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Dai F, Yuan Y, Hao J, Cheng X, Zhou X, Zhou L, Tian R, Zhao Y, Xiang T. PDCD2 as a prognostic biomarker in glioma correlates with malignant phenotype. Genes Dis 2024; 11:101106. [PMID: 39022129 PMCID: PMC11252777 DOI: 10.1016/j.gendis.2023.101106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 08/04/2023] [Indexed: 07/20/2024] Open
Abstract
Programmed cell death 2 (PDCD2) is related to cancer progression and chemotherapy sensitivity. The role of PDCD2 in solid cancers (excluding hematopoietic malignancies) and their diagnosis and prognosis remains unclear. The TCGA, CGGA, GEPIA, cBioPortal, and GTEx databases were analyzed for expression, prognostic value, and genetic modifications of PDCD2 in cancer patients. Functional enrichment analysis, CCK8, colony formation assay, transwell assay, and xenograft tumor model were undertaken to study the PDCD2's biological function in glioma (GBMLGG). The PDCD2 gene was associated with solid cancer progression. In the functional enrichment analysis results, PDCD2 was shown to participate in several important GBMLGG biological processes. GBMLGG cells may be inhibited in their proliferation, migration, invasion, and xenograft tumor growth by knocking down PDCD2. Our research can provide new insights into solid cancer prognostic biomarkers of PDCD2.
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Affiliation(s)
- Fengsheng Dai
- Department of Oncology, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400010, China
- Chongqing Key Laboratory of Translational Research for Cancer Metastasis and Individualized Treatment, Chongqing University Cancer Hospital, Chongqing 400030, China
| | - Yixiao Yuan
- Department of Oncology, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400010, China
| | - Jiaqi Hao
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
- Hunan International Scientific and Technological Cooperation Base of Brain Tumor Research, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Xing Cheng
- Department of Neuro-Oncology, Chongqing University Cancer Hospital, Chongqing 400030, China
| | - Xiangyi Zhou
- Department of Oncology, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400010, China
| | - Li Zhou
- Chongqing Key Laboratory of Translational Research for Cancer Metastasis and Individualized Treatment, Chongqing University Cancer Hospital, Chongqing 400030, China
| | - Rui Tian
- Chongqing Key Laboratory of Translational Research for Cancer Metastasis and Individualized Treatment, Chongqing University Cancer Hospital, Chongqing 400030, China
| | - Yi Zhao
- Chongqing Key Laboratory of Translational Research for Cancer Metastasis and Individualized Treatment, Chongqing University Cancer Hospital, Chongqing 400030, China
| | - Tingxiu Xiang
- Department of Oncology, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400010, China
- Chongqing Key Laboratory of Translational Research for Cancer Metastasis and Individualized Treatment, Chongqing University Cancer Hospital, Chongqing 400030, China
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Ji W, Byun WS, Lu W, Zhu X, Donovan KA, Dwyer BG, Che J, Yuan L, Abulaiti X, Corsello SM, Fischer ES, Zhang T, Gray NS. Proteomics-Based Discovery of First-in-Class Chemical Probes for Programmed Cell Death Protein 2 (PDCD2). Angew Chem Int Ed Engl 2023; 62:e202308292. [PMID: 37658265 PMCID: PMC10592021 DOI: 10.1002/anie.202308292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 08/31/2023] [Accepted: 09/01/2023] [Indexed: 09/03/2023]
Abstract
Chemical probes are essential tools for understanding biological systems and for credentialing potential biomedical targets. Programmed cell death 2 (PDCD2) is a member of the B-cell lymphoma 2 (Bcl-2) family of proteins, which are critical regulators of apoptosis. Here we report the discovery and characterization of 10 e, a first-in-class small molecule degrader of PDCD2. We discovered this PDCD2 degrader by serendipity using a chemical proteomics approach, in contrast to the conventional approach for making bivalent degraders starting from a known binding ligand targeting the protein of interest. Using 10 e as a pharmacological probe, we demonstrate that PDCD2 functions as a critical regulator of cell growth by modulating the progression of the cell cycle in T lymphoblasts. Our work provides a useful pharmacological probe for investigating PDCD2 function and highlights the use of chemical proteomics to discover selective small molecule degraders of unanticipated targets.
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Affiliation(s)
- Wenzhi Ji
- Department of Chemical and Systems Biology, Chem-H and Stanford Cancer Institute, Stanford School of Medicine, Stanford University, Stanford, CA, 94305, USA
| | - Woong Sub Byun
- Department of Chemical and Systems Biology, Chem-H and Stanford Cancer Institute, Stanford School of Medicine, Stanford University, Stanford, CA, 94305, USA
| | - Wenchao Lu
- Department of Chemical and Systems Biology, Chem-H and Stanford Cancer Institute, Stanford School of Medicine, Stanford University, Stanford, CA, 94305, USA
- Lingang Laboratory, Shanghai, 20031, China
| | - Xijun Zhu
- Department of Chemical and Systems Biology, Chem-H and Stanford Cancer Institute, Stanford School of Medicine, Stanford University, Stanford, CA, 94305, USA
| | - Katherine A Donovan
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115, USA
| | - Brendan G Dwyer
- Department of Chemical and Systems Biology, Chem-H and Stanford Cancer Institute, Stanford School of Medicine, Stanford University, Stanford, CA, 94305, USA
| | - Jianwei Che
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115, USA
| | - Linjie Yuan
- Department of Chemical and Systems Biology, Chem-H and Stanford Cancer Institute, Stanford School of Medicine, Stanford University, Stanford, CA, 94305, USA
| | - Xianmixinuer Abulaiti
- Department of Chemical and Systems Biology, Chem-H and Stanford Cancer Institute, Stanford School of Medicine, Stanford University, Stanford, CA, 94305, USA
| | - Steven M Corsello
- Department of Chemical and Systems Biology, Chem-H and Stanford Cancer Institute, Stanford School of Medicine, Stanford University, Stanford, CA, 94305, USA
| | - Eric S Fischer
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115, USA
| | - Tinghu Zhang
- Department of Chemical and Systems Biology, Chem-H and Stanford Cancer Institute, Stanford School of Medicine, Stanford University, Stanford, CA, 94305, USA
| | - Nathanael S Gray
- Department of Chemical and Systems Biology, Chem-H and Stanford Cancer Institute, Stanford School of Medicine, Stanford University, Stanford, CA, 94305, USA
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Wang L, Li C, Chen P, Liu C, Cui Z, Deng S, Yang H. Identification of PDCD2 as a Candidate Target of Andrographolide That Arrests the Tumor Cell Cycle by Human Proteome-Scale Screening. ACS Pharmacol Transl Sci 2022; 5:479-490. [DOI: 10.1021/acsptsci.2c00092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Lei Wang
- Beijing Key Laboratory of Traditional Chinese Medicine Basic Research on Prevention and Treatment for Major Diseases, Experimental Research Center, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Caifeng Li
- Beijing Key Laboratory of Traditional Chinese Medicine Basic Research on Prevention and Treatment for Major Diseases, Experimental Research Center, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Peng Chen
- Robot intelligence laboratory, Experimental Research Center, China Academy of Chinese Medical Sciences, Dongcheng District, Beijing 100700, China
| | - Chunyuan Liu
- Department of Surgery, Yantai Affiliated Hospital of Binzhou Medical University, Yantai 264100, China
| | - Zhao Cui
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Shiwen Deng
- Beijing Key Laboratory of Traditional Chinese Medicine Basic Research on Prevention and Treatment for Major Diseases, Experimental Research Center, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Hongjun Yang
- Experimental Research Center, China Academy of Chinese Medical Sciences, Dongcheng District, Beijing 100700, China
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ERRFI1 induces apoptosis of hepatocellular carcinoma cells in response to tryptophan deficiency. Cell Death Discov 2021; 7:274. [PMID: 34608122 PMCID: PMC8490388 DOI: 10.1038/s41420-021-00666-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 09/07/2021] [Accepted: 09/22/2021] [Indexed: 12/20/2022] Open
Abstract
Tryptophan metabolism is an essential regulator of tumor immune evasion. However, the effect of tryptophan metabolism on cancer cells remains largely unknown. Here, we find that tumor cells have distinct responses to tryptophan deficiency in terms of cell growth, no matter hepatocellular carcinoma (HCC) cells, lung cancer cells, or breast cancer cells. Further study shows that ERRFI1 is upregulated in sensitive HCC cells, but not in resistant HCC cells, in response to tryptophan deficiency, and ERRFI1 expression level positively correlates with HCC patient overall survival. ERRFI1 knockdown recovers tryptophan deficiency-suppressed cell growth of sensitive HCC cells. In contrast, ERRFI1 overexpression sensitizes resistant HCC cells to tryptophan deficiency. Moreover, ERRFI1 induces apoptosis by binding PDCD2 in HCC cells, PDCD2 knockdown decreases the ERRFI1-induced apoptosis in HCC cells. Thus, we conclude that ERRFI1-induced apoptosis increases the sensitivity of HCC cells to tryptophan deficiency and ERRFI1 interacts with PDCD2 to induce apoptosis in HCC cells.
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He QE, Tong YF, Ye Z, Gao LX, Zhang YZ, Wang L, Song K. A multiple genomic data fused SF2 prediction model, signature identification, and gene regulatory network inference for personalized radiotherapy. Technol Cancer Res Treat 2020; 19:1533033820909112. [PMID: 32329416 PMCID: PMC7225787 DOI: 10.1177/1533033820909112] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
Radiotherapy is one of the most important cancer treatments, but its response varies greatly among individual patients. Therefore, the prediction of radiosensitivity, identification of potential signature genes, and inference of their regulatory networks are important for clinical and oncological reasons. Here, we proposed a novel multiple genomic fused partial least squares deep regression method to simultaneously analyze multi-genomic data. Using 60 National Cancer Institute cell lines as examples, we aimed to identify signature genes by optimizing the radiosensitivity prediction model and uncovering regulatory relationships. A total of 113 signature genes were selected from more than 20,000 genes. The root mean square error of the model was only 0.0025, which was much lower than previously published results, suggesting that our method can predict radiosensitivity with the highest accuracy. Additionally, our regulatory network analysis identified 24 highly important ‘hub’ genes. The data analysis workflow we propose provides a unified and computational framework to harness the full potential of large-scale integrated cancer genomic data for integrative signature discovery. Furthermore, the regression model, signature genes, and their regulatory network should provide a reliable quantitative reference for optimizing personalized treatment options, and may aid our understanding of cancer progress mechanisms.
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Affiliation(s)
- Qi-En He
- School of Chemical Engineering and Technology, Tianjin University, 300350 Tianjin, China
| | - Yi-Fan Tong
- School of Chemical Engineering and Technology, Tianjin University, 300350 Tianjin, China
| | - Zhou Ye
- Department of Hematology and Oncology, Karamay Central Hospital of Xinjiang, 834000 Xinjiang, Uygur Autonomous Region, China
| | - Li-Xia Gao
- Department of Hematology and Oncology, Karamay Central Hospital of Xinjiang, 834000 Xinjiang, Uygur Autonomous Region, China
| | - Yi-Zhi Zhang
- Department of Hematology and Oncology, Karamay Central Hospital of Xinjiang, 834000 Xinjiang, Uygur Autonomous Region, China
| | - Ling Wang
- The First Affiliated Hospital Oncology of Dalian Medical University, 116011 Liaoning, China
| | - Kai Song
- School of Chemical Engineering and Technology, Tianjin University, 300350 Tianjin, China
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Ribosomes: An Exciting Avenue in Stem Cell Research. Stem Cells Int 2020; 2020:8863539. [PMID: 32695182 PMCID: PMC7362291 DOI: 10.1155/2020/8863539] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Revised: 06/12/2020] [Accepted: 06/16/2020] [Indexed: 02/07/2023] Open
Abstract
Stem cell research has focused on genomic studies. However, recent evidence has indicated the involvement of epigenetic regulation in determining the fate of stem cells. Ribosomes play a crucial role in epigenetic regulation, and thus, we focused on the role of ribosomes in stem cells. Majority of living organisms possess ribosomes that are involved in the translation of mRNA into proteins and promote cellular proliferation and differentiation. Ribosomes are stable molecular machines that play a role with changes in the levels of RNA during translation. Recent research suggests that specific ribosomes actively regulate gene expression in multiple cell types, such as stem cells. Stem cells have the potential for self-renewal and differentiation into multiple lineages and, thus, require high efficiency of translation. Ribosomes induce cellular transdifferentiation and reprogramming, and disrupted ribosome synthesis affects translation efficiency, thereby hindering stem cell function leading to cell death and differentiation. Stem cell function is regulated by ribosome-mediated control of stem cell-specific gene expression. In this review, we have presented a detailed discourse on the characteristics of ribosomes in stem cells. Understanding ribosome biology in stem cells will provide insights into the regulation of stem cell function and cellular reprogramming.
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王 少, 李 涛, 杜 婧, 韩 曼, 鞠 迪. [Pregnane X receptor promotes programmed cell death protein 4 expression in HepG2 cells]. NAN FANG YI KE DA XUE XUE BAO = JOURNAL OF SOUTHERN MEDICAL UNIVERSITY 2020; 40:370-375. [PMID: 32376574 PMCID: PMC7167314 DOI: 10.12122/j.issn.1673-4254.2020.03.14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Indexed: 11/24/2022]
Abstract
OBJECTIVE To investigate the role of pregnane X receptor (PXR) in the regulation of programmed cell death proteins (PDCDs) in HepG2 cells and explore the underlying molecular mechanism. METHODS HepG2 cells were treated with PXR agonist rifampicin (10 μmol/L) or SR12813 (1 μmol/L) for 24 h, using DMSO as the negative control. HepG2 cells were infected with constitutively activated PXR adenovirus (VP-PXR) for 36 h, with the cells infected with Mock as the negative control. The mRNA levels of PDCD2, PDCD4, PDCD5, and PDCD6 and the expression of miRNA21 were detected using qRT-PCR, and the protein level of PDCD4 was detected with Western blotting. Bioinformatic analysis was performed to predict the potential PXRresponsive elements (PXREs) motifs in the promotor region of human PDCD4. RESULTS The expressions of PDCD5 and PDCD6 mRNA did not differ significantly between rifampicin-treated and the control cells, while PDCD4 mRNA expression increased (t=4.209, P=0.008) and PDCD2 mRNA decreased significantly (t=-2.875, P=0.017) in rifampicin-treated cells. The mRNA expressions of PDCD2, PDCD5 and PDCD6 showed no significant difference between SR12813-treated cells and the control cells, while PDCD4 mRNA expression increased obviously in SR12813-treated cells (t=4.574, P=0.006). The PXR target gene MDR1 also increased significantly in the rifampicin- and SR12813-treated cells compared with the control cells (P=0.020 and 0.01, respectively). Infection of the cells with VP-PXR adenovirus resulted in significantly increased expression of PDCD4 and MDR1 mRNA as compared with Mock group (t=3.343, P=0.000; t=3.343, P=0.024, respectively) without causing obvious changes in PDCD2 and PDCD6 mRNA expressions. The protein level of PDCD4 increased significantly in both rifampicin (t= 2.779, P=0.025) group and VP- PXR group (t=3.066, P=0.012). The expression of miRNA21, the negative regulatory factor of PDCD4, did not differ significantly between PXR agonist group and the control group. Informatic analysis revealed the presence of putative PXREs in the 5'-flanking region of PDCD4 gene. CONCLUSIONS Our findings demonstrate that PXR agonism in HepG2 cells increases the expression of PDCD4, which is independent of miRNA21 pathway, and PDCD4 may be a target gene of PXR in HepG2 cells.
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Affiliation(s)
- 少兰 王
- />陕西中医药大学基础医学院,陕西 西安 712046School of Basic Medicine, Shaanxi University of Chinese Medicine, Xi'an 712046, China
| | - 涛 李
- />陕西中医药大学基础医学院,陕西 西安 712046School of Basic Medicine, Shaanxi University of Chinese Medicine, Xi'an 712046, China
| | - 婧 杜
- />陕西中医药大学基础医学院,陕西 西安 712046School of Basic Medicine, Shaanxi University of Chinese Medicine, Xi'an 712046, China
| | - 曼 韩
- />陕西中医药大学基础医学院,陕西 西安 712046School of Basic Medicine, Shaanxi University of Chinese Medicine, Xi'an 712046, China
| | - 迪 鞠
- />陕西中医药大学基础医学院,陕西 西安 712046School of Basic Medicine, Shaanxi University of Chinese Medicine, Xi'an 712046, China
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He J, Xing J, Yang X, Zhang C, Zhang Y, Wang H, Xu X, Wang H, Cao Y, Xu H, Zhang C, Wang C, Yu E. Silencing of Proteasome 26S Subunit ATPase 2 Regulates Colorectal Cancer Cell Proliferation, Apoptosis, and Migration. Chemotherapy 2019; 64:146-154. [PMID: 31715603 DOI: 10.1159/000502224] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Accepted: 07/19/2019] [Indexed: 11/19/2022]
Abstract
OBJECTIVE Colorectal cancer (CRC) remains a major cause of cancer-related death worldwide. Proteasome 26S subunit ATPase 2 (PSMC2) plays vital roles in regulating cell cycle and transcription and has been confirmed to be a gene potentially associated with some human tumors. However, the expression correlation and molecular mechanism of PSMC2 in CRC are still unclear. This study aimed to investigate the role of PSMC2 in malignant behaviors in CRC. METHODS The high protein levels of PSMC2 in CRC samples were identified by tissue microarray analysis. Lentivirus was used to silence PSMC2 in HCT116 and RKO cells; MTT and colony formation assay were performed to determine cell proliferation. Wound healing and Transwell assay were used to detect cell migration and invasion. Flow cytometry assay was applied to detect cell cycle and apoptosis. RESULT The results showed that, among the 96 CRC patients, the expression of PSMC2 was a positive correlation with the clinicopathological features of the patients with CRC. Furthermore, the low PSMC2 expression group showed a higher survival rate than the high PSMC2 expression group. The expression levels of PSMC2 in cancer tissue were dramatically upregulated compared with adjacent normal tissues. In vitro, shPSMC2 was designed to inhibit the expression of PSMC2 in CRC cells. Compared with shCtrl, silencing of PSMC2 significantly suppressed cell proliferation, decreased single cell colony formation, enhanced apoptosis, and accelerated G2 phase and/or S phase arrest. CONCLUSION Survival analysis indicated that high expression of PSMC2 in the CRC samples was associated with poorer survival rate than low expression of PSMC2, while the anti-tumor effect of PSMC2 silencing was also confirmed at the cellular level in vitro. Our results suggested that PSMC2 potentially worked as a regulator for CRC, and the silencing of PSMC2 may be a therapeutic strategy for CRC.
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Affiliation(s)
- Jinghu He
- Department of General Surgery, Changhai Hospital Affiliated to Navy Medical University, Shanghai, China
| | - Junjie Xing
- Department of General Surgery, Changhai Hospital Affiliated to Navy Medical University, Shanghai, China
| | - Xiaohong Yang
- Department of General Surgery, Changhai Hospital Affiliated to Navy Medical University, Shanghai, China
| | - Chenxin Zhang
- Department of General Surgery, Changhai Hospital Affiliated to Navy Medical University, Shanghai, China
| | - Yixiang Zhang
- Department of General Surgery, Changhai Hospital Affiliated to Navy Medical University, Shanghai, China
| | - Hao Wang
- Department of General Surgery, Changhai Hospital Affiliated to Navy Medical University, Shanghai, China
| | - Xiaodong Xu
- Department of General Surgery, Changhai Hospital Affiliated to Navy Medical University, Shanghai, China
| | - Hantao Wang
- Department of General Surgery, Changhai Hospital Affiliated to Navy Medical University, Shanghai, China
| | - Yi Cao
- Department of General Surgery, Changhai Hospital Affiliated to Navy Medical University, Shanghai, China
| | - Haonan Xu
- Shanghai Yangpu District New Jiangwan City Street Community Health Service Center, Shanghai, China
| | - Chuansen Zhang
- Department of Anatomy, Naval Medical University, Shanghai, China
| | - Chen Wang
- Department of Traditional Chinese Medicine, Changhai Hospital, Second Military Medical University, Shanghai, China
| | - Enda Yu
- Department of General Surgery, Changhai Hospital Affiliated to Navy Medical University, Shanghai, China,
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Aydin B, Arga KY. Co-expression Network Analysis Elucidated a Core Module in Association With Prognosis of Non-functioning Non-invasive Human Pituitary Adenoma. Front Endocrinol (Lausanne) 2019; 10:361. [PMID: 31244774 PMCID: PMC6563679 DOI: 10.3389/fendo.2019.00361] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Accepted: 05/22/2019] [Indexed: 12/21/2022] Open
Abstract
Non-functioning pituitary adenomas (NFPAs) are tumors with clinically challenging features since they have insidious progression. A complex network of gene interactions is thought to have roles in tumor formation and progression. Therefore, revealing the genetic network behind NFPA tumorigenesis is not only essential to attain further knowledge of tumor biology, but also plays a fundamental role in the development of efficacious treatment strategies. Differential co-expression network analysis is an outstanding approach for elucidation of groups of genes which show distinct co-expression patterns among phenotypes. In this study, we carried out a differential co-expression network analysis of NFPA-associated transcriptome dataset (n = 40) considering invasive (n = 22) and non-invasive (n = 18) phenotypes. Furthermore, we identified differentially co-expressed and co-regulated mRNA modules, which might be considered as potential systems biomarkers for NFPA prognosis and invasiveness. As a result, we have identified a novel 13-gene module, including CEACAM6, CYP4B1, EIF2S2, HID1, IFFO1, MYO18A, PDCD2, SGIP1, SWSAP1, and four unknown genes (A_24_P127621, A_24_P255786, A_24_P683553, and A_24_P916979), which was able to categorize the patients into two groups as invasive and non-invasive NFPA with distinct prognosis. The prognostic core module genes were associated with progression and prognosis of brain and glandular based cancers as well. Furthermore, these module genes were also expressed in blood, salivary gland, and spinal cord tissues. These results may provide the evidence on featured gene module which might play a prominent role in NFPA prognosis and sub-typing as effective biomarkers and therapeutic targets in the future.
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Liu H, Wang M, Liang N, Guan L. PDCD2 sensitizes HepG2 cells to sorafenib by suppressing epithelial‑mesenchymal transition. Mol Med Rep 2019; 19:2173-2179. [PMID: 30664177 PMCID: PMC6390009 DOI: 10.3892/mmr.2019.9860] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Accepted: 11/05/2018] [Indexed: 02/07/2023] Open
Abstract
Epithelial-mesenchymal transition (EMT) has an established role in the acquisition of therapeutic resistance. Programmed cell death domain 2 (PDCD2) is involved in the progression of multiple types of cancer. However, its mechanism underlying chemoresistance in liver cancer has not been elucidated. In the present study, it was demonstrated that the sorafenib-resistant HepG2 cell line exhibited EMT and multidrug resistance (MDR) phenotypes, and reduced expression of PDCD2, by reverse transcription-quantitative polymerase chain reaction (RT-qPCR), western blot analysis and Cell Counting Kit-8. Annexin V/fluorescein isothiocyanate and cell migration assays further demonstrated that PDCD2 effectively promoted sorafenib-induced cell apoptosis and reduced cell metastasis. Mechanistically, PDCD2 inhibited the expression of Vimentin and increased the expression of E-cadherin in a Snail-dependent manner by RT-qPCR and western blot analysis. In conclusion, the present study elucidated for the first time, to the best of our knowledge, that PDCD2 sensitizes sorafenib-resistant HepG2 cells to sorafenib by the downregulation of EMT. PDCD2 may serve as a potential therapeutic target in the treatment of sorafenib-resistant liver cancer.
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Affiliation(s)
- Hongyu Liu
- Department of Hepatobiliary‑Pancreatic Surgery, China‑Japan Union Hospital of Jilin University, Changchun, Jilin 130033, P.R. China
| | - Min Wang
- Department of Pathology, Jilin Cancer Hospital, Changchun, Jilin 130012, P.R. China
| | - Na Liang
- Office of Surgical Nursing, Changchun Medical College, Changchun, Jilin 130000, P.R. China
| | - Lianyue Guan
- Department of Hepatobiliary‑Pancreatic Surgery, China‑Japan Union Hospital of Jilin University, Changchun, Jilin 130033, P.R. China
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Li P, Fei H, Wang L, Xu H, Zhang H, Zheng L. PDCD5 regulates cell proliferation, cell cycle progression and apoptosis. Oncol Lett 2017; 15:1177-1183. [PMID: 29403562 DOI: 10.3892/ol.2017.7401] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Accepted: 08/03/2017] [Indexed: 12/14/2022] Open
Abstract
Programmed cell death (PDCD)5 is cloned from human leukemia cell line TF-1. PDCD5 is one of the members of the programmed cell death protein family that is frequently involved in tumor growth and apoptosis. To investigate the molecular and cellular functions of PDCD5, the present study established a PDCD5 stably overexpressing A431 cell line and examined the role of PDCD5 in cell proliferation, cell cycle progression and apoptosis. The data demonstrated that overexpression of PDCD5 significantly inhibited cell proliferation, induced cell cycle arrest at G2/M phase and apoptosis in A431 cells. The expression profiles of certain key regulators of these cellular events were further investigated, including P53, B cell lymphoma (BCL)-2, BCL-2 associated X protein (BAX) and caspase (CASP)3. The data demonstrated that at the transcript and protein levels, P53, BAX and CASP3 were all upregulated in the PDCD5 stably overexpressing A431 cells whereas BCL-2 was downregulated, indicating that PDCD5 acts as an important upstream regulator of P53, BCL-2, BAX and CASP3. The data suggest that PDCD5 regulates cell proliferation, cell cycle progression and apoptosis in A431 cells. PDCD5 may be a novel tumor suppressor gene, and may be potentially used for cancer treatment in the future.
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Affiliation(s)
- Penghui Li
- Department of Biogenetics, Qiqihar Medical University, Qiqihar, Heilongjiang 161006, P.R. China
| | - Hongxin Fei
- Department of Histology and Embryology, Qiqihar Medical University, Qiqihar, Heilongjiang 161006, P.R. China
| | - Lihong Wang
- Department of Immunology, Qiqihar Medical University, Qiqihar, Heilongjiang 161006, P.R. China
| | - Huiyu Xu
- Department of Immunology, Qiqihar Medical University, Qiqihar, Heilongjiang 161006, P.R. China
| | - Haiyan Zhang
- Department of Histology and Embryology, Qiqihar Medical University, Qiqihar, Heilongjiang 161006, P.R. China
| | - Lihong Zheng
- Department of Biogenetics, Qiqihar Medical University, Qiqihar, Heilongjiang 161006, P.R. China
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Ribera J, Zamora L, Morgades M, Mallo M, Solanes N, Batlle M, Vives S, Granada I, Juncà J, Malinverni R, Genescà E, Guàrdia R, Mercadal S, Escoda L, Martinez-Lopez J, Tormo M, Esteve J, Pratcorona M, Martinez-Losada C, Solé F, Feliu E, Ribera JM. Copy number profiling of adult relapsed B-cell precursor acute lymphoblastic leukemia reveals potential leukemia progression mechanisms. Genes Chromosomes Cancer 2017; 56:810-820. [PMID: 28758283 DOI: 10.1002/gcc.22486] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Revised: 07/22/2017] [Accepted: 07/22/2017] [Indexed: 12/11/2022] Open
Abstract
The outcome of relapsed adult acute lymphoblastic leukemia (ALL) remains dismal despite new therapeutic approaches. Previous studies analyzing relapse samples have shown a high degree of heterogeneity regarding gene alterations without an evident relapse signature. Bone marrow or peripheral blood samples from 31 adult B-cell precursor ALL patients at first relapse, and 21 paired diagnostic samples were analyzed by multiplex ligation probe-dependent amplification (MLPA). Nineteen paired diagnostic and relapse samples of these 21 patients were also analyzed by SNP arrays. A trend to acquire homozygous CDKN2A/B deletions and a significant increase in the number of copy number alterations (CNA) was observed from diagnosis to first relapse. Evolution from an ancestral clone was the main pattern of clonal evolution. Relapse samples were extremely heterogeneous regarding CNA frequencies. However, CDKN2A/B, PAX5, ETV6, ATM, IKZF1, VPREB1, and TP53 deletions and duplications of 1q, 8q, 17q, 21, X/Y PAR1, and Xp were frequently detected at relapse. Duplications of genes involved in cell proliferation, drug resistance and stem cell homeostasis regulation, as well as deletions of KDM6A and STAG2 genes emerged as specific alterations at relapse. Genomics of relapsed adult B-cell precursor ALL is highly heterogeneous, although some recurrent lesions involved in essential pathways deregulation were frequently observed. Selective and simultaneous targeting of these deregulated pathways may improve the results of current salvage therapies.
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Affiliation(s)
- Jordi Ribera
- Josep Carreras Leukemia Research Institute (IJC), Universitat Autònoma de Barcelona, Badalona, Spain
| | - Lurdes Zamora
- Josep Carreras Leukemia Research Institute (IJC), Universitat Autònoma de Barcelona, Badalona, Spain
- Catalan Institute of Oncology-Germans Trias i Pujol, Badalona, Spain
| | - Mireia Morgades
- Josep Carreras Leukemia Research Institute (IJC), Universitat Autònoma de Barcelona, Badalona, Spain
- Catalan Institute of Oncology-Germans Trias i Pujol, Badalona, Spain
| | - Mar Mallo
- Josep Carreras Leukemia Research Institute (IJC), Universitat Autònoma de Barcelona, Badalona, Spain
| | - Neus Solanes
- Josep Carreras Leukemia Research Institute (IJC), Universitat Autònoma de Barcelona, Badalona, Spain
| | - Montserrat Batlle
- Josep Carreras Leukemia Research Institute (IJC), Universitat Autònoma de Barcelona, Badalona, Spain
- Catalan Institute of Oncology-Germans Trias i Pujol, Badalona, Spain
| | - Susana Vives
- Josep Carreras Leukemia Research Institute (IJC), Universitat Autònoma de Barcelona, Badalona, Spain
- Catalan Institute of Oncology-Germans Trias i Pujol, Badalona, Spain
| | - Isabel Granada
- Josep Carreras Leukemia Research Institute (IJC), Universitat Autònoma de Barcelona, Badalona, Spain
- Catalan Institute of Oncology-Germans Trias i Pujol, Badalona, Spain
| | - Jordi Juncà
- Josep Carreras Leukemia Research Institute (IJC), Universitat Autònoma de Barcelona, Badalona, Spain
- Catalan Institute of Oncology-Germans Trias i Pujol, Badalona, Spain
| | - Roberto Malinverni
- Josep Carreras Leukemia Research Institute (IJC), Universitat Autònoma de Barcelona, Badalona, Spain
| | - Eulàlia Genescà
- Josep Carreras Leukemia Research Institute (IJC), Universitat Autònoma de Barcelona, Badalona, Spain
| | - Ramon Guàrdia
- Catalan Institute of Oncology-Josep Trueta, Girona, Spain
| | - Santiago Mercadal
- Catalan Institute of Oncology-Duran i Reynals, L'Hospitalet de Llobregat, Spain
| | - Lourdes Escoda
- Catalan Institute of Oncology-Joan XXIII, Tarragona, Spain
| | | | | | - Jordi Esteve
- Josep Carreras Leukemia Research Institute (IJC), Universitat Autònoma de Barcelona, Badalona, Spain
- Clinic Hospital, Barcelona, Spain
| | - Marta Pratcorona
- Josep Carreras Leukemia Research Institute (IJC), Universitat Autònoma de Barcelona, Badalona, Spain
- Sant Pau Hospital, Barcelona, Spain
| | | | - Francesc Solé
- Josep Carreras Leukemia Research Institute (IJC), Universitat Autònoma de Barcelona, Badalona, Spain
| | - Evarist Feliu
- Josep Carreras Leukemia Research Institute (IJC), Universitat Autònoma de Barcelona, Badalona, Spain
- Catalan Institute of Oncology-Germans Trias i Pujol, Badalona, Spain
| | - Josep-Maria Ribera
- Josep Carreras Leukemia Research Institute (IJC), Universitat Autònoma de Barcelona, Badalona, Spain
- Catalan Institute of Oncology-Germans Trias i Pujol, Badalona, Spain
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Pdcd2l Promotes Palmitate-Induced Pancreatic Beta-Cell Apoptosis as a FoxO1 Target Gene. PLoS One 2016; 11:e0166692. [PMID: 27861641 PMCID: PMC5115776 DOI: 10.1371/journal.pone.0166692] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Accepted: 11/02/2016] [Indexed: 01/12/2023] Open
Abstract
Transcription factor FoxO1 is a key regulator of the insulin-signaling pathway, and is reported to play important roles in pancreatic β cell differentiation, proliferation, apoptosis and stress resistance. The multifunctional nature of FoxO1 is due to its regulation of various downstream targets. Previous studies in our lab identified potential FoxO1 target genes using the ChIP-DSL technique and one of those genes, Pdcd2l, was selected for further study. We found that the expression of Pdcd2l was increased with palmitate treatment; the luciferase assay result revealed that enhanced Pdcd2l promoter activity was responsible for the elevation of Pdcd2l expression. ChIP-PCR was performed to confirm the combination of FoxO1 to Pdcd2l promoter, result showing that FoxO1 could bind to Pdcd2l promoter and this binding was further enhanced after palmitate treatment. Overexpression of FoxO1 significantly induced Pdcd2l promoter activity, leading to increased mRNA level; consistently, interference of FoxO1 abolished the increment of Pdcd2l gene expression triggered by palmitate treatment. In addition, overexpression of Pdcd2l could further increase the percentage of apoptotic cells induced by palmitate incubation, whilst interference of Pdcd2l partially reversed the palmitate-induced apoptosis together with activated Caspase-3, indicating that the latter may play a part in this process. Therefore, in this study, we confirmed the binding of FoxO1 to the Pdcd2l gene promoter and studied the role of Pdcd2l in β cells for the first time. Our results suggested that FoxO1 may exert its activity partially through the regulation of Pdcd2l in palmitate-induced β cell apoptosis and could help to clarify the molecular mechanisms of β cell failure in type 2 diabetes.
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Minakhina S, Naryshkina T, Changela N, Tan W, Steward R. Zfrp8/PDCD2 Interacts with RpS2 Connecting Ribosome Maturation and Gene-Specific Translation. PLoS One 2016; 11:e0147631. [PMID: 26807849 PMCID: PMC4726551 DOI: 10.1371/journal.pone.0147631] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Accepted: 11/25/2015] [Indexed: 11/28/2022] Open
Abstract
Zfrp8/PDCD2 is a highly conserved protein essential for stem cell maintenance in both flies and mammals. It is also required in fast proliferating cells such as cancer cells. Our previous studies suggested that Zfrp8 functions in the formation of mRNP (mRNA ribonucleoprotein) complexes and also controls RNA of select Transposable Elements (TEs). Here we show that in Zfrp8/PDCD2 knock down (KD) ovaries, specific mRNAs and TE transcripts show increased nuclear accumulation. We also show that Zfrp8/PDCD2 interacts with the (40S) small ribosomal subunit through direct interaction with RpS2 (uS5). By studying the distribution of endogenous and transgenic fluorescently tagged ribosomal proteins we demonstrate that Zfrp8/PDCD2 regulates the cytoplasmic levels of components of the small (40S) ribosomal subunit, but does not control nuclear/nucleolar localization of ribosomal proteins. Our results suggest that Zfrp8/PDCD2 functions at late stages of ribosome assembly and may regulate the binding of specific mRNA-RNPs to the small ribosomal subunit ultimately controlling their cytoplasmic localization and translation.
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Affiliation(s)
- Svetlana Minakhina
- Waksman Institute, Rutgers, The State University of New Jersey, Piscataway, New Jersey, United States of America
- * E-mail: (SM); (RS)
| | - Tatyana Naryshkina
- Waksman Institute, Rutgers, The State University of New Jersey, Piscataway, New Jersey, United States of America
| | - Neha Changela
- Waksman Institute, Rutgers, The State University of New Jersey, Piscataway, New Jersey, United States of America
| | - William Tan
- Waksman Institute, Rutgers, The State University of New Jersey, Piscataway, New Jersey, United States of America
| | - Ruth Steward
- Waksman Institute, Rutgers, The State University of New Jersey, Piscataway, New Jersey, United States of America
- * E-mail: (SM); (RS)
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15
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Zfrp8 forms a complex with fragile-X mental retardation protein and regulates its localization and function. Dev Biol 2016; 410:202-212. [PMID: 26772998 DOI: 10.1016/j.ydbio.2015.12.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2014] [Revised: 11/13/2015] [Accepted: 12/09/2015] [Indexed: 11/21/2022]
Abstract
Fragile-X syndrome is the most commonly inherited cause of autism and mental disabilities. The Fmr1 (Fragile-X Mental Retardation 1) gene is essential in humans and Drosophila for the maintenance of neural stem cells, and Fmr1 loss results in neurological and reproductive developmental defects in humans and flies. FMRP (Fragile-X Mental Retardation Protein) is a nucleo-cytoplasmic shuttling protein, involved in mRNA silencing and translational repression. Both Zfrp8 and Fmr1 have essential functions in the Drosophila ovary. In this study, we identified FMRP, Nufip (Nuclear Fragile-X Mental Retardation Protein-interacting Protein) and Tral (Trailer Hitch) as components of a Zfrp8 protein complex. We show that Zfrp8 is required in the nucleus, and controls localization of FMRP in the cytoplasm. In addition, we demonstrate that Zfrp8 genetically interacts with Fmr1 and tral in an antagonistic manner. Zfrp8 and FMRP both control heterochromatin packaging, also in opposite ways. We propose that Zfrp8 functions as a chaperone, controlling protein complexes involved in RNA processing in the nucleus.
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Ryland KE, Hawkins AG, Weisenberger DJ, Punj V, Borinstein SC, Laird PW, Martens JR, Lawlor ER. Promoter Methylation Analysis Reveals That KCNA5 Ion Channel Silencing Supports Ewing Sarcoma Cell Proliferation. Mol Cancer Res 2015; 14:26-34. [PMID: 26573141 DOI: 10.1158/1541-7786.mcr-15-0343] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2015] [Accepted: 11/04/2015] [Indexed: 02/07/2023]
Abstract
UNLABELLED Polycomb proteins are essential regulators of gene expression in stem cells and development. They function to reversibly repress gene transcription via posttranslational modification of histones and chromatin compaction. In many human cancers, genes that are repressed by polycomb in stem cells are subject to more stable silencing via DNA methylation of promoter CpG islands. Ewing sarcoma is an aggressive bone and soft-tissue tumor that is characterized by overexpression of polycomb proteins. This study investigates the DNA methylation status of polycomb target gene promoters in Ewing sarcoma tumors and cell lines and observes that the promoters of differentiation genes are frequent targets of CpG-island DNA methylation. In addition, the promoters of ion channel genes are highly differentially methylated in Ewing sarcoma compared with nonmalignant adult tissues. Ion channels regulate a variety of biologic processes, including proliferation, and dysfunction of these channels contributes to tumor pathogenesis. In particular, reduced expression of the voltage-gated Kv1.5 channel has been implicated in tumor progression. These data show that DNA methylation of the KCNA5 promoter contributes to stable epigenetic silencing of the Kv1.5 channel. This epigenetic repression is reversed by exposure to the DNA methylation inhibitor decitabine, which inhibits Ewing sarcoma cell proliferation through mechanisms that include restoration of the Kv1.5 channel function. IMPLICATIONS This study demonstrates that promoters of ion channels are aberrantly methylated in Ewing sarcoma and that epigenetic silencing of KCNA5 contributes to tumor cell proliferation, thus providing further evidence of the importance of ion channel dysregulation to tumorigenesis.
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Affiliation(s)
- Katherine E Ryland
- Department of Pharmacology, University of Michigan, Ann Arbor, Michigan. Translational Oncology Program, University of Michigan, Ann Arbor, Michigan. Department of Pediatrics, University of Michigan, Ann Arbor, Michigan
| | - Allegra G Hawkins
- Translational Oncology Program, University of Michigan, Ann Arbor, Michigan. Department of Pediatrics, University of Michigan, Ann Arbor, Michigan
| | - Daniel J Weisenberger
- Department of Biochemistry and Molecular Biology, University of Southern California, Los Angeles, California. Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Vasu Punj
- Keck School of Medicine, University of Southern California, Los Angeles, California
| | | | - Peter W Laird
- Van Andel Research Institute, Grand Rapids, Michigan
| | - Jeffrey R Martens
- Department of Pharmacology and Therapeutics, University of Florida, Gainesville, Florida
| | - Elizabeth R Lawlor
- Translational Oncology Program, University of Michigan, Ann Arbor, Michigan. Department of Pediatrics, University of Michigan, Ann Arbor, Michigan. Department of Pathology, University of Michigan, Ann Arbor, Michigan.
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Yang Y, Jin Y, Du W. Programmed cell death 2 functions as a tumor suppressor in osteosarcoma. INTERNATIONAL JOURNAL OF CLINICAL AND EXPERIMENTAL PATHOLOGY 2015; 8:10894-10900. [PMID: 26617804 PMCID: PMC4637619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 05/31/2015] [Accepted: 07/21/2015] [Indexed: 06/05/2023]
Abstract
OBJECTIVES To investigate the role of programmed cell death 2 (PDCD2) in osteosarcoma (OS), along with correlations between PDCD2 and CD4(+)/CD8(+). METHODS Sprague-Dawley (SD) rats were randomly assigned to control group and OS group. The OS group rats were subjected to induce models of OS by transplantation with UMR106 cells. Peripheral blood was collected to test the percentages of the CD4(+) and CD8(+) cell subsets using flow cytometry (FCM). Western blotting was performed to determine the PDCD2 protein level. The correlations between PDCD2 and CD4(+)/CD8(+) were analyzed by Pearson correlation coefficient. Besides, specific small interfering RNAs (siRNA) against PDCD2 and nonspecific (NS)-siRNA were transfected into UMR106 cells. Cell viability and invasive ability were determined after transfection. RESULTS CD4(+) cells percentages were significantly decreased in the OS group, while CD8(+) cells were significantly increased (P < 0.05). The PDCD2 protein levels were markedly lower than that in the control group (P < 0.05). Additionally, PDCD2 was positively correlated with CD4(+) (R(2) = 0.66, P < 0.05), but was negatively correlated with CD8(+) (R(2) = -0.94, P < 0.05). Moreover, the cell viability and invasion ability were significantly higher than that in the control group and the NS siRNA group after transfection with PDCD2 siRNA (P < 0.05). CONCLUSION These results suggest that PDCD2 is involved in the pathogenesis of OS, and PDCD2 may play an important role in tumor suppression. These mechanisms might be related to immune response induced by CD4(+) and CD8(+) T cells.
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Affiliation(s)
- Yuanxun Yang
- Department of Orthopedics, First People’s Hospital of JinanJinan 250013, Shandong, China
| | - Yan Jin
- Jinan Center for Disease Control and PreventionJinan 250021, Shandong, China
| | - Wenxi Du
- Department of Orthopedics, The First Affiliated Hospital of Zhejiang Chinese Medical UniversityHangzhou 310006, Zhejiang, China
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18
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Burroughs AM, Aravind L. Analysis of two domains with novel RNA-processing activities throws light on the complex evolution of ribosomal RNA biogenesis. Front Genet 2014; 5:424. [PMID: 25566315 PMCID: PMC4275035 DOI: 10.3389/fgene.2014.00424] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2014] [Accepted: 11/19/2014] [Indexed: 11/13/2022] Open
Abstract
Ribosomal biogenesis has been extensively investigated, especially to identify the elusive nucleases and cofactors involved in the complex rRNA processing events in eukaryotes. Large-scale screens in yeast identified two biochemically uncharacterized proteins, TSR3 and TSR4, as being key players required for rRNA maturation. Using multiple computational approaches we identify the conserved domains comprising these proteins and establish sequence and structural features providing novel insights regarding their roles. TSR3 is unified with the DTW domain into a novel superfamily of predicted enzymatic domains, with the balance of the available evidence pointing toward an RNase role with the archaeo-eukaryotic TSR3 proteins processing rRNA and the bacterial versions potentially processing tRNA. TSR4, its other eukaryotic homologs PDCD2/rp-8, PDCD2L, Zfrp8, and trus, the predominantly bacterial DUF1963 proteins, and other uncharacterized proteins are unified into a new domain superfamily, which arose from an ancient duplication event of a strand-swapped, dimer-forming all-beta unit. We identify conserved features mediating protein-protein interactions (PPIs) and propose a potential chaperone-like function. While contextual evidence supports a conserved role in ribosome biogenesis for the eukaryotic TSR4-related proteins, there is no evidence for such a role for the bacterial versions. Whereas TSR3-related proteins can be traced to the last universal common ancestor (LUCA) with a well-supported archaeo-eukaryotic branch, TSR4-related proteins of eukaryotes are derived from within the bacterial radiation of this superfamily, with archaea entirely lacking them. This provides evidence for “systems admixture,” which followed the early endosymbiotic event, playing a key role in the emergence of the uniquely eukaryotic ribosome biogenesis process.
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Affiliation(s)
- A Maxwell Burroughs
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health Bethesda, MD, USA
| | - L Aravind
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health Bethesda, MD, USA
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Zhang J, Wei W, Jin HC, Ying RC, Zhu AK, Zhang FJ. Programmed cell death 2 protein induces gastric cancer cell growth arrest at the early S phase of the cell cycle and apoptosis in a p53-dependent manner. Oncol Rep 2014; 33:103-10. [PMID: 25334010 DOI: 10.3892/or.2014.3551] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2014] [Accepted: 08/02/2014] [Indexed: 11/06/2022] Open
Abstract
Programmed cell death 2 (PDCD2) is a highly conserved nuclear protein, and aberrant PDCD2 expression alters cell apoptosis. The present study aimed to investigate PDCD2 expression in gastric cancer. Tissue specimens from 34 gastric cancer patients were collected for analysis of PDCD2 expression using immunohistochemistry, western blotting and qRT-PCR. Gastric cancer cell lines (a p53-mutated MKN28 line and a wild-type p53 MKN45 line) were used to assess the effects of PDCD2 overexpression. p53-/- nude mice were used to investigate the effect of PDCD2 on ultraviolet B (UVB)-induced skin carcinogenesis. The data showed that PDCD2 expression was reduced in gastric cancer tissue specimens, and loss of PDCD2 expression was associated with the poor survival of patients. PDCD2 expression induced gastric cancer cell growth arrest at the early S phase of the cell cycle and apoptosis. The antitumor effects of PDCD2 expression were dependent on p53 expression in gastric cancer cells. Moreover, PDCD2 expression inhibited activity of the ATM/Chk1/2/p53 signaling pathway. In addition, PDCD2 expression suppressed UVB-induced skin carcinogenesis in p53+/+ nude mice, but not in p53-/- mice. The data from the present study demonstrated that loss of PDCD2 expression could contribute to gastric cancer development and progression and that PDCD2-induced gastric cancer cell growth arrest at the early S phase of the cell cycle and apoptosis are p53-dependent.
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Affiliation(s)
- Jian Zhang
- Department of Gastroenterological Surgery, Hangzhou First People's Hospital, School of Clinical Medicine, Nanjing Medical University, Hangzhou 310006, P.R. China
| | - Wei Wei
- Department of Gastroenterological Surgery, Hangzhou First People's Hospital, School of Clinical Medicine, Nanjing Medical University, Hangzhou 310006, P.R. China
| | - Hui-Cheng Jin
- Department of Gastroenterological Surgery, Hangzhou First People's Hospital, School of Clinical Medicine, Nanjing Medical University, Hangzhou 310006, P.R. China
| | - Rong-Chao Ying
- Department of Gastroenterological Surgery, Hangzhou First People's Hospital, School of Clinical Medicine, Nanjing Medical University, Hangzhou 310006, P.R. China
| | - A-Kao Zhu
- Department of Gastroenterological Surgery, Hangzhou First People's Hospital, School of Clinical Medicine, Nanjing Medical University, Hangzhou 310006, P.R. China
| | - Fang-Jie Zhang
- Department of Gastroenterological Surgery, Hangzhou First People's Hospital, School of Clinical Medicine, Nanjing Medical University, Hangzhou 310006, P.R. China
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20
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Granier CJ, Wang W, Tsang T, Steward R, Sabaawy HE, Bhaumik M, Rabson AB. Conditional inactivation of PDCD2 induces p53 activation and cell cycle arrest. Biol Open 2014; 3:821-31. [PMID: 25150276 PMCID: PMC4163659 DOI: 10.1242/bio.20148326] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
PDCD2 (programmed cell death domain 2) is a highly conserved, zinc finger MYND domain-containing protein essential for normal development in the fly, zebrafish and mouse. The molecular functions and cellular activities of PDCD2 remain unclear. In order to better understand the functions of PDCD2 in mammalian development, we have examined PDCD2 activity in mouse blastocyst embryos, as well as in mouse embryonic stem cells (ESCs) and embryonic fibroblasts (MEFs). We have studied mice bearing a targeted PDCD2 locus functioning as a null allele through a splicing gene trap, or as a conditional knockout, by deletion of exon2 containing the MYND domain. Tamoxifen-induced knockout of PDCD2 in MEFs, as well as in ESCs, leads to defects in progression from the G1 to the S phase of cell cycle, associated with increased levels of p53 protein and p53 target genes. G1 prolongation in ESCs was not associated with induction of differentiation. Loss of entry into S phase of the cell cycle and marked induction of nuclear p53 were also observed in PDCD2 knockout blastocysts. These results demonstrate a unique role for PDCD2 in regulating the cell cycle and p53 activation during early embryonic development of the mouse.
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Affiliation(s)
- Celine J Granier
- Child Health Institute of New Jersey, Robert Wood Johnson Medical School, Rutgers University, New Brunswick, NJ 08901, USA
| | - Wei Wang
- Sequencing and Microarray Core Facility, Lewis-Sigler Institute for Integrative Genetics, Princeton University, Princeton, NJ 08854, USA
| | - Tiffany Tsang
- Child Health Institute of New Jersey, Robert Wood Johnson Medical School, Rutgers University, New Brunswick, NJ 08901, USA
| | - Ruth Steward
- Waksman Institute and Department of Molecular Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - Hatem E Sabaawy
- Rutgers Cancer Institute of New Jersey, Rutgers University, New Brunswick, NJ 08903, USA
| | - Mantu Bhaumik
- Child Health Institute of New Jersey, Robert Wood Johnson Medical School, Rutgers University, New Brunswick, NJ 08901, USA Rutgers Cancer Institute of New Jersey, Rutgers University, New Brunswick, NJ 08903, USA
| | - Arnold B Rabson
- Child Health Institute of New Jersey, Robert Wood Johnson Medical School, Rutgers University, New Brunswick, NJ 08901, USA Rutgers Cancer Institute of New Jersey, Rutgers University, New Brunswick, NJ 08903, USA
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Minakhina S, Changela N, Steward R. Zfrp8/PDCD2 is required in ovarian stem cells and interacts with the piRNA pathway machinery. Development 2014; 141:259-68. [PMID: 24381196 DOI: 10.1242/dev.101410] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The maintenance of stem cells is central to generating diverse cell populations in many tissues throughout the life of an animal. Elucidating the mechanisms involved in how stem cells are formed and maintained is crucial to understanding both normal developmental processes and the growth of many cancers. Previously, we showed that Zfrp8/PDCD2 is essential for the maintenance of Drosophila hematopoietic stem cells. Here, we show that Zfrp8/PDCD2 is also required in both germline and follicle stem cells in the Drosophila ovary. Expression of human PDCD2 fully rescues the Zfrp8 phenotype, underlining the functional conservation of Zfrp8/PDCD2. The piRNA pathway is essential in early oogenesis, and we find that nuclear localization of Zfrp8 in germline stem cells and their offspring is regulated by some piRNA pathway genes. We also show that Zfrp8 forms a complex with the piRNA pathway protein Maelstrom and controls the accumulation of Maelstrom in the nuage. Furthermore, Zfrp8 regulates the activity of specific transposable elements also controlled by Maelstrom and Piwi. Our results suggest that Zfrp8/PDCD2 is not an integral member of the piRNA pathway, but has an overlapping function, possibly competing with Maelstrom and Piwi.
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Affiliation(s)
- Svetlana Minakhina
- Rutgers University, Department of Molecular Biology, Waksman Institute, Cancer Institute of New Jersey, 190 Frelinghuysen Road, Piscataway, NJ 08854, USA
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