651
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MicroRNAs: Game Changers in the Regulation of α-Synuclein in Parkinson's Disease. PARKINSONS DISEASE 2019; 2019:1743183. [PMID: 31191899 PMCID: PMC6525811 DOI: 10.1155/2019/1743183] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/27/2019] [Revised: 03/24/2019] [Accepted: 04/10/2019] [Indexed: 12/14/2022]
Abstract
Parkinson's disease (PD) is the second most common neurodegenerative disorder. Its neuropathological hallmarks include neuronal loss in the substantia nigra pars compacta (SNpc) and the presence of Lewy bodies containing aggregates of α-synuclein (α-syn). An imbalance between the rates of α-syn synthesis, aggregation, and clearance can result in abnormal α-syn levels and contribute to the pathogenesis of PD. MicroRNAs (miRNAs) are endogenous single-stranded noncoding RNAs (∼22 nucleotides) that have recently emerged as key posttranscriptional regulators of gene expression. In this review, we summarize the functions of miRNAs that directly target α-syn. We also review miRNAs that indirectly impact α-syn levels or toxicity through different pathways, including those involved in the clearance of α-syn and neuroinflammation.
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652
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Vaschetto LM, Beccacece HM. The emerging importance of noncoding RNAs in the insecticide tolerance, with special emphasis on Plutella xylostella (Lepidoptera: Plutellidae). WILEY INTERDISCIPLINARY REVIEWS-RNA 2019; 10:e1539. [PMID: 31045325 DOI: 10.1002/wrna.1539] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 03/20/2019] [Accepted: 04/02/2019] [Indexed: 01/11/2023]
Abstract
Recently generated high-throughput sequencing data sets have shed light on the important regulatory roles of noncoding RNA (ncRNA) molecules in the development of higher organisms. Nowadays it is well-known that regulatory ncRNAs can bind complementary RNA or DNA sequences and recruit chromatin remodelers to selectively modulate gene expression. Consequently, genome sequencing and transcriptomics technologies are now being used to reveal hidden associations among ncRNAs and distinct biological mechanisms. This is the case for the diamondback moth Plutella xylostella, a worldwide pest known to infest cruciferous crops and to display resistance to most insecticides, including Bacillus thuringiensis (Bt) based biopesticides. In P. xylostella, it is thought that ncRNAs could play important roles in both development and insecticide resistance. This review will highlight recent insights into the roles of ncRNAs in P. xylostella and related lepidopterans, and will outline genetic engineering technologies which might be used to design efficient ncRNA-based pest control strategies. This article is categorized under: Regulatory RNAs/RNAi/Riboswitches > Regulatory RNAs.
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Affiliation(s)
- Luis María Vaschetto
- Instituto de Diversidad y Ecología Animal, Consejo Nacional de Investigaciones Científicas y Técnicas (IDEA, CONICET), Córdoba, Argentina.,Facultad de Ciencias Exactas, Físicas y Naturales, Universidad Nacional de Córdoba (FCEFyN, UNC), Córdoba, Argentina
| | - Hernán Mario Beccacece
- Facultad de Ciencias Exactas, Físicas y Naturales, Universidad Nacional de Córdoba (FCEFyN, UNC), Córdoba, Argentina.,Instituto de Investigaciones Biológicas y Tecnológicas Consejo Nacional de Investigaciones Científicas y Técnicas (IIByT, CONICET), Córdoba, Argentina
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653
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Characterization of the transcriptome of Haloferax volcanii, grown under four different conditions, with mixed RNA-Seq. PLoS One 2019; 14:e0215986. [PMID: 31039177 PMCID: PMC6490895 DOI: 10.1371/journal.pone.0215986] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Accepted: 04/11/2019] [Indexed: 12/21/2022] Open
Abstract
Haloferax volcanii is a well-established model species for haloarchaea. Small scale RNomics and bioinformatics predictions were used to identify small non-coding RNAs (sRNAs), and deletion mutants revealed that sRNAs have important regulatory functions. A recent dRNA-Seq study was used to characterize the primary transcriptome. Unexpectedly, it was revealed that, under optimal conditions, H. volcanii contains more non-coding sRNAs than protein-encoding mRNAs. However, the dRNA-Seq approach did not contain any length information. Therefore, a mixed RNA-Seq approach was used to determine transcript length and to identify additional transcripts, which are not present under optimal conditions. In total, 50 million paired end reads of 150 nt length were obtained. 1861 protein-coding RNAs (cdRNAs) were detected, which encoded 3092 proteins. This nearly doubled the coverage of cdRNAs, compared to the previous dRNA-Seq study. About 2/3 of the cdRNAs were monocistronic, and 1/3 covered more than one gene. In addition, 1635 non-coding sRNAs were identified. The highest fraction of non-coding RNAs were cis antisense RNAs (asRNAs). Analysis of the length distribution revealed that sRNAs have a median length of about 150 nt. Based on the RNA-Seq and dRNA-Seq results, genes were chosen to exemplify characteristics of the H. volcanii transcriptome by Northern blot analyses, e.g. 1) the transcript patterns of gene clusters can be straightforward, but also very complex, 2) many transcripts differ in expression level under the four analyzed conditions, 3) some genes are transcribed into RNA isoforms of different length, which can be differentially regulated, 4) transcripts with very long 5'-UTRs and with very long 3'-UTRs exist, and 5) about 30% of all cdRNAs have overlapping 3'-ends, which indicates, together with the asRNAs, that H. volcanii makes ample use of sense-antisense interactions. Taken together, this RNA-Seq study, together with a previous dRNA-Seq study, enabled an unprecedented view on the H. volcanii transcriptome.
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654
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Molecular Pathogenesis of Gene Regulation by the miR-150 Duplex: miR-150-3p Regulates TNS4 in Lung Adenocarcinoma. Cancers (Basel) 2019; 11:cancers11050601. [PMID: 31052206 PMCID: PMC6562801 DOI: 10.3390/cancers11050601] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Revised: 04/23/2019] [Accepted: 04/28/2019] [Indexed: 12/17/2022] Open
Abstract
Based on our miRNA expression signatures, we focused on miR-150-5p (the guide strand) and miR-150-3p (the passenger strand) to investigate their functional significance in lung adenocarcinoma (LUAD). Downregulation of miR-150 duplex was confirmed in LUAD clinical specimens. In vitro assays revealed that ectopic expression of miR-150-5p and miR-150-3p inhibited cancer cell malignancy. We performed genome-wide gene expression analyses and in silico database searches to identify their oncogenic targets in LUAD cells. A total of 41 and 26 genes were identified as miR-150-5p and miR-150-3p targets, respectively, and they were closely involved in LUAD pathogenesis. Among the targets, we investigated the oncogenic roles of tensin 4 (TNS4) because high expression of TNS4 was strongly related to poorer prognosis of LUAD patients (disease-free survival: p = 0.0213 and overall survival: p = 0.0003). Expression of TNS4 was directly regulated by miR-150-3p in LUAD cells. Aberrant expression of TNS4 was detected in LUAD clinical specimens and its aberrant expression increased the aggressiveness of LUAD cells. Furthermore, we identified genes downstream from TNS4 that were associated with critical regulators of genomic stability. Our approach (discovery of anti-tumor miRNAs and their target RNAs for LUAD) will contribute to the elucidation of molecular networks involved in the malignant transformation of LUAD.
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655
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Kim M, Civin CI, Kingsbury TJ. MicroRNAs as regulators and effectors of hematopoietic transcription factors. WILEY INTERDISCIPLINARY REVIEWS-RNA 2019; 10:e1537. [PMID: 31007002 DOI: 10.1002/wrna.1537] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2019] [Revised: 03/24/2019] [Accepted: 04/03/2019] [Indexed: 12/17/2022]
Abstract
Hematopoiesis is a highly-regulated development process orchestrated by lineage-specific transcription factors that direct the generation of all mature blood cells types, including red blood cells, megakaryocytes, granulocytes, monocytes, and lymphocytes. Under homeostatic conditions, the hematopoietic system of the typical adult generates over 1011 blood cells daily throughout life. In addition, hematopoiesis must be responsive to acute challenges due to blood loss or infection. MicroRNAs (miRs) cooperate with transcription factors to regulate all aspects of hematopoiesis, including stem cell maintenance, lineage selection, cell expansion, and terminal differentiation. Distinct miR expression patterns are associated with specific hematopoietic lineages and stages of differentiation and functional analyses have elucidated essential roles for miRs in regulating cell transitions, lineage selection, maturation, and function. MiRs function as downstream effectors of hematopoietic transcription factors and as upstream regulators to control transcription factor levels. Multiple miRs have been shown to play essential roles. Regulatory networks comprised of differentially expressed lineage-specific miRs and hematopoietic transcription factors are involved in controlling the quiescence and self-renewal of hematopoietic stem cells as well as proliferation and differentiation of lineage-specific progenitor cells during erythropoiesis, myelopoiesis, and lymphopoiesis. This review focuses on hematopoietic miRs that function as upstream regulators of central hematopoietic transcription factors required for normal hematopoiesis. This article is categorized under: RNA in Disease and Development > RNA in Development Regulatory RNAs/RNAi/Riboswitches > Regulatory RNAs.
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Affiliation(s)
- MinJung Kim
- Department of Pediatrics, Center for Stem Cell Biology and Regenerative Medicine, Marlene and Stewart Greenebaum Cancer Center, University of Maryland School of Medicine, Baltimore, Maryland
| | - Curt I Civin
- Department of Pediatrics and Physiology, Center for Stem Cell Biology and Regenerative Medicine, Marlene and Stewart Greenebaum Cancer Center, University of Maryland School of Medicine, Baltimore, Maryland
| | - Tami J Kingsbury
- Department of Physiology, Center for Stem Cell Biology and Regenerative Medicine, Marlene and Stewart Greenebaum Cancer Center, University of Maryland School of Medicine, Baltimore, Maryland
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656
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Abstract
Phytomelatonin (PM) gained the greatest interest for its application in agriculture and its use to improve human health conditions. PM based supplement has been shown to possess antioxidant capabilities because it functions as a free radical scavenger. Reactive Oxygen Species (ROS), induced by both intrinsic (peroxide production) and extrinsic (UV-radiation) factors are biochemical mediators crucial in skin aging. Skin aging is also regulated by specific microRNAs (miRs). Herein we have shown the effect of PM free radical scavengers on the human keratinocyte cell line HaCat and on ROS formation induced by both extrinsic and intrinsic factors as well as their capability to positively modulate a member of the hsa-miR-29 family linked to aging. Our result highlights the regulatory role of PM for the keratinocytes homeostasis.
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657
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Zhang B, Zhou M, Zou L, Miao J, Wang Y, Li Y, Lu S, Yu J. Long non-coding RNA LOXL1-AS1 acts as a ceRNA for miR-324-3p to contribute to cholangiocarcinoma progression via modulation of ATP-binding cassette transporter A1. Biochem Biophys Res Commun 2019; 513:827-833. [PMID: 31003776 DOI: 10.1016/j.bbrc.2019.04.089] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Accepted: 04/12/2019] [Indexed: 01/14/2023]
Abstract
Accumulating evidence has appreciated long non-coding RNAs (lncRNAs) as novel prognostic markers and therapeutic targets in malignant carcinomas. Here, we aim to investigate the value of a novel cancer-related lncRNA, LOXL1-AS1, in cholangiocarcinoma (CCA). LOXL1-AS1 was found overexpressed in CCA tissues screened by high-throughput sequencing technology. Upregulation of LOXL1-AS1 was identified by TCGA database and qRT-PCR analysis. Additionally, upregulation of LOXL1-AS1 was associated with lymph node invasion, advanced TNM stages and unfavorable prognosis. Loss-of-function and gain-of-function experiments were conducted and validated that LOXL1-AS1 could facilitate cell proliferation, migration and invasion and attenuate cell apoptosis. Moreover, luciferase reporter and rescue assays indicated that LOXL1-AS1 functioned as a ceRNA to elevate ATP-binding cassette transporter A1 (ABCA1) level by sponging miR-324-3p and exhibited the malignant phenotypes of CCA cells, thereby playing an oncogenic role in CCA. Taken together, this study reveals that LOXL1-AS1 might act as a potential biomarker and therapeutic target for CCA clinical application.
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Affiliation(s)
- Bingquan Zhang
- Department of General Medicine, The Second Affiliated Hospital of Qiqihar Medical University, Qiqihar, 161000, China
| | - Minglu Zhou
- Department of General Medicine, The Second Affiliated Hospital of Qiqihar Medical University, Qiqihar, 161000, China
| | - Liying Zou
- Department of General Medicine, The Second Affiliated Hospital of Qiqihar Medical University, Qiqihar, 161000, China
| | - Jincai Miao
- Department of Food and Drug Control, Qiqihar Institute for Food and Drug Control, Qiqihar, 161000, China
| | - Yanying Wang
- Department of Gastroenterology, East Hospital of Shanghai, 200000, Shanghai, China
| | - Yuanchun Li
- Department of General Surgery, The Second Affiliated Hospital of Qiqihar Medical University, Qiqihar, 161000, China
| | - Sidi Lu
- Department of Gastroenterology, The Second Affiliated Hospital of Qiqihar Medical University, Qiqihar, 161000, China
| | - Jing Yu
- Department of Gastroenterology, The Second Affiliated Hospital of Qiqihar Medical University, Qiqihar, 161000, China.
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658
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Ahmad M, Ahmad S, Rahman B, Haq TU, Jalil F, Shah AA. Association of MIR146A rs2910164 variation with a predisposition to sporadic breast cancer in a Pakistani cohort. Ann Hum Genet 2019; 83:325-330. [PMID: 30963551 DOI: 10.1111/ahg.12316] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Revised: 02/26/2019] [Accepted: 03/19/2019] [Indexed: 12/24/2022]
Abstract
Single-nucleotide polymorphisms (SNPs) in genes coding for microRNAs (miRNAs) play a pivotal role in the progression of breast cancer (BC). We investigated the association of miR-146a rs2910164 GC polymorphism with the risk of BC in the Pakistani population. The miR-146a rs2910164 polymorphism was genotyped in 300 BC cases and 300 age- and gender-matched healthy controls using T-ARMS-PCR. Genotype and allele frequencies were calculated and the association between genotypes and the risk of BC was calculated by odds ratio (OR) and confidence interval (95%). A significant difference in genotypic frequencies (χ2 = 63.10; P = <0.0001) and allelic frequencies (OR = 0.3955 (0.3132-0.4993); P = < 0.0001) was observed between cases and controls. Furthermore, we also found that miR-146 rs2910164 CC homozygote increased the risk of BC in the dominant (OR = 0.2397 (0.1629-0.3526); P = 0.0001; GG vs. GC + CC) and recessive (OR = 2.803 (1.865-4.213); P = <0.0001; CC vs. GC + GG) inheritance models. In summary, miR-146a rs2910164 GC is significantly associated with BC in the Pakistani population. To our knowledge, this is the first study that assessed MIR146a rs2910164 G > C SNP in Pakistani population. By analyzing the secondary structure of MIR146A variant, a significant structural modification was noted. Study with a larger sample size is needed to further confirm of these findings.
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Affiliation(s)
- Mushtaq Ahmad
- Department of Biotechnology, University of Malakand, Chakdara, Pakistan
| | - Sadia Ahmad
- Department of Biotechnology, University of Malakand, Chakdara, Pakistan
| | - Bashir Rahman
- Department of Biotechnology, University of Malakand, Chakdara, Pakistan
| | - Taqweem Ul Haq
- Department of Biotechnology, University of Malakand, Chakdara, Pakistan
| | - Fazal Jalil
- Department of Biotechnology, Abdul Wali Khan University Mardan (AWKUM), Mardan, Pakistan
| | - Aftab Ali Shah
- Department of Biotechnology, University of Malakand, Chakdara, Pakistan
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659
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Yin L, Xiao X, Georgikou C, Luo Y, Liu L, Gladkich J, Gross W, Herr I. Sulforaphane Induces miR135b-5p and Its Target Gene, RASAL2, thereby Inhibiting the Progression of Pancreatic Cancer. MOLECULAR THERAPY-ONCOLYTICS 2019; 14:74-81. [PMID: 31044154 PMCID: PMC6479751 DOI: 10.1016/j.omto.2019.03.011] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/16/2018] [Accepted: 03/27/2019] [Indexed: 12/21/2022]
Abstract
Pancreatic ductal adenocarcinoma (PDA) is one of the most lethal tumors, with poor therapeutic options in the advanced state. The broccoli-derived anti-inflammatory agent sulforaphane was shown to inhibit the progression of pancreatic cancer and other tumor entities. We examined the involvement of pancreatic cancer cell lines were evaluated by microRNA and gene expression arrays, bioinformatics, in silico analysis, qRT-PCR, western blotting, immunohistochemistry, in situ hybridization, self-renewal and differentiation assays, and in vivo xenograft studies. We selected the top nine differentially expressed microRNAs, and miR135b-5p was chosen as the most important candidate for the sulforaphane-induced upregulation of the tumor suppressor gene RASAL2. The expression of miR135b-5p and RASAL2 was almost absent in malignant pancreatic tissues and cell lines, but not in their normal counterparts. Lipofection of miR135b-5p enhanced RASAL2 expression and inhibited ERK1/2 signaling, viability, self-renewal capacity, and tumor growth. These results indicate that miR135b-5p acts as a tumor suppressor via the induction of RASAL2 in PDA.
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Affiliation(s)
- Libo Yin
- Molecular OncoSurgery, Section of Surgical Research, Department of General, Visceral, & Transplant Surgery, University of Heidelberg, Heidelberg, Germany
| | - Xi Xiao
- Molecular OncoSurgery, Section of Surgical Research, Department of General, Visceral, & Transplant Surgery, University of Heidelberg, Heidelberg, Germany
| | - Christina Georgikou
- Molecular OncoSurgery, Section of Surgical Research, Department of General, Visceral, & Transplant Surgery, University of Heidelberg, Heidelberg, Germany
| | - Yiqiao Luo
- Molecular OncoSurgery, Section of Surgical Research, Department of General, Visceral, & Transplant Surgery, University of Heidelberg, Heidelberg, Germany
| | - Li Liu
- Molecular OncoSurgery, Section of Surgical Research, Department of General, Visceral, & Transplant Surgery, University of Heidelberg, Heidelberg, Germany
| | - Jury Gladkich
- Molecular OncoSurgery, Section of Surgical Research, Department of General, Visceral, & Transplant Surgery, University of Heidelberg, Heidelberg, Germany
| | - Wolfgang Gross
- Molecular OncoSurgery, Section of Surgical Research, Department of General, Visceral, & Transplant Surgery, University of Heidelberg, Heidelberg, Germany
| | - Ingrid Herr
- Molecular OncoSurgery, Section of Surgical Research, Department of General, Visceral, & Transplant Surgery, University of Heidelberg, Heidelberg, Germany
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660
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Kang JY, Park H, Kim H, Mun D, Park H, Yun N, Joung B. Human peripheral blood‑derived exosomes for microRNA delivery. Int J Mol Med 2019; 43:2319-2328. [PMID: 30942393 PMCID: PMC6488179 DOI: 10.3892/ijmm.2019.4150] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Accepted: 03/27/2019] [Indexed: 12/20/2022] Open
Abstract
Exosomes serve important functions in cell-to-cell communication and biological functions by serving as a delivery cargo shuttle for various molecules. The application of an improved delivery method for microRNAs (miRNAs/miRs) may enhance their potential as a therapeutic tool in cardiac diseases. Thus, the present study investigated whether human peripheral blood-derived exosomes may be used as a delivery cargo system for miRNAs, and whether the delivery of miR-21 using a human peripheral blood derived-exosome may influence the degree of remodeling following myocardial infarction (MI). In H9C2 and HL-1 cells, miR-21 expression was successfully regulated by treatment with human peripheral blood derived-exosomes loaded with an miR-21 mimic or inhibitor compared with untreated cells. In addition, the mRNA and protein expression levels of SMAD family member 7 (Smad7), phosphatase and tensin homolog (PTEN) and matrix metalloproteinase 2 (MMP2), which are involved in cardiac fibrosis, were associated with the uptake of miR-21 mimic- or inhibitor-loaded exosomes. Similarly, the in vivo mRNA and protein expression of Smad7, PTEN and MMP2 were altered following treatment with miR-21 mimic- or inhibitor-loaded exosomes. Furthermore, miR-21 mimic-loaded exosomes enhanced fibrosis, whereas miR-21 inhibitor-loaded exosomes reduced fibrosis in a mouse MI model. These results suggested that miRNA-loaded human peripheral blood derived-exosomes may be used as a therapeutic tool for cardiac diseases.
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Affiliation(s)
- Ji-Young Kang
- Division of Cardiology, Yonsei University College of Medicine, Seoul 03722, Republic of Korea
| | - Hyewon Park
- Division of Cardiology, Yonsei University College of Medicine, Seoul 03722, Republic of Korea
| | - Hyoeun Kim
- Division of Cardiology, Yonsei University College of Medicine, Seoul 03722, Republic of Korea
| | - Dasom Mun
- Division of Cardiology, Yonsei University College of Medicine, Seoul 03722, Republic of Korea
| | - Hyelim Park
- Division of Cardiology, Yonsei University College of Medicine, Seoul 03722, Republic of Korea
| | - Nuri Yun
- Institute of Life Science and Biotechnology, Yonsei University, Seoul 03722, Republic of Korea
| | - Boyoung Joung
- Division of Cardiology, Yonsei University College of Medicine, Seoul 03722, Republic of Korea
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661
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Martier R, Liefhebber JM, Miniarikova J, van der Zon T, Snapper J, Kolder I, Petry H, van Deventer SJ, Evers MM, Konstantinova P. Artificial MicroRNAs Targeting C9orf72 Can Reduce Accumulation of Intra-nuclear Transcripts in ALS and FTD Patients. MOLECULAR THERAPY. NUCLEIC ACIDS 2019; 14:593-608. [PMID: 30776581 PMCID: PMC6378669 DOI: 10.1016/j.omtn.2019.01.010] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Revised: 01/22/2019] [Accepted: 01/22/2019] [Indexed: 12/13/2022]
Abstract
The most common pathogenic mutation in amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD) is an intronic GGGGCC (G4C2) repeat in the chromosome 9 open reading frame 72 (C9orf72) gene. Cellular toxicity due to RNA foci and dipeptide repeat (DPR) proteins produced by the sense and antisense repeat-containing transcripts is thought to underlie the pathogenesis of both diseases. RNA sequencing (RNA-seq) data of C9orf72-ALS patients and controls were analyzed to better understand the sequence conservation of C9orf72 in patients. MicroRNAs were developed in conserved regions to silence C9orf72 (miC), and the feasibility of different silencing approaches was demonstrated in reporter overexpression systems. In addition, we demonstrated the feasibility of a bidirectional targeting approach by expressing two concatenated miC hairpins. The efficacy of miC was confirmed by the reduction of endogenously expressed C9orf72 mRNA, in both nucleus and cytoplasm, and an ∼50% reduction of nuclear RNA foci in (G4C2)44-expressing cells. Ultimately, two miC candidates were incorporated in adeno-associated virus vector serotype 5 (AAV5), and silencing of C9orf72 was demonstrated in HEK293T cells and induced pluripotent stem cell (iPSC)-derived neurons. These data support the feasibility of microRNA (miRNA)-based and AAV-delivered gene therapy that could alleviate the gain of toxicity seen in ALS and FTD patients.
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Affiliation(s)
- Raygene Martier
- Department of Research & Development, uniQure Biopharma B.V., Amsterdam, the Netherlands; Department of Gastroenterology and Hepatology, Leiden University Medical Center, Leiden, the Netherlands
| | - Jolanda M Liefhebber
- Department of Research & Development, uniQure Biopharma B.V., Amsterdam, the Netherlands
| | - Jana Miniarikova
- Department of Research & Development, uniQure Biopharma B.V., Amsterdam, the Netherlands
| | - Tom van der Zon
- Department of Research & Development, uniQure Biopharma B.V., Amsterdam, the Netherlands
| | - Jolanda Snapper
- Department of Research & Development, uniQure Biopharma B.V., Amsterdam, the Netherlands
| | - Iris Kolder
- BaseClear B.V., Sylviusweg 74, 2333 BE, Leiden, the Netherlands
| | - Harald Petry
- Department of Research & Development, uniQure Biopharma B.V., Amsterdam, the Netherlands
| | - Sander J van Deventer
- Department of Research & Development, uniQure Biopharma B.V., Amsterdam, the Netherlands; Department of Gastroenterology and Hepatology, Leiden University Medical Center, Leiden, the Netherlands
| | - Melvin M Evers
- Department of Research & Development, uniQure Biopharma B.V., Amsterdam, the Netherlands
| | - Pavlina Konstantinova
- Department of Research & Development, uniQure Biopharma B.V., Amsterdam, the Netherlands.
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662
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Zedan AH, Hansen TF, Assenholt J, Madsen JS, Osther PJS. Circulating miRNAs in localized/locally advanced prostate cancer patients after radical prostatectomy and radiotherapy. Prostate 2019; 79:425-432. [PMID: 30537232 PMCID: PMC6587522 DOI: 10.1002/pros.23748] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Accepted: 11/08/2018] [Indexed: 12/14/2022]
Abstract
BACKGROUND Overtreatment is a well-known clinical challenge in local prostate cancer (PCa). Although risk assessment models have contributed to a better stratification of patients with local PCa, a tailored management is still in its infancy. Over the last few decades, microRNAs (miRNAs) have shown promising results as biomarkers in PCa. The aim of this study was to investigate circulating miRNAs after management of local PCa. METHODS The relative expression of four miRNAs (miRNA-21, -93, -125b, and miRNA-221) was assessed in plasma from 149 newly diagnosed patients with local or locally advanced PCa. Real-time polymerase chain reaction was used for analysis. A baseline sample at time of diagnosis and a follow-up sample after 6 months were assessed. The patients were grouped in an interventional cohort (radical prostatectomy, curative intent radiotherapy, or androgen-deprivation therapy alone) and an observational cohort (watchful waiting or active surveillance). RESULTS In the interventional cohort, levels of both miRNA-93 and miRNA-221 were significantly lower in the follow-up samples compared to baseline z = -2.738, P = 0.006, and z = -4.498, P < 0.001, respectively. The same observation was recorded for miRNA-125b in the observational cohort (z = -2.656, P = 0.008). Both miRNA-125b and miRNA-221 were correlated with risk assessment r = 0.23, P = 0.015, and r = 0.203, P = 0.016 respectively, while miRNA-93 showed tendency to significant correlation with the prostatectomy Gleason score (r = 0.276, P = 0.0576). CONCLUSIONS The current results indicate a possible role of miRNA-93 and miRNA-221 in disease monitoring in localized and locally advanced PCa. Larger studies are warranted to assess the clinical impact of these biomarkers.
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Affiliation(s)
- Ahmed H. Zedan
- Urological Research CentreDepartment of UrologyVejle HospitalVejleDenmark
- Department of OncologyVejle HospitalVejleDenmark
- Institute of Regional Health ResearchUniversity of Southern DenmarkVejleDenmark
| | - Torben F. Hansen
- Department of OncologyVejle HospitalVejleDenmark
- Institute of Regional Health ResearchUniversity of Southern DenmarkVejleDenmark
| | - Jannie Assenholt
- Department of Biochemistry and Clinical ImmunologyVejle HospitalVejleDenmark
| | - Jonna S. Madsen
- Institute of Regional Health ResearchUniversity of Southern DenmarkVejleDenmark
- Department of Biochemistry and Clinical ImmunologyVejle HospitalVejleDenmark
| | - Palle J. S. Osther
- Urological Research CentreDepartment of UrologyVejle HospitalVejleDenmark
- Institute of Regional Health ResearchUniversity of Southern DenmarkVejleDenmark
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663
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Down syndrome: Neurobiological alterations and therapeutic targets. Neurosci Biobehav Rev 2019; 98:234-255. [DOI: 10.1016/j.neubiorev.2019.01.001] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Revised: 01/02/2019] [Accepted: 01/02/2019] [Indexed: 12/12/2022]
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664
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Cattane N, Mora C, Lopizzo N, Borsini A, Maj C, Pedrini L, Rossi R, Riva MA, Pariante CM, Cattaneo A. Identification of a miRNAs signature associated with exposure to stress early in life and enhanced vulnerability for schizophrenia: New insights for the key role of miR-125b-1-3p in neurodevelopmental processes. Schizophr Res 2019; 205:63-75. [PMID: 30057098 DOI: 10.1016/j.schres.2018.07.030] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Revised: 07/13/2018] [Accepted: 07/16/2018] [Indexed: 12/17/2022]
Abstract
Epidemiological and clinical studies have provided evidence for a role of both genetic and environmental factors, such as stressful experiences early in life, in the pathogenesis of Schizophrenia (SZ) and microRNAs (miRNAs) have been suggested to play a key role in the interplay between the environment and our genome. In this study, we conducted a miRNOme analysis in different samples (blood of adult subjects exposed to childhood trauma, brain (hippocampus) of rats exposed to prenatal stress and human hippocampal progenitor cells treated with cortisol) and we identified miR-125b-1-3p as a down-regulated miRNA in all the three datasets. Interestingly, a significant down-regulation was observed also in SZ patients exposed to childhood trauma. To investigate the biological systems targeted by miR-125b-1-3p and also involved in the effects of stress, we combined the list of biological pathways modulated by predicted and validated target genes of miR-125b-1-3p, with the biological systems significantly regulated by cortisol in the in vitro model. We found, as common pathways, the CXCR4 signaling, the G-alpha signaling, and the P2Y Purigenic Receptor Signaling Pathway, which are all involved in neurodevelopmental processes. Our data, obtained from the combining of miRNAs datasets across different tissues and species, identified miR-125b-1-3p as a key marker associated with the long-term effects of stress early in life and also with the enhanced vulnerability of developing SZ. The identification of such a miRNA biomarker could allow the early detection of vulnerable subjects for SZ and could provide the basis for the development of preventive therapeutic strategies.
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Affiliation(s)
- Nadia Cattane
- Biological Psychiatry Unit, IRCCS Fatebenefratelli San Giovanni di Dio, via Pilastroni 4, Brescia, Italy
| | - Cristina Mora
- Biological Psychiatry Unit, IRCCS Fatebenefratelli San Giovanni di Dio, via Pilastroni 4, Brescia, Italy
| | - Nicola Lopizzo
- Biological Psychiatry Unit, IRCCS Fatebenefratelli San Giovanni di Dio, via Pilastroni 4, Brescia, Italy
| | - Alessandra Borsini
- Stress, Psychiatry and Immunology Laboratory, Department of Psychological Medicine, Institute of Psychiatry, King's College London, 125 Coldharbour Lane, SE5 9NU London, UK
| | - Carlo Maj
- Institute for Genomic Statistics and Bioinformatics, University Hospital, Bonn, Germany
| | - Laura Pedrini
- Psychiatry Unit, IRCCS Fatebenefratelli San Giovanni di Dio, via Pilastroni 4, Brescia, Italy
| | - Roberta Rossi
- Psychiatry Unit, IRCCS Fatebenefratelli San Giovanni di Dio, via Pilastroni 4, Brescia, Italy
| | - Marco Andrea Riva
- Department of Pharmacological and Biomolecular Sciences, University of Milan, Milan, Italy
| | - Carmine Maria Pariante
- Stress, Psychiatry and Immunology Laboratory, Department of Psychological Medicine, Institute of Psychiatry, King's College London, 125 Coldharbour Lane, SE5 9NU London, UK
| | - Annamaria Cattaneo
- Biological Psychiatry Unit, IRCCS Fatebenefratelli San Giovanni di Dio, via Pilastroni 4, Brescia, Italy; Stress, Psychiatry and Immunology Laboratory, Department of Psychological Medicine, Institute of Psychiatry, King's College London, 125 Coldharbour Lane, SE5 9NU London, UK.
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665
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Anasagasti A, Ezquerra-Inchausti M, Barandika O, Muñoz-Culla M, Caffarel MM, Otaegui D, López de Munain A, Ruiz-Ederra J. Expression Profiling Analysis Reveals Key MicroRNA-mRNA Interactions in Early Retinal Degeneration in Retinitis Pigmentosa. Invest Ophthalmol Vis Sci 2019; 59:2381-2392. [PMID: 29847644 PMCID: PMC5939684 DOI: 10.1167/iovs.18-24091] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Purpose The aim of this study was to identify differentially expressed microRNAs (miRNAs) that might play an important role in the etiology of retinal degeneration in a genetic mouse model of retinitis pigmentosa (rd10 mice) at initial stages of the disease. Methods miRNAs–mRNA interaction networks were generated for analysis of biological pathways involved in retinal degeneration. Results Of more than 1900 miRNAs analyzed, we selected 19 miRNAs on the basis of (1) a significant differential expression in rd10 retinas compared with control samples and (2) an inverse expression relationship with predicted mRNA targets involved in biological pathways relevant to retinal biology and/or degeneration. Seven of the selected miRNAs have been associated with retinal dystrophies, whereas, to our knowledge, nine have not been previously linked to any disease. Conclusions This study contributes to our understanding of the etiology and progression of retinal degeneration.
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Affiliation(s)
- Ander Anasagasti
- Neuroscience Area, Sensorial Neurodegeneration Group, Biodonostia Health Research Institute, San Sebastian, Spain
| | - Maitane Ezquerra-Inchausti
- Neuroscience Area, Sensorial Neurodegeneration Group, Biodonostia Health Research Institute, San Sebastian, Spain.,RETICS OFTARED, National Institute of Health Carlos III, Ministry of Economy and Competitiveness, Spain
| | - Olatz Barandika
- Neuroscience Area, Sensorial Neurodegeneration Group, Biodonostia Health Research Institute, San Sebastian, Spain
| | - Maider Muñoz-Culla
- Neuroscience Area, Multiple Sclerosis Group, Biodonostia Health Research Institute, San Sebastian, Spain.,Spanish Network on Multiple Sclerosis (Red Española de Esclerosis Múltiple)
| | - María M Caffarel
- Oncology Area, Biodonostia Health Research Institute, San Sebastian, Spain.,Ikerbasque, Basque Foundation for Science, Bilbao, Spain
| | - David Otaegui
- Neuroscience Area, Multiple Sclerosis Group, Biodonostia Health Research Institute, San Sebastian, Spain.,Spanish Network on Multiple Sclerosis (Red Española de Esclerosis Múltiple)
| | - Adolfo López de Munain
- Neuroscience Area, Sensorial Neurodegeneration Group, Biodonostia Health Research Institute, San Sebastian, Spain.,Department of Neurology, Donostia University Hospital, San Sebastian, Spain.,Centro de Investigaciones Biomédicas en Red Sobre Enfermedades Neurodegenerativas, Instituto Carlos III, Ministerio de Economía y Competitividad, Spain.,Department of Neuroscience, University of the Basque Country, San Sebastian, Spain
| | - Javier Ruiz-Ederra
- Neuroscience Area, Sensorial Neurodegeneration Group, Biodonostia Health Research Institute, San Sebastian, Spain.,RETICS OFTARED, National Institute of Health Carlos III, Ministry of Economy and Competitiveness, Spain
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666
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Ferreira RG, Cardoso MV, de Souza Furtado KM, Espíndola KMM, Amorim RP, Monteiro MC. Epigenetic alterations caused by aflatoxin b1: a public health risk in the induction of hepatocellular carcinoma. Transl Res 2019; 204:51-71. [PMID: 30304666 DOI: 10.1016/j.trsl.2018.09.001] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Revised: 08/27/2018] [Accepted: 09/02/2018] [Indexed: 02/07/2023]
Abstract
Aflatoxin B1 (AFB1) is currently the most commonly studied mycotoxin due to its great toxicity, its distribution in a wide variety of foods such as grains and cereals and its involvement in the development of + (hepatocellular carcinoma; HCC). HCC is one of the main types of liver cancer, and has become a serious public health problem, due to its high incidence mainly in Southeast Asia and Africa. Studies show that AFB1 acts in synergy with other risk factors such as hepatitis B and C virus leading to the development of HCC through genetic and epigenetic modifications. The genetic modifications begin in the liver through the biomorphic AFB1, the AFB1-exo-8.9-Epoxy active, which interacts with DNA to form adducts of AFB1-DNA. These adducts induce mutation in codon 249, mediated by a transversion of G-T in the p53 tumor suppressor gene, causing HCC. Thus, this review provides an overview of the evidence for AFB1-induced epigenetic alterations and the potential mechanisms involved in the development of HCC, focusing on a critical analysis of the importance of severe legislation in the detection of aflatoxins.
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Affiliation(s)
- Roseane Guimarães Ferreira
- Neurosciences and Cell Biology Post-Graduation Program, Biological Sciences Institute, Federal University of Pará/UFPA, Belém, Pará, Brazil.
| | - Magda Vieira Cardoso
- Pharmaceutical Science Post-Graduation Program, Health Science Institute, Federal University of Pará/UFPA, Belém, Pará, Brazil.
| | | | | | | | - Marta Chagas Monteiro
- Neurosciences and Cell Biology Post-Graduation Program, Pharmaceutical Science Post-Graduation Program, Health Science Institute, Federal University of Pará/UFPA, Belém, Pará, Brazil.
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667
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Pu M, Chen J, Tao Z, Miao L, Qi X, Wang Y, Ren J. Regulatory network of miRNA on its target: coordination between transcriptional and post-transcriptional regulation of gene expression. Cell Mol Life Sci 2019; 76:441-451. [PMID: 30374521 PMCID: PMC11105547 DOI: 10.1007/s00018-018-2940-7] [Citation(s) in RCA: 260] [Impact Index Per Article: 52.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Revised: 09/12/2018] [Accepted: 10/08/2018] [Indexed: 12/26/2022]
Abstract
MicroRNAs (miRNAs) are a class of endogenous small noncoding RNAs that participate in a majority of biological processes via regulating target gene expression. The post-transcriptional repression through miRNA seed region binding to 3' UTR of target mRNA is considered as the canonical mode of miRNA-mediated gene regulation. However, emerging evidence suggests that other regulatory modes exist beyond the canonical mechanism. In particular, the function of intranuclear miRNA in gene transcriptional regulation is gradually revealed, with evidence showing their contribution to gene silencing or activating. Therefore, miRNA-mediated regulation of gene transcription not only expands our understanding of the molecular mechanism underlying miRNA regulatory function, but also provides new evidence to explain its ability in the sophisticated regulation of many bioprocesses. In this review, mechanisms of miRNA-mediated gene transcriptional and post-transcriptional regulation are summarized, and the synergistic effects among these actions which form a regulatory network of a miRNA on its target are particularly elaborated. With these discussions, we aim to emphasize the importance of miRNA regulatory network on target gene regulation and further highlight the potential application of the network mode in the achievement of a more effective and stable modulation of the target gene expression.
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Affiliation(s)
- Mengfan Pu
- Center for Drug Safety Evaluation and Research, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 501 Haike Road, Shanghai, 201203, China
- School of Life Science and Technology, ShanghaiTech University, 100 Haike Road, Shanghai, 201210, China
| | - Jing Chen
- Center for Drug Safety Evaluation and Research, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 501 Haike Road, Shanghai, 201203, China
| | - Zhouteng Tao
- Center for Drug Safety Evaluation and Research, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 501 Haike Road, Shanghai, 201203, China
| | - Lingling Miao
- Center for Drug Safety Evaluation and Research, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 501 Haike Road, Shanghai, 201203, China
| | - Xinming Qi
- Center for Drug Safety Evaluation and Research, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 501 Haike Road, Shanghai, 201203, China
| | - Yizheng Wang
- The Brain Science Center, Beijing Institute of Basic Medical Sciences, 27 Taiping Road, Beijing, 100850, China
| | - Jin Ren
- Center for Drug Safety Evaluation and Research, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 501 Haike Road, Shanghai, 201203, China.
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668
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Fallah H, Ganji M, Arsang-Jang S, Sayad A, Taheri M. Consideration of the role of MALAT1 long noncoding RNA and catalytic component of RNA-induced silencing complex (Argonaute 2, AGO2) in autism spectrum disorders: Yes, or no? Meta Gene 2019. [DOI: 10.1016/j.mgene.2018.12.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
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669
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Butti Z, Patten SA. RNA Dysregulation in Amyotrophic Lateral Sclerosis. Front Genet 2019; 9:712. [PMID: 30723494 PMCID: PMC6349704 DOI: 10.3389/fgene.2018.00712] [Citation(s) in RCA: 114] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Accepted: 12/20/2018] [Indexed: 12/11/2022] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is the most common adult-onset motor neuron disease and is characterized by the degeneration of upper and lower motor neurons. It has become increasingly clear that RNA dysregulation is a key contributor to ALS pathogenesis. The major ALS genes SOD1, TARDBP, FUS, and C9orf72 are involved in aspects of RNA metabolism processes such as mRNA transcription, alternative splicing, RNA transport, mRNA stabilization, and miRNA biogenesis. In this review, we highlight the current understanding of RNA dysregulation in ALS pathogenesis involving these major ALS genes and discuss the potential of therapeutic strategies targeting disease RNAs for treating ALS.
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Affiliation(s)
- Zoe Butti
- INRS-Institut Armand-Frappier, National Institute of Scientific Research, Laval, QC, Canada
| | - Shunmoogum A Patten
- INRS-Institut Armand-Frappier, National Institute of Scientific Research, Laval, QC, Canada
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670
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Merlin S, Follenzi A. Transcriptional Targeting and MicroRNA Regulation of Lentiviral Vectors. MOLECULAR THERAPY-METHODS & CLINICAL DEVELOPMENT 2019; 12:223-232. [PMID: 30775404 PMCID: PMC6365353 DOI: 10.1016/j.omtm.2018.12.013] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Gene expression regulation is the result of complex interactions between transcriptional and post-transcriptional controls, resulting in cell-type-specific gene expression patterns that are determined by the developmental and differentiation stage of pathophysiological conditions. Understanding the complexity of gene expression regulatory networks is fundamental to gene therapy, an approach which has the potential to treat and cure inherited disorders by delivering the correct gene to patient specific cells or tissues by means of both viral and non-viral vectors. Besides the issues of biosafety, in recent years efforts have focused on achieving a robust and sustained transgene expression, which attains a phenotypic correction in several diseases, while avoiding transgene-related adverse effects, such as overexpression-associated cytotoxicity and/or immune responses to the transgene. In this sense, the use of cell-type-specific promoters and microRNA target sequences (miRTs) in gene transfer expression cassettes have allowed for a restricted expression after gene transfer in several studies. This review will focus on the use of transcriptional and post-transcriptional regulation to achieve a highly specific and safe transgene expression, as well as their application in ex vivo and in vivo gene therapeutic approaches.
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Affiliation(s)
- Simone Merlin
- Department of Health Sciences, School of Medicine, University of Piemonte Orientale, Novara, Italy
| | - Antonia Follenzi
- Department of Health Sciences, School of Medicine, University of Piemonte Orientale, Novara, Italy
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671
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Microbial Agents as Putative Inducers of B Cell Lymphoma in Sjögren's Syndrome through an Impaired Epigenetic Control: The State-of-The-Art. J Immunol Res 2019; 2019:8567364. [PMID: 30723750 PMCID: PMC6339763 DOI: 10.1155/2019/8567364] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Revised: 11/28/2018] [Accepted: 12/09/2018] [Indexed: 12/16/2022] Open
Abstract
Introduction Understanding the mechanisms underlying the pathogenesis of Sjögren's syndrome (SS) is crucially important in order to be able to discriminate the steps that lead to B cell transformation and promptly identify the patients at risk of lymphomagenesis. The aim of this narrative review is to describe the evidence concerning the role that infections or dysbiosis plays in the epigenetic control of gene expression in SS patients and their possible involvement in B cell lymphomagenesis. Materials and Methods We searched the PubMed and Google Scholar databases and selected a total of 92 articles published during the last 25 years that describe experimental and clinical studies of the potential associations of microbiota and epigenetic aberrations with the risk of B cell lymphoma in SS patients. Results and Discussion The genetic background of SS patients is characterized by the hyperexpression of genes that are mainly involved in regulating the innate and adaptive immune responses and oncogenesis. In addition, salivary gland epithelial cells and lymphocytes both have an altered epigenetic background that enhances the activation of proinflammatory and survival pathways. Dysbiosis or chronic latent infections may tune the immune response and modify the cell epigenetic machinery in such a way as to give B lymphocytes an activated or transformed phenotype. It is also worth noting that transposable integrated retroelements may participate in the pathogenesis of SS and B cell lymphomagenesis by inducing DNA breaks, modulating cell gene expression, or generating aberrant transcripts that chronically stimulate the immune system. Conclusions Microorganisms may epigenetically modify target cells and induce their transcriptome to generate an activated or transformed phenotype. The occurrence of lymphoma in more than 15% of SS patients may be the end result of a combination of genetics, epigenetics, and dysbiosis or latent infections.
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672
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Shahabi A, Naghili B, Ansarin K, Zarghami N. The relationship between microRNAs and Rab family GTPases in human cancers. J Cell Physiol 2019; 234:12341-12352. [PMID: 30609026 DOI: 10.1002/jcp.28038] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Accepted: 11/30/2018] [Indexed: 12/13/2022]
Abstract
microRNAs (miRNAs), as a group of noncoding RNAs, posttranscriptionally control gene expression by binding to 3'-untranslated region (3'-UTR). Ras-associated binding (Rab) proteins function as molecular switches for regulating vesicular transport, which mainly have oncogenic roles in cancer development and preventing the efficacy of chemotherapies. Increased evidence supported that miRNAs/Rabs interaction have been determined as potential therapeutics for cancer therapy. Nevertheless, instability and cross-targeting of miRNAs are main limitations of using miRNA-based therapeutic. The mutual interplay between Rabs and miRNAs has been poorly understood. In the present review, we focused on the essence and activity of these molecules in cancer pathogenesis. Also, numerous hindrances and potential methods in the expansion of miRNA as an anticancer therapeutics are mentioned.
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Affiliation(s)
- Arman Shahabi
- Infectious and Tropical Diseases Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.,Department of Molecular Medicine, Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran.,Student Research Committee, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Behrooz Naghili
- Infectious and Tropical Diseases Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Khalil Ansarin
- Tuberculosis and Lung Diseases Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Nosratollah Zarghami
- Infectious and Tropical Diseases Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.,Department of Molecular Medicine, Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran.,Department of Clinical Biochemistry and Laboratory Medicine, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
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673
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MicroRNAs and other non-coding RNAs in adipose tissue and obesity: emerging roles as biomarkers and therapeutic targets. Clin Sci (Lond) 2019; 133:23-40. [PMID: 30606812 DOI: 10.1042/cs20180890] [Citation(s) in RCA: 80] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Revised: 11/29/2018] [Accepted: 12/05/2018] [Indexed: 02/07/2023]
Abstract
Obesity is a metabolic condition usually accompanied by insulin resistance (IR), type 2 diabetes (T2D), and dyslipidaemia, which is characterised by excessive fat accumulation and related to white adipose tissue (WAT) dysfunction. Enlargement of WAT is associated with a transcriptional alteration of coding and non-coding RNAs (ncRNAs). For many years, big efforts have focused on understanding protein-coding RNAs and their involvement in the regulation of adipocyte physiology and subsequent role in obesity. However, diverse findings have suggested that a dysfunctional adipocyte phenotype in obesity might be also dependent on specific alterations in the expression pattern of ncRNAs, such as miRNAs. The aim of this review is to update current knowledge on the physiological roles of miRNAs and other ncRNAs in adipose tissue function and their potential impact on obesity. Therefore, we examined their regulatory role on specific WAT features: adipogenesis, adipokine secretion, inflammation, glucose metabolism, lipolysis, lipogenesis, hypoxia and WAT browning. MiRNAs can be released to body fluids and can be transported (free or inside microvesicles) to other organs, where they might trigger metabolic effects in distant tissues, thus opening new possibilities to a potential use of miRNAs as biomarkers for diagnosis, prognosis, and personalisation of obesity treatment. Understanding the role of miRNAs also opens the possibility of using these molecules on individualised dietary strategies for precision weight management. MiRNAs should be envisaged as a future therapeutic approach given that miRNA levels could be modulated by synthetic molecules (f.i. miRNA mimics and inhibitors) and/or specific nutrients or bioactive compounds.
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674
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Shieh M, Chitnis N, Clark P, Johnson FB, Kamoun M, Monos D. Computational assessment of miRNA binding to low and high expression HLA-DPB1 allelic sequences. Hum Immunol 2019; 80:53-61. [DOI: 10.1016/j.humimm.2018.09.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2018] [Revised: 08/27/2018] [Accepted: 09/12/2018] [Indexed: 12/31/2022]
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675
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Fiscon G, Conte F, Farina L, Pellegrini M, Russo F, Paci P. Identification of Disease-miRNA Networks Across Different Cancer Types Using SWIM. Methods Mol Biol 2019; 1970:169-181. [PMID: 30963493 DOI: 10.1007/978-1-4939-9207-2_10] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
MicroRNAs (miRNAs) are small noncoding RNAs (ncRNAs) involved in several biological processes and diseases. MiRNAs regulate gene expression at the posttranscriptional level, mostly downregulating their targets by binding specific regions of transcripts through imperfect sequence complementarity. Prediction of miRNA-binding sites is challenging, and target prediction algorithms are usually based on sequence complementarity. In the last years, it has been shown that by adding miRNA and protein coding gene expression, we are able to build tissue-, cell line-, or disease-specific networks improving our understanding of complex biological scenarios. In this chapter, we present an application of a recently published software named SWIM, that allows to identify key genes in a network of interactions by defining appropriate "roles" of genes according to their local/global positioning in the overall network. Furthermore, we show how the SWIM software can be used to build miRNA-disease networks, by applying the approach to tumor data obtained from The Cancer Genome Atlas (TCGA).
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Affiliation(s)
- Giulia Fiscon
- Institute for Systems Analysis and Computer Science Antonio Ruberti, National Research Council, Rome, Italy
- SysBio Centre for Systems Biology, Milan, Italy
| | - Federica Conte
- Institute for Systems Analysis and Computer Science Antonio Ruberti, National Research Council, Rome, Italy
- SysBio Centre for Systems Biology, Milan, Italy
| | - Lorenzo Farina
- Department of Computer, Control, and Management Engineering Antonio Ruberti, Sapienza University of Rome, Rome, Italy
| | - Marco Pellegrini
- Institute of Informatics and Telematics, National Research Council, Pisa, Italy
| | - Francesco Russo
- Faculty of Health and Medical Sciences¸ Novo Nordisk Foundation Center for Protein Research, Translational Disease Systems Biology, University of Copenhagen, Copenhagen, Denmark.
| | - Paola Paci
- Institute for Systems Analysis and Computer Science Antonio Ruberti, National Research Council, Rome, Italy.
- SysBio Centre for Systems Biology, Milan, Italy.
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676
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Angelin-Bonnet O, Biggs PJ, Vignes M. Gene Regulatory Networks: A Primer in Biological Processes and Statistical Modelling. Methods Mol Biol 2019; 1883:347-383. [PMID: 30547408 DOI: 10.1007/978-1-4939-8882-2_15] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Modelling gene regulatory networks requires not only a thorough understanding of the biological system depicted, but also the ability to accurately represent this system from a mathematical perspective. Throughout this chapter, we aim to familiarize the reader with the biological processes and molecular factors at play in the process of gene expression regulation. We first describe the different interactions controlling each step of the expression process, from transcription to mRNA and protein decay. In the second section, we provide statistical tools to accurately represent this biological complexity in the form of mathematical models. Among other considerations, we discuss the topological properties of biological networks, the application of deterministic and stochastic frameworks, and the quantitative modelling of regulation. We particularly focus on the use of such models for the simulation of expression data that can serve as a benchmark for the testing of network inference algorithms.
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Affiliation(s)
- Olivia Angelin-Bonnet
- Institute of Fundamental Sciences, Palmerston North, New Zealand
- School of Veterinary Science, Massey University, Palmerston North, New Zealand
| | - Patrick J Biggs
- Institute of Fundamental Sciences, Palmerston North, New Zealand
- School of Veterinary Science, Massey University, Palmerston North, New Zealand
| | - Matthieu Vignes
- Institute of Fundamental Sciences, Palmerston North, New Zealand.
- School of Veterinary Science, Massey University, Palmerston North, New Zealand.
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677
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Abdullah MI, Junit SM, Ng KL, Jayapalan JJ, Karikalan B, Hashim OH. Papillary Thyroid Cancer: Genetic Alterations and Molecular Biomarker Investigations. Int J Med Sci 2019; 16:450-460. [PMID: 30911279 PMCID: PMC6428975 DOI: 10.7150/ijms.29935] [Citation(s) in RCA: 168] [Impact Index Per Article: 33.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Accepted: 12/04/2018] [Indexed: 11/05/2022] Open
Abstract
Papillary thyroid cancer (PTC) is the most prevalent form of malignancy among all cancers of the thyroid. It is also one of the few cancers with a rapidly increasing incidence. PTC is usually contained within the thyroid gland and generally biologically indolent. Prognosis of the cancer is excellent, with less than 2% mortality at 5 years. However, more than 25% of patients with PTC developed a recurrence during a long term follow-up. The present article provides an updated condensed overview of PTC, which focuses mainly on the molecular alterations involved and recent biomarker investigations.
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Affiliation(s)
- Mardiaty Iryani Abdullah
- Department of Molecular Medicine, Faculty of Medicine, University of Malaya, 50603 Kuala Lumpur, Malaysia.,Department of Biomedical Science, Kulliyyah of Allied Health Sciences, International Islamic University Malaysia, 25200 Kuantan, Pahang, Malaysia
| | - Sarni Mat Junit
- Department of Molecular Medicine, Faculty of Medicine, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Khoon Leong Ng
- Department of Surgery, Faculty of Medicine, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Jaime Jacqueline Jayapalan
- University of Malaya Centre for Proteomics Research, Faculty of Medicine, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Barani Karikalan
- Perdana University, Jalan MAEPS Perdana, Serdang 43400, Selangor, Malaysia
| | - Onn Haji Hashim
- Department of Molecular Medicine, Faculty of Medicine, University of Malaya, 50603 Kuala Lumpur, Malaysia.,University of Malaya Centre for Proteomics Research, Faculty of Medicine, University of Malaya, 50603 Kuala Lumpur, Malaysia
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678
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Sinha P, Jaiswal P, Jainarayanan AK, Brahmachari SK. Intronic miRNA mediated gene expression regulation controls protein crowding inside the cell. Gene 2018; 679:172-178. [PMID: 30189267 DOI: 10.1016/j.gene.2018.08.082] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Revised: 07/29/2018] [Accepted: 08/30/2018] [Indexed: 01/07/2023]
Abstract
Gene regulatory effects of microRNAs at a posttranscriptional level have been established over the last decade. In this study, we analyze the interaction networks of mRNA translation regulation through intronic miRNA, under various tissue-specific cellular contexts, taking into account the thermodynamic affinity, chemical kinetics, co-localization, concentration levels, network parameters and the presence of competitive interactors. This database, and analysis has been made available through an open-access web-server, miRiam, to promote further exploration. Here we report that expression of genes involved in Apoptosis Processes, Immune System Processes, Translation Regulator Activities, and Molecular Transport Activities within the cell are predominately regulated by miRNA mediation. Our findings further indicate that this regulatory effect has a profound effect in controlling protein crowding inside the cell. A miRNA mediated gene expression regulation serves as a temporal regulator, allowing the cellular machinery to temporarily 'pause' the translation of mRNA, indicating that the miRNA-mRNA interactions may be important for governing the optimal usage of cell volume.
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Affiliation(s)
- Prashant Sinha
- Cluster Innovation Centre, University of Delhi, Delhi 110007, India
| | - Pragya Jaiswal
- Cluster Innovation Centre, University of Delhi, Delhi 110007, India
| | | | - Samir K Brahmachari
- Cluster Innovation Centre, University of Delhi, Delhi 110007, India; CSIR-Institute of Genomics and Integrative Biology, Delhi 110007, India; Academy of Scientific and Innovative Research, CRRI, New Delhi 110020, India.
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679
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Role of miRNA in the Regulatory Mechanisms of Estrogens in Cardiovascular Ageing. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2018; 2018:6082387. [PMID: 30671171 PMCID: PMC6317101 DOI: 10.1155/2018/6082387] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Accepted: 11/13/2018] [Indexed: 12/24/2022]
Abstract
Cardiovascular diseases are a worldwide health problem and are the leading cause of mortality in developed countries. Together with experimental data, the lower incidence of cardiovascular diseases in women than in men of reproductive age points to the influence of sex hormones at the cardiovascular level and suggests that estrogens play a protective role against cardiovascular disease and that this role is also modified by ageing. Estrogens affect cardiovascular function via their specific estrogen receptors to trigger gene expression changes at the transcriptional level. In addition, emerging studies have proposed a role for microRNAs in the vascular effects mediated by estrogens. miRNAs regulate gene expression by repressing translational processes and have been estimated to be involved in the regulation of approximately 30% of all protein-coding genes in mammals. In this review, we highlight the current knowledge of the role of estrogen-sensitive miRNAs, and their influence in regulating vascular ageing.
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680
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Riemann A, Reime S, Thews O. Acidic extracellular environment affects miRNA expression in tumorsin vitroandin vivo. Int J Cancer 2018; 144:1609-1618. [DOI: 10.1002/ijc.31790] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Revised: 07/13/2018] [Accepted: 07/23/2018] [Indexed: 12/15/2022]
Affiliation(s)
- Anne Riemann
- Institute of PhysiologyUniversity Halle Halle (Saale) Germany
| | - Sarah Reime
- Institute of PhysiologyUniversity Halle Halle (Saale) Germany
| | - Oliver Thews
- Institute of PhysiologyUniversity Halle Halle (Saale) Germany
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681
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Satari M, Aghadavod E, Mirhosseini N, Asemi Z. The effects of microRNAs in activating neovascularization pathways in diabetic retinopathy. J Cell Biochem 2018; 120:9514-9521. [PMID: 30556195 DOI: 10.1002/jcb.28227] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Accepted: 11/15/2018] [Indexed: 12/15/2022]
Abstract
Diabetic retinopathy (DR) is one of the major complications of diabetes mellitus that causes diabetic macular edema and visual loss. DR is categorized, based on the presence of vascular lesions and neovascularization, into non-proliferative and proliferative DR. Vascular changes in DR correlate with the cellular damage and pathological changes in the capillaries of blood-retinal barrier. Several cytokines have been involved in inducing neovascularization. These cytokines activate different signaling pathways which are mainly responsible for the complications of DR. Recently; microRNAs (miRNAs) have been introduced as the key factors in the regulation of the cytokine expression which plays a critical role in neovascularization of retinal cells. Some studies have demonstrated that changing levels of miRNAs have essential role in the pathophysiology of vascular changes in patients with DR. The aim of this study is to identify the effects of miRNAs in the pathogenesis of DR via activating neovascularization pathways.
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Affiliation(s)
- Mahbobeh Satari
- Research Center for Biochemistry and Nutrition in Metabolic Diseases, Kashan University of Medical Sciences, Kashan, Iran
| | - Esmat Aghadavod
- Research Center for Biochemistry and Nutrition in Metabolic Diseases, Kashan University of Medical Sciences, Kashan, Iran
| | | | - Zatollah Asemi
- Research Center for Biochemistry and Nutrition in Metabolic Diseases, Kashan University of Medical Sciences, Kashan, Iran
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682
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Wang L, Xu X, Yang J, Chen L, Liu B, Liu T, Jin Q. Integrated microRNA and mRNA analysis in the pathogenic filamentous fungus Trichophyton rubrum. BMC Genomics 2018; 19:933. [PMID: 30547762 PMCID: PMC6295003 DOI: 10.1186/s12864-018-5316-3] [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: 08/20/2018] [Accepted: 11/27/2018] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Trichophyton rubrum (T. rubrum) is an important model organism of dermatophytes, which are the most common fungal pathogens worldwide. Despite the severity and prevalence of the infection caused by these pathogens, current therapies are not sufficient. MicroRNA (miRNA) is a class of small noncoding RNAs that are key factors in the regulation of gene expression. These miRNAs are reported to be highly conserved in different organisms and are involved in various essential cellular processes. In this study, we performed an integrated analysis of microRNA-like RNAs (milRNAs) and mRNAs between conidial and mycelial stages to investigate the roles of milRNAs in regulating the expression of target genes in T. rubrum. RESULTS A total of 158 conserved milRNAs and 12 novel milRNAs were identified in our study, corresponding to 5470 target genes, which were involved in various essential biological pathways. In addition, 137 target genes corresponding to 21 milRNAs were concurrent differentially expressed between the conidial and mycelial stages. Among these 137 target genes, 64 genes showed the opposite trend to their corresponding milRNAs in expression difference between the two stages, indicating possible negative regulation. Furthermore, 46% of differentially expressed target genes are involved in transcription, transcriptional and post-transcriptional regulation. Our results indicate that milRNAs might associate with other regulatory elements to control gene expression at both transcriptional and post-transcriptional level. CONCLUSIONS This study provides the first analysis of milRNA expression profile in T. rubrum as well as dermatophytes in general. The results revealed the roles of milRNAs in regulating gene expression between the two major growth stages of this fungus. Our study deepens our understanding of T. rubrum and will serve as a foundation for further investigations to combat this fungus.
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Affiliation(s)
- Lingling Wang
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Xingye Xu
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Jian Yang
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Lihong Chen
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Bo Liu
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Tao Liu
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China.
| | - Qi Jin
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China.
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683
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Godbole M, Togar T, Patel K, Dharavath B, Yadav N, Janjuha S, Gardi N, Tiwary K, Terwadkar P, Desai S, Prasad R, Dhamne H, Karve K, Salunkhe S, Kawle D, Chandrani P, Dutt S, Gupta S, Badwe RA, Dutt A. Up-regulation of the kinase gene SGK1 by progesterone activates the AP-1-NDRG1 axis in both PR-positive and -negative breast cancer cells. J Biol Chem 2018; 293:19263-19276. [PMID: 30337371 PMCID: PMC6298595 DOI: 10.1074/jbc.ra118.002894] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Revised: 10/13/2018] [Indexed: 02/05/2023] Open
Abstract
Preoperative progesterone intervention has been shown to confer a survival benefit to breast cancer patients independently of their progesterone receptor (PR) status. This observation raises the question how progesterone affects the outcome of PR-negative cancer. Here, using microarray and RNA-Seq-based gene expression profiling and ChIP-Seq analyses of breast cancer cells, we observed that the serum- and glucocorticoid-regulated kinase gene (SGK1) and the tumor metastasis-suppressor gene N-Myc downstream regulated gene 1 (NDRG1) are up-regulated and that the microRNAs miR-29a and miR-101-1 targeting the 3'-UTR of SGK1 are down-regulated in response to progesterone. We further demonstrate a dual-phase transcriptional and post-transcriptional regulation of SGK1 in response to progesterone, leading to an up-regulation of NDRG1 that is mediated by a set of genes regulated by the transcription factor AP-1. We found that NDRG1, in turn, inactivates a set of kinases, impeding the invasion and migration of breast cancer cells. In summary, we propose a model for the mode of action of progesterone in breast cancer. This model helps decipher the molecular basis of observations in a randomized clinical trial of the effect of progesterone on breast cancer and has therefore the potential to improve the prognosis of breast cancer patients receiving preoperative progesterone treatment.
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Affiliation(s)
- Mukul Godbole
- From the Integrated Cancer Genomics Laboratory and
- the Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, Maharashtra 400094, India
| | - Trupti Togar
- From the Integrated Cancer Genomics Laboratory and
- the Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, Maharashtra 400094, India
| | | | - Bhasker Dharavath
- From the Integrated Cancer Genomics Laboratory and
- the Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, Maharashtra 400094, India
| | - Neelima Yadav
- From the Integrated Cancer Genomics Laboratory and
- the Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, Maharashtra 400094, India
| | | | - Nilesh Gardi
- From the Integrated Cancer Genomics Laboratory and
- the Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, Maharashtra 400094, India
| | | | | | - Sanket Desai
- From the Integrated Cancer Genomics Laboratory and
- the Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, Maharashtra 400094, India
| | | | | | - Kunal Karve
- From the Integrated Cancer Genomics Laboratory and
| | - Sameer Salunkhe
- the Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, Maharashtra 400094, India
- the Shilpee Laboratory, Advanced Centre for Treatment, Research, and Education in Cancer
| | | | | | - Shilpee Dutt
- the Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, Maharashtra 400094, India
- the Shilpee Laboratory, Advanced Centre for Treatment, Research, and Education in Cancer
| | | | - Rajendra A Badwe
- the Department of Surgical Oncology, Tata Memorial Hospital, Tata Memorial Centre, Navi Mumbai, Maharashtra 410210, India and
| | - Amit Dutt
- From the Integrated Cancer Genomics Laboratory and
- the Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, Maharashtra 400094, India
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684
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Sanchita, Trivedi R, Asif MH, Trivedi PK. Dietary plant miRNAs as an augmented therapy: cross-kingdom gene regulation. RNA Biol 2018; 15:1433-1439. [PMID: 30474479 PMCID: PMC6333437 DOI: 10.1080/15476286.2018.1551693] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Revised: 10/23/2018] [Accepted: 11/02/2018] [Indexed: 01/08/2023] Open
Abstract
Cross-kingdom gene regulation by microRNAs (miRNAs) initiated a hot debate on the effective role of orally acquired plant miRNAs on human gene expression. It resulted in the expansion of gene regulation theories and role of plant miRNAs in cross-kingdom regulation of gene expression. This opened up the discussion that 'Whether we really get what we eat?' and 'Whether the orally acquired miRNAs really have a biologically important consequences after entering our digestive and circulatory system?' The reports of orally acquired plant miRNAs inside human alimentary canal have been a topic of discussion in the scientific community. The cross-kingdom gene regulations have raised our hopes to explore the exciting world of plant miRNAs as therapeutic potential and dietary supplements. However, there are reports which have raised concerns over any such cross-kingdom regulation and argued that technical flaws in the experiments might have led to such hypothesis. This review will give the complete understanding of exogenous application and cross-kingdom regulation of plant miRNAs on human health. Here, we provide update and discuss the consequences of plant miRNA mediated cross-kingdom gene regulation and possibilities for this exciting regulatory mechanism as an augmented therapy against various diseases.
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Affiliation(s)
- Sanchita
- Genetics and Molecular Biology Division, CSIR-National Botanical Research Institute, Lucknow, Uttar Pradesh, India
| | - Ritu Trivedi
- Endocrinology Division, CSIR-Central Drug Research Institute (CSIR-CDRI), Lucknow, Uttar Pradesh, India
| | - Mehar Hasan Asif
- Genetics and Molecular Biology Division, CSIR-National Botanical Research Institute, Lucknow, Uttar Pradesh, India
- Academy of Scientific and Innovative Research (AcSIR), New Delhi, India
| | - Prabodh Kumar Trivedi
- Genetics and Molecular Biology Division, CSIR-National Botanical Research Institute, Lucknow, Uttar Pradesh, India
- Academy of Scientific and Innovative Research (AcSIR), New Delhi, India
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685
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Wang B, Ji G, Naeem H, Wang J, Kantharidis P, Powell D, Ricardo SD. The Use of Targeted Next Generation Sequencing to Explore Candidate Regulators of TGF-β1's Impact on Kidney Cells. Front Physiol 2018; 9:1755. [PMID: 30618784 PMCID: PMC6295563 DOI: 10.3389/fphys.2018.01755] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Accepted: 11/20/2018] [Indexed: 12/26/2022] Open
Abstract
Aims/Hypothesis: Transforming growth factor-beta (TGF-β1) plays an important regulatory role in the progression of chronic kidney failure. Further, damage to kidney glomerular mesangial cells is central to the progression of diabetic nephropathy. The aim of this study was to explore the genetic associations between mRNA, microRNA, and epigenetics in mesangial cells in response to TGF-β1. Methods: The regulatory effects of TGF-β1 on mesangial cells were investigated at different molecular levels by treating mesangial cells with TGF-β1 for 3 days followed by genome-wide miRNA, RNA, DNA methylation, and H3K27me3 expression profiling using next generation sequencing (NGS). Results: Our results provide the first comprehensive, computationally integrated report of RNA-Seq, miRNA-Seq, and epigenomic analyses across all genetic variations, confirming the occurrence of DNA methylation and H3K27me3 in response to TGF-β1. Our findings show that the expression of KLF7 and Gja4 are involved in TGF-β1 regulated DNA methylation. Our data also provide evidence of the association between epigenetic changes and the expression of genes closely related to TGF-β1 regulation. Conclusion: This study has advanced our current knowledge of mechanisms that contribute to the expression of TGF-β1-regulated genes involved in the pathogenesis of kidney disease. The molecular underpinnings of TGF-β1 stimulation of kidney cells was determined, thereby providing a robust platform for further target exploration.
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Affiliation(s)
- Bo Wang
- Department of Anatomy and Developmental Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Guanyu Ji
- Shenzhen E-GENE Tech Co., Ltd., Shenzhen, China
| | - Haroon Naeem
- Monash Bioinformatics Platform, Monash University, Clayton, VIC, Australia.,Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Junwen Wang
- Shenzhen E-GENE Tech Co., Ltd., Shenzhen, China
| | | | - David Powell
- Monash Bioinformatics Platform, Monash University, Clayton, VIC, Australia.,Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Sharon D Ricardo
- Department of Anatomy and Developmental Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
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686
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Ajami M, Sadeghian MH, Soleimani M, Keramati MR, Ajami M, Anbarlou A, Atashi A. Comparison of miRNA Profiles of Cord Blood Stem Cells in Identical and Fraternal Twins. CELL JOURNAL 2018; 21:78-85. [PMID: 30507092 PMCID: PMC6275421 DOI: 10.22074/cellj.2019.5683] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/29/2017] [Accepted: 02/12/2018] [Indexed: 11/16/2022]
Abstract
Objective The role of epigenetic in regulating of the gene expression profile the embryo has been documented. MicroRNAs
(miRNAs) are one of these epigenetic mechanisms. Twins are valuable models in determining the relative contributions
of genetics and the environment. In this study, we compared differences in the expression levels of 44 miRNAs in
hematopoietic stem cells (HSCs) of identical twins to that of fraternal twins as a controls.
Materials and Methods In this experimental study, CD133+ HSCs were isolated from cord blood of identical and
fraternal twins via magnetic-activated cell sorting (MACS). Variation in of gene expression levels of 44 miRNAs were
evaluated using quantitative reverse transcription-polymerase chain reaction (qRT-PCR).
Results Significant differences in expression were observed in both fraternal and identical twins to varying degrees,
but variations alteration in expression of the miRNAs were higher in fraternal twins.
Conclusion Identical twins had a positive correlation in miRNA expression, while the correlation was not statistically
significant in fraternal twins. Altogether, more differences in miRNA expression level in fraternal twins can be attributed
to the both genetics and the intrauterine environment. The contribution of the intrauterine environment and genetics to
miRNAs expression in HSCs was estimated 8 and 92%, respectively. By comparing of miRNA expression in identical
and fraternal twins and identification of their target genes and biological pathways, it could be possible to estimate the
effects of genetics and the environment on a number of biological pathways.
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Affiliation(s)
- Monireh Ajami
- Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mohammad Hadi Sadeghian
- Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran.,Cancer Molecular Pathology Research Center, Mashhad University of Medical Sciences, Mashhad, Iran. Electronic Address:
| | - Masoud Soleimani
- Department of Hematology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran. Electronic Address:
| | - Mohammad Reza Keramati
- Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran.,Cancer Molecular Pathology Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mansoureh Ajami
- Department of Hematology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Azadeh Anbarlou
- Department of Tissue Engineering, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Amir Atashi
- Stem Cell and Tissue Engineering Research Center, Shahroud University of Medical Sciences, Shahroud, Iran
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687
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Sahni A, Narra HP, Patel J, Sahni SK. MicroRNA-Regulated Rickettsial Invasion into Host Endothelium via Fibroblast Growth Factor 2 and Its Receptor FGFR1. Cells 2018; 7:cells7120240. [PMID: 30513762 PMCID: PMC6315532 DOI: 10.3390/cells7120240] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Revised: 11/20/2018] [Accepted: 11/29/2018] [Indexed: 02/07/2023] Open
Abstract
Microvascular endothelial cells (ECs) represent the primary target cells during human rickettsioses and respond to infection via the activation of immediate–early signaling cascades and the resultant induction of gene expression. As small noncoding RNAs dispersed throughout the genome, microRNAs (miRNAs) regulate gene expression post-transcriptionally to govern a wide range of biological processes. Based on our recent findings demonstrating the involvement of fibroblast growth factor receptor 1 (FGFR1) in facilitating rickettsial invasion into host cells and published reports suggesting miR-424 and miR-503 as regulators of FGF2/FGFR1, we measured the expression of miR-424 and miR-503 during R. conorii infection of human dermal microvascular endothelial cells (HMECs). Our results revealed a significant decrease in miR-424 and miR-503 expression in apparent correlation with increased expression of FGF2 and FGFR1. Considering the established phenomenon of endothelial heterogeneity and pulmonary and cerebral edema as the prominent pathogenic features of rickettsial infections, and significant pathogen burden in the lungs and brain in established mouse models of disease, we next quantified miR-424 and miR-503 expression in pulmonary and cerebral microvascular ECs. Again, R. conorii infection dramatically downregulated both miRNAs in these tissue-specific ECs as early as 30 min post-infection in correlation with higher FGF2/FGFR1 expression. Changes in the expression of both miRNAs and FGF2/FGFR1 were next confirmed in a mouse model of R. conorii infection. Furthermore, miR-424 overexpression via transfection of a mimic into host ECs reduced the expression of FGF2/FGFR1 and gave a corresponding decrease in R. conorii invasion, while an inhibitor of miR-424 had the expected opposite effect. Together, these findings implicate the rickettsial manipulation of host gene expression via regulatory miRNAs to ensure efficient cellular entry as the critical requirement to establish intracellular infection.
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Affiliation(s)
- Abha Sahni
- Department of Pathology, University of Texas Medical Branch, 301 University Boulevard, Galveston, TX 77555-0609, USA.
| | - Hema P Narra
- Department of Pathology, University of Texas Medical Branch, 301 University Boulevard, Galveston, TX 77555-0609, USA.
| | - Jignesh Patel
- Department of Pathology, University of Texas Medical Branch, 301 University Boulevard, Galveston, TX 77555-0609, USA.
| | - Sanjeev K Sahni
- Department of Pathology, University of Texas Medical Branch, 301 University Boulevard, Galveston, TX 77555-0609, USA.
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688
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Saxena S, Gupta A, Shukla V, Rani V. Functional annotation of differentially expressed fetal cardiac microRNA targets: implication for microRNA-based cardiovascular therapeutics. 3 Biotech 2018; 8:494. [PMID: 30498667 DOI: 10.1007/s13205-018-1520-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Accepted: 11/17/2018] [Indexed: 01/23/2023] Open
Abstract
Gene expression pattern of a failing heart depicts remarkable similarity with developing fetal heart. Elucidating genetic as well as epigenetic mechanisms regulating the gene expression during cardiac development will improve our understanding of cardiovascular diseases. In the present study, we aimed to validate and characterize differentially expressed known microRNAs (miRNA) obtained from next generation sequencing data of two fetal cardiac developmental stages (days 4th and 14th) from chicken (G. gallus domesticus) using bioinformatic approaches. Potential mRNA targets of individual miRNA were identified and classified according to their biological, cellular, and molecular functions. Functional annotation of putative target genes was performed to predict their association with cardiovascular diseases. We identified a total of 19 differentially expressed miRNAs between 4th and 14th day sample from the data sets obtained by next generation sequencing. A total of nearly 1522 potential targets ranging from 15 to 270 for each miRNA were predicted out of which 1221 were unique, while 301 were overlapping. Gene ontology and KEGG analysis revealed that majority of these target genes regulate critical cellular and molecular processes including transcriptional regulation, protein transport, signal transduction, matrix remodeling, Ras signaling, MAPK signaling, and TGF-beta signaling pathways indicating the complex nature of microRNA-mediated gene regulation during cardiogenesis. We found a significant association between potential target genes and cardiovascular diseases validating a link between fetal cardiac miRNAs and regulation of cardiovascular disease-related genes. These important findings may lay a foundation for further understanding the regulatory mechanisms operative in gene re-programming in the failing heart.
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689
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Cheng N, Xiao J, Ge S, Li J, Huang J, Wu X, Zhang S, Xiang T. High-Throughput Sequencing Strategy for miR-146b-regulated circRNA Expression in Hepatic Stellate Cells. Med Sci Monit 2018; 24:8699-8706. [PMID: 30504757 PMCID: PMC6286633 DOI: 10.12659/msm.910807] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND This study was designed to detect and analyze miR-146b-mediated circular RNA (circRNA) expression in hepatic stellate cells. MATERIAL AND METHODS The experiment was divided into a control group and a siRNA-miR-146b group. The interference efficiency of siRNA-miR-146b was confirmed by real-time quantitative reverse transcription PCR (qRT-PCR) and the cells were collected, and total RNA was collected for high flux sequencing. The miRNA-targeted carcass were predicted. Finally, the expression of 5 circRNAs was verified by qRT-PCR. RESULTS miR-146b expression in the siRNA-miR-146b group was significantly lower than that in the control group. The quality of the original sequencing data and the processed data satisfied with the analysis, and the expression of circRNAs was modulated after the reduction of miR-146b. Among them, 18 circRNAs were upregulated, while 77 circRNAs were downregulated in the miR-146b group compared with the control group. The gene prediction showed that hsa_circ1887 was the largest contact point in miRNA and circRNA regulatory networks. qRT-PCR showed that rno-circRNA-469, rno-circRNA-1138, rno-circRNA-2168 and rno-circRAN-1907 were significantly reduced, while circRNA-1984 was significantly promoted in the siRNA-miR-146b group compared with the control group, which were consistent with the measurements by high-throughput sequencing technique. CONCLUSIONS miR-146b could regulate the expression of circRNAs in HSCs, which might take part in the formation and development of hepatic fibrosis.
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Affiliation(s)
- Na Cheng
- Department of Infectious Diseases, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China (mainland)
| | - Juhua Xiao
- Department of Ultrasound, Jiangxi Maternal and Child Health Hospital, Nanchang, Jiangxi, China (mainland)
| | - Shanfei Ge
- Department of Infectious Diseases, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China (mainland)
| | - Juntao Li
- Department of General Surgery, GanZhou People's Hospital, Ganzhou, Jiangxi, China (mainland)
| | - Jiansheng Huang
- Department of Infectious Diseases, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China (mainland)
| | - Xiaoping Wu
- Department of Infectious Diseases, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China (mainland)
| | - Shouhua Zhang
- Department of General Surgery, Jiangxi Provincial Children's Hospital, Nanchang, Jiangxi, China (mainland)
| | - Tianxin Xiang
- Department of Infectious Diseases, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China (mainland)
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690
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Rossi UA, Hasenauer FC, Caffaro ME, Raschia MA, Maurizio E, Cortez HS, Neumann RD, Poli MA, Rossetti CA. Association of an IRF3 putative functional uORF variant with resistance to Brucella infection: A candidate gene based analysis of InDel polymorphisms in goats. Cytokine 2018; 115:109-115. [PMID: 30477986 DOI: 10.1016/j.cyto.2018.11.024] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2018] [Revised: 11/06/2018] [Accepted: 11/19/2018] [Indexed: 12/22/2022]
Abstract
Brucellosis is an important zoonotic disease caused by infection with Brucella spp. It generates major economic losses in livestock production worldwide. Goats are the principal hosts of B. melitensis, the main infection agent of caprine and human brucellosis. The selection of resistance-related genes is considered one of the best long-term means to improve control to bacterial infection in domestic ruminants. We performed a candidate gene association study to test if six short insertion/deletion polymorphisms (InDels) at bacterial-infection related genes influence the resistance to Brucella infection in female creole goats. InDels (IRF3-540: rs660531540, FKBP5-294: rs448529294, TIRAP-561: rs657494561, PTPRT-588: rs667380588, KALRN-989: rs667660989 and RAB5a-016: rs661537016) were resolved by PCR-capillary electrophoresis in samples from 64 cases and 64 controls for brucellosis. Allelic frequencies were significantly different between cases and controls at IRF3-540 and KALRN-989 (p = 0.001 and 0.005). Indeed, the minor alleles (a and k) at InDels IRF3-540 and KALRN-989 were more frequent among controls than cases, providing evidence that these alleles confer protection against Brucella infection. Moreover, IRF3-540 a-containing genotypes (Aa and aa) were associated with absence of Brucella-specific antibodies in goats (p = 0.003; OR = 3.52; 95% CI = 1.55-7.96), and more specifically, a-allele was associated with resistance to Brucella infection in a dose-dependent manner. Also, we observed that the IRF3-540 deletion (a-allele) extends a conserved upstream ORF by 75 nucleotides to the main ORF, and thus it may decrease gene expression by reducing translation efficiency from the main ORF. These results suggest a potential functional role of IRF3-540 deletion in genetic resistance to Brucella infection in goats.
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Affiliation(s)
- Ursula A Rossi
- Instituto Nacional de Tecnología Agropecuaria, CICVyA, Instituto de Patobiología, Nicolás Repetto y de Los Reseros s/n, Hurlingham, Buenos Aires B1686, Argentina
| | - Flavia C Hasenauer
- Instituto Nacional de Tecnología Agropecuaria, CICVyA, Instituto de Patobiología, Nicolás Repetto y de Los Reseros s/n, Hurlingham, Buenos Aires B1686, Argentina; CONICET, Buenos Aires, Argentina
| | - María E Caffaro
- Inst. de Genética ''Ewald A. Favret'', Nicolás Repetto y de Los Reseros s/n, Hurlingham, Buenos Aires B1686, Argentina
| | - Maria A Raschia
- Inst. de Genética ''Ewald A. Favret'', Nicolás Repetto y de Los Reseros s/n, Hurlingham, Buenos Aires B1686, Argentina
| | - Estefania Maurizio
- Instituto Nacional de Tecnología Agropecuaria, CICVyA, Instituto de Patobiología, Nicolás Repetto y de Los Reseros s/n, Hurlingham, Buenos Aires B1686, Argentina
| | - Hector S Cortez
- Instituto Nacional de Tecnología Agropecuaria, IIACS, Area de Salud Animal, RN 68 (km 172) Cerrillos, Salta, Argentina
| | - Roberto D Neumann
- Instituto Nacional de Tecnología Agropecuaria, IIACS, Area de Salud Animal, RN 68 (km 172) Cerrillos, Salta, Argentina
| | - Mario A Poli
- Inst. de Genética ''Ewald A. Favret'', Nicolás Repetto y de Los Reseros s/n, Hurlingham, Buenos Aires B1686, Argentina
| | - Carlos A Rossetti
- Instituto Nacional de Tecnología Agropecuaria, CICVyA, Instituto de Patobiología, Nicolás Repetto y de Los Reseros s/n, Hurlingham, Buenos Aires B1686, Argentina.
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691
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Sessa F, Salerno M, Di Mizio G, Bertozzi G, Messina G, Tomaiuolo B, Pisanelli D, Maglietta F, Ricci P, Pomara C. Anabolic Androgenic Steroids: Searching New Molecular Biomarkers. Front Pharmacol 2018; 9:1321. [PMID: 30524281 PMCID: PMC6256094 DOI: 10.3389/fphar.2018.01321] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2018] [Accepted: 10/29/2018] [Indexed: 12/14/2022] Open
Abstract
Even if anabolic androgenic steroid (AAS) abuse is clearly associated with a wide spectrum of collateral effects, adolescents and athletes frequently use a large group of synthetic derivatives of testosterone, both for aesthetic uses and for improving performance. Over the last few years, the development of MicroRNA (miRNA) technologies has become an essential part of research projects and their role as potential molecular biomarkers is being investigated by the scientific community. The circulating miRNAs detection as a diagnostic or prognostic tool for the diagnosis and treatment of several diseases is very useful, because with a minimal quantity of sample (peripheral blood), miRNAs are very sensitive. Even more, miRNAs remain stable both at room temperature and during freeze-thaw cycles. These characteristics highlight the important role of miRNAs in the near future as new tools for anti-doping. The article provides a systematic review and meta-analysis on the role of miRNAs as new potential molecular biomarkers of AAS use/abuse. Particularly, this paper analyzed the “miRNA signature” use as biomarkers for health disorders, focusing on the organ damages which are related to ASS use/abuse. Moreover, this review aims to provide a future prospect for less invasive or non-invasive procedures for the detection of circulating miRNA biomarkers as doping assumption signaling.
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Affiliation(s)
- Francesco Sessa
- Department of Clinical and Experimental Medicine, University of Foggia, Foggia, Italy
| | - Monica Salerno
- Department of Clinical and Experimental Medicine, University of Foggia, Foggia, Italy
| | - Giulio Di Mizio
- Department of Legal, Historical, Economic and Social Sciences, University of Catanzaro, Catanzaro, Italy
| | - Giuseppe Bertozzi
- Department of Clinical and Experimental Medicine, University of Foggia, Foggia, Italy
| | - Giovanni Messina
- Department of Clinical and Experimental Medicine, University of Foggia, Foggia, Italy
| | - Benedetta Tomaiuolo
- Department of Clinical and Experimental Medicine, University of Foggia, Foggia, Italy
| | - Daniela Pisanelli
- Department of Clinical and Experimental Medicine, University of Foggia, Foggia, Italy
| | - Francesca Maglietta
- Department of Clinical and Experimental Medicine, University of Foggia, Foggia, Italy
| | - Pietrantonio Ricci
- Department of Clinical and Experimental Medicine, University of Foggia, Foggia, Italy.,Medical and Surgical Sciences, University of Catanzaro, Catanzaro, Italy
| | - Cristoforo Pomara
- Department of Medical, Surgical and Advanced Technologies "G.F. Ingrassia", University of Catania, Catania, Italy
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692
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Yang D, Xu A, Shen P, Gao C, Zang J, Qiu C, Ouyang H, Jiang Y, He F. A two-level model for the role of complex and young genes in the formation of organism complexity and new insights into the relationship between evolution and development. EvoDevo 2018; 9:22. [PMID: 30455862 PMCID: PMC6231269 DOI: 10.1186/s13227-018-0111-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Accepted: 10/25/2018] [Indexed: 11/14/2022] Open
Abstract
Background How genome complexity affects organismal phenotypic complexity is a fundamental question in evolutionary developmental biology. Previous studies proposed various contributing factors of genome complexity and tried to find the connection between genomic complexity and organism complexity. However, a general model to answer this question is lacking. Here, we introduce a ‘two-level’ model for the realization of genome complexity at phenotypic level. Results Five representative species across Protostomia and Deuterostomia were involved in this study. The intrinsic gene properties contributing to genome complexity were classified into two generalized groups: the complexity and age degree of both protein-coding and noncoding genes. We found that young genes tend to be simpler; however, the mid-age genes, rather than the oldest genes, show the highest proportion of high complexity. Complex genes tend to be utilized preferentially in each stage of embryonic development, with maximum representation during the late stage of organogenesis. This trend is mainly attributed to mid-age complex genes. In contrast, young genes tend to be expressed in specific spatiotemporal states. An obvious correlation between the time point of the change in over- and under-representation and the order of gene age was observed, which supports the funnel-like model of the conservation pattern of development. In addition, we found some probable causes for the seemingly contradictory ‘funnel-like’ or ‘hourglass’ model. Conclusions These results indicate that complex and young genes contribute to organismal complexity at two different levels: Complex genes contribute to the complexity of individual proteomes in certain states, whereas young genes contribute to the diversity of proteomes in different spatiotemporal states. This conclusion is valid across the five species investigated, indicating it is a conserved model across Protostomia and Deuterostomia. The results in this study also support ‘funnel-like model’ from a new viewpoint and explain why there are different evo–devo relation models. Electronic supplementary material The online version of this article (10.1186/s13227-018-0111-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Dong Yang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 102206 The People's Republic of China
| | - Aishi Xu
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 102206 The People's Republic of China
| | - Pan Shen
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 102206 The People's Republic of China
| | - Chao Gao
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 102206 The People's Republic of China
| | - Jiayin Zang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 102206 The People's Republic of China
| | - Chen Qiu
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 102206 The People's Republic of China
| | - Hongsheng Ouyang
- 2Animal Sciences College of Jilin University, Changchun, 130062 The People's Republic of China
| | - Ying Jiang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 102206 The People's Republic of China
| | - Fuchu He
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 102206 The People's Republic of China
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693
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Characterization and expression profiling of microRNAs in response to plant feeding in two host-plant strains of the lepidopteran pest Spodoptera frugiperda. BMC Genomics 2018; 19:804. [PMID: 30400811 PMCID: PMC6219076 DOI: 10.1186/s12864-018-5119-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Accepted: 09/26/2018] [Indexed: 02/06/2023] Open
Abstract
Background A change in the environment may impair development or survival of living organisms leading them to adapt to the change. The resulting adaptation trait may reverse, or become fixed in the population leading to evolution of species. Deciphering the molecular basis of adaptive traits can thus give evolutionary clues. In phytophagous insects, a change in host-plant range can lead to emergence of new species. Among them, Spodoptera frugiperda is a major agricultural lepidopteran pest consisting of two host-plant strains having diverged 3 MA, based on mitochondrial markers. In this paper, we address the role of microRNAs, important gene expression regulators, in response to host-plant change and in adaptive evolution. Results Using small RNA sequencing, we characterized miRNA repertoires of the corn (C) and rice (R) strains of S. frugiperda, expressed during larval development on two different host-plants, corn and rice, in the frame of reciprocal transplant experiments. We provide evidence for 76 and 68 known miRNAs in C and R strains and 139 and 171 novel miRNAs. Based on read counts analysis, 34 of the microRNAs were differentially expressed in the C strain larvae fed on rice as compared to the C strain larvae fed on corn. Twenty one were differentially expressed on rice compared to corn in R strain. Nine were differentially expressed in the R strain compared to C strain when reared on corn. A similar ratio of microRNAs was differentially expressed between strains on rice. We could validate experimentally by QPCR, variation in expression of the most differentially expressed candidates. We used bioinformatics methods to determine the target mRNAs of known microRNAs. Comparison with the mRNA expression profile during similar reciprocal transplant experiment revealed potential mRNA targets of these host-plant regulated miRNAs. Conclusions In the current study, we performed the first systematic analysis of miRNAs in Lepidopteran pests feeding on host-plants. We identified a set of the differentially expressed miRNAs that respond to the plant diet, or differ constitutively between the two host plant strains. Among the latter, the ones that are also deregulated in response to host-plant are molecular candidates underlying a complex adaptive trait. Electronic supplementary material The online version of this article (10.1186/s12864-018-5119-6) contains supplementary material, which is available to authorized users.
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694
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Detection of a MicroRNA molecular signature of ultraviolet radiation in the superficial regions of melanocytic nevi on sun-exposed skin. Mod Pathol 2018; 31:1744-1755. [PMID: 29955145 DOI: 10.1038/s41379-018-0088-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2018] [Revised: 05/13/2018] [Accepted: 05/14/2018] [Indexed: 02/06/2023]
Abstract
How melanocytes transform into melanoma cells remains largely unknown. However, prolonged ultraviolet radiation exposure is linked with melanoma, and the DNA of melanomas arising in chronically sun-exposed skin is characterized by an elevated number of pyrimidine transitions, mainly C>T (predominantly caused by ultraviolet B), and transversions of GC>TA or AT>CG (caused by ultraviolet A over indirect mechanisms). Since ultraviolet penetrates mostly only the superficial dermis, we sought to determine the extent to which superficial and deep melanocytes of nevi in sun-exposed skin differ in their miRNA expression and consider the changes as likely secondary to ultraviolet radiation-induced damage. The differentially expressed miRNAs were analyzed for known potential oncomiRs or linked to potential oncogenes or tumor suppressors. Superficial and deep melanocytes were microdissected from the nevi of 14 patients. The suspensions were processed for hybridization to a ribonucleotide protection system with 2280 total probes, including 2256 miRNA probes targeting 2083 human miRNAs. A comprehensive analysis of all human miRNAs registered in miRBase 11.0 was performed using the HTG Molecular Diagnostic database. Statistical analysis of these data yielded for 14 samples a statistically relevant profile of 39 miRNA species at FDR<0.1 that were differentially expressed between superficial and deep melanocytes. Ingenuity Pathway Analysis based on the expression data of these 39 miRNAs suggested the gene transcripts AR, MDM2, SMAD2/3, and YBX1 as the most probable miRNA targets, which were validated at the protein level. Our findings suggest that superficial ultraviolet radiation-damaged melanocytes can be differentiated from deep melanocytes on the basis of the expression of 39 miRNAs, the most probable gene transcript and protein targets of which are AR, MDM2, SMAD2/3, and YBX1, with YBX1 expression validating the best the molecular signature in immunohistochemical analysis.
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695
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Deep sequencing and miRNA profiles in alcohol-induced neuroinflammation and the TLR4 response in mice cerebral cortex. Sci Rep 2018; 8:15913. [PMID: 30374194 PMCID: PMC6206094 DOI: 10.1038/s41598-018-34277-y] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Accepted: 10/10/2018] [Indexed: 12/12/2022] Open
Abstract
Alcohol abuse can induce brain injury and neurodegeneration, and recent evidence shows the participation of immune receptors toll-like in the neuroinflammation and brain damage. We evaluated the role of miRNAs as potential modulators of the neuroinflammation associated with alcohol abuse and the influence of the TLR4 response. Using mice cerebral cortex and next-generation sequencing (NGS), we identified miRNAs that were differentially expressed in the chronic alcohol-treated versus untreated WT or TLR4-KO mice. We observed a differentially expression of miR-183 Cluster (C) (miR-96/-182/-183), miR-200a and miR-200b, which were down-regulated, while mirR-125b was up-regulated in alcohol-treated WT versus (vs.) untreated mice. These miRNAs modulate targets genes related to the voltage-gated sodium channel, neuron hyperexcitability (Nav1.3, Trpv1, Smad3 and PP1-γ), as well as genes associated with innate immune TLR4 signaling response (Il1r1, Mapk14, Sirt1, Lrp6 and Bdnf). Functional enrichment of the miR-183C and miR-200a/b family target genes, revealed neuroinflammatory pathways networks involved in TLR4 signaling and alcohol abuse. The changes in the neuroinflammatory targets genes associated with alcohol abuse were mostly abolished in the TLR4-KO mice. Our results show the relationship between alcohol intake and miRNAs expression and open up new therapeutically targets to prevent deleterious effects of alcohol on the brain.
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696
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Panoutsopoulou K, Avgeris M, Scorilas A. miRNA and long non-coding RNA: molecular function and clinical value in breast and ovarian cancers. Expert Rev Mol Diagn 2018; 18:963-979. [DOI: 10.1080/14737159.2018.1538794] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Affiliation(s)
- Konstantina Panoutsopoulou
- Department of Biochemistry and Molecular Biology, Faculty of Biology, National and Kapodistrian University of Athens, Athens, Greece
| | - Margaritis Avgeris
- Department of Biochemistry and Molecular Biology, Faculty of Biology, National and Kapodistrian University of Athens, Athens, Greece
| | - Andreas Scorilas
- Department of Biochemistry and Molecular Biology, Faculty of Biology, National and Kapodistrian University of Athens, Athens, Greece
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697
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Vlăsceanu GM, Amărandi RM, Ioniță M, Tite T, Iovu H, Pilan L, Burns JS. Versatile graphene biosensors for enhancing human cell therapy. Biosens Bioelectron 2018; 117:283-302. [DOI: 10.1016/j.bios.2018.04.053] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Revised: 04/18/2018] [Accepted: 04/25/2018] [Indexed: 01/04/2023]
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698
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Singhvi G, Manchanda P, Krishna Rapalli V, Kumar Dubey S, Gupta G, Dua K. MicroRNAs as biological regulators in skin disorders. Biomed Pharmacother 2018; 108:996-1004. [PMID: 30372911 DOI: 10.1016/j.biopha.2018.09.090] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2018] [Revised: 09/11/2018] [Accepted: 09/15/2018] [Indexed: 12/12/2022] Open
Abstract
microRNAs are being investigated as promising therapeutic targets and biomarkers for different disease conditions. miRNAs serve as essential regulators of cell differentiation, proliferation and survival. The involvement of miRNAs in the functioning and regulation of the skin cells and skin diseases is a rapidly advancing area in dermatological research. miRNAs have been identified to play a key role in the pathogenesis, diagnosis, and treatment of the skin diseases. Skin is one of the largest organs of the body, primarily functioning as the first line of defence against external insults including bacteria, virus and other pathogens. Various miRNAs have been identified to demonstrate significant effects in various skin inflammatory conditions such as wounds, cancer, psoriasis, scleroderma, dermatomyositis. The current review explores the possible roles of the miRNAs in skin disorders and reports relating to the clinical trials involving skin diseases and miRNAs. The review has also compiled the information of the databases available, which correlates the miRNAs with different diseases and give details about targeting interactions of miRNA.
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Affiliation(s)
- Gautam Singhvi
- Department of Pharmacy, Birla Institute of Technology & Science (BITS), Pilani, Pilani Campus, Rajasthan, 333031, India.
| | - Prachi Manchanda
- Department of Pharmacy, Birla Institute of Technology & Science (BITS), Pilani, Pilani Campus, Rajasthan, 333031, India
| | - Vamshi Krishna Rapalli
- Department of Pharmacy, Birla Institute of Technology & Science (BITS), Pilani, Pilani Campus, Rajasthan, 333031, India
| | - Sunil Kumar Dubey
- Department of Pharmacy, Birla Institute of Technology & Science (BITS), Pilani, Pilani Campus, Rajasthan, 333031, India
| | - Gaurav Gupta
- School of Pharmaceutical Sciences, Jaipur National University, Jagatpura, 302017, Jaipur, India.
| | - Kamal Dua
- Discipline of Pharmacy, Graduate School of Health, University of Technology Sydney, Ultimo NSW, 2007, Australia; School of Biomedical Sciences and Pharmacy, The University of Newcastle, Callaghan, NSW, 2308, Australia; Priority Research Centre for Healthy Lungs, Hunter Medical Research Institute, Lot 1 Kookaburra Circuit, New Lambton Heights, Newcastle, NSW, 2305, Australia
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699
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Yi Y, Liu Y, Wu W, Wu K, Zhang W. The role of miR-106p-5p in cervical cancer: from expression to molecular mechanism. Cell Death Discov 2018; 4:36. [PMID: 30275981 PMCID: PMC6148547 DOI: 10.1038/s41420-018-0096-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Revised: 07/29/2018] [Accepted: 08/06/2018] [Indexed: 02/06/2023] Open
Abstract
This study aims to investigate the role of miR-106b-5p in cervical cancer by performing a comprehensive analysis on its expression and identifying its putative molecular targets and pathways based on The Cancer Genome Atlas (TCGA) dataset, Gene Expression Omnibus (GEO) dataset, and literature review. Significant upregulation of miR-106b-5p in cervical cancer is confirmed by meta-analysis with the data from TCGA, GEO, and literature. Moreover, the expression of miR-106b-5p is significantly correlated with the number of metastatic lymph nodes. Our bioinformatics analyses show that miR-106b could promote cervical cancer progression by modulating the expression of GSK3B, VEGFA, and PTK2 genes. Importantly, these three genes play a crucial role in PI3K-Akt signaling, focal adhesion, and cancer. Both the expression of miR-106b-5p and key genes are upregulated in cervical cancer. Several explanations could be implemented for this upregulation. However, the specific mechanism needs to be investigated further.
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Affiliation(s)
- Yuexiong Yi
- Department of Obstetrics and Gynecology, Zhongnan Hospital of Wuhan University, Wuhan, 430071 Hubei People's Republic of China
| | - Yanyan Liu
- Department of Obstetrics and Gynecology, Zhongnan Hospital of Wuhan University, Wuhan, 430071 Hubei People's Republic of China
| | - Wanrong Wu
- Department of Obstetrics and Gynecology, Zhongnan Hospital of Wuhan University, Wuhan, 430071 Hubei People's Republic of China
| | - Kejia Wu
- Department of Obstetrics and Gynecology, Zhongnan Hospital of Wuhan University, Wuhan, 430071 Hubei People's Republic of China
| | - Wei Zhang
- Department of Obstetrics and Gynecology, Zhongnan Hospital of Wuhan University, Wuhan, 430071 Hubei People's Republic of China
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700
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Akgül B, Erdoğan İ. Intracytoplasmic Re-localization of miRISC Complexes. Front Genet 2018; 9:403. [PMID: 30298086 PMCID: PMC6160738 DOI: 10.3389/fgene.2018.00403] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Accepted: 09/03/2018] [Indexed: 11/13/2022] Open
Abstract
MicroRNAs (miRNAs) are a conserved class of non-coding RNAs of 22 nucleotides that post-transcriptionally regulate gene expression through translational repression and/or mRNA degradation. A great progress has been made regarding miRNA biogenesis and miRNA-mediated gene regulation. Additionally, an ample amount of information exists with respect to the regulation of miRNAs. However, the cytoplasmic localization of miRNAs and its effect on gene regulatory output is still in progress. We provide a current review of the cytoplasmic miRNA localization in metazoans. We then discuss the dynamic changes in the intracytoplasmic localization of miRNAs as a means to regulate their silencing activity. We then conclude our discussion with the potential molecules that could modulate miRNA localization.
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Affiliation(s)
- Bünyamin Akgül
- Non-coding RNA Laboratory, Department of Molecular Biology and Genetics, İzmir Institute of Technology, Urla, Turkey
| | - İpek Erdoğan
- Non-coding RNA Laboratory, Department of Molecular Biology and Genetics, İzmir Institute of Technology, Urla, Turkey
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