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Xing YQ, Zhu TZ. RNA-Binding Motif Protein RBM47 Promotes Invasiveness of Glioblastoma Through Activation of Epithelial-to-Mesenchymal Transition Program. Genet Test Mol Biomarkers 2023; 27:384-392. [PMID: 38156907 DOI: 10.1089/gtmb.2023.0368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2024] Open
Abstract
Background: RNA-binding motif proteins (RBMs) have been widely implicated in the tumorigenesis of multiple human cancers but rarely investigated in glioblastoma (GBM). Methods: The expression level of RBM47 and its correlation with prognosis of GBM were examined using bioinformatics, quantitative reverse transcription PCR, and Western blot analysis. The colony formation assay and Cell Counting Kit-8 assay were used to determine the biological role of RBM47 in GBM. To measure invasiveness we used the wound healing assay and transwell assay. The regulatory relationship between RBM47 and the epithelial-to-mesenchymal transition (EMT) was examined by Western blot analysis and bioinformatic analysis. Results: Through integrative analysis of clinical proteomic and genomic tumor datasets, we found that RBM47 is significantly upregulated in GBM mesenchymal subtype, and its high expression is correlated with poor prognosis. In in vitro biological experiments, we observed a significant inhibitory effect of RBM47 knockdown on colony formation and cell growth using GBM cell lines. Conversely, overexpression of RBM47 restored and accelerated these processes. Moreover, in vitro, wound healing assays demonstrated the role of RBM46 in promoting and cell migration and invasion. Mechanistically, RBM47 enhances invasive capacity through the activation of the EMT program. In RBM47-knockdown cells, the expression levels of Vimentin and CD44 were suppressed, and the level of E-cadherin was increased. Conclusions: Taken together our results demonstrate the tumor promoting characteristics of RBM46 and suggest that it could be used both as a therapeutic target and prognostically.
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Affiliation(s)
- Yi-Qi Xing
- Institute of Neuroscience, General Hospital of Northern Theater Command, Shenyang, China
- The Second Hospital of Dalian Medical University, Dalian, China
| | - Ting-Zhun Zhu
- Institute of Neuroscience, General Hospital of Northern Theater Command, Shenyang, China
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2
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Zhou J, Xu Y, Wang L, Cong Y, Huang K, Pan X, Liu G, Li W, Dai C, Xu P, Jia X. LncRNA IDH1-AS1 sponges miR-518c-5p to suppress proliferation of epithelial ovarian cancer cell by targeting RMB47. J Biomed Res 2023; 38:51-65. [PMID: 37981573 PMCID: PMC10818171 DOI: 10.7555/jbr.37.20230097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 08/22/2023] [Accepted: 08/29/2023] [Indexed: 11/21/2023] Open
Abstract
Long noncoding RNA (lncRNA) IDH1 antisense RNA 1 ( IDH1-AS1) is involved in the progression of multiple cancers, but its role in epithelial ovarian cancer (EOC) is unknown. Therefore, we investigated the expression levels of IDH1-AS1 in EOC cells and normal ovarian epithelial cells by quantitative real-time PCR (qPCR). We first evaluated the effects of IDH1-AS1 on the proliferation, migration, and invasion of EOC cells through cell counting kit-8, colony formation, EdU, transwell, wound-healing, and xenograft assays. We then explored the downstream targets of IDH1-AS1 and verified the results by a dual-luciferase reporter, qPCR, rescue experiments, and Western blotting. We found that the expression levels of IDH1-AS1 were lower in EOC cells than in normal ovarian epithelial cells. High IDH1-AS1 expression of EOC patients from the Gene Expression Profiling Interactive Analysis database indicated a favorable prognosis, because IDH1-AS1 inhibited cell proliferation and xenograft tumor growth of EOC. IDH1-AS1 sponged miR-518c-5p whose overexpression promoted EOC cell proliferation. The miR-518c-5p mimic also reversed the proliferation-inhibiting effect induced by IDH1-AS1 overexpression. Furthermore, we found that RNA binding motif protein 47 (RBM47) was the downstream target of miR-518c-5p, that upregulation of RBM47 inhibited EOC cell proliferation, and that RBM47 overexpressing plasmid counteracted the proliferation-promoting effect caused by the IDH1-AS1 knockdown. Taken together, IDH1-AS1 may suppress EOC cell proliferation and tumor growth via the miR-518c-5p/RBM47 axis.
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Affiliation(s)
- Juan Zhou
- Department of Gynecology, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, Jiangsu 210004, China
| | - Yiran Xu
- Department of Gynecology, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, Jiangsu 210004, China
| | - Luyao Wang
- Department of Gynecology, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, Jiangsu 210004, China
| | - Yu Cong
- Department of Gynecology, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, Jiangsu 210004, China
| | - Ke Huang
- Department of Gynecology, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, Jiangsu 210004, China
| | - Xinxing Pan
- Department of Gynecology, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, Jiangsu 210004, China
| | - Guangquan Liu
- Department of Gynecology, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, Jiangsu 210004, China
| | - Wenqu Li
- Department of Gynecology, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, Jiangsu 210004, China
| | - Chenchen Dai
- Department of Gynecology, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, Jiangsu 210004, China
| | - Pengfei Xu
- Nanjing Maternity and Child Health Medical Institute, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, Jiangsu 210004, China
| | - Xuemei Jia
- Department of Gynecology, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, Jiangsu 210004, China
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Shivalingappa PKM, Singh DK, Sharma V, Arora V, Shiras A, Bapat SA. RBM47 is a Critical Regulator of Mouse Embryonic Stem Cell Differentiation. Stem Cell Rev Rep 2023; 19:475-490. [PMID: 35986129 PMCID: PMC9391069 DOI: 10.1007/s12015-022-10441-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/03/2022] [Indexed: 02/07/2023]
Abstract
RNA-binding proteins (RBPs) are pivotal for regulating gene expression as they are involved in each step of RNA metabolism. Several RBPs are essential for viable growth and development in mammals. RNA-binding motif 47 (RBM47) is an RRM-containing RBP whose role in mammalian embryonic development is poorly understood yet deemed to be essential since its loss in mouse embryos leads to perinatal lethality. In this study, we attempted to elucidate the significance of RBM47 in cell-fate decisions of mouse embryonic stem cells (mESCs). Downregulation of Rbm47 did not affect mESC maintenance and the cell cycle but perturbed the expression of primitive endoderm (PrE) markers and increased GATA4 + PrE-like cells. However, the PrE misregulation could be reversed by either overexpressing Rbm47 or treating the knockdown mESCs with the inhibitors of FGFR or MEK, suggesting an implication of RBM47 in regulating FGF-ERK signaling. Rbm47 knockdown affected the multi-lineage differentiation potential of mESCs as it regressed teratoma in NSG mice and led to a skewed expression of differentiation markers in serum-induced monolayer differentiation. Further, lineage-specific differentiation revealed that Rbm47 is essential for proper differentiation of mESCs towards neuroectodermal and endodermal fate. Taken together, we assign a hitherto unknown role(s) to RBM47 in a subtle regulation of mESC differentiation.
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Affiliation(s)
| | - Divya Kumari Singh
- National Centre for Cell Science, Savitribai Phule Pune University, Ganeshkhind, Pune, 411007, India
| | - Vaishali Sharma
- National Centre for Cell Science, Savitribai Phule Pune University, Ganeshkhind, Pune, 411007, India
| | - Vivek Arora
- National Centre for Cell Science, Savitribai Phule Pune University, Ganeshkhind, Pune, 411007, India
| | - Anjali Shiras
- National Centre for Cell Science, Savitribai Phule Pune University, Ganeshkhind, Pune, 411007, India
| | - Sharmila A Bapat
- National Centre for Cell Science, Savitribai Phule Pune University, Ganeshkhind, Pune, 411007, India.
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Ouyang J, Wu Y, Li Y, Miao J, Zheng S, Tang H, Wang C, Xiong Y, Gao Y, Wang L, Yan X, Chen H. Identification of key candidate genes for wing length-related traits by whole-genome resequencing in 772 geese. Br Poult Sci 2022; 63:747-753. [PMID: 35848598 DOI: 10.1080/00071668.2022.2102889] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
1. A total of 772, 420-day-old Xingguo gray geese (XGG) were sequenced using a low-depth (~1×) whole-genome resequencing strategy to reveal the genetic mechanism of wing length-related traits by genome-wide association analysis (GWAS).2. The results showed that 119 SNPs had genome-wide significance for wing length in five regions of chromosome 4, of which the most significant locus (P=7.95E-11) was located upstream of RBM47 and explained 7.3% of phenotypic variation.3. A total of 219 SNPs located on chromosome 4 that were associated with 2-joint-wing length, of which four SNPs reached the genome-wide significant level. However, for the length of 1-joint-wing and primary feather, we did not detect any associated locus.4. Six promising candidate genes, RBM47, SLAIN2, GRXCR1, SLC10A4, APBB2 and NSUN7 on chromosome 4, may play an important role in the growth and development of feathers, muscles and bones.
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Affiliation(s)
- Jing Ouyang
- School of life science, Jiangxi Science & Technology Normal University, Nanchang, China
| | - Yongfei Wu
- School of life science, Jiangxi Science & Technology Normal University, Nanchang, China
| | - Yaxi Li
- School of life science, Jiangxi Science & Technology Normal University, Nanchang, China
| | - Junjie Miao
- School of life science, Jiangxi Science & Technology Normal University, Nanchang, China
| | - Sumei Zheng
- School of life science, Jiangxi Science & Technology Normal University, Nanchang, China
| | - Hongbo Tang
- School of life science, Jiangxi Science & Technology Normal University, Nanchang, China
| | - Cong Wang
- School of life science, Jiangxi Science & Technology Normal University, Nanchang, China
| | - Yanpeng Xiong
- School of life science, Jiangxi Science & Technology Normal University, Nanchang, China
| | - Yuren Gao
- School of life science, Jiangxi Science & Technology Normal University, Nanchang, China
| | - Luping Wang
- School of life science, Jiangxi Science & Technology Normal University, Nanchang, China
| | | | - Hao Chen
- School of life science, Jiangxi Science & Technology Normal University, Nanchang, China
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5
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Guo T, You K, Chen X, Sun Y, Wu Y, Wu P, Jiang Y. RBM47 inhibits hepatocellular carcinoma progression by targeting UPF1 as a DNA/RNA regulator. Cell Death Dis 2022; 8:320. [PMID: 35831298 PMCID: PMC9279423 DOI: 10.1038/s41420-022-01112-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 06/30/2022] [Accepted: 06/30/2022] [Indexed: 11/16/2022]
Abstract
The mechanisms by which the tumor behaviors of hepatocellular carcinoma (HCC) support growth and metastasis remain largely unknown, and it has become increasingly apparent that molecular dysregulation is of considerable importance for cellular signaling pathways. Recently, RNA-binding motif protein 47 (RBM47) has been suggested to function as a tumor regulator by acting as an RNA binding protein (RBP), but its role in HCC remains ambiguous. Here, in HCC, we identified that RBM47 had an inhibitory influence on tumor behaviors in vitro and accordingly suppressed the growth and metastasis of xenograft tumors in vivo. Additionally, RBM47 was verified to positively regulate Upframeshift 1 (UPF1), which is a crucial protein involved in the nonsense-mediated RNA decay (NMD) process and was previously determined to be an HCC suppressor. Mechanistically, the stability of UPF1 mRNA was demonstrated to be enhanced with its 3’UTR bound by RBM47, which acted as an RNA binding protein. Meanwhile, RBM47 was also proven to promote the transcription of UPF1 as a transcription factor. Taken together, we concluded that RBM47 functioned as a tumor suppressor by upregulating UPF1, acting as a DNA/RNA binding protein at the transcriptional and posttranscriptional levels.
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Affiliation(s)
- Tao Guo
- Department of Pathophysiology, School of Basic Medical Sciences, Weifang Medical University, Weifang, 261053, China
| | - Ke You
- Department of Hepatobiliary Surgery, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, 400010, China
| | - Xi Chen
- School of Stomatology, Weifang Medical University, Weifang, 261053, China
| | - Yuqi Sun
- School of Clinical Medicine, Weifang Medical University, Weifang, 261031, China
| | - Ying Wu
- Liuzhou Key Laboratory of Infectious Disease Immunity Research, Guangxi Health Commission Key Laboratory of Clinical Biotechnology, Liuzhou People's Hospital affiliated to Guangxi Medical University, Liuzhou, 545006, China
| | - Ping Wu
- Department of Pediatric Surgery, Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, 510000, China
| | - Yingying Jiang
- School of Stomatology, Weifang Medical University, Weifang, 261053, China. .,Department of Dentistry, Affiliated Hospital of Weifang Medical University, Weifang, 261035, China.
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RNA binding motif 47 (RBM47): emerging roles in vertebrate development, RNA editing and cancer. Mol Cell Biochem 2021; 476:4493-4505. [PMID: 34499322 DOI: 10.1007/s11010-021-04256-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Accepted: 08/31/2021] [Indexed: 10/20/2022]
Abstract
RNA-binding proteins (RBPs) are critical players in the post-transcriptional regulation of gene expression and are associated with each event in RNA metabolism. The term 'RNA-binding motif' (RBM) is assigned to novel RBPs with one or more RNA recognition motif (RRM) domains that are mainly involved in the nuclear processing of RNAs. RBM47 is a novel RBP conserved in vertebrates with three RRM domains whose contributions to various aspects of cellular functions are as yet emerging. Loss of RBM47 function affects head morphogenesis in zebrafish embryos and leads to perinatal lethality in mouse embryos, thereby assigning it to be an essential gene in early development of vertebrates. Its function as an essential cofactor for APOBEC1 in C to U RNA editing of several targets through substitution for A1CF in the A1CF-APOBEC1 editosome, established a new paradigm in the field. Recent advances in the understanding of its involvement in cancer progression assigned RBM47 to be a tumor suppressor that acts by inhibiting EMT and Wnt/[Formula: see text]-catenin signaling through post-transcriptional regulation. RBM47 is also required to maintain immune homeostasis, which adds another facet to its regulatory role in cellular functions. Here, we review the emerging roles of RBM47 in various biological contexts and discuss the current gaps in our knowledge alongside future perspectives for the field.
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7
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Wang K, Huang C, Jiang T, Chen Z, Xue M, Zhang Q, Zhang J, Dai J. RNA-binding protein RBM47 stabilizes IFNAR1 mRNA to potentiate host antiviral activity. EMBO Rep 2021; 22:e52205. [PMID: 34160127 DOI: 10.15252/embr.202052205] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 05/21/2021] [Accepted: 05/25/2021] [Indexed: 12/22/2022] Open
Abstract
The type I interferon (IFN-I, IFN-α/β)-mediated immune response is the first line of host defense against invading viruses. IFN-α/β binds to IFN-α/β receptors (IFNARs) and triggers the expression of IFN-stimulated genes (ISGs). Thus, stabilization of IFNARs is important for prolonging antiviral activity. Here, we report the induction of an RNA-binding motif-containing protein, RBM47, upon viral infection or interferon stimulation. Using multiple virus infection models, we demonstrate that RBM47 has broad-spectrum antiviral activity in vitro and in vivo. RBM47 has no noticeable impact on IFN production, but significantly activates the IFN-stimulated response element (ISRE) and enhances the expression of interferon-stimulated genes (ISGs). Mechanistically, RBM47 binds to the 3'UTR of IFNAR1 mRNA, increases mRNA stability, and retards the degradation of IFNAR1. In summary, this study suggests that RBM47 is an interferon-inducible RNA-binding protein that plays an essential role in enhancing host IFN downstream signaling.
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Affiliation(s)
- Kezhen Wang
- Jiangsu Key Laboratory of Infection and Immunity, Institutes of Biology and Medical Sciences, Soochow University, Suzhou, China
| | - Chenxiao Huang
- Jiangsu Key Laboratory of Infection and Immunity, Institutes of Biology and Medical Sciences, Soochow University, Suzhou, China
| | - Tao Jiang
- Jiangsu Key Laboratory of Infection and Immunity, Institutes of Biology and Medical Sciences, Soochow University, Suzhou, China
| | - Zhiqiang Chen
- Jiangsu Key Laboratory of Infection and Immunity, Institutes of Biology and Medical Sciences, Soochow University, Suzhou, China
| | - Minfei Xue
- Jiangsu Key Laboratory of Infection and Immunity, Institutes of Biology and Medical Sciences, Soochow University, Suzhou, China
| | - Qi Zhang
- Jiangsu Key Laboratory of Infection and Immunity, Institutes of Biology and Medical Sciences, Soochow University, Suzhou, China
| | - Jinyu Zhang
- Jiangsu Key Laboratory of Infection and Immunity, Institutes of Biology and Medical Sciences, Soochow University, Suzhou, China
| | - Jianfeng Dai
- Jiangsu Key Laboratory of Infection and Immunity, Institutes of Biology and Medical Sciences, Soochow University, Suzhou, China
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Insights into the Structures and Multimeric Status of APOBEC Proteins Involved in Viral Restriction and Other Cellular Functions. Viruses 2021; 13:v13030497. [PMID: 33802945 PMCID: PMC8002816 DOI: 10.3390/v13030497] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 03/15/2021] [Accepted: 03/15/2021] [Indexed: 12/16/2022] Open
Abstract
Apolipoprotein B mRNA editing catalytic polypeptide-like (APOBEC) proteins belong to a family of deaminase proteins that can catalyze the deamination of cytosine to uracil on single-stranded DNA or/and RNA. APOBEC proteins are involved in diverse biological functions, including adaptive and innate immunity, which are critical for restricting viral infection and endogenous retroelements. Dysregulation of their functions can cause undesired genomic mutations and RNA modification, leading to various associated diseases, such as hyper-IgM syndrome and cancer. This review focuses on the structural and biochemical data on the multimerization status of individual APOBECs and the associated functional implications. Many APOBECs form various multimeric complexes, and multimerization is an important way to regulate functions for some of these proteins at several levels, such as deaminase activity, protein stability, subcellular localization, protein storage and activation, virion packaging, and antiviral activity. The multimerization of some APOBECs is more complicated than others, due to the associated complex RNA binding modes.
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Wolfe AD, Li S, Goedderz C, Chen XS. The structure of APOBEC1 and insights into its RNA and DNA substrate selectivity. NAR Cancer 2020; 2:zcaa027. [PMID: 33094286 PMCID: PMC7556403 DOI: 10.1093/narcan/zcaa027] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 09/05/2020] [Accepted: 09/10/2020] [Indexed: 02/06/2023] Open
Abstract
APOBEC1 (APO1), a member of AID/APOBEC nucleic acid cytosine deaminase family, can edit apolipoprotein B mRNA to regulate cholesterol metabolism. This APO1 RNA editing activity requires a cellular cofactor to achieve tight regulation. However, no cofactors are required for deamination on DNA by APO1 and other AID/APOBEC members, and aberrant deamination on genomic DNA by AID/APOBEC deaminases has been linked to cancer. Here, we present the crystal structure of APO1, which reveals a typical APOBEC deaminase core structure, plus a unique well-folded C-terminal domain that is highly hydrophobic. This APO1 C-terminal hydrophobic domain (A1HD) interacts to form a stable dimer mainly through hydrophobic interactions within the dimer interface to create a four-stranded β-sheet positively charged surface. Structure-guided mutagenesis within this and other regions of APO1 clarified the importance of the A1HD in directing RNA and cofactor interactions, providing insights into the structural basis of selectivity on DNA or RNA substrates.
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Affiliation(s)
- Aaron D Wolfe
- Genetics, Molecular and Cellular Biology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA
| | - Shuxing Li
- Molecular and Computational Biology, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Cody Goedderz
- Molecular and Computational Biology, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Xiaojiang S Chen
- Genetics, Molecular and Cellular Biology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA
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Shen DJ, Jiang YH, Li JQ, Xu LW, Tao KY. The RNA-binding protein RBM47 inhibits non-small cell lung carcinoma metastasis through modulation of AXIN1 mRNA stability and Wnt/β-catentin signaling. Surg Oncol 2020; 34:31-39. [PMID: 32891348 DOI: 10.1016/j.suronc.2020.02.011] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Revised: 01/29/2020] [Accepted: 02/14/2020] [Indexed: 12/25/2022]
Abstract
BACKGROUND Non-small-cell lung cancer (NSCLC) remains a highly prevalent and deadly form of cancer, with efforts to better understand the molecular basis of the progression of this disease being essential to its effective treatment. Several recent studies have highlighted the ability of RNA-binding proteins (RBPs) to regulate a wide range of cellular processes in both healthy and pathogenic contexts. Among these RBPs, RNA binding motif protein 47 (RBM47) has recently been identified as a tumor suppressor in both breast and colon cancers, whereas its role in NSCLC is poorly understood. METHODS RBM47 expression in NSCLC samples was evaluated by RT-PCR, western blotting and immunohistochemistry analysis. Molecular and cellular techniques including lentiviral vector-mediated knockdown were used to elucidate the functions and mechanisms of RBM47. RESULTS This study sought to analyze the expression and role of RBM47 in NSCLC. In the present study, we observed reduced levels of RBM47 expression in NSCLC, with these reductions corresponding to a poorer prognosis and more advanced disease including a higher TNM stage (p = 0.022), a higher likelihood of tumor thrombus (p = 0.001), and pleural invasion (p = 0.033). Through functional analyses in vitro and in vivo, we further demonstrated that these RBP was able to disrupt the proliferation, migration, and invasion of NSCLC cells. At a molecular level, we determined that RBM47 was able to bind the AXIN1 mRNA, stabilizing it and thereby enhancing the consequent suppression of Wnt/β-catentin signaling. CONCLUSION Together our findings reveal that RBM47 targets AXIN1 in order to disrupt Wnt/β-catenin signaling in NSCLC and thereby disrupting tumor progression. These results thus offer new insights into the molecular biology of NSCLC, and suggest that RBM47 may also have value as a prognostic biomarker and/or therapeutic target in NSCLC patients.
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Affiliation(s)
- Di-Jian Shen
- Department of Thoracic Surgery, Institute of Cancer Research and Basic Medical Sciences of Chinese Academy of Sciences, Cancer Hospital of University of Chinese Academy of Sciences, Zhejiang Cancer Hospital, No. 1 Banshan East Road, Gongshu District, Hangzhou, 310022, China
| | - You-Hua Jiang
- Department of Thoracic Surgery, Institute of Cancer Research and Basic Medical Sciences of Chinese Academy of Sciences, Cancer Hospital of University of Chinese Academy of Sciences, Zhejiang Cancer Hospital, No. 1 Banshan East Road, Gongshu District, Hangzhou, 310022, China
| | - Jian-Qiang Li
- Department of Thoracic Surgery, Institute of Cancer Research and Basic Medical Sciences of Chinese Academy of Sciences, Cancer Hospital of University of Chinese Academy of Sciences, Zhejiang Cancer Hospital, No. 1 Banshan East Road, Gongshu District, Hangzhou, 310022, China
| | - Li-Wei Xu
- Department of Thoracic Surgery, Institute of Cancer Research and Basic Medical Sciences of Chinese Academy of Sciences, Cancer Hospital of University of Chinese Academy of Sciences, Zhejiang Cancer Hospital, No. 1 Banshan East Road, Gongshu District, Hangzhou, 310022, China
| | - Kai-Yi Tao
- Department of Thoracic Surgery, Institute of Cancer Research and Basic Medical Sciences of Chinese Academy of Sciences, Cancer Hospital of University of Chinese Academy of Sciences, Zhejiang Cancer Hospital, No. 1 Banshan East Road, Gongshu District, Hangzhou, 310022, China.
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11
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Moreira GCM, Poleti MD, Pértille F, Boschiero C, Cesar ASM, Godoy TF, Ledur MC, Reecy JM, Garrick DJ, Coutinho LL. Unraveling genomic associations with feed efficiency and body weight traits in chickens through an integrative approach. BMC Genet 2019; 20:83. [PMID: 31694549 PMCID: PMC6836328 DOI: 10.1186/s12863-019-0783-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Accepted: 10/11/2019] [Indexed: 12/25/2022] Open
Abstract
Background Feed efficiency and growth rate have been targets for selection to improve chicken production. The incorporation of genomic tools may help to accelerate selection. We genotyped 529 individuals using a high-density SNP chip (600 K, Affymetrix®) to estimate genomic heritability of performance traits and to identify genomic regions and their positional candidate genes associated with performance traits in a Brazilian F2 Chicken Resource population. Regions exhibiting selection signatures and a SNP dataset from resequencing were integrated with the genomic regions identified using the chip to refine the list of positional candidate genes and identify potential causative mutations. Results Feed intake (FI), feed conversion ratio (FC), feed efficiency (FE) and weight gain (WG) exhibited low genomic heritability values (i.e. from 0.0002 to 0.13), while body weight at hatch (BW1), 35 days-of-age (BW35), and 41 days-of-age (BW41) exhibited high genomic heritability values (i.e. from 0.60 to 0.73) in this F2 population. Twenty unique 1-Mb genomic windows were associated with BW1, BW35 or BW41, located on GGA1–4, 6–7, 10, 14, 24, 27 and 28. Thirty-eight positional candidate genes were identified within these windows, and three of them overlapped with selection signature regions. Thirteen predicted deleterious and three high impact sequence SNPs in these QTL regions were annotated in 11 positional candidate genes related to osteogenesis, skeletal muscle development, growth, energy metabolism and lipid metabolism, which may be associated with body weight in chickens. Conclusions The use of a high-density SNP array to identify QTL which were integrated with whole genome sequence signatures of selection allowed the identification of candidate genes and candidate causal variants. One novel QTL was detected providing additional information to understand the genetic architecture of body weight traits. We identified QTL for body weight traits, which were also associated with fatness in the same population. Our findings form a basis for further functional studies to elucidate the role of specific genes in regulating body weight and fat deposition in chickens, generating useful information for poultry breeding programs.
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Affiliation(s)
| | - Mirele Daiana Poleti
- University of São Paulo (USP) / College of Animal Science and Food Engineering (FZEA), Pirassununga, São Paulo, Brazil
| | - Fábio Pértille
- Department of Animal Science, University of São Paulo, Piracicaba, SP, 13418-900, Brazil
| | - Clarissa Boschiero
- Department of Animal Science, University of São Paulo, Piracicaba, SP, 13418-900, Brazil
| | | | - Thaís Fernanda Godoy
- Department of Animal Science, University of São Paulo, Piracicaba, SP, 13418-900, Brazil
| | | | - James M Reecy
- Department of Animal Science, Iowa State University (ISU), Ames, Iowa, USA
| | - Dorian J Garrick
- School of Agriculture, Massey University, Ruakura, Hamilton, New Zealand
| | - Luiz Lehmann Coutinho
- Department of Animal Science, University of São Paulo, Piracicaba, SP, 13418-900, Brazil.
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Radine C, Peters D, Reese A, Neuwahl J, Budach W, Jänicke RU, Sohn D. The RNA-binding protein RBM47 is a novel regulator of cell fate decisions by transcriptionally controlling the p53-p21-axis. Cell Death Differ 2019; 27:1274-1285. [PMID: 31511650 DOI: 10.1038/s41418-019-0414-6] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Revised: 08/26/2019] [Accepted: 08/28/2019] [Indexed: 11/09/2022] Open
Abstract
In recent years it has become more and more apparent that the regulation of gene expression by RNA-binding proteins (RBPs) is of utmost importance for most cellular signaling pathways. RBPs control several aspects of RNA biogenesis including splicing, localization, stability, and translation efficiency. One of these RBPs is RBM47 that recently has been suggested to function as a tumor suppressor as it was shown to suppress breast and colon cancer progression. Here we demonstrate that RBM47 is an important regulator of basal and DNA damage-induced p53 and p21WAF1/CIP1 protein expression. Knockdown of RBM47 by siRNAs results in a strong reduction in p53 mRNA and protein levels due to an impaired p53 promoter activity. Accordingly, overexpression of Flag-RBM47 enhances p53 promoter activity demonstrating that RBM47 regulates p53 at the transcriptional level. By controlling p53, knockdown of RBM47 concomitantly decreases also p21 expression at the transcriptional level, driving irradiated carcinoma cell lines from different entities into cell death rather than into senescence. Thus, RBM47 represents a novel molecular switch of cell fate decisions that functions as a regulator of the p53/p21-signaling axis.
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Affiliation(s)
- Claudia Radine
- Laboratory of Molecular Radiooncology, Clinic and Policlinic for Radiation Therapy and Radiooncology, Medical Faculty, Heinrich-Heine-University, Düsseldorf, Germany
| | - Dominik Peters
- Laboratory of Molecular Radiooncology, Clinic and Policlinic for Radiation Therapy and Radiooncology, Medical Faculty, Heinrich-Heine-University, Düsseldorf, Germany
| | - Alina Reese
- Laboratory of Molecular Radiooncology, Clinic and Policlinic for Radiation Therapy and Radiooncology, Medical Faculty, Heinrich-Heine-University, Düsseldorf, Germany
| | - Judith Neuwahl
- Laboratory of Molecular Radiooncology, Clinic and Policlinic for Radiation Therapy and Radiooncology, Medical Faculty, Heinrich-Heine-University, Düsseldorf, Germany
| | - Wilfried Budach
- Laboratory of Molecular Radiooncology, Clinic and Policlinic for Radiation Therapy and Radiooncology, Medical Faculty, Heinrich-Heine-University, Düsseldorf, Germany
| | - Reiner U Jänicke
- Laboratory of Molecular Radiooncology, Clinic and Policlinic for Radiation Therapy and Radiooncology, Medical Faculty, Heinrich-Heine-University, Düsseldorf, Germany
| | - Dennis Sohn
- Laboratory of Molecular Radiooncology, Clinic and Policlinic for Radiation Therapy and Radiooncology, Medical Faculty, Heinrich-Heine-University, Düsseldorf, Germany.
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Yurchenko AA, Deniskova TE, Yudin NS, Dotsev AV, Khamiruev TN, Selionova MI, Egorov SV, Reyer H, Wimmers K, Brem G, Zinovieva NA, Larkin DM. High-density genotyping reveals signatures of selection related to acclimation and economically important traits in 15 local sheep breeds from Russia. BMC Genomics 2019; 20:294. [PMID: 32039702 PMCID: PMC7227232 DOI: 10.1186/s12864-019-5537-0] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Background Domestication and centuries of selective breeding have changed genomes of sheep breeds to respond to environmental challenges and human needs. The genomes of local breeds, therefore, are valuable sources of genomic variants to be used to understand mechanisms of response to adaptation and artificial selection. As a step toward this we performed a high-density genotyping and comprehensive scans for signatures of selection in the genomes from 15 local sheep breeds reared across Russia. Results Results demonstrated that the genomes of Russian sheep breeds contain multiple regions under putative selection. More than 50% of these regions matched with intervals identified in previous scans for selective sweeps in sheep genomes. These regions contain well-known candidate genes related to morphology, adaptation, and domestication (e.g., KITLG, KIT, MITF, and MC1R), wool quality and quantity (e.g., DSG@, DSC@, and KRT@), growth and feed intake (e.g., HOXA@, HOXC@, LCORL, NCAPG, LAP3, and CCSER1), reproduction (e.g., CMTM6, HTRA1, GNAQ, UBQLN1, and IFT88), and milk-related traits (e.g., ABCG2, SPP1, ACSS1, and ACSS2). In addition, multiple genes that are putatively related to environmental adaptations were top-ranked in selected intervals (e.g., EGFR, HSPH1, NMUR1, EDNRB, PRL, TSHR, and ADAMTS5). Moreover, we observed that multiple key genes involved in human hereditary sensory and autonomic neuropathies, and genetic disorders accompanied with an inability to feel pain and environmental temperatures, were top-ranked in multiple or individual sheep breeds from Russia pointing to a possible mechanism of adaptation to harsh climatic conditions. Conclusions Our work represents the first comprehensive scan for signatures of selection in genomes of local sheep breeds from the Russian Federation of both European and Asian origins. We confirmed that the genomes of Russian sheep contain previously identified signatures of selection, demonstrating the robustness of our integrative approach. Multiple novel signatures of selection were found near genes which could be related to adaptation to the harsh environments of Russia. Our study forms a basis for future work on using Russian sheep genomes to spot specific genetic variants or haplotypes to be used in efforts on developing next-generation highly productive breeds, better suited to diverse Eurasian environments. Electronic supplementary material The online version of this article (10.1186/s12864-019-5537-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Andrey A Yurchenko
- The Federal Research Center Institute of Cytology and Genetics, The Siberian Branch of the Russian Academy of Sciences (ICG SB RAS), Novosibirsk, Russia
| | - Tatiana E Deniskova
- L.K. Ernst Federal Science Center for Animal Husbandry, Podolsk, 142132, Russia
| | - Nikolay S Yudin
- The Federal Research Center Institute of Cytology and Genetics, The Siberian Branch of the Russian Academy of Sciences (ICG SB RAS), Novosibirsk, Russia.,Novosibirsk State University, Novosibirsk, 630090, Russia
| | - Arsen V Dotsev
- L.K. Ernst Federal Science Center for Animal Husbandry, Podolsk, 142132, Russia
| | - Timur N Khamiruev
- Research Institute of Veterinary Medicine of Eastern Siberia, The Branch of the Siberian Federal Scientific Center for Agrobiotechnologies of the Russian Academy of Sciences, Chita, Russia
| | - Marina I Selionova
- All-Russian Research Institute of Sheep and Goat Breeding - branch of the Federal State Budgetary Scientific Institution North Caucasian Agrarian Center, Stavropol, 355017, Russia
| | - Sergey V Egorov
- Siberian Research Institute of Animal Husbandry, Krasnoobsk, Russia
| | - Henry Reyer
- Institute of Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), Dummerstorf, Germany
| | - Klaus Wimmers
- Institute of Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), Dummerstorf, Germany
| | - Gottfried Brem
- L.K. Ernst Federal Science Center for Animal Husbandry, Podolsk, 142132, Russia.,Institute of Animal Breeding and Genetics, University of Veterinary Medicine, Vienna, Austria
| | - Natalia A Zinovieva
- L.K. Ernst Federal Science Center for Animal Husbandry, Podolsk, 142132, Russia.
| | - Denis M Larkin
- The Federal Research Center Institute of Cytology and Genetics, The Siberian Branch of the Russian Academy of Sciences (ICG SB RAS), Novosibirsk, Russia. .,Royal Veterinary College, University of London, London, UK.
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