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Li W, Wu H, Xu J. Construction of a genomic instability-derived predictive prognostic signature for non-small cell lung cancer patients. Cancer Genet 2023; 278-279:24-37. [PMID: 37579716 DOI: 10.1016/j.cancergen.2023.07.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 06/27/2023] [Accepted: 07/29/2023] [Indexed: 08/16/2023]
Abstract
BACKGROUND Genomic instability (GI) is an effective prognostic marker of cancer. Thus, in this work, we aimed to explore the impact of GI derived signature on prognosis in non-small cell lung cancer (NSCLC) patients using bioinformatics methods. METHODS The data of NSCLC patients were collected from The Cancer Genome Atlas. Totally 1794 immune related genes were downloaded from immport database. The optimal prognosis related genes were identified by univariate and LASSO Cox analyses. The risk score model was built to predict the NSCLC patients' prognosis. The immune cell infiltration was analyzed in CIBERSORT. RESULTS The 951 differentially expressed genes (DEGs) between the genomic stability (GS) and GI groups were enriched in 862 Gene ontology terms and 32 Kyoto Encyclopedia of Genes and Genomes pathways. Based on the 13 optimal genes, a prognostic risk score mode for NSCLC was established, and the high-risk patients exhibited worse overall survival. Moreover, the nomogram could reliably predict the clinical outcomes. The immune cell infiltration and checkpoints were significantly differential between the two groups (high-risk and low-risk). CONCLUSION The GI related 13-gene signature (TMPRSS11E, TNNC2, HLF, FOXM1, PKMYT1, TCN1, RGS20, SYT8, CD1B, LY6K, MFSD4A, KLRG2 APCDD1L) could reliably predict the prognosis of NSCLC patients.
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Affiliation(s)
- Wei Li
- Department of Pulmonary and Critical Care Medicine, The Yancheng Clinical College of Xuzhou Medical University, The First People's Hospital of Yancheng City, Yancheng, Jiangsu 224006, China
| | - Huaman Wu
- Department of Respiratory and Critical Care Medicine, Zigong First People's Hospital, Ziliujing District, Zigong, Sichuan 643000, China
| | - Juan Xu
- Department of Pulmonary and Critical Care Medicine, The Yancheng Clinical College of Xuzhou Medical University, The First People's Hospital of Yancheng City, Yancheng, Jiangsu 224006, China.
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Fouzder C, Mukhuty A, Kundu R. Kaempferol inhibits Nrf2 signalling pathway via downregulation of Nrf2 mRNA and induces apoptosis in NSCLC cells. Arch Biochem Biophys 2020; 697:108700. [PMID: 33271149 DOI: 10.1016/j.abb.2020.108700] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Revised: 11/09/2020] [Accepted: 11/24/2020] [Indexed: 02/08/2023]
Abstract
Chemoprevention failure is considered to be the most emerging problem that makes non-small cell lung cancer (NSCLC) as one of the deadliest malignancies in the world. In NSCLC cells, Nuclear factor erythroid 2-related factor 2 (Nrf2), a redox sensitive transcription factor, promotes cancer cell survival and fosters mechanism for drug resistance. Here we report identification of Kaempferol, a dietary flavonoid, as a potent Nrf2 inhibitor using Nrf2 reporter assay in NSCLC cells (A549 and NCIH460). Kaempferol selectively reduces Nrf2 mRNA and protein levels and lower level of nuclear Nrf2 downregulates transcription of Nrf2 target genes (NQO1, HO1, AKR1C1 and GST). Kaempferol (25 μM) mediated downregulation of GST, NQO1 and HO1 expression is also observed even after stimulation of Nrf2 by tert-butylhydroquinone (tBHQ). Again, Kaempferol incubation does not change the levels of NFκBp65 and phospho NFκBp65, suggesting it hampers Nrf2 signalling pathway in these cells. Nrf2 inhibition by Kaempferol induces ROS accumulation after 48 h of treatment and makes NSCLC cells sensitive to apoptosis at physiological concentration. Taken together, our study demonstrates that Kaempferol is a potent inhibitor of Nrf2 and can be used as a natural sensitizer and anti-cancer agent for lung cancer therapeutics.
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Affiliation(s)
- Chandrani Fouzder
- Cell Signalling Laboratory, Department of Zoology, Siksha- Bhavana, Visva-Bharati University, Santiniketan, 731235, India
| | - Alpana Mukhuty
- Cell Signalling Laboratory, Department of Zoology, Siksha- Bhavana, Visva-Bharati University, Santiniketan, 731235, India
| | - Rakesh Kundu
- Cell Signalling Laboratory, Department of Zoology, Siksha- Bhavana, Visva-Bharati University, Santiniketan, 731235, India.
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Ma J, Qi G, Li L. LncRNA NNT-AS1 promotes lung squamous cell carcinoma progression by regulating the miR-22/FOXM1 axis. Cell Mol Biol Lett 2020; 25:34. [PMID: 32514270 PMCID: PMC7257167 DOI: 10.1186/s11658-020-00227-8] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Accepted: 05/14/2020] [Indexed: 02/07/2023] Open
Abstract
Background Recent studies have revealed that dysregulated expression of long non-coding RNA nicotinamide nucleotide transhydrogenase antisense RNA 1 (lncRNA NNT-AS1) is associated with cell tumorigenicity in non-small cell lung cancer. However, the exact molecular mechanisms of NNT-AS1 in lung squamous cell carcinoma (LUSC) remain largely unknown. Methods The expression of NNT-AS1, microRNA (miR)-22 and Forkhead box protein M1 (FOXM1) was measured using quantitative real-time polymerase chain reaction or western blot, respectively. The interaction between miR-22 and NNT-AS1 or FOXM1 was confirmed using a dual-luciferase reporter assay and RNA immunoprecipitation assay. Cell migration and invasion abilities were measured by Transwell assay. Flow cytometry was used to detect apoptotic cells. Results NNT-AS1 and FOXM1 were up-regulated but miR-22 was down-regulated in LUSC tissues and cell lines. NNT-AS1 was a sponge of miR-22, and NNT-AS1 deletion suppressed the migration and invasion but induced apoptosis in LUSC cells. FOXM1 was a target of miR-22, and overexpression of miR-22 inhibited cell carcinogenesis in LUSC by targeting FOXM1. Additionally, NNT-AS1 could directly regulate FOXM1 expression by binding to miR-22 in LUSC cells. Conclusion LncRNA NNT-AS1 contributes to cell carcinogenesis in LUSC by regulating the miR-22/FOXM1 axis, providing a novel insight into the pathogenesis of LUSC and a new potential therapeutic target for LUSC treatment.
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Affiliation(s)
- Jing Ma
- Department of Respiratory and Critical Care Medicine, Huaihe Hospital of Henan University, NO.115 Ximen Street, Kaifeng City, Henan Province, Kaifeng, 475000 Henan China
| | - Guanbin Qi
- Department of Respiratory and Critical Care Medicine, Huaihe Hospital of Henan University, NO.115 Ximen Street, Kaifeng City, Henan Province, Kaifeng, 475000 Henan China
| | - Lei Li
- Department of Respiratory and Critical Care Medicine, Huaihe Hospital of Henan University, NO.115 Ximen Street, Kaifeng City, Henan Province, Kaifeng, 475000 Henan China
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Puderecki M, Szumiło J, Marzec-Kotarska B. Novel prognostic molecular markers in lung cancer. Oncol Lett 2020; 20:9-18. [PMID: 32565929 DOI: 10.3892/ol.2020.11541] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Accepted: 02/04/2020] [Indexed: 12/15/2022] Open
Abstract
Lung carcinoma, especially in its most commonly diagnosed non-small cell histological form, is a challenge to diagnose and treat worldwide, due to the prognosis in patients with this type of cancer being poor and mortality rates being high. However, a number of patients with this type of lung carcinoma exhibit a longer than average overall survival. The specific molecular background of non-small-cell lung cancer that favors longer survival has not yet been determined. The aim of the current study was to review articles published in the years 2017-2018 and create a list of the most important and strongest non-conventional factors that could be used in the future assessment of the prognosis of patients with adenocarcinoma and squamous cell carcinoma of the lung who cannot undergo current targeted therapy. Analysis identified multiple prognostic factors in non-small cell lung carcinoma, including tumor mutational burden, which was revealed to be independent of the tumor stage or grade as well as other factors, including age, sex or targeted therapy effects. The selected molecular factors exhibit the potential to be used in the treatment of patients with specific problematic lung cancer, and may contribute to setting recommendations for the diagnosis, prognosis and treatment of individual patients with lung cancer.
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Affiliation(s)
- Michał Puderecki
- Department of Clinical Pathomorphology, The Medical University of Lublin, 20-090 Lublin, Poland
| | - Justyna Szumiło
- Department of Clinical Pathomorphology, The Medical University of Lublin, 20-090 Lublin, Poland
| | - Barbara Marzec-Kotarska
- Department of Clinical Pathomorphology, The Medical University of Lublin, 20-090 Lublin, Poland
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Forkhead box M1 transcription factor: a novel target for pulmonary arterial hypertension therapy. World J Pediatr 2020; 16:113-119. [PMID: 31190319 DOI: 10.1007/s12519-019-00271-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Accepted: 05/23/2019] [Indexed: 02/07/2023]
Abstract
BACKGROUND Forkhead box M1 (FoxM1), a member of forkhead family, plays a key role in carcinogenesis, progression, invasion, metastasis and drug resistance. Based on the similarities between cancer and pulmonary arterial hypertension, studies on the roles and mechanisms of FoxM1 in pulmonary arterial hypertension have been increasing. This article aims to review recent advances in the mechanisms of signal transduction associated with FoxM1 in pulmonary arterial hypertension. DATA SOURCES Articles were retrieved from PubMed and MEDLINE published after 1990, including-but not limited to-FoxM1 and pulmonary arterial hypertension. RESULTS FoxM1 is overexpressed in pulmonary artery smooth muscle cells in both pulmonary arterial hypertension patients and animal models, and promotes pulmonary artery smooth muscle cell proliferation and inhibits cell apoptosis via regulating cell cycle progression. Multiple signaling molecules and pathways, including hypoxia-inducible factors, transforming growth factor-β/Smad, SET domain-containing 3/vascular endothelial growth factor, survivin, cell cycle regulatory genes and DNA damage response network, are reported to cross talk with FoxM1 in pulmonary arterial hypertension. Proteasome inhibitors are effective in the prevention and treatment of pulmonary arterial hypertension by inhibiting the expression and transcriptional activity of FoxM1. CONCLUSIONS FoxM1 has a crucial role in the pathogenesis of pulmonary arterial hypertension and may represent a novel therapeutic target. But more details of interaction between FoxM1 and other signaling pathways need to be clarified in the future.
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Abstract
Introduction: FOXM1 is one of the most frequently overexpressed proteins in human solid cancers. Here, we discuss novel direct targets of FOXM1 as well as new pathways involving FOXM1, through which this protein exerts its oncogenic activity.Areas covered: We give a detailed review of FOXM1 transcriptional targets involved in 16 different types of human cancer as published in the literature in the last 5 years. We also discuss a novel positive feedback loop between FOXM1 and AKT - both well-established master regulators of cancer.Expert opinion: Despite the discovery of several FOXM1 inhibitors over the years (by our team and others), their therapeutic use is limited by their adverse off-target effects.Newly-discovered proteins regulated by FOXM1 present a promising alternative approach to target its pro-cancer activity. In addition, targeting regulating proteins that take part in the positive feedback loop between FOXM1/AKT has the double advantage of suppressing both, and can lead to developing novel anti-cancer drugs.
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Affiliation(s)
- Soheila Borhani
- Department of Medicine, University of Illinois at Chicago, Chicago, IL, USA
| | - Andrei L Gartel
- Department of Medicine, University of Illinois at Chicago, Chicago, IL, USA
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7
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Yin L, Wang Y, Ma G, Deng Y, Zhou Q. Villi development core-related gene expression associated with lung squamous cancer prognosis. Medicine (Baltimore) 2019; 98:e14714. [PMID: 30882635 PMCID: PMC6426584 DOI: 10.1097/md.0000000000014714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/27/2018] [Revised: 01/18/2019] [Accepted: 02/06/2019] [Indexed: 02/05/2023] Open
Abstract
Similarities between embryonic development and tumorigenesis are reflected in biological behavior and gene expression. Although the gene signature during development and the clinical phenotype of different cancers show certain correlation pattern, the correlation between early embryo development and cancer remains largely unexplored. To compare the gene expression profile between development and cancer, our study analyzed the gene expression of chorionic villi samples at different gestational ages (6, 7, 8, 9, 10, 40 weeks) obtained from gene expression omnibus (GEO) datasets using correlation test. Then the villi development-related genes that gradually showed a positive correlation (upregulated) (n = 394) or negative correlation (downregulated) (n = 325) with time were used to construct protein-protein interaction (PPI) networks. Three subnetworks among the gradually upregulated genes and 3 subnetworks among the downregulated genes were identified using the molecular complex detection (MCODE) plugin in Cytoscape software. The most significant GO terms for villi-correlated genes were immune, inflammatory response and cell division. These gene clusters were also dysregulated in lung squamous cell carcinoma (SCC). Moreover the prognostic value of the gene clusters was then analyzed with TCGA lung SCC data, which showed 4 clusters that were associated with prognosis. Our results demonstrate the gene expression similarity between development and lung SCC and identified development-associated gene clusters that could contain prognostic information for lung SCC patients.
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Affiliation(s)
- Liyuan Yin
- Lung cancer centre, West China Hospital, Sichuan University, Chengdu
| | - Yonggang Wang
- Department of Respiratory Medicine, Shandong Provincial Hospital Affiliated to Shandong University, Jinan
| | - Guangzhi Ma
- Lung cancer centre, West China Hospital, Sichuan University, Chengdu
- Department of Thoracic Surgery, West China Hospital, Sichuan University, Chengdu, P. R. China
| | - Yunfu Deng
- Lung cancer centre, West China Hospital, Sichuan University, Chengdu
| | - Qinghua Zhou
- Lung cancer centre, West China Hospital, Sichuan University, Chengdu
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Yuan Y, Haiying G, Zhuo L, Ying L, Xin H. Long non-coding RNA LINC00339 facilitates the tumorigenesis of non-small cell lung cancer by sponging miR-145 through targeting FOXM1. Biomed Pharmacother 2018; 105:707-713. [PMID: 29906749 DOI: 10.1016/j.biopha.2018.06.022] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2018] [Revised: 06/03/2018] [Accepted: 06/04/2018] [Indexed: 12/16/2022] Open
Abstract
Non-small cell lung cancer (NSCLC) is one of leading causes of cancer-related death worldwide. Long noncoding RNAs (lncRNAs) has been identified to modulate the tumorigenesis of NSCLC. However, the precise molecular mechanism of lncRNAs in the course is still unclear. Results showed that LINC00339 was significantly up-regulated in NSCLC tissue and cells, which indicated the poor prognosis of NSCLC patients. Loss-of-function experiments showed that LINC00339 silencing inhibited the proliferation and invasion, accelerated the apoptosis, and suppressed the tumor growth of NSCLC cells in vitro and in vivo. Luciferase reporter assay and RNA immunoprecipitation (RIP) revealed that LINC00339 promoted the NSCLC progression via FOXM1 via targeting miR-145. In conclusion, our results identify the important role of the LINC00339/miR-145/FOXM1 axis in the NSCLC tumorigenesis, providing neoteric mechanism for the NSCLC tumorigenesis.
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Affiliation(s)
- Yuan Yuan
- Department of Respiratory Medicine, The Second Affiliated Hospital of Dalian Medical University, Dalian 116044, China
| | - Gao Haiying
- Department of General Medical, The Second Affiliated Hospital of Dalian Medical University, Dalian 116044, China
| | - Li Zhuo
- Department of General Medical, The Second Affiliated Hospital of Dalian Medical University, Dalian 116044, China
| | - Lu Ying
- Department of General Medical, The Second Affiliated Hospital of Dalian Medical University, Dalian 116044, China
| | - He Xin
- Department of Respiratory Medicine, The First Affiliated Hospital of Dalian Medical University, Zhongshan Road, No. 222, Dalian 116011, China.
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Zhang Y, Qiao WB, Shan L. Expression and functional characterization of FOXM1 in non-small cell lung cancer. Onco Targets Ther 2018; 11:3385-3393. [PMID: 29928129 PMCID: PMC6001838 DOI: 10.2147/ott.s162523] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Objectives FOXM1 is a key member of the FOX transcription factor family, which plays a vital role in a series of physiological processes. In the present study, non-small cell lung cancer (NSCLC) patients and cell lines were studied to explore the correlation between FOXM1 expression and this malignancy. Materials and methods The expression status of FOXM1 was detected in 128 cases of NSCLC tissues and NSCLC cell lines. The relationship of FOXM1 expression and clinicopathological features of NSCLC patients was evaluated by us. In addition, we also explored the biological functions of FOXM1 in NSCLC cell lines. Results The FOXM1 is highly expressed in NSCLC tissues and cell lines. FOXM1 expression was closely correlated with lymph node status and TNM stage. Cox regression analysis were performed to demonstrate the prognosis role of FOXM1. Conclusion FOXM1 conferred a proliferation and invasion advantage to NSCLC cell. The FOXM1 can be regarded as an important molecular marker in NSCLC prognosis.
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Affiliation(s)
- Yan Zhang
- Department of Thoracic Oncology, Tumor Hospital Affiliated to Xinjiang Medical University, Xinjiang, People's Republic of China
| | - Wen-Bin Qiao
- Department of Thoracic Oncology, Tumor Hospital Affiliated to Xinjiang Medical University, Xinjiang, People's Republic of China
| | - Li Shan
- Department of Thoracic Oncology, Tumor Hospital Affiliated to Xinjiang Medical University, Xinjiang, People's Republic of China
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Zhang Y, Ye X, Chen L, Wu Q, Gao Y, Li Y. PARI functions as a new transcriptional target of FOXM1 involved in gastric cancer development. Int J Biol Sci 2018; 14:531-541. [PMID: 29805304 PMCID: PMC5968845 DOI: 10.7150/ijbs.23945] [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: 11/20/2017] [Accepted: 02/16/2018] [Indexed: 12/22/2022] Open
Abstract
PARI, an element of the homologous recombination pathway of DNA repair,is involved in the regulation of cell cycle and carcinogenesis in pancreatic cancer. However, little is known about the function and regulatory mechanism of PARI in other cancers. In the present study, we evaluated the expression of PARI in gastric cancer (GC) by immunohistochemical analysis in a tissue microarray and characterized its functions using in vitro assays and in vivo animal models. We found higher expression of PARI protein was shown in GC tissues compared with related adjacent normal gastric mucosa tissues. Knockdown of PARI by RNA inference decreased cell proliferation, migration, and invasion of GC cells in vitro, as well as reduced the xenograft tumor growth and lung metastasis formation in vivo. Quantitative real-time PCR and western blot results revealed that PARI expression was activated by a well-known oncogene FOXM1 and positively correlated with FOXM1 expression at mRNA level in 38 paired of GC samples. Luciferase reporter assay and chromatin immunoprecipitation assay further demonstrated that FOXM1 directly regulated PARI transcription by binding to the specific sequences of PARI promoter. In addition, PARI knockdown blocked the effect of FOXM1 on GC cell migration. Taken together, our results suggest that PARI plays potential oncogenic roles and functions as a transcriptional target and effector of FOXM1 in GC development.
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Affiliation(s)
- Yi Zhang
- Department of Oncology, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China
| | - Xiaojuan Ye
- Department of Hematology & Oncology, the People's Hospital of Beilun District, Beilun Branch Hospital of the First Affiliated Hospital of Medical School of Zhejiang University, Ningbo 315800, China
| | - Lizhi Chen
- Department of Pharmacy, Changhai Hospital, the Second Military Medical University, Shanghai 200433, China
| | - Qiong Wu
- Department of Oncology, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China
| | - Yong Gao
- Department of Oncology, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China
| | - Yandong Li
- Department of Oncology, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China
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Erdoğan C, Kurt Z, Diri B. Estimation of the proteomic cancer co-expression sub networks by using association estimators. PLoS One 2017; 12:e0188016. [PMID: 29145449 PMCID: PMC5690670 DOI: 10.1371/journal.pone.0188016] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Accepted: 10/29/2017] [Indexed: 01/02/2023] Open
Abstract
In this study, the association estimators, which have significant influences on the gene network inference methods and used for determining the molecular interactions, were examined within the co-expression network inference concept. By using the proteomic data from five different cancer types, the hub genes/proteins within the disease-associated gene-gene/protein-protein interaction sub networks were identified. Proteomic data from various cancer types is collected from The Cancer Proteome Atlas (TCPA). Correlation and mutual information (MI) based nine association estimators that are commonly used in the literature, were compared in this study. As the gold standard to measure the association estimators’ performance, a multi-layer data integration platform on gene-disease associations (DisGeNET) and the Molecular Signatures Database (MSigDB) was used. Fisher's exact test was used to evaluate the performance of the association estimators by comparing the created co-expression networks with the disease-associated pathways. It was observed that the MI based estimators provided more successful results than the Pearson and Spearman correlation approaches, which are used in the estimation of biological networks in the weighted correlation network analysis (WGCNA) package. In correlation-based methods, the best average success rate for five cancer types was 60%, while in MI-based methods the average success ratio was 71% for James-Stein Shrinkage (Shrink) and 64% for Schurmann-Grassberger (SG) association estimator, respectively. Moreover, the hub genes and the inferred sub networks are presented for the consideration of researchers and experimentalists.
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Affiliation(s)
- Cihat Erdoğan
- Department of Computer Engineering, Namik Kemal University, Tekirdag, Turkey
- * E-mail:
| | - Zeyneb Kurt
- Department of Integrative Biology and Physiology, University of California Los Angeles, Los Angeles, California, United States of America
- Department of Computer Engineering, Yildiz Technical University, Istanbul, Turkey
| | - Banu Diri
- Department of Computer Engineering, Yildiz Technical University, Istanbul, Turkey
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Wang Y, Ung MH, Xia T, Cheng W, Cheng C. Cancer cell line specific co-factors modulate the FOXM1 cistrome. Oncotarget 2017; 8:76498-76515. [PMID: 29100329 PMCID: PMC5652723 DOI: 10.18632/oncotarget.20405] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Accepted: 08/14/2017] [Indexed: 12/11/2022] Open
Abstract
ChIP-seq has been commonly applied to identify genomic occupation of transcription factors (TFs) in a context-specific manner. It is generally assumed that a TF should have similar binding patterns in cells from the same or closely related tissues. Surprisingly, this assumption has not been carefully examined. To this end, we systematically compared the genomic binding of the cell cycle regulator FOXM1 in eight cell lines from seven different human tissues at binding signal, peaks and target genes levels. We found that FOXM1 binding in ER-positive breast cancer cell line MCF-7 are distinct comparing to those in not only other non-breast cell lines, but also MDA-MB-231, ER-negative breast cancer cell line. However, binding sites in MDA-MB-231 and non-breast cell lines were highly consistent. The recruitment of estrogen receptor alpha (ERα) caused the unique FOXM1 binding patterns in MCF-7. Moreover, the activity of FOXM1 in MCF-7 reflects the regulatory functions of ERα, while in MDA-MB-231 and non-breast cell lines, FOXM1 activities regulate cell proliferation. Our results suggest that tissue similarity, in some specific contexts, does not hold precedence over TF-cofactors interactions in determining transcriptional states and that the genomic binding of a TF can be dramatically affected by a particular co-factor under certain conditions.
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Affiliation(s)
- Yue Wang
- School of Electronic Information and Communications, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China.,Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Hanover, NH 03755, USA
| | - Matthew H Ung
- Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Hanover, NH 03755, USA
| | - Tian Xia
- School of Electronic Information and Communications, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Wenqing Cheng
- School of Electronic Information and Communications, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Chao Cheng
- Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Hanover, NH 03755, USA.,Norris Cotton Cancer Center, Geisel School of Medicine at Dartmouth, Lebanon, NH 03766, USA.,Department of Biomedical Data Sciences, Geisel School of Medicine at Dartmouth, Lebanon, NH 03766, USA
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