1
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Wu Z, Ge L, Song Y, Deng S, Duan P, Du T, Wu Y, Zhang Z, Hou X, Ma L, Zhang S. ATAD2 promotes glycolysis and tumor progression in clear cell renal cell carcinoma by regulating the transcriptional activity of c-Myc. Discov Oncol 2023; 14:79. [PMID: 37233956 DOI: 10.1007/s12672-023-00696-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 05/19/2023] [Indexed: 05/27/2023] Open
Abstract
Clear cell renal cell carcinoma (ccRCC) is a common malignant tumor of the urogenital tract. Given that ccRCC is often resistant to radiotherapy and traditional chemotherapy, the clinical treatment of patients with ccRCC remains a challenge. The present study found that ATAD2 was significantly upregulated in ccRCC tissues. In vitro and in vivo experiments showed that the inhibition of ATAD2 expression mitigated the aggressive phenotype of ccRCC. ATAD2 was also associated with glycolysis in ccRCC. Interestingly, we found that ATAD2 could physically interact with c-Myc and promote the expression of its downstream target gene, thereby enhancing the Warburg effect of ccRCC. Overall, our study emphasizes the role of ATAD2 in ccRCC. The targeted expression or functional regulation of ATAD2 could be a promising method to reduce the proliferation and progression of ccRCC.
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Affiliation(s)
- Zonglong Wu
- Department of Urology, Peking University Third Hospital, Beijing, 100191, P.R. China
| | - Liyuan Ge
- Department of Urology, Peking University Third Hospital, Beijing, 100191, P.R. China
| | - Yimeng Song
- Department of Urology, Peking University Third Hospital, Beijing, 100191, P.R. China
| | - Shaohui Deng
- Department of Urology, Peking University Third Hospital, Beijing, 100191, P.R. China
| | - Peichen Duan
- Department of Urology, Peking University Third Hospital, Beijing, 100191, P.R. China
| | - Tan Du
- Department of Urology, Peking University Third Hospital, Beijing, 100191, P.R. China
| | - Yaqian Wu
- Department of Urology, Peking University Third Hospital, Beijing, 100191, P.R. China
| | - Zhanyi Zhang
- Department of Urology, Peking University Third Hospital, Beijing, 100191, P.R. China
| | - Xiaofei Hou
- Department of Urology, Peking University Third Hospital, Beijing, 100191, P.R. China
| | - Lulin Ma
- Department of Urology, Peking University Third Hospital, Beijing, 100191, P.R. China.
| | - Shudong Zhang
- Department of Urology, Peking University Third Hospital, Beijing, 100191, P.R. China.
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2
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Czerwinska P, Mackiewicz AA. Bromodomain (BrD) Family Members as Regulators of Cancer Stemness-A Comprehensive Review. Int J Mol Sci 2023; 24:995. [PMID: 36674511 PMCID: PMC9861003 DOI: 10.3390/ijms24020995] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 12/30/2022] [Accepted: 12/31/2022] [Indexed: 01/06/2023] Open
Abstract
Epigenetic mechanisms involving DNA methylation and chromatin modifications have emerged as critical facilitators of cancer heterogeneity, substantially affecting cancer development and progression, modulating cell phenotypes, and enhancing or inhibiting cancer cell malignant properties. Not surprisingly, considering the importance of epigenetic regulators in normal stem cell maintenance, many chromatin-related proteins are essential to maintaining the cancer stem cell (CSC)-like state. With increased tumor-initiating capacities and self-renewal potential, CSCs promote tumor growth, provide therapy resistance, spread tumors, and facilitate tumor relapse after treatment. In this review, we characterized the epigenetic mechanisms that regulate the acquisition and maintenance of cancer stemness concerning selected epigenetic factors belonging to the Bromodomain (BrD) family of proteins. An increasing number of BrD proteins reinforce cancer stemness, supporting the maintenance of the cancer stem cell population in vitro and in vivo via the utilization of distinct mechanisms. As bromodomain possesses high druggable potential, specific BrD proteins might become novel therapeutic targets in cancers exhibiting de-differentiated tumor characteristics.
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Affiliation(s)
- Patrycja Czerwinska
- Department of Cancer Immunology, Poznan University of Medical Sciences, 61-866 Poznan, Poland
- Department of Diagnostics and Cancer Immunology, Greater Poland Cancer Centre, 61-866 Poznan, Poland
| | - Andrzej Adam Mackiewicz
- Department of Cancer Immunology, Poznan University of Medical Sciences, 61-866 Poznan, Poland
- Department of Diagnostics and Cancer Immunology, Greater Poland Cancer Centre, 61-866 Poznan, Poland
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3
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Zhang K, Sun X, Sun W, Wang M, Han F. Exosomal microRNA-506 inhibits biological activity of lung adenocarcinoma cells and increases sensitivity to cisplatin-based hyperthermia. Cell Signal 2022; 100:110469. [PMID: 36115547 DOI: 10.1016/j.cellsig.2022.110469] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 09/09/2022] [Accepted: 09/12/2022] [Indexed: 11/29/2022]
Abstract
Exosomal microRNAs (miRNAs) play a vital role in the occurrence and development of lung adenocarcinoma (LUAD). Based on the bioinformatics analyses, the current study sought to explore the effects of exosomal miR-506 on LUAD cell biology and the efficacy of cisplatin (CDDP)-based hyperthermia (HT). After sample preparation, we identified decreased miR-506 and elevated ATAD2. LUAD cells were subsequently transfected with miR-506 mimic, oe-ATAD2 and PI3K/AKT signaling pathway inhibitor LY294002 to analyze effects of the miR-506/ATAD2/PI3K/AKT axis on cell biological processes and chemoresistance. Effects of exosomal miR-506 on sensitivity of LUAD cells to CDDP-based HT were further assessed in a co-culture system of BMSC-derived exosomes and LUAD cells, which was also validated in tumor-bearing nude mice. miR-506 down-regulated ATAD2 to inhibit the PI3K/AKT signaling pathway, thereby inhibiting the malignant phenotypes of LUAD cells and augmenting LUAD cell sensitivity to CDDP-based HT. Further, BMSCs-derived exosomes harboring miR-506 sensitized LUAD cells to DDP/HT both in vitro and in vivo. Collectively, our findings revealed that exosomal miR-506 sensitized LUAD cells to CDDP-based HT by inhibiting ATAD2/PI3K/AKT signaling pathway, offering a potential therapeutic target for LUAD treatment.
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Affiliation(s)
- Kunming Zhang
- Department of Internal Medicine, Tongji Hospital, Tongji University School of Medicine, Shanghai 200065, PR China
| | - Xiwen Sun
- Department of Medical Imaging, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai 200433, PR China
| | - Weikai Sun
- Department of Radiotherapy, Tongji Hospital, Tongji University School of Medicine, Shanghai 200065, PR China
| | - Meng Wang
- Department of Radiotherapy, Tongji Hospital, Tongji University School of Medicine, Shanghai 200065, PR China
| | - Fushi Han
- Department of Nuclear Medicine, Tongji Hospital, Tongji University School of Medicine, Shanghai 200065, PR China.
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Yoon HJ, Kim GC, Oh S, Kim H, Kim YK, Lee Y, Kim MS, Kwon G, Ok YS, Kwon HK, Kim HS. WNK3 inhibition elicits antitumor immunity by suppressing PD-L1 expression on tumor cells and activating T-cell function. Exp Mol Med 2022; 54:1913-1926. [PMID: 36357569 PMCID: PMC9722663 DOI: 10.1038/s12276-022-00876-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 07/24/2022] [Accepted: 08/17/2022] [Indexed: 11/12/2022] Open
Abstract
Immune checkpoint therapies, such as programmed cell death ligand 1 (PD-L1) blockade, have shown remarkable clinical benefit in many cancers by restoring the function of exhausted T cells. Hence, the identification of novel PD-L1 regulators and the development of their inhibition strategies have significant therapeutic advantages. Here, we conducted pooled shRNA screening to identify regulators of membrane PD-L1 levels in lung cancer cells targeting druggable genes and cancer drivers. We identified WNK lysine deficient protein kinase 3 (WNK3) as a novel positive regulator of PD-L1 expression. The kinase-dead WNK3 mutant failed to elevate PD-L1 levels, indicating the involvement of its kinase domain in this function. WNK3 perturbation increased cancer cell death in cancer cell-immune cell coculture conditions and boosted the secretion of cytokines and cytolytic enzymes, promoting antitumor activities in CD4+ and CD8+ T cells. WNK463, a pan-WNK inhibitor, enhanced CD8+ T-cell-mediated antitumor activity and suppressed tumor growth as a monotherapy as well as in combination with a low-dose anti-PD-1 antibody in the MC38 syngeneic mouse model. Furthermore, we demonstrated that the c-JUN N-terminal kinase (JNK)/c-JUN pathway underlies WNK3-mediated transcriptional regulation of PD-L1. Our findings highlight that WNK3 inhibition might serve as a potential therapeutic strategy for cancer immunotherapy through its concurrent impact on cancer cells and immune cells.
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Affiliation(s)
- Hyun Ju Yoon
- grid.15444.300000 0004 0470 5454Severance Biomedical Science Institute, Yonsei University College of Medicine, Seoul, Korea ,grid.15444.300000 0004 0470 5454Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul, Korea
| | - Gi-Cheon Kim
- grid.15444.300000 0004 0470 5454Department of Microbiology and Immunology, Yonsei University College of Medicine, Seoul, Korea ,grid.15444.300000 0004 0470 5454Institute for Immunology and Immunological Diseases, Yonsei University College of Medicine, Seoul, Korea
| | - Sejin Oh
- grid.15444.300000 0004 0470 5454Severance Biomedical Science Institute, Yonsei University College of Medicine, Seoul, Korea ,grid.15444.300000 0004 0470 5454Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul, Korea
| | - Hakhyun Kim
- grid.15444.300000 0004 0470 5454Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul, Korea
| | - Yong Keon Kim
- grid.15444.300000 0004 0470 5454Severance Biomedical Science Institute, Yonsei University College of Medicine, Seoul, Korea ,grid.15444.300000 0004 0470 5454Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul, Korea
| | - Yunji Lee
- grid.15444.300000 0004 0470 5454Severance Biomedical Science Institute, Yonsei University College of Medicine, Seoul, Korea ,grid.15444.300000 0004 0470 5454Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul, Korea
| | - Min Seo Kim
- grid.15444.300000 0004 0470 5454Severance Biomedical Science Institute, Yonsei University College of Medicine, Seoul, Korea
| | - Gino Kwon
- grid.15444.300000 0004 0470 5454Graduate Program for Nanomedical Science, Yonsei University, Seoul, Korea
| | - Yeon-Su Ok
- grid.15444.300000 0004 0470 5454Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul, Korea ,grid.15444.300000 0004 0470 5454Department of Microbiology and Immunology, Yonsei University College of Medicine, Seoul, Korea
| | - Ho-Keun Kwon
- grid.15444.300000 0004 0470 5454Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul, Korea ,grid.15444.300000 0004 0470 5454Department of Microbiology and Immunology, Yonsei University College of Medicine, Seoul, Korea ,grid.15444.300000 0004 0470 5454Institute for Immunology and Immunological Diseases, Yonsei University College of Medicine, Seoul, Korea
| | - Hyun Seok Kim
- grid.15444.300000 0004 0470 5454Severance Biomedical Science Institute, Yonsei University College of Medicine, Seoul, Korea ,grid.15444.300000 0004 0470 5454Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul, Korea
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5
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ATAD2 drives colorectal cancer progression by regulating TRIM25 expression via a positive feedback loop with E2F transcriptional factors. Biochem Biophys Res Commun 2022; 594:146-152. [PMID: 35085891 DOI: 10.1016/j.bbrc.2022.01.036] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 01/10/2022] [Indexed: 11/23/2022]
Abstract
ATPase family AAA domain-containing protein 2 (ATAD2) is highly expressed in a variety of cancer types, and acts as a co-activator of androgen and estrogen receptors, as well as MYC and E2F transcription factors, to promote tumor cell proliferation. However, the regulation of ATAD2 and its related mechanisms are still elusive. Here, we show that ATAD2 protein was stabilized during DNA damage response in colorectal cancer (CRC) cells. TRIM25, an oncogenic ubiquitin E3 ligase, can interact with ATAD2 and stabilize ATAD2 upon genotoxic insult. We further demonstrated that ATAD2 played a tumor promoting role in CRC and acted as a transcriptional co-activator of E2Fs to promote the expression of TRIM25. Thus, our results revealed an unknown ATAD2-E2Fs-TRIM25 positive feedback loop that drove CRC progression.
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6
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Winter-Holt JJ, Bardelle C, Chiarparin E, Dale IL, Davey PRJ, Davies NL, Denz C, Fillery SM, Guérot CM, Han F, Hughes SJ, Kulkarni M, Liu Z, Milbradt A, Moss TA, Niu H, Patel J, Rabow AA, Schimpl M, Shi J, Sun D, Yang D, Guichard S. Discovery of a Potent and Selective ATAD2 Bromodomain Inhibitor with Antiproliferative Activity in Breast Cancer Models. J Med Chem 2022; 65:3306-3331. [PMID: 35133824 DOI: 10.1021/acs.jmedchem.1c01871] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
ATAD2 is an epigenetic bromodomain-containing target which is overexpressed in many cancers and has been suggested as a potential oncology target. While several small molecule inhibitors have been described in the literature, their cellular activity has proved to be underwhelming. In this work, we describe the identification of a novel series of ATAD2 inhibitors by high throughput screening, confirmation of the bromodomain region as the site of action, and the optimization campaign undertaken to improve the potency, selectivity, and permeability of the initial hit. The result is compound 5 (AZ13824374), a highly potent and selective ATAD2 inhibitor which shows cellular target engagement and antiproliferative activity in a range of breast cancer models.
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Affiliation(s)
| | - Catherine Bardelle
- BioPharmaceuticals R&D, AstraZeneca, Alderley Park, Macclesfield, Cheshire SK10 4TG, United Kingdom
| | | | | | | | | | - Christopher Denz
- Oncology R&D, AstraZeneca, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
| | | | | | - Fujin Han
- Pharmaron Beijing Co. Ltd., 6 Taihe Road, BDA, Beijing 100176, P. R. China
| | | | - Meghana Kulkarni
- Oncology R&D, AstraZeneca, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
| | - Zhaoqun Liu
- Pharmaron Beijing Co. Ltd., 6 Taihe Road, BDA, Beijing 100176, P. R. China
| | | | | | - Huijun Niu
- Pharmaron Beijing Co. Ltd., 6 Taihe Road, BDA, Beijing 100176, P. R. China
| | | | | | | | - Junjie Shi
- Pharmaron Beijing Co. Ltd., 6 Taihe Road, BDA, Beijing 100176, P. R. China
| | - Dongqing Sun
- Pharmaron Beijing Co. Ltd., 6 Taihe Road, BDA, Beijing 100176, P. R. China
| | - Dejian Yang
- Pharmaron Beijing Co. Ltd., 6 Taihe Road, BDA, Beijing 100176, P. R. China
| | - Sylvie Guichard
- Oncology R&D, AstraZeneca, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
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7
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Wu HJ, Dai WW, Wang LB, Zhang J, Wang CL. Comprehensive analysis of the molecular mechanism for gastric cancer based on competitive endogenous RNA network. WORLD JOURNAL OF TRADITIONAL CHINESE MEDICINE 2022. [DOI: 10.4103/2311-8571.355010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
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8
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Evans CM, Phillips M, Malone KL, Tonelli M, Cornilescu G, Cornilescu C, Holton SJ, Gorjánácz M, Wang L, Carlson S, Gay JC, Nix JC, Demeler B, Markley JL, Glass KC. Coordination of Di-Acetylated Histone Ligands by the ATAD2 Bromodomain. Int J Mol Sci 2021; 22:9128. [PMID: 34502039 PMCID: PMC8430952 DOI: 10.3390/ijms22179128] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 08/13/2021] [Accepted: 08/17/2021] [Indexed: 12/15/2022] Open
Abstract
The ATPase Family, AAA domain-containing protein 2 (ATAD2) bromodomain (BRD) has a canonical bromodomain structure consisting of four α-helices. ATAD2 functions as a co-activator of the androgen and estrogen receptors as well as the MYC and E2F transcription factors. ATAD2 also functions during DNA replication, recognizing newly synthesized histones. In addition, ATAD2 is shown to be up-regulated in multiple forms of cancer including breast, lung, gastric, endometrial, renal, and prostate. Furthermore, up-regulation of ATAD2 is strongly correlated with poor prognosis in many types of cancer, making the ATAD2 bromodomain an innovative target for cancer therapeutics. In this study, we describe the recognition of histone acetyllysine modifications by the ATAD2 bromodomain. Residue-specific information on the complex formed between the histone tail and the ATAD2 bromodomain, obtained through nuclear magnetic resonance spectroscopy (NMR) and X-ray crystallography, illustrates key residues lining the binding pocket, which are involved in coordination of di-acetylated histone tails. Analytical ultracentrifugation, NMR relaxation data, and isothermal titration calorimetry further confirm the monomeric state of the functionally active ATAD2 bromodomain in complex with di-acetylated histone ligands. Overall, we describe histone tail recognition by ATAD2 BRD and illustrate that one acetyllysine group is primarily engaged by the conserved asparagine (N1064), the "RVF" shelf residues, and the flexible ZA loop. Coordination of a second acetyllysine group also occurs within the same binding pocket but is essentially governed by unique hydrophobic and electrostatic interactions making the di-acetyllysine histone coordination more specific than previously presumed.
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Affiliation(s)
- Chiara M. Evans
- Department of Pharmaceutical Sciences, Albany College of Pharmacy and Health Sciences, Colchester, VT 05446, USA; (C.M.E.); (M.P.); (K.L.M.); (S.C.); (J.C.G.)
| | - Margaret Phillips
- Department of Pharmaceutical Sciences, Albany College of Pharmacy and Health Sciences, Colchester, VT 05446, USA; (C.M.E.); (M.P.); (K.L.M.); (S.C.); (J.C.G.)
- Department of Pharmacology, Larner College of Medicine, University of Vermont, Burlington, VT 05405, USA
| | - Kiera L. Malone
- Department of Pharmaceutical Sciences, Albany College of Pharmacy and Health Sciences, Colchester, VT 05446, USA; (C.M.E.); (M.P.); (K.L.M.); (S.C.); (J.C.G.)
- Department of Pharmacology, Larner College of Medicine, University of Vermont, Burlington, VT 05405, USA
| | - Marco Tonelli
- National Magnetic Resonance Facility at Madison, University of Wisconsin-Madison, Madison, WI 53706, USA; (M.T.); (G.C.); (C.C.); (J.L.M.)
| | - Gabriel Cornilescu
- National Magnetic Resonance Facility at Madison, University of Wisconsin-Madison, Madison, WI 53706, USA; (M.T.); (G.C.); (C.C.); (J.L.M.)
| | - Claudia Cornilescu
- National Magnetic Resonance Facility at Madison, University of Wisconsin-Madison, Madison, WI 53706, USA; (M.T.); (G.C.); (C.C.); (J.L.M.)
| | - Simon J. Holton
- Bayer AG, Pharmaceuticals, Research & Early Development Oncology, 13353 Berlin, Germany; (S.J.H.); (M.G.)
| | - Mátyás Gorjánácz
- Bayer AG, Pharmaceuticals, Research & Early Development Oncology, 13353 Berlin, Germany; (S.J.H.); (M.G.)
| | - Liping Wang
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, TX 78229, USA; (L.W.); (B.D.)
| | - Samuel Carlson
- Department of Pharmaceutical Sciences, Albany College of Pharmacy and Health Sciences, Colchester, VT 05446, USA; (C.M.E.); (M.P.); (K.L.M.); (S.C.); (J.C.G.)
| | - Jamie C. Gay
- Department of Pharmaceutical Sciences, Albany College of Pharmacy and Health Sciences, Colchester, VT 05446, USA; (C.M.E.); (M.P.); (K.L.M.); (S.C.); (J.C.G.)
| | - Jay C. Nix
- Molecular Biology Consortium, Advanced Light Source, Berkeley, CA 94720, USA;
| | - Borries Demeler
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, TX 78229, USA; (L.W.); (B.D.)
- Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, AB T1K 3M4, Canada
| | - John L. Markley
- National Magnetic Resonance Facility at Madison, University of Wisconsin-Madison, Madison, WI 53706, USA; (M.T.); (G.C.); (C.C.); (J.L.M.)
| | - Karen C. Glass
- Department of Pharmaceutical Sciences, Albany College of Pharmacy and Health Sciences, Colchester, VT 05446, USA; (C.M.E.); (M.P.); (K.L.M.); (S.C.); (J.C.G.)
- Department of Pharmacology, Larner College of Medicine, University of Vermont, Burlington, VT 05405, USA
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9
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Cirenajwis H, Lauss M, Planck M, Vallon-Christersson J, Staaf J. Performance of gene expression-based single sample predictors for assessment of clinicopathological subgroups and molecular subtypes in cancers: a case comparison study in non-small cell lung cancer. Brief Bioinform 2021; 21:729-740. [PMID: 30721923 PMCID: PMC7299291 DOI: 10.1093/bib/bbz008] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Revised: 12/04/2018] [Accepted: 01/07/2019] [Indexed: 12/14/2022] Open
Abstract
The development of multigene classifiers for cancer prognosis, treatment prediction, molecular subtypes or clinicopathological groups has been a cornerstone in transcriptomic analyses of human malignancies for nearly two decades. However, many reported classifiers are critically limited by different preprocessing needs like normalization and data centering. In response, a new breed of classifiers, single sample predictors (SSPs), has emerged. SSPs classify samples in an N-of-1 fashion, relying on, e.g. gene rules comparing expression values within a sample. To date, several methods have been reported, but there is a lack of head-to-head performance comparison for typical cancer classification problems, representing an unmet methodological need in cancer bioinformatics. To resolve this need, we performed an evaluation of two SSPs [k-top-scoring pair classifier (kTSP) and absolute intrinsic molecular subtyping (AIMS)] for two case examples of different magnitude of difficulty in non-small cell lung cancer: gene expression–based classification of (i) tumor histology and (ii) molecular subtype. Through the analysis of ~2000 lung cancer samples for each case example (n = 1918 and n = 2106, respectively), we compared the performance of the methods for different sample compositions, training data set sizes, gene expression platforms and gene rule selections. Three main conclusions are drawn from the comparisons: both methods are platform independent, they select largely overlapping gene rules associated with actual underlying tumor biology and, for large training data sets, they behave interchangeably performance-wise. While SSPs like AIMS and kTSP offer new possibilities to move gene expression signatures/predictors closer to a clinical context, they are still importantly limited by the difficultness of the classification problem at hand.
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Affiliation(s)
- Helena Cirenajwis
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Medicon Village, Lund, Sweden
| | - Martin Lauss
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Medicon Village, Lund, Sweden
| | - Maria Planck
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Medicon Village, Lund, Sweden
| | - Johan Vallon-Christersson
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Medicon Village, Lund, Sweden
| | - Johan Staaf
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Medicon Village, Lund, Sweden
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10
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Nayak A, Dutta M, Roychowdhury A. Emerging oncogene ATAD2: Signaling cascades and therapeutic initiatives. Life Sci 2021; 276:119322. [PMID: 33711386 DOI: 10.1016/j.lfs.2021.119322] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 02/12/2021] [Accepted: 02/27/2021] [Indexed: 12/11/2022]
Abstract
ATAD2 is a promising oncoprotein with tumor-promoting functions in many cancers. It is a valid cancer drug-target and a potential cancer-biomarker for multiple malignancies. As a cancer/testis antigen (CTA), ATAD2 could also be a probable candidate for immunotherapy. It is a unique CTA that belongs to both AAA+ ATPase and bromodomain family proteins. Since 2007, several research groups have been reported on the pleiotropic oncogenic functions of ATAD2 in diverse signaling pathways, including Rb/E2F-cMyc pathway, steroid hormone signaling pathway, p53 and p38-MAPK-mediated apoptotic pathway, AKT pathway, hedgehog signaling pathway, HIF1α signaling pathway, and Epithelial to Mesenchymal Transition (EMT) pathway in various cancers. In all these pathways, ATAD2 participates in chromatin dynamics, DNA replication, and gene transcription, demonstrating its role as an epigenetic reader and transcription factor or coactivator to promote tumorigenesis. However, despite the progress, an overall mechanism of ATAD2-mediated oncogenesis in diverse origin is elusive. In this review, we summarize the accumulated evidence to envision the overall ATAD2 signaling networks during carcinogenesis and highlight the area where missing links await further research. Besides, the structure-function aspect of ATAD2 is also discussed. Since the efforts have already been initiated to explore targeted drug molecules and RNA-based therapeutic alternatives against ATAD2, their potency and prospects have been elucidated. Together, we believe this is a well-rounded review on ATAD2, facilitating a new drift in ATAD2 research, essential for its clinical implication as a biomarker and/or cancer drug-target.
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Affiliation(s)
- Aditi Nayak
- Biochemistry and Cell Biology Laboratory, School of Basic Sciences, Indian Institute of Technology Bhubaneswar, Odisha 752050, India
| | - Madhuri Dutta
- Biochemistry and Cell Biology Laboratory, School of Basic Sciences, Indian Institute of Technology Bhubaneswar, Odisha 752050, India
| | - Anasuya Roychowdhury
- Biochemistry and Cell Biology Laboratory, School of Basic Sciences, Indian Institute of Technology Bhubaneswar, Odisha 752050, India.
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11
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Shi R, Bao X, Unger K, Sun J, Lu S, Manapov F, Wang X, Belka C, Li M. Identification and validation of hypoxia-derived gene signatures to predict clinical outcomes and therapeutic responses in stage I lung adenocarcinoma patients. Am J Cancer Res 2021; 11:5061-5076. [PMID: 33754044 PMCID: PMC7978303 DOI: 10.7150/thno.56202] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Accepted: 01/23/2021] [Indexed: 12/18/2022] Open
Abstract
Rationale: The current tumour-node-metastasis (TNM) staging system is insufficient for precise treatment decision-making and accurate survival prediction for patients with stage I lung adenocarcinoma (LUAD). Therefore, more reliable biomarkers are urgently needed to identify the high-risk subset in stage I patients to guide adjuvant therapy. Methods: This study retrospectively analysed the transcriptome profiles and clinical parameters of 1,400 stage I LUAD patients from 14 public datasets, including 13 microarray datasets from different platforms and 1 RNA-Seq dataset from The Cancer Genome Atlas (TCGA). A series of bioinformatic and machine learning approaches were combined to establish hypoxia-derived signatures to predict overall survival (OS) and immune checkpoint blockade (ICB) therapy response in stage I patients. In addition, enriched pathways, genomic and copy number alterations were analysed in different risk subgroups and compared to each other. Results: Among various hallmarks of cancer, hypoxia was identified as a dominant risk factor for overall survival in stage I LUAD patients. The hypoxia-related prognostic risk score (HPRS) exhibited more powerful capacity of survival prediction compared to traditional clinicopathological features, and the hypoxia-related immunotherapeutic response score (HIRS) outperformed conventional biomarkers for ICB therapy. An integrated decision tree and nomogram were generated to optimize risk stratification and quantify risk assessment. Conclusions: In summary, the proposed hypoxia-derived signatures are promising biomarkers to predict clinical outcomes and therapeutic responses in stage I LUAD patients.
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12
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Nayak A, Kumar S, Singh SP, Bhattacharyya A, Dixit A, Roychowdhury A. Oncogenic potential of ATAD2 in stomach cancer and insights into the protein-protein interactions at its AAA + ATPase domain and bromodomain. J Biomol Struct Dyn 2021; 40:5606-5622. [PMID: 33438526 DOI: 10.1080/07391102.2021.1871959] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
ATAD2 has recently been shown to promote stomach cancer. However, nothing is known about the functional network of ATAD2 in stomach carcinogenesis. This study illustrates the oncogenic potential of ATAD2 and the participation of its ATPase and bromodomain in stomach malignancy. Expression of ATAD2 in stomach cancer is analyzed by in silico and in vitro techniques including western blot and immunofluorescence microscopy of stomach cancer cells (SCCs) and tissues. The oncogenic potential of ATAD2 is examined thoroughly using genetic alterations, driver gene prediction, survival analysis, identification of interacting partners, and analysis of canonical pathways. To understand the protein-protein interactions (PPI) at residue level, molecular docking and molecular dynamics simulations (1200 ns) are performed. Enhanced expression of ATAD2 is observed in H. pylori-infected SCCs, patient biopsy tissues, and all stages and grades of stomach cancer. High expression of ATAD2 is found to be negatively correlated with the survival of stomach cancer patients. ATAD2 is a cancer driver gene with 37 mutational sites and a predictable factor for stomach cancer prognosis with high accuracy. The top canonical pathways of ATAD2 indicate its participation in stomach malignancy. The ATAD2-PPI in stomach cancer identify top-ranked partners; ESR1, SUMO2, SPTN2, and MYC show preference for the bromodomain whereas NCOA3 and HDA11 have preference for the ATPase domain of ATAD2. The oncogenic characterization of ATAD2 provides strong evidence to consider ATAD2 as a stomach cancer biomarker. These studies offer an insight for the first time into the ATAD2-PPI interface presenting a novel target for cancer therapeutics. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Aditi Nayak
- School of Basic Sciences, Indian Institute of Technology Bhubaneswar, Odisha, India
| | - Sugandh Kumar
- Institute of Life Sciences, Bhubaneswar, Odisha, India
| | | | - Asima Bhattacharyya
- School of Biological Sciences, National Institute of Science Education and Research (NISER) Bhubaneswar, HBNI, Khurda, Odisha, India
| | | | - Anasuya Roychowdhury
- School of Basic Sciences, Indian Institute of Technology Bhubaneswar, Odisha, India
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13
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Yao D, Zhang J, Wang J, Pan D, He Z. Discovery of novel ATAD2 bromodomain inhibitors that trigger apoptosis and autophagy in breast cells by structure-based virtual screening. J Enzyme Inhib Med Chem 2020; 35:713-725. [PMID: 32174193 PMCID: PMC7144325 DOI: 10.1080/14756366.2020.1740924] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
ATAD2 has been reported to play an important role in the processes of numerous cancers and validated to be a potential therapeutic target. This work is to discover potent ATAD2 inhibitors and elucidate the underlying mechanisms in breast cancer. A novel ATAD2 bromodomain inhibitor (AM879) was discovered by combining structure-based virtual screening with biochemical analyses. AM879 presents potent inhibitory activity towards ATAD2 bromodomain (IC50 = 3565 nM), presenting no inhibitory activity against BRD2-4. Moreover, AM879 inhibited MDA-MB-231 cells proliferation with IC50 value of 2.43 µM, suppressed the expression of c-Myc, and induced significant apoptosis. Additionally, AM978 could induce autophagy via PI3K-AKT-mTOR signalling in MDA-MB-231 cells. This study demonstrates the development of potent ATAD2 inhibitors with novel scaffolds for breast cancer therapy.
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Affiliation(s)
- Dahong Yao
- Guangdong Key Laboratory for Genome Stability & Human Disease Prevention, School of Pharmaceutical Sciences, Shenzhen University, Shenzhen, China.,Shenzhen Key Laboratory of Novel Natural Health Care Products, Innovation Platform for Natural small molecule Drugs, Engineering Laboratory of Shenzhen Natural small molecule Innovative Drugs, Shenzhen University Health Science Center, Shenzhen, China
| | - Jin Zhang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Collaborative Innovation Center for Biotherapy, Chengdu, China
| | - Jinhui Wang
- Shenzhen Honghui Bio-Pharmaceutical Co. Ltd., Shenzhen, China
| | - Dabo Pan
- Institute of Traditional Chinese Medicine & Natural Products, Guangdong Province Key Laboratory of Pharmacodynamic Constituents of TCM and New Drugs Research, College of Pharmacy, Jinan University, Guangzhou, P. R. China
| | - Zhendan He
- Guangdong Key Laboratory for Genome Stability & Human Disease Prevention, School of Pharmaceutical Sciences, Shenzhen University, Shenzhen, China.,Shenzhen Key Laboratory of Novel Natural Health Care Products, Innovation Platform for Natural small molecule Drugs, Engineering Laboratory of Shenzhen Natural small molecule Innovative Drugs, Shenzhen University Health Science Center, Shenzhen, China
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14
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Wu X, Sui Z, Zhang H, Wang Y, Yu Z. Integrated Analysis of lncRNA-Mediated ceRNA Network in Lung Adenocarcinoma. Front Oncol 2020; 10:554759. [PMID: 33042838 PMCID: PMC7523091 DOI: 10.3389/fonc.2020.554759] [Citation(s) in RCA: 94] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Accepted: 08/19/2020] [Indexed: 12/16/2022] Open
Abstract
Background A growing body of evidence indicates that long non-coding RNAs (lncRNAs) can act as competitive endogenous RNAs (ceRNAs) to bind to microRNAs (miRNAs), thereby affecting and regulating the expression of target genes. The lncRNA–miRNA–mRNA ceRNA network has been theorized to play an indispensable role in many types of tumors. However, the role of the lncRNA-related ceRNA regulatory network in lung adenocarcinoma (LUAD) remains unclear. Methods We downloaded the RNAseq and miRNAseq data of LUAD from The Cancer Genome Atlas (TCGA) data portal and identified differentially expressed lncRNAs (DElncRNAs), differentially expressed miRNAs (DEmiRNAs), and differentially expressed mRNAs (DEmRNAs) between LUAD and corresponding paracancerous tissues by using the edgeR package of R software. We constructed the lncRNA–miRNA–mRNA ceRNA network by using Cytoscape (version 3.7.2) on the basis of the interaction generated from the miRcode, miRTarBase, miRDB, and TargetScan databases. Gene Ontology (GO) annotation and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis were performed with DAVID 6.8 bioinformatics resources and plotted by using the ggplot2 package in R. The effect of genes on LUAD prognosis was assessed by applying the survival package in R in accordance with the Kaplan–Meier curve. Results In total, 1645 DElncRNAs, 117 DEmiRNAs, and 2729 DEmRNAs were identified in LUAD. The LUAD-specific ceRNA network was composed of 157 nodes and 378 edges (329 DElncRNA–DEmiRNA interactions and 49 DEmiRNA–DEmRNA interactions). GO and KEGG pathway annotations suggested that the LUAD-specific ceRNA network was related to tumor-related molecular functions and pathways. Seven lncRNAs (DISC1-IT1, SYNPR-AS1, H19, LINC00460, LINC00518, DSCR10, and STEAP2-AS1), one miRNA (hsa-mir-31), and 16 mRNAs (ATAD2, OSCAR, KIF23, E2F7, PFKP, MCM4, CEP55, CBX2, CCNE1, CLSPN, CCNB1, CDC25A, EZH2, CHEK1, SLC7A11, and PBK) were revealed to be significantly correlated with overall survival. Conclusion In this study, we described the potential regulatory mechanism of the progression of LUAD. We proposed a new lncRNA–miRNA–mRNA ceRNA network that could help further explore the molecular mechanisms of LUAD.
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Affiliation(s)
- Xianxian Wu
- Department of Esophageal Cancer, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Tianjin, China
| | - Zhilin Sui
- Department of Esophageal Cancer, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Tianjin, China
| | - Hongdian Zhang
- Department of Esophageal Cancer, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Tianjin, China
| | - Ying Wang
- Department of Esophageal Cancer, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Tianjin, China
| | - Zhentao Yu
- Department of Esophageal Cancer, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Tianjin, China
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15
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Liljedahl H, Karlsson A, Oskarsdottir GN, Salomonsson A, Brunnström H, Erlingsdottir G, Jönsson M, Isaksson S, Arbajian E, Ortiz-Villalón C, Hussein A, Bergman B, Vikström A, Monsef N, Branden E, Koyi H, de Petris L, Patthey A, Behndig AF, Johansson M, Planck M, Staaf J. A gene expression-based single sample predictor of lung adenocarcinoma molecular subtype and prognosis. Int J Cancer 2020; 148:238-251. [PMID: 32745259 PMCID: PMC7689824 DOI: 10.1002/ijc.33242] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Revised: 07/03/2020] [Accepted: 07/07/2020] [Indexed: 12/14/2022]
Abstract
Disease recurrence in surgically treated lung adenocarcinoma (AC) remains high. New approaches for risk stratification beyond tumor stage are needed. Gene expression-based AC subtypes such as the Cancer Genome Atlas Network (TCGA) terminal-respiratory unit (TRU), proximal-inflammatory (PI) and proximal-proliferative (PP) subtypes have been associated with prognosis, but show methodological limitations for robust clinical use. We aimed to derive a platform independent single sample predictor (SSP) for molecular subtype assignment and risk stratification that could function in a clinical setting. Two-class (TRU/nonTRU=SSP2) and three-class (TRU/PP/PI=SSP3) SSPs using the AIMS algorithm were trained in 1655 ACs (n = 9659 genes) from public repositories vs TCGA centroid subtypes. Validation and survival analysis were performed in 977 patients using overall survival (OS) and distant metastasis-free survival (DMFS) as endpoints. In the validation cohort, SSP2 and SSP3 showed accuracies of 0.85 and 0.81, respectively. SSPs captured relevant biology previously associated with the TCGA subtypes and were associated with prognosis. In survival analysis, OS and DMFS for cases discordantly classified between TCGA and SSP2 favored the SSP2 classification. In resected Stage I patients, SSP2 identified TRU-cases with better OS (hazard ratio [HR] = 0.30; 95% confidence interval [CI] = 0.18-0.49) and DMFS (TRU HR = 0.52; 95% CI = 0.33-0.83) independent of age, Stage IA/IB and gender. SSP2 was transformed into a NanoString nCounter assay and tested in 44 Stage I patients using RNA from formalin-fixed tissue, providing prognostic stratification (relapse-free interval, HR = 3.2; 95% CI = 1.2-8.8). In conclusion, gene expression-based SSPs can provide molecular subtype and independent prognostic information in early-stage lung ACs. SSPs may overcome critical limitations in the applicability of gene signatures in lung cancer.
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Affiliation(s)
- Helena Liljedahl
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Medicon Village, Lund, Sweden
| | - Anna Karlsson
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Medicon Village, Lund, Sweden
| | - Gudrun N Oskarsdottir
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Medicon Village, Lund, Sweden.,Department of Respiratory Medicine and Allergology, Skåne University Hospital, Lund, Sweden
| | - Annette Salomonsson
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Medicon Village, Lund, Sweden
| | - Hans Brunnström
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Medicon Village, Lund, Sweden.,Department of Pathology, Laboratory Medicine Region Skåne, Lund, Sweden
| | - Gigja Erlingsdottir
- Department of Pathology, Landspitali University Hospital, Reykjavik, Iceland.,Department of Laboratory Medicine, Department of Pathology, Skåne University Hospital, Malmö, Sweden
| | - Mats Jönsson
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Medicon Village, Lund, Sweden
| | - Sofi Isaksson
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Medicon Village, Lund, Sweden
| | - Elsa Arbajian
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Medicon Village, Lund, Sweden
| | | | - Aziz Hussein
- Department of Pathology and Cytology, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Bengt Bergman
- Department of Respiratory Medicine, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Anders Vikström
- Department of Pulmonary Medicine, University Hospital Linköping, Linköping, Sweden
| | - Nastaran Monsef
- Department of Pathology and Department of Clinical and Experimental Medicine, Linköping University, Linköping, Sweden
| | - Eva Branden
- Respiratory Medicine Unit, Department of Medicine Solna and CMM, Karolinska Institute and Karolinska University Hospital Solna, Stockholm, Sweden.,Centre for Research and Development, Uppsala University/Region Gävleborg, Gävle, Sweden
| | - Hirsh Koyi
- Respiratory Medicine Unit, Department of Medicine Solna and CMM, Karolinska Institute and Karolinska University Hospital Solna, Stockholm, Sweden.,Centre for Research and Development, Uppsala University/Region Gävleborg, Gävle, Sweden
| | - Luigi de Petris
- Thoracic Oncology Unit, Karolinska University Hospital and Department Oncology-Pathology, Karolinska Institute, Stockholm, Sweden
| | - Annika Patthey
- Department of Medical Biosciences, Pathology, Umeå University, Umeå, Sweden
| | - Annelie F Behndig
- Department of Public Health and Clinical Medicine, Division of Medicine, Umeå University, Umeå, Sweden
| | - Mikael Johansson
- Department of Radiation Sciences, Oncology, Umeå University, Umeå, Sweden
| | - Maria Planck
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Medicon Village, Lund, Sweden.,Department of Respiratory Medicine and Allergology, Skåne University Hospital, Lund, Sweden
| | - Johan Staaf
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Medicon Village, Lund, Sweden
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16
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Salomonsson A, Micke P, Mattsson JSM, La Fleur L, Isaksson J, Jönsson M, Nodin B, Botling J, Uhlén M, Jirström K, Staaf J, Planck M, Brunnström H. Comprehensive analysis of RNA binding motif protein 3 (RBM3) in non-small cell lung cancer. Cancer Med 2020; 9:5609-5619. [PMID: 32491279 PMCID: PMC7402820 DOI: 10.1002/cam4.3149] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Revised: 04/11/2020] [Accepted: 05/05/2020] [Indexed: 01/05/2023] Open
Abstract
AIMS High expression of the RNA-binding motif protein 3 (RBM3) correlates with improved prognosis in several major types of cancer. The aim of the present study was to examine the prognostic value of RBM3 protein and mRNA expression in non-small cell lung cancer (NSCLC). METHODS AND RESULTS Immunohistochemical expression of RBM3 was evaluated in surgically treated NSCLC from two independent patient populations (n = 213 and n = 306). Staining patterns were correlated with clinicopathological parameters, overall survival (OS), and recurrence-free interval (RFI). Cases with high nuclear RBM3 protein expression had a prolonged 5-year OS in both cohorts when analyzing adenocarcinomas separately (P = .02 and P = .01). RBM3 remained an independent prognostic factor for OS in multivariable analysis of cohort I (HR 0.44, 95% CI 0.21-0.90) and for RFI in cohort II (HR 0.38, 95% CI 0.22-0.74). In squamous cell carcinoma, there was instead an insignificant association to poor prognosis. Also, the expression levels of RBM3 mRNA were investigated in 2087 lung adenocarcinomas and 899 squamous cell carcinomas assembled from 13 and 8 public gene expression microarray datasets, respectively. The RBM3 mRNA levels were not clearly associated with patient outcome in either adenocarcinomas or squamous cell carcinomas. CONCLUSIONS The results from this study support that high protein expression of RBM3 is linked to improved outcome in lung adenocarcinoma.
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Affiliation(s)
- Annette Salomonsson
- Department of Clinical Sciences, Division of Oncology and Pathology, Lund University, Lund, Sweden
| | - Patrick Micke
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala University Hospital, Uppsala, Sweden
| | - Johanna S M Mattsson
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala University Hospital, Uppsala, Sweden
| | - Linnea La Fleur
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala University Hospital, Uppsala, Sweden
| | - Johan Isaksson
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala University Hospital, Uppsala, Sweden.,Department of Respiratory Medicine, Gävle Hospital, Gävle, Sweden.,Centre for Research and Development, Uppsala university/County Council of Gävleborg, Gävle, Sweden
| | - Mats Jönsson
- Department of Clinical Sciences, Division of Oncology and Pathology, Lund University, Lund, Sweden
| | - Björn Nodin
- Department of Clinical Sciences, Division of Oncology and Pathology, Lund University, Lund, Sweden
| | - Johan Botling
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala University Hospital, Uppsala, Sweden
| | - Mathias Uhlén
- Science for Life Laboratory, Royal Institute of Technology, Stockholm, Sweden.,School of Biotechnology, AlbaNova University Center, Royal Institute of Technology, Stockholm, Sweden
| | - Karin Jirström
- Department of Clinical Sciences, Division of Oncology and Pathology, Lund University, Lund, Sweden.,Department of Genetics and Pathology, Laboratory Medicine Region Skåne, Lund, Sweden
| | - Johan Staaf
- Department of Clinical Sciences, Division of Oncology and Pathology, Lund University, Lund, Sweden
| | - Maria Planck
- Department of Clinical Sciences, Division of Oncology and Pathology, Lund University, Lund, Sweden.,Department of Respiratory medicine and Allergology, Skåne University Hospital, Lund, Sweden
| | - Hans Brunnström
- Department of Clinical Sciences, Division of Oncology and Pathology, Lund University, Lund, Sweden.,Department of Genetics and Pathology, Laboratory Medicine Region Skåne, Lund, Sweden
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17
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Abo1 is required for the H3K9me2 to H3K9me3 transition in heterochromatin. Sci Rep 2020; 10:6055. [PMID: 32269268 PMCID: PMC7142091 DOI: 10.1038/s41598-020-63209-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Accepted: 03/26/2020] [Indexed: 01/24/2023] Open
Abstract
Heterochromatin regulation is critical for genomic stability. Different H3K9 methylation states have been discovered, with distinct roles in heterochromatin formation and silencing. However, how the transition from H3K9me2 to H3K9me3 is controlled is still unclear. Here, we investigate the role of the conserved bromodomain AAA-ATPase, Abo1, involved in maintaining global nucleosome organisation in fission yeast. We identified several key factors involved in heterochromatin silencing that interact genetically with Abo1: histone deacetylase Clr3, H3K9 methyltransferase Clr4, and HP1 homolog Swi6. Cells lacking Abo1 cultivated at 30 °C exhibit an imbalance of H3K9me2 and H3K9me3 in heterochromatin. In abo1∆ cells, the centromeric constitutive heterochromatin has increased H3K9me2 but decreased H3K9me3 levels compared to wild-type. In contrast, facultative heterochromatin regions exhibit reduced H3K9me2 and H3K9me3 levels in abo1∆. Genome-wide analysis showed that abo1∆ cells have silencing defects in both the centromeres and subtelomeres, but not in a subset of heterochromatin islands in our condition. Thus, our work uncovers a role of Abo1 in stabilising directly or indirectly Clr4 recruitment to allow the H3K9me2 to H3K9me3 transition in heterochromatin.
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18
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Wang H, Wang X, Xu L, Zhang J, Cao H. Integrated analysis of the E2F transcription factors across cancer types. Oncol Rep 2020; 43:1133-1146. [PMID: 32323836 PMCID: PMC7058048 DOI: 10.3892/or.2020.7504] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Accepted: 01/17/2020] [Indexed: 12/11/2022] Open
Abstract
E2F transcription factors are associated with the development of cancer. However, the E2F family genes have not yet been studied in a comprehensive manner. Using The Cancer Genome Atlas, the present study analyzed the functions of the E2F family genes across different types of tumor. It was revealed that compared with normal tissues, the E2F family genes are highly expressed in several types of tumor tissue. Furthermore, E2F transcription factors were significantly enriched in tumor samples across different types of tumor. The high expression levels of E2F family genes were associated with an unfavorable prognosis in liver hepatocellular carcinoma (LIHC) and lung adenocarcinoma (LUAD). Furthermore, patients with pathological T1 stage and iCluster2 molecular subtype of LIHC expressed particularly low levels of E2F family genes. The present study demonstrated that hypo-DNA methylation, DNA amplification and TP53 mutation contributed to the high expression levels of E2F family genes in cancer cells. Finally, the present study revealed that, compared with other types of tumor, the E2F family genes were specifically downregulated in patients with LIHC. The expression levels and prognostic effects of the E2F family genes were validated using the Gene Expression Omnibus database. The results of the present study revealed the biological functions of E2F family genes in the development of cancer and provided potential biomarkers for further therapeutic studies, particularly for patients with LIHC and LUAD.
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Affiliation(s)
- Haiwei Wang
- Fujian Provincial Prenatal Diagnosis Center, Fujian Provincial Maternity and Children's Hospital, Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian 350001, P.R. China
| | - Xinrui Wang
- Fujian Provincial Prenatal Diagnosis Center, Fujian Provincial Maternity and Children's Hospital, Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian 350001, P.R. China
| | - Liangpu Xu
- Fujian Provincial Prenatal Diagnosis Center, Fujian Provincial Maternity and Children's Hospital, Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian 350001, P.R. China
| | - Ji Zhang
- State Key Laboratory for Medical Genomics, Shanghai Institute of Hematology, Rui‑Jin Hospital Affiliated to School of Medicine, Shanghai Jiao Tong University, Shanghai 200025, P.R. China
| | - Hua Cao
- Fujian Provincial Prenatal Diagnosis Center, Fujian Provincial Maternity and Children's Hospital, Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian 350001, P.R. China
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19
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Zhou L, Yang C, Zhang N, Zhang X, Zhao T, Yu J. Silencing METTL3 inhibits the proliferation and invasion of osteosarcoma by regulating ATAD2. Biomed Pharmacother 2020; 125:109964. [PMID: 32044716 DOI: 10.1016/j.biopha.2020.109964] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 01/15/2020] [Accepted: 01/24/2020] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Osteosarcoma is the most common primary malignant bone tumor in children and young adults. RNA N6-methyladenosine (m6A) is the most abundant internal modification in mammalian mRNA, which is involved in tumorigenesis and tumor progression. It has been reported that methyltransferase-like 3 (METTL3), the first reported m6A "writer", plays critical roles in cancer progression. However, its role and molecular mechanism in osteosarcoma is poor studied. In this study, we aimed to investigate the functional role and underlying mechanism of METTL3 in the progression of osteosarcoma. METHODS We detected the mRNA expression of METTL3 in osteosarcoma cell lines, and immunofluorescence assay was performed to observe the location of METTL3. Cell lines with METTL3 gene overexpression or knockdown were established by pcDNA3.1-METTL3 or siRNA interferences in order to determine the function of METTL3 in osteosarcoma in vitro. Transcriptomic RNA sequencing (RNA-seq) were used to screen the target genes of METTL3 in osteosarcoma. RESULTS We found that METTL3 localized in cytoplasm and nucleus of osteosarcoma cells. Silencing METTL3 in SAOS-2 and MG63 cells significantly inhibited the m6A methylation level, proliferation, migration, and invasion abilities, as well as promoted cell apoptosis. However, up-regulation of METTL3 had no significant effect on the biological behaviors of U2OS cells. Further mechanism analysis suggested that METTL3 knockdown inhibited the expression of ATPase family AAA domain containing 2 (ATAD2). Moreover, ATAD2 knockdown inhibited the proliferation and invasion of SAOS-2 and MG63 cells, while its overexpression showed a significant increase in cell proliferation and invasion. Furthermore, METTL3 knockdown abrogated the promoting effects of ATAD2 overexpression on osteosarcoma cells proliferation and invasion. CONCLUSION Overall, our study revealed that METTL3 functions as an oncogene in the growth and invasion of osteosarcoma by regulating ATAD2, suggesting a potential therapeutic target for osteosarcoma treatment.
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Affiliation(s)
- Lei Zhou
- Department of Orthopedic Oncology Surgery, Shandong Cancer Hospital and Institute Affiliated to Shandong University, Jinan 250117, China; Shandong Cancer Hospital and Institute Affiliated to Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan 250117, China
| | - Changsheng Yang
- Department of Orthopedic Oncology Surgery, Shandong Cancer Hospital and Institute Affiliated to Shandong University, Jinan 250117, China; Shandong Cancer Hospital and Institute Affiliated to Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan 250117, China
| | - Ning Zhang
- Department of Orthopedics, Jinan City People's Hospital, Jinan 271100, China
| | - Xin Zhang
- Department of Orthopedic Oncology Surgery, Shandong Cancer Hospital and Institute Affiliated to Shandong University, Jinan 250117, China; Shandong Cancer Hospital and Institute Affiliated to Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan 250117, China
| | - Tingbao Zhao
- Department of Orthopedic Oncology Surgery, Shandong Cancer Hospital and Institute Affiliated to Shandong University, Jinan 250117, China; Shandong Cancer Hospital and Institute Affiliated to Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan 250117, China
| | - Jinming Yu
- Shandong Cancer Hospital and Institute Affiliated to Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan 250117, China; Department of Radiation Oncology, Shandong Cancer Hospital and Institute Affiliated to Shandong University, Jinan 250117, China.
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20
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Sun T, Du B, Diao Y, Li X, Chen S, Li Y. ATAD2 expression increases [18F]Fluorodeoxyglucose uptake value in lung adenocarcinoma via AKT-GLUT1/HK2 pathway. BMB Rep 2020. [PMID: 31186081 PMCID: PMC6675242 DOI: 10.5483/bmbrep.2019.52.7.042] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
[18F]Fluorodeoxyglucose (FDG) PET/CT imaging has been widely used in the diagnosis of malignant tumors. ATPase family AAA domain-containing protein 2 (ATAD2) plays important roles in tumor growth, invasion and metastasis. However, the relationship between [18F]FDG accumulation and ATAD2 expression remains largely unknown. This study aimed to investigate the correlation between ATAD2 expression and [18F]FDG uptake in lung adenocarcinoma (LUAD), and elucidate its underlying molecular mechanisms. The results showed that ATAD2 expression was positively correlated with maximum standardized uptake value (SUVmax), total lesion glycolysis (TLG), glucose transporter type 1 (GLUT1) expression and hexokinase2 (HK2) expression in LUAD tissues. In addition, ATAD2 knockdown significantly inhibited the proliferation, tumorigenicity, migration, [18F]FDG uptake and lactate production of LUAD cells, while, ATAD2 overexpression exhibited the opposite effects. Furthermore, ATAD2 modulated the glycometabolism of LUAD via AKT-GLUT1/HK2 pathway, as assessed using LY294002 (an inhibitor of PI3K/AKT pathway). In summary, to explore the correlation between ATAD2 expression and glycometabolism is expected to bring good news for anti-energy metabolism therapy of cancers.
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Affiliation(s)
- Tong Sun
- Department of Nuclear Medicine, The first Hospital of China Medical University, Liaoning 110001, China
| | - Bulin Du
- Department of Nuclear Medicine, The first Hospital of China Medical University, Liaoning 110001, China
| | - Yao Diao
- Department of Nuclear Medicine, The first Hospital of China Medical University, Liaoning 110001, China
| | - Xuena Li
- Department of Nuclear Medicine, The first Hospital of China Medical University, Liaoning 110001, China
| | - Song Chen
- Department of Nuclear Medicine, The first Hospital of China Medical University, Liaoning 110001, China
| | - Yaming Li
- Department of Nuclear Medicine, The first Hospital of China Medical University, Liaoning 110001, China
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21
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Wang XL, Wang S, Wu ZZ, Yang QC, Li H, Xiong HG, Wan SC, Sun ZJ. Overexpression of ATAD2 indicates Poor Prognosis in Oral Squamous Cell Carcinoma. Int J Med Sci 2020; 17:1598-1609. [PMID: 32669963 PMCID: PMC7359390 DOI: 10.7150/ijms.46809] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Accepted: 06/09/2020] [Indexed: 12/27/2022] Open
Abstract
ATPase family AAA domain-containing protein 2 (ATAD2) is highly expressed in a variety of malignancies and can promote the proliferation of tumor cells and inhibit their differentiation. However, the expression of ATAD2 and its related mechanism in oral squamous cell carcinoma (OSCC) are still unknown. Immunohistochemical staining of ATAD2, cancer stem cells (CSCs) markers and immune checkpoint molecules was conducted on human OSCC specimens to determine the expression levels of these proteins and their correlations with the clinicopathological characteristics of ATAD2 in OSCC. Moreover, the role of ATAD2 in cell proliferation, apoptosis, migration and epithelial-mesenchymal transition (EMT) were assessed by silencing ATAD2 in vitro. Immunohistochemical analysis revealed that ATAD2 expression in OSCC tissues was markedly higher than that in adjacent dysplastic tissues and normal mucosal tissues. Overexpression of ATAD2 was related to poor overall survival in OSCC patients. In addition, the protein expression of ATAD2 was notably correlated with the expression of B7-H4, PD-L1, CMTM6, Slug and ALDH1 in human OSCC. ATAD2 knockdown arrested the cell cycle, promoted the apoptosis, and inhibited the proliferation, migration, and EMT of OSCC cells. In conclusion, these findings revealed that ATAD2 is highly expressed in OSCC and can act as a poor prognostic indicator.
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Affiliation(s)
- Xiao-Long Wang
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) & Key Laboratory of Oral Biomedicine Ministry of Education, School & Hospital of Stomatology, Wuhan University, Wuhan, China.,Department of Stomatology, Xiangyang Central Hospital, Affiliated Hospital of Hubei University of Arts and Science, Xiangyang, China
| | - Shuo Wang
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) & Key Laboratory of Oral Biomedicine Ministry of Education, School & Hospital of Stomatology, Wuhan University, Wuhan, China
| | - Zhi-Zhong Wu
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) & Key Laboratory of Oral Biomedicine Ministry of Education, School & Hospital of Stomatology, Wuhan University, Wuhan, China
| | - Qi-Chao Yang
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) & Key Laboratory of Oral Biomedicine Ministry of Education, School & Hospital of Stomatology, Wuhan University, Wuhan, China
| | - Hao Li
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) & Key Laboratory of Oral Biomedicine Ministry of Education, School & Hospital of Stomatology, Wuhan University, Wuhan, China
| | - Hong-Gang Xiong
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) & Key Laboratory of Oral Biomedicine Ministry of Education, School & Hospital of Stomatology, Wuhan University, Wuhan, China
| | - Shu-Cheng Wan
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) & Key Laboratory of Oral Biomedicine Ministry of Education, School & Hospital of Stomatology, Wuhan University, Wuhan, China
| | - Zhi-Jun Sun
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) & Key Laboratory of Oral Biomedicine Ministry of Education, School & Hospital of Stomatology, Wuhan University, Wuhan, China.,Department of Oral Maxillofacial-Head Neck Oncology, School & Hospital of Stomatology, Wuhan University, Wuhan, China
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22
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Han HJ, Huang QY, Huang LJ, Chang F, Diao QZ. Prognostic value of ATPase family, AAA+ domain containing 2 expression in human cancers: A systematic review and meta-analysis. Medicine (Baltimore) 2019; 98:e17180. [PMID: 31574824 PMCID: PMC6775384 DOI: 10.1097/md.0000000000017180] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
BACKGROUND ATPase family, AAA+ domain containing 2 (ATAD2) is also known as AAA+ nuclear coregulator cancer-associated protein or PRO2000. ATAD2 has been reported as a prognostic factor in different cancer types, but the association between ATAD2 high expression and survival is still unclear. Thereby, this meta-analysis was performed to evaluate the prognostic value of ATAD2 high expression in human cancers. METHODS All of the studies included were retrieved from PubMed, EMBASE, and Cochrane Library electronic databases. The clinical outcomes were evaluated by calculating hazard ratio (HR) with their 95% confidence interval (CI). RESULTS Thirteen studies including 2689 patients were eligible for this analysis. The pooled results showed that ATAD2 over-expression was significantly associated with shorter overall survival (OS) (HR = 2.32, 95% CI = 1.77-3.02), as well as shorter recurrence-free survival (RFS), disease-free survival (DFS), and disease-specific survival (DSS) (HR = 1.83, 95% CI = 1.51-2.23) among human cancers. Subgroup analyses for OS were implemented in terms of region, tumor type, and sample size and the results were coincident with overall pooled results. Begg funnel plot and Egger test showed the presence of publication bias for OS. Sensitivity analysis indicated that both results were not affected for removing any study. CONCLUSION ATAD2 would be likely to act as a prognostic biomarker for the patients of different cancer types and provide a guide on clinical treatment. Prospective clinical studies are needed to support these findings.
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Affiliation(s)
| | | | | | | | - Qi-Zhi Diao
- The Department of Clinical Laboratory Medicine, Yongchuan Hospital, Chongqing Medical University, Yongchuan, Chongqing, China
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23
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Wu S, Han M, Zhang C. Overexpression of microRNA-186 inhibits angiogenesis in retinoblastoma via the Hedgehog signaling pathway by targeting ATAD2. J Cell Physiol 2019; 234:19059-19072. [PMID: 30993715 DOI: 10.1002/jcp.28545] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Revised: 02/27/2019] [Accepted: 03/06/2019] [Indexed: 12/13/2022]
Abstract
Retinoblastoma (RB) represents an aggressive malignancy in the eye during the period of infancy and childhood. We delineated the ability of microRNA-186 (miR-186) to influence viability, invasion, migration, angiogenesis, and apoptosis of RB via the Hedgehog signaling pathway by targeting AAA domain-containing protein 2 (ATAD2). The microarray-based analysis was adopted to identify differentially expressed genes (DEGs) related to RB. Subsequently, RB cells were treated with miR-186 mimic, miR-186 inhibitor, or si-ATAD2. The expression of miR-186, ATAD2, Hedgehog signaling pathway-related genes were evaluated, and the target relationship between miR-186 and ATAD2 was verified. Finally, cell proliferation, invasion, migration, apoptosis, and angiogenesis were assessed. ATAD2 was identified as a DEG and modulated by miR-186. Moreover, we revealed that ATAD2 was highly expressed, whereas miR-186 was lowly expressed, and the Hedgehog signaling pathway was activated in RB. Then, ATAD2 as a putative target of miR-186 was validated using a luciferase assay. miR-186 mimic or siRNA-ATAD2 in RB cells reduced cell viability, invasion, and migration coordinating with elevated apoptosis via impairing the Hedgehog signaling pathway, where repressed angiogenesis was observed. Overexpression of miR-186 attenuates RB via the inactivation of the Hedgehog signaling pathway by downregulating ATAD2.
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Affiliation(s)
- Shuai Wu
- Department of Orbital Disease & Ocular Plastic Surgery, The Second Hospital of Jilin University, Changchun, Jilin, People's Republic of China
| | - Mei Han
- Department of Strabismus & Pediatric Ophthalmology, The Second Hospital of Jilin University, Changchun, Jilin, People's Republic of China
| | - Chao Zhang
- Department of Strabismus & Pediatric Ophthalmology, The Second Hospital of Jilin University, Changchun, Jilin, People's Republic of China
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24
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Liu N, Funasaka K, Obayashi T, Miyahara R, Hirooka Y, Goto H, Senga T. ATAD2 is associated with malignant characteristics of pancreatic cancer cells. Oncol Lett 2019; 17:3489-3494. [PMID: 30867788 DOI: 10.3892/ol.2019.9960] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2015] [Accepted: 02/17/2017] [Indexed: 01/09/2023] Open
Abstract
Pancreatic cancer is one of the most aggressive human cancers and is associated with a poor prognosis. To develop a novel strategy for pancreatic cancer treatment, it is essential to elucidate the molecular mechanisms underlying the invasion and proliferation of cancer cells. ATPase family AAA domain containing protein 2 (ATAD2) is a highly conserved protein with an AAA+ domain and a bromodomain. Accumulating studies have demonstrated that ATAD2 is associated with the progression of multiple cancers. The present study demonstrated that ATAD2 depletion suppressed cell invasion and migration. In addition, ATAD2 knockdown suppressed anchorage-independent growth of pancreatic cancer cells. Finally, ATAD2 depletion was demonstrated to sensitize pancreatic cancer cells to gemcitabine. The results of the present study indicate that ATAD2 is involved in the malignant characteristics of pancreatic cancer.
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Affiliation(s)
- Nairong Liu
- Department of Gastroenterology and Hepatology, Nagoya University Graduate School of Medicine, Nagoya, Aichi 466-8550, Japan
| | - Kohei Funasaka
- Department of Gastroenterology and Hepatology, Nagoya University Graduate School of Medicine, Nagoya, Aichi 466-8550, Japan
| | - Tomohiko Obayashi
- Department of Gastroenterology and Hepatology, Nagoya University Graduate School of Medicine, Nagoya, Aichi 466-8550, Japan
| | - Ryoji Miyahara
- Department of Gastroenterology and Hepatology, Nagoya University Graduate School of Medicine, Nagoya, Aichi 466-8550, Japan
| | - Yoshiki Hirooka
- Department of Gastroenterology and Hepatology, Nagoya University Graduate School of Medicine, Nagoya, Aichi 466-8550, Japan
| | - Hidemi Goto
- Department of Gastroenterology and Hepatology, Nagoya University Graduate School of Medicine, Nagoya, Aichi 466-8550, Japan
| | - Takeshi Senga
- Division of Cancer Biology, Nagoya University Graduate School of Medicine, Nagoya, Aichi 466-8550, Japan
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25
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Gay JC, Eckenroth BE, Evans CM, Langini C, Carlson S, Lloyd JT, Caflisch A, Glass KC. Disulfide bridge formation influences ligand recognition by the ATAD2 bromodomain. Proteins 2018; 87:157-167. [PMID: 30520161 DOI: 10.1002/prot.25636] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Revised: 10/09/2018] [Accepted: 11/29/2018] [Indexed: 12/28/2022]
Abstract
The ATPase family, AAA domain-containing protein 2 (ATAD2) has a C-terminal bromodomain, which functions as a chromatin reader domain recognizing acetylated lysine on the histone tails within the nucleosome. ATAD2 is overexpressed in many cancers and its expression is correlated with poor patient outcomes, making it an attractive therapeutic target and potential biomarker. We solved the crystal structure of the ATAD2 bromodomain and found that it contains a disulfide bridge near the base of the acetyllysine binding pocket (Cys1057-Cys1079). Site-directed mutagenesis revealed that removal of a free C-terminal cysteine (C1101) residue greatly improved the solubility of the ATAD2 bromodomain in vitro. Isothermal titration calorimetry experiments in combination with the Ellman's assay demonstrated that formation of an intramolecular disulfide bridge negatively impacts the ligand binding affinities and alters the thermodynamic parameters of the ATAD2 bromodomain interaction with a histone H4K5ac peptide as well as a small molecule bromodomain ligand. Molecular dynamics simulations indicate that the formation of the disulfide bridge in the ATAD2 bromodomain does not alter the structure of the folded state or flexibility of the acetyllysine binding pocket. However, consideration of this unique structural feature should be taken into account when examining ligand-binding affinity, or in the design of new bromodomain inhibitor compounds that interact with this acetyllysine reader module.
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Affiliation(s)
- Jamie C Gay
- Department of Pharmaceutical Sciences, Albany College of Pharmacy and Health Sciences, Colchester, Vermont
| | - Brian E Eckenroth
- Department of Microbiology and Molecular Genetics, University of Vermont, Burlington, Vermont
| | - Chiara M Evans
- Department of Pharmaceutical Sciences, Albany College of Pharmacy and Health Sciences, Colchester, Vermont
| | - Cassiano Langini
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | - Samuel Carlson
- Department of Pharmaceutical Sciences, Albany College of Pharmacy and Health Sciences, Colchester, Vermont
| | - Jonathan T Lloyd
- Department of Pharmaceutical Sciences, Albany College of Pharmacy and Health Sciences, Colchester, Vermont
| | - Amedeo Caflisch
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | - Karen C Glass
- Department of Pharmaceutical Sciences, Albany College of Pharmacy and Health Sciences, Colchester, Vermont
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26
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Bamborough P, Chung CW, Furze RC, Grandi P, Michon AM, Watson RJ, Mitchell DJ, Barnett H, Prinjha RK, Rau C, Sheppard RJ, Werner T, Demont EH. Aiming to Miss a Moving Target: Bromo and Extra Terminal Domain (BET) Selectivity in Constrained ATAD2 Inhibitors. J Med Chem 2018; 61:8321-8336. [PMID: 30226378 DOI: 10.1021/acs.jmedchem.8b00862] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
ATAD2 is a cancer-associated protein whose bromodomain has been described as among the least druggable of its class. In our recent disclosure of the first chemical probe against this bromodomain, GSK8814 (6), we described the use of a conformationally constrained methoxy piperidine to gain selectivity over the BET bromodomains. Here we describe an orthogonal conformational restriction strategy of the piperidine ring to give potent and selective tropane inhibitors and show structural insights into why this was more challenging than expected. Greater understanding of why different rational approaches succeeded or failed should help in the future design of selectivity in the bromodomain family.
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Affiliation(s)
| | | | | | - Paola Grandi
- Molecular Discovery Research, Cellzome GmbH , GlaxoSmithKline , Meyerhofstrasse 1 , 69117 Heidelberg , Germany
| | - Anne-Marie Michon
- Molecular Discovery Research, Cellzome GmbH , GlaxoSmithKline , Meyerhofstrasse 1 , 69117 Heidelberg , Germany
| | | | | | | | | | - Christina Rau
- Molecular Discovery Research, Cellzome GmbH , GlaxoSmithKline , Meyerhofstrasse 1 , 69117 Heidelberg , Germany
| | | | - Thilo Werner
- Molecular Discovery Research, Cellzome GmbH , GlaxoSmithKline , Meyerhofstrasse 1 , 69117 Heidelberg , Germany
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27
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Washetine K, Heeke S, Bonnetaud C, Kara-Borni M, Ilié M, Lassalle S, Butori C, Long-Mira E, Marquette CH, Cohen C, Mouroux J, Selva E, Tanga V, Bence C, Félix JM, Gazoppi L, Skhiri T, Gormally E, Boucher P, Clément B, Dagher G, Hofman V, Hofman P. Establishing a Dedicated Lung Cancer Biobank at the University Center Hospital of Nice (France). Why and How? Cancers (Basel) 2018; 10:cancers10070220. [PMID: 29966305 PMCID: PMC6070810 DOI: 10.3390/cancers10070220] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Revised: 06/20/2018] [Accepted: 06/28/2018] [Indexed: 12/11/2022] Open
Abstract
Lung cancer is the major cause of death from cancer in the world and its incidence is increasing in women. Despite the progress made in developing immunotherapies and therapies targeting genomic alterations, improvement in the survival rate of advanced stages or metastatic patients remains low. Thus, urgent development of effective therapeutic molecules is needed. The discovery of novel therapeutic targets and their validation requires high quality biological material and associated clinical data. With this aim, we established a biobank dedicated to lung cancers. We describe here our strategy and the indicators used and, through an overall assessment, present the strengths, weaknesses, opportunities and associated risks of this biobank.
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Affiliation(s)
- Kevin Washetine
- Hospital-Integrated Biobank (BB-0033-00025), Université Côte d'Azur, CHU de Nice, 06001 Nice CEDEX 1, France.
- Laboratory of Clinical and Experimental Pathology, Université Côte d'Azur, CHU de Nice, University Hospital Federation OncoAge, 06001 Nice CEDEX 1, France.
| | - Simon Heeke
- Team 4, Institute of Research on Cancer and Aging of Nice (IRCAN), Inserm U1081, CNRS UMR7284, Université Côte d'Azur, CHU de Nice, 06107 Nice CEDEX 2, France.
| | - Christelle Bonnetaud
- Hospital-Integrated Biobank (BB-0033-00025), Université Côte d'Azur, CHU de Nice, 06001 Nice CEDEX 1, France.
| | - Mehdi Kara-Borni
- Hospital-Integrated Biobank (BB-0033-00025), Université Côte d'Azur, CHU de Nice, 06001 Nice CEDEX 1, France.
| | - Marius Ilié
- Hospital-Integrated Biobank (BB-0033-00025), Université Côte d'Azur, CHU de Nice, 06001 Nice CEDEX 1, France.
- Laboratory of Clinical and Experimental Pathology, Université Côte d'Azur, CHU de Nice, University Hospital Federation OncoAge, 06001 Nice CEDEX 1, France.
- Team 4, Institute of Research on Cancer and Aging of Nice (IRCAN), Inserm U1081, CNRS UMR7284, Université Côte d'Azur, CHU de Nice, 06107 Nice CEDEX 2, France.
- FHU OncoAge, University of Nice Sophia Antipolis, 06001 Nice CEDEX 1, France.
| | - Sandra Lassalle
- Laboratory of Clinical and Experimental Pathology, Université Côte d'Azur, CHU de Nice, University Hospital Federation OncoAge, 06001 Nice CEDEX 1, France.
- Team 4, Institute of Research on Cancer and Aging of Nice (IRCAN), Inserm U1081, CNRS UMR7284, Université Côte d'Azur, CHU de Nice, 06107 Nice CEDEX 2, France.
- FHU OncoAge, University of Nice Sophia Antipolis, 06001 Nice CEDEX 1, France.
| | - Catherine Butori
- Laboratory of Clinical and Experimental Pathology, Université Côte d'Azur, CHU de Nice, University Hospital Federation OncoAge, 06001 Nice CEDEX 1, France.
- FHU OncoAge, University of Nice Sophia Antipolis, 06001 Nice CEDEX 1, France.
| | - Elodie Long-Mira
- Laboratory of Clinical and Experimental Pathology, Université Côte d'Azur, CHU de Nice, University Hospital Federation OncoAge, 06001 Nice CEDEX 1, France.
- Team 4, Institute of Research on Cancer and Aging of Nice (IRCAN), Inserm U1081, CNRS UMR7284, Université Côte d'Azur, CHU de Nice, 06107 Nice CEDEX 2, France.
- FHU OncoAge, University of Nice Sophia Antipolis, 06001 Nice CEDEX 1, France.
| | - Charles Hugo Marquette
- Team 4, Institute of Research on Cancer and Aging of Nice (IRCAN), Inserm U1081, CNRS UMR7284, Université Côte d'Azur, CHU de Nice, 06107 Nice CEDEX 2, France.
- FHU OncoAge, University of Nice Sophia Antipolis, 06001 Nice CEDEX 1, France.
- Department of Pulmonary Medicine and Oncology, Université Côte d'Azur, CHU de Nice, University Hospital Federation OncoAge, 06001 Nice CEDEX 1, France.
| | - Charlotte Cohen
- FHU OncoAge, University of Nice Sophia Antipolis, 06001 Nice CEDEX 1, France.
- Department of Thoracic Surgery, Université Côte d'Azur, CHU de Nice, University Hospital Federation OncoAge, 06001 Nice CEDEX 1, France.
| | - Jérôme Mouroux
- Team 4, Institute of Research on Cancer and Aging of Nice (IRCAN), Inserm U1081, CNRS UMR7284, Université Côte d'Azur, CHU de Nice, 06107 Nice CEDEX 2, France.
- FHU OncoAge, University of Nice Sophia Antipolis, 06001 Nice CEDEX 1, France.
- Department of Thoracic Surgery, Université Côte d'Azur, CHU de Nice, University Hospital Federation OncoAge, 06001 Nice CEDEX 1, France.
| | - Eric Selva
- Hospital-Integrated Biobank (BB-0033-00025), Université Côte d'Azur, CHU de Nice, 06001 Nice CEDEX 1, France.
| | - Virginie Tanga
- Hospital-Integrated Biobank (BB-0033-00025), Université Côte d'Azur, CHU de Nice, 06001 Nice CEDEX 1, France.
| | - Coraline Bence
- Laboratory of Clinical and Experimental Pathology, Université Côte d'Azur, CHU de Nice, University Hospital Federation OncoAge, 06001 Nice CEDEX 1, France.
| | - Jean-Marc Félix
- Hospital-Integrated Biobank (BB-0033-00025), Université Côte d'Azur, CHU de Nice, 06001 Nice CEDEX 1, France.
| | - Loic Gazoppi
- Hospital-Integrated Biobank (BB-0033-00025), Université Côte d'Azur, CHU de Nice, 06001 Nice CEDEX 1, France.
| | - Taycir Skhiri
- FHU OncoAge, University of Nice Sophia Antipolis, 06001 Nice CEDEX 1, France.
| | | | - Pascal Boucher
- French National Cancer Institut, 92513 Boulogne Billancourt CEDEX, France.
| | - Bruno Clément
- INSERM, INRA, University of Rennes, NuMeCan, CRB Santé, CHU Rennes, 35042 Rennes, France.
| | | | - Véronique Hofman
- Hospital-Integrated Biobank (BB-0033-00025), Université Côte d'Azur, CHU de Nice, 06001 Nice CEDEX 1, France.
- Laboratory of Clinical and Experimental Pathology, Université Côte d'Azur, CHU de Nice, University Hospital Federation OncoAge, 06001 Nice CEDEX 1, France.
- Team 4, Institute of Research on Cancer and Aging of Nice (IRCAN), Inserm U1081, CNRS UMR7284, Université Côte d'Azur, CHU de Nice, 06107 Nice CEDEX 2, France.
- FHU OncoAge, University of Nice Sophia Antipolis, 06001 Nice CEDEX 1, France.
| | - Paul Hofman
- Hospital-Integrated Biobank (BB-0033-00025), Université Côte d'Azur, CHU de Nice, 06001 Nice CEDEX 1, France.
- Laboratory of Clinical and Experimental Pathology, Université Côte d'Azur, CHU de Nice, University Hospital Federation OncoAge, 06001 Nice CEDEX 1, France.
- Team 4, Institute of Research on Cancer and Aging of Nice (IRCAN), Inserm U1081, CNRS UMR7284, Université Côte d'Azur, CHU de Nice, 06107 Nice CEDEX 2, France.
- FHU OncoAge, University of Nice Sophia Antipolis, 06001 Nice CEDEX 1, France.
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NEAT1_2 functions as a competing endogenous RNA to regulate ATAD2 expression by sponging microRNA-106b-5p in papillary thyroid cancer. Cell Death Dis 2018. [PMID: 29515109 PMCID: PMC5841310 DOI: 10.1038/s41419-018-0418-z] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Nuclear paraspeckle assembly transcript 1 (NEAT1), a long non-coding RNA (lncRNA), is a core structural component of paraspeckles and is essential for paraspeckle formation. NEAT1 comprises two different isoforms: NEAT1_1 (3.7 kb) and NEAT1_2 (23 kb). Recently, NEAT1 has been shown to have oncogenic roles and to facilitate tumorigenesis in various human cancers. However, the function of NEAT1 in papillary thyroid cancer (PTC) is not well understood. The relative expression levels of NEAT1_2, ATPase family AAA domain-containing protein 2 (ATAD2), and microRNA-106b-5p (miR-106b-5p) were assessed via quantitative real-time reverse transcription polymerase chain reaction (qRT-PCR). Four PTC cell lines were used to detect the relative expression of NEAT1_2. The effects of NEAT1_2 on PTC cells were studied by RNA interference approaches in vitro. The effects of NEAT1_2 on downstream proteins were detected by western blotting. The underlying mechanism was clarified by a rescue experiment, and three dual-luciferase reporter assays. NEAT1_2 expression was markedly increased in PTC tissues and the PTC cell lines (K1 and TPC1). The relative expression level of NEAT1_2 was positively associated with TNM stage and tumor size. NEAT1_2 knockdown led to a significant inhibition of growth and metastasis, and induced apoptosis in PTC cells. Knockdown of NEAT1_2 significantly inhibited malignant biological behavior by downregulating the oncogene ATAD2. In addition, NEAT1_2 could act as a competing endogenous RNA to regulate the expression of ATAD2 through downregulating miR-106b-5p. Taken together, our results indicated that NEAT1_2 is overexpressed in PTC. NEAT1_2 could function as a competing endogenous RNA to regulate ATAD2 expression by sponging miR-106b-5p in PTC. Targeting NEAT1_2 could be a promising therapeutic strategy for patients with PTC.
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29
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An 8-gene signature for prediction of prognosis and chemoresponse in non-small cell lung cancer. Oncotarget 2018; 7:86561-86572. [PMID: 27863408 PMCID: PMC5349935 DOI: 10.18632/oncotarget.13357] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Accepted: 10/29/2016] [Indexed: 12/26/2022] Open
Abstract
Identification of a potential gene signature for improved diagnosis in non-small cell lung cancer (NSCLC) patient is necessary. Here, we aim to establish and validate the prognostic efficacy of a gene set that can predict prognosis and benefits of adjuvant chemotherapy (ACT) in NSCLC patients from various ethnicities. An 8-gene signature was calculated from the gene expression of 181 patients using univariate Cox proportional hazard regression analysis. The prognostic value of the signature was robustly validated in 1,477 patients from five microarray independent data sets and one RNA-seq data set. The 8-gene signature was identified as an independent predictor of patient survival in the presence of clinical parameters in univariate and multivariate analyses [hazard ratio (HR): 2.84, 95% confidence interval CI (1.74-4.65), p=3.06e-05, [HR] 2.62, 95% CI (1.51-4.53), p=0.001], respectively. Subset analysis demonstrated that the 8-gene signature could identify high-risk patients in stage II-III with improved survival from ACT [(HR) 1.47, 95% CI (1.01-2.14), p=0.044]. The 8-gene signature also stratified risk groups in EGFR-mutated and wild-type patients. In conclusion, the 8-gene signature is a strong and independent predictor that can significantly stratify patients into low- and high-risk groups. Our gene signature also has the potential to predict patients in stage II-III that are likely to benefit from ACT.
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Ringnér M, Staaf J. Consensus of gene expression phenotypes and prognostic risk predictors in primary lung adenocarcinoma. Oncotarget 2018; 7:52957-52973. [PMID: 27437773 PMCID: PMC5288161 DOI: 10.18632/oncotarget.10641] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Accepted: 06/13/2016] [Indexed: 11/25/2022] Open
Abstract
Transcriptional profiling of lung adenocarcinomas has identified numerous gene expression phenotype (GEP) and risk prediction (RP) signatures associated with patient outcome. However, classification agreement between signatures, underlying transcriptional programs, and independent signature validation are less studied. We classified 2395 transcriptional adenocarcinoma profiles, assembled from 17 public cohorts, using 11 GEP and seven RP signatures, finding that 16 signatures were associated with patient survival in the total cohort and in multiple individual cohorts. For significant signatures, total cohort hazard ratios were ~2 in univariate analyses (mean=1.95, range=1.4-2.6). Strong classification agreement between signatures was observed, especially for predicted low-risk patients by adenocarcinoma-derived signatures. Expression of proliferation-related genes correlated strongly with GEP subtype classifications and RP scores, driving the gene signature association with prognosis. A three-group consensus definition of samples across 10 GEP classifiers demonstrated aggregation of samples with specific smoking patterns, gender, and EGFR/KRAS mutations, while survival differences were only significant when patients were divided into low- or high-risk. In summary, our study demonstrates a consensus between GEPs and RPs in lung adenocarcinoma through a common underlying transcriptional program. This consensus generalizes reported problems with current signatures in a clinical context, stressing development of new adenocarcinoma-specific single sample predictors for clinical use.
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Affiliation(s)
- Markus Ringnér
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Medicon Village, SE 22381, Lund, Sweden
| | - Johan Staaf
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Medicon Village, SE 22381, Lund, Sweden
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Couto PP, Bastos-Rodrigues L, Schayek H, Melo FM, Lisboa RGC, Miranda DM, Vilhena A, Bale AE, Friedman E, De Marco L. Spectrum of germline mutations in smokers and non-smokers in Brazilian non-small-cell lung cancer (NSCLC) patients. Carcinogenesis 2017; 38:1112-1118. [DOI: 10.1093/carcin/bgx089] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
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The role of miR-372 in ovarian carcinoma cell proliferation. Gene 2017; 624:14-20. [DOI: 10.1016/j.gene.2017.04.043] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2017] [Accepted: 04/25/2017] [Indexed: 01/22/2023]
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Horie M, Kaczkowski B, Ohshima M, Matsuzaki H, Noguchi S, Mikami Y, Lizio M, Itoh M, Kawaji H, Lassmann T, Carninci P, Hayashizaki Y, Forrest ARR, Takai D, Yamaguchi Y, Micke P, Saito A, Nagase T. Integrative CAGE and DNA Methylation Profiling Identify Epigenetically Regulated Genes in NSCLC. Mol Cancer Res 2017; 15:1354-1365. [PMID: 28698358 DOI: 10.1158/1541-7786.mcr-17-0191] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Revised: 06/12/2017] [Accepted: 06/28/2017] [Indexed: 11/16/2022]
Abstract
Lung cancer is the leading cause of cancer-related deaths worldwide. The majority of cancer driver mutations have been identified; however, relevant epigenetic regulation involved in tumorigenesis has only been fragmentarily analyzed. Epigenetically regulated genes have a great theranostic potential, especially in tumors with no apparent driver mutations. Here, epigenetically regulated genes were identified in lung cancer by an integrative analysis of promoter-level expression profiles from Cap Analysis of Gene Expression (CAGE) of 16 non-small cell lung cancer (NSCLC) cell lines and 16 normal lung primary cell specimens with DNA methylation data of 69 NSCLC cell lines and 6 normal lung epithelial cells. A core set of 49 coding genes and 10 long noncoding RNAs (lncRNA), which are upregulated in NSCLC cell lines due to promoter hypomethylation, was uncovered. Twenty-two epigenetically regulated genes were validated (upregulated genes with hypomethylated promoters) in the adenocarcinoma and squamous cell cancer subtypes of lung cancer using The Cancer Genome Atlas data. Furthermore, it was demonstrated that multiple copies of the REP522 DNA repeat family are prominently upregulated due to hypomethylation in NSCLC cell lines, which leads to cancer-specific expression of lncRNAs, such as RP1-90G24.10, AL022344.4, and PCAT7. Finally, Myeloma Overexpressed (MYEOV) was identified as the most promising candidate. Functional studies demonstrated that MYEOV promotes cell proliferation, survival, and invasion. Moreover, high MYEOV expression levels were associated with poor prognosis.Implications: This report identifies a robust list of 22 candidate driver genes that are epigenetically regulated in lung cancer; such genes may complement the known mutational drivers.Visual Overview: http://mcr.aacrjournals.org/content/molcanres/15/10/1354/F1.large.jpg Mol Cancer Res; 15(10); 1354-65. ©2017 AACR.
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Affiliation(s)
- Masafumi Horie
- Department of Respiratory Medicine, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
- Division for Health Service Promotion, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
- Division of Genomic Technologies (DGT), RIKEN Center for Life Science Technologies, Yokohama, Kanagawa, Japan
| | - Bogumil Kaczkowski
- Division of Genomic Technologies (DGT), RIKEN Center for Life Science Technologies, Yokohama, Kanagawa, Japan.
| | - Mitsuhiro Ohshima
- Department of Biochemistry, Ohu University School of Pharmaceutical Sciences, Koriyama, Fukushima, Japan
| | - Hirotaka Matsuzaki
- Department of Respiratory Medicine, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Satoshi Noguchi
- Department of Respiratory Medicine, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Yu Mikami
- Department of Respiratory Medicine, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
- Department of Clinical Laboratory, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Marina Lizio
- Division of Genomic Technologies (DGT), RIKEN Center for Life Science Technologies, Yokohama, Kanagawa, Japan
| | - Masayoshi Itoh
- Division of Genomic Technologies (DGT), RIKEN Center for Life Science Technologies, Yokohama, Kanagawa, Japan
- RIKEN Preventive Medicine and Diagnosis Innovation Program, Wako, Saitama, Japan
| | - Hideya Kawaji
- Division of Genomic Technologies (DGT), RIKEN Center for Life Science Technologies, Yokohama, Kanagawa, Japan
- RIKEN Preventive Medicine and Diagnosis Innovation Program, Wako, Saitama, Japan
| | - Timo Lassmann
- Division of Genomic Technologies (DGT), RIKEN Center for Life Science Technologies, Yokohama, Kanagawa, Japan
- Telethon Kids Institute, the University of Western Australia, Perth, Western Australia, Australia
| | - Piero Carninci
- Division of Genomic Technologies (DGT), RIKEN Center for Life Science Technologies, Yokohama, Kanagawa, Japan
| | | | - Alistair R R Forrest
- Division of Genomic Technologies (DGT), RIKEN Center for Life Science Technologies, Yokohama, Kanagawa, Japan
- Harry Perkins Institute of Medical Research, QEII Medical Centre and Centre for Medical Research, the University of Western Australia, Nedlands, Western Australia, Australia
| | - Daiya Takai
- Department of Clinical Laboratory, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Yoko Yamaguchi
- Department of Biochemistry, Nihon University School of Dentistry, Chiyoda-ku, Tokyo, Japan
- Division of Functional Morphology Dental Research Center Nihon University School of Dentistry, Chiyoda-ku, Tokyo, Japan
| | - Patrick Micke
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Akira Saito
- Department of Respiratory Medicine, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo, Japan.
- Division for Health Service Promotion, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Takahide Nagase
- Department of Respiratory Medicine, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
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Lu WJ, Chua MS, So SK. Suppression of ATAD2 inhibits hepatocellular carcinoma progression through activation of p53- and p38-mediated apoptotic signaling. Oncotarget 2016; 6:41722-35. [PMID: 26497681 PMCID: PMC4747184 DOI: 10.18632/oncotarget.6152] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Accepted: 09/30/2015] [Indexed: 12/16/2022] Open
Abstract
The ATPase family, AAA domain containing 2 (ATAD2) is highly expressed in multiple cancers. We aim to understand the clinical and biological significance of ATAD2 over-expression in hepatocellular carcinoma (HCC), as a means to validate it as a therapeutic target in HCC. We demonstrated that ATAD2 was over-expressed in HCC patients, where high ATAD2 levels were significantly correlated with aggressive phenotypes such as high AFP levels, advanced tumor stages, and vascular invasion. Using RNA interference, suppression of ATAD2 in HCC cell lines decreased cell viability, migration, and invasion, and induced apoptosis in vitro. Furthermore, we identified p53 and p38 as key proteins that mediate apoptosis induced by ATAD2 suppression. In HCC cells, we demonstrated that ATAD2 directly interacted with MKK3/6, which prevented p38 activation and therefore inhibited p38-mediated apoptosis. In vivo, suppression of ATAD2 impaired the growth of HepG2 and Hep3B subcutaneous xenografts, accompanied by enhanced apoptosis and p-p53 and p-p38 levels. Our results validate that ATAD2 is an important negative regulator of apoptosis, and that neutralizing its activity has promising anti-tumor effects in HCC cells.
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Affiliation(s)
- Wen-Jing Lu
- Asian Liver Center, Department of Surgery, Stanford University School of Medicine, Stanford, CA, USA
| | - Mei-Sze Chua
- Asian Liver Center, Department of Surgery, Stanford University School of Medicine, Stanford, CA, USA
| | - Samuel K So
- Asian Liver Center, Department of Surgery, Stanford University School of Medicine, Stanford, CA, USA
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Xu W, Jia G, Davie JR, Murphy L, Kratzke R, Banerji S. A 10-Gene Yin Yang Expression Ratio Signature for Stage IA and IB Non-Small Cell Lung Cancer. J Thorac Oncol 2016; 11:2150-2160. [PMID: 27498386 DOI: 10.1016/j.jtho.2016.07.023] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2015] [Revised: 06/29/2016] [Accepted: 07/27/2016] [Indexed: 12/16/2022]
Abstract
INTRODUCTION Lung cancer is the leading killer cancer worldwide. There is an urgent need for easy-to-use and robust clinical gene signatures for improved prognosis and treatment prediction. METHODS We used a gene expression signature termed the Yin and Yang mean ratio (YMR), which is based on two groups of genes with opposing function, to determine lung cancer prognosis. The YMR signature represents the relative state of an individual tumor on a gene expression spectrum ranging from malignancy to the normal healthy lung. The genes in the YMR signature have therefore been determined independently of survival time, which is different from previous regression models. We then leveraged the cross-platform utility of the YMR signature to optimize the signature into a smaller set of genes that validated the robustness of the signature in many independent lung cancer expression data sets. RESULTS Four Yin and six Yang genes were optimized using 741 NSCLC cases from diverse platforms, including microarray and RNA sequencing. The 10-gene signature demonstrated significant differences in survival in eight individual independent data sets and a larger combined 1346-patient data set. When multivariate analysis taking into account other common predictors of survival was used, the 5-year recurrence-free rate of YMR (p = 6.4 × 10-6, HR =1.71 [1.36-2.16]) was secondary only to stage. The YMR signature significantly separated high- and low-risk patients with stage IA or 1B adenocarcinoma and squamous cell carcinomas of all stages. The YMR signature can also predict the benefit of adjuvant chemotherapy in high-risk patients with stage I NSCLC. CONCLUSIONS The YMR signature has great potential for guiding clinical management for NSCLC, particularly early-stage disease. The signature appears more reproducible than older signatures and functions using a variety of common gene expression platforms.
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Affiliation(s)
- Wayne Xu
- Research Institute of Oncology and Hematology, CancerCare Manitoba, Winnipeg, Manitoba, Canada; Department of Biochemistry and Medical Genetics, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Manitoba, Canada; College of Pharmacy, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Manitoba, Canada.
| | - Gaofeng Jia
- Research Institute of Oncology and Hematology, CancerCare Manitoba, Winnipeg, Manitoba, Canada
| | - James R Davie
- Research Institute of Oncology and Hematology, CancerCare Manitoba, Winnipeg, Manitoba, Canada; Department of Biochemistry and Medical Genetics, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Leigh Murphy
- Research Institute of Oncology and Hematology, CancerCare Manitoba, Winnipeg, Manitoba, Canada; Department of Biochemistry and Medical Genetics, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Robert Kratzke
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota; Division of Hematology, Oncology and Transplantation, Department of Medicine, University of Minnesota, Minneapolis, Minnesota
| | - Shantanu Banerji
- Research Institute of Oncology and Hematology, CancerCare Manitoba, Winnipeg, Manitoba, Canada; Section of Hematology and Oncology, Department of Internal Medicine, Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Manitoba, Canada; Department of Medical Oncology and Hematology, CancerCare Manitoba, Winnipeg, Manitoba, Canada
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An ANCCA/PRO2000-miR-520a-E2F2 regulatory loop as a driving force for the development of hepatocellular carcinoma. Oncogenesis 2016; 5:e229. [PMID: 27239961 PMCID: PMC4945746 DOI: 10.1038/oncsis.2016.22] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Revised: 12/16/2015] [Accepted: 12/20/2015] [Indexed: 01/09/2023] Open
Abstract
Hepatocellular carcinoma (HCC) is one of the most common malignancies in Asia especially in China. We previously identified that ANCCA/PRO2000 as an important proliferation-associated protein predicted poor prognosis of patients with HCC. However, the molecular mechanisms of ANCCA/PRO2000 leading to hepatocarcinogenesis and progression are still obscure. In the present study, we found that ANCCA/PRO2000 overexpression in HCC specimens correlated with aggressive tumor behavior and poor survival. Furthermore, ANCCA/PRO2000 exerts strong oncogenic function in HCC and promotes cell proliferation by regulating E2F2 expression, a critical cell cycle regulator. Notably, miR-520a is an intermediate regulator between ANCCA/PRO2000 and E2F2. Mechanistically, ANCCA/PRO2000 not only interacts with E2F2 but also negatively regulates miR-520a that inhibits E2F2 to cooperatively promote in vitro and in vivo growth of HCC cells. Moreover, we demonstrated that ANCCA/PRO2000 enhances the migratory capacity of HCC cells partially by suppressing ERO1L and G3BP2 expression. Additional research identified that miR-372, as a prognostic factor for HCC, could directly target ANCCA/PRO2000. Our results suggest the ANCCA/PRO2000-miR-520a-E2F2 regulatory loop as a driving force for HCC development and ANCCA/PRO2000 as a potential therapeutic target for HCC.
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Wang D, Pan Y, Hao T, Chen Y, Qiu S, Chen L, Zhao J. Clinical and Prognostic Significance of ANCCA in Squamous Cell Lung Carcinoma Patients. Arch Med Res 2016; 47:89-95. [PMID: 27131099 DOI: 10.1016/j.arcmed.2016.04.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Accepted: 04/06/2016] [Indexed: 02/01/2023]
Abstract
BACKGROUND AND AIMS AAA+ nuclear coregulatory cancer associated (ANCCA) has been demonstrated as playing important roles in diverse biological processes including tumorigenesis. However, the clinical and prognostic significance of ANCCA in squamous cell lung carcinoma (SCLC) patients is still unknown. The aim of this study is to identify the role of ANCCA in SCLC patients. METHODS ANCCA mRNA and protein expressions were detected in SCLC tissues and cell lines by real-time PCR and Western blot. We examined the ANCCA protein expression in 152 SCLC samples by immunohistochemistry and analyzed the association between the expression of ANCCA protein and clinicopathological characteristics of SCLC patients. RESULTS ANCCA mRNA and protein expression are increased in SCLC tissues and cell lines. Moreover, ANCCA protein overexpression was associated with differentiated degree, clinical stage, lymph node metastasis, and distant metastasis. In uni- and multivariate analyses, ANCCA protein overexpression was an independent poor prognostic factor for SCLC patients. CONCLUSIONS ANCCA act as a potential biomarker for therapeutic strategy and prognostic prediction for SCLC.
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Affiliation(s)
- Dingmiao Wang
- Department of Emergency Medicine, Xianning Central Hospital, Xianning City, Hubei Province, China; Department of Cardiothoracic Surgery, Zhongnan Hospital of Wuhan University, Wuhan, Hubei Province, China
| | - Yang Pan
- Department of Emergency Medicine, Xianning Central Hospital, Xianning City, Hubei Province, China
| | - Ting Hao
- Department of Emergency Medicine, Xianning Central Hospital, Xianning City, Hubei Province, China
| | - Yong Chen
- Department of Emergency Medicine, Xianning Central Hospital, Xianning City, Hubei Province, China
| | - Shiming Qiu
- Department of Emergency Medicine, Xianning Central Hospital, Xianning City, Hubei Province, China
| | - Ling Chen
- Department of Emergency Medicine, Xianning Central Hospital, Xianning City, Hubei Province, China
| | - Jinping Zhao
- Department of Cardiothoracic Surgery, Zhongnan Hospital of Wuhan University, Wuhan, Hubei Province, China.
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Hou M, Huang R, Song Y, Feng D, Jiang Y, Liu M. ATAD2 overexpression is associated with progression and prognosis in colorectal cancer. Jpn J Clin Oncol 2016; 46:222-7. [PMID: 26819280 DOI: 10.1093/jjco/hyv195] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2015] [Accepted: 11/29/2015] [Indexed: 01/05/2023] Open
Abstract
OBJECTIVES ATPase family AAA domain-containing 2 plays an important role in tumor progression including cell cycle, proliferation, apoptosis and chemoresistance. However, the expression of ATPase family AAA domain-containing 2 in colorectal cancer and its significance are still unclear. The aim of this study was to examine the expression of ATPase family AAA domain-containing 2 in colorectal cancer. METHODS Immunohistochemistry was used to determine the expression of ATPase family AAA domain-containing 2 in 155 colorectal cancer and 30 matched adjacent noncancerous tissues. The correlation of ATPase family AAA domain-containing 2 expression with clinicopathological variables was assessed using chi-square test. Patient survival was analyzed using the Kaplan-Meier and log-rank tests. Cox regression was performed for the multivariate analysis of prognostic factors. RESULTS High expression of ATPase family AAA domain-containing 2 was detected in 58.1% of the colorectal cancers and was significantly associated with advanced tumor-node-metastasis stage (P = 0.044), poor differentiation (P = 0.028), deep infiltration (P < 0.001), lymphovascular invasion (P = 0.006), lymph node metastasis (P = 0.024) and recurrence (P = 0.022). Patients with high ATPase family AAA domain-containing 2 expression had significantly poorer overall survival and disease-free survival (both P < 0.001) when compared with patients with low expression of ATPase family AAA domain-containing 2. The multivariate analysis showed that ATPase family AAA domain-containing 2 was an independent factor for both overall survival (P = 0.003; hazard ratio (HR): 2.356; 95% confidence interval (CI): 1.335-4.158) and disease-free survival (P = 0.001; HR: 2.643; 95% CI: 1.489-4.693). CONCLUSIONS These results showed that ATPase family AAA domain-containing 2 overexpression was associated with progression and prognosis of colorectal cancer.
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Affiliation(s)
- Mingming Hou
- Department of Orthopedics, The Fourth Affiliated Hospital of Harbin Medical University, Harbin
| | - Rui Huang
- Department of Colorectal Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin
| | - Yanni Song
- Department of Breast Surgery, The Third Affiliated Hospital of Harbin Medical University, Harbin
| | - Di Feng
- Department of Pathology, The Third Affiliated Hospital of Harbin Medical University, Harbin
| | - Yang Jiang
- Department of Pathology, The Third Affiliated Hospital of Harbin Medical University, Harbin
| | - Ming Liu
- Department of General Surgery, The Fourth Affiliated Hospital of Harbin Medical University, Harbin, China
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Krakstad C, Tangen IL, Hoivik EA, Halle MK, Berg A, Werner HM, Ræder MB, Kusonmano K, Zou JX, Øyan AM, Stefansson I, Trovik J, Kalland KH, Chen HW, Salvesen HB. ATAD2 overexpression links to enrichment of B-MYB-translational signatures and development of aggressive endometrial carcinoma. Oncotarget 2015; 6:28440-52. [PMID: 26308378 PMCID: PMC4695070 DOI: 10.18632/oncotarget.4955] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2015] [Accepted: 07/02/2015] [Indexed: 01/20/2023] Open
Abstract
We have explored the potential for clinical implementation of ATAD2 as a biomarker for aggressive endometrial cancer by investigating to what extent immunohistochemical (IHC) staining for ATAD2 is feasible, reflects clinical phenotype and molecular subgroups of endometrial carcinomas. Increased expression of the ATAD2 gene has been implicated in cancer development and progression in a number of tissues, but few studies have investigated ATAD2 expression using IHC. Here we show that high ATAD2 protein expression is significantly associated with established clinical-pathological variables for aggressive endometrial cancer, also in the subset of estrogen receptor α (ERα) positive tumors. Protein and mRNA expression of ATAD2 were highly correlated (P < 0.001), suggesting that IHC staining may represent a more clinically applicable measure of ATAD2 level in routinely collected formalin fixed paraffin embedded specimens. Gene expression alterations in samples with high ATAD2 expression revealed upregulation of several cancer-related genes (B-MYB, CDCs, E2Fs) and gene sets that previously have been linked to aggressive disease and potential for new targeting therapies. Our results support that IHC staining for ATAD2 may be a clinically applicable biomarker reflecting clinical phenotype and targetable alterations in endometrial carcinomas to be further explored in controlled clinical trials.
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Affiliation(s)
- Camilla Krakstad
- Centre for Cancer Biomarkers, Department of Clinical Science, University of Bergen, Bergen, Norway
- Department of Gynecology and Obstetrics, Haukeland University Hospital, Bergen, Norway
| | - Ingvild L. Tangen
- Centre for Cancer Biomarkers, Department of Clinical Science, University of Bergen, Bergen, Norway
- Department of Gynecology and Obstetrics, Haukeland University Hospital, Bergen, Norway
| | - Erling A. Hoivik
- Centre for Cancer Biomarkers, Department of Clinical Science, University of Bergen, Bergen, Norway
- Department of Gynecology and Obstetrics, Haukeland University Hospital, Bergen, Norway
| | - Mari K. Halle
- Centre for Cancer Biomarkers, Department of Clinical Science, University of Bergen, Bergen, Norway
- Department of Gynecology and Obstetrics, Haukeland University Hospital, Bergen, Norway
| | - Anna Berg
- Centre for Cancer Biomarkers, Department of Clinical Science, University of Bergen, Bergen, Norway
- Department of Gynecology and Obstetrics, Haukeland University Hospital, Bergen, Norway
| | - Henrica M. Werner
- Centre for Cancer Biomarkers, Department of Clinical Science, University of Bergen, Bergen, Norway
- Department of Gynecology and Obstetrics, Haukeland University Hospital, Bergen, Norway
| | - Maria B. Ræder
- Centre for Cancer Biomarkers, Department of Clinical Science, University of Bergen, Bergen, Norway
- Department of Gynecology and Obstetrics, Haukeland University Hospital, Bergen, Norway
| | - Kanthida Kusonmano
- Centre for Cancer Biomarkers, Department of Clinical Science, University of Bergen, Bergen, Norway
- Department of Gynecology and Obstetrics, Haukeland University Hospital, Bergen, Norway
- Computational Biology Unit, University of Bergen, Bergen, Norway
| | - June X. Zou
- Department of Internal Medicine and Department of Biochemistry and Molecular Medicine, UC Davis Comprehensive Cancer Center, University of California, Davis, CA, USA
| | - Anne M. Øyan
- Centre for Cancer Biomarkers, Department of Clinical Medicine, University of Bergen, Bergen, Norway
- Department of Microbiology, Haukeland University Hospital, Bergen, Norway
| | - Ingunn Stefansson
- Centre for Cancer Biomarkers, Department of Clinical Medicine, University of Bergen, Bergen, Norway
- Department of Pathology, Haukeland University Hospital, Bergen, Norway
| | - Jone Trovik
- Centre for Cancer Biomarkers, Department of Clinical Science, University of Bergen, Bergen, Norway
- Department of Gynecology and Obstetrics, Haukeland University Hospital, Bergen, Norway
| | - Karl-Henning Kalland
- Centre for Cancer Biomarkers, Department of Clinical Medicine, University of Bergen, Bergen, Norway
- Department of Microbiology, Haukeland University Hospital, Bergen, Norway
| | - Hong-Wu Chen
- Department of Internal Medicine and Department of Biochemistry and Molecular Medicine, UC Davis Comprehensive Cancer Center, University of California, Davis, CA, USA
| | - Helga B. Salvesen
- Centre for Cancer Biomarkers, Department of Clinical Science, University of Bergen, Bergen, Norway
- Department of Gynecology and Obstetrics, Haukeland University Hospital, Bergen, Norway
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Ringnér M, Jönsson G, Staaf J. Prognostic and Chemotherapy Predictive Value of Gene-Expression Phenotypes in Primary Lung Adenocarcinoma. Clin Cancer Res 2015; 22:218-29. [DOI: 10.1158/1078-0432.ccr-15-0529] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2015] [Accepted: 08/03/2015] [Indexed: 11/16/2022]
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Demont EH, Chung CW, Furze RC, Grandi P, Michon AM, Wellaway C, Barrett N, Bridges AM, Craggs PD, Diallo H, Dixon DP, Douault C, Emmons AJ, Jones EJ, Karamshi BV, Locke K, Mitchell DJ, Mouzon BH, Prinjha RK, Roberts AD, Sheppard RJ, Watson RJ, Bamborough P. Fragment-Based Discovery of Low-Micromolar ATAD2 Bromodomain Inhibitors. J Med Chem 2015; 58:5649-73. [PMID: 26155854 DOI: 10.1021/acs.jmedchem.5b00772] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Overexpression of ATAD2 (ATPase family, AAA domain containing 2) has been linked to disease severity and progression in a wide range of cancers, and is implicated in the regulation of several drivers of cancer growth. Little is known of the dependence of these effects upon the ATAD2 bromodomain, which has been categorized as among the least tractable of its class. The absence of any potent, selective inhibitors limits clear understanding of the therapeutic potential of the bromodomain. Here, we describe the discovery of a hit from a fragment-based targeted array. Optimization of this produced the first known micromolar inhibitors of the ATAD2 bromodomain.
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Affiliation(s)
| | | | | | - Paola Grandi
- §Molecular Discovery Research, Cellzome GmbH, GlaxoSmithKline, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Anne-Marie Michon
- §Molecular Discovery Research, Cellzome GmbH, GlaxoSmithKline, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Andy D Roberts
- ∥Drug Metabolism and Pharmacokinetics (DMPK), GlaxoSmithKline, Park Road, Ware, Hertfordshire SG12 0DP, United Kingdom
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Gnad F, Doll S, Manning G, Arnott D, Zhang Z. Bioinformatics analysis of thousands of TCGA tumors to determine the involvement of epigenetic regulators in human cancer. BMC Genomics 2015; 16 Suppl 8:S5. [PMID: 26110843 PMCID: PMC4480953 DOI: 10.1186/1471-2164-16-s8-s5] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Background Many cancer cells show distorted epigenetic landscapes. The Cancer Genome Atlas (TCGA) project profiles thousands of tumors, allowing the discovery of somatic alterations in the epigenetic machinery and the identification of potential cancer drivers among members of epigenetic protein families. Methods We integrated mutation, expression, and copy number data from 5943 tumors from 13 cancer types to train a classification model that predicts the likelihood of being an oncogene (OG), tumor suppressor (TSG) or neutral gene (NG). We applied this predictor to epigenetic regulator genes (ERGs), and used differential expression and correlation network analysis to identify dysregulated ERGs along with co-expressed cancer genes. Furthermore, we quantified global proteomic changes by mass spectrometry after EZH2 inhibition. Results Mutation-based classifiers uncovered the OG-like profile of DNMT3A and TSG-like profiles for several ERGs. Differential gene expression and correlation network analyses revealed that EZH2 is the most significantly over-expressed ERG in cancer and is co-regulated with a cell cycle network. Proteomic analysis showed that EZH2 inhibition induced down-regulation of cell cycle regulators in lymphoma cells. Conclusions Using classical driver genes to train an OG/TSG predictor, we determined the most predictive features at the gene level. Our predictor uncovered one OG and several TSGs among ERGs. Expression analyses elucidated multiple dysregulated ERGs including EZH2 as member of a co-expressed cell cycle network.
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Overexpression of ANCCA/ATAD2 in endometrial carcinoma and its correlation with tumor progression and poor prognosis. Tumour Biol 2015; 36:4479-85. [PMID: 25934333 DOI: 10.1007/s13277-015-3089-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2014] [Accepted: 01/08/2015] [Indexed: 01/22/2023] Open
Abstract
This study aimed to explore the clinical significance of AAA+ (ATPases associated with various cellular activities) nuclear coregulator cancer-associated (ANCCA) protein expression in endometrial carcinoma (EC). Correlations of ANCCA expression with clinicopathological factors and prognosis of EC patients were analyzed. Expression of ANCCA was detected in EC from 207 patients along with corresponding normal endometrium specimens by immunohistochemistry. ANCCA immunoreactivity was overexpressed in EC cases compared with that in normal endometrium (P < 0.001). High ANCCA expression was positively correlated with the International Federation of Gynecology and Obstetrics (FIGO) stage, histological grade, depth of myometrial invasion, lymph node metastasis, lymph vascular space involvement, and recurrence but not with age and histological type. Patients with high ANCCA expression exhibited significantly poorer overall survival (OS) and disease-free survival (DFS) than patients with low ANCCA expression (P = 0.001 and 0.002, respectively). Cox multivariate analysis showed that high ANCCA expression was an independent prognostic factor for both OS (hazard ratio (HR) = 4.954, 95 % confidence interval (CI) = 1.537-15.966; P = 0.007) and DFS of patients with EC (HR = 4.237, 95 % CI = 1.295-13.859; P = 0.017). We identified ANCCA protein expression as a novel independent poor prognostic indicator in EC.
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Cell cycle regulation of human DNA repair and chromatin remodeling genes. DNA Repair (Amst) 2015; 30:53-67. [PMID: 25881042 DOI: 10.1016/j.dnarep.2015.03.007] [Citation(s) in RCA: 143] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2014] [Revised: 03/03/2015] [Accepted: 03/20/2015] [Indexed: 01/10/2023]
Abstract
Maintenance of a genome requires DNA repair integrated with chromatin remodeling. We have analyzed six transcriptome data sets and one data set on translational regulation of known DNA repair and remodeling genes in synchronized human cells. These data are available through our new database: www.dnarepairgenes.com. Genes that have similar transcription profiles in at least two of our data sets generally agree well with known protein profiles. In brief, long patch base excision repair (BER) is enriched for S phase genes, whereas short patch BER uses genes essentially equally expressed in all cell cycle phases. Furthermore, most genes related to DNA mismatch repair, Fanconi anemia and homologous recombination have their highest expression in the S phase. In contrast, genes specific for direct repair, nucleotide excision repair, as well as non-homologous end joining do not show cell cycle-related expression. Cell cycle regulated chromatin remodeling genes were most frequently confined to G1/S and S. These include e.g. genes for chromatin assembly factor 1 (CAF-1) major subunits CHAF1A and CHAF1B; the putative helicases HELLS and ATAD2 that both co-activate E2F transcription factors central in G1/S-transition and recruit DNA repair and chromatin-modifying proteins and DNA double strand break repair proteins; and RAD54L and RAD54B involved in double strand break repair. TOP2A was consistently most highly expressed in G2, but also expressed in late S phase, supporting a role in regulating entry into mitosis. Translational regulation complements transcriptional regulation and appears to be a relatively common cell cycle regulatory mechanism for DNA repair genes. Our results identify cell cycle phases in which different pathways have highest activity, and demonstrate that periodically expressed genes in a pathway are frequently co-expressed. Furthermore, the data suggest that S phase expression and over-expression of some multifunctional chromatin remodeling proteins may set up feedback loops driving cancer cell proliferation.
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Zheng L, Li T, Zhang Y, Guo Y, Yao J, Dou L, Guo K. Oncogene ATAD2 promotes cell proliferation, invasion and migration in cervical cancer. Oncol Rep 2015; 33:2337-44. [PMID: 25813398 DOI: 10.3892/or.2015.3867] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2014] [Accepted: 03/08/2015] [Indexed: 11/05/2022] Open
Abstract
The ATPase family AAA domain-containing protein 2 (ATAD2) is associated with many cellular processes, such as cell proliferation, invasion and migration. However, the molecular biological function of the ATAD2 gene in cervical cancer is unclear. The purpose of this study was to explore ATAD2 expression in cervical cancer, evaluate the relationship between the development of cervical cancer, metastasis and clinicopathological characteristics, and discuss the implications for its use in clinical treatment. Protein and mRNA expression of ATAD2 was examined in tissues and cell lines. Tumor tissues from 135 cases of cervical cancer were collected for evaluation of ATAD2 expression by immunohistochemistry and western blotting. Prognostic significance was evaluated by the Cox hazards model and Kaplan-Meier survival method. HeLa and SiHa cells were transfected with two siRNAs targeting ATAD2. ATAD2 knockdown was used to analyze cell proliferation, invasion and migration. Cell viability was evaluated with the Cell Counting Κit-8 (CCK-8) assay, cell invasion by a Transwell assay and cell migration by a wound healing/scratch migration assay. ATAD2 was shown to be highly expressed in cervical cancer tissues, both at the transcriptional and protein levels, and was correlated with poor patient survival (P<0.05). Knockdown of ATAD2 in the HeLa and SiHa cells was found to reduce the capacity for invasion and migration (P<0.05), and inhibited the growth and clonogenic potential of the HeLa and SiHa cell lines. Our results suggest that cervical cancer tissues may have highly expressed ATAD2, which is associated with tumor stage and lymph node status (P<0.05). Oncogene ATAD2 may play an important role in cervical cancer proliferation, invasion and migration. It could serve as a prognostic marker and a therapeutic target for cervical cancer.
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Affiliation(s)
- Le Zheng
- Department of Gynecology, The First Hospital of China Medical University, Shenyang, Liaoning 110001, P.R. China
| | - Tianren Li
- Department of Gynecology, The First Hospital of China Medical University, Shenyang, Liaoning 110001, P.R. China
| | - Yi Zhang
- Department of Gynecology, The First Hospital of China Medical University, Shenyang, Liaoning 110001, P.R. China
| | - Yi Guo
- Department of Gynecology, The First Hospital of China Medical University, Shenyang, Liaoning 110001, P.R. China
| | - Jihang Yao
- Department of Gynecology, The First Hospital of China Medical University, Shenyang, Liaoning 110001, P.R. China
| | - Lei Dou
- Department of Gynecology, The First Hospital of China Medical University, Shenyang, Liaoning 110001, P.R. China
| | - Kejun Guo
- Department of Gynecology, The First Hospital of China Medical University, Shenyang, Liaoning 110001, P.R. China
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Starmans MHW, Pintilie M, Chan-Seng-Yue M, Moon NC, Haider S, Nguyen F, Lau SK, Liu N, Kasprzyk A, Wouters BG, Der SD, Shepherd FA, Jurisica I, Penn LZ, Tsao MS, Lambin P, Boutros PC. Integrating RAS status into prognostic signatures for adenocarcinomas of the lung. Clin Cancer Res 2015; 21:1477-86. [PMID: 25609067 DOI: 10.1158/1078-0432.ccr-14-1749] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
PURPOSE While the dysregulation of specific pathways in cancer influences both treatment response and outcome, few current prognostic markers explicitly consider differential pathway activation. Here we explore this concept, focusing on K-Ras mutations in lung adenocarcinoma (present in 25%-35% of patients). EXPERIMENTAL DESIGN The effect of K-Ras mutation status on prognostic accuracy of existing signatures was evaluated in 404 patients. Genes associated with K-Ras mutation status were identified and used to create a RAS pathway activation classifier to provide a more accurate measure of RAS pathway status. Next, 8 million random signatures were evaluated to assess differences in prognosing patients with or without RAS activation. Finally, a prognostic signature was created to target patients with RAS pathway activation. RESULTS We first show that K-Ras status influences the accuracy of existing prognostic signatures, which are effective in K-Ras-wild-type patients but fail in patients with K-Ras mutations. Next, we show that it is fundamentally more difficult to predict the outcome of patients with RAS activation (RAS(mt)) than that of those without (RAS(wt)). More importantly, we demonstrate that different signatures are prognostic in RAS(wt) and RAS(mt). Finally, to exploit this discovery, we create separate prognostic signatures for RAS(wt) and RAS(mt) patients and show that combining them significantly improves predictions of patient outcome. CONCLUSIONS We present a nested model for integrated genomic and transcriptomic data. This model is general and is not limited to lung adenocarcinomas but can be expanded to other tumor types and oncogenes.
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Affiliation(s)
- Maud H W Starmans
- Informatics and Biocomputing Program, Ontario Institute for Cancer Research, Toronto, Canada. Department of Radiation Oncology (Maastro), GROW-School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, the Netherlands
| | - Melania Pintilie
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
| | - Michelle Chan-Seng-Yue
- Informatics and Biocomputing Program, Ontario Institute for Cancer Research, Toronto, Canada
| | - Nathalie C Moon
- Informatics and Biocomputing Program, Ontario Institute for Cancer Research, Toronto, Canada
| | - Syed Haider
- Informatics and Biocomputing Program, Ontario Institute for Cancer Research, Toronto, Canada. Computer Laboratory, University of Cambridge, Cambridge, United Kingdom
| | - Francis Nguyen
- Informatics and Biocomputing Program, Ontario Institute for Cancer Research, Toronto, Canada
| | - Suzanne K Lau
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada. Department of Medical Biophysics, University of Toronto, Toronto, Canada
| | - Ni Liu
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
| | - Arek Kasprzyk
- Informatics and Biocomputing Program, Ontario Institute for Cancer Research, Toronto, Canada. Center for Translational Genomics and Bioinformatics, San Raffaelle Hospital, Milan, Italy. Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Bradly G Wouters
- Department of Radiation Oncology (Maastro), GROW-School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, the Netherlands. Princess Margaret Cancer Centre, University Health Network, Toronto, Canada. Department of Medical Biophysics, University of Toronto, Toronto, Canada. Department of Radiation Oncology, University of Toronto, Toronto, Canada
| | - Sandy D Der
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
| | - Frances A Shepherd
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
| | - Igor Jurisica
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada. Department of Medical Biophysics, University of Toronto, Toronto, Canada. Department of Computer Science, University of Toronto, Toronto, Canada
| | - Linda Z Penn
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada. Department of Medical Biophysics, University of Toronto, Toronto, Canada
| | - Ming-Sound Tsao
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada. Department of Medical Biophysics, University of Toronto, Toronto, Canada. Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
| | - Philippe Lambin
- Department of Radiation Oncology (Maastro), GROW-School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, the Netherlands
| | - Paul C Boutros
- Informatics and Biocomputing Program, Ontario Institute for Cancer Research, Toronto, Canada. Princess Margaret Cancer Centre, University Health Network, Toronto, Canada. Department of Medical Biophysics, University of Toronto, Toronto, Canada. Department of Pharmacology and Toxicology, University of Toronto, Toronto, Canada.
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Karlsson A, Ringnér M, Lauss M, Botling J, Micke P, Planck M, Staaf J. Genomic and transcriptional alterations in lung adenocarcinoma in relation to smoking history. Clin Cancer Res 2014; 20:4912-24. [PMID: 25037737 DOI: 10.1158/1078-0432.ccr-14-0246] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
PURPOSE Cigarette smoking is the major pathogenic factor for lung cancer. The precise mechanisms of tobacco-related carcinogenesis and its effect on the genomic and transcriptional landscape in lung cancer are not fully understood. EXPERIMENTAL DESIGN A total of 1,398 (277 never-smokers and 1,121 smokers) genomic and 1,449 (370 never-smokers and 1,079 smokers) transcriptional profiles were assembled from public lung adenocarcinoma cohorts, including matched next-generation DNA-sequencing data (n = 423). Unsupervised and supervised methods were used to identify smoking-related copy-number alterations (CNAs), predictors of smoking status, and molecular subgroups. RESULTS Genomic meta-analyses showed that never-smokers and smokers harbored a similar frequency of total CNAs, although specific regions (5q, 8q, 16p, 19p, and 22q) displayed a 20% to 30% frequency difference between the two groups. Importantly, supervised classification analyses based on CNAs or gene expression could not accurately predict smoking status (balanced accuracies ∼60% to 80%). However, unsupervised multicohort transcriptional profiling stratified adenocarcinomas into distinct molecular subgroups with specific patterns of CNAs, oncogenic mutations, and mutation transversion frequencies that were independent of the smoking status. One subgroup included approximately 55% to 90% of never-smokers and approximately 20% to 40% of smokers (both current and former) with molecular and clinical features of a less aggressive and smoking-unrelated disease. Given the considerable intragroup heterogeneity in smoking-defined subgroups, especially among former smokers, our results emphasize the clinical importance of accurate molecular characterization of lung adenocarcinoma. CONCLUSIONS The landscape of smoking-related CNAs and transcriptional alterations in adenocarcinomas is complex, heterogeneous, and with moderate differences. Our results support a molecularly distinct less aggressive adenocarcinoma entity, arising in never-smokers and a subset of smokers.
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Affiliation(s)
- Anna Karlsson
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden. CREATE Health Strategic Center for Translational Cancer Research, Lund University, Lund, Sweden
| | - Markus Ringnér
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden. CREATE Health Strategic Center for Translational Cancer Research, Lund University, Lund, Sweden
| | - Martin Lauss
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden
| | - Johan Botling
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Patrick Micke
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Maria Planck
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden. CREATE Health Strategic Center for Translational Cancer Research, Lund University, Lund, Sweden
| | - Johan Staaf
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden. CREATE Health Strategic Center for Translational Cancer Research, Lund University, Lund, Sweden.
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Wik E, Trovik J, Kusonmano K, Birkeland E, Raeder MB, Pashtan I, Hoivik EA, Krakstad C, Werner HMJ, Holst F, Mjøs S, Halle MK, Mannelqvist M, Mauland KK, Oyan AM, Stefansson IM, Petersen K, Simon R, Cherniack AD, Meyerson M, Kalland KH, Akslen LA, Salvesen HB. Endometrial Carcinoma Recurrence Score (ECARS) validates to identify aggressive disease and associates with markers of epithelial-mesenchymal transition and PI3K alterations. Gynecol Oncol 2014; 134:599-606. [PMID: 24995579 DOI: 10.1016/j.ygyno.2014.06.026] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2014] [Revised: 06/21/2014] [Accepted: 06/25/2014] [Indexed: 10/25/2022]
Abstract
PURPOSE Our previously reported 29-gene expression signature identified an aggressive subgroup of endometrial cancer patients with PI3K activation. We here wanted to validate these findings by independent patient series. PATIENTS AND METHODS The 29-gene expression signature was assessed in fresh frozen tumor tissue from 280 primary endometrial carcinomas (three independent cohorts), 19 metastatic lesions and in 333 primary endometrial carcinomas using TCGA data, and expression was related to clinico-pathologic features and survival. The 29-gene signature was assessed by real-time quantitative PCR, DNA oligonucleotide microarrays, or RNA sequencing. PI3K alterations were assessed by immunohistochemistry, DNA microarrays, DNA sequencing, SNP arrays or fluorescence in situ hybridization. A panel of markers of epithelial-mesenchymal transition (EMT) was also correlated to the 29-gene signature score. RESULTS High 29-gene Endometrial Carcinoma Recurrence Score (ECARS) values consistently validated to identify patients with aggressive clinico-pathologic phenotype and reduced survival. Within the presumed favorable subgroups of low grade, endometrioid tumors confined to the uterus, high ECARS still predicted a poor prognosis. The score was higher in metastatic compared to primary lesions (P<0.001) and was significantly associated with potential measures of PI3K activation, markers of EMT and vascular invasion as an indicator of metastatic spread (all P<0.001). CONCLUSIONS ECARS validates to identify aggressive endometrial carcinomas in multiple, independent patients cohorts. The higher signature score in metastatic compared to primary lesions, and the potential link to PI3K activation and EMT, support further studies of ECARS in relation to response to PI3K and EMT inhibitors in clinical trials of metastatic endometrial carcinoma.
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Affiliation(s)
- E Wik
- Centre for Cancer Biomarkers CCBIO, Department of Clinical Medicine, University of Bergen, Norway; Department of Pathology, The Gade Institute, Haukeland University Hospital, Bergen, Norway.
| | - J Trovik
- Department of Obstetrics and Gynecology, Haukeland University Hospital, Bergen, Norway; Centre for Cancer Biomarkers CCBIO, Department of Clinical Science, University of Bergen, Norway
| | - K Kusonmano
- Department of Obstetrics and Gynecology, Haukeland University Hospital, Bergen, Norway; Computational Biology Unit, University of Bergen, Bergen, Norway
| | - E Birkeland
- Centre for Cancer Biomarkers CCBIO, Department of Clinical Medicine, University of Bergen, Norway; Department of Pathology, The Gade Institute, Haukeland University Hospital, Bergen, Norway
| | - M B Raeder
- Department of Obstetrics and Gynecology, Haukeland University Hospital, Bergen, Norway; Centre for Cancer Biomarkers CCBIO, Department of Clinical Science, University of Bergen, Norway
| | - I Pashtan
- Department of Radiation Oncology, Dana-Farber/Brigham and Women's Cancer Center, Boston, MA, USA
| | - E A Hoivik
- Department of Obstetrics and Gynecology, Haukeland University Hospital, Bergen, Norway; Centre for Cancer Biomarkers CCBIO, Department of Clinical Science, University of Bergen, Norway
| | - C Krakstad
- Department of Obstetrics and Gynecology, Haukeland University Hospital, Bergen, Norway; Centre for Cancer Biomarkers CCBIO, Department of Clinical Science, University of Bergen, Norway
| | - H M J Werner
- Department of Obstetrics and Gynecology, Haukeland University Hospital, Bergen, Norway; Centre for Cancer Biomarkers CCBIO, Department of Clinical Science, University of Bergen, Norway
| | - F Holst
- Department of Obstetrics and Gynecology, Haukeland University Hospital, Bergen, Norway; Centre for Cancer Biomarkers CCBIO, Department of Clinical Science, University of Bergen, Norway
| | - S Mjøs
- Department of Obstetrics and Gynecology, Haukeland University Hospital, Bergen, Norway; Centre for Cancer Biomarkers CCBIO, Department of Clinical Science, University of Bergen, Norway
| | - M K Halle
- Department of Obstetrics and Gynecology, Haukeland University Hospital, Bergen, Norway; Centre for Cancer Biomarkers CCBIO, Department of Clinical Science, University of Bergen, Norway
| | - M Mannelqvist
- Centre for Cancer Biomarkers CCBIO, Department of Clinical Medicine, University of Bergen, Norway; Department of Pathology, The Gade Institute, Haukeland University Hospital, Bergen, Norway
| | - K K Mauland
- Department of Obstetrics and Gynecology, Haukeland University Hospital, Bergen, Norway; Centre for Cancer Biomarkers CCBIO, Department of Clinical Science, University of Bergen, Norway
| | - A M Oyan
- Department of Microbiology, Haukeland University Hospital, Bergen, Norway
| | - I M Stefansson
- Centre for Cancer Biomarkers CCBIO, Department of Clinical Medicine, University of Bergen, Norway; Department of Pathology, The Gade Institute, Haukeland University Hospital, Bergen, Norway
| | - K Petersen
- Computational Biology Unit, University of Bergen, Bergen, Norway
| | - R Simon
- Department of Pathology, University Medical Center Hamburg Eppendorf, Hamburg, Germany
| | - A D Cherniack
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - M Meyerson
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Pathology, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - K H Kalland
- Centre for Cancer Biomarkers CCBIO, Department of Clinical Science, University of Bergen, Norway; Department of Microbiology, Haukeland University Hospital, Bergen, Norway
| | - L A Akslen
- Centre for Cancer Biomarkers CCBIO, Department of Clinical Medicine, University of Bergen, Norway; Department of Pathology, The Gade Institute, Haukeland University Hospital, Bergen, Norway
| | - H B Salvesen
- Department of Obstetrics and Gynecology, Haukeland University Hospital, Bergen, Norway; Centre for Cancer Biomarkers CCBIO, Department of Clinical Science, University of Bergen, Norway
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Significance of PRO2000/ANCCA expression, a novel proliferation-associated protein in hepatocellular carcinoma. Cancer Cell Int 2014; 14:33. [PMID: 24708861 PMCID: PMC3997233 DOI: 10.1186/1475-2867-14-33] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2013] [Accepted: 03/26/2014] [Indexed: 01/01/2023] Open
Abstract
Background PRO2000/ANCCA may be an important candidate gene which located within a region of chromosome 8q in hepatocellular carcinoma (HCC). However, its significance remains unclear. The aim of this study was to explore the clinical significance of PRO2000/ANCCA expression in HCC. Methods The correlations of PRO2000/ANCCA expression with clinicopathological factors and prognosis of HCC patients were analyzed. Expression of PRO2000/ANCCA, ki-67, cyclinD1, p53 and p21 was detected in HCCs from 107 patients along with corresponding non-tumor tissues by immunohistochemistry. Results PRO2000/ANCCA expression was present in 66 of 107 (64.94%) HCC specimens in which 36 of 76 (47.37%) in well differentiated tumors and 30 of 31 (96.77%) in poorly differentiated tumors respectively, while 8 (7.48%) in adjacent non-tumor tissues with scattered positive cells. PRO2000/ANCCA expression was associated with clinicopathological features such as histological differentiation, number of tumor nodules, TNM stage, tumor microsatellite, portal vein tumor thrombus and recurrence, but not with gender, age, tumor size, cirrhosis, HBV infection and serum fetoprotein (AFP) level. There was a close relationship between PRO2000/ANCCA and ki-67 and cyclinD1 in HCC. PRO2000/ANCCA immunopositivity was independent of p53 and p21WAF1/Cip1. Conclusions Increased expression of PRO2000/ANCCA is associated with adverse outcome in patients with HCC and is a predictor of poor prognosis for HCC. PRO2000/ANCCA may be involved in the development of HCC and might promote cell proliferation through a p53/ P21WAF1/Cip1-independent pathway.
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50
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Wu G, Liu H, He H, Wang Y, Lu X, Yu Y, Xia S, Meng X, Liu Y. miR-372 down-regulates the oncogene ATAD2 to influence hepatocellular carcinoma proliferation and metastasis. BMC Cancer 2014; 14:107. [PMID: 24552534 PMCID: PMC4016509 DOI: 10.1186/1471-2407-14-107] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2013] [Accepted: 02/11/2014] [Indexed: 01/01/2023] Open
Abstract
Background ATAD2 is associated with many cellular processes, such as cell growth, migration and invasion. However, no studies have been conducted on the molecular biological function of the ATAD2 gene in hepatocellular carcinoma (HCC). Methods The protein and mRNA level expression of ATAD2 was examined in tissues and cell lines. Prognostic significance was analyzed by the Kaplan-Meier survival method and Cox regression. ATAD2 knockdown was used to analyze cell proliferation and invasion. The upstream and downstream of ATAD2 was analyzed by RT2 Profiler™ PCR array and luciferasex fluorescence system. Results ATAD2 was highly expressed in liver cancer samples and correlated with poor survival. High ATAD2 expression was positively correlated with metastasis (P = 0.005) and was an independent prognostic factor in HCC (P = 0.001). ATAD2 depletion by RNA interference reduced their capacity for invasion and proliferation and led to a G1 phase arrest in vitro. Further study revealed that miR-372 was an upstream target of ATAD2 as miR-372 was bound directly to its 3′ untranslated region (3′ UTR). In addition, ATAD2 knockdown was found to extremely up-regulate APC expression and down-regulate CTNNA1 at the mRNA level. Conclusions The findings demonstrated that miR-372 suppressed the expression of ATAD2, which was highly expressed in HCC and exerted a proto-oncogene effect in hepatic carcinogenesis. In conclusion, ATAD2 may promote HCC progression.
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Affiliation(s)
- Gang Wu
- Department of General Surgery, the First Affiliated Hospital of China Medical University, Shenyang, Liaoning 110001, China.
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