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Peter JU, Dieudonné P, Zolk O. Pharmacokinetics, Pharmacodynamics, and Side Effects of Midazolam: A Review and Case Example. Pharmaceuticals (Basel) 2024; 17:473. [PMID: 38675433 PMCID: PMC11054797 DOI: 10.3390/ph17040473] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Revised: 03/27/2024] [Accepted: 04/04/2024] [Indexed: 04/28/2024] Open
Abstract
Midazolam, a short-acting benzodiazepine, is widely used to alleviate patient anxiety, enhance compliance, and aid in anesthesia. While its side effects are typically dose-dependent and manageable with vigilant perioperative monitoring, serious cardiorespiratory complications, including fatalities and permanent neurological impairment, have been documented. Prolonged exposure to benzodiazepines, such as midazolam, has been associated with neurological changes in infants. Despite attempts to employ therapeutic drug monitoring for optimal sedation dosing, its efficacy has been limited. Consequently, efforts are underway to identify alternative predictive markers to guide individualized dosing and mitigate adverse effects. Understanding these factors is crucial for determining midazolam's suitability for future administration, particularly after a severe adverse reaction. This article aims to elucidate the factors influencing midazolam's pharmacokinetics and pharmacodynamics, potentially leading to adverse events. Finally, a case study is presented to exemplify the complex investigation into the causative factors of midazolam-related adverse events.
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Affiliation(s)
- Jens-Uwe Peter
- Institute of Clinical Pharmacology, Immanuel Klinik Rüdersdorf, Brandenburg Medical School, 15562 Rüdersdorf, Germany;
| | - Peter Dieudonné
- Department of Anesthesiology, University Hospital Ulm, 89081 Ulm, Germany
| | - Oliver Zolk
- Institute of Clinical Pharmacology, Immanuel Klinik Rüdersdorf, Brandenburg Medical School, 15562 Rüdersdorf, Germany;
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Abstract
One of the most important resources for researchers of noncoding RNAs is the information available in public databases spread over the internet. However, the effective exploration of this data can represent a daunting task, given the large amount of databases available and the variety of stored data. This chapter describes a classification of databases based on information source, type of RNA, source organisms, data formats, and the mechanisms for information retrieval, detailing the relevance of each of these classifications and its usability by researchers. This classification is used to update a 2012 review, indexing now more than 229 public databases. This review will include an assessment of the new trends for ncRNA research based on the information that is being offered by the databases. Additionally, we will expand the previous analysis focusing on the usability and application of these databases in pathogen and disease research. Finally, this chapter will analyze how currently available database schemas can help the development of new and improved web resources.
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Diseases and their clinical heterogeneity – Are we ignoring the SNiPers and micRomaNAgers? An illustration using Beta-thalassemia clinical spectrum and fetal hemoglobin levels. Genomics 2019; 111:67-75. [DOI: 10.1016/j.ygeno.2018.01.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Revised: 12/18/2017] [Accepted: 01/03/2018] [Indexed: 12/18/2022]
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Wilkins OM, Titus AJ, Salas LA, Gui J, Eliot M, Butler RA, Sturgis EM, Li G, Kelsey KT, Christensen BC. MicroRNA-Related Genetic Variants Associated with Survival of Head and Neck Squamous Cell Carcinoma. Cancer Epidemiol Biomarkers Prev 2018; 28:127-136. [PMID: 29880533 DOI: 10.1158/1055-9965.epi-18-0002] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2018] [Revised: 03/23/2018] [Accepted: 06/04/2018] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Head and neck squamous cell carcinoma (HNSCC) is commonly diagnosed at an advanced stage, and prognosis for such patients is poor. There remains a gap in our understanding of genetic variants related with HNSCC prognosis. miRNA-related single nucleotide polymorphisms (miR-SNPs) are a class of genetic variants with gene-regulatory potential. METHODS We used a genome-scale approach and independent patient populations in a two-stage approach to test 40,286 common miR-SNPs for association with HNSCC survival in the discovery population (n = 847), and selected the strongest associations for replication in validation phase cases (n = 1,236). Furthermore, we leveraged miRNA interaction databases and miRNA expression data from The Cancer Genome Atlas, to provide functional insight for the identified and replicated associations. RESULTS Joint population analyses identified novel miR-SNPs associated with overall survival in oral and laryngeal cancers. rs1816158, located within long noncoding RNA MIR100HG, was associated with overall survival in oral cavity cancer (HR, 1.56; 95% confidence interval (CI), 1.21-2.00). In addition, expression of MIR100HG-embedded miRNA, miR-100, was significantly associated with overall survival in an independent cohort of HNSCC cases (HR, 1.25; 95% CI, 1.06-1.49). A SNP in the 3'UTR of SH3BP4 (rs56161233) that overlaps predicted miRNA-binding sites and is predicted to disrupt several miRNA-mRNA interactions was associated with overall survival of laryngeal cancer (HR, 2.57; 95% CI, 1.71-3.86). CONCLUSIONS This work reveals novel miR-SNPs associated with HNSCC survival, and utilizes miRNA-mRNA interaction and expression data to provide functional support for these associations. IMPACT These findings extend our understanding of how genetic variation contributes to HNSCC survival, and may contribute to future prognostic models for improved risk stratification.
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Affiliation(s)
- Owen M Wilkins
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire
| | - Alexander J Titus
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire
| | - Lucas A Salas
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire
| | - Jiang Gui
- Department of Biomedical Data Science, Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire
| | - Melissa Eliot
- Department of Epidemiology, Brown University, Providence, Rhode Island
| | - Rondi A Butler
- Department of Epidemiology, Brown University, Providence, Rhode Island
| | - Erich M Sturgis
- Department of Head and Neck Surgery, The University of Texas M.D. Anderson Cancer Center, Houston, Texas
- Department of Epidemiology, The University of Texas M.D. Anderson Cancer Center, Houston, Texas
| | - Guojun Li
- Department of Head and Neck Surgery, The University of Texas M.D. Anderson Cancer Center, Houston, Texas
- Department of Epidemiology, The University of Texas M.D. Anderson Cancer Center, Houston, Texas
| | - Karl T Kelsey
- Department of Epidemiology, Brown University, Providence, Rhode Island
- Department of Pathology and Laboratory Medicine, Brown University, Providence, Rhode Island
| | - Brock C Christensen
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire.
- Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire
- Department of Community and Family Medicine, Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire
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Abstract
miRNA regulome is whole set of regulatory elements that regulate miRNA expression or are under control of miRNAs. Its understanding is vital for comprehension of miRNA functions. Classification of miRNA-related genetic variability is challenging because miRNA interact with different genomic elements and are studied at different omics levels. In the present study, miRNA-associated genetic variability is presented at three levels: miRNA genes and their upstream regulation, miRNA silencing machinery and miRNA targets. Several types of miRNA-associated genetic variations are known, including short and structural polymorphisms and epimutations. Differential expression can also affect miRNA regulome function. Classification of miRNA-associated genetic variability presents a baseline for complementing sequence variant nomenclature, planning of experiments, protocols for multi-omics data integration and development of biomarkers.
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Affiliation(s)
- Karin Hrovatin
- Department of Animal Science, Biotechnical Faculty, University of Ljubljana, Domžale, 1230, Slovenia
| | - Tanja Kunej
- Department of Animal Science, Biotechnical Faculty, University of Ljubljana, Domžale, 1230, Slovenia
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Ning S, Li X. Non-coding RNA Resources. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1094:1-7. [DOI: 10.1007/978-981-13-0719-5_1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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Moudi M, Montazer Zohour M. SNP in microRNA sequences or binding sites of miRNAs: association with type 2 diabetes mellitus susceptibility and in silico analysis. Int J Diabetes Dev Ctries 2017. [DOI: 10.1007/s13410-017-0587-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
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Wilkins OM, Titus AJ, Gui J, Eliot M, Butler RA, Sturgis EM, Li G, Kelsey KT, Christensen BC. Genome-scale identification of microRNA-related SNPs associated with risk of head and neck squamous cell carcinoma. Carcinogenesis 2017; 38:986-993. [PMID: 28582492 PMCID: PMC5862295 DOI: 10.1093/carcin/bgx056] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Polymorphisms in microRNAs and their target sites can disrupt microRNA-dependent gene regulation, and have been associated with cancer susceptibility. However, genome-scale analyses of microRNA-related genetic variation in cancer are lacking. We tested the associations of ~40 000 common [minor allele frequency (MAF) ≥5%], microRNA-related single nucleotide polymorphisms (miR-SNPs), with risk of head and neck squamous cell carcinoma (HNSCC) in a discovery population, and validated selected loci in an independent population among a total of 2198 cases and 2180 controls. Joint analyses across the discovery and validation populations revealed six novel miR-SNP associations with risk of HNSCC. An upstream variant of MIR548H4 (rs7834169), replicated its association with overall HNSCC risk as well as risk of oral cavity cancer. Four other variants were specifically associated with oral cavity cancer risk (rs16914640, rs1134367, rs7306991 and rs1373756). 3'UTR variant of HADH, rs221347 and rs4975616, located within known cancer risk locus 5p15.33, were specific to risk of laryngeal cancer. High confidence predicted microRNA binding sites were identified for CLEC2D, LOC37443, KDM8 and HADH overlapping rs16914640, rs7306991, rs1134367 and rs221347, respectively. Furthermore, we identified several microRNA interactions with KDM8 and HADH predicted to be disrupted by genetic variation at rs1134367 and rs221347. These results suggest microRNA-related genetic variation may contribute to the genetic susceptibility of HNSCC, and that more powerful evaluation of this class of genetic variation and their relationship with cancer risk is warranted.
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Affiliation(s)
| | | | - Jiang Gui
- Department of Biomedical Data Science, Geisel School of Medicine at Dartmouth, Lebanon, NH 03756, USA
| | - Melissa Eliot
- Department of Epidemiology, Brown University, Providence, RI 02912, USA
| | - Rondi A Butler
- Department of Epidemiology, Brown University, Providence, RI 02912, USA
| | - Erich M Sturgis
- Department of Head and Neck Surgery
- Department of Epidemiology, The University of Texas M.D. Anderson Cancer Center, TX 77030, USA
| | - Guojun Li
- Department of Head and Neck Surgery
- Department of Epidemiology, The University of Texas M.D. Anderson Cancer Center, TX 77030, USA
| | - Karl T Kelsey
- Department of Epidemiology, Brown University, Providence, RI 02912, USA
- Department of Pathology and Laboratory Medicine, Brown University, Providence, RI 02912, USA
| | - Brock C Christensen
- Department of Epidemiology
- Department of Molecular and Systems Biology and
- Department of Community and Family Medicine, Geisel School of Medicine at Dartmouth, Lebanon, NH 03756, USA
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9
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Denisenko E, Ho D, Tamgue O, Ozturk M, Suzuki H, Brombacher F, Guler R, Schmeier S. IRNdb: the database of immunologically relevant non-coding RNAs. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2016; 2016:2630531. [PMID: 31414702 PMCID: PMC5091335 DOI: 10.1093/database/baw138] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Revised: 09/22/2016] [Accepted: 09/23/2016] [Indexed: 12/27/2022]
Abstract
MicroRNAs (miRNAs), long non-coding RNAs (lncRNAs) and other functional non-coding RNAs (ncRNAs) have emerged as pivotal regulators involved in multiple biological processes. Recently, ncRNA control of gene expression has been identified as a critical regulatory mechanism in the immune system. Despite the great efforts made to discover and characterize ncRNAs, the functional role for most remains unknown. To facilitate discoveries in ncRNA regulation of immune system-related processes, we developed the database of immunologically relevant ncRNAs and target genes (IRNdb). We integrated mouse data on predicted and experimentally supported ncRNA-target interactions, ncRNA and gene annotations, biological pathways and processes and experimental data in a uniform format with a user-friendly web interface. The current version of IRNdb documents 12 930 experimentally supported miRNA-target interactions between 724 miRNAs and 2427 immune-related mouse targets. In addition, we recorded 22 453 lncRNA-immune target and 377 PIWI-interacting RNA-immune target interactions. IRNdb is a comprehensive searchable data repository which will be of help in studying the role of ncRNAs in the immune system. Database URL:http://irndb.org
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Affiliation(s)
- Elena Denisenko
- Institute of Natural and Mathematical Sciences, Massey University, Albany, Auckland 0632, New Zealand
| | - Daniel Ho
- Institute of Natural and Mathematical Sciences, Massey University, Albany, Auckland 0632, New Zealand
| | - Ousman Tamgue
- University of Cape Town, Institute of Infectious Diseases and Molecular Medicine (IDM), Division of Immunology and South African Medical Research Council (SAMRC) Immunology of Infectious Diseases, Faculty of Health Sciences, University of Cape Town, Cape Town 7925, South Africa
- International Centre for Genetic Engineering and Biotechnology, Cape Town Component, Cape Town 7925, South Africa
| | - Mumin Ozturk
- University of Cape Town, Institute of Infectious Diseases and Molecular Medicine (IDM), Division of Immunology and South African Medical Research Council (SAMRC) Immunology of Infectious Diseases, Faculty of Health Sciences, University of Cape Town, Cape Town 7925, South Africa
- International Centre for Genetic Engineering and Biotechnology, Cape Town Component, Cape Town 7925, South Africa
| | - Harukazu Suzuki
- Division of Genomic Technologies, RIKEN Center for Life Science Technologies, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Frank Brombacher
- University of Cape Town, Institute of Infectious Diseases and Molecular Medicine (IDM), Division of Immunology and South African Medical Research Council (SAMRC) Immunology of Infectious Diseases, Faculty of Health Sciences, University of Cape Town, Cape Town 7925, South Africa
- International Centre for Genetic Engineering and Biotechnology, Cape Town Component, Cape Town 7925, South Africa
| | - Reto Guler
- University of Cape Town, Institute of Infectious Diseases and Molecular Medicine (IDM), Division of Immunology and South African Medical Research Council (SAMRC) Immunology of Infectious Diseases, Faculty of Health Sciences, University of Cape Town, Cape Town 7925, South Africa
- International Centre for Genetic Engineering and Biotechnology, Cape Town Component, Cape Town 7925, South Africa
| | - Sebastian Schmeier
- Institute of Natural and Mathematical Sciences, Massey University, Albany, Auckland 0632, New Zealand
- *Corresponding author: Tel: +64 9 2136538; E-mail:
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Singh NK. microRNAs Databases: Developmental Methodologies, Structural and Functional Annotations. Interdiscip Sci 2016; 9:357-377. [PMID: 27021491 DOI: 10.1007/s12539-016-0166-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2015] [Revised: 02/08/2016] [Accepted: 03/11/2016] [Indexed: 12/31/2022]
Abstract
microRNA (miRNA) is an endogenous and evolutionary conserved non-coding RNA, involved in post-transcriptional process as gene repressor and mRNA cleavage through RNA-induced silencing complex (RISC) formation. In RISC, miRNA binds in complementary base pair with targeted mRNA along with Argonaut proteins complex, causes gene repression or endonucleolytic cleavage of mRNAs and results in many diseases and syndromes. After the discovery of miRNA lin-4 and let-7, subsequently large numbers of miRNAs were discovered by low-throughput and high-throughput experimental techniques along with computational process in various biological and metabolic processes. The miRNAs are important non-coding RNA for understanding the complex biological phenomena of organism because it controls the gene regulation. This paper reviews miRNA databases with structural and functional annotations developed by various researchers. These databases contain structural and functional information of animal, plant and virus miRNAs including miRNAs-associated diseases, stress resistance in plant, miRNAs take part in various biological processes, effect of miRNAs interaction on drugs and environment, effect of variance on miRNAs, miRNAs gene expression analysis, sequence of miRNAs, structure of miRNAs. This review focuses on the developmental methodology of miRNA databases such as computational tools and methods used for extraction of miRNAs annotation from different resources or through experiment. This study also discusses the efficiency of user interface design of every database along with current entry and annotations of miRNA (pathways, gene ontology, disease ontology, etc.). Here, an integrated schematic diagram of construction process for databases is also drawn along with tabular and graphical comparison of various types of entries in different databases. Aim of this paper is to present the importance of miRNAs-related resources at a single place.
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Affiliation(s)
- Nagendra Kumar Singh
- Department of Biological Science and Engineering, Maulana Azad National Institute of Technology, Bhopal, M.P., 462003, India.
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11
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Suresh PS, Venkatesh T, Tsutsumi R. In silico analysis of polymorphisms in microRNAs that target genes affecting aerobic glycolysis. ANNALS OF TRANSLATIONAL MEDICINE 2016; 4:69. [PMID: 27004216 DOI: 10.3978/j.issn.2305-5839.2016.01.35] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
BACKGROUND Cancer cells preferentially metabolize glucose through aerobic glycolysis, an observation known as the Warburg effect. Recently, studies have deciphered the role of oncogenes and tumor suppressor genes in regulating the Warburg effect. Furthermore, mutations in glycolytic enzymes identified in various cancers highlight the importance of the Warburg effect at the molecular and cellular level. MicroRNAs (miRNAs) are non-coding RNAs that posttranscriptionally regulate gene expression and are dysregulated in the pathogenesis of various types of human cancers. Single nucleotide polymorphisms (SNPs) in miRNA genes may affect miRNA biogenesis, processing, function, and stability and provide additional complexity in the pathogenesis of cancer. Moreover, mutations in miRNA target sequences in target mRNAs can affect expression. METHODS In silico analysis and cataloguing polymorphisms in miRNA genes that target genes directly or indirectly controlling aerobic glycolysis was carried out using different publically available databases. RESULTS miRNA SNP2.0 database revealed several SNPs in miR-126 and miR-25 in the upstream and downstream pre-miRNA flanking regions respectively should be inserted after flanking regions and miR-504 and miR-451 had the fewest. These miRNAs target genes that control aerobic glycolysis indirectly. SNPs in premiRNA genes were found in miR-96, miR-155, miR-25 and miR34a by miRNASNP. Dragon database of polymorphic regulation of miRNA genes (dPORE-miRNA) database revealed several SNPs that modify transcription factor binding sites (TFBS) or creating new TFBS in promoter regions of selected miRNA genes as analyzed by dPORE-miRNA. CONCLUSIONS Our results raise the possibility that integration of SNP analysis in miRNA genes with studies of metabolic adaptations in cancer cells could provide greater understanding of oncogenic mechanisms.
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Affiliation(s)
- Padmanaban S Suresh
- 1 Department of Biosciences, Mangalore University, Mangalagangotri, Mangalore 574 199, Karnataka, India ; 2 Nitte University Centre for Science Education and Research, Nitte University, Derlakatte, Mangalore, Karnataka, India ; 3 Department of Nutrition and Metabolism, Institute of Biomedical Science, Tokushima University, Tokushima, Japan
| | - Thejaswini Venkatesh
- 1 Department of Biosciences, Mangalore University, Mangalagangotri, Mangalore 574 199, Karnataka, India ; 2 Nitte University Centre for Science Education and Research, Nitte University, Derlakatte, Mangalore, Karnataka, India ; 3 Department of Nutrition and Metabolism, Institute of Biomedical Science, Tokushima University, Tokushima, Japan
| | - Rie Tsutsumi
- 1 Department of Biosciences, Mangalore University, Mangalagangotri, Mangalore 574 199, Karnataka, India ; 2 Nitte University Centre for Science Education and Research, Nitte University, Derlakatte, Mangalore, Karnataka, India ; 3 Department of Nutrition and Metabolism, Institute of Biomedical Science, Tokushima University, Tokushima, Japan
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12
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Dole NS, Delany AM. MicroRNA variants as genetic determinants of bone mass. Bone 2016; 84:57-68. [PMID: 26723575 PMCID: PMC4755870 DOI: 10.1016/j.bone.2015.12.016] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/09/2015] [Revised: 12/17/2015] [Accepted: 12/21/2015] [Indexed: 02/07/2023]
Abstract
Single nucleotide polymorphisms (SNPs) are the most abundant genetic variants that contribute to the heritability of bone mass. MicroRNAs (miRNAs, miRs) are key post-transcriptional regulators that modulate the differentiation and function of skeletal cells by targeting multiple genes in the same or distinct signaling pathways. SNPs in miRNA genes and miRNA binding sites can alter miRNA abundance and mRNA targeting. This review describes the potential impact of miRNA-related SNPs on skeletal phenotype. Although many associations between SNPs and bone mass have been described, this review is limited to gene variants for which a function has been experimentally validated. SNPs in miRNA genes (miR-SNPs) that impair miRNA processing and alter the abundance of mature miRNA are discussed for miR-146a, miR-125a, miR-196a, miR-149 and miR-27a. SNPs in miRNA targeting sites (miR-TS-SNPs) that alter miRNA binding are described for the bone remodeling genes bone morphogenetic protein receptor 1 (Bmpr1), fibroblast growth factor 2 (Fgf2), osteonectin (Sparc) and histone deacetylase 5 (Hdac5). The review highlights two aspects of miRNA-associated SNPs: the mechanism for altering miRNA mediated gene regulation and the potential of miR-associated SNPs to alter osteoblast, osteoclast or chondrocyte differentiation and function. Given the polygenic nature of skeletal diseases like osteoporosis and osteoarthritis, validating the function of additional miRNA-associated SNPs has the potential to enhance our understanding of the genetic determinants of bone mass and predisposition to selected skeletal diseases.
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Affiliation(s)
- Neha S Dole
- Center for Molecular Medicine, UCONN Health, Farmington, CT, USA.
| | - Anne M Delany
- Center for Molecular Medicine, UCONN Health, Farmington, CT, USA.
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Cammaerts S, Strazisar M, De Rijk P, Del Favero J. Genetic variants in microRNA genes: impact on microRNA expression, function, and disease. Front Genet 2015; 6:186. [PMID: 26052338 PMCID: PMC4439572 DOI: 10.3389/fgene.2015.00186] [Citation(s) in RCA: 88] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2015] [Accepted: 05/05/2015] [Indexed: 12/21/2022] Open
Abstract
MicroRNAs (miRNAs) are important regulators of gene expression and like any other gene, their coding sequences are subject to genetic variation. Variants in miRNA genes can have profound effects on miRNA functionality at all levels, including miRNA transcription, maturation, and target specificity, and as such they can also contribute to disease. The impact of variants in miRNA genes is the focus of the present review. To put these effects into context, we first discuss the requirements of miRNA transcripts for maturation. In the last part an overview of available databases and tools and experimental approaches to investigate miRNA variants related to human disease is presented.
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Affiliation(s)
- Sophia Cammaerts
- Applied Molecular Genomics Unit, Department of Molecular Genetics, VIB, University of Antwerp Antwerp, Belgium
| | - Mojca Strazisar
- Applied Molecular Genomics Unit, Department of Molecular Genetics, VIB, University of Antwerp Antwerp, Belgium
| | - Peter De Rijk
- Applied Molecular Genomics Unit, Department of Molecular Genetics, VIB, University of Antwerp Antwerp, Belgium
| | - Jurgen Del Favero
- Applied Molecular Genomics Unit, Department of Molecular Genetics, VIB, University of Antwerp Antwerp, Belgium ; Multiplicom N.V., Niel Belgium
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14
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Human genetic variation and its effect on miRNA biogenesis, activity and function. Biochem Soc Trans 2015; 42:1184-9. [PMID: 25110023 DOI: 10.1042/bst20140055] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
miRNAs are small non-coding regulators of gene expression that are estimated to regulate over 60% of all human genes. Each miRNA can target multiple mRNA targets and as such, miRNAs are responsible for some of the 'fine tuning' of gene expression and are implicated in regulation of all cellular processes. miRNAs bind to target genes by sequence complementarity, resulting in target degradation or translational blocking and usually a reduction in target gene expression. Like mRNA, miRNAs are transcribed from genomic DNA and are processed in several steps that are heavily reliant on correct secondary and tertiary structure. Secondary structure is determined by RNA sequence, which is in turn determined by the sequence of the genome. The human genome, however, like most eukaryotes is variable. Large numbers of SNPs (single nucleotide polymorphisms), small insertions and deletions (indels) and CNVs (copy number variants) have been described in our genome. Should this genetic variation occur in regions critical for the correct secondary structure or target binding, it may interfere with normal gene regulation and cause disease. In this review, we outline the consequences of genetic variation involving different aspects of miRNA biosynthesis, processing and regulation, with selected examples of incidences when this has potential to affect human disease.
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Paschoal AR, Maracaja-Coutinho V, Setubal JC, Simões ZLP, Verjovski-Almeida S, Durham AM. Non-coding transcription characterization and annotation. RNA Biol 2014; 9:274-82. [DOI: 10.4161/rna.19352] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
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Schmit SL, Gollub J, Shapero MH, Huang SC, Rennert HS, Finn A, Rennert G, Gruber SB. MicroRNA polymorphisms and risk of colorectal cancer. Cancer Epidemiol Biomarkers Prev 2014; 24:65-72. [PMID: 25342389 DOI: 10.1158/1055-9965.epi-14-0219] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND miRNAs act as post-transcriptional regulators of gene expression. Genetic variation in miRNA-encoding sequences or their corresponding binding sites may affect the fidelity of the miRNA-mRNA interaction and subsequently alter the risk of cancer development. METHODS This study expanded the search for miRNA-related polymorphisms contributing to the etiology of colorectal cancer across the genome using a novel platform, the Axiom miRNA Target Site Genotyping Array (237,858 markers). After quality control, the study included 596 cases and 429 controls from the Molecular Epidemiology of Colorectal Cancer study, a population-based case-control study of colorectal cancer in northern Israel. The association between each marker and colorectal cancer status was examined assuming a log-additive genetic model using logistic regression adjusted for sex, age, and two principal components. RESULTS Twenty-three markers had P values less than 5.0E-04, and the most statistically significant association involved rs2985 (chr6:34845648; intronic of UHRF1BP1; OR = 0.66; P = 3.7E-05). Furthermore, this study replicated a previously published risk locus, rs1051690, in the 3'-untranslated region of the insulin receptor gene INSR (OR = 1.38; P = 0.03), with strong evidence of differences in INSR gene expression by genotype. CONCLUSIONS This study is the first to examine associations between genetic variation in miRNA target sites and colorectal cancer using a genome-wide approach. Functional studies to identify allele-specific effects on miRNA binding are needed to confirm the regulatory capacity of genetic variation to influence risk of colorectal cancer. IMPACT This study demonstrates the potential for an miRNA-targeted genome-wide association study to identify candidate susceptibility loci and prioritize them for functional characterization.
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Affiliation(s)
- Stephanie L Schmit
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California. USC Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California
| | | | | | - Shu-Chen Huang
- USC Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Hedy S Rennert
- Department of Community Medicine and Epidemiology, Carmel Medical Center, Haifa, Israel
| | - Andrea Finn
- Affymetrix, Incorporated, Santa Clara, California
| | - Gad Rennert
- Department of Community Medicine and Epidemiology, Carmel Medical Center, Haifa, Israel. Clalit Health Services National Cancer Control Center, Haifa, Israel. Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
| | - Stephen B Gruber
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California. USC Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California.
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Obsteter J, Dovc P, Kunej T. Genetic variability of microRNA regulome in human. Mol Genet Genomic Med 2014; 3:30-9. [PMID: 25629077 PMCID: PMC4299713 DOI: 10.1002/mgg3.110] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2014] [Revised: 07/19/2014] [Accepted: 07/31/2014] [Indexed: 11/05/2022] Open
Abstract
MicroRNAs are currently being extensively studied due to their important role as post-transcriptional regulators. During miRNA biogenesis, precursors undergo two cleavage steps performed by Drosha-DGCR8 (Microprocessor) cleaving of pri-miRNA to produce pre-miRNA and Dicer-mediated cleaving to create mature miRNA. Genetic variants within human miRNA regulome have been shown to influence miRNA expression, target interaction and to affect the phenotype. In this study, we reviewed the literature, existing bioinformatics tools and catalogs associated with polymorphic miRNA regulome, and organized them into four categories: (1) polymorphisms located within miRNA genes (miR-SNPs), (2) transcription factor-binding sites/miRNA regulatory regions (miR-rSNPs), (3) miRNA target sites (miR-TS-SNPs), and 4. miRNA silencing machinery (miR-SM-SNPs). Since the miR-SM-SNPs have not been systematically studied yet, we have collected polymorphisms associated with miRNA silencing machinery. We have developed two catalogs containing genetic variability within: (1) genes encoding three main catalytic components of the silencing machinery, DROSHA, DGCR8, and DICER1; (2) miRNA genes itself, overlapping Drosha and Dicer cleavage sites. The developed resource of polymorphisms is available online (http://www.integratomics-time.com/miRNA-regulome) and will be useful for further functional studies and development of biomarkers associated with diseases and phenotypic traits.
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Affiliation(s)
- Jana Obsteter
- University of Ljubljana, Biotechnical Faculty, Department of Animal Science Groblje 3, 1230, Domzale, Slovenia
| | - Peter Dovc
- University of Ljubljana, Biotechnical Faculty, Department of Animal Science Groblje 3, 1230, Domzale, Slovenia
| | - Tanja Kunej
- University of Ljubljana, Biotechnical Faculty, Department of Animal Science Groblje 3, 1230, Domzale, Slovenia
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18
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Arrigo P. MicroRNA and noncoding RNA-related data sources. Methods Mol Biol 2014; 1107:73-89. [PMID: 24272432 DOI: 10.1007/978-1-62703-748-8_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Noncoding RNAs (ncRNAs) are ribonucleic acids capable of controlling different genetic and metabolic functions. These molecules have been recently organized into different classes, and among them microRNAs (miRNAs) are extensively studied. MicroRNAs are short oligomers mainly involved in posttranscriptional gene silencing. The specific research field, focused on structural and functional characterization of microRNAs, is commonly called mirnomics. The exploitation of the interest in microRNAs has stimulated the organization of several databases that are often integrated with analytical tools in order to predict microRNA targets, or to find those miRNAs capable to inhibit the expression of a specific protein. This work attempts to provide an overview of accessible information about microRNAs and other noncoding RNAs that has been gathered in curated databases.
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19
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Kamanu TKK, Radovanovic A, Archer JAC, Bajic VB. Exploration of miRNA families for hypotheses generation. Sci Rep 2013; 3:2940. [PMID: 24126940 PMCID: PMC3796740 DOI: 10.1038/srep02940] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2013] [Accepted: 09/25/2013] [Indexed: 12/13/2022] Open
Abstract
Technological improvements have resulted in increased discovery of new microRNAs (miRNAs) and refinement and enrichment of existing miRNA families. miRNA families are important because they suggest a common sequence or structure configuration in sets of genes that hint to a shared function. Exploratory tools to enhance investigation of characteristics of miRNA families and the functions of family-specific miRNA genes are lacking. We have developed, miRNAVISA, a user-friendly web-based tool that allows customized interrogation and comparisons of miRNA families for hypotheses generation, and comparison of per-species chromosomal distribution of miRNA genes in different families. This study illustrates hypothesis generation using miRNAVISA in seven species. Our results unveil a subclass of miRNAs that may be regulated by genomic imprinting, and also suggest that some miRNA families may be species-specific, as well as chromosome- and/or strand-specific.
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Affiliation(s)
- Timothy K K Kamanu
- King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Thuwal, Kingdom of Saudi Arabia
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20
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Bulik-Sullivan B, Selitsky S, Sethupathy P. Prioritization of genetic variants in the microRNA regulome as functional candidates in genome-wide association studies. Hum Mutat 2013; 34:1049-56. [PMID: 23595788 PMCID: PMC3807557 DOI: 10.1002/humu.22337] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2013] [Accepted: 04/03/2013] [Indexed: 02/06/2023]
Abstract
Comprehensive analyses of results from genome-wide association studies (GWAS) have demonstrated that complex disease/trait-associated loci are enriched in gene regulatory regions of the genome. The search for causal regulatory variation has focused primarily on transcriptional elements, such as promoters and enhancers. microRNAs (miRNAs) are now widely appreciated as critical posttranscriptional regulators of gene expression and are thought to impart stability to biological systems. Naturally occurring genetic variation in the miRNA regulome is likely an important contributor to phenotypic variation in the human population. However, the extent to which polymorphic miRNA-mediated gene regulation underlies GWAS signals remains unclear. In this study, we have developed the most comprehensive bioinformatic analysis pipeline to date for cataloging and prioritizing variants in the miRNA regulome as functional candidates in GWAS. We highlight specific findings, including a variant in the promoter of the miRNA let-7 that may contribute to human height variation. We also provide a discussion of how our approach can be expanded in the future. Overall, we believe that the results of this study will be valuable for researchers interested in determining whether GWAS signals implicate the miRNA regulome in their disease/trait of interest.
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Affiliation(s)
- Brendan Bulik-Sullivan
- Department of Genetics, University of North Carolina at Chapel HillChapel Hill, North Carolina
| | - Sara Selitsky
- Department of Genetics, University of North Carolina at Chapel HillChapel Hill, North Carolina
| | - Praveen Sethupathy
- Department of Genetics, University of North Carolina at Chapel HillChapel Hill, North Carolina
- Carolina Center for Genome Sciences, University of North Carolina at Chapel HillChapel Hill, North Carolina
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel HillChapel Hill, North Carolina
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21
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Zhou J, Peng R, Li T, Luo X, Peng H, Zha H, Yin P, Wen L, Zhang Z. A potentially functional polymorphism in the regulatory region of let-7a-2 is associated with an increased risk for diabetic nephropathy. Gene 2013; 527:456-61. [PMID: 23860321 DOI: 10.1016/j.gene.2013.06.088] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2013] [Revised: 06/13/2013] [Accepted: 06/26/2013] [Indexed: 01/13/2023]
Abstract
Diabetic nephropathy (DN) is a major diabetic complication. However, the initiating molecular events triggering DN are unknown. MicroRNAs (miRNAs) have recently been identified as regulators that modulate the target gene expression and are involved in DN. However, the evidence of the mechanism is still insufficient in human samples. In this study, microRNA microarray assay was used to study gene differential expression profiles in DN and diabetes mellitus (DM) patients. One of the specific differentially expressed microRNAs, let-7a, was down-expressed in DN. Additionally, the expression of let-7a was also decreased in DN by real-time RT PCR in the patients' samples. Moreover, single nucleotide polymorphism (SNP) analysis was used to evaluate the relationship between three SNPs in the regulatory region of let-7a-2 gene and the risk of DN in the Chinese Han population by means of PCR-restriction fragment length polymorphism (RFLP-PCR). Also, the genotype and allele frequencies of let-7a-2 polymorphism were tested in 274 individuals, including 108 DN, 104 DM patients and 62 health control individuals (CON). It was found that a variant rs1143770 and the distributions of CT/TT genotypes were significantly different in three groups, and the CT+TT genotypes frequencies were significantly higher in DN and DM groups than that in CON group. In conclusion, let-7a-2 might participate in the regulation of the occurrence of DN, and a potential variant rs1143770 was significantly associated with the increased risk for DN.
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Affiliation(s)
- Ji Zhou
- Department of Cell Biology and Medical Genetics, Chongqing Medical University, No.1, Medical College Road, Chongqing, China
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22
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Klein K, Zanger UM. Pharmacogenomics of Cytochrome P450 3A4: Recent Progress Toward the "Missing Heritability" Problem. Front Genet 2013; 4:12. [PMID: 23444277 PMCID: PMC3580761 DOI: 10.3389/fgene.2013.00012] [Citation(s) in RCA: 160] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2012] [Accepted: 01/26/2013] [Indexed: 12/19/2022] Open
Abstract
CYP3A4 is the most important drug metabolizing enzyme in adult humans because of its prominent expression in liver and gut and because of its broad substrate specificity, which includes drugs from most therapeutic categories and many endogenous substances. Expression and function of CYP3A4 vary extensively both intra- and interindividually thus contributing to unpredictable drug response and toxicity. A multitude of environmental, genetic, and physiological factors are known to influence CYP3A4 expression and activity. Among the best predictable sources of variation are drug–drug interactions, which are either caused by pregnane X-receptor (PXR), constitutive androstane receptor (CAR) mediated gene induction, or by inhibition through coadministered drugs or other chemicals, including also plant and food ingredients. Among physiological and pathophysiological factors are hormonal status, age, and gender, the latter of which was shown to result in higher levels in females compared to males, as well as inflammatory processes that downregulate CYP3A4 transcription. Despite the influence of these non-genetic factors, the genetic influence on CYP3A4 activity was estimated in previous twin studies and using information on repeated drug administration to account for 66% up to 88% of the interindividual variation. Although many single nucleotide polymorphisms (SNPs) within the CYP3A locus have been identified, genetic association studies have so far failed to explain a major part of the phenotypic variability. The term “missing heritability” has been used to denominate the gap between expected and known genetic contribution, e.g., for complex diseases, and is also used here in analogy. In this review we summarize CYP3A4 pharmacogenetics/genomics from the early inheritance estimations up to the most recent genetic and clinical studies, including new findings about SNPs in CYP3A4 (*22) and other genes (P450 oxidoreductase (POR), peroxisome proliferator-activated receptor alpha (PPARA)) with possible contribution to CYP3A4 variable expression.
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Affiliation(s)
- Kathrin Klein
- Dr. Margarete Fischer Bosch Institute of Clinical Pharmacology, Stuttgart Stuttgart, Germany ; University of Tübingen Tübingen, Germany
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23
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Abstract
Background MicroRNAs (miRNAs) are short non-coding RNA molecules that regulate mRNA transcript levels and translation. Deregulation of microRNAs is indicated in a number of diseases and microRNAs are seen as a promising target for biomarker identification and drug development. miRNA expression is commonly measured by microarray or real-time polymerase chain reaction (RT-PCR). The findings of RT-PCR data are highly dependent on the normalization techniques used during preprocessing of the Cycle Threshold readings from RT-PCR. Some of the commonly used endogenous controls themselves have been discovered to be differentially expressed in various conditions such as cancer, making them inappropriate internal controls. Methods We demonstrate that RT-PCR data contains a systematic bias resulting in large variations in the Cycle Threshold (CT) values of the low-abundant miRNA samples. We propose a new data normalization method that considers all available microRNAs as endogenous controls. A weighted normalization approach is utilized to allow contribution from all microRNAs, weighted by their empirical stability. Results The systematic bias in RT-PCR data is illustrated on a microRNA dataset obtained from primary cutaneous melanocytic neoplasms. We show that through a single control parameter, this method is able to emulate other commonly used normalization methods and thus provides a more general approach. We explore the consistency of RT-PCR expression data with microarray expression by utilizing a dataset where both RT-PCR and microarray profiling data is available for the same miRNA samples. Conclusions A weighted normalization method allows the contribution of all of the miRNAs, whether they are highly abundant or have low expression levels. Our findings further suggest that the normalization of a particular miRNA should rely on only miRNAs that have comparable expression levels.
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Affiliation(s)
- Rehman Qureshi
- Center for integrated Bioinformatics, School of Biomedical Engineering, Science and Health System, Drexel University, 3120 Market Street, Philadelphia, PA 19104, USA
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24
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Cytochrome P450 enzymes in drug metabolism: regulation of gene expression, enzyme activities, and impact of genetic variation. Pharmacol Ther 2013; 138:103-41. [PMID: 23333322 DOI: 10.1016/j.pharmthera.2012.12.007] [Citation(s) in RCA: 2520] [Impact Index Per Article: 229.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2012] [Accepted: 12/27/2012] [Indexed: 02/06/2023]
Abstract
Cytochromes P450 (CYP) are a major source of variability in drug pharmacokinetics and response. Of 57 putatively functional human CYPs only about a dozen enzymes, belonging to the CYP1, 2, and 3 families, are responsible for the biotransformation of most foreign substances including 70-80% of all drugs in clinical use. The highest expressed forms in liver are CYPs 3A4, 2C9, 2C8, 2E1, and 1A2, while 2A6, 2D6, 2B6, 2C19 and 3A5 are less abundant and CYPs 2J2, 1A1, and 1B1 are mainly expressed extrahepatically. Expression of each CYP is influenced by a unique combination of mechanisms and factors including genetic polymorphisms, induction by xenobiotics, regulation by cytokines, hormones and during disease states, as well as sex, age, and others. Multiallelic genetic polymorphisms, which strongly depend on ethnicity, play a major role for the function of CYPs 2D6, 2C19, 2C9, 2B6, 3A5 and 2A6, and lead to distinct pharmacogenetic phenotypes termed as poor, intermediate, extensive, and ultrarapid metabolizers. For these CYPs, the evidence for clinical significance regarding adverse drug reactions (ADRs), drug efficacy and dose requirement is rapidly growing. Polymorphisms in CYPs 1A1, 1A2, 2C8, 2E1, 2J2, and 3A4 are generally less predictive, but new data on CYP3A4 show that predictive variants exist and that additional variants in regulatory genes or in NADPH:cytochrome P450 oxidoreductase (POR) can have an influence. Here we review the recent progress on drug metabolism activity profiles, interindividual variability and regulation of expression, and the functional and clinical impact of genetic variation in drug metabolizing P450s.
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25
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Abstract
MicroRNAs (miRNAs) are a class of noncoding RNAs (ncRNAs) and posttranscriptional gene regulators shown to be involved in pathogenesis of all types of human cancers. Their aberrant expression as tumor suppressors can lead to cancerogenesis by inhibiting malignant potential, or when acting as oncogenes, by activating malignant potential. Differential expression of miRNA genes in tumorous tissues can occur owing to several factors including positional effects when mapping to cancer-associated genomic regions, epigenetic mechanisms, and malfunctioning of the miRNA processing machinery, all of which can contribute to a complex miRNA-mediated gene network misregulation. They may increase or decrease expression of protein-coding genes, can target 3'-UTR or other genic regions (5'-UTR, promoter, coding sequences), and can function in various subcellular compartments, developmental, and metabolic processes. Because expanding research on miRNA-cancer associations has already produced large amounts of data, our main objective here was to summarize main findings and critically examine the intricate network connecting the miRNAs and coding genes in regulatory mechanisms and their function and phenotypic consequences for cancer. By examining such interactions, we aimed to gain insights for the development of new diagnostic markers as well as identification of potential venues for more selective tumor therapy. To enable efficient examination of the main past and current miRNA discoveries, we developed a Web-based miRNA timeline tool that will be regularly updated (http://www.integratomics-time.com/miRNA_timeline). Further development of this tool will be directed at providing additional analyses to clarify complex network interactions between miRNAs, other classes of ncRNAs, and protein-coding genes and their involvement in development of diseases including cancer. This tool therefore provides curated relevant information about the miRNA basic research and therapeutic application all at hand on one site to help researchers and clinicians in making informed decision about their miRNA cancer-related research or clinical practice.
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26
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Li J, Zhang Z. miRNA regulatory variation in human evolution. Trends Genet 2012; 29:116-24. [PMID: 23128010 DOI: 10.1016/j.tig.2012.10.008] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2012] [Revised: 10/01/2012] [Accepted: 10/08/2012] [Indexed: 11/18/2022]
Abstract
Recent advancements have revealed a complex post-transcriptional regulatory network in humans involving miRNAs. However, the contribution of miRNAs to human evolution, especially interindividual variation associated with miRNAs, is only beginning to be studied. In this article, we illustrate the extent of variation in miRNA-mediated post-transcriptional regulation in humans. Based on evidence from recent studies, we argue that the evolution of post-transcriptional control may be adaptive, and that it not only complements the primary transcriptional regulation by transcription factors (TFs), but also diversifies gene expression phenotypes, thereby generating genetic novelty on which natural selection subsequently acts. Given that current evolutionary analyses and genotype-phenotype mapping are primarily focused on protein-coding genes and TF-mediated regulations, comprehensive examination of post-transcriptional variations should be included in future studies to add a new dimension to understanding of human phenotypic evolution.
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Affiliation(s)
- Jingjing Li
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA.
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27
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Salzman DW, Weidhaas JB. SNPing cancer in the bud: microRNA and microRNA-target site polymorphisms as diagnostic and prognostic biomarkers in cancer. Pharmacol Ther 2012; 137:55-63. [PMID: 22964086 DOI: 10.1016/j.pharmthera.2012.08.016] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2012] [Accepted: 08/17/2012] [Indexed: 12/18/2022]
Abstract
MicroRNAs are master regulators of gene expression and control many biological pathways such as cell growth, differentiation and apoptosis. Deregulation of microRNA expression and activity results in a myriad of diseases including cancer. Recently, several reports have indicated that single nucleotide polymorphisms (SNPs) in microRNAs and microRNA-target sites impact microRNA biology and associate with cancer risk, treatment response and outcome. In this review we will describe these findings and discuss the possible future of utilizing these SNPs as diagnostic and prognostic markers in the clinic.
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Affiliation(s)
- David W Salzman
- Department of Therapeutic Radiology, Yale School of Medicine, 15 York Street, Hunter Building, HRT-205, New Haven, CT 06510, USA
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28
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Kamanu FK, Medvedeva YA, Schaefer U, Jankovic BR, Archer JAC, Bajic VB. Mutations and binding sites of human transcription factors. Front Genet 2012; 3:100. [PMID: 22670148 PMCID: PMC3365286 DOI: 10.3389/fgene.2012.00100] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2011] [Accepted: 05/16/2012] [Indexed: 11/13/2022] Open
Abstract
Mutations in any genome may lead to phenotype characteristics that determine ability of an individual to cope with adaptation to environmental challenges. In studies of human biology, among the most interesting ones are phenotype characteristics that determine responses to drug treatments, response to infections, or predisposition to specific inherited diseases. Most of the research in this field has been focused on the studies of mutation effects on the final gene products, peptides, and their alterations. Considerably less attention was given to the mutations that may affect regulatory mechanism(s) of gene expression, although these may also affect the phenotype characteristics. In this study we make a pilot analysis of mutations observed in the regulatory regions of 24,667 human RefSeq genes. Our study reveals that out of eight studied mutation types, "insertions" are the only one that in a statistically significant manner alters predicted transcription factor binding sites (TFBSs). We also find that 25 families of TFBSs have been altered by mutations in a statistically significant manner in the promoter regions we considered. Moreover, we find that the related transcription factors are, for example, prominent in processes related to intracellular signaling; cell fate; morphogenesis of organs and epithelium; development of urogenital system, epithelium, and tube; neuron fate commitment. Our study highlights the significance of studying mutations within the genes regulatory regions and opens way for further detailed investigations on this topic, particularly on the downstream affected pathways.
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Affiliation(s)
- Frederick Kinyua Kamanu
- Computational Bioscience Research Center, King Abdullah University of Science and Technology Thuwal, Kingdom of Saudi Arabia
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29
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Parnell LD. Advances in Technologies and Study Design. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2012; 108:17-50. [DOI: 10.1016/b978-0-12-398397-8.00002-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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30
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Szcześniak MW, Deorowicz S, Gapski J, Kaczyński Ł, Makalowska I. miRNEST database: an integrative approach in microRNA search and annotation. Nucleic Acids Res 2011; 40:D198-204. [PMID: 22135287 PMCID: PMC3245016 DOI: 10.1093/nar/gkr1159] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
Despite accumulating data on animal and plant microRNAs and their functions, existing public miRNA resources usually collect miRNAs from a very limited number of species. A lot of microRNAs, including those from model organisms, remain undiscovered. As a result there is a continuous need to search for new microRNAs. We present miRNEST (http://mirnest.amu.edu.pl), a comprehensive database of animal, plant and virus microRNAs. The core part of the database is built from our miRNA predictions conducted on Expressed Sequence Tags of 225 animal and 202 plant species. The miRNA search was performed based on sequence similarity and as many as 10 004 miRNA candidates in 221 animal and 199 plant species were discovered. Out of them only 299 have already been deposited in miRBase. Additionally, miRNEST has been integrated with external miRNA data from literature and 13 databases, which includes miRNA sequences, small RNA sequencing data, expression, polymorphisms and targets data as well as links to external miRNA resources, whenever applicable. All this makes miRNEST a considerable miRNA resource in a sense of number of species (544) that integrates a scattered miRNA data into a uniform format with a user-friendly web interface.
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Affiliation(s)
- Michał Wojciech Szcześniak
- Laboratory of Bioinformatics, Faculty of Biology, Adam Mickiewicz University, Umultowska 89, 61-614 Poznan, Poland.
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