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Baev V, Koppers-Lalic D, Costa-Silva B. Liquid Biopsy: Current Status and Future Perspectives. Cancers (Basel) 2023; 15:3205. [PMID: 37370815 DOI: 10.3390/cancers15123205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Accepted: 06/12/2023] [Indexed: 06/29/2023] Open
Abstract
Since the discovery of the Bence Jones protein in the middle to late 1800s and the subsequent identification of the carcinoembryonic antigen and alpha-fetoprotein in the 1970s, it has been demonstrated that the analysis of biofluids is essential to the diagnostic and follow-up processes of cancer [...].
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Affiliation(s)
- Vesselin Baev
- Department of Plant Physiology and Molecular Biology, University of Plovdiv, 4000 Plovdiv, Bulgaria
| | | | - Bruno Costa-Silva
- Champalimaud Physiology and Cancer Programme, Champalimaud Foundation, 1400-038 Lisbon, Portugal
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Naydenov M, Nikolova M, Apostolov A, Glogovitis I, Salumets A, Baev V, Yahubyan G. The Dynamics of miR-449a/c Expression during Uterine Cycles Are Associated with Endometrial Development. BIOLOGY 2022; 12:biology12010055. [PMID: 36671747 PMCID: PMC9855972 DOI: 10.3390/biology12010055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 12/23/2022] [Accepted: 12/24/2022] [Indexed: 12/30/2022]
Abstract
The human endometrium is a highly dynamic tissue. Increasing evidence has shown that microRNAs (miRs) play essential roles in human endometrium development. Our previous assay, based on small RNA-sequencing (sRNA-seq) indicated the complexity and dynamics of numerous sequence variants of miRs (isomiRs) that can act together to control genes of functional relevance to the receptive endometrium (RE). Here, we used a greater average depth of sRNA-seq to detect poorly expressed small RNAs. The sequencing data confirmed the up-regulation of miR-449c and uncovered other members of the miR-449 family up-regulated in RE-among them miR-449a, as well as several isoforms of both miR-449a and miR-449c, while the third family member, miR-449b, was not identified. Stem-looped RT-qPCR analysis of miR expression at four-time points of the endometrial cycle verified the increased expression of the miR-449a/c family members in RE, among which the 5' isoform of miR-449c-miR-449c.1 was the most strongly up-regulated. Moreover, we found in a case study that the expression of miR-449c.1 and its precursor correlated with the histological assessment of the endometrial phase and patient age. We believe this study will promote the clinical investigation and application of the miR-449 family in the diagnosis and prognosis of human reproductive diseases.
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Affiliation(s)
- Mladen Naydenov
- Faculty of Biology, University of Plovdiv, Tzar Assen 24, 4000 Plovdiv, Bulgaria
| | - Maria Nikolova
- Faculty of Biology, University of Plovdiv, Tzar Assen 24, 4000 Plovdiv, Bulgaria
- Center for Women’s Health, 4000 Plovdiv, Bulgaria
| | - Apostol Apostolov
- Faculty of Biology, University of Plovdiv, Tzar Assen 24, 4000 Plovdiv, Bulgaria
- Competence Centre on Health Technologies, 50406 Tartu, Estonia
| | - Ilias Glogovitis
- Faculty of Biology, University of Plovdiv, Tzar Assen 24, 4000 Plovdiv, Bulgaria
- Department of Neurosurgery, Cancer Center Amsterdam, Amsterdam University Medical Centers, VU University Medical Center, De Boelelaan 1117, 1081 HV Amsterdam, The Netherlands
| | - Andres Salumets
- Competence Centre on Health Technologies, 50406 Tartu, Estonia
- Division of Obstetrics and Gynaecology, Department of Clinical Science, Intervention and Technology (CLINTEC), Karolinska Institute, Karolinska University Hospital, 14186 Stockholm, Sweden
- Department of Obstetrics and Gynecology, Institute of Clinical Medicine, University of Tartu, 50406 Tartu, Estonia
| | - Vesselin Baev
- Faculty of Biology, University of Plovdiv, Tzar Assen 24, 4000 Plovdiv, Bulgaria
| | - Galina Yahubyan
- Faculty of Biology, University of Plovdiv, Tzar Assen 24, 4000 Plovdiv, Bulgaria
- Correspondence:
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Ivanova Z, Minkov G, Gisel A, Yahubyan G, Minkov I, Toneva V, Baev V. The Multiverse of Plant Small RNAs: How Can We Explore It?
. Int J Mol Sci 2022; 23:ijms23073979. [PMID: 35409340 PMCID: PMC8999349 DOI: 10.3390/ijms23073979] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 03/28/2022] [Accepted: 03/31/2022] [Indexed: 12/22/2022] Open
Abstract
Plant small RNAs (sRNAs) are a heterogeneous group of noncoding RNAs with a length of 20–24 nucleotides that are widely studied due to their importance as major regulators in various biological processes. sRNAs are divided into two main classes—microRNAs (miRNAs) and small interfering RNAs (siRNAs)—which differ in their biogenesis and functional pathways. Their identification and enrichment with new structural variants would not be possible without the use of various high-throughput sequencing (NGS) techniques, allowing for the detection of the total population of sRNAs in plants. Classifying sRNAs and predicting their functional role based on such high-performance datasets is a nontrivial bioinformatics task, as plants can generate millions of sRNAs from a variety of biosynthetic pathways. Over the years, many computing tools have been developed to meet this challenge. Here, we review more than 35 tools developed specifically for plant sRNAs over the past few years and explore some of their basic algorithms for performing tasks related to predicting, identifying, categorizing, and quantifying individual sRNAs in plant samples, as well as visualizing the results of these analyzes. We believe that this review will be practical for biologists who want to analyze their plant sRNA datasets but are overwhelmed by the number of tools available, thus answering the basic question of how to choose the right one for a particular study.
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Affiliation(s)
- Zdravka Ivanova
- Institute of Molecular Biology and Biotechnologies, 4108 Markovo, Bulgaria; (Z.I.); (G.M.); (I.M.); (V.T.)
| | - Georgi Minkov
- Institute of Molecular Biology and Biotechnologies, 4108 Markovo, Bulgaria; (Z.I.); (G.M.); (I.M.); (V.T.)
- Department of Plant Physiology and Molecular Biology, University of Plovdiv, 4000 Plovdiv, Bulgaria;
| | - Andreas Gisel
- Institute of Biomedical Technologies (ITB), CNR, 70126 Bari, Italy;
| | - Galina Yahubyan
- Department of Plant Physiology and Molecular Biology, University of Plovdiv, 4000 Plovdiv, Bulgaria;
| | - Ivan Minkov
- Institute of Molecular Biology and Biotechnologies, 4108 Markovo, Bulgaria; (Z.I.); (G.M.); (I.M.); (V.T.)
- Center of Plant System Biology and Biotechnology, 4000 Plovdiv, Bulgaria
| | - Valentina Toneva
- Institute of Molecular Biology and Biotechnologies, 4108 Markovo, Bulgaria; (Z.I.); (G.M.); (I.M.); (V.T.)
- Department of Plant Physiology and Molecular Biology, University of Plovdiv, 4000 Plovdiv, Bulgaria;
| | - Vesselin Baev
- Institute of Molecular Biology and Biotechnologies, 4108 Markovo, Bulgaria; (Z.I.); (G.M.); (I.M.); (V.T.)
- Department of Plant Physiology and Molecular Biology, University of Plovdiv, 4000 Plovdiv, Bulgaria;
- Correspondence:
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Coupling miR/isomiR and mRNA Expression Signatures Unveils New Molecular Layers of Endometrial Receptivity. Life (Basel) 2021; 11:life11121391. [PMID: 34947922 PMCID: PMC8705090 DOI: 10.3390/life11121391] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 12/03/2021] [Accepted: 12/06/2021] [Indexed: 12/27/2022] Open
Abstract
Embryo implantation depends on endometrial receptivity (ER). To achieve ER, the preparation of the uterine lining requires controlled priming by ovarian hormones and the expression of numerous genes in the endometrial tissue. microRNAs (miRs) have emerged as critical genetic regulators of ER in fertility and of the diseases that are associated with infertility. With the rapid development of next-generation sequencing technologies, it has become clear that miR genes can produce canonical miRs and variants—isomiRs. Here, we describe miR/isomiR expression dynamics across the four time points of natural chorionic gonadotropin (hCG)-administered cycles. Sequencing of the small RNAs (sRNA-seq) revealed that the most significant expression changes during the transition from the pre-receptive to the receptive phase occurred in the isomiR families of miR-125a, miR-125b, miR-10a, miR-10b, miR-449c, miR-92a, miR-92b, and miR-99a. Pairing the analysis of the differentially expressed (DE) miRs/isomiRs and their predicted DE mRNA targets uncovered 280 negatively correlating pairs. In the receptive endometrium, the 5′3′-isomiRs of miR-449c, which were among the most highly up-regulated isomiRs, showed a negative correlation with their target, transcription factor (TF) MYCN, which was down-regulated. Joint analysis of the miR/isomiR and TF expression identified several regulatory interactions. Based on these data, a regulatory TF-miR/isomiR gene-target circuit including let7g-5p and miR-345; the isomiR families of miR-10a, miR-10b, miR-92a, and miR-449c; and MYCN and TWIST1 was proposed to play a key role in the establishment of ER. Our work uncovers the complexity and dynamics of the endometrial isomiRs that can act cooperatively with miRs to control the functionally important genes that are critical to ER. Further studies of miR/isomiR expression patterns that are paired with those of their target mRNAs may provide a more in-depth picture of the endometrial pathologies that are associated with implantation failure.
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