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Huang Y, Wang X, Wen C, Wang J, Zhou H, Wu L. Cancer-associated fibroblast-derived colony-stimulating factor 2 confers acquired osimertinib resistance in lung adenocarcinoma via promoting ribosome biosynthesis. MedComm (Beijing) 2024; 5:e653. [PMID: 39036343 PMCID: PMC11260172 DOI: 10.1002/mco2.653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 06/02/2024] [Accepted: 06/04/2024] [Indexed: 07/23/2024] Open
Abstract
Acquired resistance is a major obstacle to the therapeutic efficacy of osimertinib in lung adenocarcinoma (LUAD), but the underlying mechanisms are still not fully understood. Cancer-associated fibroblasts (CAFs) are the most abundant stromal cell type in LUAD tumor-microenvironment (TME) and have emerged as a key player in chemoresistance. However, the function of CAFs in osimertinib resistance is still unclear. Here, we showed that CAFs derived from osimertinib-resistant LUAD tissues (CAFOR) produced much more colony-stimulating factor 2 (CSF2) than those isolated from osimertinib-sensitive tissues. CAFOR-derived CSF2 activated the Janus kinase 2 (JAK2)/Signal transducer and activator of transcription 3 (STAT3) signaling pathway and upregulated lnc-CSRNP3 in LUAD cells. Lnc-CSRNP3 then promoted the expression of nearby gene CSRNP3 by recruiting chromodomain helicase DNA binding protein 9 (CHD9) and inhibited the phosphatase activity of the serine/threonine protein phosphatase 1 catalytic subunit α (PP1α), thereby induced osimertinib resistance by enhancing ribosome biogenesis. Collectively, our study reveals a critical role for CAFs in the development of osimertinib resistance and identifies the CSF2 pathway as an attractive target for monitoring osimertinib efficacy and overcoming osimertinib resistance in LUAD.
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Affiliation(s)
- Yutang Huang
- Institute of Life SciencesChongqing Medical UniversityChongqingChina
| | - Xiaoqing Wang
- Institute of Life SciencesChongqing Medical UniversityChongqingChina
| | - Chunjie Wen
- Institute of Life SciencesChongqing Medical UniversityChongqingChina
| | - Jingchan Wang
- School of StomatologyChongqing Medical UniversityChongqingChina
| | - Honghao Zhou
- Institute of Life SciencesChongqing Medical UniversityChongqingChina
- Pharmacogenetics Research InstituteInstitute of Clinical PharmacologyCentral South UniversityChangshaChina
| | - Lanxiang Wu
- Institute of Life SciencesChongqing Medical UniversityChongqingChina
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2
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Liu Y, Li W, Zhou S, Cui M, Zhang L. Pan-cancer analysis of the prognostic and immunological role of RPL4. Heliyon 2024; 10:e34461. [PMID: 39114029 PMCID: PMC11305218 DOI: 10.1016/j.heliyon.2024.e34461] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2024] [Revised: 06/29/2024] [Accepted: 07/09/2024] [Indexed: 08/10/2024] Open
Abstract
Ribosomal proteins (RPs) play an important role in the overall stability, function, and integrity of ribosomes. Ribosomal protein L4 (RPL4), which is encoded by RPL4, is assumed to play different roles in different cancers due to the strong correlation between them. However, research based on the underlying mechanisms of this correlations is limited. Therefore, this study investigated the biological role of RPL4 in various cancers. The Cancer Genome Atlas (TCGA) and Genotype-Tissue Expression (GTEx) databases were used to compare the differential expression of RPL4 in tumor and normal tissues. The Sangerbox database and Kaplan-Meier method were employed to assess RPL4's impact on the prognosis of pan-cancer. Analyses using the cBioPortal tool, Shiny Methylation Analysis Resource Tool (SMART), and MethSurv provided insights into the methylation and epigenetic alterations of RPL4. Gene enrichment analysis revealed that RPL4 is involved in ribosome biogenesis through multiple pathways, and its enrichment in signaling pathways directly or indirectly influence tumor development. Tumor Immune Single-cell Hub (TISCH) was used to analyze RPL4 expression levels and cellular functions in the tumor microenvironment. Tumor Immune Estimation Resource Database 2.0 (TIMER2.0) and Tumor-Immune System Interactions Database (TISIDB) tools revealed that RPL4 affected the immune infiltration potential of tumors. Furthermore, the application of the ROC mapper and CellMiner databases indicated an association between RPL4 and sensitivity to multiple antitumor drugs. Additionally, RPL4 was found to remodel the tumor immune microenvironment, leading to the development of chemoresistance. In conclusion, the findings suggest that RPL4 can be used as a potential tumor biomarker and may serve as a target for immunotherapy in various cancers. Genetic testing of RPL4 provides a foundation for the diagnosis, prognosis, and treatment of clinical tumors.
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Affiliation(s)
- Yan Liu
- Department of Plastic Surgery and Burns, Zhuhai People's Hospital (Zhuhai Clinical Medical College of Jinan University), China
| | - Wei Li
- Hepatobiliary and Pancreatic Surgery, Zhuhai People's Hospital (Zhuhai Clinical Medical College of Jinan University), China
| | - Shiyang Zhou
- Thyroid&Galactophore Surgery, Zhuhai People's Hospital (Zhuhai Clinical Medical College of Jinan University), China
| | - Min Cui
- Thyroid&Galactophore Surgery, Zhuhai People's Hospital (Zhuhai Clinical Medical College of Jinan University), China
| | - Lin Zhang
- Department of Plastic Surgery and Burns, Zhuhai People's Hospital (Zhuhai Clinical Medical College of Jinan University), China
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3
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Wang Q, Liu Y, Zhang M, Yang M, Liang J, Zuo X, Wang S, Jia X, Zhao H, Jiang H, Lin Q, Qin Q. Slc43a2 + T cell metastasis from spleen to brain in RGNNV infected teleost. SCIENCE CHINA. LIFE SCIENCES 2024; 67:733-744. [PMID: 38388846 DOI: 10.1007/s11427-023-2473-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 10/23/2023] [Indexed: 02/24/2024]
Abstract
The origin of T cells in the teleost's brain is unclear. While viewing the central nervous system (CNS) as immune privileged has been widely accepted, previous studies suggest that T cells residing in the thymus but not in the spleen of the teleost play an essential role in communicating with the peripheral organs. Here, we identified nine T cell subpopulations in the thymus and spleen of orange-spotted grouper (Epinephelus coioices) through single-cell RNA-sequencing analysis. After viral CNS infection with red-spotted grouper nervous necrosis virus (RGNNV), the number of slc43a2+ T cells synchronously increased in the spleen and brain. During the infection tests in asplenic zebrafish (tlx1▲ zebrafish model), no increase in the number of slc43a2+ T cells was observed in the brain. Single-cell transcriptomic analysis indicated that slc43a2+ T cells mature and functionally differentiate within the spleen and then migrate into the brain to trigger an immune response. This study suggests a novel route for T cell migration from the spleen to the brain during viral infection in fish.
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Affiliation(s)
- Qing Wang
- College of Marine Sciences, South China Agricultural University, Guangzhou, 510642, China
- Nansha-South China Agricultural University Fishery Research Institute, Guangzhou, 511457, China
- Joint University Laboratory of Guangdong Province, Hong Kong and Marco Region on Marine Bioresource Conservation and Exploitation, Guangzhou, 510642, China
| | - Yali Liu
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
- University of Chinese Academy of Sciences, Beijing, 100101, China
| | - Minlin Zhang
- College of Marine Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Min Yang
- College of Marine Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Jiantao Liang
- College of Marine Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Xiaoling Zuo
- College of Marine Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Shaowen Wang
- College of Marine Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Xianze Jia
- College of Marine Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Huihong Zhao
- College of Marine Sciences, South China Agricultural University, Guangzhou, 510642, China
- Nansha-South China Agricultural University Fishery Research Institute, Guangzhou, 511457, China
| | - Han Jiang
- University of Chinese Academy of Sciences, Beijing, 100101, China
| | - Qiang Lin
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China.
| | - Qiwei Qin
- College of Marine Sciences, South China Agricultural University, Guangzhou, 510642, China.
- Nansha-South China Agricultural University Fishery Research Institute, Guangzhou, 511457, China.
- Joint University Laboratory of Guangdong Province, Hong Kong and Marco Region on Marine Bioresource Conservation and Exploitation, Guangzhou, 510642, China.
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4
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Ryu HY. SUMO pathway is required for ribosome biogenesis. BMB Rep 2022; 55:535-540. [PMID: 36195568 PMCID: PMC9712707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Indexed: 12/14/2022] Open
Abstract
Ribosomes, acting as the cellular factories for protein production, are essential for all living organisms. Ribosomes are composed of both proteins and RNAs and are established through the coordination of several steps, including transcription, maturation of ribosomal RNA (rRNA), and assembly of ribosomal proteins. In particular, diverse factors required for ribosome biogenesis, such as transcription factors, small nucleolar RNA (snoRNA)-associated proteins, and assembly factors, are tightly regulated by various post-translational modifications. Among these modifications, small ubiquitin-related modifier (SUMO) targets lots of proteins required for gene expression of ribosomal proteins, rRNA, and snoRNAs, rRNA processing, and ribosome assembly. The tight control of SUMOylation affects functions and locations of substrates. This review summarizes current studies and recent progress of SUMOylation-mediated regulation of ribosome biogenesis. [BMB Reports 2022; 55(11): 535-540].
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Affiliation(s)
- Hong-Yeoul Ryu
- BK21 FOUR KNU Creative BioResearch Group, School of Life Sciences, College of National Sciences, Kyungpook National University, Daegu 41566, Korea,Brain Science and Engineering Institute, Kyungpook National University, Daegu 41566, Korea,Corresponding author. Tel: +82-53-950-6352; Fax: +82-53-955-5522; E-mail:
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5
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Ryu HY. SUMO pathway is required for ribosome biogenesis. BMB Rep 2022; 55:535-540. [PMID: 36195568 PMCID: PMC9712707 DOI: 10.5483/bmbrep.2022.55.11.130] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 09/15/2022] [Accepted: 09/26/2022] [Indexed: 12/24/2023] Open
Abstract
Ribosomes, acting as the cellular factories for protein production, are essential for all living organisms. Ribosomes are composed of both proteins and RNAs and are established through the coordination of several steps, including transcription, maturation of ribosomal RNA (rRNA), and assembly of ribosomal proteins. In particular, diverse factors required for ribosome biogenesis, such as transcription factors, small nucleolar RNA (snoRNA)-associated proteins, and assembly factors, are tightly regulated by various post-translational modifications. Among these modifications, small ubiquitin-related modifier (SUMO) targets lots of proteins required for gene expression of ribosomal proteins, rRNA, and snoRNAs, rRNA processing, and ribosome assembly. The tight control of SUMOylation affects functions and locations of substrates. This review summarizes current studies and recent progress of SUMOylation-mediated regulation of ribosome biogenesis. [BMB Reports 2022; 55(11): 535-540].
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Affiliation(s)
- Hong-Yeoul Ryu
- BK21 FOUR KNU Creative BioResearch Group, School of Life Sciences, College of National Sciences, Kyungpook National University, Daegu 41566, Korea
- Brain Science and Engineering Institute, Kyungpook National University, Daegu 41566, Korea
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6
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Chen F, Wang N, He X. Identification of Differential Genes of DNA Methylation Associated With Alzheimer's Disease Based on Integrated Bioinformatics and Its Diagnostic Significance. Front Aging Neurosci 2022; 14:884367. [PMID: 35615586 PMCID: PMC9125150 DOI: 10.3389/fnagi.2022.884367] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Accepted: 04/19/2022] [Indexed: 12/16/2022] Open
Abstract
Background Alzheimer's disease (AD) is a common neurodegenerative disease. The pathogenesis is complex and has not been clearly elucidated, and there is no effective treatment. Recent studies have demonstrated that DNA methylation is closely associated with the pathogenesis of AD, which sheds light on investigating potential biomarkers for the diagnosis of early AD and related possible therapeutic approaches. Methods Alzheimer's disease patients samples and healthy controls samples were collected from two datasets in the GEO database. Using LIMMA software package in R language to find differentially expressed genes (DEGs). Afterward, DEGs have been subjected to enrichment analysis of GO and KEGG pathways. The PPI networks and Hub genes were created and visualized based on the STRING database and Cytoscape. ROC curves were further constructed to analyze the accuracy of these genes for AD diagnosis. Results Analysis of the GSE109887 and GSE97760 datasets showed 477 significant DEGs. GO and KEGG enrichment analysis showed terms related to biological processes related to these genes. The top ten Hub genes were found on the basis of the PPI network using the CytoHubba plugin, and the AUC areas of these top ranked genes were all greater than 0.7, showing satisfactory diagnostic accuracy. Conclusion The study identified the top 10 Hub genes associated with AD-related DNA methylation, of which RPSA, RPS23, and RPLP0 have high diagnostic accuracy and excellent AD biomarker potential.
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Affiliation(s)
| | | | - Xiaping He
- School of Basic Medical Sciences, Dali University, Dali, China
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7
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Li D, Fan X, Li Y, Yang J, Lin H. The paradoxical functions of long noncoding RNAs in hepatocellular carcinoma: Implications in therapeutic opportunities and precision medicine. Genes Dis 2022; 9:358-369. [PMID: 35224152 PMCID: PMC8843871 DOI: 10.1016/j.gendis.2020.11.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 10/22/2020] [Accepted: 11/24/2020] [Indexed: 11/20/2022] Open
Abstract
Hepatocellular carcinoma (HCC) is among the most aggressive and lethal diseases with poor prognosis, worldwide. However, the mechanisms underlying HCC have not been comprehensively elucidated. With the recent application of high-throughput sequencing techniques, a diverse catalogue of differentially expressed long non-coding RNAs (lncRNA) in cancer have been shown to participate in HCC. Rather than being "transcriptional noise," they are emerging as important regulators of many biological processes, including chromatin remodelling, transcription, alternative splicing, translational and post-translational modification. Moreover, lncRNAs have dual effects in the development and progression of HCC, including oncogenic and tumour-suppressive roles. Collectively, recently data point to lncRNAs as novel diagnostic and prognostic biomarkers with satisfactory sensitivity and specificity, as well as being therapeutic targets for HCC patients. In this review, we highlight recent progress of the molecular patterns of lncRNAs and discuss their potential clinical application in human HCC.
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Affiliation(s)
- Duguang Li
- Department of General Surgery, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310058, PR China
- Biomedical Research Center, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310058, PR China
| | - Xiaoxiao Fan
- Department of General Surgery, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310058, PR China
- Biomedical Research Center, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310058, PR China
| | - Yirun Li
- Department of General Surgery, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310058, PR China
- Biomedical Research Center, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310058, PR China
| | - Jing Yang
- Department of General Surgery, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310058, PR China
- Biomedical Research Center, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310058, PR China
| | - Hui Lin
- Department of General Surgery, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310058, PR China
- Biomedical Research Center, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310058, PR China
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8
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Zhao Q, Yan S, Lu J, Parker DJ, Wu H, Sun Q, Crossman DK, Liu S, Wang Q, Sesaki H, Mitra K, Liu K, Jiao K. Drp1 regulates transcription of ribosomal protein genes in embryonic hearts. J Cell Sci 2022; 135:274456. [PMID: 35099001 PMCID: PMC8919333 DOI: 10.1242/jcs.258956] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 01/10/2022] [Indexed: 11/20/2022] Open
Abstract
Mitochondrial dysfunction causes severe congenital cardiac abnormalities and prenatal/neonatal lethality. The lack of sufficient knowledge regarding how mitochondrial abnormalities affect cardiogenesis poses a major barrier for the development of clinical applications that target mitochondrial deficiency-induced inborn cardiomyopathies. Mitochondrial morphology, which is regulated by fission and fusion, plays a key role in determining mitochondrial activity. Dnm1l encodes a dynamin-related GTPase, Drp1, which is required for mitochondrial fission. To investigate the role of Drp1 in cardiogenesis during the embryonic metabolic shift period, we specifically inactivated Dnm1l in second heart field-derived structures. Mutant cardiomyocytes in the right ventricle (RV) displayed severe defects in mitochondrial morphology, ultrastructure and activity. These defects caused increased cell death, decreased cell survival, disorganized cardiomyocytes and embryonic lethality. By characterizing this model, we reveal an AMPK-SIRT7-GABPB axis that relays the reduced cellular energy level to decrease transcription of ribosomal protein genes in cardiomyocytes. We therefore provide the first genetic evidence in mouse that Drp1 is essential for RV development. Our research provides further mechanistic insight into how mitochondrial dysfunction causes pathological molecular and cellular alterations during cardiogenesis.
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Affiliation(s)
- Qiancong Zhao
- Department of Cardiovascular Surgery, The Second Hospital of Jilin University, Changchun 130041, People's Republic of China,Department of Genetics, The University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Shun Yan
- Department of Genetics, The University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Jin Lu
- Department of Genetics, The University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Danitra J. Parker
- Department of Genetics, The University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Huiying Wu
- Department of Cardiovascular Surgery, The Second Hospital of Jilin University, Changchun 130041, People's Republic of China,Department of Genetics, The University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Qianchuang Sun
- Department of Cardiovascular Surgery, The Second Hospital of Jilin University, Changchun 130041, People's Republic of China,Department of Genetics, The University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - David K. Crossman
- Department of Genetics, The University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Shanrun Liu
- Department of Biochemistry and Molecular Genetics, The University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Qin Wang
- Department of Cell, Developmental and Integrative Biology, The University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Hiromi Sesaki
- Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Kasturi Mitra
- Department of Genetics, The University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Kexiang Liu
- Department of Cardiovascular Surgery, The Second Hospital of Jilin University, Changchun 130041, People's Republic of China,Authors for correspondence (; )
| | - Kai Jiao
- Department of Genetics, The University of Alabama at Birmingham, Birmingham, AL 35294, USA,Present address: Center for Biotechnology and Genomic Medicine, Medical College of Georgia, Augusta University, 1462 Laney Walker Blvd. CA4092, Augusta, GA 30912, USA
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Yi YW, You KS, Park JS, Lee SG, Seong YS. Ribosomal Protein S6: A Potential Therapeutic Target against Cancer? Int J Mol Sci 2021; 23:ijms23010048. [PMID: 35008473 PMCID: PMC8744729 DOI: 10.3390/ijms23010048] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Revised: 12/19/2021] [Accepted: 12/20/2021] [Indexed: 12/12/2022] Open
Abstract
Ribosomal protein S6 (RPS6) is a component of the 40S small ribosomal subunit and participates in the control of mRNA translation. Additionally, phospho (p)-RPS6 has been recognized as a surrogate marker for the activated PI3K/AKT/mTORC1 pathway, which occurs in many cancer types. However, downstream mechanisms regulated by RPS6 or p-RPS remains elusive, and the therapeutic implication of RPS6 is underappreciated despite an approximately half a century history of research on this protein. In addition, substantial evidence from RPS6 knockdown experiments suggests the potential role of RPS6 in maintaining cancer cell proliferation. This motivates us to investigate the current knowledge of RPS6 functions in cancer. In this review article, we reviewed the current information about the transcriptional regulation, upstream regulators, and extra-ribosomal roles of RPS6, with a focus on its involvement in cancer. We also discussed the therapeutic potential of RPS6 in cancer.
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Affiliation(s)
- Yong Weon Yi
- Department of Biochemistry, College of Medicine, Dankook University, Cheonan 31116, Chungcheongnam-do, Korea; (Y.W.Y.); (K.S.Y.); (J.-S.P.)
- Department of Nanobiomedical Science, Dankook University, Cheonan 31116, Chungcheongnam-do, Korea
| | - Kyu Sic You
- Department of Biochemistry, College of Medicine, Dankook University, Cheonan 31116, Chungcheongnam-do, Korea; (Y.W.Y.); (K.S.Y.); (J.-S.P.)
- Graduate School of Convergence Medical Science, Dankook University, Cheonan 31116, Chungcheongnam-do, Korea
| | - Jeong-Soo Park
- Department of Biochemistry, College of Medicine, Dankook University, Cheonan 31116, Chungcheongnam-do, Korea; (Y.W.Y.); (K.S.Y.); (J.-S.P.)
| | - Seok-Geun Lee
- Graduate School, Kyung Hee University, Seoul 02447, Korea
- Correspondence: (S.-G.L.); (Y.-S.S.); Tel.: +82-2-961-2355 (S.-G.L.); +82-41-550-3875 (Y.-S.S.); Fax: +82-2-961-9623 (S.-G.L.)
| | - Yeon-Sun Seong
- Department of Biochemistry, College of Medicine, Dankook University, Cheonan 31116, Chungcheongnam-do, Korea; (Y.W.Y.); (K.S.Y.); (J.-S.P.)
- Graduate School of Convergence Medical Science, Dankook University, Cheonan 31116, Chungcheongnam-do, Korea
- Correspondence: (S.-G.L.); (Y.-S.S.); Tel.: +82-2-961-2355 (S.-G.L.); +82-41-550-3875 (Y.-S.S.); Fax: +82-2-961-9623 (S.-G.L.)
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10
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Schott J, Reitter S, Lindner D, Grosser J, Bruer M, Shenoy A, Geiger T, Mathes A, Dobreva G, Stoecklin G. Nascent Ribo-Seq measures ribosomal loading time and reveals kinetic impact on ribosome density. Nat Methods 2021; 18:1068-1074. [PMID: 34480152 DOI: 10.1038/s41592-021-01250-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Accepted: 07/23/2021] [Indexed: 01/21/2023]
Abstract
In general, mRNAs are assumed to be loaded with ribosomes instantly upon entry into the cytoplasm. To measure ribosome density (RD) on nascent mRNA, we developed nascent Ribo-Seq by combining Ribo-Seq with progressive 4-thiouridine labeling. In mouse macrophages, we determined experimentally the lag between the appearance of nascent mRNA and its association with ribosomes, which was calculated to be 20-22 min for bulk mRNA. In mouse embryonic stem cells, nRibo-Seq revealed an even stronger lag of 35-38 min in ribosome loading. After stimulation of macrophages with lipopolysaccharide, the lag between cytoplasmic and translated mRNA leads to uncoupling between input and ribosome-protected fragments, which gives rise to distorted RD measurements under conditions where mRNA amounts are far from steady-state expression. As a result, we demonstrate that transcriptional changes affect RD in a passive way.
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Affiliation(s)
- Johanna Schott
- Mannheim Institute for Innate Immunoscience (MI3), Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany. .,Center for Molecular Biology of Heidelberg University (ZMBH), German Cancer Research Center (DKFZ)-ZMBH Alliance, Heidelberg, Germany.
| | - Sonja Reitter
- Mannheim Institute for Innate Immunoscience (MI3), Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany.,Center for Molecular Biology of Heidelberg University (ZMBH), German Cancer Research Center (DKFZ)-ZMBH Alliance, Heidelberg, Germany
| | - Doris Lindner
- Mannheim Institute for Innate Immunoscience (MI3), Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany.,Center for Molecular Biology of Heidelberg University (ZMBH), German Cancer Research Center (DKFZ)-ZMBH Alliance, Heidelberg, Germany
| | - Jan Grosser
- Mannheim Institute for Innate Immunoscience (MI3), Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany.,Center for Molecular Biology of Heidelberg University (ZMBH), German Cancer Research Center (DKFZ)-ZMBH Alliance, Heidelberg, Germany
| | - Marius Bruer
- Mannheim Institute for Innate Immunoscience (MI3), Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany.,Center for Molecular Biology of Heidelberg University (ZMBH), German Cancer Research Center (DKFZ)-ZMBH Alliance, Heidelberg, Germany
| | - Anjana Shenoy
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Tamar Geiger
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Arthur Mathes
- Department of Anatomy and Developmental Biology, European Center for Angioscience (ECAS), Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany.,German Center for Cardiovascular Research (DZHK), Heidelberg, Germany
| | - Gergana Dobreva
- Department of Anatomy and Developmental Biology, European Center for Angioscience (ECAS), Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany.,German Center for Cardiovascular Research (DZHK), Heidelberg, Germany
| | - Georg Stoecklin
- Mannheim Institute for Innate Immunoscience (MI3), Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany.,Center for Molecular Biology of Heidelberg University (ZMBH), German Cancer Research Center (DKFZ)-ZMBH Alliance, Heidelberg, Germany
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11
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Tao Y, Han Y, Yu L, Wang Q, Leng SX, Zhang H. The Predicted Key Molecules, Functions, and Pathways That Bridge Mild Cognitive Impairment (MCI) and Alzheimer's Disease (AD). Front Neurol 2020; 11:233. [PMID: 32308643 PMCID: PMC7145962 DOI: 10.3389/fneur.2020.00233] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2019] [Accepted: 03/11/2020] [Indexed: 12/11/2022] Open
Abstract
To elucidate the key molecules, functions, and pathways that bridge mild cognitive impairment (MCI) and Alzheimer's disease (AD), we investigated open gene expression data sets. Differential gene expression profiles were analyzed and combined with potential MCI- and AD-related gene expression profiles in public databases. Then, weighted gene co-expression network analysis was performed to identify the gene co-expression modules. One module was significantly negatively associated with MCI samples, in which gene ontology function and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis showed that these genes were related to cytosolic ribosome, ribosomal structure, oxidative phosphorylation, AD, and metabolic pathway. The other two modules correlated significantly with AD samples, in which functional and pathway enrichment analysis revealed strong relationships of these genes with cytoplasmic ribosome, protein binding, AD, cancer, and apoptosis. In addition, we regarded the core genes in the module network closely related to MCI and AD as bridge genes and submitted them to protein interaction network analysis to screen for major pathogenic genes according to the connectivity information. Among them, small nuclear ribonucleoprotein D2 polypeptide (SNRPD2), ribosomal protein S3a (RPS3A), S100 calcium binding protein A8 (S100A8), small nuclear ribonucleoprotein polypeptide G (SNRPG), U6 snRNA-associated Sm-like protein LSm3 (LSM3), ribosomal protein S27a (RPS27A), and ATP synthase F1 subunit gamma (ATP5C1) were not only major pathogenic genes of MCI, but also bridge genes. In addition, SNRPD2, RPS3A, S100A8, SNRPG, LSM3, thioredoxin (TXN), proteasome 20S subunit alpha 4 (PSMA4), annexin A1 (ANXA1), DnaJ heat shock protein family member A1 (DNAJA1), and prefoldin subunit 5 (PFDN5) were not only major pathogenic genes of AD, but also bridge genes. Next, we screened for differentially expressed microRNAs (miRNAs) to predict the miRNAs and transcription factors related the MCI and AD modules, respectively. The significance score of miRNAs in each module was calculated using a hypergeometric test to obtain the miRNApivot-Module interaction pair. Thirty-four bridge regulators were analyzed, among which hsa-miR-519d-3p was recognized as the bridge regulator between MCI and AD. Our study contributed to a better understanding of the pathogenic mechanisms of MCI and AD, and might lead to the development of a new strategy for clinical diagnosis and treatment.
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Affiliation(s)
- Ye Tao
- Department of Geriatrics, The First Affiliated Hospital of China Medical University, Shenyang, China
| | - Yu Han
- Department of Neurology, Jinqiu Hospital of Liaoning Province, Shenyang, China
| | - Lujiao Yu
- Department of Geriatrics, The First Affiliated Hospital of China Medical University, Shenyang, China
| | - Qi Wang
- Department of Geriatrics, The First Affiliated Hospital of China Medical University, Shenyang, China
| | - Sean X Leng
- Division of Geriatric Medicine and Gerontology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Haiyan Zhang
- Department of Geriatrics, The First Affiliated Hospital of China Medical University, Shenyang, China
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12
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Kong L, Wei Q, Hu X, Chen L, Li J. Ribosomal protein small subunit 15A (RPS15A) inhibits the apoptosis of breast cancer MDA-MB-231 cells via upregulating phosphorylated ERK1/2, Bad, and Chk1. J Cell Biochem 2019; 121:587-595. [PMID: 31535410 DOI: 10.1002/jcb.29304] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2018] [Accepted: 06/18/2019] [Indexed: 12/14/2022]
Abstract
AIM To detect the expression and identify the role of Ribosomal protein S15A (RPS15A) in human breast cancer (BC). METHODS Immunohistochemistry (IHC) was carried out for detecting the levels of RPS15A protein. Quantitative PCR was used to evaluate the mRNA level of RPS15A in one normal breast and three BC cell lines. Lentivirus-mediated shRNA targeting RPS15A was designed to investigate the impact of silencing RPS15A in MDA-MB-231 cell. RESULTS Higher RPS15A expression was detected in tumor tissues than in para-cancer tissues, and higher RPS15A expression was related to larger tumor size and higher TNM stage. Also, RPS15A mRNA expression in all three BC cell lines was higher than that in normal breast cell (all P < .005). Further, RPS15A knockdown significantly suppressed MDA-MB-231 cell proliferation and induced apoptosis. Moreover, RPS15A knockdown increased the caspase-3/-7 activity, and suppressed the phosphorylated levels of ERK1/2, Bad, and Chk1 (all P < .01). CONCLUSION RPS15A inhibits apoptosis via upregulating phosphorylated ERK1/2, Bad, and Chk1 in MDA-MB-231 cell line.
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Affiliation(s)
- Lingsuo Kong
- Department of Anesthesiology, Division of life Sciences and Medicine, West district of The First Affiliated Hospital of University of Science and Technology of China, University of Science and Technology of China, Hefei, Anhui, China
| | - Qing Wei
- Department of Anesthesiology, Division of life Sciences and Medicine, West district of The First Affiliated Hospital of University of Science and Technology of China, University of Science and Technology of China, Hefei, Anhui, China
| | - Xianwen Hu
- Department of Anesthesiology, The Second Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Lanren Chen
- Department of Anesthesiology, Division of life Sciences and Medicine, West district of The First Affiliated Hospital of University of Science and Technology of China, University of Science and Technology of China, Hefei, Anhui, China
| | - Juan Li
- Department of Anesthesia, Qilu Medical College of Shandong University, Jinan, China
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13
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Wang YH, Huang S, Zhu L, Yang Q, Yang XM, Gu JR, Zhang ZG, Nie HZ, Li J. Alternative transcription start site selection in ACSS2 controls its nuclear localization and promotes ribosome biosynthesis in hepatocellular carcinoma. Biochem Biophys Res Commun 2019; 514:632-638. [PMID: 31076106 DOI: 10.1016/j.bbrc.2019.04.193] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2019] [Accepted: 04/28/2019] [Indexed: 12/13/2022]
Abstract
Acetyl-CoA synthetase 2 (ACSS2) generates acetyl-CoA from acetate is important for histone acetylation and gene expression. ACSS2 fulfills distinct functions depending on its cellular location in tumor cells. The role and cellular localization of ACSS2 in hepatocellular carcinoma (HCC) remains to be studied. Herein, we identified that the alternative transcription start site selection of ACSS2 was significantly different between HCC and corresponding adjacent tissues. Alternative transcription start site selection produced two different ACSS2 transcripts, ACSS2-S1 and ACSS2-S2. The two isoforms of ACSS2 had different subcellular localization and different functions. Overexpression of ACSS2-S2 promoted cell proliferation and invasion, but ACSS2-S1 did not. The ACSS2-S1 was mainly present in cytoplasm, and ACSS2-S2 was distributed in both nucleus and cytoplasm. Finally, we demonstrated that alternative transcription start site selection of ACSS2 correlates ribosome biogenesis in HCC. Our findings reveal an oncogenic role of ACSS2-S2 in HCC progression via increase of ribosome biogenesis, and suggest ACSS2-S2 might be a potential therapeutic target against the HCC.
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Affiliation(s)
- Ya-Hui Wang
- Shanghai Medical College of Fudan University, Shanghai, 200032, PR China
| | - Shan Huang
- College of Animal Science, Jilin University, Changchun, Jilin, 130062, China
| | - Lei Zhu
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200240, PR China
| | - Qin Yang
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200240, PR China
| | - Xiao-Mei Yang
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200240, PR China
| | - Jian-Ren Gu
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200240, PR China
| | - Zhi-Gang Zhang
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200240, PR China
| | - Hui-Zhen Nie
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200240, PR China.
| | - Jun Li
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200240, PR China.
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14
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Hewitson JP, Shah KM, Brown N, Grevitt P, Hain S, Newling K, Sharp TV, Kaye PM, Lagos D. miR-132 suppresses transcription of ribosomal proteins to promote protective Th1 immunity. EMBO Rep 2019; 20:embr.201846620. [PMID: 30833344 DOI: 10.15252/embr.201846620] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Revised: 02/01/2019] [Accepted: 02/06/2019] [Indexed: 01/01/2023] Open
Abstract
Determining the mechanisms that distinguish protective immunity from pathological chronic inflammation remains a fundamental challenge. miR-132 has been shown to play largely immunoregulatory roles in immunity; however, its role in CD4+ T cell function is poorly understood. Here, we show that CD4+ T cells express high levels of miR-132 and that T cell activation leads to miR-132 up-regulation. The transcriptomic hallmark of splenic CD4+ T cells lacking the miR-132/212 cluster during chronic infection is an increase in mRNA levels of ribosomal protein (RP) genes. BTAF1, a co-factor of B-TFIID and novel miR-132/212-3p target, and p300 contribute towards miR-132/212-mediated regulation of RP transcription. Following infection with Leishmania donovani, miR-132 -/- CD4+ T cells display enhanced expression of IL-10 and decreased IFNγ. This is associated with reduced hepatosplenomegaly and enhanced pathogen load. The enhanced IL-10 expression in miR-132 -/- Th1 cells is recapitulated in vitro following treatment with phenylephrine, a drug reported to promote ribosome synthesis. Our results uncover that miR-132/212-mediated regulation of RP expression is critical for optimal CD4+ T cell activation and protective immunity against pathogens.
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Affiliation(s)
- James P Hewitson
- Centre for Immunology and Infection and York Biomedical Research Institute, Hull York Medical School and Department of Biology, University of York, York, UK
| | - Kunal M Shah
- Centre of Molecular Oncology, Barts Cancer Institute, John Vane Science Centre, Charterhouse Square, Queen Mary University London, London, UK
| | - Najmeeyah Brown
- Centre for Immunology and Infection and York Biomedical Research Institute, Hull York Medical School and Department of Biology, University of York, York, UK
| | - Paul Grevitt
- Centre of Molecular Oncology, Barts Cancer Institute, John Vane Science Centre, Charterhouse Square, Queen Mary University London, London, UK
| | - Sofia Hain
- Centre for Immunology and Infection and York Biomedical Research Institute, Hull York Medical School and Department of Biology, University of York, York, UK
| | - Katherine Newling
- Genomics and Bioinformatics Laboratory, Bioscience Technology Facility, Department of Biology, University of York, York, UK
| | - Tyson V Sharp
- Centre of Molecular Oncology, Barts Cancer Institute, John Vane Science Centre, Charterhouse Square, Queen Mary University London, London, UK
| | - Paul M Kaye
- Centre for Immunology and Infection and York Biomedical Research Institute, Hull York Medical School and Department of Biology, University of York, York, UK
| | - Dimitris Lagos
- Centre for Immunology and Infection and York Biomedical Research Institute, Hull York Medical School and Department of Biology, University of York, York, UK
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15
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Patra P, Izawa T, Pena-Castillo L. REPA: Applying Pathway Analysis to Genome-Wide Transcription Factor Binding Data. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2018; 15:1270-1283. [PMID: 27019499 DOI: 10.1109/tcbb.2015.2453948] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Pathway analysis has been extensively applied to aid in the interpretation of the results of genome-wide transcription profiling studies, and has been shown to successfully find associations between the biological phenomena under study and biological pathways. There are two widely used approaches of pathway analysis: over-representation analysis, and gene set analysis. Recently genome-wide transcription factor binding data has become widely available allowing for the application of pathway analysis to this type of data. In this work, we developed regulatory enrichment pathway analysis (REPA) to apply gene set analysis to genome-wide transcription factor binding data to infer associations between transcription factors and biological pathways. We used the transcription factor binding data generated by the ENCODE project, and gene sets from the Molecular Signatures and KEGG databases. Our results showed that 54 percent of the predictions examined have literature support and that REPA's recall is roughly 54 percent. This level of precision is promising as several of REPA's predictions are expected to be novel and can be used to guide new research avenues. In addition, the results of our case studies showed that REPA enhances the interpretation of genome-wide transcription profiling studies by suggesting putative regulators behind the observed transcriptional responses.
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16
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Chen Z, Bu N, Qiao X, Zuo Z, Shu Y, Liu Z, Qian Z, Chen J, Hou Y. Forkhead Box M1 Transcriptionally Regulates the Expression of Long Noncoding RNAs Snhg8 and Gm26917 to Promote Proliferation and Survival of Muscle Satellite Cells. Stem Cells 2018; 36:1097-1108. [PMID: 29575305 DOI: 10.1002/stem.2824] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2017] [Revised: 12/14/2017] [Accepted: 12/19/2017] [Indexed: 12/28/2022]
Abstract
Multiple functions have been proposed for transcription factor FoxM1, including the regulation of cell proliferation, differentiation, senescence, apoptosis, and tissue homeostasis. However, the role of FoxM1 in muscle satellite cells (SCs) remains unclear. In the present study, we demonstrated that FoxM1 was essential for the proliferation and survival of SCs. Crucially, we found that long noncoding RNAs (lncRNAs) Snhg8 and Gm26917 significantly regulated the proliferation and apoptosis of SCs, respectively, and these lncRNAs were directly regulated by FoxM1 in SCs. Mechanistically, Snhg8 sustained SCs proliferation by promoting the transcription of ribosomal proteins, while Gm26917 acted as a competing endogenous RNA for microRNA-29b, which accelerated apoptosis of SCs. In mice, conditional knockout of FoxM1 in skeletal muscle resulted in decreased proliferation and increased apoptosis of SCs. Thus, our studies revealed a previously unrecognized role of FoxM1 in SCs and uncovered two lncRNAs, Snhg8 and Gm26917, which function as novel targets of FoxM1 in the regulation of SCs proliferation and survival. Stem Cells 2018;36:1097-1108.
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Affiliation(s)
- Zhe Chen
- Department of Hematology, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, People's Republic of China
| | - Nuping Bu
- Department of Hematology, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, People's Republic of China
| | - Xiaohong Qiao
- Department of Pediatrics, Tongji Hospital, Tongji University, Shanghai, People's Republic of China
| | - Zhixiang Zuo
- Sun Yat-sen University Cancer Center, Sun Yat-sen University, Guangzhou, People's Republic of China
| | - Yahai Shu
- Department of Hematology, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, People's Republic of China
| | - Zhilong Liu
- Department of Hematology, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, People's Republic of China
| | - Zhijian Qian
- Department of Medicine, Division of Hematology/Oncology, University of Illinois at Chicago, Chicago, Illinois, USA
| | - Jieping Chen
- Department of Hematology, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, People's Republic of China
| | - Yu Hou
- Department of Hematology, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, People's Republic of China
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17
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Ahuja R, Kumar V. Stimulation of Pol III-dependent 5S rRNA and U6 snRNA gene expression by AP-1 transcription factors. FEBS J 2017; 284:2066-2077. [PMID: 28488757 DOI: 10.1111/febs.14104] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Revised: 04/15/2017] [Accepted: 05/05/2017] [Indexed: 12/31/2022]
Abstract
RNA polymerase III transcribes structurally diverse group of essential noncoding RNAs including 5S ribosomal RNA (5SrRNA) and U6 snRNA. These noncoding RNAs are involved in RNA processing and ribosome biogenesis, thus, coupling Pol III activity to the rate of protein synthesis, cell growth, and proliferation. Even though a few Pol II-associated transcription factors have been reported to participate in Pol III-dependent transcription, its activation by activator protein 1 (AP-1) factors, c-Fos and c-Jun, has remained unexplored. Here, we show that c-Fos and c-Jun bind to specific sites in the regulatory regions of 5S rRNA (type I) and U6 snRNA (type III) gene promoters and stimulate their transcription. Our chromatin immunoprecipitation studies suggested that endogenous AP-1 factors bind to their cognate promoter elements during the G1/S transition of cell cycle apparently synchronous with Pol III transcriptional activity. Furthermore, the interaction of c-Jun with histone acetyltransferase p300 promoted the recruitment of p300/CBP complex on the promoters and facilitated the occupancy of Pol III transcriptional machinery via histone acetylation and chromatin remodeling. The findings of our study, together, suggest that AP-1 factors are novel regulators of Pol III-driven 5S rRNA and U6 snRNA expression with a potential role in cell proliferation.
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Affiliation(s)
- Richa Ahuja
- Virology Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi, India
| | - Vijay Kumar
- Virology Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi, India
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18
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Herrero-Sánchez MC, Rodríguez-Serrano C, Almeida J, San Segundo L, Inogés S, Santos-Briz Á, García-Briñón J, Corchete LA, San Miguel JF, Del Cañizo C, Blanco B. Targeting of PI3K/AKT/mTOR pathway to inhibit T cell activation and prevent graft-versus-host disease development. J Hematol Oncol 2016; 9:113. [PMID: 27765055 PMCID: PMC5072323 DOI: 10.1186/s13045-016-0343-5] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Accepted: 10/08/2016] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Graft-versus-host disease (GvHD) remains the major obstacle to successful allogeneic hematopoietic stem cell transplantation, despite of the immunosuppressive regimens administered to control T cell alloreactivity. PI3K/AKT/mTOR pathway is crucial in T cell activation and function and, therefore, represents an attractive therapeutic target to prevent GvHD development. Recently, numerous PI3K inhibitors have been developed for cancer therapy. However, few studies have explored their immunosuppressive effect. METHODS The effects of a selective PI3K inhibitor (BKM120) and a dual PI3K/mTOR inhibitor (BEZ235) on human T cell proliferation, expression of activation-related molecules, and phosphorylation of PI3K/AKT/mTOR pathway proteins were analyzed. Besides, the ability of BEZ235 to prevent GvHD development in mice was evaluated. RESULTS Simultaneous inhibition of PI3K and mTOR was efficient at lower concentrations than PI3K specific targeting. Importantly, BEZ235 prevented naïve T cell activation and induced tolerance of alloreactive T cells, while maintaining an adequate response against cytomegalovirus, more efficiently than BKM120. Finally, BEZ235 treatment significantly improved the survival and decreased the GvHD development in mice. CONCLUSIONS These results support the use of PI3K inhibitors to control T cell responses and show the potential utility of the dual PI3K/mTOR inhibitor BEZ235 in GvHD prophylaxis.
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Affiliation(s)
- Mª Carmen Herrero-Sánchez
- Servicio de Hematología, Hospital Universitario de Salamanca, Paseo de San Vicente 58-182, 37007, Salamanca, Spain.,Instituto de Investigación Biomédica de Salamanca (IBSAL), Paseo de San Vicente 58-182, 37007, Salamanca, Spain.,Centro de Investigación del Cáncer, Universidad de Salamanca, Campus Miguel de Unamuno, 37007, Salamanca, Spain
| | - Concepción Rodríguez-Serrano
- Servicio de Hematología, Hospital Universitario de Salamanca, Paseo de San Vicente 58-182, 37007, Salamanca, Spain.,Instituto de Investigación Biomédica de Salamanca (IBSAL), Paseo de San Vicente 58-182, 37007, Salamanca, Spain.,Centro de Investigación del Cáncer, Universidad de Salamanca, Campus Miguel de Unamuno, 37007, Salamanca, Spain
| | - Julia Almeida
- Instituto de Investigación Biomédica de Salamanca (IBSAL), Paseo de San Vicente 58-182, 37007, Salamanca, Spain.,Centro de Investigación del Cáncer, Universidad de Salamanca, Campus Miguel de Unamuno, 37007, Salamanca, Spain.,Servicio de Citometría, Centro de Investigación del Cáncer, Universidad de Salamanca, Campus Miguel de Unamuno, 37007, Salamanca, Spain
| | - Laura San Segundo
- Instituto de Investigación Biomédica de Salamanca (IBSAL), Paseo de San Vicente 58-182, 37007, Salamanca, Spain.,Centro de Investigación del Cáncer, Universidad de Salamanca, Campus Miguel de Unamuno, 37007, Salamanca, Spain
| | - Susana Inogés
- Laboratorio de Inmunoterapia, Clínica Universidad de Navarra, Avda. Pío XII 55, 31008, Pamplona, Spain
| | - Ángel Santos-Briz
- Instituto de Investigación Biomédica de Salamanca (IBSAL), Paseo de San Vicente 58-182, 37007, Salamanca, Spain.,Departamento de Patología, Hospital Universitario de Salamanca, Paseo de San Vicente 58-182, 37007, Salamanca, Spain
| | - Jesús García-Briñón
- Instituto de Investigación Biomédica de Salamanca (IBSAL), Paseo de San Vicente 58-182, 37007, Salamanca, Spain.,Departamento de Biología Celular y Patología, Facultad de Medicina, Campus Miguel de Unamuno, 37007, Salamanca, Spain
| | - Luis Antonio Corchete
- Servicio de Hematología, Hospital Universitario de Salamanca, Paseo de San Vicente 58-182, 37007, Salamanca, Spain.,Instituto de Investigación Biomédica de Salamanca (IBSAL), Paseo de San Vicente 58-182, 37007, Salamanca, Spain.,Centro de Investigación del Cáncer, Universidad de Salamanca, Campus Miguel de Unamuno, 37007, Salamanca, Spain
| | - Jesús F San Miguel
- Clínica Universidad de Navarra, Centro de Investigación Médica Aplicada, Instituto de Investigación Sanitaria de Navarra, Avda. Pío XII 55, 31008, Pamplona, Spain
| | - Consuelo Del Cañizo
- Servicio de Hematología, Hospital Universitario de Salamanca, Paseo de San Vicente 58-182, 37007, Salamanca, Spain.,Instituto de Investigación Biomédica de Salamanca (IBSAL), Paseo de San Vicente 58-182, 37007, Salamanca, Spain.,Centro de Investigación del Cáncer, Universidad de Salamanca, Campus Miguel de Unamuno, 37007, Salamanca, Spain
| | - Belén Blanco
- Servicio de Hematología, Hospital Universitario de Salamanca, Paseo de San Vicente 58-182, 37007, Salamanca, Spain. .,Instituto de Investigación Biomédica de Salamanca (IBSAL), Paseo de San Vicente 58-182, 37007, Salamanca, Spain. .,Centro de Investigación del Cáncer, Universidad de Salamanca, Campus Miguel de Unamuno, 37007, Salamanca, Spain.
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19
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Zhu XT, Yuan JH, Zhu TT, Li YY, Cheng XY. Long noncoding RNA glypican 3 (GPC3) antisense transcript 1 promotes hepatocellular carcinoma progression via epigenetically activating GPC3. FEBS J 2016; 283:3739-3754. [DOI: 10.1111/febs.13839] [Citation(s) in RCA: 106] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2016] [Revised: 07/16/2016] [Accepted: 08/26/2016] [Indexed: 12/30/2022]
Affiliation(s)
- Xiao-ting Zhu
- Department of Anatomy, Histology and Embryology; Shanghai Jiao Tong University School of Medicine; China
| | - Ji-hang Yuan
- Department of Medical Genetics; Second Military Medical University; Shanghai China
| | - Teng-teng Zhu
- Department of Anatomy, Histology and Embryology; Shanghai Jiao Tong University School of Medicine; China
| | - Yang-yang Li
- Department of Anatomy, Histology and Embryology; Shanghai Jiao Tong University School of Medicine; China
| | - Xiao-yang Cheng
- Department of Anatomy, Histology and Embryology; Shanghai Jiao Tong University School of Medicine; China
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20
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Rajput P, Pandey V, Kumar V. Stimulation of ribosomal RNA gene promoter by transcription factor Sp1 involves active DNA demethylation by Gadd45-NER pathway. BIOCHIMICA ET BIOPHYSICA ACTA 2016; 1859:953-63. [PMID: 27156884 DOI: 10.1016/j.bbagrm.2016.05.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2016] [Revised: 04/23/2016] [Accepted: 05/04/2016] [Indexed: 01/29/2023]
Abstract
The well-studied Pol II transcription factor Sp1 has not been investigated for its regulatory role in rDNA transcription. Here, we show that Sp1 bound to specific sites on rDNA and localized into the nucleoli during the G1 phase of cell cycle to activate rDNA transcription. It facilitated the recruitment of Pol I pre-initiation complex and impeded the binding of nucleolar remodeling complex (NoRC) to rDNA resulting in the formation of euchromatin active state. More importantly, Sp1 also orchestrated the site-specific binding of Gadd45a-nucleotide excision repair (NER) complex resulting in active demethylation and transcriptional activation of rDNA. Interestingly, knockdown of Sp1 impaired rDNA transcription due to reduced engagement of the Gadd45a-NER complex and hypermethylation of rDNA. Thus, the present study unveils a novel role of Sp1 in rDNA transcription involving promoter demethylation.
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MESH Headings
- A549 Cells
- Cell Cycle Proteins/genetics
- Cell Cycle Proteins/metabolism
- Cell Nucleolus/metabolism
- DNA Methylation
- DNA Repair
- DNA, Ribosomal/genetics
- DNA, Ribosomal/metabolism
- Epigenesis, Genetic
- Euchromatin/chemistry
- Euchromatin/metabolism
- G1 Phase
- Genes, Reporter
- Green Fluorescent Proteins/genetics
- Green Fluorescent Proteins/metabolism
- HCT116 Cells
- HEK293 Cells
- Humans
- Nuclear Proteins/genetics
- Nuclear Proteins/metabolism
- Promoter Regions, Genetic
- RNA, Ribosomal/genetics
- RNA, Ribosomal/metabolism
- RNA, Small Interfering/genetics
- RNA, Small Interfering/metabolism
- Signal Transduction
- Sp1 Transcription Factor/antagonists & inhibitors
- Sp1 Transcription Factor/genetics
- Sp1 Transcription Factor/metabolism
- Transcription, Genetic
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Affiliation(s)
- Pallavi Rajput
- Virology Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi-110067, India
| | - Vijaya Pandey
- Virology Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi-110067, India
| | - Vijay Kumar
- Virology Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi-110067, India.
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21
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Jorquera R, Ortiz R, Ossandon F, Cárdenas JP, Sepúlveda R, González C, Holmes DS. SinEx DB: a database for single exon coding sequences in mammalian genomes. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2016; 2016:baw095. [PMID: 27278816 PMCID: PMC4897596 DOI: 10.1093/database/baw095] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/13/2015] [Accepted: 05/11/2016] [Indexed: 12/27/2022]
Abstract
Eukaryotic genes are typically interrupted by intragenic, noncoding sequences termed introns. However, some genes lack introns in their coding sequence (CDS) and are generally known as 'single exon genes' (SEGs). In this work, a SEG is defined as a nuclear, protein-coding gene that lacks introns in its CDS. Whereas, many public databases of Eukaryotic multi-exon genes are available, there are only two specialized databases for SEGs. The present work addresses the need for a more extensive and diverse database by creating SinEx DB, a publicly available, searchable database of predicted SEGs from 10 completely sequenced mammalian genomes including human. SinEx DB houses the DNA and protein sequence information of these SEGs and includes their functional predictions (KOG) and the relative distribution of these functions within species. The information is stored in a relational database built with My SQL Server 5.1.33 and the complete dataset of SEG sequences and their functional predictions are available for downloading. SinEx DB can be interrogated by: (i) a browsable phylogenetic schema, (ii) carrying out BLAST searches to the in-house SinEx DB of SEGs and (iii) via an advanced search mode in which the database can be searched by key words and any combination of searches by species and predicted functions. SinEx DB provides a rich source of information for advancing our understanding of the evolution and function of SEGs.Database URL: www.sinex.cl.
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Affiliation(s)
- Roddy Jorquera
- Center for Bioinformatics and Genome Biology, Fundacion Ciencia & Vida and Facultad de Ciencias Biologicas, Universidad Andres Bello, Avda Zañartu 1482, Santiago, Chile
| | - Rodrigo Ortiz
- Center for Bioinformatics and Genome Biology, Fundacion Ciencia & Vida and Facultad de Ciencias Biologicas, Universidad Andres Bello, Avda Zañartu 1482, Santiago, Chile
| | - F Ossandon
- Center for Bioinformatics and Genome Biology, Fundacion Ciencia & Vida and Facultad de Ciencias Biologicas, Universidad Andres Bello, Avda Zañartu 1482, Santiago, Chile
| | - Juan Pablo Cárdenas
- Center for Bioinformatics and Genome Biology, Fundacion Ciencia & Vida and Facultad de Ciencias Biologicas, Universidad Andres Bello, Avda Zañartu 1482, Santiago, Chile
| | - Rene Sepúlveda
- Center for Bioinformatics and Genome Biology, Fundacion Ciencia & Vida and Facultad de Ciencias Biologicas, Universidad Andres Bello, Avda Zañartu 1482, Santiago, Chile
| | - Carolina González
- Center for Bioinformatics and Genome Biology, Fundacion Ciencia & Vida and Facultad de Ciencias Biologicas, Universidad Andres Bello, Avda Zañartu 1482, Santiago, Chile
| | - David S Holmes
- Center for Bioinformatics and Genome Biology, Fundacion Ciencia & Vida and Facultad de Ciencias Biologicas, Universidad Andres Bello, Avda Zañartu 1482, Santiago, Chile
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22
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Zhang Y, Zhang G, Li X, Li B, Zhang X. The effect of ribosomal protein S15a in lung adenocarcinoma. PeerJ 2016; 4:e1792. [PMID: 26989627 PMCID: PMC4793315 DOI: 10.7717/peerj.1792] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2015] [Accepted: 02/20/2016] [Indexed: 11/20/2022] Open
Abstract
Background: RPS15A (Ribosomal Protein S15A) promotes mRNA/ribosome interactions in translation. It is critical for the process of eukaryotic protein biosynthesis. Recently, aberrantly expressed RPS15A was found in the hepatitis virus and in malignant tumors. However, the role of RPS15A has not been fully revealed on the development of lung cancer. Method: In this study, a Tissue Microarray (TMA) of primary lung adenocarcinoma tissue specimens was carried out. Furthermore, to further investigate the function of RPS15A in lung cancer, RPS15A-specific short hairpin RNA (shRNA) expressing lentivirus (Lv-shRPS15A) was constructed and used to infect H1299 and A549 cells. Result: Our data showed that RPS15A expression was increased in tumor tissues. Furthermore, the knockdown of RSP15A inhibited cancer cell growth and induced apoptosis in the cancer cells. Gene expression profile microarray also revealed that the P53 signaling pathway was activated in Lv-shRPS15A-infected cancer cells. Conclusion: Taken together, our results demonstrate that RPS15A is a novel oncogene in non-small cell lung cancer and may be a potential therapeutic target in lung cancer.
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Affiliation(s)
- Yifan Zhang
- Department of Thoracic Surgery, The Second Hospital of Jilin University , Changchun, Jilin , China
| | - Guangxin Zhang
- Department of Thoracic Surgery, The Second Hospital of Jilin University , Changchun, Jilin , China
| | - Xin Li
- Jilin provincial key laboratory on molecular and chemical genetic, The Second Hospital of Jilin University , Changchun , China
| | - Bingjin Li
- Jilin provincial key laboratory on molecular and chemical genetic, The Second Hospital of Jilin University , Changchun , China
| | - Xingyi Zhang
- Department of Thoracic Surgery, The Second Hospital of Jilin University , Changchun, Jilin , China
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23
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Herrero-Sánchez MC, Rodríguez-Serrano C, Almeida J, San-Segundo L, Inogés S, Santos-Briz Á, García-Briñón J, SanMiguel JF, Del Cañizo C, Blanco B. Effect of mTORC1/mTORC2 inhibition on T cell function: potential role in graft-versus-host disease control. Br J Haematol 2016; 173:754-68. [PMID: 26914848 DOI: 10.1111/bjh.13984] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Accepted: 12/21/2015] [Indexed: 12/17/2022]
Abstract
The mechanistic target of rapamycin (mTOR) pathway is crucial for the activation and function of T cells, which play an essential role in the development of graft-versus-host disease (GvHD). Despite its partial ability to block mTOR pathway, the mTORC1 inhibitor rapamycin has shown encouraging results in the control of GvHD. Therefore, we considered that simultaneous targeting of both mTORC1 and mTORC2 complexes could exert a more potent inhibition of T cell activation and, thus, could have utility in GvHD control. To assess this assumption, we have used the dual mTORC1/mTORC2 inhibitors CC214-1 and CC214-2. In vitro studies confirmed the superior ability of CC214-1 versus rapamycin to block mTORC1 and mTORC2 activity and to reduce T cell proliferation. Both drugs induced a similar decrease in Th1/Th2 cytokine secretion, but CC214-1 was more efficient in inhibiting naïve T cell activation and the expression of T-cell activation markers. In addition, CC214-1 induced specific tolerance against alloantigens, while preserving anti-cytomegalovirus response. Finally, in a mouse model of GvHD, the administration of CC214-2 significantly improved mice survival and decreased GvHD-induced damages. In conclusion, the current study shows, for the first time, the immunosuppressive ability of CC214-1 on T lymphocytes and illustrates the role of CC214-2 in the allogeneic transplantation setting as a possible GvHD prophylaxis agent.
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Affiliation(s)
- Ma Carmen Herrero-Sánchez
- Servicio de Hematología, Hospital Universitario de Salamanca, Salamanca, Spain.,Instituto de Investigación Biomédica de Salamanca (IBSAL), Salamanca, Spain.,Centro de Investigación del Cáncer, Universidad de Salamanca, Salamanca, Spain
| | - Concepción Rodríguez-Serrano
- Servicio de Hematología, Hospital Universitario de Salamanca, Salamanca, Spain.,Instituto de Investigación Biomédica de Salamanca (IBSAL), Salamanca, Spain.,Centro de Investigación del Cáncer, Universidad de Salamanca, Salamanca, Spain
| | - Julia Almeida
- Instituto de Investigación Biomédica de Salamanca (IBSAL), Salamanca, Spain.,Servicio de Citometría, Centro de Investigación del Cáncer, Universidad de Salamanca, Salamanca, Spain
| | - Laura San-Segundo
- Instituto de Investigación Biomédica de Salamanca (IBSAL), Salamanca, Spain.,Centro de Investigación del Cáncer, Universidad de Salamanca, Salamanca, Spain
| | - Susana Inogés
- Laboratorio de Inmunoterapia, Clínica Universidad de Navarra, Pamplona, Spain
| | - Ángel Santos-Briz
- Instituto de Investigación Biomédica de Salamanca (IBSAL), Salamanca, Spain.,Departamento de Patología, Hospital Universitario de Salamanca, Salamanca, Spain
| | - Jesús García-Briñón
- Instituto de Investigación Biomédica de Salamanca (IBSAL), Salamanca, Spain.,Departamento de Biología Celular y Patología, Facultad de Medicina, Salamanca, Spain
| | - Jesús F SanMiguel
- Clínica Universidad de Navarra, Centro de Investigación Médica Aplicada, Instituto de Investigación Sanitaria de Navarra, Pamplona, Spain
| | - Consuelo Del Cañizo
- Servicio de Hematología, Hospital Universitario de Salamanca, Salamanca, Spain.,Instituto de Investigación Biomédica de Salamanca (IBSAL), Salamanca, Spain.,Centro de Investigación del Cáncer, Universidad de Salamanca, Salamanca, Spain
| | - Belén Blanco
- Servicio de Hematología, Hospital Universitario de Salamanca, Salamanca, Spain.,Instituto de Investigación Biomédica de Salamanca (IBSAL), Salamanca, Spain
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24
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Presnell JS, Schnitzler CE, Browne WE. KLF/SP Transcription Factor Family Evolution: Expansion, Diversification, and Innovation in Eukaryotes. Genome Biol Evol 2015; 7:2289-309. [PMID: 26232396 PMCID: PMC4558859 DOI: 10.1093/gbe/evv141] [Citation(s) in RCA: 72] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/22/2015] [Indexed: 11/13/2022] Open
Abstract
The Krüppel-like factor and specificity protein (KLF/SP) genes play key roles in critical biological processes including stem cell maintenance, cell proliferation, embryonic development, tissue differentiation, and metabolism and their dysregulation has been implicated in a number of human diseases and cancers. Although many KLF/SP genes have been characterized in a handful of bilaterian lineages, little is known about the KLF/SP gene family in nonbilaterians and virtually nothing is known outside the metazoans. Here, we analyze and discuss the origins and evolutionary history of the KLF/SP transcription factor family and associated transactivation/repression domains. We have identified and characterized the complete KLF/SP gene complement from the genomes of 48 species spanning the Eukarya. We have also examined the phylogenetic distribution of transactivation/repression domains associated with this gene family. We report that the origin of the KLF/SP gene family predates the divergence of the Metazoa. Furthermore, the expansion of the KLF/SP gene family is paralleled by diversification of transactivation domains via both acquisitions of pre-existing ancient domains as well as by the appearance of novel domains exclusive to this gene family and is strongly associated with the expansion of cell type complexity.
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Affiliation(s)
| | - Christine E Schnitzler
- Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health
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25
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Sun X, Chen H, Deng Z, Hu B, Luo H, Zeng X, Han L, Cai G, Ma L. The Warsaw breakage syndrome-related protein DDX11 is required for ribosomal RNA synthesis and embryonic development. Hum Mol Genet 2015; 24:4901-15. [PMID: 26089203 DOI: 10.1093/hmg/ddv213] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Accepted: 06/04/2015] [Indexed: 12/20/2022] Open
Abstract
DDX11 was recently identified as a cause of Warsaw breakage syndrome (WABS). However, the functional mechanism of DDX11 and the contribution of clinically described mutations to the pathogenesis of WABS are elusive. Here, we show that DDX11 is a novel nucleolar protein that preferentially binds to hypomethylated active ribosomal DNA (rDNA) gene loci, where it interacts with upstream binding factor (UBF) and the RNA polymerase I (Pol I). DDX11 knockdown changed the epigenetic state of rDNA loci from euchromatic structures to more heterochromatic structures, reduced the activity of UBF, decreased the recruitment of UBF and RPA194 (a subunit of Pol I) to rDNA promoter, suppressed rRNA transcription and thereby inhibited growth and proliferation of HeLa cells. Importantly, two indentified WABS-derived mutants, R263Q and K897del, and a Fe-S deletion construct demonstrated significantly reduced binding abilities to rDNA promoters and lowered DNA-dependent ATPase activities compared with wild-type DDX11. Knockdown of the zebrafish ortholog of human DDX11 by morpholinos resulted in growth retardation and vertebral and craniofacial malformations in zebrafish, concomitant with the changes in histone epigenetic modifications at rDNA loci, the reduction of Pol I recruitment to the rDNA promoter and a significant decrease in nascent pre-RNA levels. These growth disruptions in zebrafish in response to DDX11 reduction showed similarities to the clinically described developmental abnormalities found in WABS patients for the first time in any vertebrate. Thus, our results indicate that DDX11 functions as a positive regulator of rRNA transcription and provides a novel insight into the pathogenesis of WABS.
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Affiliation(s)
- Xinliang Sun
- School of Life Sciences, Tsinghua University, Beijing, China, Division of Life Science and Health, Graduate School at Shenzhen, Tsinghua University, Shenzhen, China
| | - Hongbo Chen
- School of Life Sciences, Tsinghua University, Beijing, China, Division of Life Science and Health, Graduate School at Shenzhen, Tsinghua University, Shenzhen, China,
| | - Zaian Deng
- School of Life Sciences, Tsinghua University, Beijing, China, Division of Life Science and Health, Graduate School at Shenzhen, Tsinghua University, Shenzhen, China
| | - Bo Hu
- Department of Laboratory Medicine, The Third Affiliated Hospital of Sun Yat-sen University, Guangdong, China
| | - Hui Luo
- Department of Pharmacology, Guangdong Medical College, Zhanjiang 524023, Guangdong, China and and
| | - Xiaobin Zeng
- Department of Pharmacology, Guangdong Medical College, Zhanjiang 524023, Guangdong, China and and
| | - Liqiao Han
- Department of Laboratory Science, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangdong, China
| | - Guoping Cai
- School of Life Sciences, Tsinghua University, Beijing, China, Division of Life Science and Health, Graduate School at Shenzhen, Tsinghua University, Shenzhen, China,
| | - Lan Ma
- School of Life Sciences, Tsinghua University, Beijing, China, Division of Life Science and Health, Graduate School at Shenzhen, Tsinghua University, Shenzhen, China,
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26
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Chen B, Zhang W, Gao J, Chen H, Jiang L, Liu D, Cao Y, Zhao S, Qiu Z, Zeng J, Zhang S, Li W. Downregulation of ribosomal protein S6 inhibits the growth of non-small cell lung cancer by inducing cell cycle arrest, rather than apoptosis. Cancer Lett 2014; 354:378-89. [PMID: 25199762 DOI: 10.1016/j.canlet.2014.08.045] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2014] [Revised: 08/06/2014] [Accepted: 08/30/2014] [Indexed: 02/05/2023]
Abstract
Ribosomal protein S6 (rpS6), a component of the small 40S ribosomal subunit, has been found to be associated with multiple physiological and pathophysiological functions. However, its effects and mechanisms in non-small cell lung cancer (NSCLC) still remain unknown. Here, we showed that expressions of total rpS6 and phosphorylation rpS6 (p-rpS6) were both significantly overexpressed in NSCLC. Further survival analysis revealed the shortened overall survival (OS) and relapse-free survival (RFS) in p-rpS6 overexpressed patients and confirmed it as an independent adverse predictor. Stable downregulation of rpS6 in lung adenocarcinoma A549 and squamous cell carcinoma H520 cell lines was then achieved by two specific small hairpin RNA (shRNA) lentiviruses separately. Subsequent experiments showed that downregulation of rpS6 dramatically inhibited cell proliferation in vitro and tumorigenicity in vivo. Moreover, loss of rpS6 promoted cells arrested in G0-G1 phase and reduced in G2-M phase, along with the expression alterations of relative proteins. However, no notable change in apoptosis was observed. Collectively, these results suggested that rpS6 is overactivated in NSCLC and its downregulation suppresses the growth of NSCLC mainly by inducing G0-G1 cell cycle arrest rather than apoptosis.
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Affiliation(s)
- Bojiang Chen
- Department of Respiratory Medicine, West China Hospital of Sichuan University, Chengdu, China; State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, Chengdu, China
| | - Wen Zhang
- Department of Respiratory Medicine, West China Hospital of Sichuan University, Chengdu, China; Department of Respiratory Medicine, Second Affiliated Hospital, The Third Military Medical University, Chongqing, China
| | - Jun Gao
- Department of Toxicological Inspection, Sichuan Center for Disease Prevention and Control, Chengdu, China
| | - Hong Chen
- Department of Geriatric Medicine, Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, Chengdu, China
| | - Li Jiang
- Department of Respiratory Medicine, West China Hospital of Sichuan University, Chengdu, China; Department of Respiratory Medicine, Second Clinical Medical School, North Sichuan Medical College (Nanchong Central Hospital, Sichuan), Nanchong, China
| | - Dan Liu
- Department of Respiratory Medicine, West China Hospital of Sichuan University, Chengdu, China
| | - Yidan Cao
- Department of Pathology, West China Hospital of Sichuan University, Chengdu, China
| | - Shuang Zhao
- Department of Respiratory Medicine, West China Hospital of Sichuan University, Chengdu, China
| | - Zhixin Qiu
- Department of Respiratory Medicine, West China Hospital of Sichuan University, Chengdu, China
| | - Jing Zeng
- Department of Respiratory Medicine, West China Hospital of Sichuan University, Chengdu, China
| | - Shangfu Zhang
- Department of Pathology, West China Hospital of Sichuan University, Chengdu, China
| | - Weimin Li
- Department of Respiratory Medicine, West China Hospital of Sichuan University, Chengdu, China; State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, Chengdu, China.
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