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Matsui Y, Imai A, Izumi H, Yasumura M, Makino T, Shimizu T, Sato M, Mori H, Yoshida T. Cancer-associated point mutations within the extracellular domain of PTPRD affect protein stability and HSPG interaction. FASEB J 2024; 38:e23609. [PMID: 38593345 DOI: 10.1096/fj.202302279rr] [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: 11/05/2023] [Revised: 03/12/2024] [Accepted: 03/29/2024] [Indexed: 04/11/2024]
Abstract
PTPRD, a well-established tumor suppressor gene, encodes the protein tyrosine phosphatase-type D. This protein consists of three immunoglobulin-like (Ig) domains, four to eight fibronectin type 3 (FN) domains, a single transmembrane segment, and two cytoplasmic tandem tyrosine phosphatase domains. PTPRD is known to harbor various cancer-associated point mutations. While it is assumed that PTPRD regulates cellular functions as a tumor suppressor through the tyrosine phosphatase activity in the intracellular region, the function of its extracellular domain (ECD) in cancer is not well understood. In this study, we systematically examined the impact of 92 cancer-associated point mutations within the ECD. We found that 69.6% (64 out of 92) of these mutations suppressed total protein expression and/or plasma membrane localization. Notably, almost all mutations (20 out of 21) within the region between the last FN domain and transmembrane segment affected protein expression and/or localization, highlighting the importance of this region for protein stability. We further found that some mutations within the Ig domains adjacent to the glycosaminoglycan-binding pocket enhanced PTPRD's binding ability to heparan sulfate proteoglycans (HSPGs). This interaction is proposed to suppress phosphatase activity. Our findings therefore suggest that HSPG-mediated attenuation of phosphatase activity may be involved in tumorigenic processes through PTPRD dysregulation.
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Affiliation(s)
- Yu Matsui
- Department of Dermatology, Faculty of Medicine, University of Toyama, Toyama, Japan
| | - Ayako Imai
- Department of Molecular Neuroscience, Faculty of Medicine, University of Toyama, Toyama, Japan
- Research Center for Idling Brain Science, University of Toyama, Toyama, Japan
| | - Hironori Izumi
- Department of Molecular Neuroscience, Faculty of Medicine, University of Toyama, Toyama, Japan
- Research Center for Idling Brain Science, University of Toyama, Toyama, Japan
| | - Misato Yasumura
- Department of Anatomy and Neuroscience, Graduate School of Medicine, Osaka University, Osaka, Japan
- Division of Developmental Neuroscience, United Graduate School of Child Development (UGSCD), Osaka University, Osaka, Japan
| | - Teruhiko Makino
- Department of Dermatology, Faculty of Medicine, University of Toyama, Toyama, Japan
| | - Tadamichi Shimizu
- Department of Dermatology, Faculty of Medicine, University of Toyama, Toyama, Japan
| | - Makoto Sato
- Department of Anatomy and Neuroscience, Graduate School of Medicine, Osaka University, Osaka, Japan
- Division of Developmental Neuroscience, United Graduate School of Child Development (UGSCD), Osaka University, Osaka, Japan
| | - Hisashi Mori
- Department of Molecular Neuroscience, Faculty of Medicine, University of Toyama, Toyama, Japan
- Research Center for Idling Brain Science, University of Toyama, Toyama, Japan
| | - Tomoyuki Yoshida
- Department of Molecular Neuroscience, Faculty of Medicine, University of Toyama, Toyama, Japan
- Research Center for Idling Brain Science, University of Toyama, Toyama, Japan
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Ren Z, Wang L, Leng C. PTPRD mutation is a prognostic biomarker for sensitivity to ICIs treatment in advanced non-small cell lung cancer. Aging (Albany NY) 2023; 15:8204-8219. [PMID: 37602864 PMCID: PMC10497019 DOI: 10.18632/aging.204964] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Accepted: 07/06/2023] [Indexed: 08/22/2023]
Abstract
BACKGROUND Immune checkpoint inhibitors (ICIs) have become the standard treatment for advanced non-small cell lung cancer (NSCLC). ICIs can provide durable responses and prolong survival for some patients. With the increasing routine of next-generation sequencing (NGS) in clinical practice, it is essential to integrate prognostic factors to establish novel nomograms to improve clinical prediction ability in NSCLC with ICIs treatment. METHODS Clinical information, response data, and genome data of advanced NSCLC treated ICIs were obtained from cBioPortal. The top 20 gene alterations in durable clinical benefit (DCB) were compared with those genes in no durable benefit (NDB). Survival analyses were performed using the Kaplan-Meier plot method and selected clinical variables to develop a novel nomogram. RESULTS The mutation of PTPRD was significantly related to progression free survival (PFS) and overall survival (OS) in advanced NSCLC with ICIs treatment (PFS: p = 0.0441, OS: p = 0.0086). The PTPRD mutation was closely related to tumor mutational burden (TMB) and tumor-infiltrating immune cells (TIICs). Two novel nomograms were built to predict the PFS and OS of advanced NSCLC patients with ICIs treatment. CONCLUSIONS Our study suggested that PTPRD mutations could serve as a predictive biomarker for the sensitivity to ICIs treatment and PFS and OS in advanced NSCLC with ICIs. Our systematic nomograms showed great potential value in clinical application to predict the PFS and OS for advanced NSCLC patients with ICIs.
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Affiliation(s)
- Zhixuan Ren
- Department of Radiation Oncology, Huadong Hospital, Fudan University, Shanghai 200433, P.R. China
| | - Li Wang
- Department of Medical Oncology, Shanghai Pulmonary Hospital and Thoracic Cancer Institute, Tongji University School of Medicine, Shanghai 200433, P.R. China
| | - Chaohui Leng
- Department of Oncology, Jiujiang University Affilliated Hospital, Jiujiang 332000, P.R. China
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Herzog D, Jansen J, Mißun M, Diederichs K, Stengel F, Marx A. Chemical Proteomics of the Tumor Suppressor Fhit Covalently Bound to the Cofactor Ap 3A Elucidates Its Inhibitory Action on Translation. J Am Chem Soc 2022; 144:8613-8623. [PMID: 35522782 PMCID: PMC9121386 DOI: 10.1021/jacs.2c00815] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The tumor suppressor protein fragile histidine triad (Fhit) is known to be associated with genomic instability and apoptosis. The tumor-suppressive function of Fhit depends on the interaction with the alarmone diadenosine triphosphate (Ap3A), a noncanonical nucleotide whose concentration increases upon cellular stress. How the Fhit-Ap3A complex exerts its signaling function is unknown. Here, guided by a chemical proteomics approach employing a synthetic stable Fhit-Ap3A complex, we found that the Fhit-Ap3A complex, but not Fhit or Ap3A alone, impedes translation. Our findings provide a mechanistic model in which Fhit translocates from the nucleolus into the cytosol upon stress to form an Fhit-Ap3A complex. The Fhit-Ap3A complex impedes translation both in vitro and in vivo, resulting in reduced cell viability. Overall, our findings provide a mechanistic model by which the tumor suppressor Fhit collaborates with the alarmone Ap3A to regulate cellular proliferation.
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Feng Z, Liu Z, Peng K, Wu W. A Prognostic Model Based on Nine DNA Methylation-Driven Genes Predicts Overall Survival for Colorectal Cancer. Front Genet 2022; 12:779383. [PMID: 35126454 PMCID: PMC8814658 DOI: 10.3389/fgene.2021.779383] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Accepted: 11/12/2021] [Indexed: 01/07/2023] Open
Abstract
Background: Colorectal cancer (CRC) is the third most frequently diagnosed malignancy and the fourth leading cause of cancer-related death among common tumors in the world. We aimed to establish and validate a risk assessment model to predict overall survival (OS) for the CRC patients. Methods: DNA methylation-driven genes were identified by integrating DNA methylation profile and transcriptome data from The Cancer Genome Atlas (TCGA) CRC cohort. Then, a risk score model was built based on LASSO, univariable Cox and multivariable Cox regression analysis. After analyzing the clinicopathological factors, a nomogram was constructed and assessed. Another cohort from GEO was used for external validation. Afterward, the molecular and immune characteristics in the two risk score groups were analyzed. Results: In total, 705 methylation-driven genes were identified. Based on the LASSO and Cox regression analyses, nine genes, i.e., LINC01555, GSTM1, HSPA1A, VWDE, MAGEA12, ARHGAP, PTPRD, ABHD12B and TMEM88, were selected for the development of a risk score model. The Kaplan–Meier curve indicated that patients in the low-risk group had considerably better OS (P = 2e-08). The verification performed in subgroups demonstrated the validity of the model. Then, we established an OS-associated nomogram that included the risk score and significant clinicopathological factors. The concordance index of the nomogram was 0.81. A comprehensive molecular and immune characteristics analysis showed that the high-risk group was associated with tumor invasion, infiltration of immune cells executing pro-tumor suppression (such as myeloid-derived suppressor cells, regulatory T cells, immature dendritic cells) and higher expression of common inhibitory checkpoint molecules (ICPs). Conclusion: Our nine-gene associated risk assessment model is a promising signature to distinguish the prognosis for CRC patients. It is expected to serve as a predictive tool with high sensitivity and specificity for individualized prediction of OS in the patients with CRC.
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Affiliation(s)
| | | | | | - Wei Wu
- *Correspondence: Kangsheng Peng, ; Wei Wu,
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Príncipe C, Dionísio de Sousa IJ, Prazeres H, Soares P, Lima RT. LRP1B: A Giant Lost in Cancer Translation. Pharmaceuticals (Basel) 2021; 14:836. [PMID: 34577535 PMCID: PMC8469001 DOI: 10.3390/ph14090836] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2021] [Revised: 08/14/2021] [Accepted: 08/16/2021] [Indexed: 12/23/2022] Open
Abstract
Low-density lipoprotein receptor-related protein 1B (LRP1B) is a giant member of the LDLR protein family, which includes several structurally homologous cell surface receptors with a wide range of biological functions from cargo transport to cell signaling. LRP1B is among the most altered genes in human cancer overall. Found frequently inactivated by several genetic and epigenetic mechanisms, it has mostly been regarded as a putative tumor suppressor. Still, limitations in LRP1B studies exist, in particular associated with its huge size. Therefore, LRP1B expression and function in cancer remains to be fully unveiled. This review addresses the current understanding of LRP1B and the studies that shed a light on the LRP1B structure and ligands. It goes further in presenting increasing knowledge brought by technical and methodological advances that allow to better manipulate LRP1B expression in cells and to more thoroughly explore its expression and mutation status. New evidence is pushing towards the increased relevance of LRP1B in cancer as a potential target or translational prognosis and response to therapy biomarker.
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Affiliation(s)
- Catarina Príncipe
- i3S—Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal; (C.P.); (H.P.); (P.S.)
- Cancer Signalling and Metabolism Group, IPATIMUP—Institute of Molecular Pathology and Immunology, University of Porto, 4200-135 Porto, Portugal
| | - Isabel J. Dionísio de Sousa
- Department of Oncology, Centro Hospitalar Universitário de São João, 4200-450 Porto, Portugal;
- Faculty of Medicine, University of Porto, 4200-319 Porto, Portugal
| | - Hugo Prazeres
- i3S—Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal; (C.P.); (H.P.); (P.S.)
- IPO-Coimbra, Portuguese Oncology Institute of Coimbra, 3000-075 Coimbra, Portugal
| | - Paula Soares
- i3S—Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal; (C.P.); (H.P.); (P.S.)
- Cancer Signalling and Metabolism Group, IPATIMUP—Institute of Molecular Pathology and Immunology, University of Porto, 4200-135 Porto, Portugal
- Faculty of Medicine, University of Porto, 4200-319 Porto, Portugal
- Department of Pathology, Faculty of Medicine, University of Porto, 4200-319 Porto, Portugal
| | - Raquel T. Lima
- i3S—Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal; (C.P.); (H.P.); (P.S.)
- Cancer Signalling and Metabolism Group, IPATIMUP—Institute of Molecular Pathology and Immunology, University of Porto, 4200-135 Porto, Portugal
- Faculty of Medicine, University of Porto, 4200-319 Porto, Portugal
- Department of Pathology, Faculty of Medicine, University of Porto, 4200-319 Porto, Portugal
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Patrizi S, Pederiva F, d'Adamo AP. Whole-Genome Methylation Study of Congenital Lung Malformations in Children. Front Oncol 2021; 11:689833. [PMID: 34262872 PMCID: PMC8273538 DOI: 10.3389/fonc.2021.689833] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 06/07/2021] [Indexed: 11/30/2022] Open
Abstract
Background and Objectives The treatment of asymptomatic patients with congenital pulmonary malformations (CPMs) remains controversial, partially because the relationship between congenital lung malformations and malignancy is still undefined. Change in methylation pattern is a crucial event in human cancer, including lung cancer. We therefore studied all differentially methylated regions (DMRs) in a series of CPMs in an attempt to find methylation anomalies in genes already described in association with malignancy. Methods The DNA extracted from resected congenital lung malformations and control lung tissue was screened using Illumina MethylationEPIC arrays. Comparisons between the group of malformed samples or the malformed samples of same histology or each malformed sample and the controls and between a pleuropulmonary blastoma (PPB) and controls were performed. Moreover, each malformed sample was pairwise compared with its respective control. All differentially methylated regions (DMRs) with an adjusted p-value <0,05 were studied. Results Every comparison highlighted a number of DMRs closed to genes involved either in cell proliferation or in embryonic development or included in the Cancer Gene Census. Their abnormal methylation had been already described in lung tumors. Conclusions Methylation anomalies already described in lung tumors and also shared by the PPB were found in congenital lung malformations, regardless the histology. The presence of methylation abnormalities is suggestive of a correlation between congenital lung malformations and some step of malignant transformation.
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Affiliation(s)
- Sara Patrizi
- Medical, Surgical and Health Sciences Department, University of Trieste, Trieste, Italy
| | - Federica Pederiva
- Pediatric Surgery, Institute for Maternal and Child Health-IRCCS "Burlo Garofolo", Trieste, Italy
| | - Adamo Pio d'Adamo
- Medical, Surgical and Health Sciences Department, University of Trieste, Trieste, Italy.,Laboratory of Medical Genetics, Institute for Maternal and Child Health-IRCCS "Burlo Garofolo", Trieste, Italy
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Wang Z, Li X, Chen H, Han L, Ji X, Wang Q, Wei L, Miao Y, Wang J, Mao J, Zhang Z. Decreased HLF Expression Predicts Poor Survival in Lung Adenocarcinoma. Med Sci Monit 2021; 27:e929333. [PMID: 33979320 PMCID: PMC8127640 DOI: 10.12659/msm.929333] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Background Lung adenocarcinoma (LUAD) is a type of non-small cell carcinoma. Its pathogenesis is being explored and there is no cure for the disease. Material/Methods The Gene Expression Omnibus (GEO) was searched to obtain data on expression of messenger RNA. GEO2R, an interactive web tool, was used to calculate the differentially expressed genes (DEGs) in LUAD. All the DEGs from different datasets were imported into VENNY 2.1 (https://bioinfogp.cnb.csic.es/tools/venny/index.html) to identify the intersection of the DEGs. An online analysis tool, the Database for Annotation, Visualization, and Integrated Discovery (DAVID), was used to help understand the biological meaning of DEG enrichment in LUAD. Cytoscape 3.7.2 was used to perform centrality analysis and visualize hub genes and related networks. Furthermore, the prognostic value of the hub genes was evaluated with the Kaplan-Meier plotter survival analysis tool. Results The GEO database was used to obtain RNA sequencing information for LUAD and normal tissue from the GSE118370, GSE136043, and GSE140797 datasets. A total of 376 DEGs were identified from GSE118370, 248 were identified from GSE136403, and 718 DEGs were identified from GSE140797. The 10 genes with the highest degrees of expression – the hub genes – were CAV1, TEK, SLIT2, RHOJ, DGSX, HLF, MEIS1, PTPRD, FOXF1, and ADRB2. In addition, Kaplan-Meier survival evaluation showed that CAV1, TEK, SLIT2, HLF, MEIS1, PTPRD, FOXF1, and ADRB2 were associated with favorable outcomes for LUAD. Conclusions CAV1, TEK, SLIT2, HLF, MEIS1, PTPRD, FOXF1, and ADRB2 are hub genes in the DEG interaction network for LUAD and are involved in the development of and prognosis for the disease. The mechanisms underlying these genes should be the subject of further studies.
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Affiliation(s)
- Zaiyan Wang
- Department of Respiratory Medicine, Shanghai University of Medicine and Health Sciences Affiliated Zhoupu Hospital, Shanghai, China (mainland)
| | - Xiaoning Li
- Department of Respiratory Medicine, Shanghai University of Medicine and Health Sciences Affiliated Zhoupu Hospital, Shanghai, China (mainland)
| | - Hao Chen
- Department of Respiratory Medicine, Shanghai University of Medicine and Health Sciences Affiliated Zhoupu Hospital, Shanghai, China (mainland)
| | - Li Han
- Department of Respiratory Medicine, Shanghai University of Medicine and Health Sciences Affiliated Zhoupu Hospital, Shanghai, China (mainland)
| | - Xiaobin Ji
- Department of Respiratory Medicine, Shanghai University of Medicine and Health Sciences Affiliated Zhoupu Hospital, Shanghai, China (mainland)
| | - Qiubo Wang
- Department of Respiratory Medicine, Shanghai University of Medicine and Health Sciences Affiliated Zhoupu Hospital, Shanghai, China (mainland)
| | - Li Wei
- Department of Respiratory Medicine, Shanghai University of Medicine and Health Sciences Affiliated Zhoupu Hospital, Shanghai, China (mainland)
| | - Yafang Miao
- Department of Respiratory Medicine, Shanghai University of Medicine and Health Sciences Affiliated Zhoupu Hospital, Shanghai, China (mainland)
| | - Jing Wang
- Department of Respiratory Medicine, Shanghai University of Medicine and Health Sciences Affiliated Zhoupu Hospital, Shanghai, China (mainland)
| | - Jianfeng Mao
- Department of Respiratory Medicine, Shanghai University of Medicine and Health Sciences Affiliated Zhoupu Hospital, Shanghai, China (mainland)
| | - Zeming Zhang
- Department of Respiratory Medicine, Shanghai University of Medicine and Health Sciences Affiliated Zhoupu Hospital, Shanghai, China (mainland)
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Lin Y, Zhou X, Yang K, Chen Y, Wang L, Luo W, Li Y, Liao J, Zhou Y, Lei Y, Zhang Y, Wu D, Cai L. Protein tyrosine phosphatase receptor type D gene promotes radiosensitivity via STAT3 dephosphorylation in nasopharyngeal carcinoma. Oncogene 2021; 40:3101-3117. [PMID: 33824475 PMCID: PMC8084736 DOI: 10.1038/s41388-021-01768-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2020] [Revised: 03/09/2021] [Accepted: 03/23/2021] [Indexed: 01/07/2023]
Abstract
Radiotherapy is essential to the treatment of nasopharyngeal carcinoma (NPC) and acquired or innate resistance to this therapeutic modality is a major clinical problem. However, the underlying molecular mechanisms in the radiation resistance in NPC are not fully understood. Here, we reanalyzed the microarray data from public databases and identified the protein tyrosine phosphatase receptor type D (PTPRD) as a candidate gene. We found that PTPRD was downregulated in clinical NPC tissues and NPC cell lines with its promoter hypermethylated. Functional assays revealed that PTPRD overexpression sensitized NPC to radiation in vitro and in vivo. Importantly, miR-454-3p directly targets PTPRD to inhibit its expression and biological effect. Interestingly, mechanistic analyses indicate that PTPRD directly dephosphorylates STAT3 to enhance Autophagy-Related 5 (ATG5) transcription, resulting in triggering radiation-induced autophagy. The immunohistochemical staining of 107 NPC revealed that low PTPRD and high p-STAT3 levels predicted poor clinical outcome. Overall, we showed that PTPRD promotes radiosensitivity by triggering radiation-induced autophagy via the dephosphorylation of STAT3, thus providing a potentially useful predictive biomarker for NPC radiosensitivity and drug target for NPC radiosensitization.
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Affiliation(s)
- Yanling Lin
- Department of Radiation Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Xiaohan Zhou
- Department of Radiation Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Kaifan Yang
- Division of Spine Surgery, Department of Orthopaedics, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Yuting Chen
- Department of Radiation Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Lingzhi Wang
- First Clinical Medical College, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Wenxiao Luo
- Department of Radiation Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Yujiang Li
- Department of Thoracic and Cardiovascular Surgery/Huiqiao Medical Center, Southern Medical University, Guangzhou, China.,Department of Thoracic and Cardiovascular Surgery, Affiliated Dongguan People's Hospital, Southern Medical University (Dongguan People's Hospital), Dongguan, China
| | - Jinrong Liao
- Second Clinical Medical College, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Yingtong Zhou
- Department of Radiation Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Yiming Lei
- First Clinical Medical College, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Yanting Zhang
- First Clinical Medical College, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Dehua Wu
- Department of Radiation Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, China.
| | - Longmei Cai
- Department of Radiation Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, China.
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Zhang F, Wang B, Qin T, Wang L, Zhang Q, Lu Y, Song B, Yu X, Li L. IL-6 induces tumor suppressor protein tyrosine phosphatase receptor type D by inhibiting miR-34a to prevent IL-6 signaling overactivation. Mol Cell Biochem 2020; 473:1-13. [PMID: 32602014 DOI: 10.1007/s11010-020-03803-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Accepted: 06/18/2020] [Indexed: 12/14/2022]
Abstract
Protein tyrosine phosphatase receptor type D (PTPRD) is a tumor suppressor gene that is epigenetically silenced and mutated in several cancers, including breast cancer. Since IL-6/STAT3 signaling is often hyperactivated in breast cancer and STAT3 is a direct PTPRD substrate, we investigated the role of PTPRD in breast cancer and the association between PTPRD and IL-6/STAT3 signaling. We found that PTPRD acts as a tumor suppressor in breast cancer tissues and that high PTPRD expression is positively associated with tumor size, lymph node metastasis, PCNA expression, and patient survival. Moreover, breast cancers with high PTPRD expression tend to exhibit high IL-6 and low phosphorylated-STAT3 expression. IL-6 was found to inhibit miR-34a transcription and induce PTPRD expression in breast cancer and breast epithelial cells, whereas PTPRD was shown to mediate activated STAT3 dephosphorylation and to be a conserved, direct target of miR-34a. IL-6-induced PTPRD upregulation was blocked by miR-34a mimics, whereas experimental PTPRD overexpression suppressed MDA-MB-231 cell migration, invasion, and epithelial to mesenchymal transition, decreased STAT3 phosphorylation, and increased miR-34a transcription. Our findings suggest that PTPRD mediates activated STAT3 dephosphorylation and is induced by the IL-6/STAT3-mediated transcriptional inhibition of miR-34a, thereby establishing a negative feedback loop that inhibits IL-6/STAT3 signaling overactivation.
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Affiliation(s)
- Fan Zhang
- Department of General Surgery, The Second Affiliated Hospital of Dalian Medical University, Dalian, 116032, China
| | - Bo Wang
- Department of Pathology and Forensic Medicine, College of Basic Medical Science, Dalian Medical University, Lvshun South Road, Dalian, 116044, China
| | - Tao Qin
- Department of Pathology and Forensic Medicine, College of Basic Medical Science, Dalian Medical University, Lvshun South Road, Dalian, 116044, China
| | - Lu Wang
- Department of Pathology and Forensic Medicine, College of Basic Medical Science, Dalian Medical University, Lvshun South Road, Dalian, 116044, China
| | - Qingqing Zhang
- Department of Pathology and Forensic Medicine, College of Basic Medical Science, Dalian Medical University, Lvshun South Road, Dalian, 116044, China
| | - Ying Lu
- Department of Pathology and Forensic Medicine, College of Basic Medical Science, Dalian Medical University, Lvshun South Road, Dalian, 116044, China
| | - Bo Song
- Department of Pathology and Forensic Medicine, College of Basic Medical Science, Dalian Medical University, Lvshun South Road, Dalian, 116044, China
| | - Xiaotang Yu
- Department of Pathology and Forensic Medicine, College of Basic Medical Science, Dalian Medical University, Lvshun South Road, Dalian, 116044, China.
| | - Lianhong Li
- Department of Pathology and Forensic Medicine, College of Basic Medical Science, Dalian Medical University, Lvshun South Road, Dalian, 116044, China.
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A Novel Role for the Tumor Suppressor Gene ITF2 in Tumorigenesis and Chemotherapy Response. Cancers (Basel) 2020; 12:cancers12040786. [PMID: 32224864 PMCID: PMC7226299 DOI: 10.3390/cancers12040786] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Revised: 03/22/2020] [Accepted: 03/24/2020] [Indexed: 11/18/2022] Open
Abstract
Despite often leading to platinum resistance, platinum-based chemotherapy continues to be the standard treatment for many epithelial tumors. In this study we analyzed and validated the cytogenetic alterations that arise after treatment in four lung and ovarian paired cisplatin-sensitive/resistant cell lines by 1-million microarray-based comparative genomic hybridization (array-CGH) and qRT-PCR methodologies. RNA-sequencing, functional transfection assays, and gene-pathway activity analysis were used to identify genes with a potential role in the development of this malignancy. The results were further explored in 55 lung and ovarian primary tumors and control samples, and in two extensive in silico databases. Long-term cell exposure to platinum induces the frequent deletion of ITF2 gene. Its expression re-sensitized tumor cells to platinum and recovered the levels of Wnt/β-catenin transcriptional activity. ITF2 expression was also frequently downregulated in epithelial tumors, predicting a worse overall survival. We also identified an inverse correlation between ITF2 and HOXD9 expression, revealing that Non-small cell lung cancer (NSCLC) patients with lower expression of HOXD9 had a better overall survival rate. We defined the implication of ITF2 as a molecular mechanism behind the development of cisplatin resistance probably through the activation of the Wnt-signaling pathway. This data highlights the possible role of ITF2 and HOXD9 as novel therapeutic targets for platinum resistant tumors.
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Bae WJ, Ahn JM, Byeon HE, Kim S, Lee D. PTPRD-inactivation-induced CXCL8 promotes angiogenesis and metastasis in gastric cancer and is inhibited by metformin. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2019; 38:484. [PMID: 31805999 PMCID: PMC6896474 DOI: 10.1186/s13046-019-1469-4] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Accepted: 10/28/2019] [Indexed: 01/21/2023]
Abstract
Background Protein tyrosine phosphatase receptor delta (PTPRD) is frequently inactivated in various types of cancers. Here, we explored the underlying mechanism of PTPRD-loss-induced cancer metastasis and investigated an efficient treatment option for PTPRD-inactivated gastric cancers (GCs). Methods PTPRD expression was evaluated by immunohistochemistry. Microarray analysis was used to identify differentially expressed genes in PTPRD-inactivated cancer cells. Quantitative reverse transcription (qRT-PCR), western blotting, and/or enzyme-linked immunosorbent assays were used to investigate the PTPRD-CXCL8 axis and the expression of other related genes. An in vitro tube formation assay was performed using HUVECs. The efficacy of metformin was assessed by MTS assay. Results PTPRD was frequently downregulated in GCs and the loss of PTPRD expression was associated with advanced stage, worse overall survival, and a higher risk of distant metastasis. Microarray analysis revealed a significant increase in CXCL8 expression upon loss of PTPRD. This was validated in various GC cell lines using transient and stable PTPRD knockdown. PTPRD-loss-induced angiogenesis was mediated by CXCL8, and the increase in CXCL8 expression was mediated by both ERK and STAT3 signaling. Thus, specific inhibitors targeting ERK or STAT3 abrogated the corresponding signaling nodes and inhibited PTPRD-loss-induced angiogenesis. Additionally, metformin was found to efficiently inhibit PTPRD-loss-induced angiogenesis, decrease cell viability in PTPRD-inactivated cancers, and reverse the decrease in PTPRD expression. Conclusions Thus, the PTPRD-CXCL8 axis may serve as a potential therapeutic target, particularly for the suppression of metastasis in PTPRD-inactivated GCs. Hence, we propose that the therapeutic efficacy of metformin in PTPRD-inactivated cancers should be further investigated.
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Affiliation(s)
- Won Jung Bae
- Department of Pathology, Ajou University School of Medicine, 164, Worldcup-ro, Yeongtong-gu, Suwon-si, Gyeonggi-do, 16499, Republic of Korea
| | - Ji Mi Ahn
- Department of Pathology, Ajou University School of Medicine, 164, Worldcup-ro, Yeongtong-gu, Suwon-si, Gyeonggi-do, 16499, Republic of Korea
| | - Hye Eun Byeon
- Institute of Medical Science, Ajou University School of Medicine, Suwon, Republic of Korea
| | - Seokwhi Kim
- Department of Pathology, Ajou University School of Medicine, 164, Worldcup-ro, Yeongtong-gu, Suwon-si, Gyeonggi-do, 16499, Republic of Korea
| | - Dakeun Lee
- Department of Pathology, Ajou University School of Medicine, 164, Worldcup-ro, Yeongtong-gu, Suwon-si, Gyeonggi-do, 16499, Republic of Korea.
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Wu A, Yang X, Zhang B, Wang S, Li G. miR-516a-3p promotes proliferation, migration, and invasion and inhibits apoptosis in lung adenocarcinoma by targeting PTPRD. INTERNATIONAL JOURNAL OF CLINICAL AND EXPERIMENTAL PATHOLOGY 2019; 12:4222-4231. [PMID: 31933822 PMCID: PMC6949792] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Accepted: 09/24/2019] [Indexed: 06/10/2023]
Abstract
Background: Multiple previous studies have indicated miR-516a-3p was associated with carcinogenesis in lung cancer. However, its biologic functions in lung adenocarcinoma remain unknown. The aim of this study was to investigate the expression of miR-516a-3p in lung adenocarcinoma, its molecular mechanisms of miR-516a-3p, and its effects on cell proliferation, migration, invasion, and apoptosis. Methods: The expression of miR-516a-3p and PTPRD was tested by reverse transcription-quantitative polymerase chain reaction. Cell migration and invasion assays were used to evaluate the migration and invasion ability of cells. Flow cytometry was performed to observe the effects of miR-516a-3p on the cell apoptosis. Western blot analysis was used to assess the protein levels of PTPRD. Luciferase reporter assay was utilized to identify whether PTPRD was a direct target of miR-516a-3p. Results: There was upregulated expression of miR-516a-3p in lung adenocarcinoma tissues as well as cell lines. In addition, miR-516a-3p expression knock-down could inhibit cell proliferation, invasion, and migration, but promote apoptosis in lung adenocarcinoma. By contrast, overexpression of miR-516a-3p resulted in the opposite effect. Dual luciferase assay, RT-PCR and western blot analysis results confirmed that PTPRD was a direct target for miR-516a-3p. Further studies also found PTPRD was down-regulated in lung adenocarcinoma and there was a negative correlation between miR-516a-3p and PTPRD expression in lung adenocarcinoma. Moreover, miR-516a-3p and PTPRD were significantly correlated with the clinical stage of lung adenocarcinoma. Conclusions: Our current findings showed that miR-516a-3p was up-regulated in lung adenocarcinoma, functioning as a tumor-promoting gene by targeting PTPRD.
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Affiliation(s)
- Anhao Wu
- Department of Thoracic Surgery Ward II, Third Affiliated Hospital, Kunming Medical University, Tumor Hospital of Yunnan Kunming ProvinceKunming, Yunnan, P. R. China
| | - Xin Yang
- Department of Blood Transfusion, The First People’s Hospital of Yunnan Province, The Affiliated Hospital of Kunming University of Science and TechnologyKunming, Yunnan, P. R. China
| | - Bing Zhang
- Department of Thoracic Surgery Ward II, Third Affiliated Hospital, Kunming Medical University, Tumor Hospital of Yunnan Kunming ProvinceKunming, Yunnan, P. R. China
| | - Shuting Wang
- Department of Thoracic Surgery Ward II, Third Affiliated Hospital, Kunming Medical University, Tumor Hospital of Yunnan Kunming ProvinceKunming, Yunnan, P. R. China
| | - Gaofeng Li
- Department of Thoracic Surgery Ward II, Third Affiliated Hospital, Kunming Medical University, Tumor Hospital of Yunnan Kunming ProvinceKunming, Yunnan, P. R. China
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Loss of Tyrosine Phosphatase Delta Promotes Gastric Cancer Progression via Signal Transducer and Activator of Transcription 3 Pathways. Dig Dis Sci 2019; 64:3164-3172. [PMID: 31041642 DOI: 10.1007/s10620-019-05637-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Accepted: 04/20/2019] [Indexed: 01/16/2023]
Abstract
BACKGROUND The protein tyrosine phosphatase delta (PTPRD) is a tumor suppressor, and its role in gastric cancer (GC) remains poorly understood. METHODS The expressions of PTPRD were determined based on public data. In addition, the mRNA expressions of PTPRD in the GC samples, and the expressions of PTPRD in the GC cell lines including HGC27, SGC790, and BGC823, and gastric epithelial cell line GES-1 were determined by western blotting and quantitative real-time PCR. Furthermore, PTPRD siRNA was transfected into the HGC27 cell line, and then, cell proliferation, migration, and invasion were evaluated. The activity of signal transducer and activator of transcription 3 (STAT3) pathways in HGC27 cells transfected with PTPRD siRNA was determined by western blotting. RESULTS PTPRD deletion was found in the GC patients, and this deletion was found to be correlated with poor prognosis in the GC patients. Expression of PTPRD was significantly downregulated in gastric carcinoma specimens and tumor cell lines when compared with those in normal controls. PTPRD also plays a key role in the GC cells proliferation, invasion, and migration. Silencing PTPRD expression by siRNA dramatically promoted GC cells proliferation, invasion, and migration. Mechanism study demonstrated that phosphorylation of STAT3 was inhibited by silencing PTPRD expression and the according changes including inhibition of cell migration and invasion were observed. CONCLUSION This study supports PTPRD as a tumor suppressor and could be served as a marker for prognostic of GC. Silencing PTPRD could be a potential therapeutic in GC.
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14
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Zhao P, Peng L, Wu W, Zheng Y, Jiang W, Zhang H, Tong Z, Liu L, Ma R, Wang L, Yao M, Wang K, Fang W, Wu L. Carcinoma of Unknown Primary with EML4-ALK Fusion Response to ALK Inhibitors. Oncologist 2019; 24:449-454. [PMID: 30679319 DOI: 10.1634/theoncologist.2018-0439] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2018] [Accepted: 11/26/2018] [Indexed: 11/17/2022] Open
Abstract
With the advent of next-generation sequencing (NGS) and precision medicine, investigators have determined that tumors from different tissue sources that have the same types of genetic mutations will have a positive response to the same targeted therapy. This finding has prompted us to seek potential therapeutic targets for patients with carcinoma of unknown primary (CUP) using NGS technology. Here, we reported a case of a woman with CUP resistance to chemotherapy. We detected 450 cancer-related gene alterations using three metastatic tumor specimens and found the presence of EML4 exon13 and ALK exon20 fusion. The tumor did respond to crizotinib, a first-generation ALK inhibitor. When her tumor progressed, circulating tumor DNA detection revealed ALK L1196 M and G1269A mutation resistance to crizotinib, but she had a response to brigatinib. This case revealed that NGS technology used to detect the genetic alterations in patients with CUP might be a reliable method to find potential therapeutic targets, although the primary lesion could not always be confirmed. KEY POINTS: This case exemplifies responsiveness to ALK inhibitor in carcinoma of unknown primary (CUP) with EML4-ALK fusion.Next-generation sequencing is an important diagnostic tool to find potential therapeutic targets in CUP.Liquid biopsy may be useful to provide critical information about resistance mechanisms in CUP to guide sequential treatment decision with targeted therapy.
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Affiliation(s)
- Peng Zhao
- Cancer Biotherapy Center, the First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Ling Peng
- Department of Radiotherapy, the First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Wei Wu
- Cancer Biotherapy Center, the First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Yi Zheng
- Cancer Biotherapy Center, the First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Weiqin Jiang
- Cancer Biotherapy Center, the First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Hangyu Zhang
- Cancer Biotherapy Center, the First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Zhou Tong
- Cancer Biotherapy Center, the First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Lulu Liu
- Cancer Biotherapy Center, the First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | | | | | | | | | - Weijia Fang
- Cancer Biotherapy Center, the First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Liming Wu
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, the First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
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Qu Y, Zhang N. miR-365b-3p inhibits the cell proliferation and migration of human coronary artery smooth muscle cells by directly targeting ADAMTS1 in coronary atherosclerosis. Exp Ther Med 2018; 16:4239-4245. [PMID: 30402161 DOI: 10.3892/etm.2018.6720] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Accepted: 08/02/2018] [Indexed: 12/11/2022] Open
Abstract
Abnormal proliferation and migration of vascular smooth muscle cells serves a crucial role in the development of atherosclerosis. Previous studies have suggested that some microRNAs (miRs) are involved in this process; however, the associated underlying molecular mechanism is unclear. In present study, human coronary artery smooth muscle cells (HCASMCs) were used to explore the function of miR-365b-3p in the coronary atherosclerosis. It was indicated that platelet-derived growth factor-BB (PDGF-BB) treatment inhibited miR-365b-3p expression and upregulated the expression of a disintegrin and metalloproteinase with thrombospondin motifs 1 (ADAMTS1) in HCASMCs. Subsequently, miR-365b-3p mimic was transfected in HCASMCs to explore the function of this miR. The results of reverse transcription-quantitative polymerase chain reaction and western blot analysis indicated that overexpression of miR-365b-3p significantly downregulated ADAMTS1 expression. Functional assay results revealed that overexpression of miR-365b-3p significantly attenuated PDGF-BB-induced proliferation and migration of HCASMCs. Furthermore, the dual-luciferase reporter assay results confirmed that ADAMTS1 is a direct target gene of miR-365b-3p. This discovery proposed a novel channel of communication between ADAMTS1 and HCASMCs, and suggests a potential therapeutic approach for coronary atherosclerosis.
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Affiliation(s)
- Yunfei Qu
- Department of Cardiac Vascular Surgery, Chongqing Three Gorges Central Hospital, Chongqing 404000, P.R. China
| | - Ning Zhang
- Department of General Medicine, Chongqing Three Gorges Central Hospital, Chongqing 404000, P.R. China
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16
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Huang Y, Zhang Y, Ge L, Lin Y, Kwok HF. The Roles of Protein Tyrosine Phosphatases in Hepatocellular Carcinoma. Cancers (Basel) 2018; 10:cancers10030082. [PMID: 29558404 PMCID: PMC5876657 DOI: 10.3390/cancers10030082] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Revised: 03/12/2018] [Accepted: 03/15/2018] [Indexed: 02/08/2023] Open
Abstract
The protein tyrosine phosphatase (PTP) family is involved in multiple cellular functions and plays an important role in various pathological and physiological processes. In many chronic diseases, for example cancer, PTP is a potential therapeutic target for cancer treatment. In the last two decades, dozens of PTP inhibitors which specifically target individual PTP molecules were developed as therapeutic agents. Hepatocellular carcinoma (HCC) is one of the most common malignant tumors and is the second most lethal cancer worldwide due to a lack of effective therapies. Recent studies have unveiled both oncogenic and tumor suppressive functions of PTP in HCC. Here, we review the current knowledge on the involvement of PTP in HCC and further discuss the possibility of targeting PTP in HCC.
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Affiliation(s)
- Yide Huang
- Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation, College of Life Sciences, Fujian Normal University, Fuzhou 350117, China.
- Faculty of Health Sciences, University of Macau, Avenida de Universidade, Taipa, Macau, China.
| | - Yafei Zhang
- Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation, College of Life Sciences, Fujian Normal University, Fuzhou 350117, China.
| | - Lilin Ge
- Faculty of Health Sciences, University of Macau, Avenida de Universidade, Taipa, Macau, China.
- Jiangsu Key Laboratory for Functional Substance of Chinese Medicine, School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing 210023, China.
| | - Yao Lin
- Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation, College of Life Sciences, Fujian Normal University, Fuzhou 350117, China.
| | - Hang Fai Kwok
- Faculty of Health Sciences, University of Macau, Avenida de Universidade, Taipa, Macau, China.
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17
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Yu X, Zhang F, Mao J, Lu Y, Li J, Ma W, Fan S, Zhang C, Li Q, Wang B, Song B, Li L. Protein tyrosine phosphatase receptor-type δ acts as a negative regulator suppressing breast cancer. Oncotarget 2017; 8:98798-98811. [PMID: 29228728 PMCID: PMC5716768 DOI: 10.18632/oncotarget.22000] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Accepted: 10/03/2017] [Indexed: 01/02/2023] Open
Abstract
Protein tyrosine phosphatase receptor-type δ (PTPRD) is frequently inactivated in human cancers. This study investigated the role of PTPRD in the regulation of stemness, epithelial-mesenchymal transition (EMT), and migration and invasion in breast cancer cells. In vitro, PTPRD silencing using siRNA enhanced the stem cell-like properties of breast cancer cells, including their mammosphere- and holoclone-forming abilities, and it promoted tumorigenicity in vivo. PTPRD knockdown also increased the CD44+/CD24− breast cancer stem cell (BCSC) population and the expression of the stem cell markers ALDH1 and OCT4. It also promoted migration and invasion by breast cancer cell, EMT, and activation of signal transducer and activator of transcription 3 (STAT3). BCSCs expressed low levels of PTPRD, displayed mesenchymal phenotypes, and were more sensitive to IL-6-mediated STAT3 activation than non-BCSCs. PTPRD expression was upregulated by IL-6 in breast cancer cells, thereby establishing a negative feedback circuit by which IL-6 induced canonical STAT3 phosphorylation and transiently upregulated PTPRD, which in turn dephosphorylated STAT3 and prevented downstream signaling via the IL-6/STAT3 cascade. These data suggest that therapies aimed at restoring or enhancing PTPRD expression may be effective in controlling breast cancer progression and metastasis.
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Affiliation(s)
- Xiaotang Yu
- Department of Pathology and Forensic Medicine, Dalian Medical University, Dalian 116044, PR China
| | - Fan Zhang
- Department of General Surgery, The Second Affiliated Hospital of Dalian Medical University, Dalian 116044, PR China
| | - Jun Mao
- Department of Pathology and Forensic Medicine, Dalian Medical University, Dalian 116044, PR China
| | - Ying Lu
- Department of Pathology and Forensic Medicine, Dalian Medical University, Dalian 116044, PR China
| | - Jiazhi Li
- Department of Pathology and Forensic Medicine, Dalian Medical University, Dalian 116044, PR China
| | - Wei Ma
- Department of Human Anatomy, Dalian Medical University, Dalian 116044, PR China
| | - Shujun Fan
- Department of Pathology and Forensic Medicine, Dalian Medical University, Dalian 116044, PR China
| | - Chunying Zhang
- Department of Pathology and Forensic Medicine, Dalian Medical University, Dalian 116044, PR China
| | - Qing Li
- Department of Pathology and Forensic Medicine, Dalian Medical University, Dalian 116044, PR China
| | - Bo Wang
- Department of Pathology and Forensic Medicine, Dalian Medical University, Dalian 116044, PR China
| | - Bo Song
- Department of Pathology and Forensic Medicine, Dalian Medical University, Dalian 116044, PR China
| | - Lianhong Li
- Department of Pathology and Forensic Medicine, Dalian Medical University, Dalian 116044, PR China
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Shen T, Chen Z, Zhao ZJ, Wu J. Genetic defects of the IRF1-mediated major histocompatibility complex class I antigen presentation pathway occur prevalently in the JAK2 gene in non-small cell lung cancer. Oncotarget 2017; 8:60975-60986. [PMID: 28977839 PMCID: PMC5617399 DOI: 10.18632/oncotarget.17689] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Accepted: 04/06/2017] [Indexed: 01/05/2023] Open
Abstract
Recognition of major histocompatibility complex (MHC) class I antigens on tumor cells by cytotoxic T cells is involved in T cell-mediated tumor immune surveillance and immune checkpoint therapy. The interferon-γ (IFNγ)-IRF1 signaling pathway regulates MHC class I antigen presentation. To examine genetic defects of the IFNγ-IRF1 pathway in non-small cell lung cancer (NSCLC), we analyzed The Cancer Genome Atlas (TCGA) lung adenocarcinoma (LuAd) and lung squamous cell carcinoma (LuSc) data. Loss-of-function (LOF) genetic alterations of the IFNγ-IRF1 pathway genes (IFNGR1, IFNGR2, JAK1, JAK2, STAT1, IRF1) were found in 64 (6.3%) of 1,016 patients. These genetic defects occur prevalently in JAK2 (33 cases) and often through deletions (29 cases) of chromosome 9p24.1. JAK2 deletions were frequently, but not always, associated with deletions of PD-L1 gene (CD274), PD-L2 gene (PDCD1LG2), PTPRD, and CDKN2A/CDKN2B at the chromosome 9p24.1-9p21.3 region. IRF1 expression was correlated with immune cytolytic activity markers GZMA and PRF1 in NSCLC. IFNγ induced IRF1 expression and cell surface HLA-A/HLA-B/HLA-C (HLA-ABC) in A549, H661, H292, and H2172 cells that contained the wildtype JAK2, but not in H1573 and H1623 cells that were JAK2 defective. Deletion of JAK2 or inhibition of the JAK2 kinase activity resulted in loss of IFNγ-induced IRF1 and cell surface HLA-ABC in JAK2 wildtype NSCLC cells, whereas expression of exogenous JAK2 in H1573 cells restored the IFNγ responses. These findings show that JAK2 deficiency is the major mechanism of genetic defects of the IFNγ-IRF1 pathway in NSCLC and reveal a previously unrecognized significance of chromosome 9p deletion in NSCLC.
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Affiliation(s)
- Tao Shen
- Department of Molecular Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, USA
- Peggy and Charles Stephenson Cancer Center, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA
| | - Zhengming Chen
- Department of Molecular Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, USA
- Division of Biostatistics and Epidemiology, Department of Healthcare Policy and Research, Weill Cornell Medicine, New York, New York, USA
| | - Zhizhuang Joe Zhao
- Department of Pathology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA
| | - Jie Wu
- Department of Molecular Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, USA
- Peggy and Charles Stephenson Cancer Center, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA
- Department of Pathology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA
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Transcriptional profiling identifies the long noncoding RNA plasmacytoma variant translocation (PVT1) as a novel regulator of the asthmatic phenotype in human airway smooth muscle. J Allergy Clin Immunol 2016; 139:780-789. [PMID: 27484035 PMCID: PMC5338875 DOI: 10.1016/j.jaci.2016.06.014] [Citation(s) in RCA: 81] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Revised: 05/24/2016] [Accepted: 06/13/2016] [Indexed: 11/22/2022]
Abstract
Background The mechanism underlying nonsevere and severe asthma remains unclear, although it is commonly associated with increased airway smooth muscle (ASM) mass. Long noncoding RNAs (lncRNAs) are known to be important in regulating healthy primary airway smooth muscle cells (ASMCs), whereas changed expression has been observed in CD8 T cells from patients with severe asthma. Methods Primary ASMCs were isolated from healthy subjects (n = 9) and patients classified as having nonsevere (n = 9) or severe (n = 9) asthma. ASMCs were exposed to dexamethasone and FCS. mRNA and lncRNA expression was measured by using a microarray and quantitative real-time PCR. Bioinformatic analysis was used to examine relevant biological pathways. Finally, the lncRNA plasmacytoma variant translocation 1 (PVT1) was inhibited by transfection of primary ASMCs with small interfering RNAs, and the effect on ASMC phenotype was examined. Results The mRNA expression profile was significantly different between patient groups after exposure to dexamethasone and FCS, and these were associated with biological pathways that might be relevant to the pathogenesis of asthma, including cellular proliferation and pathways associated with glucocorticoid activity. We also observed a significant change in lncRNA expression, yet the expression of only one lncRNA (PVT1) is decreased in patients with corticosteroid-sensitive nonsevere asthma and increased in patients with corticosteroid-insensitive severe asthma. Subsequent targeting studies demonstrated the importance of this lncRNA in controlling both proliferation and IL-6 release in ASMCs from patients with severe asthma. Conclusions lncRNAs are associated with the aberrant phenotype observed in ASMCs from asthmatic patients. Targeting PVT1 might be effective in reducing airway remodeling in asthmatic patients.
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Backes C, Khaleeq QT, Meese E, Keller A. miEAA: microRNA enrichment analysis and annotation. Nucleic Acids Res 2016; 44:W110-6. [PMID: 27131362 PMCID: PMC4987907 DOI: 10.1093/nar/gkw345] [Citation(s) in RCA: 116] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2016] [Accepted: 04/18/2016] [Indexed: 12/29/2022] Open
Abstract
Similar to the development of gene set enrichment and gene regulatory network analysis tools over a decade ago, microRNA enrichment tools are currently gaining importance. Building on our experience with the gene set analysis toolkit GeneTrail, we implemented the miRNA Enrichment Analysis and Annotation tool (miEAA). MiEAA is a web-based application that offers a variety of commonly applied statistical tests such as over-representation analysis and miRNA set enrichment analysis, which is similar to Gene Set Enrichment Analysis. Besides the different statistical tests, miEAA also provides rich functionality in terms of miRNA categories. Altogether, over 14 000 miRNA sets have been added, including pathways, diseases, organs and target genes. Importantly, our tool can be applied for miRNA precursors as well as mature miRNAs. To make the tool as useful as possible we additionally implemented supporting tools such as converters between different miRBase versions and converters from miRNA names to precursor names. We evaluated the performance of miEAA on two sets of miRNAs that are affected in lung adenocarcinomas and have been detected by array analysis. The web-based application is freely accessible at: http://www.ccb.uni-saarland.de/mieaa_tool/.
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Affiliation(s)
- Christina Backes
- Chair for Clinical Bioinformatics, Saarland University, Building E 2.1, 66123 Saarbrücken, Germany
| | - Qurratulain T Khaleeq
- Chair for Clinical Bioinformatics, Saarland University, Building E 2.1, 66123 Saarbrücken, Germany
| | - Eckart Meese
- Institute of Human Genetics, Saarland University, Medical School, 66421 Homburg, Germany
| | - Andreas Keller
- Chair for Clinical Bioinformatics, Saarland University, Building E 2.1, 66123 Saarbrücken, Germany
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21
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Song L, Jiang W, Liu W, Ji J, Shi T, Zhang J, Xia C. Protein tyrosine phosphatases receptor type D is a potential tumour suppressor gene inactivated by deoxyribonucleic acid methylation in paediatric acute myeloid leukaemia. Acta Paediatr 2016; 105:e132-41. [PMID: 26607758 DOI: 10.1111/apa.13284] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/11/2015] [Revised: 09/27/2015] [Accepted: 11/20/2015] [Indexed: 01/09/2023]
Abstract
AIM Protein tyrosine phosphatases receptor type D (PTPRD) is a tumour suppressor gene, and its epigenetic silencing is frequently found in glioblastoma. As aberrant deoxyribonucleic acid (DNA) methylation patterning has been shown to play a role in leukaemogenesis, we studied the promoter methylation, expression profiles and molecular functions of PTPRD in paediatric patients with acute myeloid leukaemia (AML). METHODS Bone marrow specimens were obtained from 32 Chinese patients with a mean age of 7.2 years (range 1.1-16.5). PTPRD and methylation status were evaluated by real-time polymerase chain reaction (PCR) and methylation-specific PCR. Western blot and flow cytometry techniques were also used. RESULTS PTPRD expression was decreased by promoter region methylation in six AML cells and methylated in 21 (65.6%) of the 32 samples. In addition, PTPRD expression could be induced by the DNA demethylating agent 5-aza-2'-deoxycytidine. Furthermore, functional studies showed that overexpression of PTPRD in AML cells inhibited cell proliferation and clonogenicity as well as inducing apoptosis. However, PTPRD knockdown increased cell proliferation. These effects were associated with downregulation of cyclin D1, c-myc and upregulation of Bax. CONCLUSION The results of this study demonstrated that PTPRD was a potential tumour suppressor gene inactivated by DNA methylation in paediatric AML.
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Affiliation(s)
- Lei Song
- Department of Paediatrics The Second Affiliated Hospital of Nantong University Nantong Jiangsu China
| | - Wen Jiang
- Department of Gastroenterology Nantong Third People's Hospital Nantong Jiangsu China
| | - Wei Liu
- Department of Surgery The Second Affiliated Hospital of Nantong University Nantong Jiangsu China
| | - Ju‐Hua Ji
- Department of Gastroenterology Nantong Third People's Hospital Nantong Jiangsu China
| | - Tai‐Feng Shi
- Department of Gastroenterology Nantong Third People's Hospital Nantong Jiangsu China
| | - Jie Zhang
- School of Medicine Nantong University Nantong Jiangsu China
| | - Chun‐Qiu Xia
- Department of Surgery The Second Affiliated Hospital of Nantong University Nantong Jiangsu China
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Zhou HM, Fang YY, Weinberger PM, Ding LL, Cowell JK, Hudson FZ, Ren M, Lee JR, Chen QK, Su H, Dynan WS, Lin Y. Transgelin increases metastatic potential of colorectal cancer cells in vivo and alters expression of genes involved in cell motility. BMC Cancer 2016; 16:55. [PMID: 26847345 PMCID: PMC4741053 DOI: 10.1186/s12885-016-2105-8] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2015] [Accepted: 01/31/2016] [Indexed: 01/22/2023] Open
Abstract
Background Transgelin is an actin-binding protein that promotes motility in normal cells. Although the role of transgelin in cancer is controversial, a number of studies have shown that elevated levels correlate with aggressive tumor behavior, advanced stage, and poor prognosis. Here we sought to determine the role of transgelin more directly by determining whether experimental manipulation of transgelin levels in colorectal cancer (CRC) cells led to changes in metastatic potential in vivo. Methods Isogenic CRC cell lines that differ in transgelin expression were characterized using in vitro assays of growth and invasiveness and a mouse tail vein assay of experimental metastasis. Downstream effects of transgelin overexpression were investigated by gene expression profiling and quantitative PCR. Results Stable overexpression of transgelin in RKO cells, which have low endogenous levels, led to increased invasiveness, growth at low density, and growth in soft agar. Overexpression also led to an increase in the number and size of lung metastases in the mouse tail vein injection model. Similarly, attenuation of transgelin expression in HCT116 cells, which have high endogenous levels, decreased metastases in the same model. Investigation of mRNA expression patterns showed that transgelin overexpression altered the levels of approximately 250 other transcripts, with over-representation of genes that affect function of actin or other cytoskeletal proteins. Changes included increases in HOOK1, SDCCAG8, ENAH/Mena, and TNS1 and decreases in EMB, BCL11B, and PTPRD. Conclusions Increases or decreases in transgelin levels have reciprocal effects on tumor cell behavior, with higher expression promoting metastasis. Chronic overexpression influences steady-state levels of mRNAs for metastasis-related genes. Electronic supplementary material The online version of this article (doi:10.1186/s12885-016-2105-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Hui-Min Zhou
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, 510120, China.,Department of Gastroenterology and Hepatology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, 510120, China.,Department of Gastroenterology and Hepatology, The First Affiliated Hospital, School of Clinical Medicine of Guangdong Pharmaceutical University, Guangzhou, 510000, China
| | - Yuan-Yuan Fang
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, 510120, China.,Department of Gastroenterology and Hepatology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, 510120, China
| | - Paul M Weinberger
- Center for Biotechnology and Genomic Medicine, Georgia Regents University, Augusta, GA, 30912, USA.,GRU Cancer Center, Georgia Regents University, Augusta, GA, USA
| | | | - John K Cowell
- GRU Cancer Center, Georgia Regents University, Augusta, GA, USA
| | - Farlyn Z Hudson
- Institute of Molecular Medicine and Genetics, Georgia Regents University, Augusta, GA, USA
| | - Mingqiang Ren
- GRU Cancer Center, Georgia Regents University, Augusta, GA, USA
| | - Jeffrey R Lee
- Department of Pathology, Georgia Regents University, and Charlie Norwood Veterans Affairs Medical Center, Augusta, GA, USA
| | - Qi-Kui Chen
- Department of Gastroenterology and Hepatology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, 510120, China
| | - Hong Su
- Department of Gastroenterology and Hepatology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, 510120, China
| | - William S Dynan
- Institute of Molecular Medicine and Genetics, Georgia Regents University, Augusta, GA, USA. .,Departments of Radiation Oncology and Biochemistry, Emory University, Atlanta, GA, USA.
| | - Ying Lin
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, 510120, China. .,Department of Gastroenterology and Hepatology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, 510120, China.
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23
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Cutcutache I, Wu AY, Suzuki Y, McPherson JR, Lei Z, Deng N, Zhang S, Wong WK, Soo KC, Chan WH, Ooi LL, Welsch R, Tan P, Rozen SG. Abundant copy-number loss of CYCLOPS and STOP genes in gastric adenocarcinoma. Gastric Cancer 2016; 19. [PMID: 26205786 PMCID: PMC4824836 DOI: 10.1007/s10120-015-0514-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
BACKGROUND Gastric cancer, a leading cause of cancer death worldwide, has been little studied compared with other cancers that impose similar health burdens. Our goal is to assess genomic copy-number loss and the possible functional consequences and therapeutic implications thereof across a large series of gastric adenocarcinomas. METHODS We used high-density single-nucleotide polymorphism microarrays to determine patterns of copy-number loss and allelic imbalance in 74 gastric adenocarcinomas. We investigated whether suppressor of tumorigenesis and/or proliferation (STOP) genes are associated with genomic copy-number loss. We also analyzed the extent to which copy-number loss affects Copy-number alterations Yielding Cancer Liabilities Owing to Partial losS (CYCLOPS) genes-genes that may be attractive targets for therapeutic inhibition when partially deleted. RESULTS The proportion of the genome subject to copy-number loss varies considerably from tumor to tumor, with a median of 5.5 %, and a mean of 12 % (range 0-58.5 %). On average, 91 STOP genes were subject to copy-number loss per tumor (median 35, range 0-452), and STOP genes tended to have lower copy-number compared with the rest of the genes. Furthermore, on average, 1.6 CYCLOPS genes per tumor were both subject to copy-number loss and downregulated, and 51.4 % of the tumors had at least one such gene. CONCLUSIONS The enrichment of STOP genes in regions of copy-number loss indicates that their deletion may contribute to gastric carcinogenesis. Furthermore, the presence of several deleted and downregulated CYCLOPS genes in some tumors suggests potential therapeutic targets in these tumors.
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Affiliation(s)
- Ioana Cutcutache
- />Program in Cancer and Stem Cell Biology, Duke-NUS Graduate Medical School, Singapore, Singapore
- />Centre for Computational Biology, Duke-NUS Graduate Medical School, Singapore, Singapore
| | - Alice Yingting Wu
- />Program in Cancer and Stem Cell Biology, Duke-NUS Graduate Medical School, Singapore, Singapore
- />Centre for Computational Biology, Duke-NUS Graduate Medical School, Singapore, Singapore
- />Computation and Systems Biology, Singapore-MIT Alliance, Singapore, Singapore
| | - Yuka Suzuki
- />Program in Cancer and Stem Cell Biology, Duke-NUS Graduate Medical School, Singapore, Singapore
- />Centre for Computational Biology, Duke-NUS Graduate Medical School, Singapore, Singapore
| | - John Richard McPherson
- />Program in Cancer and Stem Cell Biology, Duke-NUS Graduate Medical School, Singapore, Singapore
- />Centre for Computational Biology, Duke-NUS Graduate Medical School, Singapore, Singapore
| | - Zhengdeng Lei
- />Program in Cancer and Stem Cell Biology, Duke-NUS Graduate Medical School, Singapore, Singapore
- />Centre for Computational Biology, Duke-NUS Graduate Medical School, Singapore, Singapore
| | - Niantao Deng
- />Program in Cancer and Stem Cell Biology, Duke-NUS Graduate Medical School, Singapore, Singapore
- />NUS Graduate School for Integrative Science and Engineering, National University of Singapore, Singapore, Singapore
| | - Shenli Zhang
- />Program in Cancer and Stem Cell Biology, Duke-NUS Graduate Medical School, Singapore, Singapore
| | - Wai Keong Wong
- />Department of General Surgery, Singapore General Hospital, Singapore, Singapore
| | - Khee Chee Soo
- />Department of General Surgery, Singapore General Hospital, Singapore, Singapore
- />Division of Surgical Oncology, National Cancer Centre Singapore, Singapore, Singapore
| | - Weng Hoong Chan
- />Department of General Surgery, Singapore General Hospital, Singapore, Singapore
| | - London Lucien Ooi
- />Department of General Surgery, Singapore General Hospital, Singapore, Singapore
- />Division of Surgical Oncology, National Cancer Centre Singapore, Singapore, Singapore
| | - Roy Welsch
- />Computation and Systems Biology, Singapore-MIT Alliance, Singapore, Singapore
- />Engineering Systems Division and Sloan School of Management, Massachusetts Institute of Technology, Cambridge, MA USA
| | - Patrick Tan
- />Program in Cancer and Stem Cell Biology, Duke-NUS Graduate Medical School, Singapore, Singapore
- />Computation and Systems Biology, Singapore-MIT Alliance, Singapore, Singapore
- />Duke-NUS Genome Biology Facility, Duke-NUS Graduate Medical School, Singapore, Singapore
- />Genome Institute of Singapore, A* STAR, Singapore, Singapore
| | - Steven G. Rozen
- />Program in Cancer and Stem Cell Biology, Duke-NUS Graduate Medical School, Singapore, Singapore
- />Centre for Computational Biology, Duke-NUS Graduate Medical School, Singapore, Singapore
- />Computation and Systems Biology, Singapore-MIT Alliance, Singapore, Singapore
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24
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Rawal RM, Joshi MN, Bhargava P, Shaikh I, Pandit AS, Patel RP, Patel S, Kothari K, Shah M, Saxena A, Bagatharia SB. Tobacco habituated and non-habituated subjects exhibit different mutational spectrums in head and neck squamous cell carcinoma. 3 Biotech 2015; 5:685-696. [PMID: 28324520 PMCID: PMC4569615 DOI: 10.1007/s13205-014-0267-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Accepted: 11/15/2014] [Indexed: 12/28/2022] Open
Abstract
Head and neck squamous cell carcinoma (HNSCC) is the sixth most common non-skin cancer in the world. Tobacco chewing is implicated with most of the cases of HNSCC but this type of cancer is increasing in non-tobacco chewers as well. This study was instigated to provide comprehensive variant and gene-level data in HNSCC subjects of the Indian population and fill the gap in the literature on comparative assessment of gene mutations in cancer subjects with a habit of tobacco and those without any habit using targeted amplicon sequencing. We performed targeted Amplicon sequencing of 409 tumor suppressor genes and oncogenes, frequently mutated across many cancer types, including head and neck. DNA from primary tumor tissues and matched blood was analyzed for HNSCC patients with a habit of tobacco and those without any habit. PDE4DIP, SYNE1, and NOTCH1 emerged as the highly mutated genes in HNSCC. A total of 39 candidate causal variants in 22 unique cancer driver genes were identified in non-habitual (WoH) and habitual (WH) subjects. Comparison of genes from both the subjects, showed seven unique cancer driver genes (KIT, ATM, RNF213, GATA2, DST, RET, CYP2C19) in WoH, while WH showed five (IL7R, PKHD1, MLL3, PTPRD, MAPK8) and 10 genes (SETD2, ATR, CDKN2A, NCOA4, TP53, SYNE1, KAT6B, THBS1, PTPRT, and FGFR3) were common to both subjects. In addition to this NOTCH1, NOTCH2, and NOTCH4 gene were found to be mutated only in habitual subjects. These findings strongly support a causal role for tobacco, acting via PI3K and MAPK pathway inhibition and stimulation of various genes leading to oncogenic transformations in case of tobacco chewers. In case of non-tobacco chewers it appears that mutations in the pathway affecting the squamous epithelial lineage and DNA repair genes lead to HNSCC. Somatic mutation in CYP2C19 gene in the non-habitual subjects suggests that this gene may have a tobacco independent role in development and progression of HNSCC. In addition to sharing high mutation rate, NOTCH gene family was found to be mutated only in habitual sample. Further, presence of mutated genes not earlier reported to be involved in HNSCC, suggest that the Indian sub-continent may have different sets of genes, as compared to other parts of the world, involved in the development and progression of HNSCC.
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Affiliation(s)
- Rakesh M Rawal
- Gujarat Cancer and Research Institute, Gujarat Cancer Society, Civil Hospital Campus, Asarwa, Ahmedabad, 380 016, Gujarat, India
| | - Madhvi N Joshi
- Gujarat State Biotechnology Mission, Department of Science and Technology, Government of Gujarat, 11th Block, 9th Floor, Udyog Bhavan, Gandhinagar, 382 011, Gujarat, India
| | - Poonam Bhargava
- Gujarat State Biotechnology Mission, Department of Science and Technology, Government of Gujarat, 11th Block, 9th Floor, Udyog Bhavan, Gandhinagar, 382 011, Gujarat, India
| | - Inayat Shaikh
- Gujarat State Biotechnology Mission, Department of Science and Technology, Government of Gujarat, 11th Block, 9th Floor, Udyog Bhavan, Gandhinagar, 382 011, Gujarat, India
| | - Aanal S Pandit
- Gujarat State Biotechnology Mission, Department of Science and Technology, Government of Gujarat, 11th Block, 9th Floor, Udyog Bhavan, Gandhinagar, 382 011, Gujarat, India
| | - Riddhi P Patel
- Gujarat State Biotechnology Mission, Department of Science and Technology, Government of Gujarat, 11th Block, 9th Floor, Udyog Bhavan, Gandhinagar, 382 011, Gujarat, India
| | - Shanaya Patel
- Gujarat Cancer and Research Institute, Gujarat Cancer Society, Civil Hospital Campus, Asarwa, Ahmedabad, 380 016, Gujarat, India
| | - Kiran Kothari
- Gujarat Cancer and Research Institute, Gujarat Cancer Society, Civil Hospital Campus, Asarwa, Ahmedabad, 380 016, Gujarat, India
| | - Manoj Shah
- Gujarat Cancer and Research Institute, Gujarat Cancer Society, Civil Hospital Campus, Asarwa, Ahmedabad, 380 016, Gujarat, India
| | - Akshay Saxena
- Gujarat State Biotechnology Mission, Department of Science and Technology, Government of Gujarat, 11th Block, 9th Floor, Udyog Bhavan, Gandhinagar, 382 011, Gujarat, India
| | - Snehal B Bagatharia
- Gujarat State Biotechnology Mission, Department of Science and Technology, Government of Gujarat, 11th Block, 9th Floor, Udyog Bhavan, Gandhinagar, 382 011, Gujarat, India.
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25
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Peyser ND, Du Y, Li H, Lui V, Xiao X, Chan TA, Grandis JR. Loss-of-Function PTPRD Mutations Lead to Increased STAT3 Activation and Sensitivity to STAT3 Inhibition in Head and Neck Cancer. PLoS One 2015; 10:e0135750. [PMID: 26267899 PMCID: PMC4534317 DOI: 10.1371/journal.pone.0135750] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2015] [Accepted: 07/25/2015] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Protein tyrosine phosphatase receptor type D (PTPRD) is a putative tumor suppressor in several cancers including head and neck squamous cell carcinoma (HNSCC). STAT3 is a frequently hyperactivated oncogene in HNSCC. As STAT3 is a direct substrate of PTPRD, we sought to determine the genetic or epigenetic alterations of PTPRD that contribute to overactive STAT3 in HNSCC. METHODS We analyzed data from The Cancer Genome Atlas (TCGA) and our previous whole-exome sequencing study and summarized the mutation, methylation, and copy number status of PTPRD in HNSCC and other cancers. In vitro studies involved standard transfection and MTT protocols, as well as methylation-specific PCR. RESULTS Our findings indicate that PTPRD mutation, rather than methylation or copy number alteration, is the primary mechanism by which PTPRD function is lost in HNSCC. We demonstrate that overexpression of wild-type PTPRD in HNSCC cells significantly inhibits growth and STAT3 activation while PTPRD mutants do not, suggesting that mutation may lead to loss of function and subsequent hyper-phosphorylation of PTPRD substrates, especially STAT3. Importantly, we determined that HNSCC cells harboring an endogenous PTPRD mutation are more sensitive to STAT3 blockade than PTPRD wild-type cells. We additionally found that PTPRD mRNA expression does not correlate with pSTAT3 expression, suggesting that alterations that manifest through altered mRNA expression, including hypermethylation and gene copy number alterations, do not significantly contribute to STAT3 overactivation in HNSCC. CONCLUSION PTPRD mutation, but not methylation or copy number loss, may serve as a predictive biomarker of sensitivity to STAT3 inhibitors in HNSCC.
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Affiliation(s)
- Noah D. Peyser
- Department of Otolaryngology, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States of America, 15213
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States of America, 15213
| | - Yu Du
- Department of Otolaryngology, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States of America, 15213
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States of America, 15213
- School of Medicine, Tsinghua University, Beijing, China, 100084
| | - Hua Li
- Department of Otolaryngology, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States of America, 15213
| | - Vivian Lui
- Pharmacogenomics and Precision Therapeutics Laboratory, Department of Pharmacology and Pharmacy, The University of Hong Kong, Hong Kong SAR, China
- Department of Biochemistry, The University of Hong Kong, Hong Kong SAR, China
| | - Xiao Xiao
- Department of Otolaryngology, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States of America, 15213
| | - Timothy A. Chan
- Human Oncology and Pathogenesis Program and Department of Radiation Oncology, Memorial Sloan-Kettering Cancer Center, 1275 York Avenue, New York, NY, United States of America, 10065
| | - Jennifer R. Grandis
- Department of Otolaryngology, University of California San Francisco, San Francisco, CA, United States of America, 94143
- * E-mail:
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26
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Chen C, Zhang Y, Loomis MM, Upton MP, Lohavanichbutr P, Houck JR, Doody DR, Mendez E, Futran N, Schwartz SM, Wang P. Genome-Wide Loss of Heterozygosity and DNA Copy Number Aberration in HPV-Negative Oral Squamous Cell Carcinoma and Their Associations with Disease-Specific Survival. PLoS One 2015; 10:e0135074. [PMID: 26247464 PMCID: PMC4527746 DOI: 10.1371/journal.pone.0135074] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2014] [Accepted: 07/17/2015] [Indexed: 01/15/2023] Open
Abstract
Oral squamous cell cancer of the oral cavity and oropharynx (OSCC) is associated with high case-fatality. For reasons that are largely unknown, patients with the same clinical and pathologic staging have heterogeneous response to treatment and different probability of recurrence and survival, with patients with Human Papillomavirus (HPV)-positive oropharyngeal tumors having the most favorable survival. To gain insight into the complexity of OSCC and to identify potential chromosomal changes that may be associated with OSCC mortality, we used Affymtrix 6.0 SNP arrays to examine paired DNA from peripheral blood and tumor cell populations isolated by laser capture microdissection to assess genome-wide loss of heterozygosity (LOH) and DNA copy number aberration (CNA) and their associations with risk factors, tumor characteristics, and oral cancer-specific mortality among 75 patients with HPV-negative OSCC. We found a highly heterogeneous and complex genomic landscape of HPV-negative tumors, and identified regions in 4q, 8p, 9p and 11q that seem to play an important role in oral cancer biology and survival from this disease. If confirmed, these findings could assist in designing personalized treatment or in the creation of models to predict survival in patients with HPV-negative OSCC.
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Affiliation(s)
- Chu Chen
- Program in Epidemiology, Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
- Department of Otolaryngology–Head and Neck Surgery, University of Washington, Seattle, Washington, United States of America
- Department of Epidemiology, University of Washington, Seattle, Washington, United States of America
- * E-mail:
| | - Yuzheng Zhang
- Program in Biostatistics and Biomathematics, Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Melissa M. Loomis
- Program in Epidemiology, Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Melissa P. Upton
- Department of Pathology, University of Washington, Seattle, Washington, United States of America
| | - Pawadee Lohavanichbutr
- Program in Epidemiology, Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - John R. Houck
- Program in Epidemiology, Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - David R. Doody
- Program in Epidemiology, Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Eduardo Mendez
- Program in Epidemiology, Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
- Department of Otolaryngology–Head and Neck Surgery, University of Washington, Seattle, Washington, United States of America
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Neal Futran
- Department of Otolaryngology–Head and Neck Surgery, University of Washington, Seattle, Washington, United States of America
| | - Stephen M. Schwartz
- Program in Epidemiology, Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
- Department of Epidemiology, University of Washington, Seattle, Washington, United States of America
| | - Pei Wang
- Program in Biostatistics and Biomathematics, Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
- Department of Genetics and Genomics Sciences, Mt. Sinai School of Medicine, New York, New York, United States of America
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Ortiz B, White JR, Wu WH, Chan TA. Deletion of Ptprd and Cdkn2a cooperate to accelerate tumorigenesis. Oncotarget 2015; 5:6976-82. [PMID: 25138050 PMCID: PMC4196177 DOI: 10.18632/oncotarget.2106] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
PTPRD encodes the protein tyrosine phosphatase receptor type D and is frequently inactivated across many human cancers. Despite its frequent inactivation, it is unknown whether loss of PTPRD promotes tumorigenesis in vivo. PTPRD is located on chromosome 9p, as is CDKN2A, and the two loci are frequently deleted together. Here, we show that co-deletion of Ptprd and Cdkn2a cooperate to accelerate tumorigenesis. Interestingly, heterozygous loss of Ptprd was sufficient to promote tumorigenesis in our model, suggesting that Ptprd may be a haploinsufficient tumor suppressor. The loss of Ptprd resulted in changes to the tumor spectrum in mice and increased the frequency of lymphomas. In total, we reveal that Ptprd is a tumor suppressor that can promote tumorigenesis in concert with Cdkn2a loss.
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Affiliation(s)
- Berenice Ortiz
- Gerstner Sloan-Kettering Graduate School, Memorial Sloan-Kettering Cancer Center, New York, NY, USA; Human Oncology and Pathogenesis Program, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - Julie R White
- The Tri-Institutional Laboratory of Comparative Pathology, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - Wei H Wu
- Human Oncology and Pathogenesis Program, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - Timothy A Chan
- Human Oncology and Pathogenesis Program, Memorial Sloan-Kettering Cancer Center, New York, NY, USA; Dept. of Radiation Oncology, Memorial Sloan-Kettering Cancer Center, New York, New York, USA; Brain Tumor Center, Memorial Sloan-Kettering Cancer Center, New York, New York, USA
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28
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Chen J, Zhang C, Xu X, Zhu X, Dai D. Downregulation of A disintegrin and metallopeptidase with thrombospondin motif type 1 by DNA hypermethylation in human gastric cancer. Mol Med Rep 2015; 12:2487-94. [PMID: 25936341 PMCID: PMC4464468 DOI: 10.3892/mmr.2015.3667] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2014] [Accepted: 03/23/2015] [Indexed: 11/06/2022] Open
Abstract
A disintegrin and metallopeptidase with thrombospondin motif type 1 (ADAMTS1) is a metalloproteinase with antiangiogenic activity. It was previously observed that the mRNA and protein levels of ADAMTS1 are downregulated in primary gastric tumors. The aim of the present study was to examine whether the reduction in the expression of ADAMTS1 is due to aberrant methylation of the gene in primary gastric tumor tissues and gastric cancer cell lines. In addition, the association between ADAMTS1 methylation and clinicopathological features in were investigated in patients with primary gastric cancer. The results revealed that the frequency of ADAMTS1 methylation in primary gastric tumor tissues was significantly higher, compared with the corresponding normal gastric tissues. The relative mRNA expression levels of ADAMTS1 were significantly lower in the methylated primary gastric tumor tissues, compared with the unmethylated primary gastric tumor tissuess. A significant association was observed between the ADAMTS1 methylation status and the depth of tumor invasion and tumor, node, metastasis stage in primary gastric cancer. The mRNA expression of ADAMTS1 was significantly lower in 60% (3 of 5) of the gastric cancer cell lines. The relative mRNA expression levels of ADAMTS1 were significantly lower in the methylated gastric cancer cell lines, compared with the unmethylated gastric cancer cell lines. Furthermore, the expression of ADAMTS1 was significantly restored following treatment with the 5-Aza-2′-deoxycytidine demethylating agent in the MGC-803, HGC-27 and AGS gastric cancer cell lines, and the demethylation of the MGC-803 cell line inhibited cell invasion. Together, these results suggested for the first time, to the best of our knowledge, ADAMTS1 as a novel antitumor protease, and this function was lost following epigenetic silencing in the gastric cancer cells and gastric tumor tissues. Therefore, the aberrant methylation of ADAMTS1 may be involved in the development and progression of gastric cancer.
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Affiliation(s)
- Jing Chen
- Department of Gastrointestinal Surgery, The Fourth Affiliated Hospital of China Medical University, Shenyang, Liaoning 110032, P.R. China
| | - Chundong Zhang
- Department of Gastrointestinal Surgery, The Fourth Affiliated Hospital of China Medical University, Shenyang, Liaoning 110032, P.R. China
| | - Xiaoyang Xu
- Department of Gastrointestinal Surgery, The Fourth Affiliated Hospital of China Medical University, Shenyang, Liaoning 110032, P.R. China
| | - Xinjiang Zhu
- Department of Gastrointestinal Surgery, The Fourth Affiliated Hospital of China Medical University, Shenyang, Liaoning 110032, P.R. China
| | - Dongqiu Dai
- Department of Gastrointestinal Surgery, The Fourth Affiliated Hospital of China Medical University, Shenyang, Liaoning 110032, P.R. China
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29
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Bian C, Li Z, Xu Y, Wang J, Xu L, Shen H. Clinical outcome and expression of mutant P53, P16, and Smad4 in lung adenocarcinoma: a prospective study. World J Surg Oncol 2015; 13:128. [PMID: 25890228 PMCID: PMC4415338 DOI: 10.1186/s12957-015-0502-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2014] [Accepted: 02/09/2015] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Whole-exome sequencing has shown that lung adenocarcinoma (LAC) can be driven by mutant genes, including TP53, P16, and Smad4. The aim of this study was to clarify protein alterations of P53, P16, and Smad4 and to explore their correlations between the protein alterations and clinical outcome. METHODS We investigated associations among P53 mutant (P53(Mut)) expression, and P16 and Smad4 loss-of-expression, with clinical outcome in 120 LAC patients who underwent curative resection, using immunohistochemical (IHC) methods. RESULTS Of the 120 patients, 76 (63.3%) expressed P53(Mut) protein, whereas 54 (45.0%) loss of P16 expressed and 75 (62.5%) loss of Smad4 expressed. P53(Mut) expression was associated with tumor size (P = 0.041) and pathological stage (P = 0.025). Loss of P16 expression was associated with lymph node metastasis (P = 0.001) and pathological stage (P < 0.001). Loss of Smad4 expression was associated with tumor size (P = 0.033), lymph node metastasis (P = 0.014), pathological stage (P = 0.017), and tumor differentiation (P = 0.022). Kaplan-Meier survival analysis showed that tumor size (P = 0.031), lymph node metastasis (P < 0.001), pathological stage (P < 0.001), P53(Mut) protein expression (P = 0.038), and loss of p16 or Smad4 expression (P < 0.001) were significantly associated with shorter overall survival(OS), whereas multivariate analysis indicated that lymph node metastasis (P = 0.014) and loss of p16 or Smad4 expression (P < 0.001) were independent prognostic factors. Analysis of protein combinations showed patients with more alterations had poorer survival (P < 0.001). Spearman correlation analysis showed that loss of Smad4 expression inversely correlated with expression of P53(Mut) (r = (-)0.196, P = 0.032) and positively with lost P16 expression (r =0.182, P = 0.047). CONCLUSIONS The findings indicate that IHC status of P53(Mut), P16, and Smad4 may predict patient outcomes in LAC.
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Affiliation(s)
- Chunan Bian
- Department of Thoracic Surgery, Nanjing Medical University-Affiliated Cancer Hospital, Nanjing, 210009, China. .,Nanjing Jiangbei Peoples' Hospital, Nanjing, 210048, China.
| | - Zhongyou Li
- Jiangsu Key Laboratory of Molecular and Translational Cancer Research, Nanjing, 210009, China.
| | - Youtao Xu
- Department of Thoracic Surgery, Nanjing Medical University-Affiliated Cancer Hospital, Nanjing, 210009, China.
| | - Jie Wang
- Jiangsu Key Laboratory of Molecular and Translational Cancer Research, Nanjing, 210009, China.
| | - Lin Xu
- Department of Thoracic Surgery, Nanjing Medical University-Affiliated Cancer Hospital, Nanjing, 210009, China.
| | - Hongbing Shen
- The Public Health College of Nanjing Medical University, Nanjing, 210029, China.
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Yan J, Kim S, Nho K, Chen R, Risacher SL, Moore JH, Saykin AJ, Shen L. Hippocampal transcriptome-guided genetic analysis of correlated episodic memory phenotypes in Alzheimer's disease. Front Genet 2015; 6:117. [PMID: 25859259 PMCID: PMC4374536 DOI: 10.3389/fgene.2015.00117] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2014] [Accepted: 03/09/2015] [Indexed: 01/18/2023] Open
Abstract
As the most common type of dementia, Alzheimer's disease (AD) is a neurodegenerative disorder initially manifested by impaired memory performances. While the diagnosis information indicates a dichotomous status of a patient, memory scores have the potential to capture the continuous nature of the disease progression and may provide more insights into the underlying mechanism. In this work, we performed a targeted genetic study of memory scores on an AD cohort to identify the associations between a set of genes highly expressed in the hippocampal region and seven cognitive scores related to episodic memory. Both main effects and interaction effects of the targeted genetic markers on these correlated memory scores were examined. In addition to well-known AD genetic markers APOE and TOMM40, our analysis identified a new risk gene NAV2 through the gene-level main effect analysis. NAV2 was found to be significantly and consistently associated with all seven episodic memory scores. Genetic interaction analysis also yielded a few promising hits warranting further investigation, especially for the RAVLT list B Score.
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Affiliation(s)
- Jingwen Yan
- BioHealth, Indiana University School of Informatics and Computing Indianapolis, IN, USA ; Center for Neuroimaging, Department of Radiology and Imaging Sciences, Indiana University School of Medicine Indianapolis, IN, USA
| | - Sungeun Kim
- Center for Neuroimaging, Department of Radiology and Imaging Sciences, Indiana University School of Medicine Indianapolis, IN, USA ; Indiana Alzheimer Disease Center, Indiana University School of Medicine Indianapolis, IN, USA
| | - Kwangsik Nho
- Center for Neuroimaging, Department of Radiology and Imaging Sciences, Indiana University School of Medicine Indianapolis, IN, USA ; Indiana Alzheimer Disease Center, Indiana University School of Medicine Indianapolis, IN, USA
| | - Rui Chen
- Center for Neuroimaging, Department of Radiology and Imaging Sciences, Indiana University School of Medicine Indianapolis, IN, USA ; Computer Science, Dartmouth College Hanover, NH, USA
| | - Shannon L Risacher
- Center for Neuroimaging, Department of Radiology and Imaging Sciences, Indiana University School of Medicine Indianapolis, IN, USA ; Indiana Alzheimer Disease Center, Indiana University School of Medicine Indianapolis, IN, USA
| | - Jason H Moore
- Genetics, Community and Family Medicine, Geisel School of Medicine at Dartmouth Lebanon, NH, USA
| | - Andrew J Saykin
- Center for Neuroimaging, Department of Radiology and Imaging Sciences, Indiana University School of Medicine Indianapolis, IN, USA ; Indiana Alzheimer Disease Center, Indiana University School of Medicine Indianapolis, IN, USA ; Medical and Molecular Genetics, Indiana University School of Medicine Indianapolis, IN, USA
| | - Li Shen
- BioHealth, Indiana University School of Informatics and Computing Indianapolis, IN, USA ; Center for Neuroimaging, Department of Radiology and Imaging Sciences, Indiana University School of Medicine Indianapolis, IN, USA ; Indiana Alzheimer Disease Center, Indiana University School of Medicine Indianapolis, IN, USA ; Center for Computational Biology and Bioinformatics, Indiana University School of Medicine Indianapolis, IN, USA
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Wang D, Wang L, Zhou J, Pan J, Qian W, Fu J, Zhang G, Zhu Y, Liu C, Wang C, Jin Z, He Z, Wu J, Shi B. Reduced expression of PTPRD correlates with poor prognosis in gastric adenocarcinoma. PLoS One 2014; 9:e113754. [PMID: 25412184 PMCID: PMC4239117 DOI: 10.1371/journal.pone.0113754] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2014] [Accepted: 10/28/2014] [Indexed: 11/18/2022] Open
Abstract
Background PTPRD, encoding protein tyrosine phosphatases receptor type D, is located at chromosome 9p23–24.1, a loci frequently lost in many types of tumors. Recently, PTPRD has been proposed to function as a tumor suppressor gene. The current study aimed to investigate PTPRD expression and its prognostic significance in primary gastric adenocarcinoma. Methods and Results Quantitative real time reverse transcription PCR (qRT-PCR) and western blotting were used to examine PTPRD expression in paired gastric tumourous and paracancerous tissues. Compared with the matched normal gastric mucosa tissues, both the mRNA (P = 0.0138) and protein (P = 0.0093) expression of PTPRD in fresh surgical specimens were significantly reduced. Clinicopathological and prognostic roles of PTPRD in gastric adenocarcinoma were investigated using immunohistochemistry with 513 paraffin-embedded gastric adenocarcinoma tissue blocks. Statistical analysis revealed that reduced PTPRD expression was significantly associated with T stage (P = 0.004), TNM stage (P<0.001) and tumor size (P = 0.003). Furthermore, Kaplan-Meier survival analysis revealed that low expression of PTPRD significantly correlated with poor survival of gastric cancer patients (P<0.001). Cox regression analysis confirmed PTPRD expression as independent predictor of the overall survival of gastric cancer patients. The MTT assay determined the effects of PTPRD on cell proliferation of MGC803 and GES1 cell lines. Restoring PTPRD expression in MGC803 cells significantly inhibited their growth rate. Silencing PTPRD expression by siRNA treatment in GES1 significantly enhanced cell proliferation compared with mock siRNA treatment. Methylation analysis of PTPRD promoter CpG island in 3 primary GC samples showed one case with partial methylation. Conclusions These results indicated that PTPRD is a candidate tumour suppressor in gastric cancer. Thus, PTPRD may play an important role in gastric tumorigenesis and serve as a valuable prognostic marker of gastric adenocarcinoma.
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Affiliation(s)
- Dandan Wang
- Key Laboratory for Biotech-Drugs Ministry of Health, Key Laboratory for Modern Medicine and Technology of Shandong Province, Key Laboratory for Rare & Uncommon Diseases of Shandong Province, Key Laboratory for Virology of Shandong Province, Back and Neck Pain Hospital of Shandong Academy of Medical Sciences, Shandong Medicinal Biotechnology Centre, Shandong Academy of Medical Sciences, Jinan, People's Republic of China
| | - Leilei Wang
- Biology Institute of Shandong Academy of Sciences, Jinan, People's Republic of China
| | - Jun Zhou
- Departments of Oncology, Provincial Hospital Affiliated to Shandong University, Jinan, People's Republic of China
| | - Jihong Pan
- Key Laboratory for Biotech-Drugs Ministry of Health, Key Laboratory for Modern Medicine and Technology of Shandong Province, Key Laboratory for Rare & Uncommon Diseases of Shandong Province, Key Laboratory for Virology of Shandong Province, Back and Neck Pain Hospital of Shandong Academy of Medical Sciences, Shandong Medicinal Biotechnology Centre, Shandong Academy of Medical Sciences, Jinan, People's Republic of China
| | - Wei Qian
- The General Hospital of Jinan Military Command, Jinan, People's Republic of China
| | - Jiafang Fu
- Key Laboratory for Biotech-Drugs Ministry of Health, Key Laboratory for Modern Medicine and Technology of Shandong Province, Key Laboratory for Rare & Uncommon Diseases of Shandong Province, Key Laboratory for Virology of Shandong Province, Back and Neck Pain Hospital of Shandong Academy of Medical Sciences, Shandong Medicinal Biotechnology Centre, Shandong Academy of Medical Sciences, Jinan, People's Republic of China
| | - Genglin Zhang
- Key Laboratory for Biotech-Drugs Ministry of Health, Key Laboratory for Modern Medicine and Technology of Shandong Province, Key Laboratory for Rare & Uncommon Diseases of Shandong Province, Key Laboratory for Virology of Shandong Province, Back and Neck Pain Hospital of Shandong Academy of Medical Sciences, Shandong Medicinal Biotechnology Centre, Shandong Academy of Medical Sciences, Jinan, People's Republic of China
| | - Youming Zhu
- Key Laboratory for Biotech-Drugs Ministry of Health, Key Laboratory for Modern Medicine and Technology of Shandong Province, Key Laboratory for Rare & Uncommon Diseases of Shandong Province, Key Laboratory for Virology of Shandong Province, Back and Neck Pain Hospital of Shandong Academy of Medical Sciences, Shandong Medicinal Biotechnology Centre, Shandong Academy of Medical Sciences, Jinan, People's Republic of China
| | - Chunshan Liu
- Key Laboratory for Biotech-Drugs Ministry of Health, Key Laboratory for Modern Medicine and Technology of Shandong Province, Key Laboratory for Rare & Uncommon Diseases of Shandong Province, Key Laboratory for Virology of Shandong Province, Back and Neck Pain Hospital of Shandong Academy of Medical Sciences, Shandong Medicinal Biotechnology Centre, Shandong Academy of Medical Sciences, Jinan, People's Republic of China
| | - Chunliang Wang
- Key Laboratory for Biotech-Drugs Ministry of Health, Key Laboratory for Modern Medicine and Technology of Shandong Province, Key Laboratory for Rare & Uncommon Diseases of Shandong Province, Key Laboratory for Virology of Shandong Province, Back and Neck Pain Hospital of Shandong Academy of Medical Sciences, Shandong Medicinal Biotechnology Centre, Shandong Academy of Medical Sciences, Jinan, People's Republic of China
| | - Zongkun Jin
- Key Laboratory for Biotech-Drugs Ministry of Health, Key Laboratory for Modern Medicine and Technology of Shandong Province, Key Laboratory for Rare & Uncommon Diseases of Shandong Province, Key Laboratory for Virology of Shandong Province, Back and Neck Pain Hospital of Shandong Academy of Medical Sciences, Shandong Medicinal Biotechnology Centre, Shandong Academy of Medical Sciences, Jinan, People's Republic of China
| | - Ziqing He
- Key Laboratory for Biotech-Drugs Ministry of Health, Key Laboratory for Modern Medicine and Technology of Shandong Province, Key Laboratory for Rare & Uncommon Diseases of Shandong Province, Key Laboratory for Virology of Shandong Province, Back and Neck Pain Hospital of Shandong Academy of Medical Sciences, Shandong Medicinal Biotechnology Centre, Shandong Academy of Medical Sciences, Jinan, People's Republic of China
| | - Jianmei Wu
- Key Laboratory for Biotech-Drugs Ministry of Health, Key Laboratory for Modern Medicine and Technology of Shandong Province, Key Laboratory for Rare & Uncommon Diseases of Shandong Province, Key Laboratory for Virology of Shandong Province, Back and Neck Pain Hospital of Shandong Academy of Medical Sciences, Shandong Medicinal Biotechnology Centre, Shandong Academy of Medical Sciences, Jinan, People's Republic of China
- * E-mail: (BS); (JW)
| | - Bin Shi
- Key Laboratory for Biotech-Drugs Ministry of Health, Key Laboratory for Modern Medicine and Technology of Shandong Province, Key Laboratory for Rare & Uncommon Diseases of Shandong Province, Key Laboratory for Virology of Shandong Province, Back and Neck Pain Hospital of Shandong Academy of Medical Sciences, Shandong Medicinal Biotechnology Centre, Shandong Academy of Medical Sciences, Jinan, People's Republic of China
- * E-mail: (BS); (JW)
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Suzuki A, Makinoshima H, Wakaguri H, Esumi H, Sugano S, Kohno T, Tsuchihara K, Suzuki Y. Aberrant transcriptional regulations in cancers: genome, transcriptome and epigenome analysis of lung adenocarcinoma cell lines. Nucleic Acids Res 2014; 42:13557-72. [PMID: 25378332 PMCID: PMC4267666 DOI: 10.1093/nar/gku885] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Here we conducted an integrative multi-omics analysis to understand how cancers harbor various types of aberrations at the genomic, epigenomic and transcriptional levels. In order to elucidate biological relevance of the aberrations and their mutual relations, we performed whole-genome sequencing, RNA-Seq, bisulfite sequencing and ChIP-Seq of 26 lung adenocarcinoma cell lines. The collected multi-omics data allowed us to associate an average of 536 coding mutations and 13,573 mutations in promoter or enhancer regions with aberrant transcriptional regulations. We detected the 385 splice site mutations and 552 chromosomal rearrangements, representative cases of which were validated to cause aberrant transcripts. Averages of 61, 217, 3687 and 3112 mutations are located in the regulatory regions which showed differential DNA methylation, H3K4me3, H3K4me1 and H3K27ac marks, respectively. We detected distinct patterns of aberrations in transcriptional regulations depending on genes. We found that the irregular histone marks were characteristic to EGFR and CDKN1A, while a large genomic deletion and hyper-DNA methylation were most frequent for CDKN2A. We also used the multi-omics data to classify the cell lines regarding their hallmarks of carcinogenesis. Our datasets should provide a valuable foundation for biological interpretations of interlaced genomic and epigenomic aberrations.
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Affiliation(s)
- Ayako Suzuki
- Department of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
| | - Hideki Makinoshima
- Division of TR, The Exploratory Oncology Research and Clinical Trial Center, National Cancer Center, Chiba, Japan
| | - Hiroyuki Wakaguri
- Department of Computational Biology, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
| | - Hiroyasu Esumi
- Division of TR, The Exploratory Oncology Research and Clinical Trial Center, National Cancer Center, Chiba, Japan
| | - Sumio Sugano
- Department of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
| | - Takashi Kohno
- Division of Genome Biology, National Cancer Center Research Institute, Tokyo, Japan Division of TR, The Exploratory Oncology Research and Clinical Trial Center, National Cancer Center, Tokyo, Japan
| | - Katsuya Tsuchihara
- Division of TR, The Exploratory Oncology Research and Clinical Trial Center, National Cancer Center, Chiba, Japan
| | - Yutaka Suzuki
- Department of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan Department of Computational Biology, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
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Du Y, Grandis JR. Receptor-type protein tyrosine phosphatases in cancer. CHINESE JOURNAL OF CANCER 2014; 34:61-9. [PMID: 25322863 PMCID: PMC4360074 DOI: 10.5732/cjc.014.10146] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Protein tyrosine phosphatases (PTPs) play an important role in regulating cell signaling events in coordination with tyrosine kinases to control cell proliferation, apoptosis, survival, migration, and invasion. Receptor-type protein tyrosine phosphatases (PTPRs) are a subgroup of PTPs that share a transmembrane domain with resulting similarities in function and target specificity. In this review, we summarize genetic and epigenetic alterations including mutation, deletion, amplification, and promoter methylation of PTPRs in cancer and consider the consequences of PTPR alterations in different types of cancers. We also summarize recent developments using PTPRs as prognostic or predictive biomarkers and/or direct targets. Increased understanding of the role of PTPRs in cancer may provide opportunities to improve therapeutic approaches.
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Affiliation(s)
- Yu Du
- Department of Otolaryngology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA.
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Zhao S, Sedwick D, Wang Z. Genetic alterations of protein tyrosine phosphatases in human cancers. Oncogene 2014; 34:3885-94. [PMID: 25263441 PMCID: PMC4377308 DOI: 10.1038/onc.2014.326] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2014] [Revised: 08/20/2014] [Accepted: 08/21/2014] [Indexed: 12/12/2022]
Abstract
Protein tyrosine phosphatases (PTPs) are enzymes that remove phosphate from tyrosine residues in proteins. Recent whole-exome sequencing of human cancer genomes reveals that many PTPs are frequently mutated in a variety of cancers. Among these mutated PTPs, protein tyrosine phosphatase T (PTPRT) appears to be the most frequently mutated PTP in human cancers. Beside PTPN11 which functions as an oncogene in leukemia, genetic and functional studies indicate that most of mutant PTPs are tumor suppressor genes. Identification of the substrates and corresponding kinases of the mutant PTPs may provide novel therapeutic targets for cancers harboring these mutant PTPs.
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Affiliation(s)
- S Zhao
- 1] Division of Gastroenterology and Hepatology and Shanghai Institution of Digestive Disease, Shanghai Jiao-Tong University School of Medicine Renji Hospital, Shanghai, China [2] Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH, USA [3] Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH, USA
| | - D Sedwick
- 1] Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH, USA [2] Department of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Z Wang
- 1] Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH, USA [2] Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH, USA
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Walia V, Prickett TD, Kim JS, Gartner JJ, Lin JC, Zhou M, Rosenberg SA, Elble RC, Solomon DA, Waldman T, Samuels Y. Mutational and functional analysis of the tumor-suppressor PTPRD in human melanoma. Hum Mutat 2014; 35:1301-10. [PMID: 25113440 DOI: 10.1002/humu.22630] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2013] [Accepted: 07/17/2014] [Indexed: 11/09/2022]
Abstract
Protein tyrosine phosphatases (PTPs) tightly regulate tyrosine phosphorylation essential for cell growth, adhesion, migration, and survival. We performed a mutational analysis of the PTP gene family in cutaneous metastatic melanoma and identified 23 phosphatase genes harboring somatic mutations. Among these, receptor-type tyrosine-protein phosphatase delta (PTPRD) was one of the most highly mutated genes, harboring 17 somatic mutations in 79 samples, a prevalence of 21.5%. Functional evaluation of six PTPRD mutations revealed enhanced anchorage-dependent and anchorage-independent growth. Interestingly, melanoma cells expressing mutant PTPRD were significantly more migratory than cells expressing wild-type PTPRD or vector alone, indicating a novel gain-of-function associated with mutant PTPRD. To understand the molecular mechanisms of PTPRD mutations, we searched for its binding partners by converting the active PTPRD enzyme into a "substrate trap" form. Using mass spectrometry and coimmunoprecipitation, we report desmoplakin, a desmosomal protein that is implicated in cell-cell adhesion, as a novel PTPRD substrate. Further analysis showed reduced phosphatase activity of mutant PTPRD against desmoplakin. Our findings identify an essential signaling cascade that is disrupted in melanoma. Moreover, because PTPRD is also mutated in glioblastomas and adenocarcinoma of the colon and lung, our data might be applicable to a large number of human cancers.
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Affiliation(s)
- Vijay Walia
- National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland
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Chen YW, Hsiao PJ, Weng CC, Kuo KK, Kuo TL, Wu DC, Hung WC, Cheng KH. SMAD4 loss triggers the phenotypic changes of pancreatic ductal adenocarcinoma cells. BMC Cancer 2014; 14:181. [PMID: 24625091 PMCID: PMC4007528 DOI: 10.1186/1471-2407-14-181] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2013] [Accepted: 02/28/2014] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND SMAD4 is a gastrointestinal malignancy-specific tumor suppressor gene found mutated in one third of colorectal cancer specimens and half of pancreatic tumors. SMAD4 inactivation by allelic deletion or intragenic mutation mainly occurs in the late stage of human pancreatic ductal adenocarcinoma (PDAC). Various studies have proposed potential SMAD4-mediated anti-tumor effects in human malignancy; however, the relevance of SMAD4 in the PDAC molecular phenotype has not yet been fully characterized. METHODS The AsPC-1, CFPAC-1 and PANC-1 human PDAC cell lines were used. The restoration or knockdown of SMAD4 expression in PDAC cells were confirmed by western blotting, luciferase reporter and immunofluorescence assays. In vitro cell proliferation, xenograft, wound healing, quantitative reverse transcriptase-polymerase chain reaction (qRT-PCR), Western blotting, and immunohistochemistry analysis were conducted using PDAC cells in which SMAD4 was either overexpressed or knocked down. RESULTS Here, we report that re-expression of SMAD4 in SMAD4-null PDAC cells does not affect tumor cell growth in vitro or in vivo, but significantly enhances cells migration in vitro. SMAD4 restoration transcriptionally activates the TGF-β1/Nestin pathway and induces expression of several transcriptional factors. In contrast, SMAD4 loss in PDAC leads to increased expression of E-cadherin, vascular endothelial growth factor (VEGF), epidermal growth factor receptor (EGFR) and CD133. Furthermore, SMAD4 loss causes alterations to multiple kinase pathways (particularly the phosphorylated ERK/p38/Akt pathways), and increases chemoresistance in vitro. Finally, PDAC cells with intact SMAD4 are more sensitive to TGF-β1 inhibitor treatment to reduced cell migration; PDAC cells lacking SMAD4 showed decreased cell motility in response to EGFR inhibitor treatment. CONCLUSIONS This study revealed the molecular basis for SMAD4-dependent differences in PDAC with the aim of identifying the subset of patients likely to respond to therapies targeting the TGF-β or EGFR signaling pathways and of identifying potential therapeutic interventions for PDAC patients with SMAD4 defects.
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Affiliation(s)
- Yu-Wen Chen
- Institute of Biomedical Sciences, National Sun Yat-Sen University, Kaohsiung 80424, Taiwan
| | - Pi-Jung Hsiao
- Division of Endocrinology and Metabolism, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
| | - Ching-Chieh Weng
- Institute of Biomedical Sciences, National Sun Yat-Sen University, Kaohsiung 80424, Taiwan
| | - Kung-Kai Kuo
- Division of Hepatobiliary Pancreatic Surgery, Department of Surgery, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Tzu-Lei Kuo
- Institute of Biomedical Sciences, National Sun Yat-Sen University, Kaohsiung 80424, Taiwan
| | - Deng-Chyang Wu
- Division of Internal Medicine, Kaohsiung Municipal Hsiao-Kang Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan
- Division of Gastroenterology, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
| | - Wen-Chun Hung
- National Institute of Cancer Research, National Health Research Institutes, Tainan 704, Taiwan
| | - Kuang-Hung Cheng
- Institute of Biomedical Sciences, National Sun Yat-Sen University, Kaohsiung 80424, Taiwan
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Theranostic Profiling for Actionable Aberrations in Advanced High Risk Osteosarcoma with Aggressive Biology Reveals High Molecular Diversity: The Human Fingerprint Hypothesis. Oncoscience 2014; 1:167-179. [PMID: 25126591 PMCID: PMC4128257 DOI: 10.18632/oncoscience.21] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
The survival of patients with advanced osteosarcoma is poor with limited therapeutic options. There is an urgent need for new targeted therapies based on biomarkers. Recently, theranostic molecular profiling services for cancer patients by CLIA-certified commercial companies as well as in-house profiling in academic medical centers have expanded exponentially. We evaluated molecular profiles of patients with advanced osteosarcoma whose tumor tissue had been analyzed by one of the following methods: 1. 182-gene next-generation exome sequencing (Foundation Medicine, Boston, MA), 2. Immunohistochemistry (IHC)/PCR-based panel (CARIS Target Now, Irving, Tx), 3.Comparative genome hybridization (Oncopath, San Antonio, TX). 4. Single-gene PCR assays, PTEN IHC (MDACC CLIA), 5. UT Houston morphoproteomics (Houston, TX). The most common actionable aberrations occur in the PI3K/PTEN/mTOR pathway. No patterns in genomic alterations beyond the above are readily identifiable, and suggest both high molecular diversity in osteosarcoma and the need for more analyses to define distinct subgroups of osteosarcoma defined by genomic alterations. Based on our preliminary observations we hypothesize that the biology of aggressive and the metastatic phenotype osteosarcoma at the molecular level is similar to human fingerprints, in that no two tumors are identical. Further large scale analyses of osteosarcoma samples are warranted to test this hypothesis.
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Walters DM, White KM, Patel U, Davis MJ, Veluci-Marlow RM, Bhupanapadu Sunkesula SR, Bonner JC, Martin JR, Gladwell W, Kleeberger SR. Genetic susceptibility to interstitial pulmonary fibrosis in mice induced by vanadium pentoxide (V2O5). FASEB J 2013; 28:1098-112. [PMID: 24285090 DOI: 10.1096/fj.13-235044] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Interstitial lung diseases (ILDs) are characterized by injury, inflammation, and scarring of alveoli, leading to impaired function. The etiology of idiopathic forms of ILD is not understood, making them particularly difficult to study due to the lack of appropriate animal models. Consequently, few effective therapies have emerged. We developed an inbred mouse model of ILD using vanadium pentoxide (V2O5), the most common form of a transition metal found in cigarette smoke, fuel ash, mineral ores, and steel alloys. Pulmonary responses to V2O5, including dose-dependent increases in lung permeability, inflammation, collagen content, and dysfunction, were significantly greater in DBA/2J mice compared to C57BL/6J mice. Inflammatory and fibrotic responses persisted for 4 mo in DBA/2J mice, while limited responses in C57BL/6J mice resolved. We investigated the genetic basis for differential responses through genetic mapping of V2O5-induced lung collagen content in BXD recombinant inbred (RI) strains and identified significant linkage on chromosome 4 with candidate genes that associate with V2O5-induced collagen content across the RI strains. Results suggest that V2O5 may induce pulmonary fibrosis through mechanisms distinct from those in other models of pulmonary fibrosis. These findings should further advance our understanding of mechanisms involved in ILD and thereby aid in identification of new therapeutic targets.
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Affiliation(s)
- Dianne M Walters
- 1Department of Physiology, Brody School of Medicine, 6N-98, East Carolina University, 600 Moye Blvd., Greenville, NC 27834, USA.
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The transcriptional consequences of somatic amplifications, deletions, and rearrangements in a human lung squamous cell carcinoma. Neoplasia 2013; 14:1075-86. [PMID: 23226101 DOI: 10.1593/neo.121380] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2012] [Revised: 09/25/2012] [Accepted: 09/28/2012] [Indexed: 12/16/2022] Open
Abstract
Lung cancer causes more deaths, worldwide, than any other cancer. Several histologic subtypes exist. Currently, there is a dearth of targeted therapies for treating one of the main subtypes: squamous cell carcinoma (SCC). As for many cancers, lung SCC karyotypes are often highly anomalous owing to large somatic structural variants, some of which are seen repeatedly in lung SCC, indicating a potential causal association for genes therein. We chose to characterize a lung SCC genome to unprecedented detail and integrate our findings with the concurrently characterized transcriptome. We aimed to ascertain how somatic structural changes affected gene expression within the cell in ways that could confer a pathogenic phenotype. We sequenced the genomes of a lung SCC cell line (LUDLU-1) and its matched lymphocyte cell line (AGLCL) to more than 50x coverage. We also sequenced the transcriptomes of LUDLU-1 and a normal bronchial epithelium cell line (LIMM-NBE1), resulting in more than 600 million aligned reads per sample, including both coding and non-coding RNA (ncRNA), in a strand-directional manner. We also captured small RNA (<30 bp). We discovered significant, but weak, correlations between copy number and expression for protein-coding genes, antisense transcripts, long intergenic ncRNA, and microRNA (miRNA). We found that miRNA undergo the largest change in overall expression pattern between the normal bronchial epithelium and the tumor cell line. We found evidence of transcription across the novel genomic sequence created from six somatic structural variants. For each part of our integrated analysis, we highlight candidate genes that have undergone the largest expression changes.
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Ninomiya H, Kato M, Sanada M, Takeuchi K, Inamura K, Motoi N, Nagano H, Nomura K, Sakao Y, Okumura S, Mano H, Ogawa S, Ishikawa Y. Allelotypes of lung adenocarcinomas featuring ALK fusion demonstrate fewer onco- and suppressor gene changes. BMC Cancer 2013; 13:8. [PMID: 23289484 PMCID: PMC3599044 DOI: 10.1186/1471-2407-13-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2012] [Accepted: 12/18/2012] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND A subset of lung adenocarcinomas harboring an EML4-ALK fusion gene resulting in dominant oncogenic activity has emerged as a target for specific therapy. EML4-ALK fusion confers a characteristic histology and is detected more frequently in never or light smokers and younger patients. METHODS To gain insights into etiology and carcinogenic mechanisms we conducted analyses to compare allelotypes of 35 ALK fusion-positive and 95 -negative tumours using single nucleotide polymorphism (SNP) arrays and especially designed software which enabled precise global genomic profiling. RESULTS Overall aberration numbers (gains + losses) of chromosomal alterations were 8.42 and 9.56 in tumours with and without ALK fusion, respectively, the difference not being statistically significant, although patterns of gain and loss were distinct. Interestingly, among selected genomic regions, oncogene-related examples such as 1p34.3(MYCL1), 7q11.2(EGFR), 7p21.1, 8q24.21(MYC), 16p13.3, 17q12(ERBB2) and 17q25.1 showed significantly less gain. Also, changes in tumour suppressor gene-related regions, such as 9p21.3 (CDKN2A) 9p23-24.1 (PTPRD), 13q14.2 (RB1), were significantly fewer in tumours with ALK fusion. CONCLUSION Global genomic comparison with SNP arrays showed tumours with ALK fusion to have fewer alterations in oncogenes and suppressor genes despite a similar overall aberration frequency, suggesting very strong oncogenic potency of ALK activation by gene fusion.
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Affiliation(s)
- Hironori Ninomiya
- Division of Pathology, The Cancer Institute, Ariake 3-8-31, Koutou-ku, Tokyo 135-8550, Japan
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Identification of unbalanced genome copy number abnormalities in patients with multiple myeloma by single-nucleotide polymorphism genotyping microarray analysis. Int J Hematol 2012; 96:492-500. [PMID: 22972171 DOI: 10.1007/s12185-012-1171-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2012] [Revised: 08/24/2012] [Accepted: 08/27/2012] [Indexed: 10/27/2022]
Abstract
Single-nucleotide polymorphism genotyping microarray (SNP array) analysis provides detailed information on chromosomal copy number aberrations. To obtain detailed information on genomic abnormalities related to pathogenesis or prognosis of multiple myeloma (MM), we performed 250K SNP array analysis in 39 MM patients and 11 cell lines. We identified an accumulation of deletions and uniparental disomies at 22q12.1. Among the hyperdiploid MM cases, chromosomal imbalance at this locus was associated with poor prognosis. On sequencing, we also found a mutation in the seizure-related 6 homolog (mouse)-like (SEZ6L) gene located at ch.22q12.1 in an MM cell line, NOP1. We further found isolated deletions in 17 genes, five of which are known tumor suppressor genes. Of these, deletion of protein tyrosine phosphatase, receptor type D (PTPRD) was found in three samples, including two patients. Consistent with previous reports, non-hyperdiploid MM, deletion of 13q (del13q) and gain of 1q in non-hyperdiploid MMs were predictive of poor prognosis (p = 0.039, p = 0.049, and p = 0.013, respectively). However, our analysis revealed that unless accompanied by gain of 1q, the prognosis of non-hyperdiploid MM was as good as that of hyperdiploid MM. Thus, SNP array analysis provides significant information useful to understanding the pathogenesis and prognosis of MM.
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Schmitz M, Driesch C, Jansen L, Runnebaum IB, Dürst M. Non-random integration of the HPV genome in cervical cancer. PLoS One 2012; 7:e39632. [PMID: 22761851 PMCID: PMC3384597 DOI: 10.1371/journal.pone.0039632] [Citation(s) in RCA: 100] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2012] [Accepted: 05/24/2012] [Indexed: 12/19/2022] Open
Abstract
HPV DNA integration into the host genome is a characteristic but not an exclusive step during cervical carcinogenesis. It is still a matter of debate whether viral integration contributes to the transformation process beyond ensuring the constitutive expression of the viral oncogenes. There is mounting evidence for a non-random distribution of integration loci and the direct involvement of cellular cancer-related genes. In this study we addressed this topic by extending the existing data set by an additional 47 HPV16 and HPV18 positive cervical carcinoma. We provide supportive evidence for previously defined integration hotspots and have revealed another cluster of integration sites within the cytogenetic band 3q28. Moreover, in the vicinity of these hotspots numerous microRNAs (miRNAs) are located and may be influenced by the integrated HPV DNA. By compiling our data and published reports 9 genes could be identified which were affected by HPV integration at least twice in independent tumors. In some tumors the viral-cellular fusion transcripts were even identical with respect to the viral donor and cellular acceptor sites used. However, the exact integration sites are likely to differ since none of the integration sites analysed thus far have shown more than a few nucleotides of homology between viral and host sequences. Therefore, DNA recombination involving large stretches of homology at the integration site can be ruled out. It is however intriguing that by sequence alignment several regions of the HPV16 genome were found to have highly homologous stretches of up to 50 nucleotides to the aforementioned genes and the integration hotspots. One common region of homologies with cellular sequences is between the viral gene E5 and L2 (nucleotides positions 4100 to 4240). We speculate that this and other regions of homology are involved in the integration process. Our observations suggest that targeted disruption, possibly also of critical cellular genes, by HPV integration remains an issue to be fully resolved.
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Affiliation(s)
- Martina Schmitz
- Klinik für Frauenheilkunde und Geburtshilfe, Universitätsklinikum Jena, Jena, Germany
| | - Corina Driesch
- Klinik für Frauenheilkunde und Geburtshilfe, Universitätsklinikum Jena, Jena, Germany
| | - Lars Jansen
- Klinik für Frauenheilkunde und Geburtshilfe, Universitätsklinikum Jena, Jena, Germany
| | - Ingo B. Runnebaum
- Klinik für Frauenheilkunde und Geburtshilfe, Universitätsklinikum Jena, Jena, Germany
| | - Matthias Dürst
- Klinik für Frauenheilkunde und Geburtshilfe, Universitätsklinikum Jena, Jena, Germany
- * E-mail:
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Meehan M, Parthasarathi L, Moran N, Jefferies CA, Foley N, Lazzari E, Murphy D, Ryan J, Ortiz B, Fabius AWM, Chan TA, Stallings RL. Protein tyrosine phosphatase receptor delta acts as a neuroblastoma tumor suppressor by destabilizing the aurora kinase A oncogene. Mol Cancer 2012; 11:6. [PMID: 22305495 PMCID: PMC3395855 DOI: 10.1186/1476-4598-11-6] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2011] [Accepted: 02/05/2012] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Protein tyrosine phosphatase receptor delta (PTPRD) is a member of a large family of protein tyrosine phosphatases which negatively regulate tyrosine phosphorylation. Neuroblastoma is a major childhood cancer arising from precursor cells of the sympathetic nervous system which is known to acquire deletions and alterations in the expression patterns of PTPRD, indicating a potential tumor suppressor function for this gene. The molecular mechanism, however, by which PTPRD renders a tumor suppressor effect in neuroblastoma is unknown. RESULTS As a molecular mechanism, we demonstrate that PTPRD interacts with aurora kinase A (AURKA), an oncogenic protein that is over-expressed in multiple forms of cancer, including neuroblastoma. Ectopic up-regulation of PTPRD in neuroblastoma dephosphorylates tyrosine residues in AURKA resulting in a destabilization of this protein culminating in interfering with one of AURKA's primary functions in neuroblastoma, the stabilization of MYCN protein, the gene of which is amplified in approximately 25 to 30% of high risk neuroblastoma. CONCLUSIONS PTPRD has a tumor suppressor function in neuroblastoma through AURKA dephosphorylation and destabilization and a downstream destabilization of MYCN protein, representing a novel mechanism for the function of PTPRD in neuroblastoma.
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Affiliation(s)
- Maria Meehan
- Department of Molecular and Cellular Therapeutics, Royal College of Surgeons in Ireland, Dublin 2, Dublin, Ireland
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Identification of novel CHD1-associated collaborative alterations of genomic structure and functional assessment of CHD1 in prostate cancer. Oncogene 2011; 31:3939-48. [PMID: 22139082 DOI: 10.1038/onc.2011.554] [Citation(s) in RCA: 78] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
A clearer definition of the molecular determinants that drive the development and progression of prostate cancer (PCa) is urgently needed. Efforts to map recurrent somatic deletions in the tumor genome, especially homozygous deletions (HODs), have provided important positional information in the search for cancer-causing genes. Analyzing HODs in the tumors of 244 patients from two independent cohorts and 22 PCa xenografts using high-resolution single-nucleotide polymorphism arrays, herein we report the identification of CHD1, a chromatin remodeler, as one of the most frequently homozygously deleted genes in PCa, second only to PTEN in this regard. The HODs observed in CHD1, including deletions affecting only internal exons of CHD1, were found to completely extinguish the expression of mRNA of this gene in PCa xenografts. Loss of this chromatin remodeler in clinical specimens is significantly associated with an increased number of additional chromosomal deletions, both hemi- and homozygous, especially on 2q, 5q and 6q. Together with the deletions observed in HEK293 cells stably transfected with CHD1 small hairpin RNA, these data suggest a causal relationship. Downregulation of Chd1 in mouse prostate epithelial cells caused dramatic morphological changes indicative of increased invasiveness, but did not result in transformation. Indicating a new role of CHD1, these findings collectively suggest that distinct CHD1-associated alterations of genomic structure evolve during and are required for the development of PCa.
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Thu KL, Pikor LA, Chari R, Wilson IM, Macaulay CE, English JC, Tsao MS, Gazdar AF, Lam S, Lam WL, Lockwood WW. Genetic disruption of KEAP1/CUL3 E3 ubiquitin ligase complex components is a key mechanism of NF-kappaB pathway activation in lung cancer. J Thorac Oncol 2011; 6:1521-9. [PMID: 21795997 PMCID: PMC3164321 DOI: 10.1097/jto.0b013e3182289479] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
INTRODUCTION Inhibitor of kappa light polypeptide gene enhancer in B-cells, kinase beta (IKBKB) (IKK-β/IKK-2), which activates NF-κB, is a substrate of the KEAP1-CUL3-RBX1 E3-ubiquitin ligase complex, implicating this complex in NF-κB pathway regulation. We investigated complex component gene disruption as a novel genetic mechanism of NF-κB activation in non-small cell lung cancer. METHODS A total of 644 tumor- and 90 cell-line genomes were analyzed for gene dosage status of the individual complex components and IKBKB. Gene expression of these genes and NF-κB target genes were analyzed in 48 tumors. IKBKB protein levels were assessed in tumors with and without complex or IKBKB genetic disruption. Complex component knockdown was performed to assess effects of the E3-ligase complex on IKBKB and NF-κB levels, and phenotypic importance of IKBKB expression was measured by pharmacological inhibition. RESULTS We observed strikingly frequent genetic disruption (42%) and aberrant expression (63%) of the E3-ligase complex and IKBKB in the samples examined. Although both adenocarcinomas and squamous cell carcinomas showed complex disruption, the patterns of gene disruption differed. IKBKB levels were elevated with complex disruption, knockdown of complex components increased activated forms of IKBKB and NF-κB proteins, and IKBKB inhibition detriments cell viability, highlighting the biological significance of complex disruption. NF-κB target genes were overexpressed in samples with complex disruption, further demonstrating the effect of complex disruption on NF-κB activity. CONCLUSIONS Gene dosage alteration is a prominent mechanism that disrupts each component of the KEAP1-CUL3-RBX1 complex and its NF-κB stimulating substrate, IKBKB. Herein, we show that, multiple component disruption of this complex represents a novel mechanism of NF-κB activation in non-small cell lung cancer.
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Affiliation(s)
- Kelsie L Thu
- Integrative Oncology Department, BC Cancer Research Centre, Vancouver, Canada.
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Wu J, Liu S, Liu G, Dombkowski A, Abrams J, Martin-Trevino R, Wicha MS, Ethier SP, Yang ZQ. Identification and functional analysis of 9p24 amplified genes in human breast cancer. Oncogene 2011; 31:333-41. [PMID: 21666724 DOI: 10.1038/onc.2011.227] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Previously, our group identified a novel amplicon at chromosome 9p24 in human esophageal and breast cancers, and cloned the novel gene, GASC1 (gene amplified in squamous cell carcinoma 1, also known as JMJD2C/KDM4C), from this amplicon. GASC1 is a histone demethylase involved in the deregulation of histone methylation in cancer cells. In the current study, we aimed to comprehensively characterize the genes in the 9p24 amplicon in human breast cancer. We performed extensive genomic analyses on a panel of cancer cell lines and narrowed the shortest region of overlap to approximately 2 Mb. Based on statistical analysis of copy number increase and overexpression, the 9p24 amplicon contains six candidate oncogenes. Among these, four genes (GASC1 UHRF2, KIAA1432 and C9orf123) are overexpressed only in the context of gene amplification while two genes (ERMP1 and IL33) are overexpressed independent of the copy number increase. We then focused our studies on the UHRF2 gene, which has a potential involvement in both DNA methylation and histone modification. Knocking down UHRF2 expression inhibited the growth of breast cancer cells specifically with 9p24 amplification. Conversely, ectopic overexpression of UHRF2 in non-tumorigenic MCF10A cells promoted cell proliferation. Furthermore, we demonstrated that UHRF2 has the ability to suppress the expression of key cell-cycle inhibitors, such as p16(INK4a), p21(Waf1/Cip1) and p27(Kip1). Taken together, our studies support the notion that the 9p24 amplicon contains multiple oncogenes that may integrate genetic and epigenetic codes and have important roles in human tumorigenesis.
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Affiliation(s)
- J Wu
- Breast Cancer Program, Wayne State University, Detroit, MI 48201, USA
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Ambatipudi S, Gerstung M, Gowda R, Pai P, Borges AM, Schäffer AA, Beerenwinkel N, Mahimkar MB. Genomic profiling of advanced-stage oral cancers reveals chromosome 11q alterations as markers of poor clinical outcome. PLoS One 2011; 6:e17250. [PMID: 21386901 PMCID: PMC3046132 DOI: 10.1371/journal.pone.0017250] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2010] [Accepted: 01/22/2011] [Indexed: 11/19/2022] Open
Abstract
Identifying oral cancer lesions associated with high risk of relapse and predicting clinical outcome remain challenging questions in clinical practice. Genomic alterations may add prognostic information and indicate biological aggressiveness thereby emphasizing the need for genome-wide profiling of oral cancers. High-resolution array comparative genomic hybridization was performed to delineate the genomic alterations in clinically annotated primary gingivo-buccal complex and tongue cancers (n = 60). The specific genomic alterations so identified were evaluated for their potential clinical relevance. Copy-number changes were observed on chromosomal arms with most frequent gains on 3q (60%), 5p (50%), 7p (50%), 8q (73%), 11q13 (47%), 14q11.2 (47%), and 19p13.3 (58%) and losses on 3p14.2 (55%) and 8p (83%). Univariate statistical analysis with correction for multiple testing revealed chromosomal gain of region 11q22.1–q22.2 and losses of 17p13.3 and 11q23–q25 to be associated with loco-regional recurrence (P = 0.004, P = 0.003, and P = 0.0003) and shorter survival (P = 0.009, P = 0.003, and P 0.0001) respectively. The gain of 11q22 and loss of 11q23-q25 were validated by interphase fluorescent in situ hybridization (I-FISH). This study identifies a tractable number of genomic alterations with few underlying genes that may potentially be utilized as biological markers for prognosis and treatment decisions in oral cancers.
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MESH Headings
- Adult
- Aged
- Aged, 80 and over
- Biomarkers, Tumor/analysis
- Biomarkers, Tumor/genetics
- Carcinoma, Squamous Cell/diagnosis
- Carcinoma, Squamous Cell/genetics
- Carcinoma, Squamous Cell/pathology
- Cells, Cultured
- Chromosome Aberrations
- Chromosomes, Human, Pair 11/genetics
- Comparative Genomic Hybridization
- Disease Progression
- Female
- Gene Expression Profiling
- Genome, Human
- HeLa Cells
- Humans
- In Situ Hybridization, Fluorescence
- Male
- Middle Aged
- Mouth Neoplasms/diagnosis
- Mouth Neoplasms/genetics
- Mouth Neoplasms/pathology
- Neoplasm Staging
- Prognosis
- Validation Studies as Topic
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Affiliation(s)
- Srikant Ambatipudi
- Tata Memorial Centre (TMC), Advanced Centre for Treatment, Research and Education in Cancer (ACTREC), Cancer Research Institute (CRI), Navi Mumbai, India
| | - Moritz Gerstung
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
- Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - Ravindra Gowda
- Tata Memorial Centre (TMC), Advanced Centre for Treatment, Research and Education in Cancer (ACTREC), Cancer Research Institute (CRI), Navi Mumbai, India
| | - Prathamesh Pai
- Head and Neck Unit, Tata Memorial Hospital, Tata Memorial Centre (TMC), Mumbai, India
| | - Anita M. Borges
- Department of Pathology and Laboratory Medicine, S. L. Raheja Hospital, Mumbai, India
| | - Alejandro A. Schäffer
- Computational Biology Branch, National Center for Biotechnology Information, National Institutes of Health (NIH), Department of Health and Human Services (DHHS), Bethesda, Maryland, United States of America
| | - Niko Beerenwinkel
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
- Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - Manoj B. Mahimkar
- Tata Memorial Centre (TMC), Advanced Centre for Treatment, Research and Education in Cancer (ACTREC), Cancer Research Institute (CRI), Navi Mumbai, India
- * E-mail:
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Shiau CK, Gu DL, Chen CF, Lin CH, Jou YS. IGRhCellID: integrated genomic resources of human cell lines for identification. Nucleic Acids Res 2010; 39:D520-4. [PMID: 21051335 PMCID: PMC3013678 DOI: 10.1093/nar/gkq1075] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Cell line identification is emerging as an essential method for every cell line user in research community to avoid using misidentified cell lines for experiments and publications. IGRhCellID (http://igrcid.ibms.sinica.edu.tw) is designed to integrate eight cell identification methods including seven methods (STR profile, gender, immunotypes, karyotype, isoenzyme profile, TP53 mutation and mutations of cancer genes) available in various public databases and our method of profiling genome alterations of human cell lines. With data validation of 11 small deleted genes in human cancer cell lines, profiles of genomic alterations further allow users to search for human cell lines with deleted gene to serve as indigenous knock-out cell model (such as SMAD4 in gene view), with amplified gene to be the cell models for testing therapeutic efficacy (such as ERBB2 in gene view) and with overlapped aberrant chromosomal loci for revealing common cancer genes (such as 9p21.3 homozygous deletion with co-deleted CDKN2A, CDKN2B and MTAP in chromosome view). IGRhCellID provides not only available methods for cell identification to help eradicating concerns of using misidentified cells but also designated genetic features of human cell lines for experiments.
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Affiliation(s)
- Cheng-Kai Shiau
- Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan
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