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Zhang Y, Gu X, Li Y, Li X, Huang Y, Ju S. Transfer RNA-derived fragment tRF-23-Q99P9P9NDD promotes progression of gastric cancer by targeting ACADSB. J Zhejiang Univ Sci B 2024; 25:438-450. [PMID: 38725342 PMCID: PMC11087185 DOI: 10.1631/jzus.b2300215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 08/07/2023] [Indexed: 05/13/2024]
Abstract
Gastric cancer (GC) is one of the most common gastrointestinal tumors. As a newly discovered type of non-coding RNAs, transfer RNA (tRNA)-derived small RNAs (tsRNAs) play a dual biological role in cancer. Our previous studies have demonstrated the potential of tRF-23-Q99P9P9NDD as a diagnostic and prognostic biomarker for GC. In this work, we confirmed for the first time that tRF-23-Q99P9P9NDD can promote the proliferation, migration, and invasion of GC cells in vitro. The dual luciferase reporter gene assay confirmed that tRF-23-Q99P9P9NDD could bind to the 3' untranslated region (UTR) site of acyl-coenzyme A dehydrogenase short/branched chain (ACADSB). In addition, ACADSB could rescue the effect of tRF-23-Q99P9P9NDD on GC cells. Next, we used Gene Ontology (GO), the Kyoto Encyclopedia of Genes and Genomes (KEGG), and Gene Set Enrichment Analysis (GSEA) to find that downregulated ACADSB in GC may promote lipid accumulation by inhibiting fatty acid catabolism and ferroptosis. Finally, we verified the correlation between ACADSB and 12 ferroptosis genes at the transcriptional level, as well as the changes in reactive oxygen species (ROS) levels by flow cytometry. In summary, this study proposes that tRF-23-Q99P9P9NDD may affect GC lipid metabolism and ferroptosis by targeting ACADSB, thereby promoting GC progression. It provides a theoretical basis for the diagnostic and prognostic monitoring value of GC and opens up new possibilities for treatment.
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Affiliation(s)
- Yu Zhang
- Medical School of Nantong University, Nantong University, Nantong 226001, China
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Nantong 226001, China
- Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Nantong 226001, China
| | - Xinliang Gu
- Medical School of Nantong University, Nantong University, Nantong 226001, China
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Nantong 226001, China
- Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Nantong 226001, China
| | - Yang Li
- Medical School of Nantong University, Nantong University, Nantong 226001, China
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Nantong 226001, China
- Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Nantong 226001, China
| | - Xun Li
- Medical School of Nantong University, Nantong University, Nantong 226001, China
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Nantong 226001, China
- Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Nantong 226001, China
| | - Yuejiao Huang
- Medical School of Nantong University, Nantong University, Nantong 226001, China.
- Department of Medical Oncology, Affiliated Hospital of Nantong University, Nantong 226001, China.
| | - Shaoqing Ju
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Nantong 226001, China. ,
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Blake D, Gazzara MR, Breuer I, Ferretti M, Lynch KW. Alternative 3'UTR expression induced by T cell activation is regulated in a temporal and signal dependent manner. Sci Rep 2024; 14:10987. [PMID: 38745101 DOI: 10.1038/s41598-024-61951-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2023] [Accepted: 05/12/2024] [Indexed: 05/16/2024] Open
Abstract
The length of 3' untranslated regions (3'UTR) is highly regulated during many transitions in cell state, including T cell activation, through the process of alternative polyadenylation (APA). However, the regulatory mechanisms and functional consequences of APA remain largely unexplored. Here we present a detailed analysis of the temporal and condition-specific regulation of APA following activation of primary human CD4+ T cells. We find that global APA changes are regulated temporally and CD28 costimulatory signals enhance a subset of these changes. Most APA changes upon T cell activation involve 3'UTR shortening, although a set of genes enriched for function in the mTOR pathway exhibit 3'UTR lengthening. While upregulation of the core polyadenylation machinery likely induces 3'UTR shortening following prolonged T cell stimulation; a significant program of APA changes occur prior to cellular proliferation or upregulation of the APA machinery. Motif analysis suggests that at least a subset of these early changes in APA are driven by upregulation of RBM3, an RNA-binding protein which competes with the APA machinery for binding. Together this work expands our understanding of the impact and mechanisms of APA in response to T cell activation and suggests new mechanisms by which APA may be regulated.
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Affiliation(s)
- Davia Blake
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Immunology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Matthew R Gazzara
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Genomic and Computational Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Isabel Breuer
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Genetics and Epigenetics Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Max Ferretti
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Kristen W Lynch
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
- Immunology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
- Genomic and Computational Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
- Genetics and Epigenetics Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
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3
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Zhong Y, Cao Y, Geng X, Yang S, Qian T, Liu C, Chen J. The role of microRNA-142a in Toxoplasma gondii infection-induced downregulation of Foxp3: implications for adverse pregnancy outcomes. BMC Infect Dis 2024; 24:490. [PMID: 38741041 DOI: 10.1186/s12879-024-09375-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Accepted: 05/03/2024] [Indexed: 05/16/2024] Open
Abstract
BACKGROUND Toxoplasma gondii (T. gondii) is capable of infecting nearly all warm-blooded animals and approximately 30% of the global population. Though most infections are subclinical in immunocompetent individuals, congenital contraction can lead to severe consequences such as spontaneous abortion, stillbirth, and a range of cranio-cerebral and/or ocular abnormalities. Previous studies reported that T. gondii-infected pregnancy mice unveiled a deficit in both the amount and suppressive functions of regulatory T (Treg) cells, accompanied with reduced levels of forkhead box p3 (Foxp3). Recently, accumulative studies have demonstrated that microRNAs (miRNAs) are, to some extent, relevant to T. gondii infection. However, the link between alterations in miRNAs and downregulation of Foxp3 triggered by T. gondii has been only sporadically studied. METHODS Quantitative reverse transcription polymerase chain reaction (RT-qPCR), protein blotting and immunofluorescence were employed to evaluate the impact of T. gondii infection and antigens on miRNA transcription and Foxp3 expression. Dual-luciferase reporter gene assays were performed to examine the fluorescence activity in EL4 cells, which were transfected with recombinant plasmids containing full-length/truncated/mutant microRNA-142a-3p (miR-142a) promoter sequence or wild type/mutant of Foxp3 3' untranslated region (3' UTR). RESULTS We found a pronounced increase in miR-142a transcription, concurrent with a decrease in Foxp3 expression in T. gondii-infected mouse placental tissue. Similarly, comparable findings have been experimentally confirmed through the treatment of EL4 cells with T. gondii antigens (TgAg) in vitro. Simultaneously, miR-142a mimics attenuated Foxp3 expression, whereas its inhibitors markedly augmented Foxp3 expression. miR-142a promoter activity was elevated upon the stimulation of T. gondii antigens, which mitigated co-transfection of mutant miR-142a promoter lacking P53 target sites. miR-142a mimics deceased the fluorescence activity of Foxp3 3' untranslated region (3' UTR), but it did not affect the fluorescence activity upon the co-transfection of mutant Foxp3 3' UTR lacking miR-142a target site. CONCLUSION In both in vivo and in vitro studies, a negative correlation was discovered between Foxp3 expression and miR-142a transcription. TgAg enhanced miR-142a promoter activity to facilitate miR-142a transcription through a P53-dependent mechanism. Furthermore, miR-142a directly targeted Foxp3 3' UTR, resulting in the downregulation of Foxp3 expression. Therefore, harnessing miR-142a may be a possible therapeutic approach for adverse pregnancy caused by immune imbalances, particularly those induced by T. gondii infection.
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Affiliation(s)
- Yue Zhong
- Department of Pathogen Biology, School of Medicine, Nantong University, 19 Qixiu Road, Nantong, Jiangsu, 226001, People's Republic of China
- ZhenJiang Provincial Blood Center, Zhenjiang, Jiangsu, 212000, People's Republic of China
| | - Yining Cao
- Department of Pathogen Biology, School of Medicine, Nantong University, 19 Qixiu Road, Nantong, Jiangsu, 226001, People's Republic of China
| | - Xiaoyu Geng
- Department of Pathogen Biology, School of Medicine, Nantong University, 19 Qixiu Road, Nantong, Jiangsu, 226001, People's Republic of China
| | - Shujin Yang
- Department of Pathogen Biology, School of Medicine, Nantong University, 19 Qixiu Road, Nantong, Jiangsu, 226001, People's Republic of China
| | - Tianmei Qian
- Engineering Research Center of Integration and Application of Digital Learning Technology, Ministry of Education, Beijing, 100034, People's Republic of China
- NMPA Key Laboratory for Research and Evaluation of Tissue Engineering Technology Products, Nantong University, Nantong, Jiangsu, 226001, People's Republic of China
| | - Chun Liu
- Laboratory Animal Center, Nantong University, 19 Qixiu Road, Nantong, Jiangsu, 226001, People's Republic of China.
| | - Jinling Chen
- Department of Pathogen Biology, School of Medicine, Nantong University, 19 Qixiu Road, Nantong, Jiangsu, 226001, People's Republic of China.
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Lee J, Hong I, Lee C, Kim D, Kim S, Lee Y. SNPs in microRNA seed region and impact of miR-375 in concurrent regulation of multiple lipid accumulation-related genes. Sci Rep 2024; 14:10924. [PMID: 38740866 DOI: 10.1038/s41598-024-61673-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2024] [Accepted: 05/08/2024] [Indexed: 05/16/2024] Open
Abstract
Bovine intramuscular fat (IMF), commonly referred to as marbling, is regulated by lipid metabolism, which includes adipogenesis, lipogenesis, glycerolipid synthesis, and lipolysis. In recent years, breeding researchers have identified single nucleotide polymorphisms (SNPs) as useful marker-assisted selection tools for improving marbling scores in national breeding programs. These included causal SNPs that induce phenotypic variation. MicroRNAs (miRNAs) are small highly conserved non-coding RNA molecules that bind to multiple non-coding regions. They are involved in post-transcriptional regulation. Multiple miRNAs may regulate a given target. Previously, three SNPs in the GPAM 3' UTR and four miRNAs were identified through in silico assays. The aim of this study is to verify the binding ability of the four miRNAs to the SNPs within the 3'UTR of GPAM, and to identify the regulatory function of miR-375 in the expression of genes related to lipid metabolism in mammalian adipocytes. It was verified that the four miRNAs bind to the GPAM 3'UTR, and identified that the miR-375 sequence is highly conserved. Furthermore, it was founded that miR-375 upregulated the GPAM gene, C/EBPα, PPARγ and lipid metabolism-related genes and promoted lipid droplet accumulation in 3T3-L1 cells. In conclusion, these results suggest that miR-375 is a multifunctional regulator of multiple lipid metabolism-related genes and may aid in obesity research as a biomarker.
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Affiliation(s)
- Jiyeon Lee
- School of Biotechnology, Hankyong National University, Anseong, Gyeonggi-do, South Korea
| | - Inpyo Hong
- School of Biotechnology, Hankyong National University, Anseong, Gyeonggi-do, South Korea
| | - Chanwoo Lee
- Nuonbio Inc., 906, A, 302 Galmachi-ro, Jungwon-gu, Seongnam-si, South Korea
| | - Daehyun Kim
- Department of Animal Science, Chonnam National University, Gwangju, South Korea
| | - Sunghak Kim
- Department of Animal Science, Chonnam National University, Gwangju, South Korea.
| | - Yoonseok Lee
- School of Biotechnology, Hankyong National University, Anseong, Gyeonggi-do, South Korea.
- Center for Genetic Information, Hankyong National University, Anseong, Gyeonggi-do, South Korea.
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5
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Zhang X, Kebaara BW. Nonsense-mediated mRNA decay of metal-binding activator MAC1 is dependent on copper levels and 3'-UTR length in Saccharomyces cerevisiae. Curr Genet 2024; 70:5. [PMID: 38709348 DOI: 10.1007/s00294-024-01291-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2023] [Revised: 04/12/2024] [Accepted: 04/22/2024] [Indexed: 05/07/2024]
Abstract
The nonsense-mediated mRNA decay (NMD) pathway was initially identified as a surveillance pathway that degrades mRNAs containing premature termination codons (PTCs). NMD is now also recognized as a post-transcriptional regulatory pathway that regulates the expression of natural mRNAs. Earlier studies demonstrated that regulation of functionally related natural mRNAs by NMD can be differential and condition-specific in Saccharomyces cerevisiae. Here, we investigated the regulation of MAC1 mRNAs by NMD in response to copper as well as the role the MAC1 3'-UTR plays in this regulation. MAC1 is a copper-sensing transcription factor that regulates the high-affinity copper uptake system. MAC1 expression is activated upon copper deprivation. We found that MAC1 mRNAs are regulated by NMD under complete minimal (CM) but escaped NMD under low and high copper conditions. Mac1 protein regulated gene, CTR1 is not regulated by NMD in conditions where MAC1 mRNAs are NMD sensitive. We also found that the MAC1 3'-UTR is the NMD targeting feature on the mRNAs, and that MAC1 mRNAs lacking 3'-UTRs were stabilized during copper deprivation. Our results demonstrate a mechanism of regulation for a metal-sensing transcription factor, at both the post-transcriptional and post-translational levels, where MAC1 mRNA levels are regulated by NMD and copper, while the activity of Mac1p is controlled by copper levels.
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Affiliation(s)
- Xinyi Zhang
- Department of Biology, Baylor University, One Bear Place #97388, Waco, TX, 76798, USA
| | - Bessie W Kebaara
- Department of Biology, Baylor University, One Bear Place #97388, Waco, TX, 76798, USA.
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6
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Guo C, Lv X, Zhang Q, Yi L, Ren Y, Li Z, Yan J, Zheng S, Sun M, Liu S. CRKL but not CRKII contributes to hemin-induced erythroid differentiation of CML. J Cell Mol Med 2024; 28:e18308. [PMID: 38683131 PMCID: PMC11057422 DOI: 10.1111/jcmm.18308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 11/22/2023] [Accepted: 03/26/2024] [Indexed: 05/01/2024] Open
Abstract
Destruction of erythropoiesis process leads to various diseases, including thrombocytopenia, anaemia, and leukaemia. miR-429-CT10 regulation of kinase-like (CRKL) axis involved in development, progression and metastasis of cancers. However, the exact role of miR-429-CRKL axis in leukaemic cell differentiation are still unknown. The current work aimed to uncover the effect of miR-429-CRKL axis on erythropoiesis. In the present study, CRKL upregulation was negatively correlated with miR-429 downregulation in both chronic myeloid leukaemia (CML) patient and CR patient samples. Moreover, CRKL expression level was significantly decreased while miR-429 expression level was increased during the erythroid differentiation of K562 cells following hemin treatment. Functional investigations revealed that overexpression and knockdown of CRKL was remarkably effective in suppressing and promoting hemin-induced erythroid differentiation of K562 cells, whereas, miR-429 exhibited opposite effects to CRKL. Mechanistically, miR-429 regulates erythroid differentiation of K562 cells by downregulating CRKL via selectively targeting CRKL-3'-untranslated region (UTR) through Raf/MEK/ERK pathway. Conversely, CRKII had no effect on erythroid differentiation of K562 cells. Taken together, our data demonstrated that CRKL (but not CRKII) and miR-429 contribute to development, progression and erythropoiesis of CML, miR-429-CRKL axis regulates erythropoiesis of K562 cells via Raf/MEK/ERK pathway, providing novel insights into effective diagnosis and therapy for CML patients.
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MESH Headings
- Humans
- Hemin/pharmacology
- MicroRNAs/genetics
- MicroRNAs/metabolism
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/pathology
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/genetics
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/metabolism
- K562 Cells
- Cell Differentiation/drug effects
- Adaptor Proteins, Signal Transducing/metabolism
- Adaptor Proteins, Signal Transducing/genetics
- Erythroid Cells/metabolism
- Erythroid Cells/drug effects
- Erythroid Cells/pathology
- Erythroid Cells/cytology
- Proto-Oncogene Proteins c-crk/metabolism
- Proto-Oncogene Proteins c-crk/genetics
- Erythropoiesis/genetics
- Erythropoiesis/drug effects
- MAP Kinase Signaling System/drug effects
- 3' Untranslated Regions
- Gene Expression Regulation, Leukemic/drug effects
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Affiliation(s)
- Chunmei Guo
- Department of Biotechnology & Liaoning Key Laboratory of Cancer Stem Cell Research, College of Basic Medical SciencesDalian Medical UniversityDalianLiaoningChina
| | - Xinxin Lv
- Department of Biotechnology & Liaoning Key Laboratory of Cancer Stem Cell Research, College of Basic Medical SciencesDalian Medical UniversityDalianLiaoningChina
| | - Qiuling Zhang
- Department of Biochemistry, College of Basic Medical SciencesDalian Medical UniversityDalianLiaoningChina
| | - Lina Yi
- Department of Biochemistry, College of Basic Medical SciencesDalian Medical UniversityDalianLiaoningChina
| | - Yingying Ren
- Department of Biotechnology & Liaoning Key Laboratory of Cancer Stem Cell Research, College of Basic Medical SciencesDalian Medical UniversityDalianLiaoningChina
| | - Zhaopeng Li
- Department of Biochemistry, College of Basic Medical SciencesDalian Medical UniversityDalianLiaoningChina
| | - Jinsong Yan
- Department of Hematology, The Second Affiliated Hospital of Dalian Medical UniversityInstitute of Stem Cell Transplantation of Dalian Medical UniversityDalianLiaoningChina
| | - Shanliang Zheng
- Department of Biochemistry, College of Basic Medical SciencesDalian Medical UniversityDalianLiaoningChina
| | - Ming‐Zhong Sun
- Department of Biotechnology & Liaoning Key Laboratory of Cancer Stem Cell Research, College of Basic Medical SciencesDalian Medical UniversityDalianLiaoningChina
| | - Shuqing Liu
- Department of Biochemistry, College of Basic Medical SciencesDalian Medical UniversityDalianLiaoningChina
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7
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Ramos-Lorente SE, Berzal-Herranz B, Romero-López C, Berzal-Herranz A. Recruitment of the 40S ribosomal subunit by the West Nile virus 3' UTR promotes the cross-talk between the viral genomic ends for translation regulation. Virus Res 2024; 343:199340. [PMID: 38387694 PMCID: PMC10907855 DOI: 10.1016/j.virusres.2024.199340] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 02/19/2024] [Accepted: 02/20/2024] [Indexed: 02/24/2024]
Abstract
Flaviviral RNA genomes are composed of discrete RNA structural units arranged in an ordered fashion and grouped into complex folded domains that regulate essential viral functions, e.g. replication and translation. This is achieved by adjusting the overall structure of the RNA genome via the establishment of inter- and intramolecular interactions. Translation regulation is likely the main process controlling flaviviral gene expression. Although the genomic 3' UTR is a key player in this regulation, little is known about the molecular mechanisms underlying this role. The present work provides evidence for the specific recruitment of the 40S ribosomal subunit by the 3' UTR of the West Nile virus RNA genome, showing that the joint action of both genomic ends contributes the positioning of the 40S subunit at the 5' end. The combination of structural mapping techniques revealed specific conformational requirements at the 3' UTR for 40S binding, involving the highly conserved SL-III, 5'DB, 3'DB and 3'SL elements, all involved in the translation regulation. These results point to the 40S subunit as a bridge to ensure cross-talk between both genomic ends during viral translation and support a link between 40S recruitment by the 3' UTR and translation control.
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Affiliation(s)
- Sara Esther Ramos-Lorente
- Instituto de Parasitología y Biomedicina "López-Neyra" (IPBLN), CSIC, Av. del Conocimiento 17, 18016 Armilla Granada, Spain
| | - Beatriz Berzal-Herranz
- Instituto de Parasitología y Biomedicina "López-Neyra" (IPBLN), CSIC, Av. del Conocimiento 17, 18016 Armilla Granada, Spain
| | - Cristina Romero-López
- Instituto de Parasitología y Biomedicina "López-Neyra" (IPBLN), CSIC, Av. del Conocimiento 17, 18016 Armilla Granada, Spain.
| | - Alfredo Berzal-Herranz
- Instituto de Parasitología y Biomedicina "López-Neyra" (IPBLN), CSIC, Av. del Conocimiento 17, 18016 Armilla Granada, Spain.
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8
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Wu Q, Gu Z, Shang B, Wan D, Zhang Q, Zhang X, Xie P, Cheng S, Zhang W, Zhang K. Circulating tumor cell clustering modulates RNA splicing and polyadenylation to facilitate metastasis. Cancer Lett 2024; 588:216757. [PMID: 38417668 DOI: 10.1016/j.canlet.2024.216757] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 02/07/2024] [Accepted: 02/20/2024] [Indexed: 03/01/2024]
Abstract
Circulating tumor cell (CTC) clusters exhibit significantly higher metastatic potential compared to single CTCs. However, the underlying mechanism behind this phenomenon remains unclear, and the role of posttranscriptional RNA regulation in CTC clusters has not been explored. Here, we conducted a comparative analysis of alternative splicing (AS) and alternative polyadenylation (APA) profiles between single CTCs and CTC clusters. We identified 994 and 836 AS events in single CTCs and CTC clusters, respectively, with ∼20% of AS events showing differential regulation between the two cell types. A key event in this differential splicing was observed in SRSF6, which disrupted AS profiles and contributed to the increased malignancy of CTC clusters. Regarding APA, we found a global lengthening of 3' UTRs in CTC clusters compared to single CTCs. This alteration was primarily governed by 14 core APA factors, particularly PPP1CA. The modified APA profiles facilitated the cell cycle progression of CTC clusters and indicated their reduced susceptibility to oxidative stress. Further investigation revealed that the proportion of H2AFY mRNA with long 3' UTR instead of short 3' UTR was higher in CTC clusters than single CTCs. The AU-rich elements (AREs) within the long 3' UTR of H2AFY mRNA enhance mRNA stability and translation activity, resulting in promoting cell proliferation and invasion, which potentially facilitate the establishment and rapid formation of metastatic tumors mediated by CTC clusters. These findings provide new insights into the mechanisms driving CTC cluster metastasis.
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Affiliation(s)
- Quanyou Wu
- Division of Abdominal Cancer, Department of Medical Oncology, Cancer Center and Laboratory of Molecular Targeted Therapy in Oncology, West China Hospital, Sichuan University, Chengdu, Sichuan Province, 610041, China; State Key Laboratory of Molecular Oncology, Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Zhaoru Gu
- State Key Laboratory of Molecular Oncology, Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Bingqing Shang
- Department of Urology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Duo Wan
- State Key Laboratory of Molecular Oncology, Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Qi Zhang
- State Key Laboratory of Molecular Oncology, Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Xiaoli Zhang
- State Key Laboratory of Molecular Oncology, Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Peipei Xie
- State Key Laboratory of Molecular Oncology, Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Shujun Cheng
- State Key Laboratory of Molecular Oncology, Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China.
| | - Wen Zhang
- Department of Immunology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China.
| | - Kaitai Zhang
- State Key Laboratory of Molecular Oncology, Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China.
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9
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Lv Y, Wang H, Zheng D, Shi M, Bi D, Hu Q, Zhi H, Lou D, Li J, Wei S, Hu Y. Environmental arsenic pollution induced liver oxidative stress injury by regulating miR-155 through inhibition of AUF1. Sci Total Environ 2024; 922:171237. [PMID: 38423337 DOI: 10.1016/j.scitotenv.2024.171237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Revised: 02/21/2024] [Accepted: 02/22/2024] [Indexed: 03/02/2024]
Abstract
Arsenic (As), a common environmental pollutant, has become a hot topic in recent years due to its potentially harmful effects. Liver damage being a central clinical feature of chronic arsenic poisoning. However, the underlying mechanisms remain unclear. We demonstrated that arsenic can lead to oxidative stress in the liver and result in structural and functional liver damage, significantly correlated with the expression of AUF1, Dicer1, and miR-155 in the liver. Interestingly, knockdown AUF1 promoted the up-regulatory effects of arsenic on Dicer1 and miR-155 and the inhibitory effects on SOD1, which exacerbated oxidative damage in rat liver. However, overexpression of AUF1 reversed the up-regulatory effects of arsenic on Dicer1 and miR-155, restored arsenic-induced SOD1 depletion, and attenuated liver oxidative stress injury. Further, we verified the mechanism and targets of miR-155 in regulating SOD1 by knockdown/overexpression of miR-155 and nonsense mutant SOD1 3'UTR experiments. In conclusion, these results powerfully demonstrate that arsenic inhibits AUF1 protein expression, which in turn reduces the inhibitory effect on Dicer1 expression, which promotes miR-155 to act on the SOD1 3'UTR region after high expression, thus inhibiting SOD1 protein expression and enzyme activity, and inducing liver injury. This finding provides a new perspective for the mechanism research and targeted prevention of arsenic poisoning, as well as scientific evidence for formulating strategies to prevent and control environmental arsenic pollution.
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Affiliation(s)
- Ying Lv
- Key Laboratory of Environmental Pollution Monitoring and Disease Control, Ministry of Education, School of Public Health, Guizhou Medical University, Guiyang 561113, Guizhou, China
| | - Hongling Wang
- Key Laboratory of Environmental Pollution Monitoring and Disease Control, Ministry of Education, School of Public Health, Guizhou Medical University, Guiyang 561113, Guizhou, China
| | - Dan Zheng
- Guiyang Maternity and Child Health Hospital, Guiyang 550003, Guizhou, China
| | - Mingyang Shi
- Key Laboratory of Environmental Pollution Monitoring and Disease Control, Ministry of Education, School of Public Health, Guizhou Medical University, Guiyang 561113, Guizhou, China
| | - Dingnian Bi
- Key Laboratory of Environmental Pollution Monitoring and Disease Control, Ministry of Education, School of Public Health, Guizhou Medical University, Guiyang 561113, Guizhou, China
| | - Qian Hu
- Key Laboratory of Environmental Pollution Monitoring and Disease Control, Ministry of Education, School of Public Health, Guizhou Medical University, Guiyang 561113, Guizhou, China
| | - Haiyan Zhi
- Key Laboratory of Environmental Pollution Monitoring and Disease Control, Ministry of Education, School of Public Health, Guizhou Medical University, Guiyang 561113, Guizhou, China
| | - Didong Lou
- Department of Forensic Medicine, Guizhou University of Traditional Chinese Medicine, Guiyang 550025, Guizhou, China; Key Laboratory of Traditional Chinese Medicine Toxicology in Forensic Medicine, Guizhou Education Department, Guiyang 550025, Guizhou, China
| | - Jun Li
- Key Laboratory of Environmental Pollution Monitoring and Disease Control, Ministry of Education, School of Public Health, Guizhou Medical University, Guiyang 561113, Guizhou, China
| | - Shaofeng Wei
- Key Laboratory of Environmental Pollution Monitoring and Disease Control, Ministry of Education, School of Public Health, Guizhou Medical University, Guiyang 561113, Guizhou, China
| | - Yong Hu
- Key Laboratory of Environmental Pollution Monitoring and Disease Control, Ministry of Education, School of Public Health, Guizhou Medical University, Guiyang 561113, Guizhou, China.
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10
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Keszler G, Vékony B, Elek Z, Nemoda Z, Angyal N, Bánlaki Z, Kovács-Nagy R, Rónai Z, Réthelyi JM. MicroRNA-Mediated Suppression of Glial Cell Line-Derived Neurotrophic Factor Expression Is Modulated by a Schizophrenia-Associated Non-Coding Polymorphism. Int J Mol Sci 2024; 25:4477. [PMID: 38674063 PMCID: PMC11050407 DOI: 10.3390/ijms25084477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Revised: 04/15/2024] [Accepted: 04/17/2024] [Indexed: 04/28/2024] Open
Abstract
Plasma levels of glial cell line-derived neurotrophic factor (GDNF), a pivotal regulator of differentiation and survival of dopaminergic neurons, are reportedly decreased in schizophrenia. To explore the involvement of GDNF in the pathogenesis of the disease, a case-control association analysis was performed between five non-coding single nucleotide polymorphisms (SNP) across the GDNF gene and schizophrenia. Of them, the 'G' allele of the rs11111 SNP located in the 3' untranslated region (3'-UTR) of the gene was found to associate with schizophrenia. In silico analysis revealed that the rs11111 'G' allele might create binding sites for three microRNA (miRNA) species. To explore the significance of this polymorphism, transient co-transfection assays were performed in human embryonic kidney 293T (HEK293T) cells with a luciferase reporter construct harboring either the 'A' or 'G' allele of the 3'-UTR of GDNF in combination with the hsa-miR-1185-1-3p pre-miRNA. It was demonstrated that in the presence of the rs11111 'G' (but not the 'A') allele, hsa-miR-1185-2-3p repressed luciferase activity in a dose-dependent manner. Deletion of the miRNA binding site or its substitution with the complementary sequence abrogated the modulatory effect. Our results imply that the rs11111 'G' allele occurring more frequently in patients with schizophrenia might downregulate GDNF expression in a miRNA-dependent fashion.
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Affiliation(s)
- Gergely Keszler
- Department of Molecular Biology, Institute of Biochemistry and Molecular Biology, Semmelweis University, 1094 Budapest, Hungary; (Z.E.); (Z.N.); (N.A.); (Z.B.); (R.K.-N.); (Z.R.)
| | - Bálint Vékony
- Doctoral School, Semmelweis University, 1085 Budapest, Hungary;
| | - Zsuzsanna Elek
- Department of Molecular Biology, Institute of Biochemistry and Molecular Biology, Semmelweis University, 1094 Budapest, Hungary; (Z.E.); (Z.N.); (N.A.); (Z.B.); (R.K.-N.); (Z.R.)
| | - Zsófia Nemoda
- Department of Molecular Biology, Institute of Biochemistry and Molecular Biology, Semmelweis University, 1094 Budapest, Hungary; (Z.E.); (Z.N.); (N.A.); (Z.B.); (R.K.-N.); (Z.R.)
| | - Nóra Angyal
- Department of Molecular Biology, Institute of Biochemistry and Molecular Biology, Semmelweis University, 1094 Budapest, Hungary; (Z.E.); (Z.N.); (N.A.); (Z.B.); (R.K.-N.); (Z.R.)
| | - Zsófia Bánlaki
- Department of Molecular Biology, Institute of Biochemistry and Molecular Biology, Semmelweis University, 1094 Budapest, Hungary; (Z.E.); (Z.N.); (N.A.); (Z.B.); (R.K.-N.); (Z.R.)
| | - Réka Kovács-Nagy
- Department of Molecular Biology, Institute of Biochemistry and Molecular Biology, Semmelweis University, 1094 Budapest, Hungary; (Z.E.); (Z.N.); (N.A.); (Z.B.); (R.K.-N.); (Z.R.)
| | - Zsolt Rónai
- Department of Molecular Biology, Institute of Biochemistry and Molecular Biology, Semmelweis University, 1094 Budapest, Hungary; (Z.E.); (Z.N.); (N.A.); (Z.B.); (R.K.-N.); (Z.R.)
| | - János M. Réthelyi
- Department of Psychiatry and Psychotherapy, Semmelweis University, 1083 Budapest, Hungary;
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11
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Zhong Y, Qin C, Wang Q, Ding M, Qiu C, Xu Y, Chen J. Inhibition of Foxp3 expression in the placenta of mice infected intraperitoneally by toxoplasma gondii tachyzoites: insights into the PPARγ/miR-7b-5p/Sp1 signaling pathway. Parasit Vectors 2024; 17:189. [PMID: 38632598 PMCID: PMC11025192 DOI: 10.1186/s13071-024-06262-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Accepted: 03/25/2024] [Indexed: 04/19/2024] Open
Abstract
BACKGROUND Toxoplasma gondii, an obligate intracellular parasitic protozoa, infects approximately 30% of the global population. Contracting T. gondii at the primary infection of the mother can result in neonatal microcephaly, chorioretinitis, hydrocephalus, or mortality. Our previous study indicated that pregnant mice infected with T. gondii displayed a decrease in both the number and the suppressive ability of regulatory T cells, accompanied by the reduced Forkhead box P3 (Foxp3). Numerous studies have proved that microRNAs (miRNAs) are implicated in T. gondii infection, but there is meager evidence on the relationship between alterations of miRNAs and downregulation of Foxp3 induced by T. gondii. METHODS Quantitative reverse transcription polymerase chain reaction was utilized to detect the transcriptions of miRNAs and Foxp3. Protein blotting and immunofluorescence were used to detect the expressions of Foxp3 and related transcription factors. The structure of mouse placenta was observed by hematoxylin and eosin (HE) staining. To examine the activity of miR-7b promoter and whether miR-7b-5p targets Sp1 to suppress Foxp3 expression, we constructed recombinant plasmids containing the full-length/truncated/mutant miR-7b promoter sequence or wildtype/mutant of Sp1 3' untranslated region (3' UTR) to detect the fluorescence activity in EL4 cells. RESULTS In T. gondii-infected mice, miR-7b transcription was significantly elevated, while Foxp3 expression was decreased in the placenta. In vitro, miR-7b mimics downregulated Foxp3 expression, whereas its inhibitors significantly upregulated Foxp3 expression. miR-7b promoter activity was elevated upon the stimulation of T. gondii antigens, which was mitigated by co-transfection of mutant miR-7b promoter lacking peroxisome proliferator-activated receptor γ (PPARγ) target sites. Additionally, miR-7b mimics diminished Sp1 expression, while miR-7b inhibitors elevated its expression. miR-7b mimics deceased the fluorescence activity of Sp1 3' untranslated region (3' UTR), but it failed to impact the fluorescence activity upon the co-transfection of mutant Sp1 3' UTR lacking miR-7b target site. CONCLUSIONS T. gondii infection and antigens promote miR-7b transcription but inhibit Foxp3 protein and gene levels. T. gondii antigens promote miR-7b promoter activity by a PPARγ-dependent mechanism. miR-7b directly binds to Sp1 3' UTR to repress Sp1 expression. Understanding the regulatory functions by which T. gondii-induced miR-7b suppresses Foxp3 expression can provide new perspectives for the possible therapeutic avenue of T. gondii-induced adverse pregnancy outcomes.
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Affiliation(s)
- Yue Zhong
- Department of Pathogen Biology, School of Medicine, Nantong University, 19 Qixiu Road, Nantong, 226001, Jiangsu, People's Republic of China
| | - Cheng Qin
- Department of Pathogen Biology, School of Medicine, Nantong University, 19 Qixiu Road, Nantong, 226001, Jiangsu, People's Republic of China
| | - Qing Wang
- Department of Pathogen Biology, School of Medicine, Nantong University, 19 Qixiu Road, Nantong, 226001, Jiangsu, People's Republic of China
| | - Maoyuan Ding
- Department of Pathogen Biology, School of Medicine, Nantong University, 19 Qixiu Road, Nantong, 226001, Jiangsu, People's Republic of China
| | - Chong Qiu
- Department of Pathogen Biology, School of Medicine, Nantong University, 19 Qixiu Road, Nantong, 226001, Jiangsu, People's Republic of China
| | - Yunzhao Xu
- Department of Obstetrics and Gynecology, Affiliated Hospital of Nantong University, Nantong, 226001, Jiangsu, People's Republic of China.
| | - Jinling Chen
- Department of Pathogen Biology, School of Medicine, Nantong University, 19 Qixiu Road, Nantong, 226001, Jiangsu, People's Republic of China.
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12
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Yang J, Zhuang H, Li J, Nunez-Nescolarde AB, Luo N, Chen H, Li A, Qu X, Wang Q, Fan J, Bai X, Ye Z, Gu B, Meng Y, Zhang X, Wu D, Sia Y, Jiang X, Chen W, Combes AN, Nikolic-Paterson DJ, Yu X. The secreted micropeptide C4orf48 enhances renal fibrosis via an RNA-binding mechanism. J Clin Invest 2024; 134:e178392. [PMID: 38625739 DOI: 10.1172/jci178392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Accepted: 03/27/2024] [Indexed: 04/17/2024] Open
Abstract
Renal interstitial fibrosis is an important mechanism in the progression of chronic kidney disease (CKD) to end-stage kidney disease. However, we lack specific treatments to slow or halt renal fibrosis. Ribosome profiling identified upregulation of a secreted micropeptide, C4orf48 (Cf48), in mouse diabetic nephropathy. Cf48 RNA and protein levels were upregulated in tubular epithelial cells in human and experimental CKD. Serum Cf48 levels were increased in human CKD and correlated with loss of kidney function, increasing CKD stage, and the degree of active interstitial fibrosis. Cf48 overexpression in mice accelerated renal fibrosis, while Cf48 gene deletion or knockdown by antisense oligonucleotides significantly reduced renal fibrosis in CKD models. In vitro, recombinant Cf48 (rCf48) enhanced TGF-β1-induced fibrotic responses in renal fibroblasts and epithelial cells independently of Smad3 phosphorylation. Cellular uptake of Cf48 and its profibrotic response in fibroblasts operated via the transferrin receptor. RNA immunoprecipitation-sequencing identified Cf48 binding to mRNA of genes involved in the fibrotic response, including Serpine1, Acta2, Ccn2, and Col4a1. rCf48 binds to the 3'UTR of Serpine1 and increases mRNA half-life. We identify the secreted Cf48 micropeptide as a potential enhancer of renal fibrosis that operates as an RNA-binding peptide to promote the production of extracellular matrix.
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Affiliation(s)
- Jiayi Yang
- Department of Nephrology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- Key Laboratory of Nephrology, National Health Commission and Guangdong Province, Guangzhou, China
| | - Hongjie Zhuang
- Department of Paediatrics, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Jinhua Li
- Department of Nephrology and
- Guangdong-Hong Kong Joint Laboratory on Immunological and Genetic Kidney Diseases, Guangdong Provincial People's Hospital and Guangdong Academy of Medical Sciences, Guangzhou, China
- The Second Clinical College, Guangdong Medical University, Dongguan, Guangdong, China
- Department of Nephrology, Monash Health and Department of Medicine and
| | - Ana B Nunez-Nescolarde
- Department of Anatomy and Developmental Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Ning Luo
- Department of Nephrology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- Key Laboratory of Nephrology, National Health Commission and Guangdong Province, Guangzhou, China
| | - Huiting Chen
- The Second Clinical College, Guangdong Medical University, Dongguan, Guangdong, China
| | - Andy Li
- Department of Nephrology, Monash Health and Department of Medicine and
| | - Xinli Qu
- Department of Anatomy and Developmental Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Qing Wang
- Department of Nephrology and
- Guangdong-Hong Kong Joint Laboratory on Immunological and Genetic Kidney Diseases, Guangdong Provincial People's Hospital and Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Jinjin Fan
- Department of Nephrology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- Key Laboratory of Nephrology, National Health Commission and Guangdong Province, Guangzhou, China
| | - Xiaoyan Bai
- Department of Nephrology and
- Guangdong-Hong Kong Joint Laboratory on Immunological and Genetic Kidney Diseases, Guangdong Provincial People's Hospital and Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Zhiming Ye
- Department of Nephrology and
- Guangdong-Hong Kong Joint Laboratory on Immunological and Genetic Kidney Diseases, Guangdong Provincial People's Hospital and Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Bing Gu
- Department of Clinical Laboratory, Guangdong Provincial People's Hospital and Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Yue Meng
- Department of Clinical Laboratory, Guangdong Provincial People's Hospital and Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Xingyuan Zhang
- Department of Biostatistics, UNC Gillings School of Global Public Health, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Di Wu
- Department of Biostatistics, UNC Gillings School of Global Public Health, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Youyang Sia
- School of Life Science, Tsinghua University, Beijing, China
| | - Xiaoyun Jiang
- Department of Paediatrics, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Wei Chen
- Department of Nephrology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- Key Laboratory of Nephrology, National Health Commission and Guangdong Province, Guangzhou, China
| | - Alexander N Combes
- Department of Anatomy and Developmental Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | | | - Xueqing Yu
- Department of Nephrology and
- Guangdong-Hong Kong Joint Laboratory on Immunological and Genetic Kidney Diseases, Guangdong Provincial People's Hospital and Guangdong Academy of Medical Sciences, Guangzhou, China
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13
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Zhang R, Liu Y, Li W, Wang P, Liu Z, Wen Y, Chu M, Wang L. A mutation in LPAR2 activates the miR-939-5p-LPAR2-PI3K/AKT axis to regulate the proliferation and apoptosis of granulosa cells in sheep. Theriogenology 2024; 219:1-10. [PMID: 38368704 DOI: 10.1016/j.theriogenology.2024.02.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 02/07/2024] [Accepted: 02/07/2024] [Indexed: 02/20/2024]
Abstract
Lysophosphatidic acid receptor-2 (LPAR2) is a G protein-coupled receptor, which is involved in various physiological processes such as cell development, proliferation, and apoptosis, and is thought to play an important role in follicular development and reproduction. There is evidence that miRNA recognition elements (MRE) in the gene 3'UTR often contain single nucleotide polymorphisms (SNPs) that can alter the binding affinity of the target miRNA, leading to dysregulation of gene expression. In this study, we detected a SNP in LPAR2 3 'UTR (rs410670692, c.*701C > T) in 384 small-tailed Han sheep using Sequenom MassARRAY®SNP genotyping. Association analysis showed that the SNP was significantly associated with litter size. Then, the effect of LPAR2 rs410670692 mutation on gene expression in sheep hosts was studied by molecular biotechnology. The results showed that the expression of LPAR2 in the TT genotype was significantly higher than that in the CC genotype, which confirmed the existence of rs410670692, a functional SNP, in LPAR2 3'UTR. We then used bioinformatics methods and double luciferase reporter gene assay to predict and confirm LPAR2 SNP rs410670692 as the direct targeting regulatory element of miR-939-5p. Cell transfection experiments further found that SNP rs410670692 down-regulated the mRNA and protein levels of LPAR2 by influencing the binding of miR-939-5p. To understand the function and mechanism of miR-939-5p in sheep granulosa cells (GCs), we conducted cell proliferation and apoptosis experiments which showed inhibited GCs proliferation along with promoted GCs apoptosis upon overexpression of miR-939-5p. Moreover, overexpression of miR-939-5p promotes apoptosis of granulosa cells by blocking the LPAR2-dependent PI3K/Akt signaling pathway. In conclusion, these results indicate that the SNP rs410670692 of LPAR2 is related to the litter size of small-tailed cold sheep, and miR-939-5p can act as a regulatory element binding to the C mutation of rs410670692 to regulate the expression of LPAR2, affect the development of GCs, and thus indirectly affect the litter size of sheep. These studies provide evidence for the involvement of LPAR2 polymorphism in sheep reproduction and are expected to provide new insights into the molecular genetic mechanisms of litter size traits in sheep.
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Affiliation(s)
- Runan Zhang
- Key Laboratory of Livestock and Poultry Multiomics, Ministry of Agriculture and Rural Affairs, College of Animal and Technology, Sichuan Agricultural University, Chengdu 611130, China; State Key Laboratory of Animal Biotech Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China
| | - Yufang Liu
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China
| | - Wentao Li
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China
| | - Peng Wang
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China
| | - Ziyi Liu
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China
| | - Yuliang Wen
- College of Animal Science and Veterinary Medicine, Henan Institute of Science and Technology, Xinxiang 453003, China
| | - Mingxing Chu
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China.
| | - Linjie Wang
- Key Laboratory of Livestock and Poultry Multiomics, Ministry of Agriculture and Rural Affairs, College of Animal and Technology, Sichuan Agricultural University, Chengdu 611130, China.
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14
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Cox ST, Haver DS, Patterson W, Cambridge CA, Turner TR, Danby RD, Hernandez D. Characterisation of RAET1E/ULBP4 exon 4 and 3' untranslated region genetic architecture reveals further diversity and allelic polymorphism. HLA 2024; 103:e15457. [PMID: 38575368 DOI: 10.1111/tan.15457] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 02/22/2024] [Accepted: 03/18/2024] [Indexed: 04/06/2024]
Abstract
NKG2D is a natural killer cell activating receptor recognising ligands on infected or tumorigenic cells, leading to their cytolysis. There are eight known genes encoding NKG2D ligands: MICA, MICB and ULBP1-6. MICA and MICB are highly polymorphic and well characterised, whilst ULBP ligands are less polymorphic and the functional implication of their diversity is not well understood. Using International HLA and Immunogenetics Workshop (IHIW) cell line DNA, we previously characterised alleles of the RAET1E gene (encoding ULBP4 proteins), including the 5' UTR promoter region and exons 1-3. We found 11 promoter haplotypes associating with alleles based on exons 1-3, revealing 19 alleles overall. The current study extends this analysis using 87 individual DNA samples from IHIW cell lines or cord blood to include RAET1E exon 4 and the 3' UTR, as polymorphism in these regions have not been previously investigated. We found two novel exon 4 polymorphisms encoding amino acid substitutions altering the transmembrane domain. An amino acid substitution at residue 233 was unique to the RAET1E*008 allele whereas the substitution at residue 237 was shared between groups of alleles. Additionally, four haplotypes were found based on 3' UTR sequences, which were unique to certain alleles or shared with allele groups based on exons 1-4 polymorphisms. Furthermore, putative microRNAs were identified that may interact with these polymorphic sites, repressing transcription and potentially affecting expression levels.
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Affiliation(s)
- Steven T Cox
- Anthony Nolan Research Institute, Royal Free Hospital, London, UK
- UCL Cancer Institute, Royal Free Campus, London, UK
| | - Daniel S Haver
- Anthony Nolan Research Institute, Royal Free Hospital, London, UK
| | - Warren Patterson
- Anthony Nolan Research Institute, Royal Free Hospital, London, UK
| | | | - Thomas R Turner
- Anthony Nolan Research Institute, Royal Free Hospital, London, UK
- UCL Cancer Institute, Royal Free Campus, London, UK
| | - Robert D Danby
- Anthony Nolan Research Institute, Royal Free Hospital, London, UK
- UCL Cancer Institute, Royal Free Campus, London, UK
- Churchill Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Diana Hernandez
- Anthony Nolan Research Institute, Royal Free Hospital, London, UK
- UCL Cancer Institute, Royal Free Campus, London, UK
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15
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Hart M, Kern F, Fecher-Trost C, Krammes L, Aparicio E, Engel A, Hirsch P, Wagner V, Keller V, Schmartz GP, Rheinheimer S, Diener C, Fischer U, Mayer J, Meyer MR, Flockerzi V, Keller A, Meese E. Experimental capture of miRNA targetomes: disease-specific 3'UTR library-based miRNA targetomics for Parkinson's disease. Exp Mol Med 2024; 56:935-945. [PMID: 38556547 PMCID: PMC11059366 DOI: 10.1038/s12276-024-01202-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 01/12/2024] [Accepted: 01/30/2024] [Indexed: 04/02/2024] Open
Abstract
The identification of targetomes remains a challenge given the pleiotropic effect of miRNAs, the limited effects of miRNAs on individual targets, and the sheer number of estimated miRNA-target gene interactions (MTIs), which is around 44,571,700. Currently, targetome identification for single miRNAs relies on computational evidence and functional studies covering smaller numbers of targets. To ensure that the targetome analysis could be experimentally verified by functional assays, we employed a systematic approach and explored the targetomes of four miRNAs (miR-129-5p, miR-129-1-3p, miR-133b, and miR-873-5p) by analyzing 410 predicted target genes, both of which were previously associated with Parkinson's disease (PD). After performing 13,536 transfections, we validated 442 of the 705 putative MTIs (62,7%) through dual luciferase reporter assays. These analyses increased the number of validated MTIs by at least 2.1-fold for miR-133b and by a maximum of 24.3-fold for miR-873-5p. Our study contributes to the experimental capture of miRNA targetomes by addressing i) the ratio of experimentally verified MTIs to predicted MTIs, ii) the sizes of disease-related miRNA targetomes, and iii) the density of MTI networks. A web service to support the analyses on the MTI level is available online ( https://ccb-web.cs.uni-saarland.de/utr-seremato ), and all the data have been added to the miRATBase database ( https://ccb-web.cs.uni-saarland.de/miratbase ).
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Affiliation(s)
- Martin Hart
- Human Genetics, Saarland University, 66421, Homburg, Germany.
| | - Fabian Kern
- Clinical Bioinformatics, Saarland University, 66123, Saarbrücken, Germany
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS)-Helmholtz Centre for Infection Research (HZI), Saarland University Campus, Saarbrücken, Germany
| | - Claudia Fecher-Trost
- Department of Experimental and Clinical Pharmacology & Toxicology, Institute of Experimental and Clinical Pharmacology and Toxicology, Center for Molecular Signaling (PZMS), Saarland University, 66421, Homburg, Germany
| | - Lena Krammes
- Human Genetics, Saarland University, 66421, Homburg, Germany
| | - Ernesto Aparicio
- Clinical Bioinformatics, Saarland University, 66123, Saarbrücken, Germany
| | - Annika Engel
- Clinical Bioinformatics, Saarland University, 66123, Saarbrücken, Germany
| | - Pascal Hirsch
- Clinical Bioinformatics, Saarland University, 66123, Saarbrücken, Germany
| | - Viktoria Wagner
- Clinical Bioinformatics, Saarland University, 66123, Saarbrücken, Germany
| | - Verena Keller
- Clinical Bioinformatics, Saarland University, 66123, Saarbrücken, Germany
- Department for Internal Medicine II, Saarland University Hospital, 66421, Homburg, Germany
| | | | | | - Caroline Diener
- Human Genetics, Saarland University, 66421, Homburg, Germany
| | - Ulrike Fischer
- Human Genetics, Saarland University, 66421, Homburg, Germany
| | - Jens Mayer
- Human Genetics, Saarland University, 66421, Homburg, Germany
| | - Markus R Meyer
- Department of Experimental and Clinical Pharmacology & Toxicology, Institute of Experimental and Clinical Pharmacology and Toxicology, Center for Molecular Signaling (PZMS), Saarland University, 66421, Homburg, Germany
| | - Veit Flockerzi
- Department of Experimental and Clinical Pharmacology & Toxicology, Institute of Experimental and Clinical Pharmacology and Toxicology, Center for Molecular Signaling (PZMS), Saarland University, 66421, Homburg, Germany
| | - Andreas Keller
- Clinical Bioinformatics, Saarland University, 66123, Saarbrücken, Germany
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS)-Helmholtz Centre for Infection Research (HZI), Saarland University Campus, Saarbrücken, Germany
| | - Eckart Meese
- Human Genetics, Saarland University, 66421, Homburg, Germany
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16
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Struhl K. How is polyadenylation restricted to 3'-untranslated regions? Yeast 2024; 41:186-191. [PMID: 38041485 PMCID: PMC11001523 DOI: 10.1002/yea.3915] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 10/30/2023] [Accepted: 11/21/2023] [Indexed: 12/03/2023] Open
Abstract
Polyadenylation occurs at numerous sites within 3'-untranslated regions (3'-UTRs) but rarely within coding regions. How does Pol II travel through long coding regions without generating poly(A) sites, yet then permits promiscuous polyadenylation once it reaches the 3'-UTR? The cleavage/polyadenylation (CpA) machinery preferentially associates with 3'-UTRs, but it is unknown how its recruitment is restricted to 3'-UTRs during Pol II elongation. Unlike coding regions, 3'-UTRs have long AT-rich stretches of DNA that may be important for restricting polyadenylation to 3'-UTRs. Recognition of the 3'-UTR could occur at the DNA (AT-rich), RNA (AU-rich), or RNA:DNA hybrid (rU:dA- and/or rA:dT-rich) level. Based on the nucleic acid critical for 3'-UTR recognition, there are three classes of models, not mutually exclusive, for how the CpA machinery is selectively recruited to 3'-UTRs, thereby restricting where polyadenylation occurs: (1) RNA-based models suggest that the CpA complex directly (or indirectly through one or more intermediary proteins) binds long AU-rich stretches that are exposed after Pol II passes through these regions. (2) DNA-based models suggest that the AT-rich sequence affects nucleosome depletion or the elongating Pol II machinery, resulting in dissociation of some elongation factors and subsequent recruitment of the CpA machinery. (3) RNA:DNA hybrid models suggest that preferential destabilization of the Pol II elongation complex at rU:dA- and/or rA:dT-rich duplexes bridging the nucleotide addition and RNA exit sites permits preferential association of the CpA machinery with 3'-UTRs. Experiments to provide evidence for one or more of these models are suggested.
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Affiliation(s)
- Kevin Struhl
- Dept. Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115
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Bolduan V, Palzer KA, Hieber C, Schunke J, Fichter M, Schneider P, Grabbe S, Pautz A, Bros M. The mRNA-Binding Protein KSRP Limits the Inflammatory Response of Macrophages. Int J Mol Sci 2024; 25:3884. [PMID: 38612694 PMCID: PMC11011855 DOI: 10.3390/ijms25073884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Revised: 03/27/2024] [Accepted: 03/29/2024] [Indexed: 04/14/2024] Open
Abstract
KH-type splicing regulatory protein (KSRP) is a single-stranded nucleic acid-binding protein with multiple functions. It is known to bind AU-rich motifs within the 3'-untranslated region of mRNA species, which in many cases encode dynamically regulated proteins like cytokines. In the present study, we investigated the role of KSRP for the immunophenotype of macrophages using bone marrow-derived macrophages (BMDM) from wild-type (WT) and KSRP-/- mice. RNA sequencing revealed that KSRP-/- BMDM displayed significantly higher mRNA expression levels of genes involved in inflammatory and immune responses, particularly type I interferon responses, following LPS stimulation. In line, time kinetics studies revealed increased levels of interferon-γ (IFN-γ), interleukin (IL)-1β and IL-6 mRNA in KSRP-/- macrophages after 6 h subsequent to LPS stimulation as compared to WT cultures. At the protein level, KSRP-/- BMDM displayed higher levels of these cytokines after overnight stimulation. Matching results were observed for primary peritoneal macrophages of KSRP-/- mice. These showed higher IL-6, tumor necrosis factor-α (TNF-α), C-X-C motif chemokine 1 (CXCL1) and CC-chemokine ligand 5 (CCL5) protein levels in response to LPS stimulation than the WT controls. As macrophages play a key role in sepsis, the in vivo relevance of KSRP deficiency for cytokine/chemokine production was analyzed in an acute inflammation model. In agreement with our in vitro findings, KSRP-deficient animals showed higher cytokine production upon LPS administration in comparison to WT mice. Taken together, these findings demonstrate that KSRP constitutes an important negative regulator of cytokine expression in macrophages.
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Affiliation(s)
- Vanessa Bolduan
- Department of Dermatology, University Medical Center, Langenbeckstr. 1, 55131 Mainz, Germany
| | - Kim-Alicia Palzer
- Department of Pharmacology, University Medical Center, Langenbeckstr. 1, 55131 Mainz, Germany (A.P.)
| | - Christoph Hieber
- Department of Dermatology, University Medical Center, Langenbeckstr. 1, 55131 Mainz, Germany
| | - Jenny Schunke
- Department of Dermatology, University Medical Center, Langenbeckstr. 1, 55131 Mainz, Germany
| | - Michael Fichter
- Department of Dermatology, University Medical Center, Langenbeckstr. 1, 55131 Mainz, Germany
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Paul Schneider
- Department of Dermatology, University Medical Center, Langenbeckstr. 1, 55131 Mainz, Germany
| | - Stephan Grabbe
- Department of Dermatology, University Medical Center, Langenbeckstr. 1, 55131 Mainz, Germany
| | - Andrea Pautz
- Department of Pharmacology, University Medical Center, Langenbeckstr. 1, 55131 Mainz, Germany (A.P.)
| | - Matthias Bros
- Department of Dermatology, University Medical Center, Langenbeckstr. 1, 55131 Mainz, Germany
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Seyres D, Gorka O, Schmidt R, Marone R, Zavolan M, Jeker LT. T helper cells exhibit a dynamic and reversible 3'-UTR landscape. RNA 2024; 30:418-434. [PMID: 38302256 PMCID: PMC10946431 DOI: 10.1261/rna.079897.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Accepted: 01/16/2024] [Indexed: 02/03/2024]
Abstract
3' untranslated regions (3' UTRs) are critical elements of messenger RNAs, as they contain binding sites for RNA-binding proteins (RBPs) and microRNAs that affect various aspects of the RNA life cycle including transcript stability and cellular localization. In response to T cell receptor activation, T cells undergo massive expansion during the effector phase of the immune response and dynamically modify their 3' UTRs. Whether this serves to directly regulate the abundance of specific mRNAs or is a secondary effect of proliferation remains unclear. To study 3'-UTR dynamics in T helper cells, we investigated division-dependent alternative polyadenylation (APA). In addition, we generated 3' end UTR sequencing data from naive, activated, memory, and regulatory CD4+ T cells. 3'-UTR length changes were estimated using a nonnegative matrix factorization approach and were compared with those inferred from long-read PacBio sequencing. We found that APA events were transient and reverted after effector phase expansion. Using an orthogonal bulk RNA-seq data set, we did not find evidence of APA association with differential gene expression or transcript usage, indicating that APA has only a marginal effect on transcript abundance. 3'-UTR sequence analysis revealed conserved binding sites for T cell-relevant microRNAs and RBPs in the alternative 3' UTRs. These results indicate that poly(A) site usage could play an important role in the control of cell fate decisions and homeostasis.
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Affiliation(s)
- Denis Seyres
- Department of Biomedicine, Basel University Hospital and University of Basel, CH-4031 Basel, Switzerland
- Transplantation Immunology and Nephrology, Basel University Hospital, CH-4031 Basel, Switzerland
| | - Oliver Gorka
- Department of Biomedicine, Basel University Hospital and University of Basel, CH-4031 Basel, Switzerland
- Transplantation Immunology and Nephrology, Basel University Hospital, CH-4031 Basel, Switzerland
| | - Ralf Schmidt
- Computational and Systems Biology, Biozentrum, University of Basel, 4056 Basel, Switzerland
| | - Romina Marone
- Department of Biomedicine, Basel University Hospital and University of Basel, CH-4031 Basel, Switzerland
- Transplantation Immunology and Nephrology, Basel University Hospital, CH-4031 Basel, Switzerland
| | - Mihaela Zavolan
- Computational and Systems Biology, Biozentrum, University of Basel, 4056 Basel, Switzerland
- Swiss Institute of Bioinformatics, Biozentrum, University of Basel, 4056 Basel, Switzerland
| | - Lukas T Jeker
- Department of Biomedicine, Basel University Hospital and University of Basel, CH-4031 Basel, Switzerland
- Transplantation Immunology and Nephrology, Basel University Hospital, CH-4031 Basel, Switzerland
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De Barros Oliveira R, Anselmi M, Marchette RCN, Roversi K, Fadanni GP, De Carvalho LM, Damasceno S, Heinrich IA, Leal RB, Cavalli J, Moreira-Júnior RE, Godard ALB, Izídio GS. Differential expression of alpha-synuclein in the hippocampus of SHR and SLA16 isogenic rat strains. Behav Brain Res 2024; 461:114835. [PMID: 38151185 DOI: 10.1016/j.bbr.2023.114835] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 12/21/2023] [Accepted: 12/22/2023] [Indexed: 12/29/2023]
Abstract
Two inbred strains, Lewis (LEW) and Spontaneously Hypertensive Rats (SHR), are well-known for their contrasting behavior related to anxiety/emotionality. Studies with these two strains led to the discovery of the Quantitative Trait Loci (QTL) on chromosome 4 (Anxrr16). To better understand the influences of this genomic region, the congenic rat strain SLA16 (SHR.LEW-Anxrr16) was developed. SLA16 rats present higher hyperactivity/impulsivity, deficits in learning and memory, and lower basal blood pressure than the SHR strain, even though genetic differences between them are only in chromosome 4. Thus, the present study proposed the alpha-synuclein and the dopaminergic system as candidates to explain the differential behavior of SHR and SLA16 strains. To accomplish this, beyond the behavioral analysis, we performed (I) the Snca gene expression and (II) quantification of the alpha-synuclein protein in the hippocampus (HPC), prefrontal cortex (PFC), and striatum (STR) of SHR and SLA16 strains; (III) sequencing of the 3'UTR of the Snca gene; and (IV) evaluation of miRNA binding in the 3'UTR site. A Single Nucleotide Polymorphism (SNP) was identified in the 3'UTR of the Snca gene, which exhibited upregulation in the HPC of SHR compared to SLA16 females. Alpha-synuclein protein was higher in the HPC of SHR males compared to SLA16 males. The results of this work suggested that differences in alpha-synuclein HPC content could be influenced by miRNA regulation and associated with behavioral differences between SHR and SLA16 animals.
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Affiliation(s)
- Rachel De Barros Oliveira
- Programa de Pós-Graduação em Biologia Celular e do Desenvolvimento, Universidade Federal de Santa Catarina, Florianópolis, Brazil
| | - Mayara Anselmi
- Programa de Pós-Graduação em Farmacologia, Universidade Federal de Santa Catarina, Florianópolis, Brazil
| | | | - Katiane Roversi
- Programa de Pós-Graduação em Farmacologia, Universidade Federal de Santa Catarina, Florianópolis, Brazil
| | - Guilherme Pasetto Fadanni
- Programa de Pós-Graduação em Farmacologia, Universidade Federal de Santa Catarina, Florianópolis, Brazil
| | - Luana Martins De Carvalho
- Departamento de Genética, Ecologia e Evolução, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Samara Damasceno
- Departamento de Genética, Ecologia e Evolução, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | | | - Rodrigo Bainy Leal
- Programa de Pós-Graduação em Bioquímica, Universidade Federal de Santa Catarina, Florianópolis, Brazil
| | - Juliana Cavalli
- Departamento de Farmacologia, Universidade Federal de Santa Catarina, Curitibanos, Brazil
| | | | - Ana Lúcia Brunialti Godard
- Departamento de Genética, Ecologia e Evolução, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Geison Souza Izídio
- Programa de Pós-Graduação em Biologia Celular e do Desenvolvimento, Universidade Federal de Santa Catarina, Florianópolis, Brazil; Programa de Pós-Graduação em Farmacologia, Universidade Federal de Santa Catarina, Florianópolis, Brazil.
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20
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Wang H, Zhang D, Chen M, Meng X, Bai S, Xin P, Yan J, Chu J, Li J, Yu H. Genome editing of 3' UTR-embedded inhibitory region enables generation of gene knock-up alleles in plants. Plant Commun 2024; 5:100745. [PMID: 37946411 PMCID: PMC10943523 DOI: 10.1016/j.xplc.2023.100745] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Revised: 10/27/2023] [Accepted: 11/07/2023] [Indexed: 11/12/2023]
Affiliation(s)
- Hongwen Wang
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Dahan Zhang
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Mingjiang Chen
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Xiangbing Meng
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Shiwei Bai
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Peiyong Xin
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Jijun Yan
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Jinfang Chu
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jiayang Li
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Yazhouwan National Laboratory, Sanya 572024, China
| | - Hong Yu
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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21
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Ji T, Yan D, Huang Y, Luo M, Zhang Y, Xu T, Gao S, Zhang L, Ruan L, Zhang C. Fibulin 1, targeted by microRNA-24-3p, promotes cell proliferation and migration in vascular smooth muscle cells, contributing to the development of atherosclerosis in APOE -/- mice. Gene 2024; 898:148129. [PMID: 38184021 DOI: 10.1016/j.gene.2024.148129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 12/05/2023] [Accepted: 01/02/2024] [Indexed: 01/08/2024]
Abstract
Extracellular matrix (ECM) and vascular smooth muscle cells (VSMCs) are the main components of atherosclerosis (AS) plaque. VSMCs participate in plaque formation through phenotypic transformation. The complex interplay between ECM and VSMCs plays vital roles in the progression of AS throughout the disease. An in-depth investigation into the functions of ECM-related molecules in VSMC development might contribute to deciphering the complexity of AS pathogenesis. In this study, the roles and molecular mechanisms of the ECM-related molecule Fibulin-1 (FBLN1) in the development of AS and VSMCs were explored using RNA sequencing, bioinformatics analysis, and cell experiments. Furthermore, the expression of FBLN1, as determined by western blot analysis, immunohistochemistry, and real-time quantitative PCR, was significantly increased in AS vascular samples compared to normal vascular samples. Silencing the FBLN1 through AAV viral injection in mice revealed an improvement in AS. Functional analyses revealed that FBLN1 promoted VSMC proliferation, migration, and wound healing. Combined with RNA sequencing and TargetScan7.2 prediction data, 22 microRNAs (miRNAs) were found to have the potential for direct interaction with the FBLN1 3'UTR in VSMCs. Among these 22 miRNAs, it was demonstrated that microRNA-24-3p (miR-24-3p) could negatively regulate FBLN1 expression by directly binding to the FBLN1 3'UTR. Moreover, miR-24-3p inhibited cell proliferation, migration, and wound healing, and suppressed the expression of Ki67, matrix metalloproteinase-2 and -9 (MMP2/9) by targeting FBLN1 in VSMCs. Meanwhile, inhibition of FBLN1 expression could restrain VSMC phenotypic transformation. In conclusion, miR-24-3p inhibited VSMC proliferation and migration by targeting FBLN1. Additionally, multiple miRNAs with the potential to interact with the FBLN1 3'UTR were identified. These findings might deepen our understanding of ECM gene regulatory networks and the complex etiology of AS.
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Affiliation(s)
- Tianyi Ji
- Department of Geriatrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China
| | - Dan Yan
- Department of Geriatrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China
| | - Yi Huang
- Department of Geriatrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China
| | - Mandi Luo
- Department of Geriatrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China
| | - Yucong Zhang
- Department of Geriatrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China
| | - Ting Xu
- Department of Geriatrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China
| | - Shangbang Gao
- Department of Geriatrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China; Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Sciences and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Le Zhang
- Department of Geriatrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China
| | - Lei Ruan
- Department of Geriatrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China.
| | - Cuntai Zhang
- Department of Geriatrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China.
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Li Y, Gong J, Sun Q, Vong EG, Cheng X, Wang B, Yuan Y, Jin L, Gamazon ER, Zhou D, Lai M, Zhang D. Alternative polyadenylation quantitative trait methylation mapping in human cancers provides clues into the molecular mechanisms of APA. Am J Hum Genet 2024; 111:562-583. [PMID: 38367620 PMCID: PMC10940021 DOI: 10.1016/j.ajhg.2024.01.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 01/19/2024] [Accepted: 01/22/2024] [Indexed: 02/19/2024] Open
Abstract
Genetic variants are involved in the orchestration of alternative polyadenylation (APA) events, while the role of DNA methylation in regulating APA remains unclear. We generated a comprehensive atlas of APA quantitative trait methylation sites (apaQTMs) across 21 different types of cancer (1,612 to 60,219 acting in cis and 4,448 to 142,349 in trans). Potential causal apaQTMs in non-cancer samples were also identified. Mechanistically, we observed a strong enrichment of cis-apaQTMs near polyadenylation sites (PASs) and both cis- and trans-apaQTMs in proximity to transcription factor (TF) binding regions. Through the integration of ChIP-signals and RNA-seq data from cell lines, we have identified several regulators of APA events, acting either directly or indirectly, implicating novel functions of some important genes, such as TCF7L2, which is known for its involvement in type 2 diabetes and cancers. Furthermore, we have identified a vast number of QTMs that share the same putative causal CpG sites with five different cancer types, underscoring the roles of QTMs, including apaQTMs, in the process of tumorigenesis. DNA methylation is extensively involved in the regulation of APA events in human cancers. In an attempt to elucidate the potential underlying molecular mechanisms of APA by DNA methylation, our study paves the way for subsequent experimental validations into the intricate biological functions of DNA methylation in APA regulation and the pathogenesis of human cancers. To present a comprehensive catalog of apaQTM patterns, we introduce the Pancan-apaQTM database, available at https://pancan-apaqtm-zju.shinyapps.io/pancanaQTM/.
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Affiliation(s)
- Yige Li
- Department of Pathology, and Department of Medical Oncology of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, China; Department of Pathology, Key Laboratory of Disease Proteomics of Zhejiang Province, School of Medicine, Zhejiang University, Hangzhou, Zhejiang Province, China; Department of Pathology, the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, China
| | - Jingwen Gong
- Department of Pathology, and Department of Medical Oncology of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, China; Department of Pathology, Key Laboratory of Disease Proteomics of Zhejiang Province, School of Medicine, Zhejiang University, Hangzhou, Zhejiang Province, China; Alibaba-Zhejiang University Joint Research Center of Future Digital Healthcare, Hangzhou, Zhejiang Province, China
| | - Qingrong Sun
- Department of Pathology, Key Laboratory of Disease Proteomics of Zhejiang Province, School of Medicine, Zhejiang University, Hangzhou, Zhejiang Province, China; Alibaba-Zhejiang University Joint Research Center of Future Digital Healthcare, Hangzhou, Zhejiang Province, China; Liangzhu Laboratory, Zhejiang University Medical Center, 1369 West Wenyi Road, Hangzhou, Zhejiang Province, China; College of Information Science and Technology, ZheJiang Shuren University, Hangzhou 310015, ZheJiang, China
| | - Eu Gene Vong
- Department of Pathology, Key Laboratory of Disease Proteomics of Zhejiang Province, School of Medicine, Zhejiang University, Hangzhou, Zhejiang Province, China; Department of Biochemistry and Genetics, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, China; The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, China
| | - Xiaoqing Cheng
- Department of Pathology, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang Province, China
| | - Binghong Wang
- Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang Province, China
| | - Ying Yuan
- Department of Medical Oncology, the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, China; Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, Chinese National Ministry of Education), the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, China
| | - Li Jin
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute, Zhangjiang Fudan International Innovation Center, Fudan University, Shanghai, China; Research Unit of Dissecting the Population Genetics and Developing New Technologies for Treatment and Prevention of Skin Phenotypes and Dermatological Diseases (2019RU058), Chinese Academy of Medical Sciences, Shanghai, China
| | - Eric R Gamazon
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA; Data Science Institute, Vanderbilt University Medical Center, Nashville, TN, USA; Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Dan Zhou
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, USA; School of Public Health and the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Maode Lai
- Department of Pathology, Key Laboratory of Disease Proteomics of Zhejiang Province, School of Medicine, Zhejiang University, Hangzhou, Zhejiang Province, China; Alibaba-Zhejiang University Joint Research Center of Future Digital Healthcare, Hangzhou, Zhejiang Province, China; Department of Pathology, Research Unit of Intelligence Classification of Tumor Pathology and Precision Therapy, Chinese Academy of Medical Sciences (2019RU042), Key Laboratory of Disease Proteomics of Zhejiang Province, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, China.
| | - Dandan Zhang
- Department of Pathology, and Department of Medical Oncology of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, China; Department of Pathology, Key Laboratory of Disease Proteomics of Zhejiang Province, School of Medicine, Zhejiang University, Hangzhou, Zhejiang Province, China; Alibaba-Zhejiang University Joint Research Center of Future Digital Healthcare, Hangzhou, Zhejiang Province, China; Department of Pathology, Research Unit of Intelligence Classification of Tumor Pathology and Precision Therapy, Chinese Academy of Medical Sciences (2019RU042), Key Laboratory of Disease Proteomics of Zhejiang Province, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, China.
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Bi X, Ye W, Cheng X, Yang N, Wu X. vizAPA: visualizing dynamics of alternative polyadenylation from bulk and single-cell data. Bioinformatics 2024; 40:btae099. [PMID: 38485700 PMCID: PMC10950478 DOI: 10.1093/bioinformatics/btae099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Revised: 01/11/2024] [Indexed: 03/21/2024] Open
Abstract
MOTIVATION Alternative polyadenylation (APA) is a widespread post-transcriptional regulatory mechanism across all eukaryotes. With the accumulation of genome-wide APA sites, especially those with single-cell resolution, it is imperative to develop easy-to-use visualization tools to guide APA analysis. RESULTS We developed an R package called vizAPA for visualizing APA dynamics from bulk and single-cell data. vizAPA implements unified data structures for APA data and genome annotations. vizAPA also enables identification of genes with differential APA usage across biological samples and/or cell types. vizAPA provides four unique modules for extensively visualizing APA dynamics across biological samples and at the single-cell level. vizAPA could serve as a plugin in many routine APA analysis pipelines to augment studies for APA dynamics. AVAILABILITY AND IMPLEMENTATION https://github.com/BMILAB/vizAPA.
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Affiliation(s)
- Xingyu Bi
- Pasteurien College, Suzhou Medical College of Soochow University, Soochow University, Suzhou 215000, China
| | - Wenbin Ye
- Division of Computational Biomedicine, Department of Biological Chemistry, School of Medicine, University of California, Irvine, CA 92697, United States
| | - Xin Cheng
- Pasteurien College, Suzhou Medical College of Soochow University, Soochow University, Suzhou 215000, China
| | - Ning Yang
- College of Industrial Design, Pukyong National University, Busan 48513, Korea
| | - Xiaohui Wu
- Pasteurien College, Suzhou Medical College of Soochow University, Soochow University, Suzhou 215000, China
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24
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Kouniaki D, Tarassi K, Tsirogianni A. A novel HLA-C*17 variant, HLA-C*17:01:01:29, identified in a healthy individual from Greece. HLA 2024; 103:e15447. [PMID: 38526343 DOI: 10.1111/tan.15447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Accepted: 03/11/2024] [Indexed: 03/26/2024]
Abstract
HLA-C*17:01:01:29 differs from the HLA-C*17:01:01:05 allele by one nucleotide substitution in the 3'UTR.
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Affiliation(s)
- Diamanto Kouniaki
- Immunology and Histocompatibility Department, Evangelismos General Hospital, Athens, Greece
| | - Katerina Tarassi
- Immunology and Histocompatibility Department, Evangelismos General Hospital, Athens, Greece
| | - Alexandra Tsirogianni
- Immunology and Histocompatibility Department, Evangelismos General Hospital, Athens, Greece
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Hu T, Zeng C, Song Z, Liu Q, Chen S, Huang W, Ma Q, Li H. HNRNPA2B1 and HNRNPR stabilize ASCL1 in an m6A-dependent manner to promote neuroblastoma progression. Biochim Biophys Acta Mol Basis Dis 2024; 1870:167050. [PMID: 38331110 DOI: 10.1016/j.bbadis.2024.167050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 01/28/2024] [Accepted: 01/30/2024] [Indexed: 02/10/2024]
Abstract
HNRNPA2B1 and HNRNPR stabilize ASCL1 mRNA in neuroblastoma, but whether their regulatory effects depend on m6A modification and whether their function involves ASCL1 remain unknown. This study investigated the m6A-dependent binding of HNRNPA2B1 and HNRNPR to ASCL1 and subsequent regulation, as well as the expression, clinical significance, and function of HNRNPA2B1 and HNRNPR in neuroblastoma. We revealed that METTL14 mediated ASCL1 m6A modification to stabilize ASCL1. HNRNPA2B1 and HNRNPR significantly enriched ASCL1 mRNA by binding to the 5' and 3' untranslated regions, respectively, and METTL14 knockdown reduced this enrichment. Mutations in m6A sites in the untranslated regions of ASCL1 mRNA considerably decreased probe capacity to engage HNRNPA2B1 and HNRNPR. HNRNPR interacts with IGF2BP1, and knocking down either impaired binding to ASCL1 mRNA. HNRNPA2B1 and HNRNPR knockdown suppressed neuroblastoma cell growth and invasion, while ASCL1 overexpression restored these effects. The high HNRNPA2B1 and HNRNPR expression in neuroblastoma correlated with ASCL1 expression. Thus, HNRNPA2B1 and HNRNPR bind and stabilize ASCL1 mRNA in an m6A-dependent manner to promote neuroblastoma progression. This study not only discovered a new mechanism underlying the high ASCL1 expression in neuroblastoma but also identified the HNRNPA2B1/HNRNPR/ASCL1 axis as a promising target for inhibiting neuroblastoma progression.
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Affiliation(s)
- Ting Hu
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha 410008, China; Institute of Skull Base Surgery and Neurooncology at Hunan Province, Changsha 410008, China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Chong Zeng
- Department of Medicine, The Seventh Affiliated Hospital, Hengyang Medical School, University of South China, Changsha 410119, China
| | - Zhihao Song
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha 410008, China; Institute of Skull Base Surgery and Neurooncology at Hunan Province, Changsha 410008, China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Qing Liu
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha 410008, China; Institute of Skull Base Surgery and Neurooncology at Hunan Province, Changsha 410008, China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Si Chen
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha 410008, China; Department of Ophthalmology, Xiangya Hospital, Central South University, Changsha 410008, China; Hunan Key Laboratory of Ophthalmology, Changsha 410008, China
| | - Wei Huang
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha 410008, China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha 410008, China; Research Center of Carcinogenesis and Targeted Therapy, Xiangya Hospital, Central South University, Changsha 410008, China.
| | - Qianquan Ma
- Department of Neurosurgery, Peking University Third Hospital, Peking University, Beijing 100191, China.
| | - Haoyu Li
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha 410008, China; Institute of Skull Base Surgery and Neurooncology at Hunan Province, Changsha 410008, China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha 410008, China.
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26
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Yuan H, Zou JH, Luo Y, Zhang J, Pan H, Cao S, Chen H, Song Y. Cellular nuclear-localized U2AF2 protein is hijacked by the flavivirus 3'UTR for viral replication complex formation and RNA synthesis. Vet Microbiol 2024; 290:109977. [PMID: 38185072 DOI: 10.1016/j.vetmic.2023.109977] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 12/14/2023] [Accepted: 12/29/2023] [Indexed: 01/09/2024]
Abstract
Japanese encephalitis virus (JEV) is a zoonotic pathogen belonging to the Flavivirus genus, causing viral encephalitis in humans and reproductive failure in swine. The 3' untranslated region (3'UTR) of JEV contains highly conservative secondary structures required for viral translation, RNA synthesis, and pathogenicity. Identification of host factors interacting with JEV 3'UTR is crucial for elucidating the underlying mechanism of flavivirus replication and pathogenesis. In this study, U2 snRNP auxiliary factor 2 (U2AF2) was identified as a novel cellular protein that interacts with the JEV genomic 3'UTR (the SL-I, SL-II, SL-III, and DB region) via its 1 to 148 amino acids. JEV infection or JEV 3' UTR on its own triggered the nuclear-localized U2AF2 redistributed to the cytoplasm and colocalized with viral replication complex. U2AF2 also interacts with JEV NS3 and NS5 protein, the downregulation of U2AF2 nearly abolished the formation of flavivirus replication vesicles. The production of JEV protein, RNA, and viral titers were all increased by U2AF2 overexpression and decreased by knockdown. U2AF2 also functioned as a pro-viral factor for Zika virus (ZIKV) and West Nile virus (WNV), but not for vesicular stomatitis virus (VSV). Mechanically, U2AF2 facilitated the synthesis of both positive- and negative-strand flavivirus RNA without affecting viral attachment, internalization or release process. Collectively, our work paves the way for developing U2AF2 as a potential flavivirus therapeutic target.
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Affiliation(s)
- Honggen Yuan
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China; College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Jia Hui Zou
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China; College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Yun Luo
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China; College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Jinhua Zhang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China; College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Hong Pan
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China; College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Shengbo Cao
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China; College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Huanchun Chen
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China; College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Yunfeng Song
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China; College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China.
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Sun M, Song P, Zhao Y, Li B, Wang P, Cong Z, Hua S. Mechanisms of LPS-induced epithelial mesenchymal transition in bEECs. Theriogenology 2024; 216:30-41. [PMID: 38154204 DOI: 10.1016/j.theriogenology.2023.12.027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 12/17/2023] [Accepted: 12/21/2023] [Indexed: 12/30/2023]
Abstract
High-concentrate diets cause subacute ruminal acidosis, resulting in increased blood lipopolysaccharide (LPS) levels in cows. We found that the peak LPS in cows fed with high-concentrate diets coincides the period of embryo implantation in a large-scale dairy farm. As epithelial-mesenchymal transition (EMT) should be tightly regulated during normal embryo implantation in cows, we speculated that increased LPS may cause abnormal EMT, thereby inhibiting embryo implantation in cows. To confirm that elevated LPS levels induce abnormal EMT in cows, we treated bovine endometrial epithelial cells (bEECs) with LPS for 48 h and analyzed the protein levels of ZEB1, a major EMT-related transcription factor, which is positively regulated by the TGFβ/SMAD3 pathway. In addition, we analyzed the changes in expression of three EMT-related genes (E-cadherin, N-cadherin, and Vimentin), and examined the morphology and migratory ability of the cells. The results showed that elevated LPS levels increased protein expression of ZEB1, vimentin, and N-cadherin, and reduced that of E-cadherin. Elevated LPS also increased bEECs migration rate, and induced the cells to acquire a mesenchymal phenotype. Furthermore, benzyl butyl phthalate (BBP)-induced ZEB1 overexpression significantly decreased E-cadherin levels and increased N-cadherin levels. As LPS treatment also decreased the expression of Bta-miR-200b, we further found that Bta-miR-200b targets to the 3'UTR of ZEB1 through the confirmation of dual-luciferase reporter system. And the increased level of Bta-miR-200b by mimic enhanced the expression of E-cadherin and yet inhibited the expression of N-cadherin in protein, which exactly opposite to the results induced by LPS. In conclusion, LPS induced EMT in bEECs by upregulating ZEB1, while Bta-miR-200b could inhibit the occurrence of EMT by binding ZEB1 3'UTR. These results provide a new insight for low reproductive rate of dairy cows under the background of high-concentrate diets.
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Affiliation(s)
- Mingkun Sun
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, China; Key Laboratory of Animal Biotechnology, Ministry of Agriculture and Rural Affairs, Northwest A&F University, Yangling, Shaanxi, China
| | - Pengjie Song
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, China; Key Laboratory of Animal Biotechnology, Ministry of Agriculture and Rural Affairs, Northwest A&F University, Yangling, Shaanxi, China
| | - Yu Zhao
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, China; Key Laboratory of Animal Biotechnology, Ministry of Agriculture and Rural Affairs, Northwest A&F University, Yangling, Shaanxi, China
| | - Bowen Li
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, China; Key Laboratory of Animal Biotechnology, Ministry of Agriculture and Rural Affairs, Northwest A&F University, Yangling, Shaanxi, China
| | - Ping Wang
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, China; Key Laboratory of Animal Biotechnology, Ministry of Agriculture and Rural Affairs, Northwest A&F University, Yangling, Shaanxi, China
| | - Zhipeng Cong
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, China; Key Laboratory of Animal Biotechnology, Ministry of Agriculture and Rural Affairs, Northwest A&F University, Yangling, Shaanxi, China
| | - Song Hua
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, China; Key Laboratory of Animal Biotechnology, Ministry of Agriculture and Rural Affairs, Northwest A&F University, Yangling, Shaanxi, China.
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Chowdhury IR, Viktorova E, Samal SK, Belov GA. The effect of 5' and 3' non-translated regions on the expression of a transgene from a Newcastle disease virus vector. Virus Res 2024; 341:199309. [PMID: 38181903 PMCID: PMC10818242 DOI: 10.1016/j.virusres.2024.199309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 12/25/2023] [Accepted: 01/03/2024] [Indexed: 01/07/2024]
Abstract
Newcastle disease virus (NDV) is an avian virus and a promising vector for the development of vaccines for veterinary and human use. The optimal vaccine vector performance requires a stable high-level expression of a transgene. The foreign genes are usually incorporated in the genome of NDV as individual transcription units, whose transcription and subsequent translation of the mRNA are regulated by the 5' and 3' untranslated regions (UTRs) flanking the open reading frame of the transgene. Here, we investigated if the UTRs derived from the cognate NDV genes would increase the expression of a model protective antigene from an NDV vector. Our results show that in chicken DF1 cells, none of the UTRs tested significantly outperformed generic short sequences flanking the transgene, while in human HeLa cells, UTRs derived from the M gene of NDV statistically significantly increased the expression of the transgene. The UTRs derived from the HN gene significantly downregulated the transgene expression in both cell cultures. Further experiments demonstrated that NDV UTRs differently affect the mRNA abundance and translation efficacy. While both M and HN UTRs decreased the level of the transgene mRNA in infected cells compared to the mRNA flanked by generic UTRs, M, and particularly, HN UTRs strongly increased the mRNA translation efficacy. The major determinants of translation enhancement are localized in the 5'UTR of HN. Thus, our data reveal a direct role of NDV UTRs in translational regulation, and inform future optimization of NDV vectors for vaccine and therapeutic use.
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Affiliation(s)
- Ishita Roy Chowdhury
- Virginia-Maryland College of Veterinary Medicine and the Department of Veterinary Medicine, University of Maryland, College Park, MD, USA
| | - Ekaterina Viktorova
- Virginia-Maryland College of Veterinary Medicine and the Department of Veterinary Medicine, University of Maryland, College Park, MD, USA
| | - Siba K Samal
- Virginia-Maryland College of Veterinary Medicine and the Department of Veterinary Medicine, University of Maryland, College Park, MD, USA
| | - George A Belov
- Virginia-Maryland College of Veterinary Medicine and the Department of Veterinary Medicine, University of Maryland, College Park, MD, USA.
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29
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Zhang T, Li C, Zhu J, Li Y, Wang Z, Tong CY, Xi Y, Han Y, Koiwa H, Peng X, Zhang X. Structured 3' UTRs destabilize mRNAs in plants. Genome Biol 2024; 25:54. [PMID: 38388963 PMCID: PMC10885604 DOI: 10.1186/s13059-024-03186-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Accepted: 02/14/2024] [Indexed: 02/24/2024] Open
Abstract
BACKGROUND RNA secondary structure (RSS) can influence the regulation of transcription, RNA processing, and protein synthesis, among other processes. 3' untranslated regions (3' UTRs) of mRNA also hold the key for many aspects of gene regulation. However, there are often contradictory results regarding the roles of RSS in 3' UTRs in gene expression in different organisms and/or contexts. RESULTS Here, we incidentally observe that the primary substrate of miR159a (pri-miR159a), when embedded in a 3' UTR, could promote mRNA accumulation. The enhanced expression is attributed to the earlier polyadenylation of the transcript within the hybrid pri-miR159a-3' UTR and, resultantly, a poorly structured 3' UTR. RNA decay assays indicate that poorly structured 3' UTRs could promote mRNA stability, whereas highly structured 3' UTRs destabilize mRNA in vivo. Genome-wide DMS-MaPseq also reveals the prevailing inverse relationship between 3' UTRs' RSS and transcript accumulation in the transcriptomes of Arabidopsis, rice, and even human. Mechanistically, transcripts with highly structured 3' UTRs are preferentially degraded by 3'-5' exoribonuclease SOV and 5'-3' exoribonuclease XRN4, leading to decreased expression in Arabidopsis. Finally, we engineer different structured 3' UTRs to an endogenous FT gene and alter the FT-regulated flowering time in Arabidopsis. CONCLUSIONS We conclude that highly structured 3' UTRs typically cause reduced accumulation of the harbored transcripts in Arabidopsis. This pattern extends to rice and even mammals. Furthermore, our study provides a new strategy of engineering the 3' UTRs' RSS to modify plant traits in agricultural production and mRNA stability in biotechnology.
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Affiliation(s)
- Tianru Zhang
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, 77843, USA
- Molecular and Environmental Plant Sciences, Texas A&M University, College Station, TX, 77843, USA
| | - Changhao Li
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, 77843, USA
| | - Jiaying Zhu
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, 77843, USA.
| | - Yanjun Li
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, 77843, USA
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Plant Virology, Ningbo University, Ningbo, 315211, China
| | - Zhiye Wang
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, 77843, USA
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Chun-Yip Tong
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, 77843, USA
| | - Yu Xi
- Department of Medical Physiology, College of Medicine, Texas A&M University, Bryan, TX, 77807, USA
| | - Yi Han
- National Engineering Laboratory of Crop Stress Resistence Breeding, School of Life Sciences, Anhui Agricultural University, Hefei, 230036, China
| | - Hisashi Koiwa
- Department of Horticultural Sciences, Texas A&M University, College Station, TX, 77843, USA
| | - Xu Peng
- Department of Medical Physiology, College of Medicine, Texas A&M University, Bryan, TX, 77807, USA
| | - Xiuren Zhang
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, 77843, USA.
- Molecular and Environmental Plant Sciences, Texas A&M University, College Station, TX, 77843, USA.
- Department of Biology, Texas A&M University, College Station, TX, 77843, USA.
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Stachowiak M, Nowacka-Woszuk J, Szabelska-Beresewicz A, Zyprych-Walczak J, Krzeminska P, Sosinski O, Nowak T, Switonski M. A massive alteration of gene expression in undescended testicles of dogs and the association of KAT6A variants with cryptorchidism. Proc Natl Acad Sci U S A 2024; 121:e2312724121. [PMID: 38315849 PMCID: PMC10873591 DOI: 10.1073/pnas.2312724121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 12/26/2023] [Indexed: 02/07/2024] Open
Abstract
Cryptorchidism is the most common form of disorder of sex development in male dogs, but its hereditary predisposition is poorly elucidated. The gonadal transcriptome of nine unilaterally cryptorchid dogs and seven control dogs was analyzed using RNA-seq. Comparison between the scrotal and inguinal gonads of unilateral cryptorchid dogs revealed 8,028 differentially expressed genes (DEGs) (3,377 up-regulated and 4,651 down-regulated). A similar number of DEGs (7,619) was found by comparing the undescended testicles with the descended testicles of the control dogs. The methylation status of the selected DEGs was also analyzed, with three out of nine studied DEGs showing altered patterns. Bioinformatic analysis of the cDNA sequences revealed 20,366 SNP variants, six of which showed significant differences in allelic counts between cryptorchid and control dogs. Validation studies in larger cohorts of cryptorchid (n = 122) and control (n = 173) dogs showed that the TT genotype (rs850666472, p.Ala1230Val) and the AA genotype in 3'UTR (16:23716202G>A) in KATA6, responsible for acetylation of lysine 9 in histone H3, are associated with cryptorchidism (P = 0.0383). Both the transcript level of KAT6A and H3K9 acetylation were lower in undescended testes, and additionally, the acetylation depended on the genotypes in exon 17 and the 3'UTR. Our study showed that the massive alteration of the transcriptome in undescended testicles is not caused by germinal DNA variants in DEG regulatory sequences but is partly associated with an aberrant DNA methylation and H3K9 acetylation patterns. Moreover, variants of KAT6A can be considered markers associated with the risk of this disorder.
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Affiliation(s)
- Monika Stachowiak
- Department of Genetics and Animal Breeding, Poznan University of Life Sciences, 60-637Poznan, Poland
| | - Joanna Nowacka-Woszuk
- Department of Genetics and Animal Breeding, Poznan University of Life Sciences, 60-637Poznan, Poland
| | - Alicja Szabelska-Beresewicz
- Department of Mathematical and Statistical Methods, Poznan University of Life Sciences, 60-637Poznan, Poland
| | - Joanna Zyprych-Walczak
- Department of Mathematical and Statistical Methods, Poznan University of Life Sciences, 60-637Poznan, Poland
| | - Paulina Krzeminska
- Department of Genetics and Animal Breeding, Poznan University of Life Sciences, 60-637Poznan, Poland
- Department of Ribonucleoprotein Biochemistry, Institute of Bioorganic Chemistry Polish Academy of Sciences, 61-704Poznan, Poland
| | - Oskar Sosinski
- Department of Genetics and Animal Breeding, Poznan University of Life Sciences, 60-637Poznan, Poland
| | - Tomasz Nowak
- Department of Genetics and Animal Breeding, Poznan University of Life Sciences, 60-637Poznan, Poland
| | - Marek Switonski
- Department of Genetics and Animal Breeding, Poznan University of Life Sciences, 60-637Poznan, Poland
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Xiang Y, Sun M, Wu Y, Hu Y. MiR-205-5p-Mediated MAGI1 Inhibition Attenuates the Injury Induced by Diabetic Nephropathy. Pharmacology 2024; 109:98-109. [PMID: 38325349 DOI: 10.1159/000535670] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 12/04/2023] [Indexed: 02/09/2024]
Abstract
INTRODUCTION Membrane-associated guanylate kinase with an inverted domain structure-1 (MAGI1) is dysregulated in diabetes; however, its role in diabetic nephropathy (DN) remains unclear. In this study, we determined the function and associated mechanisms of MAGI1 in DN. METHODS Serum samples from 28 patients with DN and 28 normal volunteers were collected. High-glucose (HG)-treated human renal mesangial cells (HRMCs) and streptozotocin-treated rats were used as cell and animal models of DN, respectively. MAGI1 mRNA expression was measured by quantitative reverse transcription polymerase chain reaction. An 5-Ethynyl-2'-deoxyuridine assay was used to assess cell proliferation, whereas Western blot analysis was performed to quantitate the levels of markers associated with proliferation, the extracellular matrix (ECM), and inflammation. These included collagens I, collagen IV, cyclin D1, AKT, phosphorylated-AKT (p-AKT), PI3K, and phosphorylated-PI3K (p-PI3K). The predicted binding of miR-205-5p with the MAGI1 3'UTR was verified using a luciferase assay. RESULTS MAGI1 expression was increased in serum samples from DN patients and in HRMCs treated with HG. MAGI1 knockdown attenuated excessive proliferation, ECM accumulation, and inflammation in HG-induced HRMCs as well as injury to DN rats. MiR-205-5p potentially interacted with the 3'UTR of MAGI1 and binding was verified using a dual-luciferase reporter assay. Moreover, miR-205-5p repression offset the inhibitory influence of MAGI1 knockdown on proliferation, collagen deposition, and inflammation in HG-treated HRMCs. CONCLUSION MAGI1 contributes to injury caused by DN. Furthermore, miR-205-5p binds to MAGI1 and suppresses MAGI1 function. These findings suggest that miR-205-5p-mediates MAGI1 inhibition, which represents a potential treatment for DN.
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Affiliation(s)
- Yuanbing Xiang
- Nephropathy Rheumatology Department, Clinical Medical College and Affiliated Hospital of Chengdu University, Chengdu, China
| | - Min Sun
- Nephropathy Rheumatology Department, Clinical Medical College and Affiliated Hospital of Chengdu University, Chengdu, China
| | - Yuxi Wu
- Nephropathy Rheumatology Department, Clinical Medical College and Affiliated Hospital of Chengdu University, Chengdu, China
| | - Yao Hu
- Nephropathy Rheumatology Department, Clinical Medical College and Affiliated Hospital of Chengdu University, Chengdu, China
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Shan W, Wang J, Cheng R, Xuan Y, Yin Z. Erythropoietin alleviates astrocyte pyroptosis by targeting the miR-325-3p/Gsdmd axis in rat spinal cord injury. Inflammopharmacology 2024; 32:523-536. [PMID: 37578618 DOI: 10.1007/s10787-023-01311-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 07/27/2023] [Indexed: 08/15/2023]
Abstract
BACKGROUND Neuroinflammation plays an important role in spinal cord injury (SCI), and an increasing number of studies have focused on the role of astrocytes in neuroinflammation. Pyroptosis is an inflammation-related form of programmed cell death, and neuroinflammation induced by astrocytes in the form of pyroptosis has been widely reported in many central nervous system diseases. Recent studies have found that erythropoietin has significant anti-inflammatory and neuroprotective effects in SCI; however, it has not been reported whether erythropoietin can reduce neuroinflammation by inhibiting neural cell pyroptosis in SCI. METHODS A GEO dataset (GSE153720) was used to analyse the expression of pyroptosis-related genes in sham astrocytes and astrocytes 7 days, 1 month and 3 months after SCI. TargetScan and miRDB databases were used to predict the miRNA that could bind to the 3'UTR of rat Gsdmd. Primary rat spinal astrocytes were used for in vitro experiments, and the modified version of Allen's method was used to establish the rat SCI model. Western blotting, quantitative real-time polymerase chain reaction, flow cytometry, immunofluorescence, lactate dehydrogenase release assay and propidium iodide staining were used to detect the pyroptosis phenotype. A dual luciferase reporter gene assay was used to verify that miR-325-3p can bind to the 3'UTR of Gsdmd. RESULTS We found that pyroptosis-related genes mediated by the canonical NLRP3 inflammasome were highly expressed in astrocytes in an SCI animal model by bioinformatic analysis. We also observed that erythropoietin could reduce astrocyte pyroptosis in vivo and in vitro. In addition, we predicted miRNAs that regulate Gsdmd, the pyroptosis executor, and verified that erythropoietin inhibits astrocyte pyroptosis in SCI through the miR-325-3p/Gsdmd axis. CONCLUSIONS We demonstrated that erythropoietin can inhibit astrocyte pyroptosis through the miR-325-3p/Gsdmd axis. This study is expected to provide a new mechanism for erythropoietin in the treatment of SCI and a more reliable theoretical basis for clinical research.
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Affiliation(s)
- Wenshan Shan
- Department of Orthopaedics, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
| | - Jiawei Wang
- Department of Orthopaedics, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
| | - Rui Cheng
- Department of Orthopaedics, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
| | - Yong Xuan
- Department of Orthopaedics, The Second People's Hospital of Hefei, Hefei, Anhui, China.
- Department of Orthopaedics, Hefei Hospital Affiliated to Anhui Medical University, Hefei, Anhui, China.
| | - Zongsheng Yin
- Department of Orthopaedics, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China.
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Niño Ramírez JE, Gil-Etayo FJ, Jiménez Hernaz I, Arroyo-Sánchez D, Tejeda Velarde A. Next-generation sequencing identifies four novel HLA class I alleles with nucleotide substitutions in the 3' UTR. HLA 2024; 103:e15371. [PMID: 38372571 DOI: 10.1111/tan.15371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Revised: 01/22/2024] [Accepted: 01/23/2024] [Indexed: 02/20/2024]
Abstract
Characterization by next-generation sequencing of four novel HLA alleles: C*17:03:01:07, C*16:01:01:39, B*15:17:01:07, and B*44:03:01:57.
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Affiliation(s)
- Jairo Eduardo Niño Ramírez
- Laboratorio de HLA-Biología Molecular, Servicio de Hematología, Hospital Universitario de Salamanca, Salamanca, Spain
- Instituto de Investigación Biomédica de Salamanca, Salamanca, Spain
- Universidad de Salamanca, Salamanca, Spain
| | - Francisco Javier Gil-Etayo
- Laboratorio de HLA-Biología Molecular, Servicio de Hematología, Hospital Universitario de Salamanca, Salamanca, Spain
- Instituto de Investigación Biomédica de Salamanca, Salamanca, Spain
| | - Isabel Jiménez Hernaz
- Laboratorio de HLA-Biología Molecular, Servicio de Hematología, Hospital Universitario de Salamanca, Salamanca, Spain
| | - Daniel Arroyo-Sánchez
- Laboratorio de HLA-Biología Molecular, Servicio de Hematología, Hospital Universitario de Salamanca, Salamanca, Spain
| | - Amalia Tejeda Velarde
- Laboratorio de HLA-Biología Molecular, Servicio de Hematología, Hospital Universitario de Salamanca, Salamanca, Spain
- Instituto de Investigación Biomédica de Salamanca, Salamanca, Spain
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Sharma A, Bagchi S, Barwad AW, Agarwal SK, Kanga U. One nucleotide substitution in the 3'UTR generated the novel allele HLA-B*40:01:02:47 in a North Indian individual. HLA 2024; 103:e15377. [PMID: 38342777 DOI: 10.1111/tan.15377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2024] [Revised: 01/19/2024] [Accepted: 01/24/2024] [Indexed: 02/13/2024]
Abstract
HLA-B*40:01:02:47 differs from HLA-B*40:01:02:01 by one nucleotide change in the 3'UTR at position 2739 (A>T).
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Affiliation(s)
- Akanksha Sharma
- Department of Transplant Immunology and Immunogenetics, Clinical Immunogenetics Laboratory, Centre for Excellence in Molecular Medicine (ICMR), All India Institute of Medical Sciences, New Delhi, India
| | - Soumita Bagchi
- Department of Nephrology, All India Institute of Medical Sciences, New Delhi, India
| | - Adarsh W Barwad
- Department of Pathology, All India Institute of Medical Sciences, New Delhi, India
| | - Sanjay Kumar Agarwal
- Department of Nephrology, All India Institute of Medical Sciences, New Delhi, India
| | - Uma Kanga
- Department of Transplant Immunology and Immunogenetics, Clinical Immunogenetics Laboratory, Centre for Excellence in Molecular Medicine (ICMR), All India Institute of Medical Sciences, New Delhi, India
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Chhichholiya Y, Singh HV, Vashistha R, Singh S, Munshi A. Deciphering the role of KRAS gene in oncogenesis: Focus on signaling pathways, genetic alterations in 3'UTR, KRAS specific miRNAs and therapeutic interventions. Crit Rev Oncol Hematol 2024; 194:104250. [PMID: 38143047 DOI: 10.1016/j.critrevonc.2023.104250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 12/05/2023] [Accepted: 12/20/2023] [Indexed: 12/26/2023] Open
Abstract
Cancer is a significant cause of death after cardiovascular disease. The genomic, epigenetic and environmental factors have been found to be the risk factor for the disease. The most important genes that develop cancer are oncogenes and tumor suppressor genes. Among oncogenes, KRAS has emerged as a significant player in the development of many cancers. Dysregulation of the RAS signaling pathway either on account of mutation in significant genes involved in the pathway or aberrant expression of different miRNAs targeting these genes including KRAS. The focus is also on the alterations in 3'UTR of the KRAS gene sequence as well as the changes in the miRNA encoding genes especially the one targeting the KRAS gene. Efforts are also being put in to target the dysregulated KRAS gene as a therapeutic approach to treat different cancers. However, there are some challenges like resistance to KRAS inhibitors that need to be addressed.
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Affiliation(s)
- Yogita Chhichholiya
- Department of Human Genetics and Molecular Medicine, Central University of Punjab, Bathinda, Punjab, India
| | - Harsh Vikram Singh
- Department of Human Genetics and Molecular Medicine, Central University of Punjab, Bathinda, Punjab, India
| | | | - Sandeep Singh
- Department of Human Genetics and Molecular Medicine, Central University of Punjab, Bathinda, Punjab, India
| | - Anjana Munshi
- Department of Human Genetics and Molecular Medicine, Central University of Punjab, Bathinda, Punjab, India.
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Xu Z, Zhang S, Zhang Y, Zhou D, Ming R, Song L. [The mechanism of Xuebijing injection in preventing and treating lung injury induced by cardiopulmonary bypass by regulating the apoptosis of alveolar polymorphonuclear neutrophil]. Zhonghua Wei Zhong Bing Ji Jiu Yi Xue 2024; 36:166-171. [PMID: 38442933 DOI: 10.3760/cma.j.cn121430-20230128-00038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 03/07/2024]
Abstract
OBJECTIVE To investigate the protective effect of Xuebijing injection on acute lung injury (ALI) associated with cardiopulmonary bypass (CPB) by regulating the apoptosis of polymorphonuclear neutrophils (PMN). METHODS Thirty male Sprague-Dawley (SD) rats were randomly divided into sham operation group (Sham group), CPB model group (CPB group) and Xuebijing pretreatment group (XBJ group) according to the random number table method, with 10 rats in each group. Rats in the CPB group and XBJ group undergoing CPB procedures for 60 minutes. Rats in the Sham group did not undergo CPB. Rats in the XBJ group received intraperitoneal injection of 4 mL/kg Xuebijing injection 2 hours before CPB. Rats in the Sham group and CPB group were injected with an equal amount of normal saline. 4 hours after CPB, arterial blood was collected for blood gas analysis to calculate respiratory index (RI), and lung tissue of rats was collected for determination of lung index (LI) and pulmonary water containing rate. PMN in bronchoalveolar lavage fluid (BALF) were collected and the activity of caspase-3 was detected. The apoptosis rate was detected by flow cytometry. The expressions of microRNA-142-3p (miR-142-3p) and FoxO1 mRNA were detected by real-time fluorescence quantitative polymerase chain reaction (RT-qPCR). The protein expression of FoxO1 was detected by Western blotting. In addition, HL-60 cells were divided into control oligonucleotide transfection group, miR-142-3p mimics transfection group, and miR-142-3p inhibitor transfection group. After 48 hours of transfection, the activity of miR-142-3p binding to FoxO1 was detected using dual luciferase reporter genes. RESULTS Compared with Sham group, RI, LI and pulmonary water containing rate were significantly increased in CPB group. The caspase-3 activity and apoptosis rate of PMN obtained from BALF were significantly decreased, the expression of miR-142-3p was decreased, and the expression of FoxO1 protein was increased. However, compared with CPB group, RI, LI and pulmonary water containing rate were significantly decreased in XBJ group [RI: 0.281±0.066 vs. 0.379±0.071, LI: 4.50±0.26 vs. 5.71±0.42, pulmonary water containing rate: (80.31±32.50)% vs. (84.59±3.41)%, all P < 0.01]. The caspase-3 activity and apoptosis rate of PMN obtained from BALF were significantly increased [caspase-3 activity: 0.350±0.021 vs. 0.210±0.014, apoptosis rate: (15.490±1.382)% vs. (8.700±0.701)%, both P < 0.01], the expression of miR-142-3p was significantly up-regulated (2-ΔΔCt: 2.61±0.17 vs. 0.62±0.05, P < 0.01), and the protein expression of FoxO1 was decreased [FoxO1/GAPDH (relative expression level): 0.81±0.04 vs. 1.22±0.06, P < 0.01]. However, there was no statistically significant difference in FoxO1 mRNA expression among the three groups. The bioinformatics analysis results showed that miR-142-3p can bind to the FoxO1 3'untranslated region (3'UTR). In HL-60 cells, compared with control oligonucleotide transfection group, the transfection of miR-142-3p mimics could reduce the expression of FoxO1 protein [FoxO1/GAPDH (relative expression level): 0.48±0.06 vs. 1.00±0.05, P < 0.01], however, the transfection of miR-142-3p inhibitor increased the expression of FoxO1 protein [FoxO1/GAPDH (relative expression level): 1.37±0.21 vs. 1.00±0.05, P < 0.05]. But, transfection with miR-142-3p mimics or inhibitor had no effect on FoxO1 mRNA expression. The luciferase reporter gene showed that miR-142-3p could bind to the FoxO1 3'UTR to inhibit FoxO1 expression. CONCLUSIONS Xuebijing injection may promote the apoptosis of pulmonary alveolar PMN through the miR-142-3p/FoxO1 axis, and play a role in the prevention and treatment of CPB-induced ALI.
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Affiliation(s)
- Zhaojun Xu
- Department of Cardiothoracic Surgery, the First Affiliated Hospital, Hunan University of Chinese Medicine, Changsha 410007, Hunan, China
| | - Shengkang Zhang
- Department of Cardiothoracic Surgery, the First Affiliated Hospital, Hunan University of Chinese Medicine, Changsha 410007, Hunan, China
| | - Yi Zhang
- Department of Cardiothoracic Surgery, the First Affiliated Hospital, Hunan University of Chinese Medicine, Changsha 410007, Hunan, China
| | - Daiyong Zhou
- Department of Cardiothoracic Surgery, the First Affiliated Hospital, Hunan University of Chinese Medicine, Changsha 410007, Hunan, China
| | - Runyu Ming
- Department of Cardiothoracic Surgery, the First Affiliated Hospital, Hunan University of Chinese Medicine, Changsha 410007, Hunan, China
| | - Lan Song
- Department of Biochemistry and Molecular Biology, Hunan University of Chinese Medicine, Changsha 410208, Hunan, China. Corresponding author: Song Lan,
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Tanaka-Yano M, Zong L, Park B, Yanai H, Tekin-Turhan F, Blackshear PJ, Beerman I. Tristetraprolin overexpression drives hematopoietic changes in young and middle-aged mice generating dominant mitigating effects on induced inflammation in murine models. GeroScience 2024; 46:1271-1284. [PMID: 37535204 PMCID: PMC10828162 DOI: 10.1007/s11357-023-00879-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 07/17/2023] [Indexed: 08/04/2023] Open
Abstract
Tristetraprolin (TTP), encoded by Zfp36 in mice, is one of the best-characterized tandem zinc-finger mRNA binding proteins involved in mRNA deadenylation and decay. TTPΔARE mice lack an AU-rich motif in the 3'-untranslated regions of TTP mRNA, leading to increased TTP mRNA stability and more TTP protein, resulting in elevated mRNA decay rates of TTP targets. We examined the effect of TTP overexpression on the hematopoietic system in both young and middle-aged mice using TTPΔARE mice and found alterations in blood cell frequencies, with loss of platelets and B220 cells and gains of eosinophils and T cells. TTPΔARE mice also have skewed primitive populations in the bone marrow, with increases in myeloid-biased hematopoietic stem cells (HSCs) but decreases in granulocyte/macrophage-biased multipotent progenitors (MPP3) in both young and middle-aged mice. Changes in the primitive cells' frequencies were associated with transcriptional alterations in the TTP overexpression cells specific to age as well as cell type. Regardless of age, there was a consistent elevation of transcripts regulated by TNFα and TGFβ signaling pathways in both the stem and multipotent progenitor populations. HSCs with TTP overexpression had decreased reconstitution potential in murine transplants but generated hematopoietic environments that mitigated the inflammatory response to the collagen antibody-induced arthritis (CAIA) challenge, which models rheumatoid arthritis and other autoimmune disorders. This dampening of the inflammatory response was even present when there was only a small frequency of TTP overexpressing cells present in the middle-aged mice. We provide an analysis of the early hematopoietic compartments with elevated TTP expression in both young and middle-aged mice which inhibits the reconstitution potential of the HSCs but generates a hematopoietic system that provides dominant repression of induced inflammation.
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Affiliation(s)
- Mayuri Tanaka-Yano
- Epigenetics and Stem Cell Unit, Translational Gerontology Branch, National Institute On Aging, National Institutes of Health, 251 Bayview Boulevard, Baltimore, MD, 21224, USA
| | - Le Zong
- Epigenetics and Stem Cell Unit, Translational Gerontology Branch, National Institute On Aging, National Institutes of Health, 251 Bayview Boulevard, Baltimore, MD, 21224, USA
| | - Bongsoo Park
- Epigenetics and Stem Cell Unit, Translational Gerontology Branch, National Institute On Aging, National Institutes of Health, 251 Bayview Boulevard, Baltimore, MD, 21224, USA
| | - Hagai Yanai
- Epigenetics and Stem Cell Unit, Translational Gerontology Branch, National Institute On Aging, National Institutes of Health, 251 Bayview Boulevard, Baltimore, MD, 21224, USA
| | - Ferda Tekin-Turhan
- Epigenetics and Stem Cell Unit, Translational Gerontology Branch, National Institute On Aging, National Institutes of Health, 251 Bayview Boulevard, Baltimore, MD, 21224, USA
| | - Perry J Blackshear
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, Durham, NC, 27709, USA
| | - Isabel Beerman
- Epigenetics and Stem Cell Unit, Translational Gerontology Branch, National Institute On Aging, National Institutes of Health, 251 Bayview Boulevard, Baltimore, MD, 21224, USA.
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Farhana A, Alsrhani A, Alghsham RS, Derafa W, Khan YS, Rasheed Z. Gold Nanoparticles Downregulate IL-6 Expression/Production by Upregulating microRNA-26a-5p and Deactivating the RelA and NF-κBp50 Transcription Pathways in Activated Breast Cancer Cells. Int J Mol Sci 2024; 25:1404. [PMID: 38338683 PMCID: PMC10855246 DOI: 10.3390/ijms25031404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 12/27/2023] [Accepted: 01/04/2024] [Indexed: 02/12/2024] Open
Abstract
MicroRNAs (miRNAs) are involved in the modulation of pathogenic genes by binding to their mRNA sequences' 3' untranslated regions (3'UTR). Interleukin-6 (IL-6) is known to promote cancer progression and treatment resistance. In this study, we aimed to explore the therapeutic effects of gold nanoparticles (GNP) against IL-6 overexpression and the modulation of miRNA-26a-5p in breast cancer (BC) cells. GNP were synthesized using the trisodium citrate method and characterized through UV-Vis spectroscopy, dynamic light scattering (DLS), and transmission electron microscopy (TEM). To predict the binding of miR-26a-5p in the IL-6 mRNA's 3'UTR, we utilized bioinformatics algorithms. Luciferase reporter clone assays and anti-miRNA-26a-5p transfection were employed to validate the binding of miR26a-5p in the IL-6 mRNA's 3'UTR. The activity of RelA and NF-κBp50 was assessed and confirmed using Bay 11-7082. The synthesized GNP were spherical with a mean size of 28.3 nm, exhibiting high stability, and were suitable for BC cell treatment. We found that miR-26a-5p directly regulated IL-6 overexpression in MCF-7 cells activated with PMA. Treatment of MCF-7 cells with GNP resulted in the inhibition of IL-6 overexpression and secretion through the increase of miR26a-5p. Furthermore, GNP deactivated NF-κBp65/NF-κBp50 transcription activity. The newly engineered GNP demonstrated safety and showed promise as a therapeutic approach for reducing IL-6 overexpression. The GNP suppressed IL-6 overexpression and secretion by deactivating NF-κBp65/NF-κBp50 transcription activity and upregulating miR-26a-5p expression in activated BC cells. These findings suggest that GNP have potential as a therapeutic intervention for BC by targeting IL-6 expression and associated pathways.
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Affiliation(s)
- Aisha Farhana
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Jouf University, Sakaka 72388, Saudi Arabia;
| | - Abdullah Alsrhani
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Jouf University, Sakaka 72388, Saudi Arabia;
| | - Ruqaih S. Alghsham
- Department of Pathology, College of Medicine, Qassim University, Buraidah 51452, Saudi Arabia; (R.S.A.); (Z.R.)
| | - Wassila Derafa
- Department of Chemistry, College of Science, Jouf University, Aljouf 72388, Saudi Arabia;
| | - Yusuf Saleem Khan
- Department of Anatomy, College of Medicine, Jouf University, Sakaka 72388, Saudi Arabia;
| | - Zafar Rasheed
- Department of Pathology, College of Medicine, Qassim University, Buraidah 51452, Saudi Arabia; (R.S.A.); (Z.R.)
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Niederau PA, Eglé P, Willig S, Parsons J, Hoernstein SNW, Decker EL, Reski R. Multifactorial analysis of terminator performance on heterologous gene expression in Physcomitrella. Plant Cell Rep 2024; 43:43. [PMID: 38246952 PMCID: PMC10800305 DOI: 10.1007/s00299-023-03088-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 11/02/2023] [Indexed: 01/23/2024]
Abstract
KEY MESSAGE Characterization of Physcomitrella 3'UTRs across different promoters yields endogenous single and double terminators for usage in molecular pharming. The production of recombinant proteins for health applications accounts for a large share of the biopharmaceutical market. While many drugs are produced in microbial and mammalian systems, plants gain more attention as expression hosts to produce eukaryotic proteins. In particular, the good manufacturing practice (GMP)-compliant moss Physcomitrella (Physcomitrium patens) has outstanding features, such as excellent genetic amenability, reproducible bioreactor cultivation, and humanized protein glycosylation patterns. In this study, we selected and characterized novel terminators for their effects on heterologous gene expression. The Physcomitrella genome contains 53,346 unique 3'UTRs (untranslated regions) of which 7964 transcripts contain at least one intron. Over 91% of 3'UTRs exhibit more than one polyadenylation site, indicating the prevalence of alternative polyadenylation in Physcomitrella. Out of all 3'UTRs, 14 terminator candidates were selected and characterized via transient Dual-Luciferase assays, yielding a collection of endogenous terminators performing equally high as established heterologous terminators CaMV35S, AtHSP90, and NOS. High performing candidates were selected for testing as double terminators which impact reporter levels, dependent on terminator identity and positioning. Testing of 3'UTRs among the different promoters NOS, CaMV35S, and PpActin5 showed an increase of more than 1000-fold between promoters PpActin5 and NOS, whereas terminators increased reporter levels by less than tenfold, demonstrating the stronger effect promoters play as compared to terminators. Among selected terminator attributes, the number of polyadenylation sites as well as polyadenylation signals were found to influence terminator performance the most. Our results improve the biotechnology platform Physcomitrella and further our understanding of how terminators influence gene expression in plants in general.
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Affiliation(s)
| | - Pauline Eglé
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Sandro Willig
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Juliana Parsons
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Freiburg, Germany
| | | | - Eva L Decker
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Ralf Reski
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Freiburg, Germany.
- Signalling Research Centre BIOSS and CIBSS, University of Freiburg, Freiburg, Germany.
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Łabuz J, Banaś AK, Zgłobicki P, Bażant A, Sztatelman O, Giza A, Lasok H, Prochwicz A, Kozłowska-Mroczek A, Jankowska U, Hermanowicz P. Phototropin2 3'UTR overlaps with the AT5G58150 gene encoding an inactive RLK kinase. BMC Plant Biol 2024; 24:55. [PMID: 38238701 PMCID: PMC10795372 DOI: 10.1186/s12870-024-04732-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 01/05/2024] [Indexed: 01/22/2024]
Abstract
BACKGROUND This study examines the biological implications of an overlap between two sequences in the Arabidopsis genome, the 3'UTR of the PHOT2 gene and a putative AT5G58150 gene, encoded on the complementary strand. AT5G58150 is a probably inactive protein kinase that belongs to the transmembrane, leucine-rich repeat receptor-like kinase family. Phot2 is a membrane-bound UV/blue light photoreceptor kinase. Thus, both proteins share their cellular localization, on top of the proximity of their loci. RESULTS The extent of the overlap between 3'UTR regions of AT5G58150 and PHOT2 was found to be 66 bp, using RACE PCR. Both the at5g58150 T-DNA SALK_093781C (with insertion in the promoter region) and 35S::AT5G58150-GFP lines overexpress the AT5G58150 gene. A detailed analysis did not reveal any substantial impact of PHOT2 or AT5G58150 on their mutual expression levels in different light and osmotic stress conditions. AT5G58150 is a plasma membrane protein, with no apparent kinase activity, as tested on several potential substrates. It appears not to form homodimers and it does not interact with PHOT2. Lines that overexpress AT5G58150 exhibit a greater reduction in lateral root density due to salt and osmotic stress than wild-type plants, which suggests that AT5G58150 may participate in root elongation and formation of lateral roots. In line with this, mass spectrometry analysis identified proteins with ATPase activity, which are involved in proton transport and cell elongation, as putative interactors of AT5G58150. Membrane kinases, including other members of the LRR RLK family and BSK kinases (positive regulators of brassinosteroid signalling), can also act as partners for AT5G58150. CONCLUSIONS AT5G58150 is a membrane protein that does not exhibit measurable kinase activity, but is involved in signalling through interactions with other proteins. Based on the interactome and root architecture analysis, AT5G58150 may be involved in plant response to salt and osmotic stress and the formation of roots in Arabidopsis.
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Affiliation(s)
- Justyna Łabuz
- Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7A, 30-387, Kraków, Poland.
| | - Agnieszka Katarzyna Banaś
- Department of Plant Biotechnology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387, Kraków, Poland
| | - Piotr Zgłobicki
- Department of Plant Biotechnology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387, Kraków, Poland
| | - Aneta Bażant
- Department of Plant Biotechnology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387, Kraków, Poland
| | - Olga Sztatelman
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, 02-106, Warsaw, Poland
| | - Aleksandra Giza
- Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7A, 30-387, Kraków, Poland
- Doctoral School of Exact and Natural Sciences, Jagiellonian University, Łojasiewicza 11, 30-348, Kraków, Poland
| | - Hanna Lasok
- Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7A, 30-387, Kraków, Poland
| | - Aneta Prochwicz
- Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7A, 30-387, Kraków, Poland
- Doctoral School of Exact and Natural Sciences, Jagiellonian University, Łojasiewicza 11, 30-348, Kraków, Poland
| | - Anna Kozłowska-Mroczek
- Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7A, 30-387, Kraków, Poland
| | - Urszula Jankowska
- Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7A, 30-387, Kraków, Poland
| | - Paweł Hermanowicz
- Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7A, 30-387, Kraków, Poland
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Zhang Z, Jin F, Huang J, Mandal SD, Zeng L, Zafar J, Xu X. MicroRNA Targets PAP1 to Mediate Melanization in Plutella xylostella (Linnaeus) Infected by Metarhizium anisopliae. Int J Mol Sci 2024; 25:1140. [PMID: 38256210 PMCID: PMC10816858 DOI: 10.3390/ijms25021140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2023] [Revised: 01/10/2024] [Accepted: 01/11/2024] [Indexed: 01/24/2024] Open
Abstract
MicroRNAs (miRNAs) play a pivotal role in important biological processes by regulating post-transcriptional gene expression and exhibit differential expression patterns during development, immune responses, and stress challenges. The diamondback moth causes significant economic damage to crops worldwide. Despite substantial advancements in understanding the molecular biology of this pest, our knowledge regarding the role of miRNAs in regulating key immunity-related genes remains limited. In this study, we leveraged whole transcriptome resequencing data from Plutella xylostella infected with Metarhizium anisopliae to identify specific miRNAs targeting the prophenoloxidase-activating protease1 (PAP1) gene and regulate phenoloxidase (PO) cascade during melanization. Seven miRNAs (pxy-miR-375-5p, pxy-miR-4448-3p, pxy-miR-279a-3p, pxy-miR-3286-3p, pxy-miR-965-5p, pxy-miR-8799-3p, and pxy-miR-14b-5p) were screened. Luciferase reporter assays confirmed that pxy-miR-279a-3p binds to the open reading frame (ORF) and pxy-miR-965-5p to the 3' untranslated region (3' UTR) of PAP1. Our experiments demonstrated that a pxy-miR-965-5p mimic significantly reduced PAP1 expression in P. xylostella larvae, suppressed PO activity, and increased larval mortality rate. Conversely, the injection of pxy-miR-965-5p inhibitor could increase PAP1 expression and PO activity while decreasing larval mortality rate. Furthermore, we identified four LncRNAs (MSTRG.32910.1, MSTRG.7100.1, MSTRG.6802.1, and MSTRG.22113.1) that potentially interact with pxy-miR-965-5p. Interference assays using antisense oligonucleotides (ASOs) revealed that silencing MSTRG.7100.1 and MSTRG.22113.1 increased the expression of pxy-miR-965-5p. These findings shed light on the potential role of pxy-miR-965-5p in the immune response of P. xylostella to M. anisopliae infection and provide a theoretical basis for biological control strategies targeting the immune system of this pest.
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Affiliation(s)
| | | | | | | | | | | | - Xiaoxia Xu
- National Key Laboratory of Green Pesticide, College of Plant Protection, South China Agricultural University, Guangzhou 510642, China; (Z.Z.); (F.J.); (J.H.); (S.D.M.); (L.Z.); (J.Z.)
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Muazzen Z, Moghrabi W, Bakheet T, Mahmoud L, Al-Saif M, Khabar KSA, Hitti EG. Global analysis of the abundance of AU-rich mRNAs in response to glucocorticoid treatment. Sci Rep 2024; 14:913. [PMID: 38195703 PMCID: PMC10776588 DOI: 10.1038/s41598-024-51301-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Accepted: 01/02/2024] [Indexed: 01/11/2024] Open
Abstract
Glucocorticoids (GC) like dexamethasone (Dex) are potent anti-inflammatory agents with diverse cellular functions including the potentiation of the activity of AU-rich elements (AREs). AREs are cis-acting instability sequence elements located in the 3'UTRs of many inflammatory mediator mRNAs. Here, available RNA-seq data were used to investigate the effect of GCs on the ARE-mRNA-transcriptome. At a global scale, ARE-mRNAs had a tendency to be downregulated after GC-treatment of the A549 lung cancer cell-line, but with notable cases of upregulation. mRNA stability experiments indicated that not only the downregulated, but also the upregulated ARE-mRNAs are destabilized by Dex-treatment. Several of the most upregulated ARE-mRNAs code for anti-inflammatory mediators including the established GC targets DUSP1 and ZFP36; both code for proteins that target ARE-containing mRNAs for destruction. GCs are widely used in the treatment of COVID-19 patients; we show that ARE-mRNAs are more likely to regulate in opposite directions between Dex-treatment and SARS-CoV-2 infections compared to non-ARE mRNAs. The effect of GC treatment on ARE-mRNA abundance was also investigated in blood monocytes of COVID-19 patients. The results were heterogeneous; however, in agreement with in vitro observations, ZFP36 and DUSP1 were often amongst the most differentially expressed mRNAs. The results of this study propose a universal destabilization of ARE-mRNAs by GCs, but a diverse overall outcome in vitro likely due to induced transcription or due to the heterogeneity of COVID-19 patient's responses in vivo.
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Affiliation(s)
- Zeyad Muazzen
- Molecular BioMedicine Department, Research and Innovation, King Faisal Specialist Hospital and Research Centre, 11211, Riyadh, Saudi Arabia
| | - Walid Moghrabi
- Molecular BioMedicine Department, Research and Innovation, King Faisal Specialist Hospital and Research Centre, 11211, Riyadh, Saudi Arabia
| | - Tala Bakheet
- Molecular BioMedicine Department, Research and Innovation, King Faisal Specialist Hospital and Research Centre, 11211, Riyadh, Saudi Arabia
| | - Linah Mahmoud
- Molecular BioMedicine Department, Research and Innovation, King Faisal Specialist Hospital and Research Centre, 11211, Riyadh, Saudi Arabia
| | - Maher Al-Saif
- Molecular BioMedicine Department, Research and Innovation, King Faisal Specialist Hospital and Research Centre, 11211, Riyadh, Saudi Arabia
| | - Khalid S A Khabar
- Molecular BioMedicine Department, Research and Innovation, King Faisal Specialist Hospital and Research Centre, 11211, Riyadh, Saudi Arabia
| | - Edward G Hitti
- Molecular BioMedicine Department, Research and Innovation, King Faisal Specialist Hospital and Research Centre, 11211, Riyadh, Saudi Arabia.
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Cazares T, Higgs RE, Wang J, Ozer HG. SeedMatchR: identify off-target effects mediated by siRNA seed regions in RNA-seq experiments. Bioinformatics 2024; 40:btae011. [PMID: 38192001 PMCID: PMC10799297 DOI: 10.1093/bioinformatics/btae011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 12/20/2023] [Accepted: 01/05/2024] [Indexed: 01/10/2024] Open
Abstract
MOTIVATION On-target gene knockdown, using siRNA, ideally results from binding fully complementary regions in mRNA transcripts to induce direct cleavage. Off-target siRNA gene knockdown can occur through several modes, one being a seed-mediated mechanism mimicking miRNA gene regulation. Seed-mediated off-target effects occur when the ∼8 nucleotides at the 5' end of the guide strand, called a seed region, bind the 3' untranslated regions of mRNA, causing reduced translation. Experiments using siRNA knockdown paired with RNA-seq can be used to detect siRNA sequences with off-target effects driven by the seed region. However, there are limited computational tools designed specifically for detecting siRNA off-target effects mediated by the seed region in differential gene expression experiments. RESULTS SeedMatchR is an R package developed to provide users a single, unified resource for detecting and visualizing seed-mediated off-target effects of siRNA using RNA-seq experiments. SeedMatchR is designed to extend current differential expression analysis tools, such as DESeq2, by annotating results with predicted seed matches. Using publicly available data, we demonstrate the ability of SeedMatchR to detect cumulative changes in differential gene expression attributed to siRNA seed region activity. AVAILABILITY SeedMatchR is available on CRAN. Documentation and example workflows are available through the SeedMatchR GitHub page at https://github.com/tacazares/SeedMatchR.
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Affiliation(s)
- Tareian Cazares
- Genetic Medicine, Eli Lilly and Company, Indianapolis, IN 46225, United States
| | - Richard E Higgs
- Genetic Medicine, Eli Lilly and Company, Indianapolis, IN 46225, United States
| | - Jibo Wang
- Genetic Medicine, Eli Lilly and Company, Indianapolis, IN 46225, United States
| | - Hatice Gulcin Ozer
- Genetic Medicine, Eli Lilly and Company, Indianapolis, IN 46225, United States
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Lin B, Fan L, Jackson S, Matunis AR, Lou D, Chen K, Trevejo-Nuñez G. Lung Epithelial Regnase-1 Dampens Local Immune Response but Does Not Worsen Susceptibility to Klebsiella pneumoniae. Immunohorizons 2024; 8:89-96. [PMID: 38226923 PMCID: PMC10835647 DOI: 10.4049/immunohorizons.2300082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 12/22/2023] [Indexed: 01/17/2024] Open
Abstract
Klebsiella pneumoniae (KP) presents a global health threat, leading to significant morbidity and mortality due to its multidrug-resistant profile and the limited availability of therapeutic options. To eliminate KP lung infection, the host initiates a robust inflammatory response. One of the host's mechanisms for mitigating excessive inflammation involves the RNA-binding protein regnase-1 (Reg1, MCPIP1, or ZC3H12A). Reg1 has an RNA binding domain that recognizes stem-loop structures in the 3' untranslated region of various proinflammatory transcripts, leading to mRNA decay. However, excessive suppression of inflammation by Reg1 results in suboptimal KP control. Reg1 deficiency within the nonhematopoietic compartment confers resistance to KP in the lung. Given that lung epithelium is crucial for KP resistance, we hypothesized that selective deletion of Reg1 in lung epithelial cells might enhance proinflammatory signals, leading to a better control of KP. Our transcriptomic analysis of epithelial cells in KP-infected wild-type mice revealed the presence of three distinct alveolar type 2 cell (AT2) subpopulations (conventional, inflammatory, and cycling) and enrichment of Reg1 in inflammatory AT2 cells. We conditionally deleted Reg1 in lung AT2 cells (ΔReg1), which amplified the local inflammatory response in the lung and increased macrophage cell numbers compared with controls. However, when ΔReg1 mice were subjected to KP infection, there were no significant differences in bacterial burden or survival compared with controls. These findings suggest that the local inflammatory response enhanced by Reg1 deletion in AT2 cells is insufficient to control KP infection.
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Affiliation(s)
- Becky Lin
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA
| | - Li Fan
- Division of Pulmonary, Allergy and Critical Care Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA
| | - Shaterra Jackson
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA
| | - Aidan R Matunis
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA
| | - Dequan Lou
- Division of Pulmonary, Allergy and Critical Care Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA
| | - Kong Chen
- Division of Pulmonary, Allergy and Critical Care Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA
| | - Giraldina Trevejo-Nuñez
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA
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Cheng ZA, Bian C, Lin KQ, Sun H, Yang ZQ. Determination of the 3'UTR region of HLA-B*53:01:03 sequence by next generation sequencing. HLA 2024; 103:e15322. [PMID: 38174641 DOI: 10.1111/tan.15322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 11/23/2023] [Accepted: 11/25/2023] [Indexed: 01/05/2024]
Abstract
The 3'UTR of the HLA-B*53:01:03 allele has been determined by next generation sequencing.
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Affiliation(s)
- Zi-An Cheng
- Department of Medical Genetics, Institute of Medical Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Kunming, China
| | - Cheng Bian
- Department of Medical Genetics, Institute of Medical Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Kunming, China
| | - Ke-Qin Lin
- Department of Medical Genetics, Institute of Medical Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Kunming, China
| | - Hao Sun
- Department of Medical Genetics, Institute of Medical Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Kunming, China
| | - Zhao-Qing Yang
- Department of Medical Genetics, Institute of Medical Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Kunming, China
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Aslan-Kara K, Dündar-Yenilmez E, Ateş E, Alparslan MM, Peköz T, Bozdemir H, Tuli A. EFHC1 gene mutation profile of Turkish JME patients and its association with disease risk. Seizure 2024; 114:79-83. [PMID: 38088014 DOI: 10.1016/j.seizure.2023.12.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2023] [Revised: 11/28/2023] [Accepted: 12/01/2023] [Indexed: 01/23/2024] Open
Abstract
OBJECTIVES Juvenile myoclonic epilepsy (JME) is a common form of generalized epilepsy with an important genetic component. This cohort study aimed to examine the frequency of EFHC1 gene variants in Turkish JME patients and a healthy control group and evaluate the association between these mutations and disease risk. METHODS We screened 72 JME patients with a mean age of 31.8 ± 9.9 (20-65) years and 35 controls with a mean age of 29.1 ± 7.6 (17-50) years from southern Turkey using direct sequencing analyses. RESULTS EFCH1 single nucleotide variants were detected in 24 of 72 JME patients and 3 of 35 controls. The most common mutations were R182H in JME patients (p = 0.010) and 3'UTR in the control group (p < 0.001). The R182H mutation is a common variant in JME (95 % CI: 1.232-76.580, p = 0.031) and the 3'UTR mutation may be associated with lower risk of JME in the Turkish population (95 % CI: 13.89-166.67, p < 0.001). SIGNIFICANCE Our results indicate that EFHC1 gene variants carry a risk for JME and the 3'UTR variant may have a protective role against JME in the Turkish population. Screening for other genes is needed to further clarify the genetic inheritance of JME in Turkish patients.
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Affiliation(s)
- Kezban Aslan-Kara
- Department of Neurology, School of Medicine, Çukurova University Faculty of Medicine, Sarıçam-Adana 01330, Türkiye.
| | - Ebru Dündar-Yenilmez
- Department of Medical Biochemistry, Çukurova University Faculty of Medicine, Türkiye
| | - Elçin Ateş
- Department of Neurology, School of Medicine, Çukurova University Faculty of Medicine, Sarıçam-Adana 01330, Türkiye
| | | | - Taylan Peköz
- Department of Neurology, School of Medicine, Çukurova University Faculty of Medicine, Sarıçam-Adana 01330, Türkiye
| | - Hacer Bozdemir
- Department of Neurology, School of Medicine, Çukurova University Faculty of Medicine, Sarıçam-Adana 01330, Türkiye
| | - Abdullah Tuli
- Department of Medical Biochemistry, Çukurova University Faculty of Medicine, Türkiye
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Nulali J, Zhang K, Long M, Wan Y, Liu Y, Zhang Q, Yang L, Hao J, Yang L, Song H. ALYREF-mediated RNA 5-Methylcytosine modification Promotes Hepatocellular Carcinoma Progression Via Stabilizing EGFR mRNA and pSTAT3 activation. Int J Biol Sci 2024; 20:331-346. [PMID: 38164181 PMCID: PMC10750289 DOI: 10.7150/ijbs.82316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Accepted: 09/23/2023] [Indexed: 01/03/2024] Open
Abstract
5-Methylcytosine (m5C) is one of the most ubiquitous modifications of mRNA and contributes to cancer pathogenesis. Aly/REF export factor (ALYREF), an m5C reader, is associated with the prognosis of liver hepatocellular carcinoma (LIHC). However, the effects of ALYREF on the progression of LIHC and the underlying molecular mechanisms remains elusive. Through an analysis of an online database and 3 independent LIHC cohorts, we found that ALYREF was markedly elevated in human liver cancer tissues and was significantly correlated with LIHC clinicopathological parameters, including Ki67+ cell rate, high-grade TNM stage, and poor prognosis. Several experiments were conducted to investigate the molecular basis and functional role of ALYREF-related progression in this study. ALYREF could enhance LIHC cell proliferation, migration, invasion, and epithelial-mesenchymal transition (EMT) in vitro and tumor formation in vivo. Mechanistically, ALYREF promoted the progression of human LIHC through EGFR pathways. Furthermore, ALYREF could directly bind to the m5C modification site of EGFR 3' untranslated region (3' UTR) to stabilize EGFR mRNA. Collectively, ALYREF played a crucial oncogenic role in LIHC via the stabilization of EGFR mRNA and subsequent activation of the STAT3 signaling pathway. Our results may help to elucidate the potential mechanisms of ALYREF-induced m5C modification in the progression of human LIHC.
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Affiliation(s)
- Jiayida Nulali
- The Core Laboratory in Medical Center of Clinical Research, Department of Molecular Diagnostics and Endocrinology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200011, China
| | - Kaiwen Zhang
- The Core Laboratory in Medical Center of Clinical Research, Department of Molecular Diagnostics and Endocrinology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200011, China
| | - Manmei Long
- Department of Pathology, Shanghai Ninth People's Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Yueyue Wan
- The Core Laboratory in Medical Center of Clinical Research, Department of Molecular Diagnostics and Endocrinology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200011, China
| | - Yu Liu
- Department of Respiration, Yangpu Hospital, Tongji University School of Medicine, Shanghai, China
| | - Qianyue Zhang
- The Core Laboratory in Medical Center of Clinical Research, Department of Molecular Diagnostics and Endocrinology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200011, China
| | - Liu Yang
- The Core Laboratory in Medical Center of Clinical Research, Department of Molecular Diagnostics and Endocrinology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200011, China
| | - Jun Hao
- Department of Liver Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Linhua Yang
- Department of Biliary-Pancreatic Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Huaidong Song
- The Core Laboratory in Medical Center of Clinical Research, Department of Molecular Diagnostics and Endocrinology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200011, China
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Tian Y, Wang Y, Wang Z. CIRCESPL1 SILENCING PROTECTS AGAINST LPS-INDUCED LUNG FIBROBLAST DYSFUNCTION PARTLY BY TARGETING THE MIR-146B-3P/TRAF1 AXIS IN PNEUMONIA. Shock 2024; 61:157-164. [PMID: 38010117 DOI: 10.1097/shk.0000000000002268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
ABSTRACT Background: Neonatal pneumonia is a common disease in the neonatal period with high mortality. The present work concentrated on the role and mechanism of circular RNA extra spindle pole bodies like 1, separase (circESPL1) in LPS-induced dysfunction of lung fibroblasts. Methods: Reverse transcription-quantitative polymerase chain reaction and Western blot assay were conducted to analyze RNA and protein expression, respectively. Cell viability, proliferation, apoptosis, and inflammation were assessed by Cell Counting Kit-8 assay, 5-ethynyl-2'-deoxyuridine assay, flow cytometry, and enzyme-linked immunosorbent assay, respectively. Dual-luciferase reporter assay and RNA immunoprecipitation assay were conducted to verify the intermolecular interactions among circESPL1, miR-146b-3p, and TRAF1. Results: CircESPL1 expression was upregulated in the serum samples of pneumonia patients and LPS-induced lung fibroblasts. CircESPL1 silencing protected lung fibroblasts against LPS-induced dysfunction. CircESPL1 bound to microRNA-146b-3p (miR-146b-3p) in lung fibroblasts. CircESPL1 knockdown-mediated protective effects on LPS-induced lung fibroblasts were largely reversed by the silence of miR-146b-3p. miR-146b-3p directly interacted with the 3' untranslated region of TNF receptor associated factor 1 (TRAF1), and TRAF1 expression was regulated by the circESPL1/miR-146b-3p axis in lung fibroblasts. TRAF1 overexpression largely reversed miR-146b-3p accumulation-mediated protective effects on LPS-induced lung fibroblasts. Conclusion: CircESPL1 knockdown protected lung fibroblasts from LPS-induced injury partly by targeting the miR-146b-3p/TRAF1 axis.
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Affiliation(s)
- Yubo Tian
- Department of Child Health, Women's and Children's Hospital, Zhumadian Central Hospital, Zhumadian, China
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Chen L, Zhou Y, Cheng H, Lu W, Cai M, Jiang K. Circ-SATB2 (hsa_circ_0008928) and miR-150-5p are regulators of TRIM66 in the regulation of NSCLC cell growth and metastasis of NSCLC cells via the ceRNA pathway. J Biochem Mol Toxicol 2024; 38:e23615. [PMID: 38084627 DOI: 10.1002/jbt.23615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 07/27/2023] [Accepted: 11/28/2023] [Indexed: 01/18/2024]
Abstract
Circular RNA (circRNA) was an important modulator and potential molecular target of nonsmall cell lung cancer (NSCLC). CircSATB2 was reported to be upregulated in NSCLC. However, the role and mechanism of circSATB2 in NSCLC progression remain to be illustrated. The RNA and protein expression was detected by quantitative real-time polymerase chain reaction, western blot, and immunohistochemistry assay. Cell counting kit-8, cell colony formation, and 5-ethynyl-2'-deoxyuridine assays were applied to assess cell growth. The migrated and invaded cells were examined by transwell assay. Flow cytometry was performed to measure apoptotic cells. The interaction among circSATB2, microRNA-150-5p (miR-150-5p), and tripartite motif-containing protein 66 (TRIM66) was identified by dual-luciferase reporter assay and RNA immunoprecipitation assay. An in vivo experiment was conducted to investigate the effect of circSATB2 on tumor growth. CircSATB2 expression was highly expressed in NSCLC tissues and cell lines. CircSATB2 and TRIM66 silencing both suppressed NSCLC cell growth, migration, and invasion whereas promoted NSCLC cell apoptosis. CircSATB2 acted as a molecular sponge for miR-150-5p, and miR-150-5p interacted with the 3' untranslated region (3'UTR) of TRIM66. Moreover, circSATB2 knockdown-induced effects were partly reversed by TRIM66 overexpression in NSCLC cells. Besides, cirSATB2 expression was negatively correlated with miR-150-5p level and positively correlated with TRIM66 level in NSCLC tumor tissues. CircSATB2 knockdown blocked xenograft tumor growth in vivo. In summary, this study verified that circSATB2 stimulated NSCLC cell malignant behaviors by miR-150-5p/TRIM66 pathway, providing a possible circRNA-targeted therapy for NSCLC.
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Affiliation(s)
- Liangji Chen
- Medical Clinical Laboratory, Xiantao First People's Hospital Affiliated to Yangtze University, Xiantao City, Hubei Province, China
| | - Yuting Zhou
- Medical Clinical Laboratory, Xiantao First People's Hospital Affiliated to Yangtze University, Xiantao City, Hubei Province, China
| | - Hongbing Cheng
- Thoracic Surgery, Xiantao First People's Hospital Affiliated to Yangtze University, Xiantao City, Hubei Province, China
| | - Wenjing Lu
- Department of Oncology, Xiantao First People's Hospital Affiliated to Yangtze University, Xiantao City, Hubei Province, China
| | - Mengyang Cai
- Medical Clinical Laboratory, Xiantao First People's Hospital Affiliated to Yangtze University, Xiantao City, Hubei Province, China
| | - Kaifeng Jiang
- Clinical Laboratory, The Central Hospital of Yongzhou, Yongzhou City, Hunan Province, China
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He P, Liu Z, Qi J, Shan J, Sheng J. Long noncoding RNA LINC00885 upregulates NCK1 to promote cell viability and migration of triple-negative breast cancer cells through sponging miR-654-3p. Cancer Biomark 2024; 39:63-78. [PMID: 37694355 DOI: 10.3233/cbm-230143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
BACKGROUND LINC00885 is a novel oncogenic long noncoding RNA (LncRNA) which is upregulated in various types of cancer, but its function in triple-negative breast cancer (TNBC) remains unknown. OBJECTIVE This study aimed to determine the role of LINC00885 on TNBC development. METHODS Clinical interrelation and survival analysis were determined using online database. The CCK-8 and Transwell assays were used to detect the proliferation and migration behaviors in TNBC cell lines. The interaction among genes was detected by RNA pull down assay. RESULTS LncRNA LINC00885 was highly expressed in TNBC compared to normal breast like. Low levels of LINC00885 was related to good prognosis in TNBC patients compared to TNBC patients with high LINC00885. LINC00885-downregulation inhibited, whereas LINC00885-overexpression promoted the proliferation and migration capability of TNBC cell lines. In TNBC cell lines, noncatalytic region of tyrosine kinase 1 (NCK1) expression was positively associated with LINC00885 expression, and shRNA-mediated the depletion of NCK1 significantly abolished LINC00885 upregulation-mediated pro-tumor effects. Combined with online databases, miR-654-3p was screened as the direct target gene of LINC00885, which could directly bind to 3'-untranslated regions (3'-UTR) of NCK1, resulting in the decreased expression of NCK1 in TNBC cell lines. LINC00885 overexpression-mediated the upregulation of NCK1 was abrogated by miR-654-3p mimics. MiR-654-3p mimics significantly rescued the tumor promotive role caused by LINC00885-overexpression. However, exogenous NCK1 notably eliminated the anti-tumor effects caused by miR-654-3p mimics in LINC00885-overexpressed cells. CONCLUSIONS LINC00885 is expressed at a high level in TNBC. LINC00885 promoted proliferation and migration by regulating the miR-654-3p/NCK1 axis in TNBC cell lines. Possibly, LINC00885 can be served as a potential therapeutic target for TNBC.
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Affiliation(s)
- Peina He
- Department of Medicine, Pingdingshan University, Pingdingshan, Henan, China
| | - Zhi Liu
- Department of Medicine, Pingdingshan University, Pingdingshan, Henan, China
| | - Jinxu Qi
- Department of Medicine, Pingdingshan University, Pingdingshan, Henan, China
| | - Junrao Shan
- Department of Medicine, Pingdingshan University, Pingdingshan, Henan, China
| | - Jianyun Sheng
- Department of Gynecotokology, The First People's Hospital of Pingdingshan, Pingdingshan, Henan, China
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