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Shuaib M, Prajapati KS, Singh AK, Kumar S. Discovery of differentially expressed novel miRNAs in breast normal cells and their putative targets. Mol Cell Biochem 2023; 478:2361-2378. [PMID: 36680668 DOI: 10.1007/s11010-023-04665-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2022] [Accepted: 01/11/2023] [Indexed: 01/22/2023]
Abstract
MicroRNAs (miRNAs) play critical role in normal breast development and their altered expression may lead to breast cancer. Identification of new miRNAs allows us to understand the normal physiological process and associated disease pathophysiology. In the present study we identify the novel miRNAs in withaferin A treated breast normal cells (MCF-10A) using small RNA sequencing. The pathophysiological potential of the identified miRNAs was checked by studying their expression pattern in MDA-MB-231 and MCF-7 breast cancer cells using qRT-PCR technique. The secondary/tertiary structure of the identified miRNAs, target gene enrichment in Gene Ontology terms and KEGG pathway, miRNA-mRNA interaction of the sorted target genes, miRNA-mRNA/miRNA-argonaute protein/miRNA-mRNA-argonaute protein interaction and stability, were studied using bioinformatics tools/software, and molecular dynamics simulations. Hsa-miR-N88585 and hsa-miR-N461089 were identified and validated as novel miRNAs in normal breast cells. Up-expression of identified miRNAs in MDA-MB-231 and MCF-7 cells indicates their oncogenic nature. Identified target genes were enriched in classical signaling pathways (AMPK and Ras) and important GO terms. PLXDC2, BHLHE40, ARMC8, and PECAM1, CDC27, KCNK3 genes were sorted as putative targets for hsa-miR-N88585 and hsa-miR-N461089, respectively. MD simulation revealed stable hsa-miR-N88585/hsa-miR-N461089-AGO protein complex formation which indicates their further processing. In conclusion, the study identifies hsa-miR-N88585 and hsa-miR-N461089 as novel miRNAs in breast normal cells which are significantly inversely expressed in breast cancer cells. Further experiments are required to study the role of identified novel miRNAs in normal breast development and pathophysiology of breast cancer.
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Affiliation(s)
- Mohd Shuaib
- Molecular Signaling & Drug Discovery Laboratory, Department of Biochemistry, Central University of Punjab, Bathinda, Punjab, 151401, India
| | - Kumari Sunita Prajapati
- Molecular Signaling & Drug Discovery Laboratory, Department of Biochemistry, Central University of Punjab, Bathinda, Punjab, 151401, India
| | - Atul Kumar Singh
- Molecular Signaling & Drug Discovery Laboratory, Department of Biochemistry, Central University of Punjab, Bathinda, Punjab, 151401, India
| | - Shashank Kumar
- Molecular Signaling & Drug Discovery Laboratory, Department of Biochemistry, Central University of Punjab, Bathinda, Punjab, 151401, India.
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2
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Abstract
Circulating microRNAs (miRNAs) have been used effectively as peripheral biomarkers and mechanistic targets for human diseases such as stroke, Alzheimer's, and cancer. The purpose of our study is to determine noninvasive, blood-based early detectable biomarkers for ischemic stroke (IS). Based on our previous global miRNA sequencing study, four miRNAs were previously unreported (novel) in IS condition. Among these, miRNA PC-5P-12969 was exclusively expressed in the IS condition; otherwise, it was not expressed in normal condition, and therefore, we focused on miRNA PC-5P-12969 for further studies. In the present study, we investigated novel miRNA PC-5P-12969 for its expression levels using quantitative real-time PCR assay (qRT-PCR) in an in vitro, oxygen, and glucose deprivation/reoxygenation (OGD/R)-treated mouse primary hippocampal neuronal cells (HT22) and in an in vivo using a photothrombotic stroke model. In an in vitro study of stroke-induced HT22 cells, we found a two fold increase of PC-5P-12969 expression levels, in agreement with our original global miRNA study. In the cerebral cortex of photothrombotic stroke mice, we found significantly upregulated levels of PC-5P-12969 in 4 hours and 1 day post-stroke relative to the control mice. However, we did not find any change in the expression of PC-5P-12969 in the cerebellum (unaffected in IS) of both stroke and control mice. Based on findings from this study, together with our earlier original global microRNA study results, we conclude that PC-5P-12969 is a potential candidate of the peripheral marker and also a drug target for IS. This is the first study validating that the miRNA PC-5P-12969, might be a potential biomarker for IS.
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Affiliation(s)
- Murali Vijayan
- Department of Internal Medicine, Texas Tech University Health Sciences Center, Lubbock, TX, USA
| | - Faisal F Alamri
- Department of Pharmaceutical Sciences, School of Pharmacy, Texas Tech University Health Sciences Center, Amarillo, TX, USA
| | - Abdullah Al Shoyaib
- Department of Pharmaceutical Sciences, School of Pharmacy, Texas Tech University Health Sciences Center, Amarillo, TX, USA
| | - Vardan T Karamyan
- Department of Pharmaceutical Sciences, School of Pharmacy, Texas Tech University Health Sciences Center, Amarillo, TX, USA
- Center for Blood Brain Barrier Research, School of Pharmacy, Texas Tech University Health Sciences Center, Amarillo, TX, USA
| | - P Hemachandra Reddy
- Department of Internal Medicine, Texas Tech University Health Sciences Center, Lubbock, TX, USA.
- Garrison Institute on Aging, Texas Tech University Health Sciences Center, Lubbock, TX, USA.
- Garrison Institute on Aging, South West Campus, Texas Tech University Health Sciences Center, Lubbock, TX, 79430, USA.
- Cell Biology & Biochemistry Department, Texas Tech University Health Sciences Center, Lubbock, TX, USA.
- Pharmacology & Neuroscience Department, Texas Tech University Health Sciences Center, Lubbock, TX, USA.
- Neurology Department, Texas Tech University Health Sciences Center, Lubbock, TX, USA.
- Speech, Language and Hearing Sciences Department, Texas Tech University Health Sciences Center, Lubbock, TX, USA.
- Department of Public Health, Graduate School of Biomedical Sciences, Lubbock, TX, USA.
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Liu X, Chen M, Zhou X, Cao Z. Identification of novel miRNAs and their target genes from Populus szechuanica infected with Melampsora larici-populina. Mol Biol Rep 2019; 46:3083-3092. [PMID: 30859446 DOI: 10.1007/s11033-019-04746-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Accepted: 03/05/2019] [Indexed: 01/21/2023]
Abstract
Two novel miRNAs were selected from a pre-constructed RNA library of Populus szechuanica infected with the foliar rust fungus Melampsora larici-populina in order to detect the genes regulated as targets of the miRNAs novel_mir_11 and novel_mir_357. The novel miRNAs were identified from P. szechuanica using stem-loop methods and their precursors were able to fold into a complete stem loop structure. The predicted target genes of the novel miRNAs were verified with RNA ligase-mediated 5' rapid amplification of cDNA ends (RLM-5'RACE). The full-length sequences of target genes, RPM1 and RPS2/5, in P. szechuanica were obtained through rapid amplification of cDNA ends (RACE) and officially named PsRPM1 and PsRPS2/5. These genes contain nucleotide binding site-leucine-rich repeats (NBS-LRR) domains typical of resistance genes. The expression levels of miRNAs and their target genes in different periods post infection were analysed with quantitative real-time PCR (qRT-PCR). After infection with the foliar rust fungus, the expression levels of the novel miRNAs and their target genes were dynamic. Both novel_mir_11 and novel_mir_357 negatively regulated the expression of their target genes. In this study, the regulatory effects of two novel miRNAs through their target genes were characterized to provide further mechanistic information regarding the interaction between Populus and a foliar rust fungus. Results of this study improve our understanding of the defence response mechanisms of Populus and will stimulate future work to characterize strategies to prevent and control Populus diseases.
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Affiliation(s)
- Xin Liu
- College of Forestry, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Min Chen
- College of Forestry, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Xue Zhou
- College of Forestry, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Zhimin Cao
- College of Forestry, Northwest A&F University, Yangling, Shaanxi, 712100, China.
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Zhao L, Yang X, Cui L, Wei J, Ni P, Li M, Wang Y, He Y, Li X, Liang S, Tian Y, Wang Q, Cui W, Lin D, Ma X, Li T. Increased expression of a novel miRNA in peripheral blood is negatively correlated with hippocampal volume in patients with major depressive disorder. J Affect Disord 2019; 245:205-212. [PMID: 30408638 DOI: 10.1016/j.jad.2018.10.363] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Revised: 10/19/2018] [Accepted: 10/31/2018] [Indexed: 10/28/2022]
Abstract
BACKGROUND Major depressive disorder (MDD) is a serious psychiatric illness with unclear pathophysiology. As one of the post-transcriptional regulators, prior research has indicated that miRNAs are involved in the pathophysiology of MDD. The aim of this study was to screen the MDD-related miRNAs in the peripheral blood and investigate the target genes of the differentially expressed miRNAs and their potential functions in MDD pathophysiology. METHODS miRNA sequencing was performed using the peripheral blood of patients with MDD and matched controls (cohort A, 10 vs 10). The nominal significant results were validated in an independent sample (cohort B, 72 vs 75) by real-time quantitative polymerase chain reaction (PCR). The target genes of verified miRNAs were predicted using Miranda software. Luciferase assay was used to verify one of the predicted target genes. Furthermore, we analyzed the correlations between the expression of pmiR-chr11 and hippocampal volume. RESULTS Ten miRNAs were nominally significantly dysregulated in patients with MDD in cohort A. One of the 10 miRNAs, pmiR-chr11, was significantly dysregulated in cohort B. The pmiR-chr11 could regulate one of the target genes, BRPF1 (bromodomain and PHD finger containing 1), via binding its 3' untranslated region (UTR). The expression of pmiR-chr11 was negatively correlated with hippocampal volume in patients with MDD. LIMITATIONS The expression of the miRNAs and mRNAs detected in the peripheral blood may not reflect the expression in the brain. CONCLUSIONS Our findings suggested that the pmiR-chr11 may influence hippocampal volume by regulating BRPF1 in MDD.
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Affiliation(s)
- Liansheng Zhao
- Psychiatric Laboratory and Mental Health Center, the State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, Chengdu, China; Huaxi Brain Research Center, West China Hospital of Sichuan University, Chengdu, China
| | - Xiao Yang
- Psychiatric Laboratory and Mental Health Center, the State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, Chengdu, China; Huaxi Brain Research Center, West China Hospital of Sichuan University, Chengdu, China
| | - Lijun Cui
- Hebei Mental Health Center, Baoding, China
| | - Jinxue Wei
- Psychiatric Laboratory and Mental Health Center, the State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, Chengdu, China; Huaxi Brain Research Center, West China Hospital of Sichuan University, Chengdu, China
| | - Peiyan Ni
- Psychiatric Laboratory and Mental Health Center, the State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, Chengdu, China; Huaxi Brain Research Center, West China Hospital of Sichuan University, Chengdu, China
| | - Mingli Li
- Psychiatric Laboratory and Mental Health Center, the State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, Chengdu, China; Huaxi Brain Research Center, West China Hospital of Sichuan University, Chengdu, China
| | - Yingcheng Wang
- Psychiatric Laboratory and Mental Health Center, the State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, Chengdu, China; Huaxi Brain Research Center, West China Hospital of Sichuan University, Chengdu, China
| | - Yin He
- Psychiatric Laboratory and Mental Health Center, the State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, Chengdu, China; Huaxi Brain Research Center, West China Hospital of Sichuan University, Chengdu, China
| | - Xiaojing Li
- Psychiatric Laboratory and Mental Health Center, the State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, Chengdu, China; Huaxi Brain Research Center, West China Hospital of Sichuan University, Chengdu, China
| | - Sugai Liang
- Psychiatric Laboratory and Mental Health Center, the State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, Chengdu, China; Huaxi Brain Research Center, West China Hospital of Sichuan University, Chengdu, China
| | - Yang Tian
- Psychiatric Laboratory and Mental Health Center, the State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, Chengdu, China; Huaxi Brain Research Center, West China Hospital of Sichuan University, Chengdu, China
| | - Qiang Wang
- Psychiatric Laboratory and Mental Health Center, the State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, Chengdu, China; Huaxi Brain Research Center, West China Hospital of Sichuan University, Chengdu, China
| | - Wei Cui
- Hebei Mental Health Center, Baoding, China
| | - Dongtao Lin
- College of Foreign Languages and Cultures, Sichuan University, Chengdu, China
| | - Xiaohong Ma
- Psychiatric Laboratory and Mental Health Center, the State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, Chengdu, China; Huaxi Brain Research Center, West China Hospital of Sichuan University, Chengdu, China.
| | - Tao Li
- Psychiatric Laboratory and Mental Health Center, the State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, Chengdu, China; Huaxi Brain Research Center, West China Hospital of Sichuan University, Chengdu, China
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Minatel BC, Martinez VD, Ng KW, Sage AP, Tokar T, Marshall EA, Anderson C, Enfield KSS, Stewart GL, Reis PP, Jurisica I, Lam WL. Large-scale discovery of previously undetected microRNAs specific to human liver. Hum Genomics 2018; 12:16. [PMID: 29587854 PMCID: PMC5870816 DOI: 10.1186/s40246-018-0148-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Accepted: 03/19/2018] [Indexed: 12/18/2022] Open
Abstract
MicroRNAs (miRNAs) are crucial regulators of gene expression in normal development and cellular homeostasis. While miRNA repositories contain thousands of unique sequences, they primarily contain molecules that are conserved across several tissues, largely excluding lineage and tissue-specific miRNAs. By analyzing small non-coding RNA sequencing data for abundance and secondary RNA structure, we discovered 103 miRNA candidates previously undescribed in liver tissue. While expression of some of these unannotated sequences is restricted to non-malignant tissue, downregulation of most of the sequences was detected in liver tumors, indicating their importance in the maintenance of liver homeostasis. Furthermore, target prediction revealed the involvement of the unannotated miRNA candidates in fatty-acid metabolism and tissue regeneration, which are key pathways in liver biology. Here, we provide a comprehensive analysis of the undiscovered liver miRNA transcriptome, providing new resources for a deeper exploration of organ-specific biology and disease.
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Affiliation(s)
- Brenda C Minatel
- Department of Integrative Oncology, British Columbia Cancer Research Centre, Vancouver, BC, Canada.
| | - Victor D Martinez
- Department of Integrative Oncology, British Columbia Cancer Research Centre, Vancouver, BC, Canada
| | - Kevin W Ng
- Department of Integrative Oncology, British Columbia Cancer Research Centre, Vancouver, BC, Canada
| | - Adam P Sage
- Department of Integrative Oncology, British Columbia Cancer Research Centre, Vancouver, BC, Canada
| | - Tomas Tokar
- Krembil Research Institute, University Health Network, Toronto, ON, Canada
| | - Erin A Marshall
- Department of Integrative Oncology, British Columbia Cancer Research Centre, Vancouver, BC, Canada
| | - Christine Anderson
- Department of Integrative Oncology, British Columbia Cancer Research Centre, Vancouver, BC, Canada
| | - Katey S S Enfield
- Department of Integrative Oncology, British Columbia Cancer Research Centre, Vancouver, BC, Canada
| | - Greg L Stewart
- Department of Integrative Oncology, British Columbia Cancer Research Centre, Vancouver, BC, Canada
| | - Patricia P Reis
- Faculty of Medicine, São Paulo State University (UNESP), Botucatu, SP, Brazil
| | - Igor Jurisica
- Krembil Research Institute, University Health Network, Toronto, ON, Canada
| | - Wan L Lam
- Department of Integrative Oncology, British Columbia Cancer Research Centre, Vancouver, BC, Canada
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Samad AFA, Nazaruddin N, Murad AMA, Jani J, Zainal Z, Ismail I. Deep sequencing and in silico analysis of small RNA library reveals novel miRNA from leaf Persicaria minor transcriptome. 3 Biotech 2018; 8:136. [PMID: 29479512 DOI: 10.1007/s13205-018-1164-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Accepted: 02/08/2018] [Indexed: 01/25/2023] Open
Abstract
In current era, majority of microRNA (miRNA) are being discovered through computational approaches which are more confined towards model plants. Here, for the first time, we have described the identification and characterization of novel miRNA in a non-model plant, Persicaria minor (P. minor) using computational approach. Unannotated sequences from deep sequencing were analyzed based on previous well-established parameters. Around 24 putative novel miRNAs were identified from 6,417,780 reads of the unannotated sequence which represented 11 unique putative miRNA sequences. PsRobot target prediction tool was deployed to identify the target transcripts of putative novel miRNAs. Most of the predicted target transcripts (mRNAs) were known to be involved in plant development and stress responses. Gene ontology showed that majority of the putative novel miRNA targets involved in cellular component (69.07%), followed by molecular function (30.08%) and biological process (0.85%). Out of 11 unique putative miRNAs, 7 miRNAs were validated through semi-quantitative PCR. These novel miRNAs discoveries in P. minor may develop and update the current public miRNA database.
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Affiliation(s)
- Abdul Fatah A Samad
- 1School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 Bangi, Selangor Malaysia
| | - Nazaruddin Nazaruddin
- 1School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 Bangi, Selangor Malaysia
- 3Department of Chemistry, Faculty of Mathematics and Natural Sciences, University of Syiah Kuala, Darussalam, Banda Aceh, 23111 Indonesia
| | - Abdul Munir Abdul Murad
- 1School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 Bangi, Selangor Malaysia
| | - Jaeyres Jani
- BioEasy Sdn. Bhd. and ScienceVision Sdn. Bhd., Setia Alam, Seksyen U13, 40170 Shah Alam, Selangor Malaysia
| | - Zamri Zainal
- 1School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 Bangi, Selangor Malaysia
- 2Institute of Systems Biology, Universiti Kebangsaan Malaysia, 43600 Bangi, Selangor Malaysia
| | - Ismanizan Ismail
- 1School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 Bangi, Selangor Malaysia
- 2Institute of Systems Biology, Universiti Kebangsaan Malaysia, 43600 Bangi, Selangor Malaysia
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