1
|
Yi SA, Pongkulapa T, Nevins S, Goldston LL, Chen M, Lee KB. Developing MiR-133a Zipper Nanoparticles for Targeted Enhancement of Thermogenic Adipocyte Generation. Adv Healthc Mater 2024:e2400654. [PMID: 38795000 DOI: 10.1002/adhm.202400654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Revised: 05/17/2024] [Indexed: 05/27/2024]
Abstract
Existing delivery methods for RNAi therapeutics encounter challenges, including stability, specificity, and off-target effects, which restrict their clinical effectiveness. In this study, a novel miR-133a zipper nanoparticle (NP) system that integrates miRNA zipper technology with rolling circle transcription (RCT) to achieve targeted delivery and specific regulation of miR-133a in adipocytes, is presented. This innovative approach can greatly enhance the delivery and release of miR-133a zippers, increasing the expression of thermogenic genes and mitochondrial biogenesis. he miR-133a zipper NP is utilized for the delivery of miRNA zipper-blocking miR-133a, an endogenous inhibitor of Prdm16 expression, to enhance the thermogenic activity of adipocytes by modulating their transcriptional program. Inhibition of miR-133a through the miR-133a zipper NP leads to more significant upregulation of thermogenic gene expression (Prdm16 and Ucp1) than with the free miR-133a zipper strand. Furthermore, miR-133a zipper NPs increase the number of mitochondria and induce heat production, reducing the size of 3D adipose spheroids. In short, this study emphasizes the role of RNA NPs in improving RNAi stability and specificity and paves the way for broader applications in gene therapy. Moreover, this research represents a significant advancement in RNAi-based treatments, pointing toward a promising direction for future therapeutic strategies.
Collapse
Affiliation(s)
- Sang Ah Yi
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, 123 Bevier Road, Piscataway, NJ, 08854, USA
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Thanapat Pongkulapa
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, 123 Bevier Road, Piscataway, NJ, 08854, USA
| | - Sarah Nevins
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, 123 Bevier Road, Piscataway, NJ, 08854, USA
| | - Li Ling Goldston
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, 123 Bevier Road, Piscataway, NJ, 08854, USA
| | - Meizi Chen
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, 123 Bevier Road, Piscataway, NJ, 08854, USA
| | - Ki-Bum Lee
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, 123 Bevier Road, Piscataway, NJ, 08854, USA
| |
Collapse
|
2
|
Kazancioglu E, Tug E, Ergun MA, Kazan HH, Karaoguz MY. The interrelation between the high expression level of MIR34a and the trisomic abortion materials. J Obstet Gynaecol Res 2024; 50:842-848. [PMID: 38452772 DOI: 10.1111/jog.15913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 02/12/2024] [Indexed: 03/09/2024]
Abstract
AIMS The underlying mechanism and constitution of spontaneous abortions are complicated and heterogeneous. Many factors, including epigenetic scenarios like micro-ribonucleic acids (miRNAs, MIRs), can additively affect the progression of pregnancy losses. This study aimed to evaluate whether the expression levels of placental inhibitor and/or activator miRNAs had a difference between the numerically abnormal and normal karyotyped spontaneous abortions. METHODS The case-control study included 100 spontaneous abortion materials consisting of trophoblastic tissues with 42 disomies (controls), 43 aneuploidies (including trisomy 16, 21, 22, and monosomy X), and 15 triploidies. Disomic abortion materials with XX normal karyotypes were omitted from the study to exclude possible maternal decidual cell contamination. Total RNA isolation was performed with TRIzol™ reagent directly from frozen trophoblastic tissues, and the mature miRNAs were obtained by reverse transcription via quantitative real-time polymerase chain reaction (qRT-PCR). Then, the expression levels of placental activators MIR378a-5p, MIR376c, MIR195, and inhibitors MIR34a and MIR210 were relatively evaluated using MIR130 as a reference. RESULTS The expression level of placental inhibitor MIR34a was detected to be high in trisomic abortion materials (trisomy 16 and 21) when compared to the disomic ones (p = 0.0324). MIR195 (p = 0.0484) and MIR34a (p = 0.0346) expression levels were increased in numerically abnormal cases with advanced maternal age compared to the disomic ones within all maternal ages. CONCLUSIONS It seems likely that the high expression level of MIR34a and the coexistence of trisomic abortion materials are quite interrelated with the additive effect of advanced maternal age.
Collapse
Affiliation(s)
- Elvin Kazancioglu
- Department of Medical Genetics, Medical Faculty, Gazi University, Ankara, Turkey
| | - Esra Tug
- Department of Medical Genetics, Medical Faculty, Gazi University, Ankara, Turkey
| | - Mehmet Ali Ergun
- Department of Medical Genetics, Medical Faculty, Gazi University, Ankara, Turkey
| | - Hasan Huseyin Kazan
- Department of Medical Genetics, Medical Faculty, Near East University, Nicosia, Cyprus
| | | |
Collapse
|
3
|
Wang Q, Deng J, Jiang Y, Wang Z, Xia B, Chen T. A medaka gonad-specific lncRNA may act as pri-miR-202 to regulate testicular endocrine homeostasis and spermatogenesis. Theriogenology 2024; 214:273-285. [PMID: 37948817 DOI: 10.1016/j.theriogenology.2023.10.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 10/09/2023] [Accepted: 10/15/2023] [Indexed: 11/12/2023]
Abstract
A large number of long non-coding RNAs (lncRNAs) are expressed in animal gonads, but their functions are poorly understood. In this study, a gonad-specific lncRNA, termed lnc4, was identified and characterized in the model fish medaka (Oryzias latipes). The expression pattern and in vitro functional analyses indicated that lnc4 was likely to be a primary transcript of miR-202 (pri-miR-202). Results of single-molecule fluorescence in situ hybridization demonstrated that the precursor miR-202 (pre-miR-202) was highly expressed in the nuclei of testicular somatic cells, including Leydig and Sertoli cells, whereas only a small amount of lnc4 molecules could be detected co-expressed with pre-miR-202 in Sertoli cells due to its low expression level. Deletion of the lnc4 locus led to a significant reduction in testis size and a dramatic decrease in the number of male germ cells, as well as a reduction in sperm viability. Moreover, lnc4 knockout resulted in enhanced synthesis and secretion of testicular somatic cells and accelerated differentiation of immature male germ cells. Taken together, functional studies of lnc4 and its mature transcript miR-202 will contribute to the understanding of the important role of non-coding RNAs in animal or human reproductive disorders.
Collapse
Affiliation(s)
- Qian Wang
- College of Animal Science and Technology, Yangtze University, Jingzhou, Hubei, 434024, China; College of Fisheries, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Jiajie Deng
- State Key Laboratory of Freshwater Ecology and Biotechnology, Hubei Hongshan Laboratory, Institute of Hydrobiology, Innovation Academy for Seed Design (INASEED), Chinese Academy of Sciences, Wuhan, Hubei, 430072, China
| | - Yuewen Jiang
- College of Fisheries, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Zhi Wang
- College of Fisheries, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Bilin Xia
- College of Fisheries, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Tiansheng Chen
- Fisheries College of Jimei University, Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture and Rural Affairs, Engineering Research Center of the Modern Technology for Eel Industry, Ministry of Education, Xiamen, Fujian, 361021, China; College of Fisheries, Huazhong Agricultural University, Wuhan, Hubei, 430070, China.
| |
Collapse
|
4
|
Carvalho LB, Dos Santos Sanna PL, Dos Santos Afonso CC, Bondan EF, da Silva Feltran G, Ferreira MR, Birbrair A, Andia DC, Latini A, Foganholi da Silva RA. MicroRNA biogenesis machinery activation and lncRNA and REST overexpression as neuroprotective responses to fight inflammation in the hippocampus. J Neuroimmunol 2023; 382:578149. [PMID: 37481910 DOI: 10.1016/j.jneuroim.2023.578149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 06/05/2023] [Accepted: 07/09/2023] [Indexed: 07/25/2023]
Abstract
Brain Long non-coding RNA (lncRNA) and microRNAs (miRs) play essential roles in the regulation of several important biological processes, including neuronal activity, cognitive processes, neurogenesis, angiogenesis, and neuroinflammation. In this context, the transcriptional repressor, RE1 silencing transcription factor (Rest), acts regulating the expression of neuronal genes as well as of lncRNAs and multiple miRNAs in the central nervous system. Nevertheless, its role in neuroinflammation was less explored. Here, we demonstrate, using an in vivo model of neuroinflammation induced by i.p. injection of LPS (0.33 mg/kg), that neuroinflammation increases gene expression of pro-inflammatory cytokines concomitant with the native and truncated forms of Rest and of non-coding RNAs. Additionally, the increased expression of enzymes Drosha ribonuclease III) (Drosha), Exportin 5 (Xpo5) and Endoribonuclease dicer (Dicer), associated with high expression of neuroprotective miRs 22 and 132 are indicative that the activation of biogenesis of miRs in the hippocampal region is a Central Nervous System (CNS) protective mechanism for the deleterious effects of neuroinflammation. Our results indicate that positive regulation of Rest gene expression in the hippocampal region by neuroinflammation correlates directly with the expression of miRs 22 and 132 and inversely with miR 335. In parallel, the confirmation of the possible alignment between the lncRNAs with miR 335 by bioinformatics corroborates with the sponge effect of Hottip and Hotair hybridizing and inhibiting the pro-inflammatory action of miR 335. This suggests the existence of a possible correlation between the activation of miR biogenesis machinery with increased expression of the transcription factor Rest, contributing to neuroprotection.
Collapse
Affiliation(s)
| | | | | | - Eduardo F Bondan
- CEEpiRG - Center for Epigenetic Study and Genic Regulation, Program in Environmental and Experimental Pathology, Paulista University, São Paulo, SP, Brazil
| | - Geórgia da Silva Feltran
- Lab. of Bioassays and Cellular Dynamics, Department of Chemical and Biological Sciences, Institute of Biosciences, UNESP - São Paulo State University, Botucatu, SP, Brazil
| | - Marcel Rodrigues Ferreira
- Molecular Genetics and Bioinformatics Laboratory, Experimental Research Unity, Botucatu Medical School, São Paulo State University, USA
| | - Alexander Birbrair
- Department of Pathology, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil; Department of Dermatology, University of Wisconsin-Madison, Madison, WI, USA; Department of Radiology, Columbia University Medical Center, New York, NY, USA
| | - Denise Carleto Andia
- School of Dentistry, Health Science Institute, Paulista University, São Paulo 04026-002, São Paulo, Brazil
| | - Alexandra Latini
- Laboratory of Bioenergetics and Oxidative Stress, LABOX, Department of Biochemistry, Center for Biological Sciences, Federal University of Santa Catarina, Florianopolis, Brazil
| | - Rodrigo A Foganholi da Silva
- Dentistry, University of Taubaté, Taubaté, São Paulo, SP, Brazil; CEEpiRG - Center for Epigenetic Study and Genic Regulation, Program in Environmental and Experimental Pathology, Paulista University, São Paulo, SP, Brazil.
| |
Collapse
|
5
|
Ste-Croix DT, Bélanger RR, Mimee B. Characterization of microRNAs in the cyst nematode Heterodera glycines identifies possible candidates involved in cross-kingdom interactions with its host Glycine max. RNA Biol 2023; 20:614-628. [PMID: 37599428 PMCID: PMC10443972 DOI: 10.1080/15476286.2023.2244790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 07/21/2023] [Accepted: 07/31/2023] [Indexed: 08/22/2023] Open
Abstract
The soybean cyst nematode (SCN - Heterodera glycines) is one of the most damaging pests to the cultivated soybean worldwide. Using a wide array of stylet-secreted effector proteins, this nematode can restructure its host cells into a complex and highly active feeding structure called the syncytium. Tight regulation of these proteins is thought to be essential to the successful formation of this syncytium. To date, multiple mechanisms have been proposed to regulate the expression of these proteins including through post-transcriptional regulation. MicroRNAs (miRNAs) are a class of small, roughly 22-nucleotide-long, non-coding RNA shown to regulate gene expression through its interaction with the 3' untranslated region of genes. These same small RNAs have also been hypothesized to be able to cross over kingdom barriers and regulate genes in other species in a process called cross-kingdom interactions. In this study, we characterized the miRNome of the SCN via sequencing of small-RNAs isolated from whole nematodes and exosomes representing all developmental stages. We identified 121 miRNA loci encoding 96 distinct miRNA families including multiple lineage- and species-specific candidates. Using a combination of plant- and animal-specific miRNA target predictors, we generated a unique repertoire of miRNA:mRNA interacting partners in the nematode and its host plant leading to the identification of a set of nine probable cross-kingdom miRNA candidates.
Collapse
Affiliation(s)
- Dave T. Ste-Croix
- Saint-Jean-Sur-Richelieu Research and Development Centre, Agriculture and Agri-Food Canada, Saint-Jean-Sur-Richelieu, Canada
- Département de Phytologie, Université Laval, Québec, Canada
| | - Richard R. Bélanger
- Département de Phytologie, Université Laval, Québec, Canada
- Centre de Recherche et d’Innovation sur les Végétaux (CRIV), Université Laval, Québec, Canada
| | - Benjamin Mimee
- Saint-Jean-Sur-Richelieu Research and Development Centre, Agriculture and Agri-Food Canada, Saint-Jean-Sur-Richelieu, Canada
| |
Collapse
|
6
|
Xie Y, Xu Z, Wu C, Zhou C, Zhang X, Gu T, Yang J, Yang H, Zheng E, Xu Z, Cai G, Li Z, Liu D, Wu Z, Hong L. Extracellular vesicle-encapsulated miR-21-5p in seminal plasma prevents sperm capacitation via Vinculin inhibition. Theriogenology 2022; 193:103-113. [PMID: 36156422 DOI: 10.1016/j.theriogenology.2022.09.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2021] [Revised: 07/11/2022] [Accepted: 09/10/2022] [Indexed: 10/31/2022]
Abstract
To penetrate the zona pellucida before sperm-egg binding, sperm must undergo highly time-controlled capacitation and acrosome reaction in the female reproductive tract. Our previous study demonstrated that miR-21-5p is the most abundant miRNA in boar seminal plasma (SP)-derived extracellular vesicles (EVs) and can target Vinculin (VCL) gene, which may participate in boar sperm capacitation. Thus, this study aims to explore the potential role of miR-21-5p from SP-derived EVs in preventing sperm capacitation and its underlying mechanism. We observed that sperm could incorporate miR-21-5p from SP-derived EVs. The roles of SP-derived EVs miR-21-5p in sperm capacitation were then determined using gain- and loss-of-function analyses. In addition, the expression levels of miR-21-5p, VCL, and VCL protein in liquid-preserved boar sperm following transfection were determined using RT-qPCR and Western blotting. Our results revealed that miR-21-5p overexpression inhibited sperm capacitation and acrosome reaction. Similarly, miR-21-5p expression was significantly lower (P < 0.05) in capacitated sperm than un-capacitated sperm. However, the protein level of VCL was also significantly lower (P < 0.05) in capacitated sperm than un-capacitated sperm. Furthermore, immunofluorescence analysis showed that VCL protein mainly located in sperm head and sperm capacitation was inhibited after treating with VCL protein inhibitor (Chrysin). In conclusion, our study provides reasonable evidence that miR-21-5p expression in SP-derived EVs could prevent sperm capacitation via VCL inhibition.
Collapse
Affiliation(s)
- Yanshe Xie
- National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, China; Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China; Lingnan Guangdong Laboratory of Modern Agriculture, Guangzhou, China
| | - Zhiqian Xu
- National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, China; Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China; Lingnan Guangdong Laboratory of Modern Agriculture, Guangzhou, China
| | - Changhua Wu
- National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, China; Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China; Lingnan Guangdong Laboratory of Modern Agriculture, Guangzhou, China
| | - Chen Zhou
- National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, China; Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China; Lingnan Guangdong Laboratory of Modern Agriculture, Guangzhou, China
| | | | - Ting Gu
- National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, China; Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China; Lingnan Guangdong Laboratory of Modern Agriculture, Guangzhou, China
| | - Jie Yang
- National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, China; Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China; Lingnan Guangdong Laboratory of Modern Agriculture, Guangzhou, China
| | - Huaqiang Yang
- National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, China; Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China; Lingnan Guangdong Laboratory of Modern Agriculture, Guangzhou, China
| | - Enqin Zheng
- National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, China; Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China; Lingnan Guangdong Laboratory of Modern Agriculture, Guangzhou, China
| | - Zheng Xu
- National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, China; Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China; Lingnan Guangdong Laboratory of Modern Agriculture, Guangzhou, China
| | - Gengyuan Cai
- National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, China; Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China; Lingnan Guangdong Laboratory of Modern Agriculture, Guangzhou, China
| | - Zicong Li
- National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, China; Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China; Lingnan Guangdong Laboratory of Modern Agriculture, Guangzhou, China; State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangzhou, 510642, China
| | - Dewu Liu
- National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, China; Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China; Lingnan Guangdong Laboratory of Modern Agriculture, Guangzhou, China
| | - Zhenfang Wu
- National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, China; Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China; Lingnan Guangdong Laboratory of Modern Agriculture, Guangzhou, China; State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangzhou, 510642, China.
| | - Linjun Hong
- National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, China; Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China; Lingnan Guangdong Laboratory of Modern Agriculture, Guangzhou, China.
| |
Collapse
|
7
|
Dozier C, Montigny A, Viladrich M, Culerrier R, Combier JP, Besson A, Plaza S. Small ORFs as New Regulators of Pri-miRNAs and miRNAs Expression in Human and Drosophila. Int J Mol Sci 2022; 23:5764. [PMID: 35628573 PMCID: PMC9144653 DOI: 10.3390/ijms23105764] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 05/19/2022] [Indexed: 02/01/2023] Open
Abstract
MicroRNAs (miRNAs) are small regulatory non-coding RNAs, resulting from the cleavage of long primary transcripts (pri-miRNAs) in the nucleus by the Microprocessor complex generating precursors (pre-miRNAs) that are then exported to the cytoplasm and processed into mature miRNAs. Some miRNAs are hosted in pri-miRNAs annotated as long non-coding RNAs (lncRNAs) and defined as MIRHGs (for miRNA Host Genes). However, several lnc pri-miRNAs contain translatable small open reading frames (smORFs). If smORFs present within lncRNAs can encode functional small peptides, they can also constitute cis-regulatory elements involved in lncRNA decay. Here, we investigated the possible involvement of smORFs in the regulation of lnc pri-miRNAs in Human and Drosophila, focusing on pri-miRNAs previously shown to contain translatable smORFs. We show that smORFs regulate the expression levels of human pri-miR-155 and pri-miR-497, and Drosophila pri-miR-8 and pri-miR-14, and also affect the expression and activity of their associated miRNAs. This smORF-dependent regulation is independent of the nucleotidic and amino acidic sequences of the smORFs and is sensitive to the ribosome-stalling drug cycloheximide, suggesting the involvement of translational events. This study identifies smORFs as new cis-acting elements involved in the regulation of pri-miRNAs and miRNAs expression, in both Human and Drosophila melanogaster.
Collapse
Affiliation(s)
- Christine Dozier
- Molecular, Cellular and Developmental Biology Department (MCD), Centre de Biologie Integrative (CBI), University of Toulouse, CNRS, UPS, 31062 Toulouse, France; (R.C.); (A.B.)
| | - Audrey Montigny
- Laboratoire de Recherche en Sciences Végétales, UMR5546 CNRS, UPS Université de Toulouse, INP, 31320 Auzeville-Tolosan, France; (A.M.); (M.V.); (J.-P.C.)
| | - Mireia Viladrich
- Laboratoire de Recherche en Sciences Végétales, UMR5546 CNRS, UPS Université de Toulouse, INP, 31320 Auzeville-Tolosan, France; (A.M.); (M.V.); (J.-P.C.)
| | - Raphael Culerrier
- Molecular, Cellular and Developmental Biology Department (MCD), Centre de Biologie Integrative (CBI), University of Toulouse, CNRS, UPS, 31062 Toulouse, France; (R.C.); (A.B.)
| | - Jean-Philippe Combier
- Laboratoire de Recherche en Sciences Végétales, UMR5546 CNRS, UPS Université de Toulouse, INP, 31320 Auzeville-Tolosan, France; (A.M.); (M.V.); (J.-P.C.)
| | - Arnaud Besson
- Molecular, Cellular and Developmental Biology Department (MCD), Centre de Biologie Integrative (CBI), University of Toulouse, CNRS, UPS, 31062 Toulouse, France; (R.C.); (A.B.)
| | - Serge Plaza
- Laboratoire de Recherche en Sciences Végétales, UMR5546 CNRS, UPS Université de Toulouse, INP, 31320 Auzeville-Tolosan, France; (A.M.); (M.V.); (J.-P.C.)
| |
Collapse
|
8
|
Li S, Wang C, Xu Y, Wang W, Zhao X, Qian Q, Mi X. A designer DNA tetrahedron-based molecular beacon for tumor-related microRNA fluorescence imaging in living cells. Analyst 2022; 147:2231-2237. [DOI: 10.1039/d2an00418f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A designer nanoprobe of tetrahedral DNA framework (TDF) combined with MB (termed TDFM nanoprobe) for the efficient fluorescence imaging of tumor-related miRNA-214 in living cells.
Collapse
Affiliation(s)
- Shuainan Li
- Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chenguang Wang
- Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yi Xu
- Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China
| | - Wei Wang
- Shanghai Pudong New District Zhoupu Hospital (Shanghai University of Medicine & Health Sciences Affiliated Zhoupu Hospital), Shanghai 201318, China
| | - Xiaoshuang Zhao
- Key Laboratory of Functional Materials for Informatics, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, Shanghai 200050, China
| | - Qiuling Qian
- Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xianqiang Mi
- Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Key Laboratory of Functional Materials for Informatics, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, Shanghai 200050, China
- CAS Center for Excellence in Superconducting Electronics (CENSE), Shanghai 200050, China
- Key Laboratory of Systems Biology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Hangzhou, 310024, China
| |
Collapse
|
9
|
He F, Ni N, Wang H, Zeng Z, Zhao P, Shi D, Xia Y, Chen C, Hu D, Qin K, Wagstaff W, Qin D, Hendren-Santiago B, Ho S, Haydon R, Luu H, Reid R, Shen L, Gan H, Fan J, He TC. OUHP: an optimized universal hairpin primer system for cost-effective and high-throughput RT-qPCR-based quantification of microRNA (miRNA) expression. Nucleic Acids Res 2021; 50:e22. [PMID: 34850128 PMCID: PMC8887422 DOI: 10.1093/nar/gkab1153] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Revised: 11/03/2021] [Accepted: 11/08/2021] [Indexed: 12/16/2022] Open
Abstract
MicroRNAs (miRNAs or miRs) are single-stranded, ∼22-nucleotide noncoding RNAs that regulate many cellular processes. While numerous miRNA quantification technologies are available, a recent analysis of 12 commercial platforms revealed high variations in reproducibility, sensitivity, accuracy, specificity and concordance within and/or between platforms. Here, we developed a universal hairpin primer (UHP) system that negates the use of miRNA-specific hairpin primers (MsHPs) for quantitative reverse transcription PCR (RT-qPCR)-based miRNA quantification. Specifically, we analyzed four UHPs that share the same hairpin structure but are anchored with two, three, four and six degenerate nucleotides at 3'-ends (namely UHP2, UHP3, UHP4 and UHP6), and found that the four UHPs yielded robust RT products and quantified miRNAs with high efficiency. UHP-based RT-qPCR miRNA quantification was not affected by long transcripts. By analyzing 14 miRNAs, we demonstrated that UHP4 closely mimicked MsHPs in miRNA quantification. Fine-tuning experiments identified an optimized UHP (OUHP) mix with a molar composition of UHP2:UHP4:UHP6 = 8:1:1, which closely recapitulated MsHPs in miRNA quantification. Using synthetic LET7 isomiRs, we demonstrated that the OUHP-based qPCR system exhibited high specificity and sensitivity. Collectively, our results demonstrate that the OUHP system can serve as a reliable and cost-effective surrogate of MsHPs for RT-qPCR-based miRNA quantification for basic research and precision medicine.
Collapse
Affiliation(s)
| | | | - Hao Wang
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA,Ministry of Education Key Laboratory of Diagnostic Medicine, and the School of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, China
| | - Zongyue Zeng
- Departments of Nephrology, Gastroenterology, Laboratory Diagnostic Medicine, and Orthopaedic Surgery, the First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China,Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA,Ministry of Education Key Laboratory of Diagnostic Medicine, and the School of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, China
| | - Piao Zhao
- Departments of Nephrology, Gastroenterology, Laboratory Diagnostic Medicine, and Orthopaedic Surgery, the First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China,Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA
| | - Deyao Shi
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA,Department of Orthopaedic Surgery, Union Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Yinglin Xia
- Division of Gastroenterology and Hepatology, Department of Medicine, University of Illinois at Chicago, Chicago, IL 60612, USA
| | - Connie Chen
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA
| | - Daniel A Hu
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA
| | - Kevin H Qin
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA
| | - William Wagstaff
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA
| | - David Qin
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA
| | - Bryce Hendren-Santiago
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA
| | - Sherwin H Ho
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA
| | - Rex C Haydon
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA
| | - Hue H Luu
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA
| | - Russell R Reid
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA,Section of Plastic Surgery, Department of Surgery, The University of Chicago Medical Center, Chicago, IL 60637, USA
| | - Le Shen
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA,Section of Plastic Surgery, Department of Surgery, The University of Chicago Medical Center, Chicago, IL 60637, USA
| | - Hua Gan
- Correspondence may also be addressed to Hua Gan. Tel: +86 23 8901 2019; Fax: +86 23 8901 2019;
| | - Jiaming Fan
- Correspondence may also be addressed to Jiaming Fan. Tel: +86 23 6848 5240;
| | - Tong-Chuan He
- To whom correspondence should be addressed. Tel: +1 773 702 7169; Fax: +1 773 834 4598;
| |
Collapse
|
10
|
Assis RIF, Feltran GDS, Silva MES, Palma ICDR, Rovai ES, Miranda TBD, Ferreira MR, Zambuzzi WF, Birbrair A, Andia DC, da Silva RA. Non-coding RNAs repressive role in post-transcriptional processing of RUNX2 during the acquisition of the osteogenic phenotype of periodontal ligament mesenchymal stem cells. Dev Biol 2021; 470:37-48. [PMID: 33152274 DOI: 10.1016/j.ydbio.2020.10.012] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2020] [Revised: 10/06/2020] [Accepted: 10/22/2020] [Indexed: 02/08/2023]
Abstract
Mesenchymal stem cells are candidates for therapeutic strategies in periodontal repair due to their osteogenic potential. In this study, we identified epigenetic markers during osteogenic differentiation, taking advantage of the individual pattern of mesenchymal cells of the periodontal ligament with high (h-PDLCs) and low (l-PDLCs) osteogenic capacity. We found that the involvement of non-coding RNAs in the regulation of the RUNX2 gene is strongly associated with high osteogenic potential. Moreover, we evaluated miRs and genes that encode enzymes to process miRs and their biogenesis. Our data show the high expression of the XPO5 gene, and miRs 7 and 22 observed in the l-PDLCs might be involved in acquiring osteogenic potential, suppressing RUNX2 gene expression. Further, an inversely proportional correlation between lncRNAs (HOTAIR and HOTTIP) and RUNX2 gene expression was observed in both l- and h-PDLCs, and it was also related to the distinct osteogenic phenotypes. Thus, our results indicate the low expression of XPO5 in h-PDLC might be the limiting point for blocking the miRs biogenesis, allowing the high gene expression of RUNX2. In accordance, the low expression of miRs, HOTAIR, and HOTTIP could be a prerequisite for increased osteogenic potential in h-PDLCs. These results will help us to better understand the underlying mechanisms of osteogenesis, considering the heterogeneity in the osteogenic potential of PDLCs that might be related to a distinct transcriptional profile of lncRNAs and the biogenesis machinery.
Collapse
Affiliation(s)
- Rahyza I F Assis
- Department of Prosthodontics and Periodontics, Piracicaba Dental School, University of Campinas, Piracicaba, São Paulo, Brazil
| | - Geórgia da S Feltran
- Lab. of Bioassays and Cellular Dynamics, Department of Chemical and Biological Sciences, Institute of Biosciences, UNESP - São Paulo State University, 18618-970, Botucatu, São Paulo, Brazil
| | | | | | - Emanuel Silva Rovai
- Faculty of Dentistry, University of Taubaté, 12020-340, Taubaté, São Paulo, Brazil
| | | | - Marcel Rodrigues Ferreira
- Lab. of Bioassays and Cellular Dynamics, Department of Chemical and Biological Sciences, Institute of Biosciences, UNESP - São Paulo State University, 18618-970, Botucatu, São Paulo, Brazil
| | - Willian F Zambuzzi
- Lab. of Bioassays and Cellular Dynamics, Department of Chemical and Biological Sciences, Institute of Biosciences, UNESP - São Paulo State University, 18618-970, Botucatu, São Paulo, Brazil
| | - Alexander Birbrair
- Department of Pathology, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil; Department of Radiology, Columbia University Medical Center, New York, NY, USA
| | - Denise C Andia
- School of Dentistry, Health Science Institute, Paulista University, 04026-002, São Paulo, Brazil.
| | - Rodrigo A da Silva
- Faculty of Dentistry, University of Taubaté, 12020-340, Taubaté, São Paulo, Brazil; Program in Environmental and Experimental Pathology, Paulista University, São Paulo, 04026-002, São Paulo, Brazil.
| |
Collapse
|
11
|
Li X, Xiao J, Li K, Zhou Y. MiR-199-3p modulates the onset of puberty in rodents probably by regulating the expression of Kiss1 via the p38 MAPK pathway. Mol Cell Endocrinol 2020; 518:110994. [PMID: 32818586 DOI: 10.1016/j.mce.2020.110994] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 08/13/2020] [Accepted: 08/13/2020] [Indexed: 12/27/2022]
Abstract
The Kiss1 gene plays an indispensable role in modulating the onset of puberty and fertility in mammals. Although an increasing number of genetic and environmental factors that influence reproduction through Kiss1 have been identified, the function of microRNAs, a class of posttranscriptional regulators, in regulating Kiss1 expression remains poorly understood. This study aimed at investigating the mechanism by which Kiss1 expression is regulated by microRNAs. A simplified miRNome screen by a dual-fluorescence reporter system based on Kiss1 was performed to identify microRNAs that affect the expression of Kiss1. The expression patterns of the identified microRNAs during the period of murine sexual development were investigated, and only miR-199-3p was studied further. Aided by bioinformatics algorithms, miR-199-3p was demonstrated to be a repressor of Kiss1 expression, as it blocked the expression of Kiss1 through the p38 MAPK pathway by simultaneously inhibiting several targets in both GT1-7 cells and primary hypothalamic neurons. Both the inhibition of the p38 MAPK pathway by the intracerebroventricular administration of chemical agents in rats and the ectopic expression of miR-199-3p by lentivirus injection in the hypothalamus in mice delayed puberty onset and gonad development. Our results presented a novel regulatory mechanism of puberty onset which the sustained downregulation of miR-199-3p might gradually release the inhibition of the p38 MAPK/Fos/CREB/Kiss1 pathway during puberty development.
Collapse
Affiliation(s)
- Xiaoning Li
- Key Laboratory of Science & Technology of Eco-Textile, Ministry of Education, Donghua University, Shanghai, China; College of Chemistry, Chemical Engineering & Biotechnology, Donghua University, Shanghai, China
| | - Junhua Xiao
- College of Chemistry, Chemical Engineering & Biotechnology, Donghua University, Shanghai, China
| | - Kai Li
- College of Chemistry, Chemical Engineering & Biotechnology, Donghua University, Shanghai, China
| | - Yuxun Zhou
- Key Laboratory of Science & Technology of Eco-Textile, Ministry of Education, Donghua University, Shanghai, China; College of Chemistry, Chemical Engineering & Biotechnology, Donghua University, Shanghai, China.
| |
Collapse
|
12
|
Popa N, Boyer F, Jaouen F, Belzeaux R, Gascon E. Social Isolation and Enrichment Induce Unique miRNA Signatures in the Prefrontal Cortex and Behavioral Changes in Mice. iScience 2020; 23:101790. [PMID: 33294798 PMCID: PMC7701176 DOI: 10.1016/j.isci.2020.101790] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 09/14/2020] [Accepted: 11/06/2020] [Indexed: 01/19/2023] Open
Abstract
An extensive body of evidence supports the notion that exposure to an enriched/impoverished environment alters brain functions via epigenetic changes. However, how specific modifications of social environment modulate brain functions remains poorly understood. To address this issue, we investigate the molecular and behavioral consequences of briefly manipulating social settings in young and middle-aged wild-type mice. We observe that, modifications of the social context, only affect the performance in socially related tasks. Social enrichment increases sociability whereas isolation leads to the opposite effect. Our work also pointed out specific miRNA signatures associated to each social environment. These miRNA alterations are reversible and found selectively in the medial prefrontal cortex. Finally, we show that miRNA modifications linked to social enrichment or isolation might target rather different intracellular pathways. Together, these observations suggest that the prefrontal cortex may be a key brain area integrating social information via the modification of precise miRNA networks.
Collapse
Affiliation(s)
- Natalia Popa
- Aix-Marseille Université, CNRS, INT, Inst Neurosci Timone, UMR7289, 27, Boulevard Jean Moulin, 13005 Marseille, France
| | - Flora Boyer
- Aix-Marseille Université, CNRS, INT, Inst Neurosci Timone, UMR7289, 27, Boulevard Jean Moulin, 13005 Marseille, France
| | - Florence Jaouen
- Aix-Marseille Université, CNRS, INT, Inst Neurosci Timone, UMR7289, 27, Boulevard Jean Moulin, 13005 Marseille, France
- NeuroBioTools Facility (NeuroVir), Aix Marseille Université, CNRS, INT, Inst Neurosci Timone, Marseille, France
| | - Raoul Belzeaux
- Aix-Marseille Université, CNRS, INT, Inst Neurosci Timone, UMR7289, 27, Boulevard Jean Moulin, 13005 Marseille, France
- Assistance Publique Hôpitaux de Marseille, Sainte Marguerite Hospital, Pôle de Psychiatrie Universitaire Solaris, Marseille, France
| | - Eduardo Gascon
- Aix-Marseille Université, CNRS, INT, Inst Neurosci Timone, UMR7289, 27, Boulevard Jean Moulin, 13005 Marseille, France
- Corresponding author
| |
Collapse
|
13
|
da Silva RA, Ferreira MR, Gomes AM, Zambuzzi WF. LncRNA HOTAIR is a novel endothelial mechanosensitive gene. J Cell Physiol 2019; 235:4631-4642. [PMID: 31637716 DOI: 10.1002/jcp.29340] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2019] [Accepted: 09/30/2019] [Indexed: 12/17/2022]
Abstract
To better address whether the long noncoding RNAs (lncRNAs) HOTAIR and HOTTIP are mechanosensitive genes, they were investigated in differentially challenged endothelial cells with respect to a circuit of tensional forces, considering the performance of both arterial and venous endothelial cells. We subjected arterial- and venous-obtained endothelial cells to a circuit of tensional forces within a shear stress model in vitro. Real-time quantitative polymerase chain reaction analysis indicated that microRNA (miRNA)-related processing machinery is significantly required in shear stressed arterial endothelial cell metabolism, which orchestrates miRNA (small noncoding RNA) involvement, and their involvement suggests lncRNA involvement. Of lncRNAs HOTAIR and HOTTIP, only HOTAIR was mechanosensitive considering both arterial and venous endothelial cells, presenting a positive correlation between methylation signature and gene expression. Thereafter, using bioinformatics tools, lncRNA HOTAIR was predicted to modulate miRNA185, miRNA-21, and miRNA23b downregulation. We compared the values of gene expression with a Pearson's correlation test, and expected correlations were observed for miRNA185 (r = 0.8664), miRNA-21 (r = 0.8605), and miRNA23b (0.9128). Taken together, these findings clearly show that lncRNA HOTAIR responds to the shear stress and emerges as a novel mechanosensitive gene in endothelial cells. Altogether, this understanding of mechanosensitive transcriptional and posttranscriptional control involving HOTAIR can also lead to new forms of therapeutic intervention for various diseases, as well as new strategies for tissue engineering and regenerative medicine.
Collapse
Affiliation(s)
- Rodrigo A da Silva
- Laboratory of Bioassays and Cellular Dynamics, Department of Chemistry and Biochemistry, Institute of Biosciences, São Paulo State University - UNESP, Botucatu, São Paulo, Brazil.,Division of Dental Biology, Department of Dentistry, University of Taubaté, Taubaté, São Paulo, Brazil
| | - Marcel Rodrigues Ferreira
- Laboratory of Bioassays and Cellular Dynamics, Department of Chemistry and Biochemistry, Institute of Biosciences, São Paulo State University - UNESP, Botucatu, São Paulo, Brazil
| | - Anderson Moreira Gomes
- Laboratory of Bioassays and Cellular Dynamics, Department of Chemistry and Biochemistry, Institute of Biosciences, São Paulo State University - UNESP, Botucatu, São Paulo, Brazil
| | - Willian F Zambuzzi
- Laboratory of Bioassays and Cellular Dynamics, Department of Chemistry and Biochemistry, Institute of Biosciences, São Paulo State University - UNESP, Botucatu, São Paulo, Brazil
| |
Collapse
|
14
|
Forero DA, González-Giraldo Y, Castro-Vega LJ, Barreto GE. qPCR-based methods for expression analysis of miRNAs. Biotechniques 2019; 67:192-199. [PMID: 31560239 DOI: 10.2144/btn-2019-0065] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Several approaches for miRNA expression analysis have been developed in recent years. In this article, we provide an updated and comprehensive review of available qPCR-based methods for miRNA expression analysis and discuss their advantages and disadvantages. Existing techniques involve the use of stem-loop reverse transcriptase-PCR, polyadenylation of RNAs, ligation of adapters or RT with complex primers, using universal or miRNA-specific qPCR primers and/or probes. Many of these methods are oriented towards the expression analysis of mature miRNAs and few are designed for the study of pre-miRNAs and pri-miRNAs. We also discuss findings from articles that compare results from existing methods. Finally, we suggest key points for the improvement of available techniques and for the future development of additional methods.
Collapse
Affiliation(s)
- Diego A Forero
- Laboratory of NeuroPsychiatric Genetics, Biomedical Sciences Research Group, School of Medicine, Universidad Antonio Nariño, Bogotá, Colombia.,PhD Program in Health Sciences, School of Medicine, Universidad Antonio Nariño, Bogotá, Colombia
| | - Yeimy González-Giraldo
- Departamento de Nutrición y Bioquímica, Pontificia Universidad Javeriana, Bogotá, Colombia
| | - Luis J Castro-Vega
- INSERM, UMR970, Paris-Cardiovascular Research Center, Equipe Labellisée par la Ligue contre le Cancer, Paris, France.,Université Paris Descartes, Sorbonne Paris Cité, Faculté de Médecine, Paris, France
| | - George E Barreto
- Departamento de Nutrición y Bioquímica, Pontificia Universidad Javeriana, Bogotá, Colombia
| |
Collapse
|
15
|
da Silva RA, Fernandes CJDC, Feltran GDS, Gomes AM, Andrade AF, Andia DC, Peppelenbosch MP, Zambuzzi WF. Laminar shear stress‐provoked cytoskeletal changes are mediated by epigenetic reprogramming of
TIMP1
in human primary smooth muscle cells. J Cell Physiol 2018; 234:6382-6396. [DOI: 10.1002/jcp.27374] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2018] [Accepted: 08/17/2018] [Indexed: 12/28/2022]
Affiliation(s)
- Rodrigo A. da Silva
- Department of Chemistry and Biochemistry Laboratory of Bioassays and Cellular Dynamics, São Paulo State University (UNESP), Institute of Biosciences, Campus Botucatu Botucatu Brazil
| | - Célio Jr da C. Fernandes
- Department of Chemistry and Biochemistry Laboratory of Bioassays and Cellular Dynamics, São Paulo State University (UNESP), Institute of Biosciences, Campus Botucatu Botucatu Brazil
| | - Geórgia da S. Feltran
- Department of Chemistry and Biochemistry Laboratory of Bioassays and Cellular Dynamics, São Paulo State University (UNESP), Institute of Biosciences, Campus Botucatu Botucatu Brazil
| | - Anderson M. Gomes
- Department of Chemistry and Biochemistry Laboratory of Bioassays and Cellular Dynamics, São Paulo State University (UNESP), Institute of Biosciences, Campus Botucatu Botucatu Brazil
| | - Amanda Fantini Andrade
- Department of Chemistry and Biochemistry Laboratory of Bioassays and Cellular Dynamics, São Paulo State University (UNESP), Institute of Biosciences, Campus Botucatu Botucatu Brazil
| | - Denise C. Andia
- Faculdade de Odontologia Área de Pesquisa em Epigenética, Universidade Paulista, UNIP São Paulo São Paulo Brazil
| | - Maikel P. Peppelenbosch
- Department of Gastroenterology & Hepatology Erasmus MC, University Medical Center Rotterdam Rotterdam The Netherlands
| | - Willian F. Zambuzzi
- Department of Chemistry and Biochemistry Laboratory of Bioassays and Cellular Dynamics, São Paulo State University (UNESP), Institute of Biosciences, Campus Botucatu Botucatu Brazil
- Electron Microscopy Center, São Paulo State University (UNESP), Institute of Biosciences, campus Botucatu Botucatu Brazil
| |
Collapse
|
16
|
XIE HL, WU TT, XIE ZH, FAN JL, TONG CY. Quantitative Detection of PremicroRNA-21 Based on Chimeric Molecular Beacon. CHINESE JOURNAL OF ANALYTICAL CHEMISTRY 2018. [DOI: 10.1016/s1872-2040(18)61099-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
|
17
|
Sison SL, Patitucci TN, Seminary ER, Villalon E, Lorson CL, Ebert AD. Astrocyte-produced miR-146a as a mediator of motor neuron loss in spinal muscular atrophy. Hum Mol Genet 2018. [PMID: 28637335 DOI: 10.1093/hmg/ddx230] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Spinal muscular atrophy (SMA), the leading genetic cause of infant mortality, is caused by the loss of the survival motor neuron-1 (SMN1) gene, which leads to motor neuron loss, muscle atrophy, respiratory distress, and death. Motor neurons exhibit the most profound loss, but the mechanisms underlying disease pathogenesis are not fully understood. Recent evidence suggests that motor neuron extrinsic influences, such as those arising from astrocytes, contribute to motor neuron malfunction and loss. Here we investigated both loss-of-function and toxic gain-of-function astrocyte mechanisms that could play a role in SMA pathology. We had previously found that glial derived neurotrophic factor (GDNF) is reduced in SMA astrocytes. However, reduced GDNF expression does not play a major role in SMA pathology as viral-mediated GDNF re-expression did not improve astrocyte function or motor neuron loss. In contrast, we found that SMA astrocytes increased microRNA (miR) production and secretion compared to control astrocytes, suggesting potential toxic gain-of-function properties. Specifically, we found that miR-146a was significantly upregulated in SMA induced pluripotent stem cell (iPSC)-derived astrocytes and SMNΔ7 mouse spinal cord. Moreover, increased miR-146a was sufficient to induce motor neuron loss in vitro, whereas miR-146a inhibition prevented SMA astrocyte-induced motor neuron loss. Together, these data indicate that altered astrocyte production of miR-146a may be a contributing factor in astrocyte-mediated SMA pathology.
Collapse
Affiliation(s)
- Samantha L Sison
- Department of Cell Biology, Neurobiology and Anatomy, Medical College of Wisconsin, Milwaukee, 53226 WI, USA
| | - Teresa N Patitucci
- Department of Cell Biology, Neurobiology and Anatomy, Medical College of Wisconsin, Milwaukee, 53226 WI, USA
| | - Emily R Seminary
- Department of Cell Biology, Neurobiology and Anatomy, Medical College of Wisconsin, Milwaukee, 53226 WI, USA
| | - Eric Villalon
- Department of Veterinary Pathobiology, Bond Life Sciences Center, University of Missouri, Columbia, 65211 MO, USA
| | - Christian L Lorson
- Department of Veterinary Pathobiology, Bond Life Sciences Center, University of Missouri, Columbia, 65211 MO, USA
| | - Allison D Ebert
- Department of Cell Biology, Neurobiology and Anatomy, Medical College of Wisconsin, Milwaukee, 53226 WI, USA
| |
Collapse
|