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He K, Zhou X, Zhao J, Du H, Guo J, Deng R, Wang J. Identification and Functional Mechanism Verification of Novel MicroRNAs Associated with the Fibrosis Progression in Chronic Kidney Disease. Biochem Genet 2024:10.1007/s10528-024-10688-7. [PMID: 38316653 DOI: 10.1007/s10528-024-10688-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Accepted: 01/04/2024] [Indexed: 02/07/2024]
Abstract
Chronic kidney disease (CKD) is a serious threat to human health worldwide, and its incidence is increasing annually. A growing amount of information is emerging about the role of micoRNAs (miRNAs) in the regulation of renal fibrosis, which has aroused interest in the development of drugs that block pathogenic miRNAs or restore protective miRNAs levels. To clarify the role of miRNAs in CKD, we selected patients with significant renal fibrotic disease (diabetic nephropathy (DN) and focal segmental glomerulosclerosis (FSGS)) as the disease group, and patients with little or no renal fibrotic disease (minimal change disease (MCD) and renal carcinoma adjacent to normal kidney) as controls. Significantly differentially expressed miRNAs were obtained by human kidney tissue sequencing, subsequently verified in mice models of DN and FSGS, and subsequently inhibited or overexpressed in human renal tubular epithelial cells (HK-2) stimulated by high glucose (HG) and TGF-β1 in vitro. Therefore, the mechanism of its action in renal fibrosis was further elaborated. Finally, the downstream target genes of the corresponding miRNAs were verified by bioinformatics analysis, qRT-PCR, western blot and double luciferase report analysis. Two novel miRNAs, hsa-miR-1470-3p (miR-1470) and hsa-miR-4483-3p (miR-4483), were detected by renal tissue sequencing in the disease group with significant renal fibrosis (DN and FSGS) and the control group with little or no renal fibrosis (MCD and normal renal tissue adjacent to renal carcinoma). Subsequent human renal tissue qRT-PCR verified that the expression of miR-1470 was significantly increased, while the expression of miR-4483 was markedly decreased in the disease group (p < 0.05). Moreover, in vivo DN and FSGS mice models, the expression levels of miR-1470 and miR-4483 were consistent with the results of human kidney tissue. In vitro, miR-4483 was suppressed, whereas miR-1470 was induced by treatment with TGF-β1 or HG. Inhibition of miR-1470 or overexpression of miR-4483 promoted HG or TGF-β1-induced fibrosis in HK-2 cells. Further study revealed that MMP-13 and TIMP1 were the target genes ofmiR-1470 and miR-4483, respectively. Our study identifies newly dysregulated miRNA profiles related to fibrosis kidneys. miR-1470 and miR-4483 are demonstrated to participate in kidney fibrosis by regulation of MMP-13, TIMP1 respectively. Our results may represent a promising research direction for renal disorders and help identify new biomarkers and therapeutic targets for CKD.
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Affiliation(s)
- Kaiying He
- Lanzhou University, Lanzhou, Gansu, China
- Department of Nephrology, The Second Hospital & Clinical Medical School, Lanzhou University, No. 82 Cuiyingmen, Lanzhou, Gansu, China
| | - Xiaochun Zhou
- Department of Nephrology, The Second Hospital & Clinical Medical School, Lanzhou University, No. 82 Cuiyingmen, Lanzhou, Gansu, China
| | - Jing Zhao
- Lanzhou University, Lanzhou, Gansu, China
- Department of Nephrology, The Second Hospital & Clinical Medical School, Lanzhou University, No. 82 Cuiyingmen, Lanzhou, Gansu, China
| | - Hongxuan Du
- Lanzhou University, Lanzhou, Gansu, China
- Department of Nephrology, The Second Hospital & Clinical Medical School, Lanzhou University, No. 82 Cuiyingmen, Lanzhou, Gansu, China
| | - Juan Guo
- Xi'an Huyi District Hospital Of Traditional Chinese Medicine, Xi'an, Shaanxi, China
| | - Rongrong Deng
- Lanzhou University, Lanzhou, Gansu, China
- Department of Nephrology, The Second Hospital & Clinical Medical School, Lanzhou University, No. 82 Cuiyingmen, Lanzhou, Gansu, China
| | - Jianqin Wang
- Department of Nephrology, The Second Hospital & Clinical Medical School, Lanzhou University, No. 82 Cuiyingmen, Lanzhou, Gansu, China.
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Gómez-Martín C, Zhou H, Medina JM, Aparicio-Puerta E, Hackenberg M, Shi B. Comprehensive, integrative genomic analysis of microRNA expression profiles in different tissues of two wheat cultivars with different traits. Funct Integr Genomics 2022; 23:15. [PMID: 36562829 DOI: 10.1007/s10142-022-00920-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 06/29/2022] [Revised: 11/04/2022] [Accepted: 11/29/2022] [Indexed: 12/24/2022]
Abstract
Wheat is one of the most important food sources on Earth. MicroRNAs (miRNA) play important roles in wheat productivity. To identify wheat miRNAs, we constructed and sequenced sRNA libraries from leaves and roots of two wheat cultivars (RAC875 and Kukri) with many different traits. Given that available miRNA wheat complement in the plant-specific database PmiREN ( https://pmiren.com ) does not include root tissues and root-associated miRNAs might thus be missing, we performed first the prediction of novel miRNAs using the sRNAbench tool. We found a total of 150 putatively novel miRNA genes with expression of both arms from 289 unique mature sequences and nearly 30% of all miRNA reads in roots corresponded to novel miRNAs. In contrast, this figure in leaves dropped to under 3%, confirming the undersampling of roots in the complement of known miRNAs. By using 120 publicly available wheat datasets, 598 Zea mays small RNA libraries, 64 plant species genomes, wheat degradome library, and functional enrichment analysis, a subset of novel miRNAs were confirmed as bona-fide miRNAs. Of the total 605 miRNAs identified in this study inclusive of 316 known miRNAs, 528 miRNAs were shared by both cultivars, 429 miRNAs were shared by both root tissues and 329 miRNAs were shared by both leaf tissues. In addition, 32 miRNAs were specific to Kukri while 45 miRNAs were specific to RAC875. These miRNAs had diverse functions, such as regulation of gene transcription, protein translation, energy metabolism, and cell cycle progression. Our data provide a genome-wide miRNA expression profile in these two wheat cultivars and help functional studies of wheat genomics.
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Affiliation(s)
- Cristina Gómez-Martín
- Department of Pathology, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Hui Zhou
- School of Agriculture, Food and Wine, University of Adelaide, Urrbrae, SA, 5064, Australia
| | - José Maria Medina
- Computational Genomics and Bioinformatics Group, Genetics Department, University of Granada, 18071, Granada, Spain.,Bioinformatics Laboratory, Centro de Investigación Biomédica, Biotechnology Institute, PTS, Avda. del Conocimiento S/N, 18100, Granada, Spain
| | - Ernesto Aparicio-Puerta
- Computational Genomics and Bioinformatics Group, Genetics Department, University of Granada, 18071, Granada, Spain.,Bioinformatics Laboratory, Centro de Investigación Biomédica, Biotechnology Institute, PTS, Avda. del Conocimiento S/N, 18100, Granada, Spain.,Instituto de Investigación Biosanitaria Ibs.GRANADA, University of Granada, 18071, Granada, Spain.,Excellence Research Unit "Modelling Nature" (MNat), University of Granada, 18071, Granada, Spain
| | - Michael Hackenberg
- Computational Genomics and Bioinformatics Group, Genetics Department, University of Granada, 18071, Granada, Spain. .,Bioinformatics Laboratory, Centro de Investigación Biomédica, Biotechnology Institute, PTS, Avda. del Conocimiento S/N, 18100, Granada, Spain. .,Instituto de Investigación Biosanitaria Ibs.GRANADA, University of Granada, 18071, Granada, Spain. .,Excellence Research Unit "Modelling Nature" (MNat), University of Granada, 18071, Granada, Spain.
| | - Bujun Shi
- School of Agriculture, Food and Wine, University of Adelaide, Urrbrae, SA, 5064, Australia.
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Saxena S, Mathur P, Shukla V, Rani V. Differential expression of novel MicroRNAs from developing fetal heart of Gallus gallus domesticus implies a role in cardiac development. Mol Cell Biochem 2019; 462:157-165. [PMID: 31494815 DOI: 10.1007/s11010-019-03618-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [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: 04/02/2019] [Accepted: 08/24/2019] [Indexed: 01/26/2023]
Abstract
Heart development is a complex process regulated by multi-layered genetic as well epigenetic regulators many of which are still unknown. Besides their critical role during cardiac development, these molecular regulators emerge as key modulators of cardiovascular pathologies, where fetal cardiac genes' re-expression is witnessed. MicroRNAs have recently emerged as a crucial part of signalling cascade in both development and diseases. We aimed to identify, validate, and perform functional annotation of putative novel miRNAs using chicken as a cardiac development model system. Novel miRNAs were obtained through deep sequencing of small RNAs extracted from chicken embryonic cardiac tissue of different developmental stages. After filtering out real pre-miRNAs, their expression analysis, potential target gene's prediction and functional annotations were performed. Expression analysis revealed that miRNAs were differentially expressed during different developmental stages of chicken heart. The expression of selected putative novel miRNAs was further validated by real-time PCR. Our analysis indicated the presence of novel cardiac miRNAs that might be regulating critical cardiac development events such as cardiac cell growth, differentiation, cardiac action potential generation and signal transduction.
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Affiliation(s)
- Sharad Saxena
- Transcriptome Laboratory, Centre for Emerging Diseases, Department of Biotechnology, Jaypee Institute of Information Technology, A-10, Sector-62, Noida, UP, 201307, India
| | - Priyanka Mathur
- Transcriptome Laboratory, Centre for Emerging Diseases, Department of Biotechnology, Jaypee Institute of Information Technology, A-10, Sector-62, Noida, UP, 201307, India
| | - Vaibhav Shukla
- Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India
| | - Vibha Rani
- Transcriptome Laboratory, Centre for Emerging Diseases, Department of Biotechnology, Jaypee Institute of Information Technology, A-10, Sector-62, Noida, UP, 201307, India.
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Thanjeem Begum ME, Baul HS, Venkatesh K, Sen D. Novel miRNA expression in the delta opioid signaling pathway mediated cell survivability in an in vitro model of ER stress. Nanomedicine 2019; 17:150-187. [PMID: 30716419 DOI: 10.1016/j.nano.2019.01.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Revised: 12/21/2018] [Accepted: 01/11/2019] [Indexed: 10/27/2022]
Abstract
Micro RNAs (miRNAs) are small non-coding RNAs which bind to the 3'-untranslated region of a mature mRNA to induce degradation; thereby regulating gene expression. It is reported that dysregulated miRNAs involved in neurodegenerative diseases including Parkinson's disease, could play a significant role as prognostic markers and therapeutic targets. Neuroprotective effect of delta opioid receptors (DOR) and its known miRNA regulation against endoplasmic reticulum (ER) stress have been reported previously by our lab. Current study focuses on understanding the regulation of novel miRNAs by DOR under ER stress. Novel miRNAs were identified for three different samples; control, tunicamycin (ER stress inducer), and tunicamycin+DADLE (DOR agonist). Differentially regulated miRNAs between the different samples were identified and pathway/target genes analysis was carried out. The results suggest that following DOR activation novel miRNAs like xxx-m0073-3p, xxx-m0225-3p, xxx-m0088-3p, xxx-m0098-5p etc. could regulate cell survival mechanisms in neuronal cells (SH-SY5Y) under ER stress.
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Affiliation(s)
- M Erfath Thanjeem Begum
- Cellular and Molecular Therapeutics Laboratory, Centre for Biomaterials, Cellular and Molecular Theranostics, Vellore Institute of Technology (VIT), Vellore, Tamil Nadu, India
| | - Himadri Shekhaar Baul
- Cellular and Molecular Therapeutics Laboratory, Centre for Biomaterials, Cellular and Molecular Theranostics, Vellore Institute of Technology (VIT), Vellore, Tamil Nadu, India
| | - Katari Venkatesh
- Cellular and Molecular Therapeutics Laboratory, Centre for Biomaterials, Cellular and Molecular Theranostics, Vellore Institute of Technology (VIT), Vellore, Tamil Nadu, India
| | - Dwaipayan Sen
- Cellular and Molecular Therapeutics Laboratory, Centre for Biomaterials, Cellular and Molecular Theranostics, Vellore Institute of Technology (VIT), Vellore, Tamil Nadu, India..
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Guo N, Zhang Y, Sun X, Fan H, Gao J, Chao Y, Liu A, Yu X, Cai Y, Lin Y. Genome-wide identification of differentially expressed miRNAs induced by ethephon treatment in abscission layer cells of cotton (Gossypium hirsutum). Gene 2018; 676:263-268. [PMID: 30125660 DOI: 10.1016/j.gene.2018.08.057] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [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: 01/31/2018] [Revised: 07/19/2018] [Accepted: 08/16/2018] [Indexed: 12/20/2022]
Abstract
Cotton is one of the most important economic crops and its production is influenced by various adverse factors. Boll shedding at an inappropriate period causes the severe loss of cotton yield. Ethephon can promote the formation of abscission layer cells, resulting in boll shedding. To genome-widely investigate the differentially expressed miRNAs involved in the formation of abscission layer cells, two sRNA libraries were constructed using abscission tissues of cotton pedicels treated with ethephon or water. A total of 55,264,755 and 59,069,866 clean reads were generated in two libraries. 460 mature miRNAs were identified, including 301 known miRNAs and 159 novel miRNAs. Among them, one known gra-MIR530b and seven novel miRNAs (gar-novel-miR88-3p/gra-novel-miR8-3p, gar-novel-miR16-5p, gar-novel-miR100-3p, gar-novel-miR75-3p/gra-novel-miR92-3p,gar-novel-miR32-5p/gra-novel-miR30-5p, gar-novel-miR9-5p and gra-novel-miR61-3p) were expressed differentially in abscission tissues. Seven-two genes were predicted as potential targets of the eight miRNAs. Gene ontology (GO) analyses revealed that most of these target genes are auxin response factors (ARFs), GTPase activators, and the regulators of oxidative phosphorylation and photosynthesis. Hence, we speculate that these miRNAs might regulate cell separation and aging to affect the formation of bscission layer cells. Our findings will provide a new insight into the regulatory mechanism of miRNAs involved in boll shedding.
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Affiliation(s)
- Ning Guo
- School of Life Science, Anhui Agricultural University, 130 Changjiang West Road, Hefei 230036, PR China.
| | - Yujiang Zhang
- School of Life Science, Anhui University, 111 Jiu Long Road, Hefei 230601, PR China.
| | - Xu Sun
- School of Life Science, Anhui Agricultural University, 130 Changjiang West Road, Hefei 230036, PR China
| | - Honghong Fan
- School of Life Science, Anhui Agricultural University, 130 Changjiang West Road, Hefei 230036, PR China
| | - Junsan Gao
- School of Life Science, Anhui Agricultural University, 130 Changjiang West Road, Hefei 230036, PR China
| | - Yunpeng Chao
- School of Life Science, Anhui Agricultural University, 130 Changjiang West Road, Hefei 230036, PR China.
| | - Anfeng Liu
- School of Life Science, Anhui Agricultural University, 130 Changjiang West Road, Hefei 230036, PR China
| | - Xiantao Yu
- School of Life Science, Anhui Agricultural University, 130 Changjiang West Road, Hefei 230036, PR China
| | - Yongping Cai
- School of Life Science, Anhui Agricultural University, 130 Changjiang West Road, Hefei 230036, PR China.
| | - Yi Lin
- School of Life Science, Anhui Agricultural University, 130 Changjiang West Road, Hefei 230036, PR China.
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Gupta H, Tiwari T, Patel M, Mehta A, Ghosh A. An approach to identify the novel miRNA encoded from H. Annuus EST sequences. Genom Data 2015; 6:139-44. [PMID: 26697356 DOI: 10.1016/j.gdata.2015.09.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Accepted: 09/06/2015] [Indexed: 01/15/2023]
Abstract
MicroRNAs are a newly discovered class of non-protein small RNAs with 22-24 nucleotides. They play multiple roles in biological processes including development, cell proliferation, apoptosis, stress responses and many other cell functions. In this research, several approaches were combined to make a computational prediction of potential miRNAs and their targets in Helianthus annuus (H. annuus). The already available information of the plant miRNAs present in miRBase v21 was used against expressed sequence tags (ESTs). A total of three miRNAs were detected from which one potential novel miRNA was identified following a range of strict filtering criteria. The target prediction was carried out for these three miRNAs having various targets. These targets were functionally annotated and GO terms were assigned. To study the conserved nature of the miRNAs, predicted phylogenetic analysis was carried out. These findings will significantly provide the broader picture for understanding the functions in H. annuus.
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Khan MS, Khraiwesh B, Pugalenthi G, Gupta RS, Singh J, Duttamajumder SK, Kapur R. Subtractive hybridization-mediated analysis of genes and in silico prediction of associated microRNAs under waterlogged conditions in sugarcane (Saccharum spp.). FEBS Open Bio 2014; 4:533-41. [PMID: 25009768 DOI: 10.1016/j.fob.2014.05.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2014] [Revised: 05/28/2014] [Accepted: 05/30/2014] [Indexed: 01/03/2023] Open
Abstract
Waterlogging adversely affects sugarcane productivity and quality. A subtractive cDNA library was prepared from sugarcane leaf tissue and sequenced to generate ESTs. EST sequences were used to identify transcripts induced by waterlogging. The sequenced clones were classified by predicted functions and stress-related genes formed the largest class. EST sequences were also used to identify putative novel microRNAs and their targets.
Sugarcane is an important tropical cash crop meeting 75% of world sugar demand and it is fast becoming an energy crop for the production of bio-fuel ethanol. A considerable area under sugarcane is prone to waterlogging which adversely affects both cane productivity and quality. In an effort to elucidate the genes underlying plant responses to waterlogging, a subtractive cDNA library was prepared from leaf tissue. cDNA clones were sequenced and annotated for their putative functions. Major groups of ESTs were related to stress (15%), catalytic activity (13%), cell growth (10%) and transport related proteins (6%). A few stress-related genes were identified, including senescence-associated protein, dehydration-responsive family protein, and heat shock cognate 70 kDa protein. A bioinformatics search was carried out to discover novel microRNAs (miRNAs) that can be regulated in sugarcane plants subjected to waterlogging stress. Taking advantage of the presence of miRNA precursors in the related sorghum genome, seven candidate mature miRNAs were identified in sugarcane. The application of subtraction technology allowed the identification of differentially expressed sequences and novel miRNAs in sugarcane under waterlogging stress. The comparative global transcript profiling in sugarcane plants undertaken in this study suggests that proteins associated with stress response, signal transduction, metabolic activity and ion transport play important role in conferring waterlogging tolerance in sugarcane.
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Ruiz Esparza-Garrido R, Velázquez-Flores MÁ, Diegopérez-Ramírez J, López-Aguilar E, Siordia-Reyes G, Hernández-Ortiz M, Martínez-Batallar AG, Encarnación-Guevara S, Salamanca-Gómez F, Arenas-Aranda DJ. A proteomic approach of pediatric astrocytomas: MiRNAs and network insight. J Proteomics 2013; 94:162-75. [PMID: 24060999 DOI: 10.1016/j.jprot.2013.09.009] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [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: 05/17/2013] [Revised: 07/23/2013] [Accepted: 09/12/2013] [Indexed: 12/13/2022]
Abstract
UNLABELLED Pediatric astrocytomas, a leading cause of death associated with cancer, are the most common primary central nervous system tumors found in children. Most studies of these tumors focus on adults, not on children. We examined the global protein and microRNA expression pattern by 2D SDS-PAGE, mass spectrometry (MALDI-TOF), and RT(2) miRNA PCR Array System. Proteomic studies revealed 49 proteins with changes on the expression. Interactome showed that vimentin, calreticulin, and 14-3-3 epsilon protein are hub proteins in these neoplasms. MicroRNA analyses demonstrated for the first time novel microRNAs involved in the astrocytoma biology. In conclusion, our results show that novel proteins and microRNAs with expression changes on pediatric astrocytoma could serve as biomarkers of tumor progression. BIOLOGICAL SIGNIFICANCE Astrocytomas are tumors that progress rapidly and that invade surrounding tissues. Although some drugs have been developed to treat these neoplasms, the mortality of patients is still very high. In this study, we describe for the first time, to our knowledge, some proteins and miRNAs associated with the biology of astrocytic tumors that could be postulated as possible diagnostic or prognostic biomarkers. Altogether, our results indicate that large-scale analyses allow making a fairly accurate prediction of different cellular processes altered in astrocytic tumors.
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Affiliation(s)
- Ruth Ruiz Esparza-Garrido
- Unidad de Investigación Médica en Genética Humana, Hospital de Pediatría, Centro Médico Nacional Siglo XXI, IMSS, 06720 México, D.F., Mexico; Posgrado en Ciencias Biológicas, Universidad Nacional Autónoma de México, Av. Universidad 3000, C.P. 04510 Coyoacán, D. F., Mexico
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