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Small RNA Targets: Advances in Prediction Tools and High-Throughput Profiling. BIOLOGY 2022; 11:biology11121798. [PMID: 36552307 PMCID: PMC9775672 DOI: 10.3390/biology11121798] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 11/27/2022] [Accepted: 12/08/2022] [Indexed: 12/14/2022]
Abstract
MicroRNAs (miRNAs) are an abundant class of small non-coding RNAs that regulate gene expression at the post-transcriptional level. They are suggested to be involved in most biological processes of the cell primarily by targeting messenger RNAs (mRNAs) for cleavage or translational repression. Their binding to their target sites is mediated by the Argonaute (AGO) family of proteins. Thus, miRNA target prediction is pivotal for research and clinical applications. Moreover, transfer-RNA-derived fragments (tRFs) and other types of small RNAs have been found to be potent regulators of Ago-mediated gene expression. Their role in mRNA regulation is still to be fully elucidated, and advancements in the computational prediction of their targets are in their infancy. To shed light on these complex RNA-RNA interactions, the availability of good quality high-throughput data and reliable computational methods is of utmost importance. Even though the arsenal of computational approaches in the field has been enriched in the last decade, there is still a degree of discrepancy between the results they yield. This review offers an overview of the relevant advancements in the field of bioinformatics and machine learning and summarizes the key strategies utilized for small RNA target prediction. Furthermore, we report the recent development of high-throughput sequencing technologies, and explore the role of non-miRNA AGO driver sequences.
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Feitosa RM, Prieto-Oliveira P, Brentani H, Machado-Lima A. MicroRNA target prediction tools for animals: Where we are at and where we are going to - A systematic review. Comput Biol Chem 2022; 100:107729. [DOI: 10.1016/j.compbiolchem.2022.107729] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 07/08/2022] [Accepted: 07/09/2022] [Indexed: 11/26/2022]
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Yin D, Lin D, Guo H, Gu H, Ying C, Zhang Y, Zhang J, Liu K, Tang W. Integrated analysis of blood mRNAs and microRNAs reveals immune changes with age in the Yangtze finless porpoise (Neophocaena asiaeorientalis). Comp Biochem Physiol B Biochem Mol Biol 2021; 256:110635. [PMID: 34119650 DOI: 10.1016/j.cbpb.2021.110635] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 05/31/2021] [Accepted: 06/07/2021] [Indexed: 12/13/2022]
Abstract
Populations of Yangtze finless porpoises (YFPs) have rapidly declined in recent decades, raising the specter of extinction. In order to protect YFPs, a greater understanding of their biology is needed, including studying how their immune functioning changes with age. Here, we systematically studied the hematologic and biochemical parameters, as well as mRNAs and miRNAs profiles of old, adult, and young YFPs. The lymphocyte (LYMPH), neutrophils (NEUT) and eosinophils (EOS) counts in old YFPs were lower than those in young or adult YFPs. When comparing old to adult YFPs, the latter showed higher expression of genes associated with the innate and adaptive immune systems, including complement components, major histocompatibility complex, interleukins, TNF receptors, and chemokines/cytokines. When comparing old to young YFPs, the most striking difference was in higher toll-like receptor signaling in the latter. When comparing adult to young YFPs, the former exhibited higher expression of genes related to adaptive immunity and the FoxO signaling pathway, but lower expression of genes associated with the PI3K-Akt signaling pathway. Negative miRNA-mRNA interactions were predicted in comparisons of the old and adult (326), old and young (316), adult and young (211) groups. Overall, these results delineate a progression from early innate immune function dominance to adaptive immune function enhancement (young to adult) and deterioration (adult to old), and the changes in miRNAs profile correlate with the effects of age on immune functions. This study is the first to observe the changes of immune function of Yangtze finless porpoise with age using transcriptome method, and the study's findings are of great significance for protecting this endangered species.
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Affiliation(s)
- Denghua Yin
- Shanghai Universities Key Laboratory of Marine Animal Taxonomy and Evolution, Shanghai Ocean University, Shanghai 201306, China; Scientific Observing and Experimental Station of Fishery Resources and Environment in the Lower Reaches of the Changjiang River, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, CAFS, WuXi 214081, China
| | - Danqing Lin
- Scientific Observing and Experimental Station of Fishery Resources and Environment in the Lower Reaches of the Changjiang River, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, CAFS, WuXi 214081, China
| | - Hongyi Guo
- Shanghai Universities Key Laboratory of Marine Animal Taxonomy and Evolution, Shanghai Ocean University, Shanghai 201306, China
| | - Hailong Gu
- Shanghai Universities Key Laboratory of Marine Animal Taxonomy and Evolution, Shanghai Ocean University, Shanghai 201306, China
| | - Congping Ying
- Scientific Observing and Experimental Station of Fishery Resources and Environment in the Lower Reaches of the Changjiang River, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, CAFS, WuXi 214081, China
| | - Ya Zhang
- Shanghai Universities Key Laboratory of Marine Animal Taxonomy and Evolution, Shanghai Ocean University, Shanghai 201306, China
| | - Jialu Zhang
- Scientific Observing and Experimental Station of Fishery Resources and Environment in the Lower Reaches of the Changjiang River, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, CAFS, WuXi 214081, China
| | - Kai Liu
- Scientific Observing and Experimental Station of Fishery Resources and Environment in the Lower Reaches of the Changjiang River, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, CAFS, WuXi 214081, China.
| | - Wenqiao Tang
- Shanghai Universities Key Laboratory of Marine Animal Taxonomy and Evolution, Shanghai Ocean University, Shanghai 201306, China.
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Zhang J, Cai R, Liang J, Izaz A, Shu Y, Pan T, Wu X. Molecular mechanism of Chinese alligator (Alligator sinensis) adapting to hibernation. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2020; 336:32-49. [PMID: 33231934 DOI: 10.1002/jez.b.23013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Revised: 10/22/2020] [Accepted: 10/28/2020] [Indexed: 12/22/2022]
Abstract
Hibernation is a physiological state for Chinese alligators to cope with cold weather. In mammals, gene expression changes during hibernation and their regulatory mechanisms have been extensively studied, however, these studies in reptiles are still rare. Here, integrated analysis of messenger RNA (mRNA), microRNA (miRNA), and long noncoding RNA (lncRNA) reveals the molecular mechanisms of the hypothalamus, liver, and skeletal muscle in hibernating and active individuals. During hibernation, the number of genes increased in the hypothalamus, liver, and skeletal muscle was 585, 282, and 297, while the number of genes decreased was 215, 561, and 627, respectively, as compared with active individuals. Through Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analysis, the differential expressed genes were mainly enriched in DNA damage repair, biological rhythm, energy metabolism, myoprotein degradation, and other related items and pathways. Besides, 4740 miRNAs were identified in three tissues. Through the comprehensive analysis of miRNA and mRNA abundance profiles, 12,291, 6997, and 8232 miRNA-mRNA pairs all showed a negative correlation in the hypothalamus, liver, and skeletal muscle, respectively. Some miRNA target genes were related tobiological rhythm and energy metabolism, suggesting that miRNA may play an important role in the physiological metabolism of the hibernating adaptability of Chinese alligators. Moreover, 402, 230, and 130 differentially expressed lncRNAs were identified in the hypothalamus, liver, and skeletal muscle, respectively. The targeting relationship of four lncRNA-mRNA pairs were predicted, with the main function of target genes involved in the amino acid transportation. These results are helpful to further understand the molecular regulatory basis of the hibernation adaptation in Chinese alligators.
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Affiliation(s)
- Jihui Zhang
- Key Laboratory for the Conservation and Utilization of Important Biological Resources of Anhui Province, Wuhu, China.,College of Life Sciences, Anhui Normal University, Wuhu, China
| | - Ruiqing Cai
- Key Laboratory for the Conservation and Utilization of Important Biological Resources of Anhui Province, Wuhu, China.,College of Life Sciences, Anhui Normal University, Wuhu, China
| | - Juanjuan Liang
- Key Laboratory for the Conservation and Utilization of Important Biological Resources of Anhui Province, Wuhu, China.,College of Life Sciences, Anhui Normal University, Wuhu, China
| | - Ali Izaz
- Key Laboratory for the Conservation and Utilization of Important Biological Resources of Anhui Province, Wuhu, China.,College of Life Sciences, Anhui Normal University, Wuhu, China
| | - Yilin Shu
- Key Laboratory for the Conservation and Utilization of Important Biological Resources of Anhui Province, Wuhu, China.,College of Life Sciences, Anhui Normal University, Wuhu, China
| | - Tao Pan
- Key Laboratory for the Conservation and Utilization of Important Biological Resources of Anhui Province, Wuhu, China.,College of Life Sciences, Anhui Normal University, Wuhu, China
| | - Xiaobing Wu
- Key Laboratory for the Conservation and Utilization of Important Biological Resources of Anhui Province, Wuhu, China.,College of Life Sciences, Anhui Normal University, Wuhu, China
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Shu Y, Zhang H, Cai Q, Tang D, Wang G, Liu T, Lv B, Wu H. Integrated mRNA and miRNA expression profile analyses reveal the potential roles of sex-biased miRNA-mRNA pairs in gonad tissues of the Chinese concave-eared torrent frog (Odorrana tormota). JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2019; 332:69-80. [PMID: 30964604 DOI: 10.1002/jez.b.22851] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Revised: 02/21/2019] [Accepted: 03/20/2019] [Indexed: 12/20/2022]
Abstract
The Chinese concave-eared torrent frog (Odorrana tormota) is typically sexually dimorphic. Females are significantly less common than males in the wild. Until now, the molecular mechanisms of reproduction and sex differentiation of frogs remain unclear. Here, we integrated mRNA and microRNA (miRNA) expression profiles to reveal the molecular mechanisms of reproduction and sex differentiation in O. tormota. We identified 234 differentially expressed miRNAs (DEMs) and 18,551 differentially expressed transcripts. Of these, 12,053 mRNAs and 64 miRNAs were upregulated in testes, and 6,498 mRNAs and 170 miRNAs were upregulated in ovaries. Integrated analysis of the miRNA and mRNA expression profiles predicted 75,602 potential miRNA-mRNA interaction sites, with 42,065 negative miRNA-mRNA interactions. We found 36 differentially expressed genes (DEGs) related to reproduction and sex differentiation, of which 15 DEGs formed 92 negative miRNA-mRNA interactions with 34 known DEMs. Thus, miRNAs may play other important roles in O. tormota. Furthermore, Gene Ontology enrichment and Kyoto Encyclopedia of Genes and Genomes pathway analyses showed reproductive-related processes, such as the gonadotropinreleasing hormone signaling pathway and ovarian steroidogenesis. Based on functional annotation and the literature, the retinoic acid signaling pathway, the SOX9-AMH pathway, and the process of spermatogenesis may be involved in the molecular mechanisms of reproduction and sex differentiation in O. tormota, and may be regulated by miRNAs. The miRNA-mRNA pairs described may provide further understanding of the regulatory mechanisms associated with reproduction and sex differentiation, and the molecular mechanism of reproduction in O. tormota.
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Affiliation(s)
- Yilin Shu
- Key Laboratory for the Conservation and Utilization of Important Biological Resources of Anhui Province, Wuhu, China
- College of Life Sciences, Anhui Normal University, Wuhu, China
| | - Huijuan Zhang
- Key Laboratory for the Conservation and Utilization of Important Biological Resources of Anhui Province, Wuhu, China
- College of Life Sciences, Anhui Normal University, Wuhu, China
| | - Qijia Cai
- Key Laboratory of Algal Biology of the Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- University of the Chinese Academy of Sciences, Beijing, China
| | - Dong Tang
- Key Laboratory for the Conservation and Utilization of Important Biological Resources of Anhui Province, Wuhu, China
- College of Life Sciences, Anhui Normal University, Wuhu, China
| | - Gang Wang
- Key Laboratory for the Conservation and Utilization of Important Biological Resources of Anhui Province, Wuhu, China
- College of Life Sciences, Anhui Normal University, Wuhu, China
| | - Ting Liu
- Key Laboratory for the Conservation and Utilization of Important Biological Resources of Anhui Province, Wuhu, China
- College of Life Sciences, Anhui Normal University, Wuhu, China
| | - Bihua Lv
- Department of Pharmacy, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Hailong Wu
- Key Laboratory for the Conservation and Utilization of Important Biological Resources of Anhui Province, Wuhu, China
- College of Life Sciences, Anhui Normal University, Wuhu, China
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Shu Y, Xia J, Yu Q, Wang G, Zhang J, He J, Wang H, Zhang L, Wu H. Integrated analysis of mRNA and miRNA expression profiles reveals muscle growth differences between adult female and male Chinese concave-eared frogs (Odorrana tormota). Gene 2018; 678:241-251. [PMID: 30103010 DOI: 10.1016/j.gene.2018.08.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2018] [Revised: 07/24/2018] [Accepted: 08/02/2018] [Indexed: 02/07/2023]
Abstract
The Chinese concave-eared torrent frog (Odorrana tormota) is the first known non-mammalian vertebrate that can communicate using ultrasound. In this species, females are approximately four times as large as males, in which the female growth rate is obviously higher than that of male. Until now, the molecular mechanisms underlying muscle growth development differences between male and female frogs have not been reported. Here, we integrated mRNA and miRNA expression profiles to reveal growth differences in the hindlimb muscles of 2-year-old frogs. Among 569 differentially expressed genes (DEGs), 69 were associated with muscle growth and regeneration. Fifty-one up-regulated genes in females were potentially involved in promoting muscle growth and regeneration, whereas 18 up-regulated genes in males may lead to muscle growth inhibition and fast-twitch muscle fiber contraction. 244 DEGs were enriched in mTOR and other protein synthesis signaling pathways, and protein degradation pathways, including lysosomal protease, calpain, caspase, and ubiquitin-proteasome system pathways. It may interpret why female muscles grow faster than males. Based on expression differences of genes involved in glycolysis and oxidative metabolism, we speculated that the proportion of slow muscle fiber was higher and that of fast muscle fiber was lower in female compared with male muscle. Additionally, 767 miRNAs were identified, including 217 new miRNAs, and 6248 miRNA-negatively regulated mRNAs were predicted. The miRNA target genes were enriched in pathways related to muscle growth, protein synthesis, and degradation. Thus, in addition to the identified mRNA differential expressions, miRNAs may play other important roles in the differential regulation of hindlimb muscle growth between female and male O. tormota.
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Affiliation(s)
- Yilin Shu
- Key Laboratory for the Conservation and Utilization of Important Biological Resources of Anhui Province, Wuhu 241000, China; College of Life Sciences, Anhui Normal University, Wuhu 241000, China
| | - Jinquan Xia
- Key Laboratory for the Conservation and Utilization of Important Biological Resources of Anhui Province, Wuhu 241000, China; College of Life Sciences, Anhui Normal University, Wuhu 241000, China
| | - Qiang Yu
- Key Laboratory for the Conservation and Utilization of Important Biological Resources of Anhui Province, Wuhu 241000, China; College of Life Sciences, Anhui Normal University, Wuhu 241000, China
| | - Gang Wang
- Key Laboratory for the Conservation and Utilization of Important Biological Resources of Anhui Province, Wuhu 241000, China; College of Life Sciences, Anhui Normal University, Wuhu 241000, China
| | - Jihui Zhang
- Key Laboratory for the Conservation and Utilization of Important Biological Resources of Anhui Province, Wuhu 241000, China; College of Life Sciences, Anhui Normal University, Wuhu 241000, China
| | - Jun He
- Key Laboratory for the Conservation and Utilization of Important Biological Resources of Anhui Province, Wuhu 241000, China; College of Life Sciences, Anhui Normal University, Wuhu 241000, China
| | - Huan Wang
- Key Laboratory for the Conservation and Utilization of Important Biological Resources of Anhui Province, Wuhu 241000, China; College of Life Sciences, Anhui Normal University, Wuhu 241000, China
| | - Ling Zhang
- Department of Occupational and Environmental Health, School of Public Health, Wuhan University of Science and Technology, China; Hubei Province Key Laboratory of Occupational Hazard Identification and Control, Wuhan University of Science and Technology, China.
| | - Hailong Wu
- Key Laboratory for the Conservation and Utilization of Important Biological Resources of Anhui Province, Wuhu 241000, China; College of Life Sciences, Anhui Normal University, Wuhu 241000, China.
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Bagla S, Cukovic D, Asano E, Sood S, Luat A, Chugani HT, Chugani DC, Dombkowski AA. A distinct microRNA expression profile is associated with α[ 11C]-methyl-L-tryptophan (AMT) PET uptake in epileptogenic cortical tubers resected from patients with tuberous sclerosis complex. Neurobiol Dis 2018; 109:76-87. [PMID: 28993242 PMCID: PMC6070303 DOI: 10.1016/j.nbd.2017.10.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Revised: 09/09/2017] [Accepted: 10/06/2017] [Indexed: 10/18/2022] Open
Abstract
Tuberous sclerosis complex (TSC) is characterized by hamartomatous lesions in various organs and arises due to mutations in the TSC1 or TSC2 genes. TSC mutations lead to a range of neurological manifestations including epilepsy, cognitive impairment, autism spectrum disorders (ASD), and brain lesions that include cortical tubers. There is evidence that seizures arise at or near cortical tubers, but it is unknown why some tubers are epileptogenic while others are not. We have previously reported increased tryptophan metabolism measured with α[11C]-methyl-l-tryptophan (AMT) positron emission tomography (PET) in epileptogenic tubers in approximately two-thirds of patients with tuberous sclerosis and intractable epilepsy. However, the underlying mechanisms leading to seizure onset in TSC remain poorly characterized. MicroRNAs are enriched in the brain and play important roles in neurodevelopment and brain function. Recent reports have shown aberrant microRNA expression in epilepsy and TSC. In this study, we performed microRNA expression profiling in brain specimens obtained from TSC patients undergoing epilepsy surgery for intractable epilepsy. Typically, in these resections several non-seizure onset tubers are resected together with the seizure-onset tubers because of their proximity. We directly compared seizure onset tubers, with and without increased tryptophan metabolism measured with PET, and non-onset tubers to assess the role of microRNAs in epileptogenesis associated with these lesions. Whether a particular tuber was epileptogenic or non-epileptogenic was determined with intracranial electrocorticography, and tryptophan metabolism was measured with AMT PET. We identified a set of five microRNAs (miR-142-3p, 142-5p, 223-3p, 200b-3p and 32-5p) that collectively distinguish among the three primary groups of tubers: non-onset/AMT-cold (NC), onset/AMT-cold (OC), and onset/AMT-hot (OH). These microRNAs were significantly upregulated in OH tubers compared to the other two groups, and microRNA expression was most significantly associated with AMT-PET uptake. The microRNAs target a group of genes enriched for synaptic signaling and epilepsy risk, including SLC12A5, SYT1, GRIN2A, GRIN2B, KCNB1, SCN2A, TSC1, and MEF2C. We confirmed the interaction between miR-32-5p and SLC12A5 using a luciferase reporter assay. Our findings provide a new avenue for subsequent mechanistic studies of tuber epileptogenesis in TSC.
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Affiliation(s)
- Shruti Bagla
- Department of Pediatrics, Wayne State University School of Medicine, Detroit, MI, USA
| | - Daniela Cukovic
- Department of Pediatrics, Wayne State University School of Medicine, Detroit, MI, USA
| | - Eishi Asano
- Department of Pediatrics, Wayne State University School of Medicine, Detroit, MI, USA
| | - Sandeep Sood
- Department of Neurosurgery, Wayne State University School of Medicine, Detroit, MI, USA
| | - Aimee Luat
- Department of Pediatrics, Wayne State University School of Medicine, Detroit, MI, USA
| | - Harry T Chugani
- Department of Neurology, Nemours/Alfred I. duPont Hospital for Children, Wilmington, DE, USA
| | - Diane C Chugani
- Research Department, Nemours/Alfred I. duPont Hospital for Children, Wilmington, DE, USA; Communication Sciences and Disorders Department, College of Health Sciences, University of Delaware, Newark, DE, USA
| | - Alan A Dombkowski
- Department of Pediatrics, Wayne State University School of Medicine, Detroit, MI, USA.
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Surveying computational algorithms for identification of miRNA–mRNA regulatory modules. THE NUCLEUS 2017. [DOI: 10.1007/s13237-017-0208-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
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Venkatesan N, Deepa PR, Khetan V, Krishnakumar S. Computational and in vitro Investigation of miRNA-Gene Regulations in Retinoblastoma Pathogenesis: miRNA Mimics Strategy. Bioinform Biol Insights 2015; 9:89-101. [PMID: 25983556 PMCID: PMC4429751 DOI: 10.4137/bbi.s21742] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2014] [Revised: 01/13/2015] [Accepted: 01/17/2015] [Indexed: 12/14/2022] Open
Abstract
PURPOSE Retinoblastoma (RB), a primary pediatric intraocular tumor, arises from primitive retinal layers. Several novel molecular strategies are being developed for the clinical management of RB. miRNAs are known to regulate cancer-relevant biological processes. Here, the role of selected miRNAs, namely, miR-532-5p and miR-486-3p, has been analyzed for potential therapeutic targeting in RB. METHODS A comprehensive bioinformatic analysis was performed to predict the posttranscriptional regulators (miRNAs) of the select panel of genes [Group 1: oncogenes (HMGA2, MYCN, SYK, FASN); Group 2: cancer stem cell markers (TACSTD, ABCG2, CD133, CD44, CD24) and Group 3: cell cycle regulatory proteins (p53, MDM2)] using Microcosm, DIANALAB, miRBase v 18, and REFSEQ database, and RNA hybrid. The expressions of five miRNAs, namely, miR-146b-5p, miR-532-5p, miR-142-5p, miR-328, and miR-486-3p, were analyzed by qRT–PCR on primary RB tumor samples (n = 30; including 17 invasive RB tumors and 13 noninvasive RB tumors). Detailed complementary alignment between 5’ seed sequence of differentially expressed miRNAs and the sequence of target genes was determined. Based on minimum energy level and piCTAR scores, the gene targets were selected. Functional roles of these miRNA clusters were studied by using mimics in cultured RB (Y79, Weri Rb-1) cells in vitro. The gene targets (SYK and FASN) of the studied miRNAs were confirmed by qRT-PCR and western blot analysis. Cell proliferation and apoptotic studies were performed. RESULTS Nearly 1948 miRNAs were identified in the in silico analysis, From this list, only 9 upregulated miRNAs (miR-146b-5p, miR-305, miR-663b, miR-299, miR-532-5p, miR-892b, miR-501, miR-142-5p, and miR-513b) and 10 downregulated miRNAs (miR-1254, miR-328, miR-133a, miR-1287, miR-1299, miR-375, miR-486-3p, miR-720, miR-98, and miR-122*) were found to be common with the RB serum miRNA profile. Downregulation of five miRNAs (miR-146b-5p, miR-532-5p, miR-142-5p, miR-328, and miR-486-3p) was confirmed experimentally. Predicted common oncogene targets (SYK and FASN) of miR-486-3p and miR-532-5p were evaluated for their mRNA and protein expression in these miRNA mimic-treated RB cells. Experimental overexpression of these miRNAs mediated apoptotic cell death without significantly altering the cell cycle in RB cells. CONCLUSION Key miRNAs in RB pathogenesis were identified by an in silico approach. Downregulation of miR-486-3p and miR-532-5p in primary retinoblastoma tissues implicates their role in tumorigenesis. Prognostic and therapeutic potential of these miRNA was established by the miRNA mimic strategy.
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Affiliation(s)
- Nalini Venkatesan
- Larsen & Toubro Department of Ocular Pathology, Vision Research Foundation, Sankara Nethralaya, Chennai, India. ; Department of Biological Sciences, Birla Institute of Technology and Science (BITS), Pilani, Rajasthan, India
| | - Perinkulam Ravi Deepa
- Department of Biological Sciences, Birla Institute of Technology and Science (BITS), Pilani, Rajasthan, India
| | - Vikas Khetan
- Department of Vitreoretina and Oncology, Medical Research Foundation, Sankara Nethralaya, Chennai, India
| | - Subramanian Krishnakumar
- Larsen & Toubro Department of Ocular Pathology, Vision Research Foundation, Sankara Nethralaya, Chennai, India
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