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Eynard SE, Klopp C, Canale-Tabet K, Marande W, Vandecasteele C, Roques C, Donnadieu C, Boone Q, Servin B, Vignal A. The black honey bee genome: insights on specific structural elements and a first step towards pangenomes. Genet Sel Evol 2024; 56:51. [PMID: 38943059 PMCID: PMC11212449 DOI: 10.1186/s12711-024-00917-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2024] [Accepted: 06/04/2024] [Indexed: 07/01/2024] Open
Abstract
BACKGROUND The honey bee reference genome, HAv3.1, was produced from a commercial line sample that was thought to have a largely dominant Apis mellifera ligustica genetic background. Apis mellifera mellifera, often referred to as the black bee, has a separate evolutionary history and is the original type in western and northern Europe. Growing interest in this subspecies for conservation and non-professional apicultural practices, together with the necessity of deciphering genome backgrounds in hybrids, triggered the necessity for a specific genome assembly. Moreover, having several high-quality genomes is becoming key for taking structural variations into account in pangenome analyses. RESULTS Pacific Bioscience technology long reads were produced from a single haploid black bee drone. Scaffolding contigs into chromosomes was done using a high-density genetic map. This allowed for re-estimation of the recombination rate, which was over-estimated in some previous studies due to mis-assemblies, which resulted in spurious inversions in the older reference genomes. The sequence continuity obtained was very high and the only limit towards continuous chromosome-wide sequences seemed to be due to tandem repeat arrays that were usually longer than 10 kb and that belonged to two main families, the 371 and 91 bp repeats, causing problems in the assembly process due to high internal sequence similarity. Our assembly was used together with the reference genome to genotype two structural variants by a pangenome graph approach with Graphtyper2. Genotypes obtained were either correct or missing, when compared to an approach based on sequencing depth analysis, and genotyping rates were 89 and 76% for the two variants. CONCLUSIONS Our new assembly for the Apis mellifera mellifera honey bee subspecies demonstrates the utility of multiple high-quality genomes for the genotyping of structural variants, with a test case on two insertions and deletions. It will therefore be an invaluable resource for future studies, for instance by including structural variants in GWAS. Having used a single haploid drone for sequencing allowed a refined analysis of very large tandem repeat arrays, raising the question of their function in the genome. High quality genome assemblies for multiple subspecies such as presented here, are crucial for emerging projects using pangenomes.
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Affiliation(s)
- Sonia E Eynard
- GenPhySE, Université de Toulouse, INRAE, INPT, INP-ENVT, Castanet Tolosan, France
| | | | - Kamila Canale-Tabet
- GenPhySE, Université de Toulouse, INRAE, INPT, INP-ENVT, Castanet Tolosan, France
| | | | | | - Céline Roques
- INRAE, US 1426, GeT-PlaGe, Genotoul, Castanet-Tolosan, France
| | | | - Quentin Boone
- GenPhySE, Université de Toulouse, INRAE, INPT, INP-ENVT, Castanet Tolosan, France
- Sigenae, MIAT, INRAE, Castanet Tolosan, France
| | - Bertrand Servin
- GenPhySE, Université de Toulouse, INRAE, INPT, INP-ENVT, Castanet Tolosan, France
| | - Alain Vignal
- GenPhySE, Université de Toulouse, INRAE, INPT, INP-ENVT, Castanet Tolosan, France.
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Xu D, Gareev I, Beylerli O, Pavlov V, Le H, Shi H. Integrative bioinformatics analysis of miRNA and mRNA expression profiles and identification of associated miRNA-mRNA network in intracranial aneurysms. Noncoding RNA Res 2024; 9:471-485. [PMID: 38511055 PMCID: PMC10950608 DOI: 10.1016/j.ncrna.2024.01.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Revised: 01/08/2024] [Accepted: 01/08/2024] [Indexed: 03/22/2024] Open
Abstract
Background Intracranial aneurysms (IAs) represent protrusions in the vascular wall, with their growth and wall thinning influenced by various factors. These processes can culminate in the rupture of the aneurysm, leading to subarachnoid hemorrhage (SAH). Unfortunately, over half of the patients prove unable to withstand SAH, succumbing to adverse outcomes despite intensive therapeutic interventions, even in premier medical facilities. This study seeks to discern the pivotal microRNAs (miRNAs) and genes associated with the formation and progression of IAs. Methods The investigation gathered expression data of miRNAs (from GSE66240) and mRNAs (from GSE158558) within human aneurysm tissue and superficial temporal artery (STA) samples, categorizing them into IA and normal groups. This classification was based on the Gene Expression Omnibus (GEO) database. Results A total of 70 differentially expressed microRNAs (DEMs) and 815 differentially expressed mRNAs (DEGs) were pinpointed concerning IA. Subsequently, a miRNA-mRNA network was constructed, incorporating 9 significantly upregulated DEMs and 211 significantly downregulated DEGs. Simultaneously, functional enrichment and pathway analyses were conducted on both DEMs and DEGs. Through protein-protein interaction (PPI) network analysis and functional enrichment, 9 significantly upregulated DEMs (hsa-miR-188-5p, hsa-miR-590-5p, hsa-miR-320b, hsa-miR-423-5p, hsa-miR-140-5p, hsa-miR-486-5p, hsa-miR-320a, hsa-miR-342-3p, and hsa-miR-532-5p) and 50 key genes (such as ATP6V1G1, KBTBD6, VIM, PA2G4, DYNLL1, METTL21A, MDH2, etc.) were identified, suggesting their potential significant role in IA. Among these genes, ten were notably negatively regulated by at least two key miRNAs. Conclusions The findings of this study provide valuable insights into the potential pathogenic mechanisms underlying IA by elucidating a miRNA-mRNA network. This comprehensive approach sheds light on the intricate interplay between miRNAs and genes, offering a deeper understanding of the molecular dynamics involved in IA development and progression.
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Affiliation(s)
- Dongxiao Xu
- Department of Neurosurgery, The First Affiliated Hospital of Henan University of Science and Technology, Luoyang, China
| | - Ilgiz Gareev
- Central Research Laboratory, Bashkir State Medical University, Ufa, Republic of Bashkortostan, 3 Lenin street, 450008, Russia
| | - Ozal Beylerli
- Central Research Laboratory, Bashkir State Medical University, Ufa, Republic of Bashkortostan, 3 Lenin street, 450008, Russia
| | - Valentin Pavlov
- Department of Urology, Bashkir State Medical University, 3 Lenin Street, 450008, Ufa, Russia
| | - Huang Le
- Department of Neurosurgery, The First Affiliated Hospital of Harbin Medical University, Harbin, 150001, China
| | - Huaizhang Shi
- Department of Neurosurgery, The First Affiliated Hospital of Harbin Medical University, Harbin, 150001, China
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Wang J, Yue XQ, Li YT, Jiang M, Liu JC, Zhao ZG, Niu CY. ANALYSIS AND IDENTIFICATION OF FERROPTOSIS-RELATED GENE SIGNATURE FOR ACUTE LUNG INJURY. Shock 2024; 61:728-739. [PMID: 37878471 DOI: 10.1097/shk.0000000000002247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2023]
Abstract
ABSTRACT Background: Recent studies have shown that ferroptosis is involved in the evolution of acute lung injury (ALI), a serious respiratory pathological process leading to death. However, the regulatory mechanisms underlying ferroptosis in ALI remain largely unknown. The current study analyzed and identified a ferroptosis-related gene signature for ALI. Methods: Key genes associated with ferroptosis in ALI were identified by bioinformatics analysis. GSE104214, GSE18341, and GSE17355 datasets were downloaded from the Gene Expression Omnibus database. The signature genes were screened by least absolute shrinkage and selection operator regression, and the key genes of ALI were screened by weighted correlation network analysis (WGCNA), followed by immune infiltration analysis and functional enrichment analysis. In addition, mRNA expression of key genes in the lungs of mice with hemorrhagic shock (HS) and sepsis was verified. Results: A total of 2,132 differential genes were identified by various analyses, and 9 characteristic genes were detected using Lasso regression. We intersected nine signature genes with WGCNA module genes and finally determined four key genes ( PROK2 , IL6 , TNF , SLC7A11 ). All four key genes were closely correlated with immune cells and regulatory genes of ALI, and the expression of the four genes was significantly different in the lung tissues of HS and sepsis models. Besides, the ferroptosis-related molecules GPX4 and ACSL4 showed remarkable difference in these models. Conclusion: These results indicate that PROK2 , IL6 , TNF , and SLC7A11 may be key regulatory targets of ferroptosis during ALI. This study proved that ferroptosis is a common pathophysiological process in three ALI models.
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Affiliation(s)
- Jing Wang
- Department of Pathophysiology in Basic Medical College, Hebei Medical University, Shijiazhuang, China
| | - Xiao-Qi Yue
- Institute of Microcirculation, Basic Medical College, Hebei North University, Zhangjiakou, China
| | - Yu-Ting Li
- Institute of Microcirculation, Basic Medical College, Hebei North University, Zhangjiakou, China
| | - Miao Jiang
- Department of Pathophysiology in Basic Medical College, Hebei Medical University, Shijiazhuang, China
| | - Jun-Chao Liu
- The First Affiliated Hospital, Hebei North University, Zhangjiakou, China
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Granda-Díaz R, Manterola L, Hermida-Prado F, Rodríguez R, Santos L, García-de-la-Fuente V, Fernández MT, Corte-Torres MD, Rodrigo JP, Álvarez-Teijeiro S, Lawrie CH, Garcia-Pedrero JM. Targeting oncogenic functions of miR-301a in head and neck squamous cell carcinoma by PI3K/PTEN and MEK/ERK pathways. Biomed Pharmacother 2023; 161:114512. [PMID: 36931033 DOI: 10.1016/j.biopha.2023.114512] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 03/07/2023] [Accepted: 03/09/2023] [Indexed: 03/18/2023] Open
Abstract
Treatment of head and neck squamous cell carcinomas (HNSCC), the sixth most frequent cancer worldwide, remains challenging. miRNA dysregulation is closely linked to tumorigenesis and tumor progression, thus emerging as suitable targets for cancer treatment. Transcriptomic analysis of TCGA HNSCC dataset revealed that miR-301a expression levels significantly increased in primary tumors, as compared to patient-matched normal tissue. This prompted us to investigate its pathobiological role and potential as new therapeutic target using different preclinical HNSCC models. miR-301a overexpression in HNSCC-derived cell lines led to enhanced proliferation and invasion, whereas miR-301 inhibition reduced these effects. In vivo validation was performed using an orthotopic mouse model. Results concordantly showed that the mitotic counts, the percentage of infiltration depth and Ki67 proliferative index were significantly augmented in the subgroup of mice harboring miR-301a-overexpressing tumors. Further mechanistic characterization revealed PI3K/PTEN/AKT and MEK/ERK pathways as central signaling nodes responsible for mediating the oncogenic activity of miR-301a observed in HNSCC cells. Notably, pharmacological disruption of PI3K and ERK signals with BYL-719 and PD98059, respectively, was effective to completely revert/abolish miR-301a-promoted tumor cell growth and invasion. Altogether, these findings demonstrate that miR-301a dysregulation plays an oncogenic role in HNSCC, thus emerging as a candidate therapeutic target for this disease. Importantly, available PI3K and ERK inhibitors emerge as promising anti-tumor agents to effectively target miR-301a-mediated signal circuit hampering growth-promoting and pro-invasive functions.
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Affiliation(s)
- Rocío Granda-Díaz
- Instituto Universitario de Oncología del Principado de Asturias (IUOPA), University of Oviedo, Oviedo, Spain; Department of Otolaryngology, Hospital Universitario Central de Asturias and Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), University of Oviedo, Oviedo, Spain; CIBERONC, Instituto de Salud Carlos III, Madrid, Spain
| | - Lorea Manterola
- Molecular Oncology group, Biodonostia Research Institute, San Sebastián, Spain
| | - Francisco Hermida-Prado
- Instituto Universitario de Oncología del Principado de Asturias (IUOPA), University of Oviedo, Oviedo, Spain; Department of Otolaryngology, Hospital Universitario Central de Asturias and Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), University of Oviedo, Oviedo, Spain; CIBERONC, Instituto de Salud Carlos III, Madrid, Spain
| | - René Rodríguez
- CIBERONC, Instituto de Salud Carlos III, Madrid, Spain; Instituto Universitario de Oncología del Principado de Asturias (IUOPA), University of Oviedo, Oviedo, Spain; Sarcomas and Experimental Therapies, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), University of Oviedo, Oviedo, Spain
| | - Laura Santos
- Instituto Universitario de Oncología del Principado de Asturias (IUOPA), University of Oviedo, Oviedo, Spain; Department of Otolaryngology, Hospital Universitario Central de Asturias and Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), University of Oviedo, Oviedo, Spain
| | - Vanessa García-de-la-Fuente
- Instituto Universitario de Oncología del Principado de Asturias (IUOPA), University of Oviedo, Oviedo, Spain; Department of Otolaryngology, Hospital Universitario Central de Asturias and Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), University of Oviedo, Oviedo, Spain
| | - María Teresa Fernández
- Histopathology Unit, Instituto Universitario de Oncología del Principado de Asturias (IUOPA), University of Oviedo, Oviedo, Spain
| | - M Daniela Corte-Torres
- Biobank of Principado de Asturias, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain
| | - Juan P Rodrigo
- Instituto Universitario de Oncología del Principado de Asturias (IUOPA), University of Oviedo, Oviedo, Spain; Department of Otolaryngology, Hospital Universitario Central de Asturias and Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), University of Oviedo, Oviedo, Spain; CIBERONC, Instituto de Salud Carlos III, Madrid, Spain
| | - Saúl Álvarez-Teijeiro
- Instituto Universitario de Oncología del Principado de Asturias (IUOPA), University of Oviedo, Oviedo, Spain; Department of Otolaryngology, Hospital Universitario Central de Asturias and Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), University of Oviedo, Oviedo, Spain; CIBERONC, Instituto de Salud Carlos III, Madrid, Spain.
| | - Charles H Lawrie
- Molecular Oncology group, Biodonostia Research Institute, San Sebastián, Spain; IKERBASQUE, Basque Foundation for Science, Bilbao, Spain; Radcliffe Department of Medicine, University of Oxford, Oxford, United Kingdom; Sino-Swiss Institute of Advanced Technology (SSIAT), Shanghai University, Shanghai, China.
| | - Juana M Garcia-Pedrero
- Instituto Universitario de Oncología del Principado de Asturias (IUOPA), University of Oviedo, Oviedo, Spain; Department of Otolaryngology, Hospital Universitario Central de Asturias and Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), University of Oviedo, Oviedo, Spain; CIBERONC, Instituto de Salud Carlos III, Madrid, Spain.
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Tang Y, Ma D, Liang M, Hou Y, Zhang M, Wang J, Yuan C, Li M, Sun C, Xie J, Wang C, Zhang J. Stress-inducible IL-6 is regulated by KLF7 in brown adipocytes. Heliyon 2023; 9:e14931. [PMID: 37025783 PMCID: PMC10070148 DOI: 10.1016/j.heliyon.2023.e14931] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 03/19/2023] [Accepted: 03/22/2023] [Indexed: 03/30/2023] Open
Abstract
Stress-inducible interleukin 6 (IL-6) is generated in brown adipocytes via beta-3 adrenergic receptor (ADRB3) signaling, which is necessary in stress hyperglycemia, the kind of metabolic adaptation enabling "fight or flight" response by means of liver gluconeogenesis. Nevertheless, the mechanism of ADRB3 signaling mediates IL-6 in brown adipocytes remains unclear. As a result, it is critical to understand how brown adipocytes produce IL-6 via ADRB3 signaling. We found that the ADRB3 agonist and cold stimulation promoted the expression of KLF7 and IL-6 in brown adipocytes of mice. In parallel to these results in vivo, treatment with ADRB3 agonist promoted the expression of KLF7 and the release of IL-6 in primary brown adipocytes of mice. Notably, we discovered that KLF7 positively controls the expression of IL-6 and downregulated KLF7 largely blunted ADRB3 agonist induced IL-6 expressions in brown adipocytes. Our findings suggest that KLF7 is required for the generation of IL-6 when ADRB3 signaling is activated in brown adipocytes.
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Aravindraja C, Vekariya KM, Botello-Escalante R, Rahaman SO, Chan EKL, Kesavalu L. Specific microRNA Signature Kinetics in Porphyromonas gingivalis-Induced Periodontitis. Int J Mol Sci 2023; 24:2327. [PMID: 36768651 PMCID: PMC9916963 DOI: 10.3390/ijms24032327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 01/17/2023] [Accepted: 01/19/2023] [Indexed: 01/26/2023] Open
Abstract
Porphyromonas gingivalis is one of the major bacteria constituting the subgingival pathogenic polymicrobial milieu during periodontitis. Our objective is to determine the global microRNA (miRNA, miR) expression kinetics in 8- and 16-weeks duration of P. gingivalis infection in C57BL/6J mice and to identify the miRNA signatures at specific time-points in mice. We evaluated differential expression (DE) miRNAs in mandibles (n = 10) using high-throughput NanoString nCounter® miRNA expression panels. The bacterial colonization, alveolar bone resorption (ABR), serum immunoglobulin G (IgG) antibodies, and bacterial dissemination were confirmed. In addition, all the infected mice showed bacterial colonization on the gingival surface, significant increases in ABR (p < 0.0001), and specific IgG antibody responses (p < 0.05-0.001). The miRNA profiling showed 26 upregulated miRNAs (e.g., miR-804, miR-690) and 14 downregulated miRNAs (e.g., miR-1902, miR-1937a) during an 8-weeks infection, whereas 7 upregulated miRNAs (e.g., miR-145, miR-195) and one downregulated miR-302b were identified during a 16-weeks infection. Both miR-103 and miR-30d were commonly upregulated at both time-points, and all the DE miRNAs were unique to the specific time-points. However, miR-31, miR-125b, miR-15a, and miR-195 observed in P. gingivalis-infected mouse mandibles were also identified in the gingival tissues of periodontitis patients. None of the previously identified miRNAs reported in in vitro studies using cell lines (periodontal ligament cells, gingival epithelial cells, human leukemia monocytic cell line (THP-1), and B cells) exposed to P. gingivalis lipopolysaccharide were observed in the in vivo study. Most of the pathways (endocytosis, bacterial invasion, and FcR-mediated phagocytosis) targeted by the DE miRNAs were linked with bacterial pathogen recognition and clearance. Further, eighteen miRNAs were closely associated with the bacterial invasion of epithelial cells. This study highlights the altered expression of miRNA in gingiva, and their expression depends on the time-points of infection. This is the first in vivo study that identified specific signature miRNAs (miR-103 and miR-30d) in P. gingivalis invasion of epithelial cells, establishes a link between miRNA and development of periodontitis and helping to better understand the pathobiology of periodontitis.
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Affiliation(s)
- Chairmandurai Aravindraja
- Department of Periodontology, College of Dentistry, University of Florida, Gainesville, FL 32610, USA
| | - Krishna Mukesh Vekariya
- Department of Periodontology, College of Dentistry, University of Florida, Gainesville, FL 32610, USA
| | - Ruben Botello-Escalante
- Department of Periodontology, College of Dentistry, University of Florida, Gainesville, FL 32610, USA
| | - Shaik O. Rahaman
- Department of Nutrition and Food Science, University of Maryland, College Park, MD 20742, USA
| | - Edward K. L. Chan
- Department of Oral Biology, College of Dentistry, University of Florida, Gainesville, FL 32610, USA
| | - Lakshmyya Kesavalu
- Department of Periodontology, College of Dentistry, University of Florida, Gainesville, FL 32610, USA
- Department of Oral Biology, College of Dentistry, University of Florida, Gainesville, FL 32610, USA
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7
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2'-5' oligoadenylate synthetase‑like 1 (OASL1) protects against atherosclerosis by maintaining endothelial nitric oxide synthase mRNA stability. Nat Commun 2022; 13:6647. [PMID: 36333342 PMCID: PMC9636244 DOI: 10.1038/s41467-022-34433-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 10/26/2022] [Indexed: 11/06/2022] Open
Abstract
Endothelial nitric oxide synthase (eNOS) decreases following inflammatory stimulation. As a master regulator of endothelial homeostasis, maintaining optimal eNOS levels is important during cardiovascular events. However, little is known regarding the mechanism of eNOS protection. In this study, we demonstrate a regulatory role for endothelial expression of 2'-5' oligoadenylate synthetase-like 1 (OASL1) in maintaining eNOS mRNA stability during athero-prone conditions and consider its clinical implications. A lack of endothelial Oasl1 accelerated plaque progression, which was preceded by endothelial dysfunction, elevated vascular inflammation, and decreased NO bioavailability following impaired eNOS expression. Mechanistically, knockdown of PI3K/Akt signaling-dependent OASL expression increased Erk1/2 and NF-κB activation and decreased NOS3 (gene name for eNOS) mRNA expression through upregulation of the negative regulatory, miR-584, whereas a miR-584 inhibitor rescued the effects of OASL knockdown. These results suggest that OASL1/OASL regulates endothelial biology by protecting NOS3 mRNA and targeting miR-584 represents a rational therapeutic strategy for eNOS maintenance in vascular disease.
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8
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Liu Z, Ma F, Kang Y, Liu X. Gene ssa-miR-301a-3p improves rainbow trout ( Oncorhynchus mykiss) resistance to heat stress by targeting hsp90b2. PeerJ 2022; 10:e13476. [PMID: 35811807 PMCID: PMC9266697 DOI: 10.7717/peerj.13476] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Accepted: 05/01/2022] [Indexed: 01/17/2023] Open
Abstract
Rainbow trout (Oncorhynchus mykiss) is a cold-water fish that is commonly harmed by high temperatures. MicroRNAs (miRNAs) are being investigated intensively because they act as essential metabolic regulators and have a role in the heat stress response. Although there have been numerous studies on rainbow trout heat stress, research on miRNA implicated in rainbow trout heat stress is quite restricted. Rainbow trout were sampled at 18 and 24 °C, respectively, to examine the mechanism of miRNA under heat stress, and we identified a heat stress-induced miRNA, ssa-miR-301a-3p, for further investigation based on our bioinformatics analysis of rainbow trout small RNA sequencing data. Bioinformatics research suggested that hsp90b2 is a probable target gene for ssa-miR-301a-3p. QRT-PCR was used to confirm the expression levels of ssa-miR-301a-3p and hsp90b2. Meanwhile, the dual-luciferase reporter assay was employed to validate the ssa-miR-301a-3p-hsp90b2 targeted connection. The results indicated that at 24 °C, the relative expression of ssa-miR-301a-3p was considerably lower than at 18 °C. On the other hand, hsp90b2 expression, followed the opposite pattern. The binding of ssa-miR-301a-3p to the 3'-UTR of hsp90b2 resulted in a substantial decrease in luciferase activity. The findings showed that ssa-miR-301a-3p was implicated in heat stress, and our findings provide fresh insights into the processes of miRNA in response to heat stress in rainbow trout.
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Affiliation(s)
- Zhe Liu
- Gansu Agricultural University, Lanzhou, China
| | - Fang Ma
- Tianshui Normal University, Tianshui, China
| | - Yujun Kang
- Gansu Agricultural University, Lanzhou, China
| | - Xiaoxia Liu
- Gansu Agricultural University, Lanzhou, China
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LncRNA HOTAIR sponges miR-301a-3p to promote glioblastoma proliferation and invasion through upregulating FOSL1. Cell Signal 2022; 94:110306. [PMID: 35292358 PMCID: PMC9058208 DOI: 10.1016/j.cellsig.2022.110306] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 03/07/2022] [Accepted: 03/08/2022] [Indexed: 01/29/2023]
Abstract
Glioblastoma, one of the most fatal brain tumors, is associated with a dismal prognosis and an extremely short overall survival. We previously reported that the overexpressed transient receptor potential channel TRPM7 is an essential glioblastoma regulator. Accumulating evidence suggests that long noncoding RNAs (lncRNAs) play an important role in glioma's initiation and progression. However, the function of lncRNA, HOX transcript antisense intergenic RNA (HOTAIR) mediated by TRPM7 in glioma remains unclear. In this study, HOTAIR expression was found to be positively regulated by TRPM7, significantly upregulated in glioma tissues, and is a poor prognosis factor for glioma patients. Moreover, reduced HOTAIR expression impeded the proliferation and invasion of glioma cells. Mechanistically, HOTAIR directly interacted with miR-301a-3p, and downregulation of miR-301a-3p efficiently reversed FOSL1 suppression induced by siRNA HOTAIR, which implied that HOTAIR positively regulated FOSL1 level through sponging miR-301a-3p and played an oncogenic role in glioma progression. In contrast to HOTAIR's role, miR-301a-3p alone served as a tumor suppressor to decrease glioma cell viability and migration/invasion. In agreement with HOTAIR's role, FOSL1 functioned as a tumorigenic gene in glioma pathogenesis, which was highly expressed in glioma tissues, and was shown to be an unfavorable prognostic factor for glioma patients. Mechanically, FOSL1 inhibition by siRNA FOSL1 efficiently rescued the oncogenic-like phenotypes caused by the miR-301a-3p inhibitor in glioma pathogenesis. SIGNIFICANCE: Our study elucidated the role of TRPM7-mediated HOTAIR as a miRNA sponge to target downstream FOSL1 oncogene and therefore consequently contribute to gliomagenesis, which shed new light on TRPM7/lncRNA-directed diagnostic and therapeutic approach in glioma.
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Wang Y, Du J, Liu Y, Yang S, Wang Q. microRNA-301a-3p is a potential biomarker in venous ulcers vein and gets involved in endothelial cell dysfunction. Bioengineered 2022; 13:14138-14158. [PMID: 35734851 PMCID: PMC9342147 DOI: 10.1080/21655979.2022.2083821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 05/23/2022] [Accepted: 05/24/2022] [Indexed: 11/04/2022] Open
Abstract
Venous ulcer is a common contributor to chronic venous insufficiency (CVI) of lower limbs, which seriously affects the life quality of patients. In this study, we researched the expression characteristics of microRNA-301a-3p (miR-301a-3p) in patients with CVI and investigated the impact of miR-301a-3p on the dysfunction of human umbilical vein endothelial cells (HUVECs). The plasma level of miR-301a-3p in normal controls, patients with varicose great saphenous vein, and patients with the venous ulcer of lower limbs were measured. We adopted Interleukin-1β (IL-1β), H2O2, and oxygen and glucose deprivation (OGD) to induce endothelial cell injury in vitro. In this way, we evaluated the influence of miR-301a-3p on HUVEC viability, apoptosis, inflammatory response, and oxidative stress. Our data showed that miR-301a-3p was substantially overexpressed in patients with lower limb venous ulcers. The viability of HUVECs decreased, and miR-301a-3p was up-regulated after IL-1β, H2O2, and OGD treatment. miR-301a-3p inhibition greatly ameliorated the dysfunction and cell damage of HUVECs, promoted IGF1/PI3K/Akt/PPARγ, and down-regulated NF-κB/MMPs. The phosphatidylinositol 3-kinase (PI3K) inhibitor (LY294002) or the peroxisome proliferator-activated receptor-γ (PPARγ) inhibitor (GW9661) reversed the anti-inflammatory, antioxidant, and anti-apoptotic effects mediated by miR-301a-3p down-regulation. The nuclear factor-κB (NF-κB) inhibitor lessened cell injury mediated by miR-301a-3p overexpression. In terms of the mechanism, miR-301a-3p targeted the 3'UTR of Insulin-like growth factor-1 (IGF1) and repressed the profile of IGF1. Thus, miR-301a-3p mediates venous endothelial cell damage by targeting IGF1 and regulating the IGF1/PI3K/Akt/PPARγ/NF-κB/MMPs pathway.
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Affiliation(s)
- Ying Wang
- Department of Vascular Surgery, The Second Affiliated Hospital of Qiqihar Medical College, Qiqihar, Heilongjiang, China
| | - Jingchen Du
- Department of Vascular Surgery, Heilongjiang Provincial Hospital, Harbin, Heilongjiang, China
| | - Yu Liu
- Department of Vascular Surgery, The First Hospital of Qiqihar, Qiqihar, Heilongjiang, China
| | - Shuhui Yang
- Department of Vascular Surgery, Heilongjiang Provincial Hospital, Harbin, Heilongjiang, China
| | - Qingshan Wang
- Department of Vascular Surgery, Heilongjiang Provincial Hospital, Harbin, Heilongjiang, China
- Department of Vascular Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China
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Chen F, Li J, Zheng T, Chen T, Yuan Z. KLF7 Alleviates Atherosclerotic Lesions and Inhibits Glucose Metabolic Reprogramming in Macrophages by Regulating HDAC4/miR-148b-3p/NCOR1. Gerontology 2022; 68:1291-1310. [PMID: 35439761 DOI: 10.1159/000524029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 03/09/2022] [Indexed: 11/19/2022] Open
Abstract
OBJECTIVES Atherosclerosis (AS) remains a major contributor to death worldwide. This study sought to explore the role of Krüppel-like factor 7 (KLF7) in AS lesions via regulating glucose metabolic reprogramming (GMR) in macrophages. METHODS AS mouse and cell models were established via high-fat-diet feeding and oxidized low-density lipoprotein (ox-LDL) induction. KLF7, histone deacetylase 4 (HDAC4), miR-148b-3p, and nuclear receptor corepressor 1 (NCOR1) expressions in aortic tissue and cells were detected via reverse transcription quantitative polymerase chain reaction or Western blotting. Parameters of AS lesions and mouse metabolism were detected via hematoxylin-eosin, oil red O, and Masson staining, assay kits, glucose tolerance test, and enzymatic analysis. Peritoneal macrophages of mice were isolated and cellular metabolism was detected via Seahorse metabolic flux analysis, assay kits, ELISA, and Western blotting. Bindings among KLF7, HDAC4, microRNA (miR)-148b-3p, and NCOR1 were testified via the dual-luciferase assay and chromatin immunoprecipitation assay. RESULTS KLF7 was poorly expressed in AS mice and ox-LDL-induced RAW264.7 cells. KLF7 overexpression attenuated AS lesions and rescued metabolic abnormities in AS mice, and reduced glucose intake and GMR in ox-LDL-induced RAW264.7 cells. Mechanically, KLF7 bound to the HDAC4 promoter to activate HDAC4. HDAC4 reduced H3 and H4 acetylation levels in the miR-148b promoter to inhibit miR-148b-3p and promote NCOR1 transcription. HDAC4 downregulation abolished the protective role of KLF7 overexpression in AS mice and ox-LDL-induced RAW264.7 cells via the miR-148b-3p/NCOR1 axis. CONCLUSION KLF7 bound to the HDAC4 promoter to activate HDAC4, inhibit miR-148b-3p via reducing acetylation level, and promote NCOR1 transcription, thereby limiting GMR in macrophages and alleviating AS lesions.
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Affiliation(s)
- Fangyuan Chen
- Department of Cardiovascular Medicine, First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Juanli Li
- Department of Cardiovascular Medicine, First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Tao Zheng
- Department of Cardiovascular Medicine, First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Tao Chen
- Department of Cardiovascular Medicine, First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Zuyi Yuan
- Department of Cardiovascular Medicine, First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
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Zuo J, Zhang Z, Li M, Yang Y, Zheng B, Wang P, Huang C, Zhou S. The crosstalk between reactive oxygen species and noncoding RNAs: from cancer code to drug role. Mol Cancer 2022; 21:30. [PMID: 35081965 PMCID: PMC8790843 DOI: 10.1186/s12943-021-01488-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 12/26/2021] [Indexed: 02/08/2023] Open
Abstract
Oxidative stress (OS), characterized by the excessive accumulation of reactive oxygen species (ROS), is an emerging hallmark of cancer. Tumorigenesis and development driven by ROS require an aberrant redox homeostasis, that activates onco-signaling and avoids ROS-induced programmed death by orchestrating antioxidant systems. These processes are revealed to closely associate with noncoding RNAs (ncRNAs). On the basis of the available evidence, ncRNAs have been widely identified as multifarious modulators with the involvement of several key redox sensing pathways, such as NF-κB and Nrf2 signaling, therefore potentially becoming effective targets for cancer therapy. Furthermore, the vast majority of ncRNAs with property of easy detected in fluid samples (e.g., blood and urine) facilitate clinicians to monitor redox homeostasis, indicating a novel method for cancer diagnosis. Herein, focusing on carcinoma initiation, metastasis and chemoradiotherapy resistance, we aimed to discuss the ncRNAs-ROS network involved in cancer progression, and the potential clinical application as biomarkers and therapeutic targets.
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Affiliation(s)
- Jing Zuo
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, 610041, People's Republic of China
| | - Zhe Zhang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, 610041, People's Republic of China
| | - Maomao Li
- Department of Obstetrics and Gynecology, Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE and State Key Laboratory of Biotherapy, West China Second University Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, People's Republic of China
| | - Yun Yang
- Department of Obstetrics and Gynecology, Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE and State Key Laboratory of Biotherapy, West China Second University Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, People's Republic of China
| | - Bohao Zheng
- Department of Obstetrics and Gynecology, Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE and State Key Laboratory of Biotherapy, West China Second University Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, People's Republic of China
| | - Ping Wang
- Department of Obstetrics and Gynecology, Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE and State Key Laboratory of Biotherapy, West China Second University Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, People's Republic of China.
| | - Canhua Huang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, 610041, People's Republic of China.
| | - Shengtao Zhou
- Department of Obstetrics and Gynecology, Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE and State Key Laboratory of Biotherapy, West China Second University Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, People's Republic of China.
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Luo S, Wu R, Li Q, Zhang G. MiR-301a-3p Advances IRAK1-Mediated Differentiation of Th17 Cells to Promote the Progression of Systemic Lupus Erythematosus via Targeting PELI1. JOURNAL OF HEALTHCARE ENGINEERING 2021; 2021:2982924. [PMID: 34931135 PMCID: PMC8684520 DOI: 10.1155/2021/2982924] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 11/24/2021] [Accepted: 11/30/2021] [Indexed: 01/11/2023]
Abstract
Systemic lupus erythematosus (SLE) is a common autoimmune disease with high incidence in females. The pathogenesis of SLE is complex, and healing SLE has become a serious challenge for clinical treatment. Aberrant expression of miR-301a-3p involves the progressions of multiple diseases, and some studies have indicated that increased miR-301a-3p could induce the inflammatory injury of some organs. However, the role and molecular mechanism of miR-301a-3p in SLE remain unclear. In this study, the miR-301a-3p levels in peripheral blood mononuclear cells (PBMCs) of the patients with SLE and health subjects were measured with qRT-PCR. The ELISA assay was used to investigate the effect of miR-301a-3p on the levels of inflammatory factors in PBMCs, and flow cytometry assays were used to observe the effect of miR-301a-3p on the levels of CD4+ T cells and Th17 cells in PBMCs. Moreover, TargetScan, dual-luciferase reporter assay, and western blot were used to reveal the downstream targets and regulation mechanism of miR-301a-3p in SLE. The results showed that miR-301a-3p was significantly upregulated in PBMCs of the SLE patients, and increased miR-301a-3p could boost the expression of IL-6, IL-17, and INF-γ in PBMCs and promote the differentiation of Th17 cells. It was found that PELI1 was a target of miR-301a-3p, and PELI1 upregulation could effectively reverse the effect of miR-301a-3p on PBMCs. Besides, this study also found that miR-301a-3p could promote the expression of IRAK1 to involve the progression of SLE via targeting PELI1. In conclusion, this study suggests that increased miR-301a-3p serves as a pathogenic factor in SLE to promote IRAK1-mediated differentiation of Th17 cells via targeting PELI1.
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Affiliation(s)
- Shuaihantian Luo
- Department of Dermatology, The Second Xiangya Hospital of Central South University, Changsha 410011, Hunan Province, China
| | - Ruifang Wu
- Department of Dermatology, The Second Xiangya Hospital of Central South University, Changsha 410011, Hunan Province, China
| | - Qianwen Li
- Department of Dermatology, The Second Xiangya Hospital of Central South University, Changsha 410011, Hunan Province, China
| | - Guiying Zhang
- Department of Dermatology, The Second Xiangya Hospital of Central South University, Changsha 410011, Hunan Province, China
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Zhao B, Pan Y, Qiao L, Liu J, Yang K, Liang Y, Liu W. miR-301a inhibits adipogenic differentiation of adipose-derived stromal vascular fractions by targeting HOXC8 in sheep. Anim Sci J 2021; 92:e13661. [PMID: 34856652 DOI: 10.1111/asj.13661] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 10/09/2021] [Accepted: 10/21/2021] [Indexed: 01/13/2023]
Abstract
MicroRNAs (miRNAs) regulate adipogenic differentiation in stromal vascular fractions (SVFs) through post-transcriptional regulation of transcription factors and other functional genes. miR-301 and the homeobox C8 (HOXC8) gene are involved in lipid homeostasis; however, their roles in the adipogenic differentiation of ovine SVFs are unknown. Here, we explored the effects of miR-301 and HOXC8 on adipogenic differentiation in ovine SVFs and the regulatory role of miR-301a in HOXC8 expression. Additionally, we evaluated the effect of miR-301a and HOXC8 on the mRNA abundance of adipogenic markers and the ability of ovine SVFs to accumulate lipids. We found that miR-301a regulates adipogenic differentiation in ovine SVFs by directly targeting the 3'-untranslated region of HOXC8, resulting in significant downregulation of the HOXC8 mRNA and protein. Moreover, miR-301a overexpression suppressed adipogenic differentiation in ovine SVFs and significantly inhibited the expression of adipogenesis-related genes-including adiponectin, C/EBPα, PPARγ, and FABP4. Conversely, HOXC8 overexpression in ovine SVFs increased the accumulation of lipid droplets and remarkably promoted the expression of adipogenic markers. Taken together, our results indicate that miR-301a attenuates the adipogenic differentiation of ovine SVFs by targeting HOXC8. These findings improve our understanding of the mechanism of lipid accumulation and metabolism in sheep.
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Affiliation(s)
- Bishi Zhao
- College of Animal Science, Shanxi Agricultural University, Taigu, China
| | - Yangyang Pan
- College of Animal Science, Shanxi Agricultural University, Taigu, China
| | - Liying Qiao
- College of Animal Science, Shanxi Agricultural University, Taigu, China
| | - Jianhua Liu
- College of Animal Science, Shanxi Agricultural University, Taigu, China
| | - Kaijie Yang
- College of Animal Science, Shanxi Agricultural University, Taigu, China
| | - Yu Liang
- College of Animal Science, Shanxi Agricultural University, Taigu, China
| | - Wenzhong Liu
- College of Animal Science, Shanxi Agricultural University, Taigu, China
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