1
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Agrawal S, Buyan A, Severin J, Koido M, Alam T, Abugessaisa I, Chang HY, Dostie J, Itoh M, Kere J, Kondo N, Li Y, Makeev VJ, Mendez M, Okazaki Y, Ramilowski JA, Sigorskikh AI, Strug LJ, Yagi K, Yasuzawa K, Yip CW, Hon CC, Hoffman MM, Terao C, Kulakovskiy IV, Kasukawa T, Shin JW, Carninci P, de Hoon MJL. Annotation of nuclear lncRNAs based on chromatin interactions. PLoS One 2024; 19:e0295971. [PMID: 38709794 PMCID: PMC11073715 DOI: 10.1371/journal.pone.0295971] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Accepted: 12/02/2023] [Indexed: 05/08/2024] Open
Abstract
The human genome is pervasively transcribed and produces a wide variety of long non-coding RNAs (lncRNAs), constituting the majority of transcripts across human cell types. Some specific nuclear lncRNAs have been shown to be important regulatory components acting locally. As RNA-chromatin interaction and Hi-C chromatin conformation data showed that chromatin interactions of nuclear lncRNAs are determined by the local chromatin 3D conformation, we used Hi-C data to identify potential target genes of lncRNAs. RNA-protein interaction data suggested that nuclear lncRNAs act as scaffolds to recruit regulatory proteins to target promoters and enhancers. Nuclear lncRNAs may therefore play a role in directing regulatory factors to locations spatially close to the lncRNA gene. We provide the analysis results through an interactive visualization web portal at https://fantom.gsc.riken.jp/zenbu/reports/#F6_3D_lncRNA.
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Affiliation(s)
- Saumya Agrawal
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Andrey Buyan
- Autosome.org, Russia
- FANTOM Consortium, Dolgoprudny, Russia
| | - Jessica Severin
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Masaru Koido
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Tanvir Alam
- College of Science and Engineering, Hamad Bin Khalifa University, Doha, Qatar
| | | | - Howard Y. Chang
- Center for Personal Dynamic Regulome, Stanford University, Stanford, California, United States of America
| | - Josée Dostie
- Department of Biochemistry, Rosalind and Morris Goodman Cancer Research Center, McGill University, Montréal, Québec, Canada
| | - Masayoshi Itoh
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- RIKEN Preventive Medicine and Diagnosis Innovation Program, Wako, Japan
| | - Juha Kere
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
- Stem Cells and Metabolism Research Program, University of Helsinki and Folkhälsan Research Center, Helsinki, Finland
| | - Naoto Kondo
- RIKEN Center for Life Science Technologies, Yokohama, Japan
| | - Yunjing Li
- Division of Biostatistics, Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada
| | | | - Mickaël Mendez
- Department of Computer Science, University of Toronto, Toronto, Ontario, Canada
| | - Yasushi Okazaki
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Jordan A. Ramilowski
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Advanced Medical Research Center, Yokohama City University, Yokohama, Japan
| | | | - Lisa J. Strug
- Division of Biostatistics, Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada
- Department of Computer Science, University of Toronto, Toronto, Ontario, Canada
- Department of Statistical Sciences, University of Toronto, Ontario, Canada
- The Centre for Applied Genomics and Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Ken Yagi
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Kayoko Yasuzawa
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Chi Wai Yip
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Chung Chau Hon
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Michael M. Hoffman
- Department of Computer Science, University of Toronto, Toronto, Ontario, Canada
- Princess Margaret Cancer Centre, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
- Vector Institute, Toronto, Ontario, Canada
| | - Chikashi Terao
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | | | - Takeya Kasukawa
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Jay W. Shin
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore, Republic of Singapore
| | - Piero Carninci
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Human Technopole, Milan, Italy
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2
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Wang Y, Wei J, Hong K, Zhou N, Liu X, Hong X, Li W, Zhao J, Chen C, Wu L, Yu L, Zhu X. Transcriptome Analysis Reveals the Molecular Response to Salinity Challenge in Larvae of the Giant Freshwater Prawn Macrobrachium rosenbergii. Front Physiol 2022; 13:885035. [PMID: 35574435 PMCID: PMC9099292 DOI: 10.3389/fphys.2022.885035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Accepted: 03/11/2022] [Indexed: 11/15/2022] Open
Abstract
Salinity is a crucial factor influencing the growth, development, immunity, and reproduction of aquatic organisms; however, little is known about the molecular mechanism of the response to salinity challenge in larvae of the giant freshwater prawn Macrobrachium rosenbergii. Herein, larvae cultured in three treatment groups with salinities of 10, 13, and 16‰ (S10, S13, and S16) were collected, and then transcriptome analysis was conducted by RNA-seq. A total of 6,473, 3,830 and 3,584 differentially expressed genes (DEGs) were identified in the S10 vs. S13 comparison, S10 vs. S16 comparison and S13 vs. S16 comparison, respectively. These genes are involved in osmoregulation, energy metabolism, molting, and the immune response. qPCR analysis was used to detect the expression patterns of 16 DEGs to verify the accuracy of the transcriptome data. Protein–protein interaction (PPI) analysis for DEGs and microsatellite marker screening were also conducted to reveal the molecular mechanism of salinity regulation. Together, our results will provide insight into the molecular genetic basis of adaptation to salinity challenge for larvae of M. rosenbergii.
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Affiliation(s)
- Yakun Wang
- Key Laboratory of Tropical and Subtropical Fishery Resource Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
| | - Jie Wei
- Key Laboratory of Tropical and Subtropical Fishery Resource Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
- College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China
| | - Kunhao Hong
- Key Laboratory of Tropical and Subtropical Fishery Resource Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
| | - Nan Zhou
- Key Laboratory of Tropical and Subtropical Fishery Resource Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
- School of Fishery, Zhejiang Ocean University, Zhoushan, China
| | - Xiaoli Liu
- Key Laboratory of Tropical and Subtropical Fishery Resource Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
| | - Xiaoyou Hong
- Key Laboratory of Tropical and Subtropical Fishery Resource Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
| | - Wei Li
- Key Laboratory of Tropical and Subtropical Fishery Resource Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
| | - Jian Zhao
- Key Laboratory of Tropical and Subtropical Fishery Resource Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
| | - Chen Chen
- Key Laboratory of Tropical and Subtropical Fishery Resource Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
| | - Liang Wu
- Sisal and Sisal Products Quality Supervision, Inspection and Testing Center, Ministry of Agriculture and Rural Affairs, Zhanjiang, China
| | - Lingyun Yu
- Key Laboratory of Tropical and Subtropical Fishery Resource Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
- *Correspondence: Lingyun Yu, ; Xinping Zhu,
| | - Xinping Zhu
- Key Laboratory of Tropical and Subtropical Fishery Resource Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
- *Correspondence: Lingyun Yu, ; Xinping Zhu,
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Ji Z, Tang T, Chen M, Dong B, Sun W, Wu N, Chen H, Feng Q, Yang X, Jin R, Jiang L. C-Myc-activated long non-coding RNA LINC01050 promotes gastric cancer growth and metastasis by sponging miR-7161-3p to regulate SPZ1 expression. J Exp Clin Cancer Res 2021; 40:351. [PMID: 34749766 PMCID: PMC8573944 DOI: 10.1186/s13046-021-02155-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 10/25/2021] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Growing evidence shows that long non-coding RNAs (lncRNAs) play significant roles in cancer development. However, the functions of most lncRNAs in human gastric cancer are still not fully understood. Here, we explored the role of a novel c-Myc-activated lncRNA, LINC01050, in gastric cancer progression. METHODS The expression of LINC01050 in the context of gastric cancer was assessed using The Cancer Genome Atlas datasets. Its functions in gastric cancer were investigated through gain- and loss-of-function experiments combined with the Cell Counting Kit-8 assays, colony-forming assays, Transwell assays, flow cytometry, Western blot analyses, and xenograft tumor and mouse metastasis models. Potential LINC01050 transcription activators were screened via bioinformatics and validated by chromatin immunoprecipitation and luciferase assays. The interaction between LINC01050 and miR-7161-3p and the targets of miR-7161-3p were predicted by bioinformatics analysis and confirmed by a luciferase assay, RNA immunoprecipitation, RNA pull-down, and rescue experiments. RESULTS LINC01050 was significantly up-regulated in gastric cancer, and its high expression was positively correlated with a poor prognosis. The transcription factor c-Myc was found to directly bind to the LINC01050 promoter region and activate its transcription. Furthermore, overexpression of LINC01050 was confirmed to promote gastric cancer cell proliferation, migration, invasion, and epithelial-mesenchymal transition in vitro and tumor growth in vivo. At the same time, its knockdown inhibited gastric cancer cell proliferation, migration, invasion, and epithelial-mesenchymal transition in vitro along with tumor growth and metastasis in vivo. Moreover, mechanistic investigations revealed that LINC01050 functions as a molecular sponge to absorb cytosolic miR-7161-3p, which reduces the miR-7161-3p-mediated translational repression of SPZ1, thus contributing to gastric cancer progression. CONCLUSIONS Taken together, our results identified a novel gastric cancer-associated lncRNA, LINC01050, which is activated by c-Myc. LINC01050 may be considered a potential therapeutic target for gastric cancer.
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Affiliation(s)
- Ziwei Ji
- Department of Gastroenterology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325000, China
| | - Tianbin Tang
- Central Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325000, China
| | - Mengxia Chen
- Department of Gastroenterology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325000, China
| | - Buyuan Dong
- Department of Gastroenterology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325000, China
| | - Wenjing Sun
- Central Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325000, China
| | - Nan Wu
- Department of Gastroenterology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325000, China
| | - Hao Chen
- Department of Gastroenterology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325000, China
| | - Qian Feng
- Department of Gastroenterology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325000, China
| | - Xingyi Yang
- Department of Gastroenterology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325000, China
| | - Rong Jin
- Department of Gastroenterology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325000, China.
| | - Lei Jiang
- Central Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325000, China.
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4
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SPZ1 promotes deregulation of Bim to boost apoptosis resistance in colorectal cancer. Biosci Rep 2021; 134:155-167. [PMID: 31934723 DOI: 10.1042/cs20190865] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Revised: 12/24/2019] [Accepted: 01/14/2020] [Indexed: 12/26/2022] Open
Abstract
Colorectal cancer (CRC) is the third most common malignancies in adults. Similar to other solid tumors, CRC cells show increased proliferation and suppressed apoptosis during the development and progression of the disease. Previous studies have shown that a novel tumor oncogene, spermatogenic basic helix-loop-helix transcription factor zip 1 (SPZ1), can promote proliferation. However, it is unclear whether SPZ1 plays a role in suppressing apoptosis, and the molecular mechanism behind SPZ1's suppression of apoptosis in CRC remains unclear. Here, we found that silencing endogenous SPZ1 inhibits cell growth and induces apoptosis, and overexpression of SPZ1 promotes cell growth. These findings were corroborated by in vitro and in vivo studies. Interestingly, SPZ1 overexpressing cells were resistant to 5-fluorouracil, a drug commonly used to treat cancer. Moreover, knocking down SPZ1 led to the activation of caspase through the deregulation of Bim by ERK1/2, we found that CRC tissues had significantly higher SPZ1 and lower Bim expression, and SPZ1HBimL were associated with advanced clinical stage of CRC. Collectively, our findings demonstrate that SPZ1 contributes to tumor progression by limiting apoptosis. SPZ1 reduces apoptosis by altering the stability of Bim, suggesting SPZ1 may serve as a biomarker and therapeutic target for CRC.
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5
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Landscape of somatic single nucleotide variants and indels in colorectal cancer and impact on survival. Nat Commun 2020; 11:3644. [PMID: 32686686 PMCID: PMC7371703 DOI: 10.1038/s41467-020-17386-z] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Accepted: 06/23/2020] [Indexed: 02/07/2023] Open
Abstract
Colorectal cancer (CRC) is a biologically heterogeneous disease. To characterize its mutational profile, we conduct targeted sequencing of 205 genes for 2,105 CRC cases with survival data. Our data shows several findings in addition to enhancing the existing knowledge of CRC. We identify PRKCI, SPZ1, MUTYH, MAP2K4, FETUB, and TGFBR2 as additional genes significantly mutated in CRC. We find that among hypermutated tumors, an increased mutation burden is associated with improved CRC-specific survival (HR = 0.42, 95% CI: 0.21–0.82). Mutations in TP53 are associated with poorer CRC-specific survival, which is most pronounced in cases carrying TP53 mutations with predicted 0% transcriptional activity (HR = 1.53, 95% CI: 1.21–1.94). Furthermore, we observe differences in mutational frequency of several genes and pathways by tumor location, stage, and sex. Overall, this large study provides deep insights into somatic mutations in CRC, and their potential relationships with survival and tumor features. Large scale sequencing study is of paramount importance to unravel the heterogeneity of colorectal cancer. Here, the authors sequenced 205 cancer genes in more than 2000 tumours and identified additional mutated driver genes, determined that mutational burden and specific mutations in TP53 are associated with survival odds.
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6
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Wang LT, Wang SN, Chiou SS, Liu KY, Chai CY, Chiang CM, Huang SK, Yokoyama KK, Hsu SH. TIP60-dependent acetylation of the SPZ1-TWIST complex promotes epithelial-mesenchymal transition and metastasis in liver cancer. Oncogene 2019; 38:518-532. [PMID: 30154425 PMCID: PMC6345675 DOI: 10.1038/s41388-018-0457-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Revised: 05/28/2018] [Accepted: 06/03/2018] [Indexed: 02/08/2023]
Abstract
Metastasis is the main cause of cancer mortality. However, the triggering mechanisms and regulation of epithelial-mesenchymal transition (EMT) factors in the commitment of metastasis have not been well characterized. Spermatogenic Zip 1 (SPZ1) acts as a proto-oncogene and an upstream regulator of EMT during tumorigenesis. Here we report that the HIV-1 Tat-interacting protein 60 kDa (Tip60) acetyltransferase mediates acetylation at lysine residues of SPZ1 at positions 369 and 374, and of TWIST1 at positions 73 and 76, which are required for SPZ1-TWIST1 complex formation and cancer cell migration in vitro and in vivo. Ectopic SPZ1 and TWIST1 expression, but not that of TWIST1 alone, enhanced vascular endothelial growth factor (VEGF) expression via the recruitment of bromodomain-containing protein 4 (BRD4), thus enhancing RNA-Pol II-dependent transcription and inducing metastasis. Neutralization of VEGF using humanized monoclonal antibodies such as Avastin, effectively abrogated the EMT and oncogenesis induced by the acetylated SPZ1-TWIST1 complex. Our findings highlight the importance of acetylation signaling in the SPZ1-TWIST1-BRD4 axis in the mediation of EMT and its regulation during tumor initiation and metastasis.
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Affiliation(s)
- Li-Ting Wang
- Graduate Institute of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan
| | - Shen-Nien Wang
- Department of Surgery, Kaohsiung Medical University Hospital, Kaohsiung 807, Taiwan
- Pingtung Hospital, Ministry of Health and Welfare, Pingtung 900, Taiwan
| | - Shyh-Shin Chiou
- Department of Pediatrics, Kaohsiung Medical University Hospital, Kaohsiung 807, Taiwan
- Division of Hematology-Oncology, Kaohsiung Medical University Hospital, Kaohsiung 807, Taiwan
| | - Kwei-Yan Liu
- Graduate Institute of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan
| | - Chee-Yin Chai
- Department of Pathology, Kaohsiung Medical University Hospital, Kaohsiung 807, Taiwan
| | - Cheng-Ming Chiang
- Simmons Comprehensive Cancer Center, Departments of Pharmacology and Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX, 75390-8807, USA
| | - Shau-Ku Huang
- Division of Environmental Health and Occupational Medicine, National Health Research Institutes, 115, Zhunan, Taiwan
| | - Kazunari K Yokoyama
- Graduate Institute of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan.
- Center of Infectious Disease and Cancer Research, Kaohsiung Medical University, Kaohsiung 807, Taiwan.
- Center for Stem Cell Research, Kaohsiung Medical University, Kaohsiung 807, Taiwan.
- Department of Molecular Preventive Medicine, Graduate School of Medicine, the University of Tokyo, Tokyo, 113-0033, Japan.
| | - Shih-Hsien Hsu
- Graduate Institute of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan.
- Department of Medical Research, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 807, Taiwan.
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7
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Liu X, Han X, Wan X, He C, Wang Y, Mao A, Yu F, Zhou T, Feng L, Zhang P, Jin J, Ma X. SPZ1 is critical for chemoresistance and aggressiveness in drug-resistant breast cancer cells. Biochem Pharmacol 2018; 156:43-51. [PMID: 30076850 DOI: 10.1016/j.bcp.2018.07.046] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2018] [Accepted: 07/31/2018] [Indexed: 12/24/2022]
Abstract
It is believed that chemotherapeutic agents can enhance the malignancy of treated cancer cells in clinical situations, which is a major problem for chemotherapy. However, the underlying molecular mechanisms are still not fully understood. Here, we demonstrated that chemotherapy up-regulates the levels of spermatogenic bHLH transcription factor zip 1 (SPZ1), and knockdown of SPZ1 in drug resistant breast cancers showed that SPZ1 is critical for regulating the chemoresistance, migration, invasion and epithelial-mesenchymal transition (EMT) in a Twist1-dependent manner. Moreover, suppressing SPZ1-Twist1 axis decreased the growth of tumor xenografts. Notably, we found a positive correlation between SPZ1 and Twist1 in breast cancer samples from patients with anthracycline or taxane-based chemotherapy. Thus, our results revealed a novel role of SPZ1 as an inducer of chemoresistance and aggressiveness under chemotherapy, and this suggests that therapeutic targeting of SPZ1 may not only enhance the sensitivity of breast cancer to chemotherapy, but also suppress breast cancer invasion and metastases.
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Affiliation(s)
- Xiaoyu Liu
- School of Medicine and School of Pharmaceutical Sciences, Jiangnan University, Wuxi, China; School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Xiping Han
- School of Medicine and School of Pharmaceutical Sciences, Jiangnan University, Wuxi, China
| | - Xu Wan
- School of Medicine and School of Pharmaceutical Sciences, Jiangnan University, Wuxi, China
| | - Chao He
- Department of Emergency and Critical Care, Changzheng Hospital, Naval Medical University, Shanghai, China
| | - Yan Wang
- Key Laboratory of Cardiovascular Medicine and Clinical Pharmacology of Shanxi Province, Taiyuan, China
| | - Aiqin Mao
- School of Medicine and School of Pharmaceutical Sciences, Jiangnan University, Wuxi, China
| | - Fan Yu
- School of Medicine and School of Pharmaceutical Sciences, Jiangnan University, Wuxi, China
| | - Tingting Zhou
- School of Medicine and School of Pharmaceutical Sciences, Jiangnan University, Wuxi, China
| | - Lei Feng
- School of Medicine and School of Pharmaceutical Sciences, Jiangnan University, Wuxi, China
| | - Peng Zhang
- School of Medicine and School of Pharmaceutical Sciences, Jiangnan University, Wuxi, China.
| | - Jian Jin
- School of Medicine and School of Pharmaceutical Sciences, Jiangnan University, Wuxi, China.
| | - Xin Ma
- School of Medicine and School of Pharmaceutical Sciences, Jiangnan University, Wuxi, China.
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8
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Wang SN, Wang LT, Sun DP, Chai CY, Hsi E, Kuo HT, Yokoyama KK, Hsu SH. Intestine-specific homeobox (ISX) upregulates E2F1 expression and related oncogenic activities in HCC. Oncotarget 2018; 7:36924-36939. [PMID: 27175585 PMCID: PMC5095049 DOI: 10.18632/oncotarget.9228] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Accepted: 04/16/2016] [Indexed: 01/29/2023] Open
Abstract
Intestine-specific homeobox (ISX), a newly identified proto-oncogene, is involved in cell proliferation and progression of hepatocellular carcinoma (HCC). However, the underlying mechanisms linking gene expression and tumor formation remain unclear. In this study, we found that ISX transcriptionally activated E2F transcription factor 1 (E2F1) and associated oncogenic activity by directly binding to the E2 site of its promoter. Forced expression of ISX increased the expression of and phosphorylated the serine residue at position 332 of E2F1, which may be translocated into the nucleus to form the E2F1–DP-1 complex, suggesting that the promotion of oncogenic activities of the ISX–E2F1 axis plays a critical role in hepatoma cells. Coexpression of ISX and E2F1 significantly promoted p53 and RB-mediated cell proliferation and anti-apoptosis, and repressed apoptosis and autophagy. In contrast, short hairpin RNAi-mediated attenuation of ISX and E2F1 decreased cell proliferation and malignant transformation, respectively, in hepatoma cells in vitro and in vivo. The mRNA expression of E2F1 and ISX in 238 paired specimens from human HCC patients, and the adjacent, normal tissues exhibited a tumor-specific expression pattern which was highly correlated with disease pathogenesis, patient survival time, progression stage, and poor prognosis. Therefore, our results indicate that E2F1 is an important downstream gene of ISX in hepatoma progression.
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Affiliation(s)
- Shen-Nien Wang
- Division of Hepatobiliary Surgery, Department of Surgery, Faculty of Medicine, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan.,Graduate Institute of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Li-Ting Wang
- Graduate Institute of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Ding-Ping Sun
- Division of General Surgery, Department of Surgery, Chi-Mei Medical Center, Tainan, Taiwan.,Department of Food Science and Technology, Chia Nan University of Pharmacy and Science, Tainan, Taiwan
| | - Chee-Yin Chai
- Department of Pathology, Faculty of Medicine, College of Medicine, Kaohsiung, Taiwan
| | - Edward Hsi
- Department of Genome Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Hsing-Tao Kuo
- Department of Internal Medicine, Division of Hepatogastroenterology, Chi-Mei Medical Center, Tainan, Taiwan.,Department of Senior Citizen Service Management, Chia Nan University of Pharmacy & Science, Tainan, Taiwan
| | - Kazunari K Yokoyama
- Graduate Institute of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan.,Research Center for Stem Cell Research, Kaohsiung Medical University, Kaohsiung, Taiwan.,Center for Environmental Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan.,Department of Molecular Preventive Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.,Faculty of Science and Engineering, Tokushima Bunri University, Sanuki, Japan.,Center of Infectious Disease and Cancer Research, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Shih-Hsien Hsu
- Graduate Institute of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan.,Center of Infectious Disease and Cancer Research, Kaohsiung Medical University, Kaohsiung, Taiwan
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9
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Watanabe M. Transcription factor SPZ1 may promote TWIST-mediated epithelial-mesenchymal transition in thoracic malignancies. J Thorac Dis 2017; 9:2740-2742. [PMID: 29221228 DOI: 10.21037/jtd.2017.07.112] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Masayuki Watanabe
- Department of Gastroenterological Surgery, Cancer Institute Hospital of Japanese Foundation for Cancer Research, Tokyo, Japan
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10
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Zhang S, Liu W, Liu X, Qi J, Deng C. Biomarkers identification for acute myocardial infarction detection via weighted gene co-expression network analysis. Medicine (Baltimore) 2017; 96:e8375. [PMID: 29381915 PMCID: PMC5708914 DOI: 10.1097/md.0000000000008375] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
The study aimed to seek potential biomarkers for acute myocardial infarction (AMI) detection and treatment.The dataset GSE48060 was used, consisting of 52 peripheral blood samples (31 AMI samples and 21 normal controls). By limma package, differentially expressed genes (DEGs) between 2 kinds of samples were identified, followed by enrichment analysis, subpathway analysis, protein-protein interaction (PPI) network analysis, and transcription factor network (TFN) analysis. Weighted gene co-expression network analysis was used to further extract key modules relating to AMI, followed by enrichment and TFN analyses. Expression validation was performed via meta-analysis of 2 datasets, GSE22229 and GSE29111.A set of 428 DEGs in AMI were screened out, and the upregulated toll-like receptor (TLR) family genes (TLR1, TLR2, and TLR10) were enriched in wound response, immune response and inflammatory response functions, and downregulated genes (GBP5, CXCL5, GZMA, CCL5, and CCL4) were correlated with immune response. CCL5, GZMA, GZMB, TLR2, and formyl peptide receptor 1 (FPR1) were predicted as crucial nodes in the PPI network. Signal transducer and activator of transcription 1 (STAT1) was the key transcription factor (TF) with multiple targets. The grey module was highly related to AMI. Genes in this module were closely related to regulation of macrophage activation, and spermatogenic leucine zipper 1 (SPZ1) was identified as a TF. Expressions of TLR2 and FPR1 were confirmed via the integrated matrix.Several potential biomarkers for AMI detection were identified, such as GZMB, GBP5, FPR1, TLR2, STAT1, and SPZ1. They might exert their functions via regulation of immune and inflammation responses. Genes in grey module play significant roles in AMI via regulation of macrophage activation.
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11
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HOTAIR genetic variants are associated with prostate cancer and benign prostate hyperplasia in an Iranian population. Gene 2017; 613:20-24. [DOI: 10.1016/j.gene.2017.02.031] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Revised: 02/17/2017] [Accepted: 02/27/2017] [Indexed: 01/02/2023]
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12
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Transcription factor SPZ1 promotes TWIST-mediated epithelial-mesenchymal transition and oncogenesis in human liver cancer. Oncogene 2017; 36:4405-4414. [PMID: 28368406 PMCID: PMC5543259 DOI: 10.1038/onc.2017.69] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2016] [Revised: 01/31/2017] [Accepted: 02/04/2017] [Indexed: 12/17/2022]
Abstract
The epithelial-mesenchymal transition (EMT) is an important process in the progression of cancer. However, its occurrence and mechanism of regulation are not fully understood. We propose a regulatory pathway in which spermatogenic leucine zipper 1 (SPZ1) promotes EMT through its transactivating ability in increasing TWIST1 expression. We compared the expression of SPZ1 and TWIST1 in specimens of hepatocarcinoma cells (HCCs) and non-HCCs. Expression of SPZ1 exhibited a tumor-specific expression pattern and a high correlation with patients' survival time, tumor size, tumor number and progression stage. Moreover, forced expression and knockdown of SPZ1 in hepatoma cells showed that SPZ1 was able to regulate the cellular proliferation, invasion, and tumorigenic activity in a TWIST1-dependent manner in vitro and in vivo. These data demonstrate that SPZ1, a newly dscribed molecule, transactivates TWIST1 promoters, and that this SPZ1-TWIST axis mediates EMT signaling and exerts significant regulatory effects on tumor oncogenesis.
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DNA methylation of the Fthl17 5'-upstream region regulates differential Fthl17 expression in lung cancer cells and germline stem cells. PLoS One 2017; 12:e0172219. [PMID: 28207785 PMCID: PMC5312872 DOI: 10.1371/journal.pone.0172219] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Accepted: 02/01/2017] [Indexed: 12/13/2022] Open
Abstract
The Ferritin heavy polypeptide-like 17 (Fthl17) gene is a member of the cancer/testis antigen gene family, and is preferentially expressed in cancer cells and in testis. Although DNA methylation has been linked to the regulation of human FTHL17 gene expression, detailed epigenetic regulation of its expression has not been investigated. To address this, we assessed the epigenetic regulation of murine Fthl17 gene expression in cancer cells and germ cells. Fthl17 was more highly expressed in testis, a murine lung cancer cell line, KLN205, and in germline stem cells (GSCs) than in normal lung tissues. Furthermore, the Fthl17 expression level in GSCs was significantly higher than in KLN205 cells. We performed bisulfite-sequencing and luciferase (luc) reporter assays to examine the role of DNA methylation of the Fthl17 promoter in the regulation of Fthl17 expression. In KLN205 cells, testis, and GSCs, the Fthl17 5’-upstream region was hypo-methylated compared with normal lung tissues. Luc reporter assays indicated that hypo-methylation of the -0.6 kb to 0 kb region upstream from the transcription start site (TSS) was involved in the up-regulation of Fthl17 expression in KLN205 cells and GSCs. Because the -0.6 kb to -0.3 kb or the -0.3 kb to 0 kb region were relatively more hypo-methylated in KLN205 cells and in GSCs, respectively, compared with other regions between -0.6 kb to 0 kb, those regions may contribute to Fthl17 up-regulation in each cell type. Following treatment with 5-Azacytidine, the -0.3 kb to 0 kb region became hypo-methylated, and Fthl17 expression was up-regulated in KLN205 cells to a level comparable to that in GSCs. Together, the results suggest that hypo-methylation of different but adjacent regions immediately upstream of the Fthl17 gene contribute to differential expression levels in lung cancer cells and GSCs, and hypo-methylation of the TSS-proximal region may be critical for high level expression.
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Erickson A, Moreau R. The regulation of FGF21 gene expression by metabolic factors and nutrients. Horm Mol Biol Clin Investig 2016; 30:/j/hmbci.ahead-of-print/hmbci-2016-0016/hmbci-2016-0016.xml. [PMID: 27285327 DOI: 10.1515/hmbci-2016-0016] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2016] [Accepted: 05/08/2016] [Indexed: 12/26/2022]
Abstract
Fibroblast growth factor 21 (FGF21) gene expression is altered by a wide array of physiological, metabolic, and environmental factors. Among dietary factors, high dextrose, low protein, methionine restriction, short-chain fatty acids (butyric acid and lipoic acid), and all-trans-retinoic acid were repeatedly shown to induce FGF21 expression and circulating levels. These effects are usually more pronounced in liver or isolated hepatocytes than in adipose tissue or isolated fat cells. Although peroxisome proliferator-activated receptor α (PPARα) is a key mediator of hepatic FGF21 expression and function, including the regulation of gluconeogenesis, ketogenesis, torpor, and growth inhibition, there is increasing evidence of PPARα-independent transactivation of the FGF21 gene by dietary molecules. FGF21 expression is believed to follow the circadian rhythm and be placed under the control of first order clock-controlled transcription factors, retinoic acid receptor-related orphan receptors (RORs) and nuclear receptors subfamily 1 group D (REV-ERBs), with FGF21 rhythm being anti-phase to REV-ERBs. Key metabolic hormones such as glucagon, insulin, and thyroid hormone have presumed or clearly demonstrated roles in regulating FGF21 transcription and secretion. The control of the FGF21 gene by glucagon and insulin appears more complex than first anticipated. Some discrepancies are noted and will need continued studies. The complexity in assessing the significance of FGF21 gene expression resides in the difficulty to ascertain (i) when transcription results in local or systemic increase of FGF21 protein; (ii) if FGF21 is among the first or second order genes upregulated by physiological, metabolic, and environmental stimuli, or merely an epiphenomenon; and (iii) whether FGF21 may have some adverse effects alongside beneficial outcomes.
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15
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Xia M, Erickson A, Yi X, Moreau R. Mapping the response of human fibroblast growth factor 21 (FGF21) promoter to serum availability and lipoic acid in HepG2 hepatoma cells. Biochim Biophys Acta Gen Subj 2015; 1860:498-507. [PMID: 26691139 DOI: 10.1016/j.bbagen.2015.12.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Revised: 11/23/2015] [Accepted: 12/11/2015] [Indexed: 12/15/2022]
Abstract
The hormone-like polypeptide, fibroblast growth factor 21 (FGF21), is a major modulator of lipid and glucose metabolism and an exploratory treatment strategy for obesity related metabolic disorders. The costs of recombinant FGF21 and mode of delivery by injection are important constraints to its wide therapeutic use. The stimulation of endogenous FGF21 production through diet is being explored as an alternative approach. To that end, we examined the mechanism(s) by which serum manipulation and lipoic acid (a dietary activator of FGF21) induce FGF21 in human hepatocellular carcinoma HepG2 cells. Serum withdrawal markedly induced FGF21 mRNA levels (88 fold) and FGF21 secreted in the media (19 fold). Lipoic acid induced FGF21 mRNA 7 fold above DMSO-treated control cells and FGF21 secretion 3 fold. These effects were several-fold greater than those of PPARα agonist, Wy14643, which failed to induce FGF21 above and beyond the induction seen with serum withdrawal. The use of transcription inhibitor, actinomycin D, revealed that de novo mRNA synthesis drives FGF21 secretion in response to serum starvation. Four previously unrecognized loci in FGF21 promoter were nucleosome depleted and enriched in acetylated histone H3 revealing their role as transcriptional enhancers and putative transcription factor binding sites. FGF21 did not accumulate to a significant degree in induced HepG2 cells, which secreted FGF21 time dependently in media. We conclude that lipoic acid cell signaling connects with the transcriptional upregulation of FGF21 and it may prove to be a safe and affordable means to stimulate FGF21 production.
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Affiliation(s)
- Mengna Xia
- Department of Nutrition and Health Sciences, University of Nebraska-Lincoln, Lincoln, NE 68583, USA
| | - Anjeza Erickson
- Department of Nutrition and Health Sciences, University of Nebraska-Lincoln, Lincoln, NE 68583, USA
| | - Xiaohua Yi
- Department of Nutrition and Health Sciences, University of Nebraska-Lincoln, Lincoln, NE 68583, USA
| | - Régis Moreau
- Department of Nutrition and Health Sciences, University of Nebraska-Lincoln, Lincoln, NE 68583, USA.
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16
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Chiou SS, Wang LT, Huang SB, Chai CY, Wang SN, Liao YM, Lin PC, Liu KY, Hsu SH. Wntless (GPR177) expression correlates with poor prognosis in B-cell precursor acute lymphoblastic leukemia via Wnt signaling. Carcinogenesis 2014; 35:2357-2364. [DOI: 10.1093/carcin/bgu166] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/30/2023] Open
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17
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Rat Stem-Cell Leukemia Gene Expression Increased during Testis Maturation. Biosci Biotechnol Biochem 2014; 76:2118-23. [DOI: 10.1271/bbb.120503] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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18
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Sammut SJ, Feichtinger J, Stuart N, Wakeman JA, Larcombe L, McFarlane RJ. A novel cohort of cancer-testis biomarker genes revealed through meta-analysis of clinical data sets. Oncoscience 2014; 1:349-359. [PMID: 25594029 PMCID: PMC4278308 DOI: 10.18632/oncoscience.37] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2014] [Accepted: 05/06/2014] [Indexed: 12/12/2022] Open
Abstract
The identification of cancer-specific biomolecules is of fundamental importance to the development of diagnostic and/or prognostic markers, which may also serve as therapeutic targets. Some antigenic proteins are only normally present in male gametogenic tissues in the testis and not in normal somatic cells. When these proteins are aberrantly produced in cancer they are referred to as cancer/testis (CT) antigens (CTAs). Some CTA genes have been proven to encode immunogenic proteins that have been used as successful immunotherapy targets for various forms of cancer and have been implicated as drug targets. Here, a targeted in silico analysis of cancer expressed sequence tag (EST) data sets resulted in the identification of a significant number of novel CT genes. The expression profiles of these genes were validated in a range of normal and cancerous cell types. Subsequent meta-analysis of gene expression microarray data sets demonstrates that these genes are clinically relevant as cancer-specific biomarkers, which could pave the way for the discovery of new therapies and/or diagnostic/prognostic monitoring technologies.
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Affiliation(s)
| | - Julia Feichtinger
- Institute for Knowledge Discovery, Graz University of Technology, Austria.,Core Facility Bioinformatics, Austrian Centre of Industrial Biotechnology, Austria
| | | | - Jane A Wakeman
- North West Cancer Research Institute, Bangor University, Bangor, UK
| | - Lee Larcombe
- North West Cancer Research Institute, Bangor University, Bangor, UK
| | - Ramsay J McFarlane
- North West Cancer Research Institute, Bangor University, Bangor, UK.,NISCHR Cancer Genetics Biomedical Research Unit
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Survival of motor neuron protein downregulates miR-9 expression in patients with spinal muscular atrophy. Kaohsiung J Med Sci 2014; 30:229-34. [PMID: 24751385 DOI: 10.1016/j.kjms.2013.12.007] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2013] [Accepted: 09/26/2013] [Indexed: 11/23/2022] Open
Abstract
Spinal muscular atrophy (SMA) is a lethal hereditary disease caused by homozygous absence of the survival of the motor neuron (SMN) 1 gene (SMN1), and it is the leading genetic cause of infant mortality. The severity of SMA is directly correlated with SMN protein levels in affected patients; however, the cellular regulatory mechanisms for SMN protein expression are not completely understood. In this study, we investigated the regulatory effects between SMN expression and miR-9a, a downstream noncoding small RNA. Using an inducible SMN short hairpin RNA interference (shRNAi) system in NSC 34 and human skin fibroblast cells, cellular miR-9 levels and SMN protein repression were time-dependently upregulated. Conversely, cellular miR-9 levels decreased when HeLa cells were transfected with SMN protein fused with green fluorescent protein. In SMA-like mice spinal cords and human primary skin fibroblasts isolated from patients with different degrees of SMA, human SMN exhibited a disease severity-dependent decrease, whereas cellular miR-9 levels increased. These results clearly suggested that cellular SMN proteins regulated miR-9 expression and that miR-9 expression was related to SMA severity. Thus, miR-9 may be a marker for SMA prognosis.
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20
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Transcriptional regulatory network analysis of the over-expressed genes in adipose tissue. Genes Genomics 2013. [DOI: 10.1007/s13258-013-0145-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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21
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Functional characterization of mammalian Wntless homolog in mammalian system. Kaohsiung J Med Sci 2012; 28:355-61. [DOI: 10.1016/j.kjms.2012.02.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2011] [Accepted: 08/24/2011] [Indexed: 11/20/2022] Open
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Vilborg A, Bersani C, Wilhelm MT, Wiman KG. The p53 target Wig-1: a regulator of mRNA stability and stem cell fate? Cell Death Differ 2011; 18:1434-40. [PMID: 21394102 DOI: 10.1038/cdd.2011.20] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Wig-1 is a transcriptional target of the tumor suppressor p53 and encodes an unusual zinc-finger protein involved in post-transcriptional gene regulation. Wig-1 is expressed in all cell types investigated so far, with the highest levels in the brain, and is enriched in stem cells as compared with more differentiated cells of the same lineage. Wig-1 binds to both long double-stranded (ds) RNA and short microRNA-like dsRNA. We have shown that Wig-1 acts in a positive feedback loop that stabilizes p53 mRNA through an AU-rich element (ARE) in the p53 3'untranslated region. Our preliminary data indicate a more general effect of Wig-1 on ARE-containing mRNA. Here we shall summarize current knowledge about Wig-1 and discuss possible implications on p53 function and other cellular processes.
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Affiliation(s)
- A Vilborg
- Karolinska Institutet, Department of Oncology-Pathology, Cancer Center Karolinska, Stockholm, Sweden
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23
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Functional interaction of Ugene and EBV infection mediates tumorigenic effects. Oncogene 2011; 30:2921-32. [PMID: 21317926 DOI: 10.1038/onc.2011.16] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Epstein-Barr virus (EBV) infection is associated with many human neoplasms, in which EBV-derived latent membrane protein-1 (LMP1) appears to be critical, but its exact oncogenic mechanism remains to be defined. To this end, our initial microarray analyses identified a LMP1-inducible gene, Ugene, originally characterized as a binding partner for uracil DNA glycosylase 2, which is highly expressed in malignant colon cancer. In this report, it was found that Ugene, designated herein as LMP1-induced protein (LMPIP), was induced, in a time-dependent manner, in EBV-infected peripheral blood mononuclear cells and LMP1-transfected 293 cells. Functionally, when compared with mock-transfected cells, overexpression of LMPIP in nasopharyngeal carcinoma (NPC) cell lines resulted in a decrease in reactive oxygen species production and maintained mitochondria membrane potential (Δψ) loss induced by H(2)O(2). The NPC cells transfected with LMPIP also showed a decrease in G1 population and an increase in the cell population in sub-G1 and multiploid phase, concomitant with increased levels of cell cycle activators, including cyclin D1 and CDK4. In contrast, silencing of LMPIP expression in the NPC tumor cell lines with short hairpin RNA interference revealed significantly decreased cell population at G1/S phase, while the number of cells in multiploid phase increased. Significantly, NPC cells with LMPIP knock-down also showed a decrease in tumorigenic and transforming activity induced by ectopic LMP1 expression, as determined by analyses of soft agar foci and tumor size in nude mice. Further, elevated LMPIP expression was also noted in cytoplasm and nuclei in EBV-infected NPC tumor cell mass and non-EBV-infected tumor cell lines. These results suggested that LMPIP may have an important mediator role in EBV-mediated neoplasm and may serve as a new target for therapy of tumors induced by EBV infection.
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Hsu SH, Lai MC, Er TK, Yang SN, Hung CH, Tsai HH, Lin YC, Chang JG, Lo YC, Jong YJ. Ubiquitin carboxyl-terminal hydrolase L1 (UCHL1) regulates the level of SMN expression through ubiquitination in primary spinal muscular atrophy fibroblasts. Clin Chim Acta 2010; 411:1920-8. [PMID: 20713032 DOI: 10.1016/j.cca.2010.07.035] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2010] [Revised: 07/28/2010] [Accepted: 07/30/2010] [Indexed: 02/04/2023]
Abstract
BACKGROUND Spinal muscular atrophy (SMA), a lethal hereditary disease caused by mutations of the survival of motor neuron 1 (SMN1) gene, is the leading genetic cause of infant mortality. Its severity directly correlates to the expression level of SMN protein in patients with SMA, but the regulatory mechanisms of SMN protein expression remain incompletely defined. In the present study, we aimed to identify candidate proteins to distinguish SMA fibroblasts from normal fibroblasts. METHODS To identify cellular targets regulating the expression of SMN, we initially utilized a proteomics approach combining 2D electrophoresis and LC-MS/MS, wherein the total proteins extracted from type I SMA patients and normal skin fibroblast cells were compared. RESULTS Our initial proteomics analysis discovered significant increase of ubiquitin carboxyl-terminal hydrolase L1 (UCHL1) in type I SMA fibroblasts when compared to normal fibroblasts. Significantly, UCHL1 proteins directly interacted with SMN protein, as determined by immunoprecipitation and immunofluorescence assays in P19 and NSC34 cells. Over-expression of UCHL1 in P19 and NSC34 cells significantly reduced the level of SMN proteins in vivo, and, in fact, purified UCHL1 was shown to be able to enhance, in a dose-dependent manner, the level of ubiquitinated SMN in vitro. Further, inhibition of UCHL1 activity by UCHL1 inhibitor (LDN-57444) increased cellular SMN protein and gems number in the nucleus in NSC34 and SMA skin fibroblasts. The same results were observed in cells with UCHL1-specific knockdown. CONCLUSIONS These results suggested that UCHL1 may be a critical regulator in controlling cellular SMN protein turnover, and that it may serve as an attractive therapeutic target for SMA.
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Affiliation(s)
- Shih-Hsien Hsu
- Graduate Institute of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
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25
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Fuchs J, Mueller JC, Lichtner P, Schulte C, Munz M, Berg D, Wüllner U, Illig T, Sharma M, Gasser T. The transcription factor PITX3 is associated with sporadic Parkinson's disease. Neurobiol Aging 2009; 30:731-8. [PMID: 17905480 DOI: 10.1016/j.neurobiolaging.2007.08.014] [Citation(s) in RCA: 81] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2007] [Revised: 08/02/2007] [Accepted: 08/20/2007] [Indexed: 11/28/2022]
Abstract
Parkinson's disease (PD) is a progressive neurodegenerative disease with typical motor symptoms due to the preferential loss of midbrain dopaminergic (mDA) neurons in the Substantia nigra pars compacta. Several proteins of the homeodomain family are crucial for the development of mDA neurons. These proteins remain expressed into adulthood with largely unknown functions, but potentially influence mDA neuronal survival. To determine whether genetic variation in these genes plays a role in sporadic PD, we performed a genetic association study in a screening sample of 340 PD patients and 680 controls and a large replication sample of 669 PD patients and 669 controls using 54 single nucleotide polymorphisms in and around the Engrailed 1/2, PITX3, LMX1B and OTX2 genes. We provide evidence for a novel, strong and reproducible association of the PITX3 promoter SNP rs3758549: C>T (p=0.004) with PD. The C-allele appears to be a recessive risk allele with an estimated population frequency of 83%. An allele-dependent dysregulation of PITX3 expression might contribute to the susceptibility to PD.
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Affiliation(s)
- Julia Fuchs
- Hertie-Institute for Clinical Brain Research, Department of Neurodegenerative Diseases, University of Tübingen, Otfried-Müller-Strasse 27, 72076 Tübingen, Germany.
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26
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Lombard Z, Tiffin N, Hofmann O, Bajic VB, Hide W, Ramsay M. Computational selection and prioritization of candidate genes for fetal alcohol syndrome. BMC Genomics 2007; 8:389. [PMID: 17961254 PMCID: PMC2194724 DOI: 10.1186/1471-2164-8-389] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2007] [Accepted: 10/25/2007] [Indexed: 01/07/2023] Open
Abstract
Background Fetal alcohol syndrome (FAS) is a serious global health problem and is observed at high frequencies in certain South African communities. Although in utero alcohol exposure is the primary trigger, there is evidence for genetic- and other susceptibility factors in FAS development. No genome-wide association or linkage studies have been performed for FAS, making computational selection and -prioritization of candidate disease genes an attractive approach. Results 10174 Candidate genes were initially selected from the whole genome using a previously described method, which selects candidate genes according to their expression in disease-affected tissues. Hereafter candidates were prioritized for experimental investigation by investigating criteria pertinent to FAS and binary filtering. 29 Criteria were assessed by mining various database sources to populate criteria-specific gene lists. Candidate genes were then prioritized for experimental investigation using a binary system that assessed the criteria gene lists against the candidate list, and candidate genes were scored accordingly. A group of 87 genes was prioritized as candidates and for future experimental validation. The validity of the binary prioritization method was assessed by investigating the protein-protein interactions, functional enrichment and common promoter element binding sites of the top-ranked genes. Conclusion This analysis highlighted a list of strong candidate genes from the TGF-β, MAPK and Hedgehog signalling pathways, which are all integral to fetal development and potential targets for alcohol's teratogenic effect. We conclude that this novel bioinformatics approach effectively prioritizes credible candidate genes for further experimental analysis.
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Affiliation(s)
- Zané Lombard
- Division of Human Genetics, National Health Laboratory Service & School of Pathology, University of the Witwatersrand, Johannesburg, 2001, South Africa.
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Suzuki T, Minami N, Kono T, Imai H. Zygotically activated genes are suppressed in mouse nuclear transferred embryos. CLONING AND STEM CELLS 2007; 8:295-304. [PMID: 17196094 DOI: 10.1089/clo.2006.8.295] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Mammalian oocytes have the ability to confer totipotency to terminally differentiated somatic cell nuclei. Viable cloned animals have been produced by somatic cell nuclear transfer (NT) into oocytes in many mammalian species including mouse. However, the success rates of the production were quite low in all species. Many studies have measured differences in gene expression between NT and fertilized embryos in relatively advanced stages of development such as pre- and post-natal stages or the blastocyst stage. In the present study, we compared gene expression patterns using differential display RT-PCR (DDRT-PCR) between the NT and IVF embryos at the 2-cell stage to detect some abnormalities affecting later development of NT embryos. Aberrant gene expression was detected in NT embryos compared with IVF embryos, and MuERV-L and Dnaja2 genes were down-regulated and Inpp5b and Chst12 genes were up-regulated in the NT embryos. Further analysis showed that the expression of zygotically activated genes such as Interferon-gamma, Dub-1, Spz1, DD2106 (unknown gene), and DD2111 (unknown gene) were suppressed in NT embryos, suggesting that the cellular process involved in the nuclear reprogramming of somatic nucleus is not appropriately regulated.
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Affiliation(s)
- Toru Suzuki
- Laboratory of Reproductive Biology, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
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