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Zhu X, Wang H. Revisiting the role and mechanism of ELF3 in circadian clock modulation. Gene 2024; 913:148378. [PMID: 38490512 DOI: 10.1016/j.gene.2024.148378] [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: 12/06/2023] [Revised: 03/08/2024] [Accepted: 03/12/2024] [Indexed: 03/17/2024]
Abstract
The gene encoding EARLY FLOWERING3 (ELF3) is necessary for photoperiodic flowering and the normal regulation of circadian rhythms. It provides important information at the cellular level to uncover the biological mechanisms that improve plant growth and development. ELF3 interactions with transcription factors such as BROTHER OF LUX ARRHYTHMO (BOA), LIGHT-REGULATED WD1 (LWD1), PHYTOCHROME-INTERACTING FACTOR 4 (PIF4), PHYTOCHROME-INTERACTING FACTOR 7 (PIF7), and LUX ARRHYTHMO (LUX) suggest a role in evening complex (EC) independent pathways, demanding further investigation to elucidate the EC-dependent versus EC-independent mechanisms. The ELF3 regulation of flowering time about photoperiod and temperature variations can also optimize crop cultivation across diverse latitudes. In this review paper, we summarize how ELF3's role in the circadian clock and light-responsive flowering control in crops offers substantial potential for scientific advancement and practical applications in biotechnology and agriculture. Despite its essential role in crop adaptation, very little is known in many important crops. Consequently, comprehensive and targeted research is essential for extrapolating ELF3-related insights from Arabidopsis to other crops, utilizing both computational and experimental methodologies. This research should prioritize investigations into ELF3's protein-protein interactions, post-translational modifications, and genomic targets to elucidate its contribution to accurate circadian clock regulation.
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Affiliation(s)
- Xingzun Zhu
- College of Landscape Architecture, Changchun University, No.1 Weixinglu Changchun, Jilin, China.
| | - Hongtao Wang
- College of Life Sciences, Tonghua Normal University, Tonghua, 950, Yucai Road, China.
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2
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Ju Y, Fang S, Liu L, Ma H, Zheng L. The function of the ELF3 gene and its mechanism in cancers. Life Sci 2024; 346:122637. [PMID: 38614305 DOI: 10.1016/j.lfs.2024.122637] [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: 01/28/2024] [Revised: 04/01/2024] [Accepted: 04/10/2024] [Indexed: 04/15/2024]
Abstract
E74-like factor 3 (ELF3) is an important member of the E-twenty-six (ETS) transcription factor family. ELF3 is expressed in various types of cells and regulates a variety of biological behaviors, such as cell proliferation, differentiation, apoptosis, migration, and invasion, by binding to DNA to regulate the expression of other genes. In recent years, studies have shown that ELF3 plays an important role in the occurrence and development of many tumors and inflammation and immune related diseases. ELF3 has different functions and expression patterns in different tumors; it can function as a tumor suppressor gene or an oncogene, highlighting its dual effects of tumor promotion and inhibition. ELF3 also affects the levels of tumor immunity-related cytokines and is involved in the regulation and expression of multiple signaling pathways. In tumor therapy, ELF3 is a complex and multifunctional gene and has become a key focus of targeted treatment research. An in-depth study of the biological function of ELF3 can help to elucidate its role in biological processes and provide ideas and a basis for the development and clinical application of ELF3-related therapeutic methods. This review introduces the structure and physiological and cellular functions of the ELF3 gene, summarizes the mechanisms of action of ELF3 in different types of malignant tumors and its role in immune regulation, inflammation, etc., and discusses treatment methods for ELF3-related diseases, providing significant reference value for scholars studying the ELF3 gene and related diseases.
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Affiliation(s)
- Yiheng Ju
- Affiliated Hospital of Qingdao University, Qingdao, China
| | - Sheng Fang
- Yantai Penglai People's Hospital, Yantai, China
| | - Lei Liu
- Affiliated Hospital of Qingdao University, Qingdao, China
| | - Hui Ma
- Affiliated Hospital of Qingdao University, Qingdao, China.
| | - Longbo Zheng
- Affiliated Hospital of Qingdao University, Qingdao, China.
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3
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Arriojas A, Patalano S, Macoska J, Zarringhalam K. A Bayesian Noisy Logic Model for Inference of Transcription Factor Activity from Single Cell and Bulk Transcriptomic Data. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.03.539308. [PMID: 37205561 PMCID: PMC10187261 DOI: 10.1101/2023.05.03.539308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
The advent of high-throughput sequencing has made it possible to measure the expression of genes at relatively low cost. However, direct measurement of regulatory mechanisms, such as Transcription Factor (TF) activity is still not readily feasible in a high-throughput manner. Consequently, there is a need for computational approaches that can reliably estimate regulator activity from observable gene expression data. In this work, we present a noisy Boolean logic Bayesian model for TF activity inference from differential gene expression data and causal graphs. Our approach provides a flexible framework to incorporate biologically motivated TF-gene regulation logic models. Using simulations and controlled over-expression experiments in cell cultures, we demonstrate that our method can accurately identify TF activity. Moreover, we apply our method to bulk and single cell transcriptomics measurements to investigate transcriptional regulation of fibroblast phenotypic plasticity. Finally, to facilitate usage, we provide user-friendly software packages and a web-interface to query TF activity from user input differential gene expression data: https://umbibio.math.umb.edu/nlbayes/.
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Affiliation(s)
- Argenis Arriojas
- Department of Mathematics, University of Massachusetts Boston, Boston, MA 02125, USA
- Department of Physics, University of Massachusetts Boston, Boston, MA 02125, USA
- Center for Personalized Cancer Therapy, University of Massachusetts Boston, Boston, MA 02125, USA
| | - Susan Patalano
- Center for Personalized Cancer Therapy, University of Massachusetts Boston, Boston, MA 02125, USA
| | - Jill Macoska
- Center for Personalized Cancer Therapy, University of Massachusetts Boston, Boston, MA 02125, USA
| | - Kourosh Zarringhalam
- Department of Mathematics, University of Massachusetts Boston, Boston, MA 02125, USA
- Center for Personalized Cancer Therapy, University of Massachusetts Boston, Boston, MA 02125, USA
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4
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Subbalakshmi AR, Sahoo S, Manjunatha P, Goyal S, Kasiviswanathan VA, Mahesh Y, Ramu S, McMullen I, Somarelli JA, Jolly MK. The ELF3 transcription factor is associated with an epithelial phenotype and represses epithelial-mesenchymal transition. J Biol Eng 2023; 17:17. [PMID: 36864480 PMCID: PMC9983220 DOI: 10.1186/s13036-023-00333-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Accepted: 02/09/2023] [Indexed: 03/04/2023] Open
Abstract
BACKGROUND Epithelial-mesenchymal plasticity (EMP) involves bidirectional transitions between epithelial, mesenchymal and multiple intermediary hybrid epithelial/mesenchymal phenotypes. While the process of epithelial-mesenchymal transition (EMT) and its associated transcription factors are well-characterised, the transcription factors that promote mesenchymal-epithelial transition (MET) and stabilise hybrid E/M phenotypes are less well understood. RESULTS Here, we analyse multiple publicly-available transcriptomic datasets at bulk and single-cell level and pinpoint ELF3 as a factor that is strongly associated with an epithelial phenotype and is inhibited during EMT. Using mechanism-based mathematical modelling, we also show that ELF3 inhibits the progression of EMT. This behaviour was also observed in the presence of an EMT inducing factor WT1. Our model predicts that the MET induction capacity of ELF3 is stronger than that of KLF4, but weaker than that of GRHL2. Finally, we show that ELF3 levels correlates with worse patient survival in a subset of solid tumour types. CONCLUSION ELF3 is shown to be inhibited during EMT progression and is also found to inhibit the progression of complete EMT suggesting that ELF3 may be able to counteract EMT induction, including in the presence of EMT-inducing factors, such as WT1. The analysis of patient survival data indicates that the prognostic capacity of ELF3 is specific to cell-of-origin or lineage.
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Affiliation(s)
- Ayalur Raghu Subbalakshmi
- grid.34980.360000 0001 0482 5067Centre for BioSystems Science and Engineering, Indian Institute of Science, 560012 Bangalore, India
| | - Sarthak Sahoo
- grid.34980.360000 0001 0482 5067Centre for BioSystems Science and Engineering, Indian Institute of Science, 560012 Bangalore, India
| | - Prakruthi Manjunatha
- grid.444321.40000 0004 0501 2828Department of Medical Electronics, M S Ramaiah Institute of Technology, 560054 Bangalore, India
| | - Shaurya Goyal
- grid.429017.90000 0001 0153 2859Department of Humanities and Social Sciences, Indian Institute of Technology, 721302 Kharagpur, India
| | - Vignesh A Kasiviswanathan
- grid.512757.30000 0004 1761 9897Department of Biotechnology, JSS Science and Technology University, 570006 Mysore, India
| | - Yeshwanth Mahesh
- grid.34980.360000 0001 0482 5067Centre for BioSystems Science and Engineering, Indian Institute of Science, 560012 Bangalore, India
| | - Soundharya Ramu
- grid.419655.a0000 0001 0008 3668Department of Biotechnology, National Institute of Technology Warangal, 506004 Warangal, India
| | - Isabelle McMullen
- grid.26009.3d0000 0004 1936 7961Department of Medicine, Duke University, NC 27708 Durham, USA
| | - Jason A. Somarelli
- grid.26009.3d0000 0004 1936 7961Department of Medicine, Duke University, NC 27708 Durham, USA ,grid.26009.3d0000 0004 1936 7961Duke Cancer Institute, Duke University, NC 27708 Durham, USA
| | - Mohit Kumar Jolly
- Centre for BioSystems Science and Engineering, Indian Institute of Science, 560012, Bangalore, India.
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Xu HJ, Bai J, Tian Y, Feng X, Chen AP, Wang J, Wu J, Jin XR, Zhang F, Quan MY, Chen C, Lee KY, Zhang JS. ESE1/AGR2 axis antagonizes TGF-β-induced epithelial-mesenchymal transition in low-grade pancreatic cancer. Cancer Med 2023; 12:5979-5993. [PMID: 36329620 PMCID: PMC10028153 DOI: 10.1002/cam4.5397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 10/12/2022] [Accepted: 10/21/2022] [Indexed: 11/06/2022] Open
Abstract
Epithelium-specific ETS transcription factor 1 (ESE1) has been implicated in epithelial homeostasis, inflammation, as well as tumorigenesis, and cancer progression. However, numerous studies have reported contradictory roles-as an oncogene or a tumor suppressor of ESE1 in different cancers, and its function in the development and progression of pancreatic ductal adenocarcinoma (PDAC) has remained largely unexplored. Herein, we report that ESE1 was found upregulated in primary PDAC compared to normal pancreatic tissue, but high expression of ESE1 correlated to better relapse-free survival in patients with PDAC. Interestingly, ESE1 was found to exhibit dual roles in regulation of malignant properties of PDAC cells in that its overexpression promoted cell proliferation, whereas its downregulation enhanced epithelial-mesenchymal transition (EMT) phenotype. In the context of TGF-β-induced EMT, ESE1 is markedly downregulated at post-transcriptional level, and reconstituted ESE1 expression partially reversed TGF-β-induced EMT marker expression. Furthermore, we identify AGR2 as a novel transcriptional target of ESE1 that participates in TGF-β-induced EMT in PDAC. Collectively, our findings reveal an ESE1/AGR2 axis that interacts with TGF-β signaling to modulate EMT phenotype in PDAC.
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Affiliation(s)
- Hui-Jing Xu
- International Collaborative Center on Growth Factor Research, and School of Pharmaceutical Sciences, Wenzhou Medical University, Zhejiang, China
- College of Pharmacy and Research Institute of Drug Development, Chonnam National University, Gwangju, Republic of Korea
| | - Jing Bai
- International Collaborative Center on Growth Factor Research, and School of Pharmaceutical Sciences, Wenzhou Medical University, Zhejiang, China
| | - Ye Tian
- International Collaborative Center on Growth Factor Research, and School of Pharmaceutical Sciences, Wenzhou Medical University, Zhejiang, China
| | - Xiao Feng
- International Collaborative Center on Growth Factor Research, and School of Pharmaceutical Sciences, Wenzhou Medical University, Zhejiang, China
| | - Ai-Ping Chen
- International Collaborative Center on Growth Factor Research, and School of Pharmaceutical Sciences, Wenzhou Medical University, Zhejiang, China
| | - Jie Wang
- International Collaborative Center on Growth Factor Research, and School of Pharmaceutical Sciences, Wenzhou Medical University, Zhejiang, China
| | - Jin Wu
- International Collaborative Center on Growth Factor Research, and School of Pharmaceutical Sciences, Wenzhou Medical University, Zhejiang, China
| | - Xu-Ru Jin
- The Quzhou Affiliated Hospital of Wenzhou Medical University, Quzhou People's Hospital, Zhejiang, China
| | - Feng Zhang
- The Quzhou Affiliated Hospital of Wenzhou Medical University, Quzhou People's Hospital, Zhejiang, China
| | - Mei-Yu Quan
- Medical Research Center, and Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Wenzhou Medical University, Zhejiang, China
| | - Chengshui Chen
- The Quzhou Affiliated Hospital of Wenzhou Medical University, Quzhou People's Hospital, Zhejiang, China
| | - Kwang-Youl Lee
- College of Pharmacy and Research Institute of Drug Development, Chonnam National University, Gwangju, Republic of Korea
| | - Jin-San Zhang
- The Quzhou Affiliated Hospital of Wenzhou Medical University, Quzhou People's Hospital, Zhejiang, China
- Medical Research Center, and Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Wenzhou Medical University, Zhejiang, China
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Poonaki E, Kahlert UD, Meuth SG, Gorji A. The role of the ZEB1–neuroinflammation axis in CNS disorders. J Neuroinflammation 2022; 19:275. [PMCID: PMC9675144 DOI: 10.1186/s12974-022-02636-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Accepted: 10/31/2022] [Indexed: 11/21/2022] Open
Abstract
Zinc finger E-box binding homeobox 1 (ZEB1) is a master modulator of the epithelial–mesenchymal transition (EMT), a process whereby epithelial cells undergo a series of molecular changes and express certain characteristics of mesenchymal cells. ZEB1, in association with other EMT transcription factors, promotes neuroinflammation through changes in the production of inflammatory mediators, the morphology and function of immune cells, and multiple signaling pathways that mediate the inflammatory response. The ZEB1–neuroinflammation axis plays a pivotal role in the pathogenesis of different CNS disorders, such as brain tumors, multiple sclerosis, cerebrovascular diseases, and neuropathic pain, by promoting tumor cell proliferation and invasiveness, formation of the hostile inflammatory micromilieu surrounding neuronal tissues, dysfunction of microglia and astrocytes, impairment of angiogenesis, and dysfunction of the blood–brain barrier. Future studies are needed to elucidate whether the ZEB1–neuroinflammation axis could serve as a diagnostic, prognostic, and/or therapeutic target for CNS disorders.
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Affiliation(s)
- Elham Poonaki
- grid.411327.20000 0001 2176 9917Department of Neurology, Faculty of Medicine, Heinrich-Heine-University, Düsseldorf, Germany ,grid.5949.10000 0001 2172 9288Epilepsy Research Center, Department of Neurosurgery, Westfälische Wilhelms-Universität Münster, Domagkstr. 11, 48149 Münster, Germany
| | - Ulf Dietrich Kahlert
- grid.5807.a0000 0001 1018 4307Molecular and Experimental Surgery, Faculty of Medicine, University Clinic for General-, Visceral-, Vascular- and Transplantation Surgery, Otto-Von-Guericke-University, Magdeburg, Germany
| | - Sven G. Meuth
- grid.411327.20000 0001 2176 9917Department of Neurology, Faculty of Medicine, Heinrich-Heine-University, Düsseldorf, Germany
| | - Ali Gorji
- grid.5949.10000 0001 2172 9288Epilepsy Research Center, Department of Neurosurgery, Westfälische Wilhelms-Universität Münster, Domagkstr. 11, 48149 Münster, Germany ,grid.512981.60000 0004 0612 1380Shefa Neuroscience Research Center, Khatam Alanbia Hospital, Tehran, Iran ,grid.411583.a0000 0001 2198 6209Neuroscience Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
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7
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Barillari G, Bei R, Manzari V, Modesti A. Infection by High-Risk Human Papillomaviruses, Epithelial-to-Mesenchymal Transition and Squamous Pre-Malignant or Malignant Lesions of the Uterine Cervix: A Series of Chained Events? Int J Mol Sci 2021; 22:13543. [PMID: 34948338 PMCID: PMC8703928 DOI: 10.3390/ijms222413543] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 12/13/2021] [Accepted: 12/14/2021] [Indexed: 12/19/2022] Open
Abstract
Wound healing requires static epithelial cells to gradually assume a mobile phenotype through a multi-step process termed epithelial-to-mesenchymal transition (EMT). Although it is inherently transient and reversible, EMT perdures and is abnormally activated when the epithelium is chronically exposed to pathogens: this event deeply alters the tissue and eventually contributes to the development of diseases. Among the many of them is uterine cervical squamous cell carcinoma (SCC), the most frequent malignancy of the female genital system. SCC, whose onset is associated with the persistent infection of the uterine cervix by high-risk human papillomaviruses (HR-HPVs), often relapses and/or metastasizes, being resistant to conventional chemo- or radiotherapy. Given that these fearsome clinical features may stem, at least in part, from the exacerbated and long-lasting EMT occurring in the HPV-infected cervix; here we have reviewed published studies concerning the impact that HPV oncoproteins, cellular tumor suppressors, regulators of gene expression, inflammatory cytokines or growth factors, and the interactions among these effectors have on EMT induction and cervical carcinogenesis. It is predictable and desirable that a broader comprehension of the role that EMT inducers play in SCC pathogenesis will provide indications to flourish new strategies directed against this aggressive tumor.
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Affiliation(s)
- Giovanni Barillari
- Department of Clinical Sciences and Translational Medicine, University of Rome Tor Vergata, 1 via Montellier, 00133 Rome, Italy; (R.B.); (V.M.); (A.M.)
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Na L, Wang Z, Bai Y, Sun Y, Dong D, Wang W, Zhao C. WNT7B represses epithelial-mesenchymal transition and stem-like properties in bladder urothelial carcinoma. Biochim Biophys Acta Mol Basis Dis 2021; 1868:166271. [PMID: 34562599 DOI: 10.1016/j.bbadis.2021.166271] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2021] [Revised: 09/01/2021] [Accepted: 09/15/2021] [Indexed: 12/18/2022]
Abstract
BACKGROUND Recurrence and metastasis are the major problems of bladder urothelial carcinoma, which mainly attribute to tumor cell stemness, epithelial-mesenchymal transition (EMT) and chemoresistance. METHODS TCGA database was interrogated for gene mRNA expression in bladder urothelial carcinoma samples. CCLE database was interrogated for gene mRNA expression in bladder cancer cell lines. The correlation between two genes was analyzed by Pearson statistics. 37 human bladder urothelial carcinoma specimens were adopted for immunohistochemistry. Bladder cancer cells RT4, J82, and UM-UC-3 were used to carry out loss and gain of function studies. Kaplan-Meier method was performed to analyze the overall survival. FINDINGS WNT7B is downregulated in high-grade bladder urothelial carcinomas. Low WNT7B expression is associated with unfavorable prognosis. Loss and gain of function studies showed that WNT7B inhibits bladder urothelial carcinoma cell EMT, stem-like properties and chemoresistance. FZD5, a specific receptor for WNT7B, mediates WNT7B signaling. ELF3 is a downstream component of WNT7B signaling, which transcriptionally modulates NOTCH1, a tumor suppressor in bladder urothelial carcinoma. INTERPRETATION These data demonstrate that WNT7B/FZD5-ELF3-NOTCH1 signaling functions as a tumor-suppressing pathway in bladder urothelial carcinoma.
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Affiliation(s)
- Lei Na
- Department of Pathophysiology, College of Basic Medical Science, China Medical University, Shenyang, China; Department of Urology, Shengjing Hospital of China Medical University, Shenyang, China
| | - Zhuo Wang
- Department of Pathophysiology, College of Basic Medical Science, China Medical University, Shenyang, China
| | - Yu Bai
- Department of Pathophysiology, College of Basic Medical Science, China Medical University, Shenyang, China; Department of Nephrology, Shengjing Hospital of China Medical University, Shenyang, China
| | - Yu Sun
- Department of Pathophysiology, College of Basic Medical Science, China Medical University, Shenyang, China
| | - Dan Dong
- Department of Pathophysiology, College of Basic Medical Science, China Medical University, Shenyang, China
| | - Wei Wang
- Department of Pathophysiology, College of Basic Medical Science, China Medical University, Shenyang, China.
| | - Chenghai Zhao
- Department of Pathophysiology, College of Basic Medical Science, China Medical University, Shenyang, China.
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9
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Dong D, Na L, Zhou K, Wang Z, Sun Y, Zheng Q, Gao J, Zhao C, Wang W. FZD5 prevents epithelial-mesenchymal transition in gastric cancer. Cell Commun Signal 2021; 19:21. [PMID: 33618713 PMCID: PMC7898745 DOI: 10.1186/s12964-021-00708-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Accepted: 01/18/2021] [Indexed: 12/11/2022] Open
Abstract
Background Frizzled (FZD) proteins function as receptors for WNT ligands. Members in FZD family including FZD2, FZD4, FZD7, FZD8 and FZD10 have been demonstrated to mediate cancer cell epithelial-mesenchymal transition (EMT). Methods CCLE and TCGA databases were interrogated to reveal the association of FZD5 with EMT. EMT was analyzed by investigating the alterations in CDH1 (E-cadherin), VIM (Vimentin) and ZEB1 expression, cell migration and cell morphology. Transcriptional modulation was determined by ChIP in combination with Real-time PCR. Survival was analyzed by Kaplan–Meier method. Results In contrast to other FZDs, FZD5 was identified to prevent EMT in gastric cancer. FZD5 maintains epithelial-like phenotype and is negatively modulated by transcription factors SNAI2 and TEAD1. Epithelial-specific factor ELF3 is a downstream effecter, and protein kinase C (PKC) links FZD5 to ELF3. ELF3 represses ZEB1 expression, further guarding against EMT. Moreover, FZD5 signaling requires its co-receptor LRP5 and WNT7B is a putative ligand for FZD5. FZD5 and ELF3 are associated with longer survival, whereas SNAI2 and TEAD1 are associated with shorter survival. Conclusions Taken together, FZD5-ELF3 signaling blocks EMT, and plays a potential tumor-suppressing role in gastric cancer. ![]()
Video Abstract
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Affiliation(s)
- Dan Dong
- Department of Pathophysiology, College of Basic Medical Science, China Medical University, Shenyang, People's Republic of China
| | - Lei Na
- Department of Pathophysiology, College of Basic Medical Science, China Medical University, Shenyang, People's Republic of China.,Department of Urology, Shengjing Hospital of China Medical University, Shenyang, People's Republic of China
| | - Kailing Zhou
- Department of Pathophysiology, College of Basic Medical Science, China Medical University, Shenyang, People's Republic of China
| | - Zhuo Wang
- Department of Pathophysiology, College of Basic Medical Science, China Medical University, Shenyang, People's Republic of China
| | - Yu Sun
- Department of Pathophysiology, College of Basic Medical Science, China Medical University, Shenyang, People's Republic of China
| | - Qianqian Zheng
- Department of Pathophysiology, College of Basic Medical Science, China Medical University, Shenyang, People's Republic of China
| | - Jian Gao
- Center of Laboratory Technology and Experimental Medicine, China Medical University, Shenyang, People's Republic of China
| | - Chenghai Zhao
- Department of Pathophysiology, College of Basic Medical Science, China Medical University, Shenyang, People's Republic of China.
| | - Wei Wang
- Department of Pathophysiology, College of Basic Medical Science, China Medical University, Shenyang, People's Republic of China.
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10
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Ghaffari S, Hanson C, Schmidt RE, Bouchonville KJ, Offer SM, Sinha S. An integrated multi-omics approach to identify regulatory mechanisms in cancer metastatic processes. Genome Biol 2021; 22:19. [PMID: 33413550 PMCID: PMC7789593 DOI: 10.1186/s13059-020-02213-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Accepted: 11/25/2020] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Metastatic progress is the primary cause of death in most cancers, yet the regulatory dynamics driving the cellular changes necessary for metastasis remain poorly understood. Multi-omics approaches hold great promise for addressing this challenge; however, current analysis tools have limited capabilities to systematically integrate transcriptomic, epigenomic, and cistromic information to accurately define the regulatory networks critical for metastasis. RESULTS To address this limitation, we use a purposefully generated cellular model of colon cancer invasiveness to generate multi-omics data, including expression, accessibility, and selected histone modification profiles, for increasing levels of invasiveness. We then adopt a rigorous probabilistic framework for joint inference from the resulting heterogeneous data, along with transcription factor binding profiles. Our approach uses probabilistic graphical models to leverage the functional information provided by specific epigenomic changes, models the influence of multiple transcription factors simultaneously, and automatically learns the activating or repressive roles of cis-regulatory events. Global analysis of these relationships reveals key transcription factors driving invasiveness, as well as their likely target genes. Disrupting the expression of one of the highly ranked transcription factors JunD, an AP-1 complex protein, confirms functional relevance to colon cancer cell migration and invasion. Transcriptomic profiling confirms key regulatory targets of JunD, and a gene signature derived from the model demonstrates strong prognostic potential in TCGA colorectal cancer data. CONCLUSIONS Our work sheds new light into the complex molecular processes driving colon cancer metastasis and presents a statistically sound integrative approach to analyze multi-omics profiles of a dynamic biological process.
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Affiliation(s)
- Saba Ghaffari
- Department of Computer Science, University of Illinois at Urbana-Champaign, Urbana, USA
| | - Casey Hanson
- Department of Genetics, Stanford University, Stanford, USA
| | - Remington E Schmidt
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Gonda 19-476, 200 First St SW, Rochester, MN, 55905, USA
| | - Kelly J Bouchonville
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Gonda 19-476, 200 First St SW, Rochester, MN, 55905, USA
| | - Steven M Offer
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Gonda 19-476, 200 First St SW, Rochester, MN, 55905, USA.
| | - Saurabh Sinha
- Department of Computer Science, Carl R. Woese Institute of Genomic Biology, and Cancer Center of Illinois, University of Illinois at Urbana-Champaign, 2122, Siebel Center, 201 N. Goodwin Ave., Urbana, IL, 61801, USA.
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11
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Saxena K, Jolly MK, Balamurugan K. Hypoxia, partial EMT and collective migration: Emerging culprits in metastasis. Transl Oncol 2020; 13:100845. [PMID: 32781367 PMCID: PMC7419667 DOI: 10.1016/j.tranon.2020.100845] [Citation(s) in RCA: 105] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2020] [Revised: 07/12/2020] [Accepted: 07/27/2020] [Indexed: 02/07/2023] Open
Abstract
Epithelial-mesenchymal transition (EMT) is a cellular biological process involved in migration of primary cancer cells to secondary sites facilitating metastasis. Besides, EMT also confers properties such as stemness, drug resistance and immune evasion which can aid a successful colonization at the distant site. EMT is not a binary process; recent evidence suggests that cells in partial EMT or hybrid E/M phenotype(s) can have enhanced stemness and drug resistance as compared to those undergoing a complete EMT. Moreover, partial EMT enables collective migration of cells as clusters of circulating tumor cells or emboli, further endorsing that cells in hybrid E/M phenotypes may be the 'fittest' for metastasis. Here, we review mechanisms and implications of hybrid E/M phenotypes, including their reported association with hypoxia. Hypoxia-driven activation of HIF-1α can drive EMT. In addition, cyclic hypoxia, as compared to acute or chronic hypoxia, shows the highest levels of active HIF-1α and can augment cancer aggressiveness to a greater extent, including enriching for a partial EMT phenotype. We also discuss how metastasis is influenced by hypoxia, partial EMT and collective cell migration, and call for a better understanding of interconnections among these mechanisms. We discuss the known regulators of hypoxia, hybrid EMT and collective cell migration and highlight the gaps which needs to be filled for connecting these three axes which will increase our understanding of dynamics of metastasis and help control it more effectively.
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Affiliation(s)
- Kritika Saxena
- Centre for BioSystems Science and Engineering, Indian Institute of Science, Bangalore 560012, India
| | - Mohit Kumar Jolly
- Centre for BioSystems Science and Engineering, Indian Institute of Science, Bangalore 560012, India.
| | - Kuppusamy Balamurugan
- Laboratory of Cell and Developmental Signaling, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA.
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12
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Ramos PIP, Arge LWP, Lima NCB, Fukutani KF, de Queiroz ATL. Leveraging User-Friendly Network Approaches to Extract Knowledge From High-Throughput Omics Datasets. Front Genet 2019; 10:1120. [PMID: 31798629 PMCID: PMC6863976 DOI: 10.3389/fgene.2019.01120] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Accepted: 10/16/2019] [Indexed: 11/13/2022] Open
Abstract
Recent technological advances for the acquisition of multi-omics data have allowed an unprecedented understanding of the complex intricacies of biological systems. In parallel, a myriad of computational analysis techniques and bioinformatics tools have been developed, with many efforts directed towards the creation and interpretation of networks from this data. In this review, we begin by examining key network concepts and terminology. Then, computational tools that allow for their construction and analysis from high-throughput omics datasets are presented. We focus on the study of functional relationships such as co-expression, protein-protein interactions, and regulatory interactions that are particularly amenable to modeling using the framework of networks. We envisage that many potential users of these analytical strategies may not be completely literate in programming languages and code adaptation, and for this reason, emphasis is given to tools' user-friendliness, including plugins for the widely adopted Cytoscape software, an open-source, cross-platform tool for network analysis, visualization, and data integration.
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Affiliation(s)
- Pablo Ivan Pereira Ramos
- Center for Data and Knowledge Integration for Health (CIDACS), Instituto Gonçalo Moniz, Fundação Oswaldo Cruz, Salvador, Brazil
| | - Luis Willian Pacheco Arge
- Laboratório de Genética Molecular e Biotecnologia Vegetal, Centro de Ciências da Saúde, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | | | - Kiyoshi F. Fukutani
- Multinational Organization Network Sponsoring Translational and Epidemiological Research (MONSTER) Initiative, Fundação José Silveira, Salvador, Brazil
| | - Artur Trancoso L. de Queiroz
- Center for Data and Knowledge Integration for Health (CIDACS), Instituto Gonçalo Moniz, Fundação Oswaldo Cruz, Salvador, Brazil
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13
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Rabalski AJ, Bogdan AR, Baranczak A. Evaluation of Chemically-Cleavable Linkers for Quantitative Mapping of Small Molecule-Cysteinome Reactivity. ACS Chem Biol 2019; 14:1940-1950. [PMID: 31430117 DOI: 10.1021/acschembio.9b00424] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Numerous reagents have been developed to enable chemical proteomic analysis of small molecule-protein interactomes. However, the performance of these reagents has not been systematically evaluated and compared. Herein, we report our efforts to conduct a parallel assessment of two widely used chemically cleavable linkers equipped with dialkoxydiphenylsilane (DADPS linker) and azobenzene (AZO linker) moieties. Profiling a cellular cysteinome using the iodoacetamide alkyne probe demonstrated a significant discrepancy between the experimental results obtained through the application of each of the reagents. To better understand the source of observed discrepancy, we evaluated the key sample preparation steps. We also performed a mass tolerant database search strategy using MSFragger software. This resulted in identifying a previously unreported artifactual modification on the residual mass of the azobenzene linker. Furthermore, we conducted a comparative analysis of enrichment modes using both cleavable linkers. This effort determined that enrichment of proteolytic digests yielded a far greater number of identified cysteine residues than the enrichment conducted prior to protein digest. Inspired by recent studies where multiplexed quantitative labeling strategies were applied to cleavable biotin linkers, we combined this further optimized protocol using the DADPS cleavable linker with tandem mass tag (TMT) labeling to profile the FDA-approved covalent EGFR kinase inhibitor dacomitinib against the cysteinome of an epidermoid cancer cell line. Our analysis resulted in the detection and quantification of over 10,000 unique cysteine residues, a nearly 3-fold increase over previous studies that used cleavable biotin linkers for enrichment. Critically, cysteine residues corresponding to proteins directly as well as indirectly modulated by dacomitinib treatment were identified. Overall, our study suggests that the dialkoxydiphenylsilane linker could be broadly applied wherever chemically cleavable linkers are required for chemical proteomic characterization of cellular proteomes.
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Affiliation(s)
- Adam J. Rabalski
- Drug Discovery Science & Technology, AbbVie Inc., 1 North Waukegan Road, North Chicago, Illinois 60064-6101, United States
| | - Andrew R. Bogdan
- Drug Discovery Science & Technology, AbbVie Inc., 1 North Waukegan Road, North Chicago, Illinois 60064-6101, United States
| | - Aleksandra Baranczak
- Drug Discovery Science & Technology, AbbVie Inc., 1 North Waukegan Road, North Chicago, Illinois 60064-6101, United States
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14
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Zhao H, He L, Yin D, Song B. Identification of β-catenin target genes in colorectal cancer by interrogating gene fitness screening data. Oncol Lett 2019; 18:3769-3777. [PMID: 31516589 PMCID: PMC6733007 DOI: 10.3892/ol.2019.10724] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Accepted: 07/12/2019] [Indexed: 11/06/2022] Open
Abstract
β-catenin regulates its target genes which are associated with proliferation, differentiation, migration and angiogenesis, and the dysregulation of Wnt/β-catenin signaling facilitates hallmarks of colorectal cancer (CRC). Identification of β-catenin targets and their potential roles in tumorigenesis has gained increased interest. However, the number of identified targets remains limited. The present study implemented a novel strategy, interrogating gene fitness profiles derived from large-scale RNA interference and CRISPR-CRISPR associated protein 9 screening data to identify β-catenin target genes in CRC cell lines. Using these data sets, pair wise gene fitness similarities were determined which highlighted a total of 13 genes whose functions were highly correlated with β-catenin. It was further demonstrated that the expression of these genes were altered in CRC, illustrating their potential roles in the progression of CRC. The present study further demonstrated that these targets could be used to predict disease-free survival in CRC. In conclusion, the findings provided novel approaches for the identification of β-catenin targets, which may become prognostic biomarkers or drug targets for the management of CRC.
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Affiliation(s)
- Haomin Zhao
- Department of Vascular Surgery, China-Japan Union Hospital of Jilin University, Changchun, Jilin 130033, P.R. China
| | - Liang He
- Department of Gastrointestinal Surgery, First Hospital of Jilin University, Changchun, Jilin 130033, P.R. China
| | - Dexin Yin
- Department of Vascular Surgery, China-Japan Union Hospital of Jilin University, Changchun, Jilin 130033, P.R. China
| | - Bin Song
- Department of Gastrointestinal Surgery, China-Japan Union Hospital of Jilin University, Changchun, Jilin 130033, P.R. China
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15
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Li D, Cheng P, Wang J, Qiu X, Zhang X, Xu L, Liu Y, Qin S. IRF6 Is Directly Regulated by ZEB1 and ELF3, and Predicts a Favorable Prognosis in Gastric Cancer. Front Oncol 2019; 9:220. [PMID: 31019894 PMCID: PMC6458252 DOI: 10.3389/fonc.2019.00220] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Accepted: 03/12/2019] [Indexed: 01/09/2023] Open
Abstract
Interferon regulatory factor 6 (IRF6) acts as a tumor suppressor and controls cell differentiation in ectodermal and craniofacial tissues by regulating expression of target genes. However, its function in gastric cancer (GC) remains unknown to date. In this study, we found that the IRF6 expression was significantly downregulated in GC. And the decreased expression of IRF6 was clinically correlated with poor prognosis of GC. Moreover, loss-of-function and gain-of-function studies showed that IRF6 was negatively regulated by ZEB1 but positively regulated by ELF3. Additionally, transcription factor ZEB1 and ELF3 could directly bind on IRF6 promoter, which suggested that transcription factor IRF6 is transcriptionally regulated by ZEB1 and ELF3. Nevertheless, we found that IRF6 expression was negatively related to its promoter methylation in TCGA stomach cancer cohorts. The downregulation of IRF6 in GC might be due to the overexpression of ZEB1 and the DNA methylation of IRF6 promoter.
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Affiliation(s)
- Dandan Li
- Institute of Basic Medical Sciences, School of Basic Medical Sciences, Hubei University of Medicine, Shiyan, China.,School of Biomedical Engineering, Hubei University of Medicine, Shiyan, China
| | - Ping Cheng
- Shiyan Hospital of Traditional Chinese Medicine, Shiyan, China
| | - Jingjie Wang
- Institute of Basic Medical Sciences, School of Basic Medical Sciences, Hubei University of Medicine, Shiyan, China.,School of Biomedical Engineering, Hubei University of Medicine, Shiyan, China
| | - Xuemei Qiu
- Institute of Basic Medical Sciences, School of Basic Medical Sciences, Hubei University of Medicine, Shiyan, China.,School of Biomedical Engineering, Hubei University of Medicine, Shiyan, China
| | - Xudong Zhang
- Institute of Basic Medical Sciences, School of Basic Medical Sciences, Hubei University of Medicine, Shiyan, China
| | - Li Xu
- School of Biomedical Engineering, Hubei University of Medicine, Shiyan, China
| | - Ying Liu
- Institute of Basic Medical Sciences, School of Basic Medical Sciences, Hubei University of Medicine, Shiyan, China.,School of Biomedical Engineering, Hubei University of Medicine, Shiyan, China
| | - Shanshan Qin
- Institute of Basic Medical Sciences, School of Basic Medical Sciences, Hubei University of Medicine, Shiyan, China.,School of Biomedical Engineering, Hubei University of Medicine, Shiyan, China.,Hubei Key Laboratory of Wudang Local Chinese Medicine Research, Shiyan, China
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16
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Li Y, Zhao W, Shi R, Jia J, Li X, Cheng J. Rs4759314 polymorphism located in HOTAIR is associated with the risk of congenital heart disease by alternating downstream signaling via reducing its expression. J Cell Biochem 2018; 119:8112-8122. [DOI: 10.1002/jcb.26736] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2017] [Accepted: 01/29/2018] [Indexed: 12/17/2022]
Affiliation(s)
- Yunyun Li
- Department of obstetrics and gynecologyEast HospitalTongji University School of MedicineShanghaiChina
| | - Wenrong Zhao
- Department of obstetrics and gynecologyEast HospitalTongji University School of MedicineShanghaiChina
| | - Ri Shi
- Department of obstetrics and gynecologyEast HospitalTongji University School of MedicineShanghaiChina
| | - Jun Jia
- Department of obstetrics and gynecologyEast HospitalTongji University School of MedicineShanghaiChina
| | - Xiaona Li
- Department of obstetrics and gynecologyEast HospitalTongji University School of MedicineShanghaiChina
| | - Jingxin Cheng
- Department of obstetrics and gynecologyEast HospitalTongji University School of MedicineShanghaiChina
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