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The phosphatase CTDSPL2 is phosphorylated in mitosis and a target for restraining tumor growth and motility in pancreatic cancer. Cancer Lett 2022; 526:53-65. [PMID: 34813892 PMCID: PMC8702485 DOI: 10.1016/j.canlet.2021.11.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 10/29/2021] [Accepted: 11/12/2021] [Indexed: 02/03/2023]
Abstract
Carboxy-terminal domain (CTD) small phosphatase like 2 (CTDSPL2), also known as SCP4 or HSPC129, is a new member of the small CTD phosphatase (SCP) family and its role in cancers remains unclear. Here, we used a Phos-tag technique to screen a series of phosphatases and identified CTDSPL2 as a mitotic regulator. We demonstrated that CTDSPL2 was phosphorylated at T86, S104, and S134 by cyclin-dependent kinase 1 (CDK1) in mitosis. Depletion of CTDSPL2 led to mitotic defects and prolonged mitosis. Resultantly, CTDSPL2 deletion restrained proliferation, migration, and invasion in pancreatic cancer cells. We further confirmed the dominant negative effects of a phosphorylation-deficient mutant form of CTDSPL2, implying the biological significance of CTDSPL2 mitotic phosphorylation. Moreover, RT2 cell cycle array analysis revealed p21 and p27 as downstream regulators of CTDSPL2, and inhibition of p21 and/or p27 partially rescued the phenotype in CTDSPL2-deficient cell lines. Importantly, both CTDSPL2 depletion and phosphorylation-deficient mutant CTDSPL2 hindered tumor growth in xenograft models. Together, our findings for the first time highlight the novel role of CTDSPL2 in regulating cell mitosis, proliferation and motility in pancreatic cancer and point out the implications of CTDSPL2 in regulating two critical cell cycle participants (p21 and p27), providing an alternative molecular target for pancreatic cancer treatment.
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Xu L, Gao Z, Yang Z, Qu M, Li H, Chen L, Lv Y, Fan Z, Yue W, Li C, Xie X, Pei X. Evaluation of Reliable Reference Genes for In Vitro Erythrocyte Generation from Cord Blood CD34 + Cells. DNA Cell Biol 2021; 40:1200-1210. [PMID: 34227876 DOI: 10.1089/dna.2021.0185] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
In vitro generation of red blood cells has the potential to circumvent shortfalls in the global demand for blood for transfusion applications. However, cell differentiation and proliferation are often regulated by precise changes in gene expression, but the underlying mechanisms and molecular changes remain unclear. Quantitative reverse transcription-polymerase chain reaction (qRT-PCR) can be used to evaluate multiple target genes. To make the results more reliable, suitable reference genes should be used to calibrate the error associated with qRT-PCR. In this study, we utilized bioinformatics to screen 3 novel candidate reference genes (calcium and integrin binding family member 2 [CIB2], olfactory receptor family 8 subfamily B member 8 [OR8B8], and zinc finger protein 425 [ZNF425]) along with eight traditional reference genes (glyceraldehyde-3-phosphate dehydrogenase [GAPDH], β-actin [ACTB], 18S RNA, β2-microglobulin [β2-MG], peptidylprolyl isomerase A [PPIA], TATA box-binding protein [TBP], hydroxymethylbilane synthase [HMBS], and hypoxanthine phosphoribosyltransferase 1 [HPRT1]). Two software algorithms (geNorm and NormFinder) were used to evaluate the stability of expression of the 11 genes at different stages of erythrocyte development. Comprehensive analysis showed that expression of GAPDH and TBP was the most stable, whereas ZNF425 and OR8B8 were the least suitable candidate genes. These results suggest that appropriate reference genes should be selected before performing gene expression analysis during erythroid differentiation and that GAPDH and TBP are suitable reference genes for gene expression studies on erythropoiesis.
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Affiliation(s)
- Lei Xu
- Stem Cell and Regenerative Medicine Lab, Institute of Health Service and Transfusion Medicine, Beijing, China.,South China Research Center for Stem Cell & Regenerative Medicine, SCIB, Guangzhou, China
| | - Zhan Gao
- Clinical Medical College of Air Force, Anhui Medical University, Hefei, China.,Air Force Medical Center, PLA, Beijing, China
| | - Zhou Yang
- Stem Cell and Regenerative Medicine Lab, Institute of Health Service and Transfusion Medicine, Beijing, China.,South China Research Center for Stem Cell & Regenerative Medicine, SCIB, Guangzhou, China
| | - Mingyi Qu
- Stem Cell and Regenerative Medicine Lab, Institute of Health Service and Transfusion Medicine, Beijing, China.,South China Research Center for Stem Cell & Regenerative Medicine, SCIB, Guangzhou, China.,Beijing Institute of Radiation Medicine, Beijing, China
| | - Huilin Li
- Stem Cell and Regenerative Medicine Lab, Institute of Health Service and Transfusion Medicine, Beijing, China.,South China Research Center for Stem Cell & Regenerative Medicine, SCIB, Guangzhou, China
| | - Lin Chen
- Stem Cell and Regenerative Medicine Lab, Institute of Health Service and Transfusion Medicine, Beijing, China.,South China Research Center for Stem Cell & Regenerative Medicine, SCIB, Guangzhou, China
| | - Yang Lv
- Stem Cell and Regenerative Medicine Lab, Institute of Health Service and Transfusion Medicine, Beijing, China.,South China Research Center for Stem Cell & Regenerative Medicine, SCIB, Guangzhou, China
| | - Zeng Fan
- Stem Cell and Regenerative Medicine Lab, Institute of Health Service and Transfusion Medicine, Beijing, China.,South China Research Center for Stem Cell & Regenerative Medicine, SCIB, Guangzhou, China
| | - Wen Yue
- Stem Cell and Regenerative Medicine Lab, Institute of Health Service and Transfusion Medicine, Beijing, China.,South China Research Center for Stem Cell & Regenerative Medicine, SCIB, Guangzhou, China
| | - Cuiying Li
- Clinical Medical College of Air Force, Anhui Medical University, Hefei, China.,Air Force Medical Center, PLA, Beijing, China
| | - Xiaoyan Xie
- Stem Cell and Regenerative Medicine Lab, Institute of Health Service and Transfusion Medicine, Beijing, China.,South China Research Center for Stem Cell & Regenerative Medicine, SCIB, Guangzhou, China
| | - Xuetao Pei
- Stem Cell and Regenerative Medicine Lab, Institute of Health Service and Transfusion Medicine, Beijing, China.,South China Research Center for Stem Cell & Regenerative Medicine, SCIB, Guangzhou, China
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Hirano T, Tsuruda T, Tanaka Y, Harada H, Yamazaki T, Ishida A. Long noncoding RNA CCDC26 as a modulator of transcriptional switching between fetal and embryonic globins. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2020; 1868:118931. [PMID: 33340546 DOI: 10.1016/j.bbamcr.2020.118931] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 12/04/2020] [Accepted: 12/11/2020] [Indexed: 01/04/2023]
Abstract
The CCDC26 gene is considered to encode a functional noncoding RNA associated with acute myeloid leukemia and other cancers. However, investigations into the physiological roles of CCDC26 are rare. Previously, we reported that CCDC26 regulated proliferation and cell death of leukemia cells through KIT, a receptor tyrosine kinase, by using K562 leukemia cells and their derivative CCDC26-knockdown (KD) cells. Here we propose a new role of CCDC26 in the differentiation of erythroid cells. We showed that expression of embryonic (ε- and ζ-) globins was markedly upregulated in CCDC26-KD cells compared with K562 control cells during hemin-induced differentiation. In contrast, expression of fetal-type γ-globin, a major globin expressed in original K562 cells, was decreased. These changes in the expression of globin genes mainly took place at the transcriptional level, with significant suppression of transcription of adult (β-, δ-) globins in CCDC26-KD cells. Re-introduction of exogenous CCDC26 into the CCDC26-KD cells recovered low-level expression of the embryonal globins. These results suggest CCDC26 has a role in switching transcription of globin genes in the differentiation of erythroid cells. The expression profile of the CCDC26-KD cells and control cells suggests FOG-2, a transcriptional modulator, as a candidate for a mediator of the CCDC26-associated regulation. We showed that both embryonic globins were transcriptionally activated in FOG-2-KD K562 cells. The KIT inhibitor ISCK03 suppressed the production of hemoglobin in K562 cells but did not affect transcription of globin genes. To summarize, FOG-2, but not KIT, is responsible for globin transcriptional regulation by CCDC26.
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Affiliation(s)
- Tetsuo Hirano
- Graduate School of Integrated Sciences for Life, Hiroshima University, 1-7-1 Kagamiyama, Higashihiroshima, Hiroshima 739-8521, Japan.
| | - Tomomi Tsuruda
- School of Integrated Arts and Sciences, Hiroshima University, 1-7-1 Kagamiyama, Higashihiroshima, Hiroshima 739-8521, Japan
| | - Yuka Tanaka
- Graduate School of Integrated Sciences for Life, Hiroshima University, 1-7-1 Kagamiyama, Higashihiroshima, Hiroshima 739-8521, Japan
| | - Hironori Harada
- Laboratory of Oncology, School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo 192-0392, Japan.
| | - Takeshi Yamazaki
- Graduate School of Integrated Sciences for Life, Hiroshima University, 1-7-1 Kagamiyama, Higashihiroshima, Hiroshima 739-8521, Japan.
| | - Atsuhiko Ishida
- Graduate School of Integrated Sciences for Life, Hiroshima University, 1-7-1 Kagamiyama, Higashihiroshima, Hiroshima 739-8521, Japan.
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Affiliation(s)
- X Charlie Dong
- Department of Biochemistry and Molecular Biology, Center for Diabetes and Metabolic Diseases, Indiana University School of Medicine, Indianapolis, IN
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Chen J, Dong X, Lei X, Xia Y, Zeng Q, Que P, Wen X, Hu S, Peng B. Non-small-cell lung cancer pathological subtype-related gene selection and bioinformatics analysis based on gene expression profiles. Mol Clin Oncol 2017; 8:356-361. [PMID: 29435303 DOI: 10.3892/mco.2017.1516] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Accepted: 11/21/2017] [Indexed: 02/06/2023] Open
Abstract
Lung cancer is one of the most common malignant diseases and a major threat to public health on a global scale. Non-small-cell lung cancer (NSCLC) has a higher degree of malignancy and a lower 5-year survival rate compared with that of small-cell lung cancer. NSCLC may be mainly divided into two pathological subtypes, adenocarcinoma and squamous cell carcinoma. The aim of the present study was to identify disease genes based on the gene expression profile and the shortest path analysis of weighted functional protein association networks with the existing protein-protein interaction data from the Search Tool for the Retrieval of Interacting Genes. The gene expression profile (GSE10245) was downloaded from the National Center for Biotechnology Information Gene Expression Omnibus database, including 40 lung adenocarcinoma and 18 lung squamous cell carcinoma tissues. A total of 8 disease genes were identified using Naïve Bayesian Classifier based on the Maximum Relevance Minimum Redundancy feature selection method following preprocessing. An additional 21 candidate genes were selected using the shortest path analysis with Dijkstra's algorithm. The AURKA and SLC7A2 genes were selected three and two times in the shortest path analysis, respectively. All those genes participate in a number of important pathways, such as oocyte meiosis, cell cycle and cancer pathways with Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis. The present findings may provide novel insights into the pathogenesis of NSCLC and enable the development of novel therapeutic strategies. However, further investigation is required to confirm these findings.
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Affiliation(s)
- Jiangpeng Chen
- School of Public Health and Management, Chongqing Medical University, Chongqing 400016, P.R. China
| | - Xiaoqi Dong
- Department of Respiratory Diseases, The First Affiliated Hospital of Zhejiang University, Hangzhou, Zhejiang 310003, P.R. China
| | - Xun Lei
- School of Public Health and Management, Chongqing Medical University, Chongqing 400016, P.R. China
| | - Yinyin Xia
- School of Public Health and Management, Chongqing Medical University, Chongqing 400016, P.R. China
| | - Qing Zeng
- School of Public Health and Management, Chongqing Medical University, Chongqing 400016, P.R. China
| | - Ping Que
- School of Public Health and Management, Chongqing Medical University, Chongqing 400016, P.R. China
| | - Xiaoyan Wen
- School of Public Health and Management, Chongqing Medical University, Chongqing 400016, P.R. China
| | - Shan Hu
- School of Public Health and Management, Chongqing Medical University, Chongqing 400016, P.R. China
| | - Bin Peng
- School of Public Health and Management, Chongqing Medical University, Chongqing 400016, P.R. China
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Kang N, Koo J, Wang S, Hur SJ, Bahk YY. A systematic study of nuclear interactome of C-terminal domain small phosphatase-like 2 using inducible expression system and shotgun proteomics. BMB Rep 2017; 49:319-24. [PMID: 26674342 PMCID: PMC5070719 DOI: 10.5483/bmbrep.2016.49.6.240] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2015] [Indexed: 11/24/2022] Open
Abstract
RNA polymerase II C-terminal domain phosphatases are newly emerging family of phosphatases that contain FCPH domain with Mg+2-binding DXDX(T/V) signature motif. Its subfamily includes small CTD phosphatases (SCPs). Recently, we identified several interacting partners of human SCP1 with appearance of dephosphorylation and O-GlcNAcylation. In this study, using an established cell line with inducible CTDSPL2 protein (a member of the new phosphatase family), proteomic screening was conducted to identify binding partners of CTDSPL2 in nuclear extract through immunoprecipitation of CTDSPL2 with its associated. This approach led to the identification of several interacting partners of CTDSPL2. This will provide a better understanding on CTDSPL2. [BMB Reports 2016; 49(6): 319-324]
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Affiliation(s)
- NaNa Kang
- Department of Brain & Cognitive Sciences, DGIST, Daegu 42988, Korea
| | - JaeHyung Koo
- Department of Brain & Cognitive Sciences, DGIST, Daegu 42988, Korea
| | - Sen Wang
- Qiqihar Medical University, Qiqihar City, Heilongjiang, 161006, China
| | - Sun Jin Hur
- Department of Animal Science and Technology, Chung-Ang University, Anseong 17546, Korea
| | - Young Yil Bahk
- Department of Biotechnology, Konkuk University, Chungju 27478, Korea
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Wani S, Sugita A, Ohkuma Y, Hirose Y. Human SCP4 is a chromatin-associated CTD phosphatase and exhibits the dynamic translocation during erythroid differentiation. J Biochem 2016; 160:111-20. [DOI: 10.1093/jb/mvw018] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2016] [Accepted: 02/01/2016] [Indexed: 12/24/2022] Open
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Ma Y, Yao N, Liu G, Dong L, Liu Y, Zhang M, Wang F, Wang B, Wei X, Dong H, Wang L, Ji S, Zhang J, Wang Y, Huang Y, Yu J. Functional screen reveals essential roles of miR-27a/24 in differentiation of embryonic stem cells. EMBO J 2014; 34:361-78. [PMID: 25519956 DOI: 10.15252/embj.201489957] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
MicroRNAs play important roles in controlling the embryonic stem cell (ESC) state. Although much is known about microRNAs maintaining ESC state, microRNAs that are responsible for promoting ESC differentiation are less reported. Here, by screening 40 microRNAs pre-selected by their expression patterns and predicted targets in Dgcr8-null ESCs, we identify 14 novel differentiation-associated microRNAs. Among them, miR-27a and miR-24, restrained by c-Myc in ESC, exert their roles of silencing self-renewal through directly targeting several important pluripotency-associated factors, such as Oct4, Foxo1 and Smads. CRISPR/Cas9-mediated knockout of all miR-27/24 in ESCs leads to serious deficiency in ESC differentiation in vitro and in vivo. Moreover, depleting of them in mouse embryonic fibroblasts can evidently promote somatic cell reprogramming. Altogether, our findings uncover the essential role of miR-27 and miR-24 in ESC differentiation and also demonstrate novel microRNAs responsible for ESC differentiation.
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Affiliation(s)
- Yanni Ma
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, China Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, China
| | - Nan Yao
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, China Department of Medical Genetics, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, China
| | - Guang Liu
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, China Department of Medical Genetics, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, China
| | - Lei Dong
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, China Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, China
| | - Yufang Liu
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, China Department of Medical Genetics, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, China
| | - Meili Zhang
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, China Department of Medical Genetics, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, China
| | - Fang Wang
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, China Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, China
| | - Bin Wang
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, China Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, China
| | - Xueju Wei
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, China Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, China
| | - He Dong
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, China Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, China
| | - Lanlan Wang
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, China Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, China
| | - Shaowei Ji
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, China Department of Medical Genetics, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, China
| | - Junwu Zhang
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, China Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, China
| | - Yangming Wang
- Peking-Tsinghua Joint Center for Life Sciences, Institute of Molecular Medicine, Peking University, Beijing, China
| | - Yue Huang
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, China Department of Medical Genetics, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, China
| | - Jia Yu
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, China Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, China
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Omolo B, Carson C, Chu H, Zhou Y, Simpson DA, Hesse JE, Paules RS, Nyhan KC, Ibrahim JG, Kaufmann WK. A prognostic signature of G(2) checkpoint function in melanoma cell lines. Cell Cycle 2013; 12:1071-82. [PMID: 23454897 PMCID: PMC3646863 DOI: 10.4161/cc.24067] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2013] [Accepted: 02/21/2013] [Indexed: 12/31/2022] Open
Abstract
As DNA damage checkpoints are barriers to carcinogenesis, G(2) checkpoint function was quantified to test for override of this checkpoint during melanomagenesis. Primary melanocytes displayed an effective G(2) checkpoint response to ionizing radiation (IR)-induced DNA damage. Thirty-seven percent of melanoma cell lines displayed a significant defect in G(2) checkpoint function. Checkpoint function was melanoma subtype-specific with "epithelial-like" melanoma lines, with wild type NRAS and BRAF displaying an effective checkpoint, while lines with mutant NRAS and BRAF displayed defective checkpoint function. Expression of oncogenic B-Raf in a checkpoint-effective melanoma attenuated G(2) checkpoint function significantly but modestly. Other alterations must be needed to produce the severe attenuation of G(2) checkpoint function seen in some BRAF-mutant melanoma lines. Quantitative trait analysis tools identified mRNA species whose expression was correlated with G(2) checkpoint function in the melanoma lines. A 165 gene signature was identified with a high correlation with checkpoint function (p < 0.004) and low false discovery rate (≤ 0.077). The G(2) checkpoint gene signature predicted G(2) checkpoint function with 77-94% accuracy. The signature was enriched in lysosomal genes and contained numerous genes that are associated with regulation of chromatin structure and cell cycle progression. The core machinery of the cell cycle was not altered in checkpoint-defective lines but rather numerous mediators of core machinery function were. When applied to an independent series of primary melanomas, the predictive G(2) checkpoint signature was prognostic of distant metastasis-free survival. These results emphasize the value of expression profiling of primary melanomas for understanding melanoma biology and disease prognosis.
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Affiliation(s)
- Bernard Omolo
- Division of Mathematics and Computer Science; University of South Carolina Upstate; Spartanburg, SC USA
| | - Craig Carson
- Department of Dermatology; University of North Carolina at Chapel Hill; Chapel Hill, NC USA
| | - Haitao Chu
- Division of Biostatistics; University of Minnesota, Minneapolis, MN USA
| | - Yingchun Zhou
- Pathology and Laboratory Medicine; University of North Carolina at Chapel Hill; Chapel Hill, NC USA
| | - Dennis A. Simpson
- Pathology and Laboratory Medicine; University of North Carolina at Chapel Hill; Chapel Hill, NC USA
| | - Jill E. Hesse
- Environmental Stress and Cancer Group; National Institute of Environmental Health Sciences; Research Triangle Park, NC USA
| | - Richard S. Paules
- Environmental Stress and Cancer Group; National Institute of Environmental Health Sciences; Research Triangle Park, NC USA
| | - Kristine C. Nyhan
- Department of Radiation Oncology; University of California-San Francisco; San Francisco, CA USA
| | - Joseph G. Ibrahim
- Departments of Biostatistics; University of North Carolina at Chapel Hill; Chapel Hill, NC USA
- Center for Environmental Health and Susceptibility; University of North Carolina at Chapel Hill; Chapel Hill, NC USA
- Lineberger Comprehensive Cancer Center; University of North Carolina at Chapel Hill; Chapel Hill, NC USA
| | - William K. Kaufmann
- Pathology and Laboratory Medicine; University of North Carolina at Chapel Hill; Chapel Hill, NC USA
- Center for Environmental Health and Susceptibility; University of North Carolina at Chapel Hill; Chapel Hill, NC USA
- Lineberger Comprehensive Cancer Center; University of North Carolina at Chapel Hill; Chapel Hill, NC USA
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