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Zhao L, Wu X, Zhang Z, Fang L, Yang B, Li Y. ELF1 suppresses autophagy to reduce cisplatin resistance via the miR-152-3p/NCAM1/ERK axis in lung cancer cells. Cancer Sci 2023. [PMID: 36846943 DOI: 10.1111/cas.15770] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 02/12/2023] [Accepted: 02/23/2023] [Indexed: 03/01/2023] Open
Abstract
Resistance to chemotherapeutic drugs limits the efficacy of chemotherapy in non-small cell lung cancer (NSCLC). Autophagy is an essential mechanism which involves in drug resistance. Our previous research has revealed that miR-152-3p represses NSCLC progression. However, the mechanism of miR-152-3p in autophagy-mediated chemoresistance in NSCLC remains unclear. Cisplatin-resistant cell lines (A549/DDP and H446/DDP) were transfected with related vectors and subjected to cisplatin, autophagy inhibitor, activator, or extracellular signal-regulated kinase (ERK) activator. Flow cytometry, CCK8 and colony formation assays were performed for testing apoptosis and cell viability. The related RNAs or proteins were detected by qRT-PCR or Western blot. Chromatin immunoprecipitation, luciferase reporter assay or RNA immunoprecipitation were used for validating the interaction between miR-152-3p and ELF1 or NCAM1. Co-IP verified the binding between NCAM1 and ERK. The role of miR-152-3p in cisplatin resistance of NSCLC was also validated in vivo. The results showed that miR-152-3p and ELF1 were decreased in NSCLC tissues. miR-152-3p reversed cisplatin resistance by inhibiting autophagy through NCAM1. NCAM1 promoted autophagy through the ERK pathway and facilitated cisplatin resistance. ELF1 positively regulated miR-152-3p level by directly interacting with miR-152-3p promoter. miR-152-3p targeted NCAM1 to regulate NCAM1 level and then affected the binding of NCAM1 to ERK1/2. ELF1 inhibited autophagy and reversed cisplatin resistance through miR-152-3p/NCAM1. miR-152-3p inhibited autophagy and cisplatin resistance of xenograft tumor in mice. In conclusion, our study revealed that ELF1 inhibited autophagy to attenuate cisplatin resistance through the miR-152-3p/NCAM1/ERK pathway in H446/DDP and A549/DDP cells, suggesting a potential novel treatment strategy for NSCLC.
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Affiliation(s)
- Lifeng Zhao
- Departments of Oncology, The Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, China
| | - Xiangsheng Wu
- School of Clinical Medicine, Graduate School of Youjiang Medical University for Nationalities, Baise, China
| | - Zhiwen Zhang
- School of Clinical Medicine, Graduate School of Youjiang Medical University for Nationalities, Baise, China
| | - Lini Fang
- Departments of Oncology, The Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, China
| | - Bo Yang
- Departments of Oncology, The Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, China
| | - Yepeng Li
- Departments of Oncology, The Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, China
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Tiong KL, Sintupisut N, Lin MC, Cheng CH, Woolston A, Lin CH, Ho M, Lin YW, Padakanti S, Yeang CH. An integrated analysis of the cancer genome atlas data discovers a hierarchical association structure across thirty three cancer types. PLOS DIGITAL HEALTH 2022; 1:e0000151. [PMID: 36812605 PMCID: PMC9931374 DOI: 10.1371/journal.pdig.0000151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 10/31/2022] [Indexed: 06/18/2023]
Abstract
Cancer cells harbor molecular alterations at all levels of information processing. Genomic/epigenomic and transcriptomic alterations are inter-related between genes, within and across cancer types and may affect clinical phenotypes. Despite the abundant prior studies of integrating cancer multi-omics data, none of them organizes these associations in a hierarchical structure and validates the discoveries in extensive external data. We infer this Integrated Hierarchical Association Structure (IHAS) from the complete data of The Cancer Genome Atlas (TCGA) and compile a compendium of cancer multi-omics associations. Intriguingly, diverse alterations on genomes/epigenomes from multiple cancer types impact transcriptions of 18 Gene Groups. Half of them are further reduced to three Meta Gene Groups enriched with (1) immune and inflammatory responses, (2) embryonic development and neurogenesis, (3) cell cycle process and DNA repair. Over 80% of the clinical/molecular phenotypes reported in TCGA are aligned with the combinatorial expressions of Meta Gene Groups, Gene Groups, and other IHAS subunits. Furthermore, IHAS derived from TCGA is validated in more than 300 external datasets including multi-omics measurements and cellular responses upon drug treatments and gene perturbations in tumors, cancer cell lines, and normal tissues. To sum up, IHAS stratifies patients in terms of molecular signatures of its subunits, selects targeted genes or drugs for precision cancer therapy, and demonstrates that associations between survival times and transcriptional biomarkers may vary with cancer types. These rich information is critical for diagnosis and treatments of cancers.
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Affiliation(s)
- Khong-Loon Tiong
- Institute of Statistical Science, Academia Sinica, Section 2, Taipei, Taiwan
| | - Nardnisa Sintupisut
- Institute of Statistical Science, Academia Sinica, Section 2, Taipei, Taiwan
| | - Min-Chin Lin
- Institute of Statistical Science, Academia Sinica, Section 2, Taipei, Taiwan
- Psomagen, Rockville, Maryland, United States of America
| | - Chih-Hung Cheng
- Institute of Statistical Science, Academia Sinica, Section 2, Taipei, Taiwan
| | - Andrew Woolston
- Institute of Statistical Science, Academia Sinica, Section 2, Taipei, Taiwan
- Translational Cancer Immunotherapy & Genomics Lab, Barts Cancer Institute, Charterhouse Square, London, United Kingdom
| | - Chih-Hsu Lin
- Institute of Statistical Science, Academia Sinica, Section 2, Taipei, Taiwan
- C3.ai, Redwood City, California, United States of America
| | - Mirrian Ho
- Institute of Statistical Science, Academia Sinica, Section 2, Taipei, Taiwan
| | - Yu-Wei Lin
- Institute of Statistical Science, Academia Sinica, Section 2, Taipei, Taiwan
- AiLife Diagnostics, Pearland, Texas, United States of America
| | - Sridevi Padakanti
- Institute of Statistical Science, Academia Sinica, Section 2, Taipei, Taiwan
| | - Chen-Hsiang Yeang
- Institute of Statistical Science, Academia Sinica, Section 2, Taipei, Taiwan
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Fang H, Sun Z, Chen Z, Chen A, Sun D, Kong Y, Fang H, Qian G. Bioinformatics and systems-biology analysis to determine the effects of Coronavirus disease 2019 on patients with allergic asthma. Front Immunol 2022; 13:988479. [PMID: 36211429 PMCID: PMC9537444 DOI: 10.3389/fimmu.2022.988479] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 08/30/2022] [Indexed: 12/05/2022] Open
Abstract
Background The coronavirus disease (COVID-19) pandemic has posed a significant challenge for global health systems. Increasing evidence shows that asthma phenotypes and comorbidities are major risk factors for COVID-19 symptom severity. However, the molecular mechanisms underlying the association between COVID-19 and asthma are poorly understood. Therefore, we conducted bioinformatics and systems biology analysis to identify common pathways and molecular biomarkers in patients with COVID-19 and asthma, as well as potential molecular mechanisms and candidate drugs for treating patients with both COVID-19 and asthma. Methods Two sets of differentially expressed genes (DEGs) from the GSE171110 and GSE143192 datasets were intersected to identify common hub genes, shared pathways, and candidate drugs. In addition, murine models were utilized to explore the expression levels and associations of the hub genes in asthma and lung inflammation/injury. Results We discovered 157 common DEGs between the asthma and COVID-19 datasets. A protein–protein-interaction network was built using various combinatorial statistical approaches and bioinformatics tools, which revealed several hub genes and critical modules. Six of the hub genes were markedly elevated in murine asthmatic lungs and were positively associated with IL-5, IL-13 and MUC5AC, which are the key mediators of allergic asthma. Gene Ontology and pathway analysis revealed common associations between asthma and COVID-19 progression. Finally, we identified transcription factor–gene interactions, DEG–microRNA coregulatory networks, and potential drug and chemical-compound interactions using the hub genes. Conclusion We identified the top 15 hub genes that can be used as novel biomarkers of COVID-19 and asthma and discovered several promising candidate drugs that might be helpful for treating patients with COVID-19 and asthma.
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Affiliation(s)
- Hongwei Fang
- Affiliated Cancer Hospital and Institute of Guangzhou Medical University, Guangzhou, China
- Department of Anesthesiology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Zhun Sun
- Affiliated Cancer Hospital and Institute of Guangzhou Medical University, Guangzhou, China
| | - Zhouyi Chen
- Department of Anesthesiology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Anning Chen
- Affiliated Cancer Hospital and Institute of Guangzhou Medical University, Guangzhou, China
| | - Donglin Sun
- Affiliated Cancer Hospital and Institute of Guangzhou Medical University, Guangzhou, China
| | - Yan Kong
- Department of Anesthesiology (High-Tech Branch), The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Hao Fang
- Department of Anesthesiology, Zhongshan Hospital, Fudan University, Shanghai, China
- Department of Anesthesiology, Minhang Hospital, Fudan University, Shanghai, China
- *Correspondence: Guojun Qian, ; Hao Fang,
| | - Guojun Qian
- Affiliated Cancer Hospital and Institute of Guangzhou Medical University, Guangzhou, China
- *Correspondence: Guojun Qian, ; Hao Fang,
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Xu H, Wang H, Li G, Jin X, Chen B. The Immune-Related Gene ELF3 is a Novel Biomarker for the Prognosis of Ovarian Cancer. Int J Gen Med 2021; 14:5537-5548. [PMID: 34531679 PMCID: PMC8439714 DOI: 10.2147/ijgm.s332320] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2021] [Accepted: 08/25/2021] [Indexed: 12/24/2022] Open
Abstract
Background Ovarian cancer (OC) is a fatal gynaecological malignancy. The study aimed to conduct a comprehensive study to determine the role of ELF3 in OC through bioinformatic analysis. Methods Kruskal-Wallis test, Wilcoxon sign-rank test, and logistic regression were used to evaluate the relationship between clinical characteristics and ELF3 expression. Kaplan-Meier method and Cox regression analysis were used to evaluate the prognostic factors. Gene set enrichment analysis (GSEA) and immuno-infiltration analysis were used to evaluate the significant involvement of ELF3 in function. Results High ELF3 expression in OC was associated with age (P< 0.001). High ELF3 expression predicted a poorer overall survival (OS) (HR: 1.37; 95% CI: 1.05-1.78; P=0.019) and disease specific survival (DSS) (HR: 1.43; 95% CI: 1.08-1.89; P=0.013). And ELF3 expression (HR: 1.779; 95% CI: 1.281-2.472; P<0.001) was independently correlated with OS in OC patients. GSEA demonstrated that pathways including GPCR-ligand binding, neuronal system, signaling by WNT, translation, neuroactive ligand-receptor interaction, and TCF dependent signaling in response to WNT were differentially enriched in ELF3 low expression phenotype. Immune infiltration analysis showed that ELF3 expression was correlated with immune infiltrates. Conclusion ELF3 expression in OC patients was significantly associated with poor survival and immune infiltration and a promising prognostic biomarker in OC.
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Affiliation(s)
- Hao Xu
- Department of Gynecology, Huangshi Love & Health Hospital Affiliated to Hubei Polytechnic University, Huangshi, 435000, Hubei, People's Republic of China
| | - Haihong Wang
- Department of Gynecology, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, 221000, Jiangsu, People's Republic of China
| | - Guilin Li
- Department of Gynecology, Maternal and Child Health Care Hospital Affiliated to Xuzhou Medical University, Xuzhou, 221000, Jiangsu, People's Republic of China
| | - Xin Jin
- Department of Gynecology, Maternal and Child Health Care Hospital Affiliated to Xuzhou Medical University, Xuzhou, 221000, Jiangsu, People's Republic of China
| | - Buze Chen
- Department of Gynecology, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, 221000, Jiangsu, People's Republic of China.,Xuzhou Medical University, Xuzhou, 221000, Jiangsu, People's Republic of China
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Yaşar P, Kars G, Yavuz K, Ayaz G, Oğuztüzün Ç, Bilgen E, Suvacı Z, Çetinkol ÖP, Can T, Muyan M. A CpG island promoter drives the CXXC5 gene expression. Sci Rep 2021; 11:15655. [PMID: 34341443 PMCID: PMC8329181 DOI: 10.1038/s41598-021-95165-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Accepted: 07/16/2021] [Indexed: 02/06/2023] Open
Abstract
CXXC5 is a member of the zinc-finger CXXC family that binds to unmethylated CpG dinucleotides. CXXC5 modulates gene expressions resulting in diverse cellular events mediated by distinct signaling pathways. However, the mechanism responsible for CXXC5 expression remains largely unknown. We found here that of the 14 annotated CXXC5 transcripts with distinct 5' untranslated regions encoding the same protein, transcript variant 2 with the highest expression level among variants represents the main transcript in cell models. The DNA segment in and at the immediate 5'-sequences of the first exon of variant 2 contains a core promoter within which multiple transcription start sites are present. Residing in a region with high G-C nucleotide content and CpG repeats, the core promoter is unmethylated, deficient in nucleosomes, and associated with active RNA polymerase-II. These findings suggest that a CpG island promoter drives CXXC5 expression. Promoter pull-down revealed the association of various transcription factors (TFs) and transcription co-regulatory proteins, as well as proteins involved in histone/chromatin, DNA, and RNA processing with the core promoter. Of the TFs, we verified that ELF1 and MAZ contribute to CXXC5 expression. Moreover, the first exon of variant 2 may contain a G-quadruplex forming region that could modulate CXXC5 expression.
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Affiliation(s)
- Pelin Yaşar
- Department of Biological Sciences, Middle East Technical University, Ankara, 06800, Turkey.
- Epigenetics and Stem Cell Biology Laboratory, Single Cell Dynamics Group, National Institute of Environmental Health Sciences, Research Triangle Park, NC, 27709, USA.
| | - Gizem Kars
- Department of Biological Sciences, Middle East Technical University, Ankara, 06800, Turkey
| | - Kerim Yavuz
- Department of Biological Sciences, Middle East Technical University, Ankara, 06800, Turkey
| | - Gamze Ayaz
- Department of Biological Sciences, Middle East Technical University, Ankara, 06800, Turkey
- Cancer and Stem Cell Epigenetics Section, Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Çerağ Oğuztüzün
- Department of Computer Engineering, Bilkent University, Ankara, 06800, Turkey
| | - Ecenaz Bilgen
- Department of Chemistry, Middle East Technical University, Ankara, 06800, Turkey
| | - Zeynep Suvacı
- Department of Chemistry, Middle East Technical University, Ankara, 06800, Turkey
| | | | - Tolga Can
- Department of Computer Engineering, Middle East Technical University, Ankara, 06800, Turkey
| | - Mesut Muyan
- Department of Biological Sciences, Middle East Technical University, Ankara, 06800, Turkey.
- Cansyl Laboratories, Middle East Technical University, Ankara, 06800, Turkey.
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6
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Seifert LL, Si C, Saha D, Sadic M, de Vries M, Ballentine S, Briley A, Wang G, Valero-Jimenez AM, Mohamed A, Schaefer U, Moulton HM, García-Sastre A, Tripathi S, Rosenberg BR, Dittmann M. The ETS transcription factor ELF1 regulates a broadly antiviral program distinct from the type I interferon response. PLoS Pathog 2019; 15:e1007634. [PMID: 31682641 PMCID: PMC6932815 DOI: 10.1371/journal.ppat.1007634] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Revised: 12/26/2019] [Accepted: 10/11/2019] [Indexed: 12/20/2022] Open
Abstract
Induction of vast transcriptional programs is a central event of innate host responses to viral infections. Here we report a transcriptional program with potent antiviral activity, driven by E74-like ETS transcription factor 1 (ELF1). Using microscopy to quantify viral infection over time, we found that ELF1 inhibits eight diverse RNA and DNA viruses after multi-cycle replication. Elf1 deficiency results in enhanced susceptibility to influenza A virus infections in mice. ELF1 does not feed-forward to induce interferons, and ELF1’s antiviral effect is not abolished by the absence of STAT1 or by inhibition of JAK phosphorylation. Accordingly, comparative expression analyses by RNA-seq revealed that the ELF1 transcriptional program is distinct from interferon signatures. Thus, ELF1 provides an additional layer of the innate host response, independent from the action of type I interferons. After decades of research on the innate immune system, we still struggle to understand exactly how this first line of defense protects cells against viral infections. Our gap in knowledge stems, on one hand, from the sheer number of effector genes, few of which have been characterized in mechanistic detail. On the other hand, our understanding of innate gene transcription is constantly evolving. We know that different regulatory mechanisms greatly influence the quality, magnitude, and timing of gene expression, all of which may contribute to the antiviral power of the innate response. Deciphering these regulatory mechanisms is indispensable for harnessing the power of innate immunity in novel antiviral therapies. Here, we report a novel transcriptional program as part of the cell-intrinsic immune system, raised by E74-like ETS transcription factor 1 (ELF1). ELF1 potently restricts multi-cycle propagation of all viruses tested in our study. Reduced levels of ELF1 significantly diminish host defenses against influenza A virus in vitro and in vivo, suggesting a critical but previously overlooked role of this ETS transcription factor. The ELF1 program is complex and comprises over 300 potentially antiviral genes, which are almost entirely distinct from those known to be induced by interferon. Taken together, our data provide evidence for a program of antiviral protection that expands the previously known arsenal of the innate immune response.
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Affiliation(s)
- Leon Louis Seifert
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, New York, United States of America
| | - Clara Si
- Department of Microbiology, New York University School of Medicine, New York, New York, United States of America
| | - Debjani Saha
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Mohammad Sadic
- Department of Microbiology, New York University School of Medicine, New York, New York, United States of America
| | - Maren de Vries
- Department of Microbiology, New York University School of Medicine, New York, New York, United States of America
| | - Sarah Ballentine
- Department of Microbiology, New York University School of Medicine, New York, New York, United States of America
| | - Aaron Briley
- Department of Microbiology, New York University School of Medicine, New York, New York, United States of America
| | - Guojun Wang
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Ana M. Valero-Jimenez
- Department of Microbiology, New York University School of Medicine, New York, New York, United States of America
| | - Adil Mohamed
- Department of Microbiology, New York University School of Medicine, New York, New York, United States of America
| | - Uwe Schaefer
- Laboratory of Immune Cell Epigenetics and Signaling, The Rockefeller University, New York, New York, United States of America
| | - Hong M. Moulton
- Carlson College of Veterinary Medicine, Oregon State University, Corvallis, Oregon, United States of America
| | - Adolfo García-Sastre
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Shashank Tripathi
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- Microbiology and Cell Biology Department, Centre for Infectious Disease Research, Indian Institute of Science, Bangalore, India
| | - Brad R. Rosenberg
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Meike Dittmann
- Department of Microbiology, New York University School of Medicine, New York, New York, United States of America
- * E-mail:
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Hamada H, Goto Y, Arakawa J, Murayama E, Ogawa Y, Konno M, Oyama T, Asai M, Sato A, Tanuma SI, Uchiumi F. Characterization of the human E2F4 promoter region and its response to 12-O-tetradecanoylphorbol-13-acetate. J Biochem 2019; 166:363-373. [PMID: 31199460 DOI: 10.1093/jb/mvz047] [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: 09/03/2018] [Accepted: 06/11/2019] [Indexed: 12/23/2022] Open
Abstract
The E2F transcription factors (TFs), which control the progression of the cell cycle in response to DNA-damage and various stresses, are known to interact with a tumour suppressor, Retinoblastoma 1 (RB1). We previously showed that the response of the human RB1 promoter to a 12-O-tetradecanoylphorbol-13-acetate (TPA) in HL-60 cells is mediated by a duplicated GGAA motif, which is also present in the 5'-upstream of the E2F family genes. The motifs are especially rich in the 5'-upstream of the E2F4 gene. In the present study, we constructed luciferase (Luc) expression vectors containing a 466 bp of the 5'-upstream of the human E2F4 gene. The transfection of this plasmid and deletion/mutation-introduced derivatives into HL-60 cells and a Luc reporter assay showed that duplicated and triplicated GGAA (TTCC) motifs in the E2F4 promoter respond to TPA. As expected, electrophoretic mobility shift assay indicated that SPI1 (PU.1) binds to the GGAA motif-containing element. A quantitative RT-PCR and western blotting showed that the E2F4 transcripts and its encoding proteins accumulate during the differentiation of HL-60 into macrophage-like cells. In contrast, the expression of the E2F1 gene and the protein, which possibly acts as a cell cycle accelerator, was greatly diminished.
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Affiliation(s)
- Hiroshi Hamada
- Department of Gene Regulation, Faculty of Pharmaceutical Sciences, Tokyo University of Science, Noda-shi, Chiba-ken, Japan
| | - Yuta Goto
- Department of Gene Regulation, Faculty of Pharmaceutical Sciences, Tokyo University of Science, Noda-shi, Chiba-ken, Japan
| | - Jun Arakawa
- Department of Gene Regulation, Faculty of Pharmaceutical Sciences, Tokyo University of Science, Noda-shi, Chiba-ken, Japan
| | - Erisa Murayama
- Department of Gene Regulation, Faculty of Pharmaceutical Sciences, Tokyo University of Science, Noda-shi, Chiba-ken, Japan
| | - Yui Ogawa
- Department of Gene Regulation, Faculty of Pharmaceutical Sciences, Tokyo University of Science, Noda-shi, Chiba-ken, Japan
| | - Midori Konno
- Department of Gene Regulation, Faculty of Pharmaceutical Sciences, Tokyo University of Science, Noda-shi, Chiba-ken, Japan
| | - Takahiro Oyama
- Hinoki Shinyaku Co., Ltd, 9-6 Nibancho, Chiyoda-ku, Tokyo, Japan
- Department of Biochemistry, Faculty of Pharmaceutical Sciences, Tokyo University of Science, Noda-shi, Chiba-ken, Japan
| | - Masashi Asai
- Department of Gene Regulation, Faculty of Pharmaceutical Sciences, Tokyo University of Science, Noda-shi, Chiba-ken, Japan
| | - Akira Sato
- Department of Biochemistry, Faculty of Pharmaceutical Sciences, Tokyo University of Science, Noda-shi, Chiba-ken, Japan
| | - Sei-Ichi Tanuma
- Department of Biochemistry, Faculty of Pharmaceutical Sciences, Tokyo University of Science, Noda-shi, Chiba-ken, Japan
- Genomic Medical Science, Research Institute of Science and Technology, Tokyo University of Science, Noda-shi, Chiba-ken, Japan
| | - Fumiaki Uchiumi
- Department of Gene Regulation, Faculty of Pharmaceutical Sciences, Tokyo University of Science, Noda-shi, Chiba-ken, Japan
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8
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Hamada H, Yamamura M, Ohi H, Kobayashi Y, Niwa K, Oyama T, Mano Y, Asai M, Tanuma SI, Uchiumi F. Characterization of the human zinc finger nfx‑1‑type containing 1 encoding ZNFX1 gene and its response to 12‑O‑tetradecanoyl‑13‑acetate in HL‑60 cells. Int J Oncol 2019; 55:896-904. [PMID: 31432148 DOI: 10.3892/ijo.2019.4860] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Accepted: 07/19/2019] [Indexed: 11/06/2022] Open
Abstract
Human promyelocytic HL‑60 cells can be differentiated into macrophage‑like cells by treatment with 12‑O‑tetra decanoylphorbol‑13‑acetate (TPA). Certain 5' upstream regions of the zinc finger protein (ZNF)‑encoding genes contain duplicated GGAA motifs, which are frequently found in the TPA‑responding gene promoter regions. To examine transcriptional responses to TPA, 5'flanking regions of human zinc finger CCCH‑type containing, antiviral, ZNF252, ZNF343, ZNF555, ZNF782 and zinc finger nfx‑1‑type containing 1 (ZNFX1) genes were isolated by polymerase chain reaction (PCR) and ligated into a multiple‑cloning site of the pGL4.10[luc2] vector. Transient transfection and a luciferase assay revealed that the ZNFX1 promoter most prominently responded to the TPA treatment. Deletion and point mutation experiments indicated that the duplicated GGAA motif in the 100‑bp region positively responded to TPA. In addition, reverse transcription‑quantitative PCR and western blotting showed that the mRNA and protein of ZNFX1 accumulate during the differentiation of HL‑60 cells. These results indicated that expression of the TPA‑inducible ZNFX1 gene, which belongs to the group of interferon‑responsive genes, is regulated by the cis‑action of the duplicated GGAA motif.
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Affiliation(s)
- Hiroshi Hamada
- Department of Gene Regulation, Faculty of Pharmaceutical Sciences, Tokyo University of Science, Noda‑shi, Chiba‑ken 278‑8510, Japan
| | - Mayu Yamamura
- Department of Gene Regulation, Faculty of Pharmaceutical Sciences, Tokyo University of Science, Noda‑shi, Chiba‑ken 278‑8510, Japan
| | - Hiroto Ohi
- Department of Gene Regulation, Faculty of Pharmaceutical Sciences, Tokyo University of Science, Noda‑shi, Chiba‑ken 278‑8510, Japan
| | - Yota Kobayashi
- Department of Gene Regulation, Faculty of Pharmaceutical Sciences, Tokyo University of Science, Noda‑shi, Chiba‑ken 278‑8510, Japan
| | - Kuniyoshi Niwa
- Department of Gene Regulation, Faculty of Pharmaceutical Sciences, Tokyo University of Science, Noda‑shi, Chiba‑ken 278‑8510, Japan
| | - Takahiro Oyama
- Department of Gene Regulation, Faculty of Pharmaceutical Sciences, Tokyo University of Science, Noda‑shi, Chiba‑ken 278‑8510, Japan
| | - Yasunari Mano
- Department of Clinical Drug Informatics, Faculty of Pharmaceutical Sciences, Tokyo University of Science, Noda‑shi, Chiba‑ken 278‑8510, Japan
| | - Masashi Asai
- Department of Gene Regulation, Faculty of Pharmaceutical Sciences, Tokyo University of Science, Noda‑shi, Chiba‑ken 278‑8510, Japan
| | - Sei-Ichi Tanuma
- Department of Biochemistry, Faculty of Pharmaceutical Sciences, Tokyo University of Science, Noda‑shi, Chiba‑ken 278‑8510, Japan
| | - Fumiaki Uchiumi
- Department of Gene Regulation, Faculty of Pharmaceutical Sciences, Tokyo University of Science, Noda‑shi, Chiba‑ken 278‑8510, Japan
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9
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Sinnamon JR, Torkenczy KA, Linhoff MW, Vitak SA, Mulqueen RM, Pliner HA, Trapnell C, Steemers FJ, Mandel G, Adey AC. The accessible chromatin landscape of the murine hippocampus at single-cell resolution. Genome Res 2019; 29:857-869. [PMID: 30936163 PMCID: PMC6499306 DOI: 10.1101/gr.243725.118] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Accepted: 03/21/2019] [Indexed: 11/29/2022]
Abstract
Here we present a comprehensive map of the accessible chromatin landscape of the mouse hippocampus at single-cell resolution. Substantial advances of this work include the optimization of a single-cell combinatorial indexing assay for transposase accessible chromatin (sci-ATAC-seq); a software suite, scitools, for the rapid processing and visualization of single-cell combinatorial indexing data sets; and a valuable resource of hippocampal regulatory networks at single-cell resolution. We used sci-ATAC-seq to produce 2346 high-quality single-cell chromatin accessibility maps with a mean unique read count per cell of 29,201 from both fresh and frozen hippocampi, observing little difference in accessibility patterns between the preparations. By using this data set, we identified eight distinct major clusters of cells representing both neuronal and nonneuronal cell types and characterized the driving regulatory factors and differentially accessible loci that define each cluster. Within pyramidal neurons, we identified four major clusters, including CA1 and CA3 neurons, and three additional subclusters. We then applied a recently described coaccessibility framework, Cicero, which identified 146,818 links between promoters and putative distal regulatory DNA. Identified coaccessibility networks showed cell-type specificity, shedding light on key dynamic loci that reconfigure to specify hippocampal cell lineages. Lastly, we performed an additional sci-ATAC-seq preparation from cultured hippocampal neurons (899 high-quality cells, 43,532 mean unique reads) that revealed substantial alterations in their epigenetic landscape compared with nuclei from hippocampal tissue. This data set and accompanying analysis tools provide a new resource that can guide subsequent studies of the hippocampus.
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Affiliation(s)
- John R Sinnamon
- The Vollum Institute, Oregon Health and Science University, Portland, Oregon 97239, USA
| | - Kristof A Torkenczy
- Department of Molecular and Medical Genetics, Oregon Health and Science University, Portland, Oregon 97239, USA
| | - Michael W Linhoff
- The Vollum Institute, Oregon Health and Science University, Portland, Oregon 97239, USA
| | - Sarah A Vitak
- Department of Molecular and Medical Genetics, Oregon Health and Science University, Portland, Oregon 97239, USA
| | - Ryan M Mulqueen
- Department of Molecular and Medical Genetics, Oregon Health and Science University, Portland, Oregon 97239, USA
| | - Hannah A Pliner
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
| | - Cole Trapnell
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
| | | | - Gail Mandel
- The Vollum Institute, Oregon Health and Science University, Portland, Oregon 97239, USA
| | - Andrew C Adey
- Department of Molecular and Medical Genetics, Oregon Health and Science University, Portland, Oregon 97239, USA
- Knight Cardiovascular Institute, Oregon Health and Science University, Portland, Oregon 97239, USA
- Knight Cancer Institute, Oregon Health and Science University, Portland, Oregon 97239, USA
- Knight Center for Early Detection Advanced Research, Oregon Health and Science University, Portland, Oregon 97239, USA
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O-GlcNAc cycling and the regulation of nucleocytoplasmic dynamics. Biochem Soc Trans 2017; 45:427-436. [DOI: 10.1042/bst20160171] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Revised: 02/05/2017] [Accepted: 02/09/2017] [Indexed: 01/01/2023]
Abstract
The dynamic carbohydrate post-translational modification (PTM) O-linked β-N-acetyl glucosamine (O-GlcNAc) is found on thousands of proteins throughout the nucleus and cytoplasm, and rivals phosphorylation in terms of the number of substrates and pathways influenced. O-GlcNAc is highly conserved and essential in most organisms, with disruption of O-GlcNAc cycling linked to diseases ranging from cancer to neurodegeneration. Nuclear pore proteins were the first identified O-GlcNAc-modified substrates, generating intense and ongoing interest in understanding the role of O-GlcNAc cycling in nuclear pore complex structure and function. Recent advances in detecting and altering O-GlcNAcylation levels have provided insights into many mechanisms by which O-GlcNAcylation influences the nucleocytoplasmic localization and stability of protein targets. The emerging view is that the multifunctional enzymes of O-GlcNAc cycling are critical nutrient-sensing components of a complex network of signaling cascades involving multiple PTMs. Furthermore, O-GlcNAc plays a role in maintaining the structural integrity of the nuclear pore and regulating its function as the gatekeeper of nucleocytoplasmic trafficking.
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11
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Characterization of the 5'-flanking region of the human DNA helicase B (HELB) gene and its response to trans-Resveratrol. Sci Rep 2016; 6:24510. [PMID: 27079536 PMCID: PMC4832242 DOI: 10.1038/srep24510] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2016] [Accepted: 03/30/2016] [Indexed: 12/17/2022] Open
Abstract
Human DNA helicase B (HELB/HDHB) regulates DNA replication through association with human DNA polymerase α-primase. In the present study, an 866-base pair (bp) of the 5′-flanking region of the human HELB gene-containing Luciferase (Luc) reporter plasmid, pHDHB-Luc was transfected into various cell lines and Luc activity was analyzed. Deletion analyses revealed that a 121-bp containing the major transcription start site (TSS) was essential for the basal promoter activity in all tested cells. TF-SEARCH analysis indicated that GC-box/Sp1 and duplicated GGAA-motifs containing putative STAT-x and c-ETS binding sites are located close to the TSS. Furthermore, chromatin immunoprecipitation (ChIP) analysis showed that PU.1 and Sp1 bind to the 121-bp region. Reverse transcriptase-polymerase chain reaction (RT-PCR) and western blot analyses showed the HELB gene and protein expression was up-regulated by trans-Resveratrol (Rsv) treatment in HeLa S3 cells. Moreover, transfection experiment indicated that mutations on the GC-boxes and the duplicated GGAA-motif greatly reduced promoter activity and the response to Rsv in HeLa S3 cells. These results suggest that Rsv, which is a natural compound that has been found to elongate the lifespan of various organisms, regulates HELB promoter activity through co-operation of the GC-boxes and the duplicated GGAA-motif in the 121-bp.
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