeutic approaches against AE. Various infectious diseases in humans have been associated with altered expression patterns of microRNAs (miRNAs), a class of small non-coding RNAs involved in negative regulation of gene expression. Herein, we revealed that significant alteration of miRNAs expression occurred in murine liver subsequently to experimental infection with E. multilocularis eggs when compared to non-infected controls. At the early stage of murine AE, hepatic miRNAs were mainly down-regulated. Respective target genes of the most extensively down-regulated miRNAs were involved in angiogenesis and fatty acid synthesis. Furthermore, we found higher mRNA levels of three angiogenic and two lipogenic genes in E. multilocularis infected livers compared to non-infected controls. Angiogenesis and fatty acid biosynthesis may be beneficial for development of the E. multilocularis metacestodes. In fact the formation of new blood vessels in the periparasitic area may ensure that parasites are supplied with oxygen and nutrients and get rid of waste products. Additionally, E. multilocularis is not able to undertake de novo fatty acid synthesis, thus lipids must be scavenged from its host. More research on the regulation of the hepatic miRNA transcriptome at more advanced stages of AE is needed.
Collapse
Affiliation(s)
- Ghalia Boubaker
- Department of Infectious Diseases and Pathobiology, Institute of Parasitology, University of Bern, Bern, Switzerland
- Department of Clinical Biology B, Laboratory of Parasitology and Mycology, University of Monastir, Monastir, Tunisia
- * E-mail: (GB); (BG)
| | | | - Andrew Hemphill
- Department of Infectious Diseases and Pathobiology, Institute of Parasitology, University of Bern, Bern, Switzerland
| | - Norbert Müller
- Department of Infectious Diseases and Pathobiology, Institute of Parasitology, University of Bern, Bern, Switzerland
| | - Junhua Wang
- Department of Infectious Diseases and Pathobiology, Institute of Parasitology, University of Bern, Bern, Switzerland
| | - Bruno Gottstein
- Department of Infectious Diseases and Pathobiology, Institute of Parasitology, University of Bern, Bern, Switzerland
- Institute of Infectious Diseases, Faculty of Medicine, University of Berne, Berne, Switzerland
- * E-mail: (GB); (BG)
| | - Markus Spiliotis
- Department of Infectious Diseases and Pathobiology, Institute of Parasitology, University of Bern, Bern, Switzerland
| |
Collapse
|
9
|
Lin MH, Chen YZ, Lee MY, Weng KP, Chang HT, Yu SY, Dong BJ, Kuo FR, Hung LT, Liu LF, Chen WS, Tsai KW. Comprehensive identification of microRNA arm selection preference in lung cancer: miR-324-5p and -3p serve oncogenic functions in lung cancer. Oncol Lett 2018; 15:9818-9826. [PMID: 29844840 PMCID: PMC5958786 DOI: 10.3892/ol.2018.8557] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Accepted: 11/16/2017] [Indexed: 12/31/2022] Open
Abstract
MicroRNA (miRNA/miR) dysfunction is a hallmark of lung cancer, and results in the dysregulation of tumor suppressors and oncogenes during lung cancer progression. Selection of the 5p and 3p arms of miRNA is a mechanism that improves the modulation of miRNA biological functions and complicates the regulatory network in human types of cancer. However, the involvement of arm selection preference of miRNA in lung cancer remains unclear. In the present study, changes in miRNA arm selection preference were comprehensively identified in lung cancer and corresponding adjacent normal tissues by analyzing The Cancer Genome Atlas. Arm selection was revealed to be consistent in the majority of miRNAs in lung cancer. Only a few miRNAs had significantly altered arm selection preference in lung cancer. Among these, the biological functions of the individual arms of miR-324 were investigated further. The data revealed that miR-324-5p and -3p were significantly overexpressed in lung cancer cells. Ectopic expression of miR-324-5p significantly promoted cell proliferation and invasion in lung cancer cells, while miR-324-3p overexpression significantly increased cell proliferation but did not alter the invasion of lung cancer cells. In conclusion, the arm selection preference of miRNA may be an additional mechanism through which biological functions are modulated. The results of the present study provide a novel insight into the underlying mechanisms of lung cancer and may direct research into future therapies.
Collapse
Affiliation(s)
- Min-Hsi Lin
- Division of Chest Medicine, Kaohsiung Veterans General Hospital, Kaohsiung 813, Taiwan, R.O.C.,School of Medicine, National Yang-Ming University, Taipei 112, Taiwan, R.O.C
| | - You-Zuo Chen
- Department of Medical Education and Research, Kaohsiung Veterans General Hospital, Kaohsiung 813, Taiwan, R.O.C
| | - Mei-Yu Lee
- Department of Medical Education and Research, Kaohsiung Veterans General Hospital, Kaohsiung 813, Taiwan, R.O.C.,Department of Biological Science and Technology, I-Shou University, Kaohsiung 813, Taiwan, R.O.C
| | - Ken-Pen Weng
- School of Medicine, National Yang-Ming University, Taipei 112, Taiwan, R.O.C.,Department of Pediatrics, Kaohsiung Veterans General Hospital, Kaohsiung 813, Taiwan, R.O.C.,Department of Physical Therapy, Shu-Zen College of Medicine and Management, Kaohsiung 813, Taiwan, R.O.C
| | - Hong-Tai Chang
- Center for Geriatrics and Gerontology, Kaohsiung Veterans General Hospital, Kaohsiung 813, Taiwan, R.O.C.,Department of Surgery, Kaohsiung Veterans General Hospital, Kaohsiung 813, Taiwan, R.O.C
| | - Shou-Yu Yu
- Department of Medical Education and Research, Kaohsiung Veterans General Hospital, Kaohsiung 813, Taiwan, R.O.C
| | - Bo-Jhu Dong
- Department of Chemical Biology, National Pingtung University of Education, Pingtung 900, Taiwan, R.O.C
| | - Fan-Rong Kuo
- Department of Chemical Biology, National Pingtung University of Education, Pingtung 900, Taiwan, R.O.C
| | - Li-Tzu Hung
- Department of Chemical Biology, National Pingtung University of Education, Pingtung 900, Taiwan, R.O.C
| | - Li-Feng Liu
- Department of Biological Science and Technology, I-Shou University, Kaohsiung 813, Taiwan, R.O.C
| | - Wei-Shone Chen
- School of Medicine, National Yang-Ming University, Taipei 112, Taiwan, R.O.C.,Department of Surgery, Veterans General Hospital, Taipei 112, Taiwan, R.O.C
| | - Kuo-Wang Tsai
- Department of Medical Education and Research, Kaohsiung Veterans General Hospital, Kaohsiung 813, Taiwan, R.O.C.,Department of Chemical Biology, National Pingtung University of Education, Pingtung 900, Taiwan, R.O.C.,Institute of Biomedical Sciences, National Sun Yat-sen University, Kaohsiung 813, Taiwan, R.O.C
| |
Collapse
|
10
|
Pagès A, Dotu I, Pallarès-Albanell J, Martí E, Guigó R, Eyras E. The discovery potential of RNA processing profiles. Nucleic Acids Res 2018; 46:e15. [PMID: 29155959 PMCID: PMC5814818 DOI: 10.1093/nar/gkx1115] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2016] [Revised: 10/13/2017] [Accepted: 11/10/2017] [Indexed: 12/27/2022] Open
Abstract
Small non-coding RNAs (sncRNAs) are highly abundant molecules that regulate essential cellular processes and are classified according to sequence and structure. Here we argue that read profiles from size-selected RNA sequencing capture the post-transcriptional processing specific to each RNA family, thereby providing functional information independently of sequence and structure. We developed SeRPeNT, a new computational method that exploits reproducibility across replicates and uses dynamic time-warping and density-based clustering algorithms to identify, characterize and compare sncRNAs by harnessing the power of read profiles. We applied SeRPeNT to: (i) generate an extended human annotation with 671 new sncRNAs from known classes and 131 from new potential classes, (ii) show pervasive differential processing of sncRNAs between cell compartments and (iii) predict new molecules with miRNA-like behaviour from snoRNA, tRNA and long non-coding RNA precursors, potentially dependent on the miRNA biogenesis pathway. Furthermore, we validated experimentally four predicted novel non-coding RNAs: a miRNA, a snoRNA-derived miRNA, a processed tRNA and a new uncharacterized sncRNA. SeRPeNT facilitates fast and accurate discovery and characterization of sncRNAs at an unprecedented scale. SeRPeNT code is available under the MIT license at https://github.com/comprna/SeRPeNT.
Collapse
Affiliation(s)
- Amadís Pagès
- Pompeu Fabra University (UPF), E08003 Barcelona, Spain
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, E08003 Barcelona, Spain
| | - Ivan Dotu
- Pompeu Fabra University (UPF), E08003 Barcelona, Spain
- IMIM—Hospital del Mar Medical Research Institute, E08003 Barcelona, Spain
| | - Joan Pallarès-Albanell
- Pompeu Fabra University (UPF), E08003 Barcelona, Spain
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, E08003 Barcelona, Spain
| | - Eulàlia Martí
- Pompeu Fabra University (UPF), E08003 Barcelona, Spain
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, E08003 Barcelona, Spain
| | - Roderic Guigó
- Pompeu Fabra University (UPF), E08003 Barcelona, Spain
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, E08003 Barcelona, Spain
| | - Eduardo Eyras
- Pompeu Fabra University (UPF), E08003 Barcelona, Spain
- Catalan Institution for Research and Advanced Studies (ICREA), E08010 Barcelona, Spain
| |
Collapse
|
11
|
Xu L, Hu Y, Cao Y, Li J, Ma L, Li Y, Qi Y. An expression atlas of miRNAs in Arabidopsis thaliana. SCIENCE CHINA-LIFE SCIENCES 2017; 61:178-189. [PMID: 29197026 DOI: 10.1007/s11427-017-9199-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Accepted: 10/16/2017] [Indexed: 01/21/2023]
Abstract
MicroRNAs (miRNAs) are small non-coding RNAs that regulate a variety of biological processes. MiRNA expression often exhibits spatial and temporal specificity. However, genome-wide miRNA expression patterns in different organs during development of Arabidopsis thaliana have not yet been systemically investigated. In this study, we sequenced small RNA libraries generated from 27 different organ/tissue types, which cover the entire life cycle of Arabidopsis. Analysis of the sequencing data revealed that most miRNAs are ubiquitously expressed, whereas a small set of miRNAs display highly specific expression patterns. In addition, different miRNA members within the same family have distinct spatial and temporal expression patterns. Moreover, we found that some miRNAs are produced from different arms of their hairpin precursors at different developmental stages. This work provides new insights into the regulation of miRNA biogenesis and a rich resource for future investigation of miRNA functions in Arabidopsis.
Collapse
Affiliation(s)
- Le Xu
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Yugang Hu
- College of Biological Sciences, China Agricultural University, Beijing, 100094, China
| | - Ying Cao
- College of Life Sciences-Beijing Key Laboratory of Plant Gene Resources and Biotechnology for Carbon Reduction and Environmental Improvement, Capital Normal University, Beijing, 100048, China
| | - Jingrui Li
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China.,Tsinghua-Peking Center for Life Sciences, Beijing, 100084, China
| | - Ligeng Ma
- College of Life Sciences-Beijing Key Laboratory of Plant Gene Resources and Biotechnology for Carbon Reduction and Environmental Improvement, Capital Normal University, Beijing, 100048, China
| | - Yan Li
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China. .,Tsinghua-Peking Center for Life Sciences, Beijing, 100084, China.
| | - Yijun Qi
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China. .,Tsinghua-Peking Center for Life Sciences, Beijing, 100084, China.
| |
Collapse
|
12
|
MicroRNA-34 directly targets pair-rule genes and cytoskeleton component in the honey bee. Sci Rep 2017; 7:40884. [PMID: 28098233 PMCID: PMC5241629 DOI: 10.1038/srep40884] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Accepted: 12/12/2016] [Indexed: 01/06/2023] Open
Abstract
MicroRNAs (miRNAs) are key regulators of developmental processes, such as cell fate determination and differentiation. Previous studies showed Dicer knockdown in honeybee embryos disrupt the processing of functional mature miRNAs and impairs embryo patterning. Here we investigated the expression profiles of miRNAs in honeybee embryogenesis and the role of the highly conserved miR-34-5p in the regulation of genes involved in insect segmentation. A total of 221 miRNAs were expressed in honey bee embryogenesis among which 97 mature miRNA sequences have not been observed before. Interestingly, we observed a switch in dominance between the 5-prime and 3-prime arm of some miRNAs in different embryonic stages; however, most miRNAs present one dominant arm across all stages of embryogenesis. Our genome-wide analysis of putative miRNA-target networks and functional pathways indicates miR-34-5p is one of the most conserved and connected miRNAs associated with the regulation of genes involved in embryonic patterning and development. In addition, we experimentally validated that miR-34-5p directly interacts to regulatory elements in the 3'-untranslated regions of pair-rule (even-skipped, hairy, fushi-tarazu transcription factor 1) and cytoskeleton (actin5C) genes. Our study suggests that miR-34-5p may regulate the expression of pair-rule and cytoskeleton genes during early development and control insect segmentation.
Collapse
|
13
|
Gardiner AS, Gutierrez HL, Luo L, Davies S, Savage DD, Bakhireva LN, Perrone-Bizzozero NI. Alcohol Use During Pregnancy is Associated with Specific Alterations in MicroRNA Levels in Maternal Serum. Alcohol Clin Exp Res 2016; 40:826-37. [PMID: 27038596 PMCID: PMC4825401 DOI: 10.1111/acer.13026] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2015] [Accepted: 01/25/2016] [Indexed: 12/12/2022]
Abstract
Background Given the challenges of confirming prenatal alcohol exposure (PAE) during pregnancy using currently established biomarkers of alcohol consumption, we examined whether serum microRNAs (miRNAs) may serve as stable biomarkers for PAE. Alterations in the levels of specific circulating miRNAs have been associated with various disease states and in animal models of fetal alcohol spectrum disorder. Methods Pregnant women in this prospective study were recruited from substance abuse and general maternity clinics affiliated with the University of New Mexico. Serum was collected at the time of admission for delivery from 14 subjects who reported ≥1 binge‐drinking episode or ≥3 drinks/wk during pregnancy and 16 subjects who reported abstinence during pregnancy and tested negative for 5 ethanol biomarkers. Total RNA was isolated from serum and used for microarray analysis. Results False discovery rate‐corrected analyses of covariance revealed that 55 miRNAs were significantly altered between the 2 groups. Hierarchical clustering using only the significantly altered miRNAs grouped samples into alcohol‐consuming and non‐alcohol‐consuming individuals. Discriminant analysis then identified miRs‐122*, ‐126, ‐216b, ‐221*, ‐3119, ‐3942‐5p, ‐4704‐3p, ‐4743, ‐514‐5p, and ‐602 as the top 10 discriminators between the 2 groups. Ingenuity Pathway Analysis of putative miRNA targets illustrated that miRNAs identified in this study are involved in biological pathways that mediate the effects of alcohol, such as brain‐derived neurotrophic factor, ERK1/2, and PI3K/AKT signaling. Conclusions This is the first report of alterations in serum miRNA expression that are associated with alcohol use during human pregnancy. These results suggest that serum miRNAs could be useful as biomarkers of alcohol exposure.
Collapse
Affiliation(s)
- Amy S Gardiner
- Department of Neurosciences, University of New Mexico Health Sciences Center, Albuquerque, New Mexico
| | - Hilda L Gutierrez
- Department of Pharmacy Practice and Administrative Sciences, University of New Mexico Health Sciences Center, Albuquerque, New Mexico
| | - Li Luo
- Department of Internal Medicine, University of New Mexico Health Sciences Center, Albuquerque, New Mexico
| | - Suzy Davies
- Department of Neurosciences, University of New Mexico Health Sciences Center, Albuquerque, New Mexico
| | - Daniel D Savage
- Department of Neurosciences, University of New Mexico Health Sciences Center, Albuquerque, New Mexico.,Department of Pediatrics, University of New Mexico Health Sciences Center, Albuquerque, New Mexico
| | - Ludmila N Bakhireva
- Department of Pharmacy Practice and Administrative Sciences, University of New Mexico Health Sciences Center, Albuquerque, New Mexico.,Department of Internal Medicine, University of New Mexico Health Sciences Center, Albuquerque, New Mexico.,Department of Family and Community Medicine, University of New Mexico Health Sciences Center, Albuquerque, New Mexico
| | - Nora I Perrone-Bizzozero
- Department of Neurosciences, University of New Mexico Health Sciences Center, Albuquerque, New Mexico.,Department of Psychiatry and Behavioral Sciences, University of New Mexico Health Sciences Center, Albuquerque, New Mexico
| |
Collapse
|
14
|
Tsai KW, Leung CM, Lo YH, Chen TW, Chan WC, Yu SY, Tu YT, Lam HC, Li SC, Ger LP, Liu WS, Chang HT. Arm Selection Preference of MicroRNA-193a Varies in Breast Cancer. Sci Rep 2016; 6:28176. [PMID: 27307030 PMCID: PMC4910092 DOI: 10.1038/srep28176] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Accepted: 05/31/2016] [Indexed: 01/28/2023] Open
Abstract
MicroRNAs (miRNAs) are short noncoding RNAs derived from the 3′ and 5′ ends of the same precursor. However, the biological function and mechanism of miRNA arm expression preference remain unclear in breast cancer. We found significant decreases in the expression levels of miR-193a-5p but no significant differences in those of miR-193a-3p in breast cancer. MiR-193a-3p suppressed breast cancer cell growth and migration and invasion abilities, whereas miR-193a-5p suppressed cell growth but did not influence cell motility. Furthermore, NLN and CCND1, PLAU, and SEPN1 were directly targeted by miR-193a-5p and miR-193a-3p, respectively, in breast cancer cells. The endogenous levels of miR-193a-5p and miR-193a-3p were significantly increased by transfecting breast cancer cells with the 3′UTR of their direct targets. Comprehensive analysis of The Cancer Genome Atlas database revealed significant differences in the arm expression preferences of several miRNAs between breast cancer and adjacent normal tissues. Our results collectively indicate that the arm expression preference phenomenon may be attributable to the target gene amount during breast cancer progression. The miRNA arm expression preference may be a means of modulating miRNA function, further complicating the mRNA regulatory network. Our findings provide a new insight into miRNA regulation and an application for breast cancer therapy.
Collapse
Affiliation(s)
- Kuo-Wang Tsai
- Department of Medical Education and Research, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan.,Department of Chemical Biology, National Pingtung University of Education, Pingtung, Taiwan
| | - Chung-Man Leung
- Department of Radiation Oncology, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan
| | - Yi-Hao Lo
- Department of Family Medicine, Zuoying Branch of Kaohsiung Armed Forces General Hospital, Kaohsiung, Taiwan
| | - Ting-Wen Chen
- Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan.,Bioinformatics Center, Chang Gung University, Taoyuan, Taiwan
| | - Wen-Ching Chan
- Genomics &Proteomics Core Laboratory, Department of medical research, Kaohsiung, Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan
| | - Shou-Yu Yu
- Department of Medical Education and Research, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan
| | - Ya-Ting Tu
- Department of Medical Education and Research, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan
| | - Hing-Chung Lam
- Center For Geriatrics and Gerontology, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan
| | - Sung-Chou Li
- Genomics &Proteomics Core Laboratory, Department of medical research, Kaohsiung, Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan
| | - Luo-Ping Ger
- Department of Medical Education and Research, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan.,Institute of Biomedical Sciences, National Sun Yat-Sen University, Kaohsiung, Taiwan
| | - Wen-Shan Liu
- Department of Radiation Oncology, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan.,Department of Radiation Oncology, Tri-Service General Hospital, Taipei, Twiwan
| | - Hong-Tai Chang
- Center For Geriatrics and Gerontology, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan.,Department of Surgery, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan
| |
Collapse
|
15
|
Zhang Y, Zang Q, Xu B, Zheng W, Ban R, Zhang H, Yang Y, Hao Q, Iqbal F, Li A, Shi Q. IsomiR Bank: a research resource for tracking IsomiRs. Bioinformatics 2016; 32:2069-71. [DOI: 10.1093/bioinformatics/btw070] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Accepted: 02/01/2016] [Indexed: 12/14/2022] Open
|
16
|
Laganà A, Veneziano D, Spata T, Tang R, Zhu H, Mohler PJ, Kilic A. Identification of General and Heart-Specific miRNAs in Sheep (Ovis aries). PLoS One 2015; 10:e0143313. [PMID: 26599010 PMCID: PMC4657999 DOI: 10.1371/journal.pone.0143313] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Accepted: 11/03/2015] [Indexed: 12/18/2022] Open
Abstract
MicroRNAs (miRNAs or miRs) are small regulatory RNAs crucial for modulation of signaling pathways in multiple organs. While the link between miRNAs and heart disease has grown more readily apparent over the past three years, these data are primarily limited to small animal models or cell-based systems. Here, we performed a high-throughput RNA sequencing (RNAseq) analysis of left ventricle and other tissue from a pre-clinical ovine model. We identified 172 novel miRNA precursors encoding a total of 264 mature miRNAs. Notably, 84 precursors were detected in both the left ventricle and other tissues. However, 10 precursors, encoding 11 mature sequences, were specific to the left ventricle. Moreover, the total 168 novel miRNA precursors included 22 non-conserved ovine-specific sequences. Our data identify and characterize novel miRNAs in the left ventricle of sheep, providing fundamental new information for our understanding of protein regulation in heart and other tissues.
Collapse
Affiliation(s)
- Alessandro Laganà
- Department of Molecular Virology, Immunology and Medical Genetics, Comprehensive Cancer Center, The Ohio State University, Columbus, OH, United States of America
- * E-mail: (AL); (AK)
| | - Dario Veneziano
- Department of Molecular Virology, Immunology and Medical Genetics, Comprehensive Cancer Center, The Ohio State University, Columbus, OH, United States of America
- Department of Clinical and Molecular Biomedicine, University of Catania, Catania, Italy
| | - Tyler Spata
- Department of Surgery, The Ohio State University, Columbus, OH, United States of America
| | - Richard Tang
- Department of Surgery, The Ohio State University, Columbus, OH, United States of America
| | - Hua Zhu
- Department of Surgery, The Ohio State University, Columbus, OH, United States of America
| | - Peter J. Mohler
- The Davis Heart and Lung Research Institute, Departments of Physiology & Cell Biology and Internal Medicine, The Ohio State University Medical Center, Columbus, OH, United States of America
| | - Ahmet Kilic
- Department of Surgery, The Ohio State University, Columbus, OH, United States of America
- * E-mail: (AL); (AK)
| |
Collapse
|
17
|
Song J, Song J, Mo B, Chen X. Uridylation and adenylation of RNAs. SCIENCE CHINA. LIFE SCIENCES 2015; 58:1057-66. [PMID: 26563174 PMCID: PMC5089844 DOI: 10.1007/s11427-015-4954-9] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/05/2015] [Accepted: 10/15/2015] [Indexed: 11/26/2022]
Abstract
The posttranscriptional addition of nontemplated nucleotides to the 3' ends of RNA molecules can have a significant impact on their stability and biological function. It has been recently discovered that nontemplated addition of uridine or adenosine to the 3' ends of RNAs occurs in different organisms ranging from algae to humans, and on different kinds of RNAs, such as histone mRNAs, mRNA fragments, U6 snRNA, mature small RNAs and their precursors etc. These modifications may lead to different outcomes, such as increasing RNA decay, promoting or inhibiting RNA processing, or changing RNA activity. Growing pieces of evidence have revealed that such modifications can be RNA sequence-specific and subjected to temporal or spatial regulation in development. RNA tailing and its outcomes have been associated with human diseases such as cancer. Here, we review recent developments in RNA uridylation and adenylation and discuss the future prospects in this research area.
Collapse
Affiliation(s)
- JianBo Song
- Shenzhen Key Laboratory of Microbial Genetic Engineering, College of Life Science, Shenzhen University, Shenzhen, 518060, China
- Department of Biochemistry and Molecular Biology, College of Science, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Jun Song
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen, 518060, China
| | - BeiXin Mo
- Shenzhen Key Laboratory of Microbial Genetic Engineering, College of Life Science, Shenzhen University, Shenzhen, 518060, China.
| | - XueMei Chen
- Shenzhen Key Laboratory of Microbial Genetic Engineering, College of Life Science, Shenzhen University, Shenzhen, 518060, China.
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, CA, 92521, USA.
- Howard Hughes Medical Institute, University of California, Riverside, CA, 92521, USA.
| |
Collapse
|
18
|
Li R, Beaudoin F, Ammah AA, Bissonnette N, Benchaar C, Zhao X, Lei C, Ibeagha-Awemu EM. Deep sequencing shows microRNA involvement in bovine mammary gland adaptation to diets supplemented with linseed oil or safflower oil. BMC Genomics 2015; 16:884. [PMID: 26519053 PMCID: PMC4628385 DOI: 10.1186/s12864-015-1965-7] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2015] [Accepted: 09/30/2015] [Indexed: 11/29/2022] Open
Abstract
BACKGROUND Bovine milk fat composition is responsive to dietary manipulation providing an avenue to modify the content of fatty acids and especially some specific unsaturated fatty acid (USFA) isomers of benefit to human health. MicroRNAs (miRNAs) regulate gene expression but their specific roles in bovine mammary gland lipogenesis are unclear. The objective of this study was to determine the expression pattern of miRNAs following mammary gland adaptation to dietary supplementation with 5 % linseed or safflower oil using next generation RNA-sequencing. METHODS Twenty-four Canadian Holstein dairy cows (twelve per treatment) in mid lactation were fed a control diet (total mixed ration of corn:grass silages) for 28 days followed by a treatment period (control diet supplemented with 5 % linseed or safflower oil) of 28 days. Milk samples were collected weekly for fat and individual fatty acid determination. RNA from mammary gland biopsies harvested on day-14 (control period) and on days +7 and +28 (treatment period) from six randomly selected cows per treatment was subjected to small RNA sequencing. RESULTS Milk fat percentage decreased significantly (P < 0.001) during treatment with the two diets as compared to the control period. The individual saturated fatty acids C4:0, C6:0, C8:0, C14:0 and C16:0 decreased significantly (P < 0.05) while five USFAs (C14:1, C18:1n11t, C20:3n3, C20:5n3 and CLA:t10c12) increased remarkably (P < 0.05) in response to both treatments. Analysis of 361 million sequence reads generated 321 known bovine miRNAs and 176 novel miRNAs. The expression of fourteen and twenty-two miRNAs was affected (P < 0.05) by linseed and safflower oil treatments, respectively. Seven miRNAs including six up-regulated (bta-miR-199c, miR-199a-3p, miR-98, miR-378, miR-148b and miR-21-5p) and one down-regulated (bta-miR-200a) were found to be regulated (P < 0.05) by both treatments, and thus considered core differentially expressed (DE) miRNAs. The gene targets of core DE miRNAs have functions related to gene expression and general cellular metabolism (P < 0.05) and are enriched in four pathways of lipid metabolism (3-phosphoinositide biosynthesis, 3-phosphoinositide degradation, D-myo-inisitol-5-phosphate metabolism and the superpathway of inositol phosphate compounds). CONCLUSION Our results suggest that DE miRNAs in this study might be important regulators of bovine mammary lipogenesis and metabolism. The novel miRNAs identified in this study will further enrich the bovine miRNome repertoire and contribute to understanding mammary gland biology.
Collapse
Affiliation(s)
- Ran Li
- Agriculture and Agri-Food Canada, Dairy and Swine Research and Development Centre, Sherbrooke, Quebec, J1M 0C8, Canada
- College of Animal Science and Technology, Northwest A&F University, Xi'an, Shaanxi, 712100, China
| | - Frédéric Beaudoin
- Agriculture and Agri-Food Canada, Dairy and Swine Research and Development Centre, Sherbrooke, Quebec, J1M 0C8, Canada
| | - Adolf A Ammah
- Agriculture and Agri-Food Canada, Dairy and Swine Research and Development Centre, Sherbrooke, Quebec, J1M 0C8, Canada
| | - Nathalie Bissonnette
- Agriculture and Agri-Food Canada, Dairy and Swine Research and Development Centre, Sherbrooke, Quebec, J1M 0C8, Canada
| | - Chaouki Benchaar
- Agriculture and Agri-Food Canada, Dairy and Swine Research and Development Centre, Sherbrooke, Quebec, J1M 0C8, Canada
| | - Xin Zhao
- Department of Animal Science, McGill University, Ste-Anne-de-Bellevue, Quebec, H9X 3V9, Canada
| | - Chuzhao Lei
- College of Animal Science and Technology, Northwest A&F University, Xi'an, Shaanxi, 712100, China
| | - Eveline M Ibeagha-Awemu
- Agriculture and Agri-Food Canada, Dairy and Swine Research and Development Centre, Sherbrooke, Quebec, J1M 0C8, Canada.
| |
Collapse
|
19
|
Saiselet M, Gacquer D, Spinette A, Craciun L, Decaussin-Petrucci M, Andry G, Detours V, Maenhaut C. New global analysis of the microRNA transcriptome of primary tumors and lymph node metastases of papillary thyroid cancer. BMC Genomics 2015; 16:828. [PMID: 26487287 PMCID: PMC4618137 DOI: 10.1186/s12864-015-2082-3] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Accepted: 10/14/2015] [Indexed: 01/21/2023] Open
Abstract
Background Papillary Thyroid Cancer (PTC) is the most prevalent type of endocrine cancer. Its incidence has rapidly increased in recent decades but little is known regarding its complete microRNA transcriptome (miRNome). In addition, there is a need for molecular biomarkers allowing improved PTC diagnosis. Methods We performed small RNA deep-sequencing of 3 PTC, their matching normal tissues and lymph node metastases (LNM). We designed a new bioinformatics framework to handle each aspect of the miRNome: whole expression profiles, isomiRs distribution, non-templated additions distributions, RNA-editing or mutation. Results were validated experimentally by qRT-PCR on normal samples, tumors and LNM from 14 independent patients and in silico using the dataset from The Cancer Genome Atlas (small RNA deepsequencing of 59 normal samples, 495 PTC, and 8 LNM). Results We performed small RNA deep-sequencing of 3 PTC, their matching normal tissues and lymph node metastases (LNM). We designed a new bioinformatics framework to handle each aspect of the miRNome: whole expression profiles, isomiRs distribution, non-templated additions distributions, RNA-editing or mutation. Results were validated experimentally by qRT-PCR on normal samples, tumors and LNM from 14 independent patients and in silico using the dataset from The Cancer Genome Atlas (small RNA deep-sequencing of 59 normal samples, 495 PTC, and 8 LNM). We confirmed already described up-regulations of microRNAs in PTC, such as miR-146b-5p or miR-222-3p, but we also identified down-regulated microRNAs, such as miR-7-5p or miR-30c-2-3p. We showed that these down-regulations are linked to the tumorigenesis process of thyrocytes. We selected the 14 most down-regulated microRNAs in PTC and we showed that they are potential biomarkers of PTC samples. Nevertheless, they can distinguish histological classical variants and follicular variants of PTC in the TCGA dataset. In addition, 12 of the 14 down-regulated microRNAs are significantly less expressed in aggressive PTC compared to non-aggressive PTC. We showed that the associated aggressive expression profile is mainly due to the presence of the BRAF V600E mutation. In general, primary tumors and LNM presented similar microRNA expression profiles but specific variations like the down-regulation of miR-7-2-3p and miR-30c-2-3p in LNM were observed. Investigations of the 5p-to-3p arm expression ratios, non-templated additions or isomiRs distributions revealed no major implication in PTC tumorigenesis process or LNM appearance. Conclusions Our results showed that down-regulated microRNAs can be used as new potential common biomarkers of PTC and to distinguish main subtypes of PTC. MicroRNA expressions can be linked to the development of LNM of PTC. The bioinformatics framework that we have developed can be used as a starting point for the global analysis of any microRNA deep-sequencing data in an unbiased way. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-2082-3) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Manuel Saiselet
- IRIBHM, Université libre de Bruxelles, 808 route de Lennik, B-1070, Brussels, Belgium.
| | - David Gacquer
- IRIBHM, Université libre de Bruxelles, 808 route de Lennik, B-1070, Brussels, Belgium.
| | - Alex Spinette
- Tumor Bank of the J. Bordet Cancer Institute, 1000, Brussels, Belgium.
| | - Ligia Craciun
- Tumor Bank of the J. Bordet Cancer Institute, 1000, Brussels, Belgium.
| | - Myriam Decaussin-Petrucci
- Service d'anatomie et cytologie pathologiques, Centre Hospitalier Lyon Sud, 69495, Pierre Benite Cedex, France.
| | - Guy Andry
- J. Bordet Cancer Institute, Surgery Department, 1000, Brussels, Belgium.
| | - Vincent Detours
- IRIBHM, Université libre de Bruxelles, 808 route de Lennik, B-1070, Brussels, Belgium.
| | - Carine Maenhaut
- IRIBHM, Université libre de Bruxelles, 808 route de Lennik, B-1070, Brussels, Belgium. .,Welbio, Université libre de Bruxelles, Brussels, Belgium.
| |
Collapse
|
20
|
Kaushik A, Saraf S, Mukherjee SK, Gupta D. miRMOD: a tool for identification and analysis of 5' and 3' miRNA modifications in Next Generation Sequencing small RNA data. PeerJ 2015; 3:e1332. [PMID: 26623179 PMCID: PMC4662591 DOI: 10.7717/peerj.1332] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Accepted: 09/27/2015] [Indexed: 12/27/2022] Open
Abstract
In the past decade, the microRNAs (miRNAs) have emerged to be important regulators of gene expression across various species. Several studies have confirmed different types of post-transcriptional modifications at terminal ends of miRNAs. The reports indicate that miRNA modifications are conserved and functionally significant as it may affect miRNA stability and ability to bind mRNA targets, hence affecting target gene repression. Next Generation Sequencing (NGS) of the small RNA (sRNA) provides an efficient and reliable method to explore miRNA modifications. The need for dedicated software, especially for users with little knowledge of computers, to determine and analyze miRNA modifications in sRNA NGS data, motivated us to develop miRMOD. miRMOD is a user-friendly, Microsoft Windows and Graphical User Interface (GUI) based tool for identification and analysis of 5′ and 3′ miRNA modifications (non-templated nucleotide additions and trimming) in sRNA NGS data. In addition to identification of miRNA modifications, the tool also predicts and compares the targets of query and modified miRNAs. In order to compare binding affinities for the same target, miRMOD utilizes minimum free energies of the miRNA:target and modified-miRNA:target interactions. Comparisons of the binding energies may guide experimental exploration of miRNA post-transcriptional modifications. The tool is available as a stand-alone package to overcome large data transfer problems commonly faced in web-based high-throughput (HT) sequencing data analysis tools. miRMOD package is freely available at http://bioinfo.icgeb.res.in/miRMOD.
Collapse
Affiliation(s)
- Abhinav Kaushik
- Bioinformatics Laboratory, SCB Group, International Centre for Genetic Engineering & Biotechnology, New Delhi, India
| | - Shradha Saraf
- Bioinformatics Laboratory, SCB Group, International Centre for Genetic Engineering & Biotechnology, New Delhi, India
| | - Sunil K Mukherjee
- Department of Genetics, University of Delhi, South Campus, Delhi, India
| | - Dinesh Gupta
- Bioinformatics Laboratory, SCB Group, International Centre for Genetic Engineering & Biotechnology, New Delhi, India
| |
Collapse
|
21
|
Basanta-Sanchez M, Temple S, Ansari SA, D'Amico A, Agris PF. Attomole quantification and global profile of RNA modifications: Epitranscriptome of human neural stem cells. Nucleic Acids Res 2015; 44:e26. [PMID: 26438536 PMCID: PMC4756851 DOI: 10.1093/nar/gkv971] [Citation(s) in RCA: 82] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Accepted: 09/15/2015] [Indexed: 01/09/2023] Open
Abstract
Exploration of the epitranscriptome requires the development of highly sensitive and accurate technologies in order to elucidate the contributions of the more than 100 RNA modifications to cell processes. A highly sensitive and accurate ultra-high performance liquid chromatography—tandem mass spectrometry method was developed to simultaneously detect and quantify 28 modified and four major nucleosides in less than 20 min. Absolute concentrations were calculated using extinction coefficients of each of the RNA modifications studied. A comprehensive RNA modifications database of UV profiles and extinction coefficient is reported within a 2.3–5.2 % relative standard deviation. Excellent linearity was observed 0.99227–0.99999 and limit of detection values ranged from 63.75 attomoles to 1.21 femtomoles. The analytical performance was evaluated by analyzing RNA modifications from 100 ng of RNA from human pluripotent stem cell-derived neural cells. Modifications were detected at concentrations four orders of magnitude lower than the corresponding parental nucleosides, and as low as 23.01 femtograms, 64.09 attomoles. Direct and global quantitative analysis of RNA modifications are among the advantages of this new approach.
Collapse
Affiliation(s)
| | | | | | - Anna D'Amico
- The RNA Institute, University at Albany, Albany, NY, USA
| | - Paul F Agris
- The RNA Institute, University at Albany, Albany, NY, USA
| |
Collapse
|
22
|
Vitsios DM, Enright AJ. Chimira: analysis of small RNA sequencing data and microRNA modifications. Bioinformatics 2015; 31:3365-7. [PMID: 26093149 PMCID: PMC4595902 DOI: 10.1093/bioinformatics/btv380] [Citation(s) in RCA: 77] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2015] [Accepted: 06/16/2015] [Indexed: 01/01/2023] Open
Abstract
Summary: Chimira is a web-based system for microRNA (miRNA) analysis from small RNA-Seq data. Sequences are automatically cleaned, trimmed, size selected and mapped directly to miRNA hairpin sequences. This generates count-based miRNA expression data for subsequent statistical analysis. Moreover, it is capable of identifying epi-transcriptomic modifications in the input sequences. Supported modification types include multiple types of 3′-modifications (e.g. uridylation, adenylation), 5′-modifications and also internal modifications or variation (ADAR editing or single nucleotide polymorphisms). Besides cleaning and mapping of input sequences to miRNAs, Chimira provides a simple and intuitive set of tools for the analysis and interpretation of the results (see also Supplementary Material). These allow the visual study of the differential expression between two specific samples or sets of samples, the identification of the most highly expressed miRNAs within sample pairs (or sets of samples) and also the projection of the modification profile for specific miRNAs across all samples. Other tools have already been published in the past for various types of small RNA-Seq analysis, such as UEA workbench, seqBuster, MAGI, OASIS and CAP-miRSeq, CPSS for modifications identification. A comprehensive comparison of Chimira with each of these tools is provided in the Supplementary Material. Chimira outperforms all of these tools in total execution speed and aims to facilitate simple, fast and reliable analysis of small RNA-Seq data allowing also, for the first time, identification of global microRNA modification profiles in a simple intuitive interface. Availability and implementation: Chimira has been developed as a web application and it is accessible here: http://www.ebi.ac.uk/research/enright/software/chimira. Contact:aje@ebi.ac.uk Supplementary information:Supplementary data are available at Bioinformatics online.
Collapse
Affiliation(s)
- Dimitrios M Vitsios
- European Molecular Biology Laboratory-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Anton J Enright
- European Molecular Biology Laboratory-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| |
Collapse
|
23
|
Evolutionary and expression analysis of miR-#-5p and miR-#-3p at the miRNAs/isomiRs levels. BIOMED RESEARCH INTERNATIONAL 2015; 2015:168358. [PMID: 26075215 PMCID: PMC4436453 DOI: 10.1155/2015/168358] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/12/2014] [Revised: 09/27/2014] [Accepted: 09/29/2014] [Indexed: 11/18/2022]
Abstract
We mainly discussed miR-#-5p and miR-#-3p under three aspects: (1) primary evolutionary analysis of human miRNAs; (2) evolutionary analysis of miRNAs from different arms across the typical 10 vertebrates; (3) expression pattern analysis of miRNAs at the miRNA/isomiR levels using public small RNA sequencing datasets. We found that no bias can be detected between the numbers of 5p-miRNA and 3p-miRNA, while miRNAs from miR-#-5p and miR-#-3p show variable nucleotide compositions. IsomiR expression profiles from the two arms are always stable, but isomiR expressions in diseased samples are prone to show larger degree of dispersion. miR-#-5p and miR-#-3p have relative independent evolution/expression patterns and datasets of target mRNAs, which might also contribute to the phenomena of arm selection and/or arm switching. Simultaneously, miRNA/isomiR expression profiles may be regulated via arm selection and/or arm switching, and the dynamic miRNAome and isomiRome will adapt to functional and/or evolutionary pressures. A comprehensive analysis and further experimental study at the miRNA/isomiR levels are quite necessary for miRNA study.
Collapse
|
24
|
Asikainen S, Heikkinen L, Juhila J, Holm F, Weltner J, Trokovic R, Mikkola M, Toivonen S, Balboa D, Lampela R, Icay K, Tuuri T, Otonkoski T, Wong G, Hovatta O. Selective microRNA-Offset RNA expression in human embryonic stem cells. PLoS One 2015; 10:e0116668. [PMID: 25822230 PMCID: PMC4378994 DOI: 10.1371/journal.pone.0116668] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2014] [Accepted: 12/11/2014] [Indexed: 12/26/2022] Open
Abstract
Small RNA molecules, including microRNAs (miRNAs), play critical roles in regulating pluripotency, proliferation and differentiation of embryonic stem cells. miRNA-offset RNAs (moRNAs) are similar in length to miRNAs, align to miRNA precursor (pre-miRNA) loci and are therefore believed to derive from processing of the pre-miRNA hairpin sequence. Recent next generation sequencing (NGS) studies have reported the presence of moRNAs in human neurons and cancer cells and in several tissues in mouse, including pluripotent stem cells. In order to gain additional knowledge about human moRNAs and their putative development-related expression, we applied NGS of small RNAs in human embryonic stem cells (hESCs) and fibroblasts. We found that certain moRNA isoforms are notably expressed in hESCs from loci coding for stem cell-selective or cancer-related miRNA clusters. In contrast, we observed only sparse moRNAs in fibroblasts. Consistent with earlier findings, most of the observed moRNAs derived from conserved loci and their expression did not appear to correlate with the expression of the adjacent miRNAs. We provide here the first report of moRNAs in hESCs, and their expression profile in comparison to fibroblasts. Moreover, we expand the repertoire of hESC miRNAs. These findings provide an expansion on the known repertoire of small non-coding RNA contents in hESCs.
Collapse
Affiliation(s)
- Suvi Asikainen
- Department of Clinical Science, Intervention and Technology, Karolinska Institutet, 17177, Stockholm, Sweden
- Research Programs Unit, Molecular Neurology and Biomedicum Stem Cell Centre, University of Helsinki, 00014, Helsinki, Finland
- * E-mail:
| | - Liisa Heikkinen
- A.I. Virtanen Institute, University of Eastern Finland, 70211, Kuopio, Finland
- Department of Biological and Environmental Science, University of Jyvaskyla, 40014, Jyvaskyla, Finland
| | - Juuso Juhila
- Research Programs Unit, Molecular Neurology and Biomedicum Stem Cell Centre, University of Helsinki, 00014, Helsinki, Finland
| | - Frida Holm
- Department of Clinical Science, Intervention and Technology, Karolinska Institutet, 17177, Stockholm, Sweden
| | - Jere Weltner
- Research Programs Unit, Molecular Neurology and Biomedicum Stem Cell Centre, University of Helsinki, 00014, Helsinki, Finland
| | - Ras Trokovic
- Research Programs Unit, Molecular Neurology and Biomedicum Stem Cell Centre, University of Helsinki, 00014, Helsinki, Finland
| | - Milla Mikkola
- Research Programs Unit, Molecular Neurology and Biomedicum Stem Cell Centre, University of Helsinki, 00014, Helsinki, Finland
| | - Sanna Toivonen
- Research Programs Unit, Molecular Neurology and Biomedicum Stem Cell Centre, University of Helsinki, 00014, Helsinki, Finland
| | - Diego Balboa
- Research Programs Unit, Molecular Neurology and Biomedicum Stem Cell Centre, University of Helsinki, 00014, Helsinki, Finland
| | - Riina Lampela
- Department of Clinical Science, Intervention and Technology, Karolinska Institutet, 17177, Stockholm, Sweden
| | - Katherine Icay
- Research Programs Unit, Molecular Neurology and Biomedicum Stem Cell Centre, University of Helsinki, 00014, Helsinki, Finland
| | - Timo Tuuri
- Research Programs Unit, Molecular Neurology and Biomedicum Stem Cell Centre, University of Helsinki, 00014, Helsinki, Finland
| | - Timo Otonkoski
- Research Programs Unit, Molecular Neurology and Biomedicum Stem Cell Centre, University of Helsinki, 00014, Helsinki, Finland
- Children’s Hospital, Helsinki University Central Hospital, 00029, Helsinki, Finland
| | - Garry Wong
- A.I. Virtanen Institute, University of Eastern Finland, 70211, Kuopio, Finland
- Faculty of Health Sciences, University of Macau, Taipa, Macau S.A.R., China
| | - Outi Hovatta
- Department of Clinical Science, Intervention and Technology, Karolinska Institutet, 17177, Stockholm, Sweden
| |
Collapse
|
25
|
Evaluation and application of the strand-specific protocol for next-generation sequencing. BIOMED RESEARCH INTERNATIONAL 2015; 2015:182389. [PMID: 25893191 PMCID: PMC4393923 DOI: 10.1155/2015/182389] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/11/2014] [Accepted: 02/03/2015] [Indexed: 12/02/2022]
Abstract
Next-generation sequencing (NGS) has become a powerful sequencing tool, applied in a wide range of biological studies. However, the traditional sample preparation protocol for NGS is non-strand-specific (NSS), leading to biased estimates of expression for transcripts overlapped at the antisense strand. Strand-specific (SS) protocols have recently been developed. In this study, we prepared the same RNA sample by using the SS and NSS protocols, followed by sequencing with Illumina HiSeq platform. Using real-time quantitative PCR as a standard, we first proved that the SS protocol more precisely estimates gene expressions compared with the NSS protocol, particularly for those overlapped at the antisense strand. In addition, we also showed that the sequence reads from the SS protocol are comparable with those from conventional NSS protocols in many aspects. Finally, we also mapped a fraction of sequence reads back to the antisense strand of the known genes, originally without annotated genes located. Using sequence assembly and PCR validation, we succeeded in identifying and characterizing the novel antisense genes. Our results show that the SS protocol performs more accurately than the traditional NSS protocol and can be applied in future studies.
Collapse
|
26
|
Zhang H, Yang S, Guo L, Zhao Y, Shao F, Chen F. Comparisons of isomiR patterns and classification performance using the rank-based MANOVA and 10-fold cross-validation. Gene 2014; 569:21-6. [PMID: 25447923 DOI: 10.1016/j.gene.2014.11.026] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2014] [Revised: 11/07/2014] [Accepted: 11/11/2014] [Indexed: 12/29/2022]
Abstract
Next generation sequencing technology has identified a series of miRNA variants (named "isomiRs"), which might be associated with cancer progression. We provide a new strategy to reanalyze the miR-seq datasets through a view of the isomiR spectrum. Firstly, differentially expressed (DE) isomiRs were detected with the DESeq algorithm based on negative binomial distribution. Secondly, the rank-based MANOVA was adopted to compare the isomiR patterns between normal and tumor tissues. Moreover, a comprehensive survey on classification performance of three features was conducted, including the logistic regression, k-nearest neighbors and Random Forest. Finally, functional enrichment analysis was performed with the putative targets of specific isomiRs to elucidate their biological functions. Furthermore, the methods were applied to the downloaded miR-seq datasets of breast invasive carcinoma from TCGA. We found that the expression levels of multiple isomiRs derived from the same miRNA locus showed significant inconsistency between normal and tumor samples. In most cases, logistic regression with multiple DE isomiRs was superior to the others, with highest AUC and lowest AIC. Similarly, DE isomiRs performed best in the average accuracy of standard classifiers. Integrated targets were significantly enriched in some cancer-related pathways, including MAPK signaling pathway, and focal adhesion. Collectively, we could recommend the rank-based MANOVA for comparing different isomiR patterns, and further investigation on isomiRs needs to be considered in miRNA sequencing research.
Collapse
Affiliation(s)
- Hui Zhang
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing 211166, China
| | - Sheng Yang
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing 211166, China
| | - Li Guo
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing 211166, China
| | - Yang Zhao
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing 211166, China
| | - Fang Shao
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing 211166, China
| | - Feng Chen
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing 211166, China.
| |
Collapse
|
27
|
miRSeq: a user-friendly standalone toolkit for sequencing quality evaluation and miRNA profiling. BIOMED RESEARCH INTERNATIONAL 2014; 2014:462135. [PMID: 25114903 PMCID: PMC4119685 DOI: 10.1155/2014/462135] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/07/2014] [Revised: 05/24/2014] [Accepted: 05/25/2014] [Indexed: 11/17/2022]
Abstract
MicroRNAs (miRNAs) present diverse regulatory functions in a wide range of biological activities. Studies on miRNA functions generally depend on determining miRNA expression profiles between libraries by using a next-generation sequencing (NGS) platform. Currently, several online web services are developed to provide small RNA NGS data analysis. However, the submission of large amounts of NGS data, conversion of data format, and limited availability of species bring problems. In this study, we developed miRSeq to provide alternatives. To test the performance, we had small RNA NGS data from four species, including human, rat, fly, and nematode, analyzed with miRSeq. The alignments results indicate that miRSeq can precisely evaluate the sequencing quality of samples regarding percentage of self-ligation read, read length distribution, and read category. miRSeq is a user-friendly standalone toolkit featuring a graphical user interface (GUI). After a simple installation, users can easily operate miRSeq on a PC or laptop by using a mouse. Within minutes, miRSeq yields useful miRNA data, including miRNA expression profiles, 3′ end modification patterns, and isomiR forms. Moreover, miRSeq supports the analysis of up to 105 animal species, providing higher flexibility.
Collapse
|
28
|
Hu W, Wang T, Yue E, Zheng S, Xu JH. Flexible microRNA arm selection in rice. Biochem Biophys Res Commun 2014; 447:526-30. [PMID: 24746469 DOI: 10.1016/j.bbrc.2014.04.036] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2014] [Accepted: 04/07/2014] [Indexed: 10/25/2022]
Abstract
MicroRNAs act at the post-transcriptional level and guide Argonaute proteins to cleave their corresponding target transcripts. However, little attention has been paid to arm selection in miRNA precursors. In this study, small RNA high-throughput sequencing data from 29 different rice libraries were pooled to investigate tissue- and abiotic stress-specific dynamic expression of miRNAs. We found that more than half of pre-miRNAs showed changes in arm selection in different tissues and/or under different abiotic stresses. Our findings suggest that miRNA selection is remarkably prevalent in plants, providing new insights into the role of miRNAs in plant growth and development.
Collapse
Affiliation(s)
- Wangxiong Hu
- College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China; Institute of Crop Science, Zhejiang Key Laboratory of Crop Germplasm, Zhejiang University, Hangzhou, Zhejiang 310058, China; Zhejiang-California International Nanosystems Institute, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Tingzhang Wang
- Institute of Crop Science, Zhejiang Key Laboratory of Crop Germplasm, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Erkui Yue
- Institute of Crop Science, Zhejiang Key Laboratory of Crop Germplasm, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Shu Zheng
- Zhejiang-California International Nanosystems Institute, Zhejiang University, Hangzhou, Zhejiang 310058, China; Cancer Institute, Second Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang 310009, China.
| | - Jian-Hong Xu
- Institute of Crop Science, Zhejiang Key Laboratory of Crop Germplasm, Zhejiang University, Hangzhou, Zhejiang 310058, China.
| |
Collapse
|
29
|
Leung CM, Li SC, Chen TW, Ho MR, Hu LY, Liu WS, Wu TT, Hsu PC, Chang HT, Tsai KW. Comprehensive microRNA profiling of prostate cancer cells after ionizing radiation treatment. Oncol Rep 2014; 31:1067-78. [PMID: 24452514 PMCID: PMC3926670 DOI: 10.3892/or.2014.2988] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2013] [Accepted: 12/23/2013] [Indexed: 12/19/2022] Open
Abstract
MicroRNAs (miRNAs) are small, non-coding RNAs that negatively regulate gene expression and have emerged as potential biomarkers in radiation response to human cancer. Only a few miRNAs have been identified in radiation response to prostate cancer and the involvement of the radiation-associated miRNA machinery in the response of prostate cancer cells to radiation is not thoroughly understood. Therefore, the purpose of the present study was to comprehensively investigate the expression levels, arm selection preference and isomiRs of radiation-response miRNAs in radiation-treated PC3 cells using a next-generation sequencing (NGS) approach. Our data revealed that the arm selection preference and 3′ modification of miRNAs may be altered in prostate cancer after radiation exposure. In addition, the proportion of AA dinucleotide modifications at the end of the read gradually increased in a time-dependent manner after PC3 radiation treatment. We also identified 6 miRNAs whose expression increased and 16 miRNAs whose expression decreased after exposure to 10 Gy of radiation. A pathway enrichment analysis revealed that the target genes of these radiation-induced miRNAs significantly co-modulated the radiation response pathway, including the mitogen-activated protein kinase (MAPK), Wnt, transforming growth factor-β (TGF-β) and ErbB signaling pathways. Furthermore, analysis of The Cancer Genome Atlas (TCGA) database revealed that the expression of these radiation-induced miRNAs was frequently dysregulated in prostate cancer. Our study identified radiation-induced miRNA candidates which may contribute to radiosensitivity and can be used as biomarkers for radiotherapy.
Collapse
Affiliation(s)
- Chung-Man Leung
- Department of Radiation Oncology, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan, R.O.C
| | - Sung-Chou Li
- Genomics and Proteomics Core Laboratory, Department of Medical Research, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan, R.O.C
| | - Ting-Wen Chen
- Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan, R.O.C
| | - Meng-Ru Ho
- Genomics Research Center, Academia Sinica, Taipei, Taiwan, R.O.C
| | - Ling-Yueh Hu
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan, R.O.C
| | - Wen-Shan Liu
- Department of Radiation Oncology, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan, R.O.C
| | - Tony T Wu
- Department of Surgery, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan, R.O.C
| | - Ping-Chi Hsu
- Department of Safety, Health and Environmental Engineering, National Kaohsiung First University of Science and Technology, Kaohsiung, Taiwan, R.O.C
| | - Hong-Tai Chang
- Department of Surgery, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan, R.O.C
| | - Kuo-Wang Tsai
- Department of Medical Education and Research, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan, R.O.C
| |
Collapse
|
30
|
Abstract
A mature miRNA may be generated from 5p or 3p arm of a hairpin precursor. The selection may be flexible via "arm switching". However, accumulating evidences suggest that both arms of many pre-miRNAs can yield mature functional miRNAs. Herein, we attempted to compare the isomiR expression profiles between the two arms through analyzing in-house and published small RNA deep sequencing datasets. Although many miR-#-5p and miR-#-3p have been reported as functional miRNAs, fewer miRNA pairs (11 and 6 pairs are collected in tumor and normal cells, respectively) are simultaneously identified as abundant miRNA species. According to isomiR types and dominant isomiR species, miR-#-5p and miR-#-3p show various isomiR expression profiles as well as diverse enrichment levels. IsomiR profiles of non-dominant arm are not well-conserved in 5' ends as well as isomiR profiles of dominant arm. If both the miR-#-5p and miR-#-3p are abundantly expressed, their isomiR expression profiles are always stable across different samples. Similar to diverse enrichment levels of miR-#-5p and miR-#-3p, the isomiR expression patterns may also be influenced by the phenomenon of "arm switching". The diverged isomiR expression profiles further enrich the complexity of multiple isomiRs, and complicate the coding-non-coding RNA regulatory network.
Collapse
|
31
|
Mathelier A, Carbone A. Large scale chromosomal mapping of human microRNA structural clusters. Nucleic Acids Res 2013; 41:4392-408. [PMID: 23444140 PMCID: PMC3632110 DOI: 10.1093/nar/gkt112] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2012] [Revised: 01/08/2013] [Accepted: 02/03/2013] [Indexed: 02/06/2023] Open
Abstract
MicroRNAs (miRNAs) can group together along the human genome to form stable secondary structures made of several hairpins hosting miRNAs in their stems. The few known examples of such structures are all involved in cancer development. A large scale computational analysis of human chromosomes crossing sequence analysis and deep sequencing data revealed the presence of >400 structural clusters of miRNAs in the human genome. An a posteriori analysis validates predictions as bona fide miRNAs. A functional analysis of structural clusters position along the chromosomes co-localizes them with genes involved in several key cellular processes like immune systems, sensory systems, signal transduction and development. Immune systems diseases, infectious diseases and neurodegenerative diseases are characterized by genes that are especially well organized around structural clusters of miRNAs. Target genes functional analysis strongly supports a regulatory role of most predicted miRNAs and, notably, a strong involvement of predicted miRNAs in the regulation of cancer pathways. This analysis provides new fundamental insights on the genomic organization of miRNAs in human chromosomes.
Collapse
Affiliation(s)
| | - Alessandra Carbone
- Université Pierre et Marie Curie, UMR7238, 15, rue de l’Ecole de Médecine, 75006 Paris, France and CNRS, UMR7238, Laboratoire de Génomique des Microorganismes, 75006 Paris, France
| |
Collapse
|