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Binder M, Szalat RE, Talluri S, Fulciniti M, Avet-Loiseau H, Parmigiani G, Samur MK, Munshi NC. Bone marrow stromal cells induce chromatin remodeling in multiple myeloma cells leading to transcriptional changes. Nat Commun 2024; 15:4139. [PMID: 38755155 PMCID: PMC11098817 DOI: 10.1038/s41467-024-47793-5] [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: 01/06/2023] [Accepted: 04/12/2024] [Indexed: 05/18/2024] Open
Abstract
The natural history of multiple myeloma is characterized by its localization to the bone marrow and its interaction with bone marrow stromal cells. The bone marrow stromal cells provide growth and survival signals, thereby promoting the development of drug resistance. Here, we show that the interaction between bone marrow stromal cells and myeloma cells (using human cell lines) induces chromatin remodeling of cis-regulatory elements and is associated with changes in the expression of genes involved in the cell migration and cytokine signaling. The expression of genes involved in these stromal interactions are observed in extramedullary disease in patients with myeloma and provides the rationale for survival of myeloma cells outside of the bone marrow microenvironment. Expression of these stromal interaction genes is also observed in a subset of patients with newly diagnosed myeloma and are akin to the transcriptional program of extramedullary disease. The presence of such adverse stromal interactions in newly diagnosed myeloma is associated with accelerated disease dissemination, predicts the early development of therapeutic resistance, and is of independent prognostic significance. These stromal cell induced transcriptomic and epigenomic changes both predict long-term outcomes and identify therapeutic targets in the tumor microenvironment for the development of novel therapeutic approaches.
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Affiliation(s)
- Moritz Binder
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston, MA, USA
| | - Raphael E Szalat
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston, MA, USA
- Department of Data Science, Dana Farber Cancer Institute, Boston, MA, USA
| | - Srikanth Talluri
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston, MA, USA
| | | | - Hervé Avet-Loiseau
- University Cancer Center of Toulouse, Institut National de la Santé, Toulouse, France
| | - Giovanni Parmigiani
- Department of Data Science, Dana Farber Cancer Institute, Boston, MA, USA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Mehmet K Samur
- Department of Data Science, Dana Farber Cancer Institute, Boston, MA, USA.
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
| | - Nikhil C Munshi
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston, MA, USA.
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2
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Wu HX, He PM, Jia R. Effects of µ-Conotoxin GIIIB on the cellular activity of mouse skeletal musculoblast: combined transcriptome and proteome analysis. Proteome Sci 2023; 21:17. [PMID: 37828502 PMCID: PMC10568904 DOI: 10.1186/s12953-023-00221-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Accepted: 10/03/2023] [Indexed: 10/14/2023] Open
Abstract
µ-Conotoxin GIIIB (µ-CTX GIIIB) is a polypeptide containing three disulfide bridges, produced by the sea snail Conus geographus. This study was aimed to explored the cytotoxic effects of µ-CTX GIIIB on mouse skeletal musculoblast (Sol8). Sol8 cells were exposed to ouabain and veratridine to establish the cell injury model, and then treated with µ-CTX GIIIB. CCK-8 was adopted to evaluate the cytotoxicity of µ-CTX GIIIB. Then, proteomics and transcriptome were conducted, and the explore the differentially expressed genes (DEGs) and differentially expressed proteins (DEPs) affected by µ-CTX GIIIB were found. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis was used to investigate the affected signaling pathways. µ-CTX GIIIB increased the cell survival rate of injured Sol8 cells. We found and identified 1,663 DEGs and 444 DEPs influenced by µ-CTX GIIIB. 106 pairs of correlated DEGs and DEPs were selected by combining transcriptome and proteome data. The results of KEGG and GO analysis showed that µ-CTX GIIB affected the cell cycle, apoptosis, DNA damage and repair, lipid metabolism and other biological processes of Sol8 cells. µ-CTX GIIIB could affected cell cycle regulation, DNA damage repair, and activation of tumor factors, with potential carcinogenic effects. Our results provide an important basis for the study of in vitro toxicity, the mechanism of toxicity and injury prevention by µ-CTX GIIIB.
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Affiliation(s)
- Han-Xi Wu
- College of Marine Ecology and Environment, Shanghai Ocean University, No.999, Huchenghuan Rd, Nanhui New City, Shanghai, 201306, P.R. China
| | - Pei-Min He
- College of Marine Ecology and Environment, Shanghai Ocean University, No.999, Huchenghuan Rd, Nanhui New City, Shanghai, 201306, P.R. China
| | - Rui Jia
- College of Marine Ecology and Environment, Shanghai Ocean University, No.999, Huchenghuan Rd, Nanhui New City, Shanghai, 201306, P.R. China.
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3
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Li T, Xu L, Teng J, Ma Y, Liu W, Wang Y, Chi X, Shao S, Dong Y, Zhan Q, Liu X. GADD45G Interacts with E-cadherin to Suppress the Migration and Invasion of Esophageal Squamous Cell Carcinoma. Dig Dis Sci 2020; 65:1032-1041. [PMID: 31562612 DOI: 10.1007/s10620-019-05836-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Accepted: 09/08/2019] [Indexed: 01/06/2023]
Abstract
BACKGROUND/AIMS Esophageal squamous cell carcinoma (ESCC) is one of the most prevalent cancers with poor prognosis. Metastasis is the leading cause of cancer-related deaths. The growth arrest and DNA damage-inducible 45 gamma (GADD45G) has been reported to correlate with survival, invasion, and metastasis of ESCC. This study was aimed to investigate the role and mechanism of GADD45G in ESCC cell migration and invasion. METHODS Both the effects of GADD45G and its need for E-cadherin to function on ESCC cell migration and invasion were determined through loss- and gain-of-function approaches via Transwell assays. The interaction between GADD45G and E-cadherin was detected by GST-pull down and IP assays. The expression of E-cadherin upon GADD45G overexpression was evaluated by RT-qPCR and western blot. The level of E-cadherin in cytoplasmic, nuclear, and membrane fractions was examined by western blot following subcellular fractionation. RESULTS Knockdown of GADD45G increased the migration and invasion abilities of KYSE150 cells, while overexpression of GADD45G showed the opposite effects on YES2 and KYSE30 cells. GADD45G could interact with E-cadherin and enhanced its membrane level. Knockdown of E-cadherin abolished the inhibitory effects of GADD45G on ESCC cell migration and invasion. Intriguingly, dimer-dissociating mutant of GADD45G could not interact with E-cadherin and almost lost its ability to suppress the ESCC cell migration and invasion. CONCLUSIONS This study reveals a novel role for GADD45G in inhibiting the ESCC cell migration and invasion, which will provide a new insight in understanding the ESCC metastatic mechanism.
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Affiliation(s)
- Tongtong Li
- Institute of Cancer Stem Cell, Dalian Medical University, No. 9 West Section, Lvshun South Road, Lvshunkou District, Dalian, 116044, China
| | - Lele Xu
- Institute of Cancer Stem Cell, Dalian Medical University, No. 9 West Section, Lvshun South Road, Lvshunkou District, Dalian, 116044, China
| | - Jinglei Teng
- Institute of Cancer Stem Cell, Dalian Medical University, No. 9 West Section, Lvshun South Road, Lvshunkou District, Dalian, 116044, China
| | - Yunping Ma
- Institute of Cancer Stem Cell, Dalian Medical University, No. 9 West Section, Lvshun South Road, Lvshunkou District, Dalian, 116044, China
| | - Wenzhong Liu
- Institute of Cancer Stem Cell, Dalian Medical University, No. 9 West Section, Lvshun South Road, Lvshunkou District, Dalian, 116044, China
| | - Yan Wang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Laboratory of Molecular Oncology, Peking University Cancer Hospital & Institute, No. 52 Fucheng Road, Haidian District, Beijing, 100142, China
| | - Xinming Chi
- Liaoning Key Laboratory of Proteomics, Dalian Medical University, No. 9 West Section, Lvshun South Road, Lvshunkou District, Dalian, 116044, China
| | - Shujuan Shao
- Liaoning Key Laboratory of Proteomics, Dalian Medical University, No. 9 West Section, Lvshun South Road, Lvshunkou District, Dalian, 116044, China
| | - Yan Dong
- College of Stomatology, Dalian Medical University, No. 9 West Section, Lvshun South Road, Lvshunkou District, Dalian, 116044, China
| | - Qimin Zhan
- Institute of Cancer Stem Cell, Dalian Medical University, No. 9 West Section, Lvshun South Road, Lvshunkou District, Dalian, 116044, China.,Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Laboratory of Molecular Oncology, Peking University Cancer Hospital & Institute, No. 52 Fucheng Road, Haidian District, Beijing, 100142, China.,State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, No. 17 Panjiayuan Nanli, Chaoyang District, Beijing, 100021, China
| | - Xuefeng Liu
- Institute of Cancer Stem Cell, Dalian Medical University, No. 9 West Section, Lvshun South Road, Lvshunkou District, Dalian, 116044, China.
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Shi Q, Sutariya V, Varghese Gupta S, Bhatia D. GADD45α-targeted suicide gene therapy driven by synthetic CArG promoter E9NS sensitizes NSCLC cells to cisplatin, resveratrol, and radiation regardless of p53 status. Onco Targets Ther 2019; 12:3161-3170. [PMID: 31114253 PMCID: PMC6497884 DOI: 10.2147/ott.s192061] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Accepted: 03/12/2019] [Indexed: 12/12/2022] Open
Abstract
Background: GADD45α is a tumor suppressor protein often upregulated by environmental stresses and DNA-damage agents to cause growth arrest, apoptosis, tumor growth inhibition, and anti-angiogenesis. A novel suicide gene therapy vector pE9NS.G45α was engineered by cloning GADD45α opening reading frame downstream to the synthetic CArG promoter E9NS, which contains nine repeats of CArG element with modified core A/T sequence and functions as a molecular switch to drive the expression of GADD45α. The current study aims to determine the efficacy of this suicide gene therapy vector in combination with cisplatin, resveratrol, and radiation in NSCLC cell lines with various p53 statuses. Methods: Three NSCLC cell lines, H1299 (deleted p53), A549 (wild-type p53), and H23 (mutated p53), were examined in the present investigation to represent NSCLC with different p53 functions. MTT assay was conducted to select suitable doses of cisplatin, resveratrol, and radiation for gene therapy, and dual luciferase assay was performed to validate the activation of promoter E9NS. The efficacy of gene therapy combinations was evaluated by the amount of GADD45α expression, cell survival, and apoptosis. Results: All the combinations successfully activated promoter E9NS to elevate intracellular GADD45α protein levels and subsequently enhanced cell viability reduction and apoptosis induction regardless of p53 status. Conclusion: Our study demonstrates that GADD45α-targeted suicide gene therapy controlled by synthetic promoter E9NS sensitizes NSCLC cells to cisplatin, resveratrol, and radiation and is effective against NSCLC at least in vitro.
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Affiliation(s)
- Qiwen Shi
- Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou, Zhejiang, People's Republic of China
| | | | | | - Deepak Bhatia
- Bernard J. Dunn School of Pharmacy, Shenandoah University, Ashburn, VA, USA
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5
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Tan Y, Xiao D, Xu Y, Wang C. Long non-coding RNA DLX6-AS1 is upregulated in preeclampsia and modulates migration and invasion of trophoblasts through the miR-376c/GADD45A axis. Exp Cell Res 2018; 370:718-724. [PMID: 30055134 DOI: 10.1016/j.yexcr.2018.07.039] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Revised: 07/23/2018] [Accepted: 07/24/2018] [Indexed: 12/20/2022]
Abstract
Long non-coding RNA (lncRNA) are key regulatory molecules that are implicated in diverse biological processes and human diseases, including preeclampsia. However, their expression and functions in the progression of preeclampsia remains largely unclear. In this study, lncRNA DLX6-AS1 was confirmed to be significantly upregulated in the placentas of patients with preeclampsia, compared with normal controls. Overexpression of DLX6-AS1 dramatically decreased proliferation, migration and invasion in trophoblast JEG3 and HTR-8/SVneo cells. Luciferase activity and RNA pull-down assays showed that DLX6-AS1 interacted with miR-376c, and that overexpression of DLX6-AS1 significantly reduced expression of miR-376c in HTR-8/SVneo cells. Also, miR-376c targeted and downregulated GADD45A in HTR-8/SVneo cells. Overexpression of GADD45A effectively attenuated a miR-376c-induced increase in the proliferation, migration and invasion of HTR-8/SVneo cells. Further research showed that DLX6-AS1-induced inhibition of trophoblast proliferation, migration and invasion was effectively neutralized by GADD45A knockdown and miR-376c overexpression. Taken together, these findings suggest that DLX6-AS1 may contribute to preeclampsia by impairing proliferative, migratory and invasive abilities of trophoblasts via the miR-376c/GADD45A axis.
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Affiliation(s)
- Yan Tan
- Department of Gynecology and Obstetrics, Affiliated Shenzhen Maternity & Child Healthcare Hospital, Southern Medical University (Shenzhen Maternity & Child Healthcare Hospital), Shenzhen 518028, Guangdong, China
| | - Di Xiao
- Department of Gynecology and Obstetrics, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou 510150, Guangdong, China
| | - Yanbin Xu
- Department of Gynecology and Obstetrics, Affiliated Shenzhen Maternity & Child Healthcare Hospital, Southern Medical University (Shenzhen Maternity & Child Healthcare Hospital), Shenzhen 518028, Guangdong, China
| | - Chenhong Wang
- Department of Gynecology and Obstetrics, Affiliated Shenzhen Maternity & Child Healthcare Hospital, Southern Medical University (Shenzhen Maternity & Child Healthcare Hospital), Shenzhen 518028, Guangdong, China; Department of Gynecology and Obstetrics, Shenzhen Hospital, Southern Medical University, Shenzhen 518000, Guangdong, China.
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6
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The Curcumin Analog CH-5 Exerts Anticancer Effects in Human Osteosarcoma Cells via Modulation of Transcription Factors p53/Sp1. Int J Mol Sci 2018; 19:ijms19071909. [PMID: 29966255 PMCID: PMC6073932 DOI: 10.3390/ijms19071909] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2018] [Revised: 04/15/2018] [Accepted: 04/16/2018] [Indexed: 12/11/2022] Open
Abstract
Curcumin is a potential anticancer drug with poor bioavailability, which limits its clinical use as a therapeutic agent. The aim of this study was a preliminary evaluation of the curcumin analogue CH-5 as a cytotoxic agent in human osteosarcoma cell lines U2OS, MG-63, and Saos-2. CH-5 inhibited cell viability at lower concentrations than curcumin, leading to the induction of apoptosis. The cellular levels of the transcription factors p53 and Sp1 affect the expression of cellular pathways that lead to apoptosis. CH-5 increased p53 protein levels in U2OS cells and reduced Sp1 levels, with a consequent effect on the expression of their target genes DNA methyltransferase 1 (DNMT1) and growth arrest and DNA damage-inducible 45 alpha gene (Gadd45a). CH-5 repressed DNMT1 and increased Gadd45a mRNA expression, which was dependent on p53, as this effect was only observed in the colorectal cancer cell line HCT116 with active p53, but not in the isogenic p53-deficient HCT116 cells. CH-5 also reduced the protein levels of DNMT1, which led to the upregulation of Gadd45a. These results suggest that CH-5 has potentially higher anticancer activity than curcumin, which is associated with the expression of apoptosis-associated genes regulated by the transcription factors Sp1 and p53. Future work on CH-5 will define the therapeutic potential of this compound in vivo.
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Saladino S, Salamone M, Ghersi G. MDA-MB-231 and 8701BC breast cancer lines promote the migration and invasiveness of ECV304 cells on 2D and 3D type-I collagen matrix. Cell Biol Int 2018; 41:1030-1038. [PMID: 28678446 DOI: 10.1002/cbin.10817] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Accepted: 06/27/2017] [Indexed: 01/15/2023]
Abstract
Tumor angiogenesis is a multiphasic process, having the extracellular matrix remodeling as critical step. Different classes of proteolytic enzymes in matrix digestion/remodeling are involved. The role of lytic enzymes and their activation mode have not been completely elucidated. Herein, the crosstalk between endothelia and tumor cells, by realization of bi- and three-dimensional endothelial and breast cancer cells co-cultures, were studied in vitro. Particularly, the effects of two tumor conditioned media (TCM) were assessed about endothelial proliferation, migration, and invasiveness. An increase in expression of pro-MMP9 was detected when endothelial cells were cultured in the presence of both TCM; such as an up-regulation of MMP1 and MMP14 and a down-regulation of MMP7. Moreover the increased MMP2 gene expression from one of them and the stimulation MMP3 synthesis from the other one were observed; an increases of β3-integrin, VEGFA, and DPP4 molecules were detected when endothelia cells are cultured with both TCM. The selection/characterization of elements present in conditioned media from breast cancer cells differently affect endothelial cells, make them potential effectors useful in breast cancer treatment.
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Affiliation(s)
- Silvia Saladino
- Dipartimento STEBICEF, Università di Palermo, viale delle Scienze 90128 Palermo, Sicilia, Italy
| | - Monica Salamone
- ABIEL s.r.l via del Mare 3, 91021 Campobello di Mazara (TP), Palermo, Italy
| | - Giulio Ghersi
- Dipartimento STEBICEF, Università di Palermo, viale delle Scienze 90128 Palermo, Sicilia, Italy.,ABIEL s.r.l via del Mare 3, 91021 Campobello di Mazara (TP), Palermo, Italy
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8
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The β-catenin/CBP-antagonist ICG-001 inhibits pediatric glioma tumorigenicity in a Wnt-independent manner. Oncotarget 2018; 8:27300-27313. [PMID: 28460484 PMCID: PMC5432336 DOI: 10.18632/oncotarget.15934] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Accepted: 02/20/2017] [Indexed: 12/12/2022] Open
Abstract
Pediatric high-grade gliomas (pedHGG) belong to the most aggressive cancers in children with a poor prognosis due to a lack of efficient therapeutic strategies. The β-catenin/Wnt-signaling pathway was shown to hold promising potential as a treatment target in adult high-grade gliomas by abrogating tumor cell invasion and the acquisition of stem cell-like characteristics. Since pedHGG differ from their adult counterparts in genetically and biologically we aimed to investigate the effects of β-catenin/Wnt-signaling pathway-inhibition by the β-catenin/CBP antagonist ICG-001 in pedHGG cell lines. In contrast to adult HGG, pedHGG cells displayed minimal detectable canonical Wnt-signaling activity. Nevertheless, low doses of ICG-001 inhibited cell migration/invasion, tumorsphere- and colony formation, proliferation in vitro as well as tumor growth in vivo/ovo, suggesting that ICG-001 affects pedHGG tumor cell characteristics independent of β-catenin/Wnt-signaling. RNA-sequencing analyses support a Wnt/β-catenin-independent effect of ICG-001 on target gene transcription, revealing strong effects on genes involved in cellular metabolic/biosynthetic processes and cell cycle progression. Among these, high mRNA expression of cell cycle regulator JDP2 was found to confer a better prognosis for pedHGG patients. In conclusion, ICG-001 might offer an effective treatment option for pedHGG patients functioning to regulate cell phenotype and gene expression programs in absence of Wnt/β-catenin signaling-activity.
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9
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Effects of microRNA-374 on proliferation, migration, invasion, and apoptosis of human SCC cells by targeting Gadd45a through P53 signaling pathway. Biosci Rep 2017; 37:BSR20170710. [PMID: 28679648 PMCID: PMC6435473 DOI: 10.1042/bsr20170710] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Revised: 06/30/2017] [Accepted: 07/04/2017] [Indexed: 12/20/2022] Open
Abstract
The present study investigated the effects of microRNA-374 (miR-374) on human squamous cell carcinoma (SCC) cell proliferation, migration, invasion, and apoptosis through P53 signaling pathway by targeting growth arrest and DNA-damage-inducible protein 45 α (Gadd45a). Skin samples were collected from patients with skin SCC and normal skin samples. Expression of miR-374, Gadd45a, P53, P73, P16, c-myc, bcl-2, Bax, caspase-3, and caspase-9 were detected using quantitative real-time polymerase chain reaction (qRT-PCR) and Western blotting. A431 and SCL-1 cells were divided into blank, negative control (NC), miR-374 mimics, miR374 inhibitors, siRNA–Gadd45a, and miR-374 inhibitors + siRNA–Gadd45a groups. Their proliferation, migration, invasion, cell cycle, and apoptosis were evaluated by 3-[4,5-dimethylthiazol-2-yl]-2,5 diphenyl tetrazolium bromide (MTT) assay, scratch test, Transwell assay, and flow cytometry. SCC skin tissues exhibited decreased expression of miR-374, P73, P16, Bax caspase-3 and caspase-9, and increased levels of Gadd45a, P53, c-myc, and Bcl-2 compared with the normal skin tissues. The miR-374 inhibitors group exhibited decreased expression of miR-374, P73, P16, Bax caspase-3 and caspase-9, and increased expression of Gadd45a, P53, c-myc, and Bcl-2, enhanced cell proliferation, migration, and invasion, and reduced apoptosis compared with the blank and NC groups; the miR-374 mimics group followed opposite trends. Compared with the blank and NC groups, the miR-374 inhibitors + siRNA–Gadd45a group showed decreased miR-374 level; the siRNA–Gadd45a group showed elevated levels of P73, P16, Bax, caspase-3 and caspase-9, decreased levels of Gadd45a, P53, c-myc, and Bcl-2, reduced cell proliferation, migration, and invasion, and accelerated apoptosis. miR-374 induces apoptosis and inhibits proliferation, migration, and invasion of SCC cells through P53 signaling pathway by down-regulating Gadd45a.
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10
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Comprehensive Analysis of the Transcriptional and Mutational Landscape of Follicular and Papillary Thyroid Cancers. PLoS Genet 2016; 12:e1006239. [PMID: 27494611 PMCID: PMC4975456 DOI: 10.1371/journal.pgen.1006239] [Citation(s) in RCA: 232] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2016] [Accepted: 07/13/2016] [Indexed: 12/30/2022] Open
Abstract
Follicular thyroid carcinoma (FTC) and benign follicular adenoma (FA) are indistinguishable by preoperative diagnosis due to their similar histological features. Here we report the first RNA sequencing study of these tumors, with data for 30 minimally invasive FTCs (miFTCs) and 25 FAs. We also compared 77 classical papillary thyroid carcinomas (cPTCs) and 48 follicular variant of PTCs (FVPTCs) to observe the differences in their molecular properties. Mutations in H/K/NRAS, DICER1, EIF1AX, IDH1, PTEN, SOS1, and SPOP were identified in miFTC or FA. We identified a low frequency of fusion genes in miFTC (only one, PAX8–PPARG), but a high frequency of that in PTC (17.60%). The frequencies of BRAFV600E and H/K/NRAS mutations were substantially different in miFTC and cPTC, and those of FVPTC were intermediate between miFTC and cPTC. Gene expression analysis demonstrated three molecular subtypes regardless of their histological features, including Non–BRAF–Non–RAS (NBNR), as well as BRAF–like and RAS–like. The novel molecular subtype, NBNR, was associated with DICER1, EIF1AX, IDH1, PTEN, SOS1, SPOP, and PAX8–PPARG. The transcriptome of miFTC or encapsulated FVPTC was indistinguishable from that of FA, providing a molecular explanation for the similarly indolent behavior of these tumors. We identified upregulation of genes that are related to mitochondrial biogenesis including ESRRA and PPARGC1A in oncocytic follicular thyroid neoplasm. Arm-level copy number variations were correlated to histological and molecular characteristics. These results expanded the current molecular understanding of thyroid cancer and may lead to new diagnostic and therapeutic approaches to the disease. Recently, The Cancer Genome Atlas proposed an improved classification of the subtypes of papillary thyroid carcinoma (PTC) based on gene expression profiles, which better represents cell signaling and differentiation. However, a molecular characterization of follicular thyroid carcinoma (FTC), which has a greater tendency for hematogenous spread to lung and bone is not yet fully elucidated. In this study, we describe the first RNA sequencing data of minimally invasive FTC (miFTC) and benign follicular adenoma (FA), which cause diagnostic difficulties due to their similar histological features. Additionally, classical PTC and follicular variant of PTC (FVPTC) were sequenced to compare their transcriptional and mutational landscape. BRAF, H/K/NRAS, fusion genes, and copy number variations were associated with tumor histology. Based on gene expression profiles, thyroid tumors were classified as three molecular subtypes regardless of histological subtypes, BRAF–like, RAS–like, and Non–BRAF–Non–RAS. In particular, we found identical gene expression profiles between miFTC, FA, and encapsulated FVPTC. Oncocytic follicular thyroid tumors have gene expression signatures related to mitochondrial biogenesis including ESRRA and PPARGC1A. These results expanded the current molecular understanding of thyroid cancer to its follicular types.
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11
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Genetic alterations of JAK/STAT cascade and histone modification in extranodal NK/T-cell lymphoma nasal type. Oncotarget 2016; 6:17764-76. [PMID: 25980440 PMCID: PMC4627344 DOI: 10.18632/oncotarget.3776] [Citation(s) in RCA: 116] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2014] [Accepted: 04/13/2015] [Indexed: 01/05/2023] Open
Abstract
Extranodal NK/T-cell lymphoma nasal type (ENKL) is a rare type of non-Hodgkin lymphoma that more frequently occurs in East Asia and Latin America. Even though its molecular background has been discussed in the last few years, the current knowledge does not explain the disease pathogenesis in most cases of ENKL. Here, we performed multiple types of next-generation sequencing on 34 ENKL samples, including whole-exome sequencing (9 cancer tissues and 4 cancer cell lines), targeted sequencing (21 cancer tissues), and RNA sequencing (3 cancer tissues and 4 cancer cell lines). Mutations were found most frequently in 3 genes, STAT3, BCOR, and MLL2 (which were present in 9, 7, and 6 cancer samples, respectively), whereas there were only 2 cases of JAK3 mutation. In total, JAK/STAT pathway- and histone modification-related genes accounted for 55.9% and 38.2% of cancer samples, respectively, and their involvement in ENKL pathogenesis was also supported by gene expression analysis. In addition, we provided 177 genes upregulated only in cancer tissues, which appear to be linked with angiocentric and angiodestructive growth of ENKL. In this study, we propose several novel driver genes of ENKL, and show that these genes and their functional groups may be future therapeutic targets of this disease.
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12
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Hibsh D, Buetow KH, Yaari G, Efroni S. Quantification of read species behavior within whole genome sequencing of cancer genomes for the stratification and visualization of genomic variation. Nucleic Acids Res 2016; 44:e81. [PMID: 26809676 PMCID: PMC4872078 DOI: 10.1093/nar/gkw031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2015] [Accepted: 01/11/2016] [Indexed: 11/13/2022] Open
Abstract
The cancer genome is abnormal genome, and the ability to monitor its sequence had undergone a technological revolution. Yet prognosis and diagnosis remain an expert-based decision, with only limited abilities to provide machine-based decisions. We introduce a heterogeneity-based method for stratifying and visualizing whole-genome sequencing (WGS) reads. This method uses the heterogeneity within WGS reads to markedly reduce the dimensionality of next-generation sequencing data; it is available through the tool HiBS (Heterogeneity-Based Subclassification) that allows cancer sample classification. We validated HiBS using >200 WGS samples from nine different cancer types from The Cancer Genome Atlas (TCGA). With HiBS, we show progress with two WGS related issues: (i) differentiation between normal (NB) and tumor (TP) samples based solely on the information structure of their WGS data, and (ii) identification of specific regions of chromosomal amplification/deletion and their association with tumor stage. By comparing results to those obtained through available WGS analyses tools, we demonstrate some of the novelties obtained by the approach implemented in HiBS and also show nearly perfect normal/tumor classification, used to identify known and unknown chromosomal aberrations. Finally, the HiBS index has been associated with breast cancer tumor stage.
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Affiliation(s)
- Dror Hibsh
- Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 52900, Israel
| | - Kenneth H Buetow
- Computational Sciences and Informatics Program, Complex Adaptive Systems Initiative, Arizona State University, Tempe AZ 85281, USA
| | - Gur Yaari
- Faculty of Engineering, Bar-Ilan University, Ramat Gan 52900, Israel
| | - Sol Efroni
- Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 52900, Israel
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Liu X, Deng Q, Luo X, Chen Y, Shan N, Qi H. Oxidative stress-induced Gadd45α inhibits trophoblast invasion and increases sFlt1/sEng secretions via p38 MAPK involving in the pathology of pre-eclampsia. J Matern Fetal Neonatal Med 2016; 29:3776-85. [PMID: 26809169 DOI: 10.3109/14767058.2016.1144744] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
BACKGROUND Pre-eclampsia (PE) is one of the most common pregnancy-related complications. We have previously reported that growth arrest and DNA damage-inducible 45 alpha (Gadd45α) is over-expressed in trophoblasts in pre-eclamptic placentas, with an excessive activation of p38 mitogen-activated protein kinase (MAPK) and increased levels of soluble Fms-like tyrosine kinase 1 (sFlt-1) and soluble endoglin (sEng) in maternal sera. Now we further investigate how Gadd45α regulates trophoblast functions and anti-angiogenesis factors secretions during placental development in patients with PE. METHODS Human placental villous explants were used to verify the effects of Gadd45α and p38 MAPK in placentation. Then HRT8/SVneo cells exposed to hypoxia/reoxygenation (H/R) were employed as an oxidative stress model to investigate the effects of Gadd45α on invasion and sFlt-1/sEng secretions. Through silencing Gadd45α with lentiviral vector-based short-hairpin RNA and inhibiting p38 MAPK with SB203580, we demonstrated that Gadd45α and its downstream p38 protein played roles in the pathology of pre-eclampsia. RESULTS Gadd45α was found to have increased expression in H/R-treated villous explants and HTR8/SVneo cells. Gadd45α knockdown or p38 blockage could promote trophoblast outgrowth and migration in H/R-exposed villous explants, and enhance the potentials of trophoblast migration/invasion and network formation in H/R-exposed HTR8/SVneo cells. These functional changes might be related to the increased activities of MMP2/9. Meanwhile, Gadd45α knockdown or p38 inhibition also decreases sFlt-1/sEng secretions via suppressing oxidative stress. CONCLUSIONS Oxidative stress-induced overexpression of Gadd45α might influence the activity of MMPs through activation of p38 MAPK signaling to affect the invasion of trophoblast cells, and increase the secretions of sFlt-1/sEng, which then participate in the pathogenesis of pre-eclampsia.
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Affiliation(s)
- Xiru Liu
- a Department of Obstetrics and Gynecology , the First Affiliated Hospital of Chongqing Medical University , Chongqing , China
| | - Qinyin Deng
- a Department of Obstetrics and Gynecology , the First Affiliated Hospital of Chongqing Medical University , Chongqing , China
| | - Xin Luo
- a Department of Obstetrics and Gynecology , the First Affiliated Hospital of Chongqing Medical University , Chongqing , China
| | - Ying Chen
- a Department of Obstetrics and Gynecology , the First Affiliated Hospital of Chongqing Medical University , Chongqing , China
| | - Nan Shan
- a Department of Obstetrics and Gynecology , the First Affiliated Hospital of Chongqing Medical University , Chongqing , China
| | - Hongbo Qi
- a Department of Obstetrics and Gynecology , the First Affiliated Hospital of Chongqing Medical University , Chongqing , China
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14
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Comparative transcriptomic profiling of hydrogen peroxide signaling networks in zebrafish and human keratinocytes: Implications toward conservation, migration and wound healing. Sci Rep 2016; 6:20328. [PMID: 26846883 PMCID: PMC4742856 DOI: 10.1038/srep20328] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2015] [Accepted: 12/30/2015] [Indexed: 12/31/2022] Open
Abstract
Skin wounds need to be repaired rapidly after injury to restore proper skin barrier function. Hydrogen peroxide (H2O2) is a conserved signaling factor that has been shown to promote a variety of skin wound repair processes, including immune cell migration, angiogenesis and sensory axon repair. Despite growing research on H2O2 functions in wound repair, the downstream signaling pathways activated by this reactive oxygen species in the context of injury remain largely unknown. The goal of this study was to provide a comprehensive analysis of gene expression changes in the epidermis upon exposure to H2O2 concentrations known to promote wound repair. Comparative transcriptome analysis using RNA-seq data from larval zebrafish and previously reported microarray data from a human epidermal keratinocyte line shows that H2O2 activates conserved cell migration, adhesion, cytoprotective and anti-apoptotic programs in both zebrafish and human keratinocytes. Further assessment of expression characteristics and signaling pathways revealed the activation of three major H2O2–dependent pathways, EGF, FOXO1, and IKKα. This study expands on our current understanding of the clinical potential of low-level H2O2 for the promotion of epidermal wound repair and provides potential candidates in the treatment of wound healing deficits.
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15
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Li Y, Wang X, Yao L. Directional migration and transcriptional analysis of oligodendrocyte precursors subjected to stimulation of electrical signal. Am J Physiol Cell Physiol 2015; 309:C532-40. [PMID: 26269459 DOI: 10.1152/ajpcell.00175.2015] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2015] [Accepted: 08/05/2015] [Indexed: 12/28/2022]
Abstract
Loss of oligodendrocytes as the result of central nervous system disease causes demyelination that impairs axon function. Effective directional migration of endogenous or grafted oligodendrocyte precursor cells (OPCs) to a lesion is crucial in the neural remyelination process. In this study, the migration of OPCs in electric fields (EFs) was investigated. We found that OPCs migrated anodally in applied EFs, and the directedness and displacement of anodal migration increased significantly when the EF strength increased from 50 to 200 mV/mm. However, EFs did not significantly affect the cell migration speed. The transcriptome of OPCs subjected to EF stimulation (100 and 200 mV/mm) was analyzed using RNA sequencing (RNA-Seq), and results were verified by the reverse transcription quantitative polymerase chain reaction. A Kyoto Encyclopedia of Genes and Genomes pathway analysis revealed that the mitogen-activated protein kinase pathway that signals cell migration was significantly upregulated in cells treated with an EF of 200 mV/mm compared with control cells. Gene ontology enrichment analysis showed the downregulation of differentially expressed genes in chemotaxis. This study suggests that an applied EF is an effective cue to guiding OPC migration in neural regeneration and that transcriptional analysis contributes to the understanding of the mechanism of EF-guided cell migration.
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Affiliation(s)
- Yongchao Li
- Department of Biological Sciences, Wichita State University, Wichita, Kansas; and
| | - Xinkun Wang
- Genome Sequencing Core and Genomics Facility, University of Kansas, Lawrence, Kansas
| | - Li Yao
- Department of Biological Sciences, Wichita State University, Wichita, Kansas; and
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16
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Cheah NP, Pennings JL, Vermeulen JP, Godschalk RW, van Schooten FJ, Opperhuizen A. In vitro effects of low-level aldehyde exposures on human umbilical vein endothelial cells. Toxicol Res (Camb) 2015. [DOI: 10.1039/c4tx00213j] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Aldehydes cause gene expression changes for genes associated with cardiovascular disease. Exposure to aldehydes from tobacco smoke needs to be controlled.
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Affiliation(s)
- Nuan P. Cheah
- Department of Toxicology
- Maastricht University
- Maastricht
- The Netherlands
- Centre for Health Protection
| | - Jeroen L.A. Pennings
- Centre for Health Protection
- National Institute for Public Health and the Environment (RIVM)
- Bilthoven
- The Netherlands
| | - Jolanda P. Vermeulen
- Centre for Health Protection
- National Institute for Public Health and the Environment (RIVM)
- Bilthoven
- The Netherlands
| | | | | | - Antoon Opperhuizen
- Department of Toxicology
- Maastricht University
- Maastricht
- The Netherlands
- Netherlands Food and Consumer Product Safety Authority (NVWA)
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17
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Liu X, Mu H, Luo X, Xiao X, Ding Y, Yin N, Deng Q, Qi H. Expression of Gadd45α in human early placenta and its role in trophoblast invasion. Placenta 2014; 35:370-7. [DOI: 10.1016/j.placenta.2014.03.020] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/22/2014] [Revised: 03/21/2014] [Accepted: 03/27/2014] [Indexed: 01/04/2023]
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18
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Abstract
DNA damage response genes play vital roles in the maintenance of a healthy genome. Defects in cell cycle checkpoint and DNA repair genes, especially mutation or aberrant downregulation, are associated with a wide spectrum of human disease, including a predisposition to the development of neurodegenerative conditions and cancer. On the other hand, upregulation of DNA damage response and repair genes can also cause cancer, as well as increase resistance of cancer cells to DNA damaging therapy. In recent years, it has become evident that many of the genes involved in DNA damage repair have additional roles in tumorigenesis, most prominently by acting as transcriptional (co-)factors. Although defects in these genes are causally connected to tumor initiation, their role in tumor progression is more controversial and it seems to depend on tumor type. In some tumors like melanoma, cell cycle checkpoint/DNA repair gene upregulation is associated with tumor metastasis, whereas in a number of other cancers the opposite has been observed. Several genes that participate in the DNA damage response, such as RAD9, PARP1, BRCA1, ATM and TP53 have been associated with metastasis by a number of in vitro biochemical and cellular assays, by examining human tumor specimens by immunohistochemistry or by DNA genome-wide gene expression profiling. Many of these genes act as transcriptional effectors to regulate other genes implicated in the pathogenesis of cancer. Furthermore, they are aberrantly expressed in numerous human tumors and are causally related to tumorigenesis. However, whether the DNA damage repair function of these genes is required to promote metastasis or another activity is responsible (e.g., transcription control) has not been determined. Importantly, despite some compelling in vitro evidence, investigations are still needed to demonstrate the role of cell cycle checkpoint and DNA repair genes in regulating metastatic phenotypes in vivo.
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Affiliation(s)
- Constantinos G. Broustas
- Center for Radiological Research, Columbia University College of Physicians and Surgeons, New York, New York 10032
| | - Howard B. Lieberman
- Center for Radiological Research, Columbia University College of Physicians and Surgeons, New York, New York 10032
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, New York 10032
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CXCR2-driven ovarian cancer progression involves upregulation of proinflammatory chemokines by potentiating NF-κB activation via EGFR-transactivated Akt signaling. PLoS One 2013; 8:e83789. [PMID: 24376747 PMCID: PMC3869803 DOI: 10.1371/journal.pone.0083789] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2013] [Accepted: 11/08/2013] [Indexed: 01/19/2023] Open
Abstract
Ovarian cancer is an inflammation-associated malignancy with a high mortality rate. CXCR2 expressing ovarian cancers are aggressive with poorer outcomes. We therefore investigated molecular mechanisms involved in CXCR2-driven cancer progression by comparing CXCR2 positive and negative ovarian cancer cell lines. Stably CXCR2 transfected SKOV-3 cells had a faster growth rate as compared to control cells transfected with empty vector. Particularly, tumor necrosis factor (TNF), abundantly expressed in ovarian cancer, enhanced cell proliferation by decreasing the G0-G1 phase in CXCR2 transfected cells. TNF increased nuclear factor-κB (NF-κB) activity to a greater degree in CXCR2 transfected cells than control cells as well as provided a greater activation of IκB. CXCR2 transfected cells expressed higher levels of its proinflammatory ligands, CXCL1/2 and enhanced more proliferation, migration, invasion and colony formation. CXCR2 positive cells also activated more EGFR, which led to higher Akt activation. Enhanced NF-κB activity in CXCR2 positive cells was reduced by a PI3K/Akt inhibitor rather than an Erk inhibitor. CXCL1 added to CXCR2 positive cells led to an increased activation of IκB. CXCL1 also led to a significantly greater number of invasive cells in CXCR2 transfected cells, which was blocked by the NF-κB inhibitor, Bay 11-7082. In addition, enhanced cell proliferation in CXCR2 positive cells was more sensitive to CXCL1 antibody or an NF-κB inhibitor. Finally, CXCR2 transfection of parental cells increased CXCL1 promoter activity via an NF-κB site. Thus augmentation of proinflammatory chemokines CXCL1/2, by potentiating NF-κB activation through EGFR-transactivated Akt, contributes to CXCR2-driven ovarian cancer progression.
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WANG HUIYONG, ZHANG YANQING, QIAN JIANG, ZHANG MINGUI, WANG XIANGNING. Radiotherapy-induced Gadd45a impairs lacrimal gland epithelial cell migration and proliferation. Mol Med Rep 2013; 8:1049-54. [DOI: 10.3892/mmr.2013.1636] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2013] [Accepted: 08/12/2013] [Indexed: 11/05/2022] Open
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