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Shinde A, Chandak N, Singh J, Roy M, Mane M, Tang X, Vasiyani H, Currim F, Gohel D, Shukla S, Goyani S, Saranga MV, Brindley DN, Singh R. TNF-α induced NF-κB mediated LYRM7 expression modulates the tumor growth and metastatic ability in breast cancer. Free Radic Biol Med 2024; 211:158-170. [PMID: 38104742 DOI: 10.1016/j.freeradbiomed.2023.12.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 12/11/2023] [Accepted: 12/14/2023] [Indexed: 12/19/2023]
Abstract
Tumor microenvironment (TME) of solid tumors including breast cancer is complex and contains a distinct cytokine pattern including TNF-α, which determines the progression and metastasis of breast tumors. The metastatic potential of triple negative breast cancer subtypes is high as compared to other subtypes of breast cancer. NF-κB is key transcription factor regulating inflammation and mitochondrial bioenergetics including oxidative phosphorylation (OXPHOS) genes which determine its oxidative capacity and generating reducing equivalents for synthesis of key metabolites for proliferating breast cancer cells. The differential metabolic adaptation and OXPHOS function of breast cancer subtypes in inflammatory conditions and its contribution to metastasis is not well understood. Here we demonstrated that different subunits of NF-κB are differentially expressed in subtypes of breast cancer patients. RELA, one of the major subunits in regulation of the NF-κB pathway is positively correlated with high level of TNF-α in breast cancer patients. TNF-α induced NF-κB regulates the expression of LYRM7, an assembly factor for mitochondrial complex III. Downregulation of LYRM7 in MDA-MB-231 cells decreases mitochondrial super complex assembly and enhances ROS levels, which increases the invasion and migration potential of these cells. Further, in vivo studies using Infliximab, a monoclonal antibody against TNF-α showed decreased expression of LYRM7 in tumor tissue. Large scale breast cancer databases and human patient samples revealed that LYRM7 levels decreased in triple negative breast cancer patients compared to other subtypes and is determinant of survival outcome in patients. Our results indicate that TNF-α induced NF-κB is a critical regulator of LYRM7, a major factor for modulating mitochondrial functions under inflammatory conditions, which determines growth and survival of breast cancer cells.
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Affiliation(s)
- Anjali Shinde
- Department of Biochemistry, Faculty of Science, The MS University of Baroda, Vadodara, 390002, Gujarat, India
| | - Nisha Chandak
- Department of Biochemistry, Faculty of Science, The MS University of Baroda, Vadodara, 390002, Gujarat, India
| | - Jyoti Singh
- Department of Biochemistry, Faculty of Science, The MS University of Baroda, Vadodara, 390002, Gujarat, India
| | - Milton Roy
- Institute for Cell Engineering, John Hopkins University School of Medicine, 733 North Broadway, MRB 731, Baltimore, MD, 21205, USA
| | - Minal Mane
- Department of Biochemistry, Faculty of Science, The MS University of Baroda, Vadodara, 390002, Gujarat, India
| | - Xiaoyun Tang
- Cancer Research Institute of Northern Alberta, Department of Biochemistry, University of Alberta, Edmonton, Alberta, T6G2S2, Canada
| | - Hitesh Vasiyani
- Department of Pharmacology and Toxicology, Virginia Commonwealth University, Richmond, VA-23284, USA
| | - Fatema Currim
- Department of Biochemistry, Faculty of Science, The MS University of Baroda, Vadodara, 390002, Gujarat, India
| | - Dhruv Gohel
- Department of Genomic Medicine, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, 44195, USA
| | - Shatakshi Shukla
- Department of Biochemistry, Faculty of Science, The MS University of Baroda, Vadodara, 390002, Gujarat, India
| | - Shanikumar Goyani
- Department of Biochemistry, Faculty of Science, The MS University of Baroda, Vadodara, 390002, Gujarat, India
| | - M V Saranga
- Department of Biochemistry, Faculty of Science, The MS University of Baroda, Vadodara, 390002, Gujarat, India
| | - David N Brindley
- Cancer Research Institute of Northern Alberta, Department of Biochemistry, University of Alberta, Edmonton, Alberta, T6G2S2, Canada
| | - Rajesh Singh
- Department of Biochemistry, Faculty of Science, The MS University of Baroda, Vadodara, 390002, Gujarat, India; Department of Molecular and Human Genetics, Banaras Hindu University (BHU) (IoE), Varanasi, 221005, UP, India.
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2
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Bhowmick C, Rahaman M, Bhattacharya S, Mukherjee M, Chakravorty N, Dutta PK, Mahadevappa M. Identification of hub genes to determine drug-disease correlation in breast carcinomas. Med Oncol 2023; 41:36. [PMID: 38153604 DOI: 10.1007/s12032-023-02246-9] [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: 08/26/2023] [Accepted: 11/11/2023] [Indexed: 12/29/2023]
Abstract
The exact molecular mechanism underlying the heterogeneous drug response against breast carcinoma remains to be fully understood. It is urgently required to identify key genes that are intricately associated with varied clinical response of standard anti-cancer drugs, clinically used to treat breast cancer patients. In the present study, the utility of transcriptomic data of breast cancer patients in discerning the clinical drug response using machine learning-based approaches were evaluated. Here, a computational framework has been developed which can be used to identify key genes that can be linked with clinical drug response and progression of cancer, offering an immense opportunity to predict potential prognostic biomarkers and therapeutic targets. The framework concerned utilizes DeSeq2, Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), Cytoscape, and machine learning techniques to find these crucial genes. Total RNA extraction and qRT-PCR were performed to quantify relative expression of few hub genes selected from the networks. In our study, we have experimentally checked the expression of few key hub genes like APOA2, DLX5, APOC3, CAMK2B, and PAK6 that were predicted to play an immense role in breast cancer tumorigenesis and progression in response to anti-cancer drug Paclitaxel. However, further experimental validations will be required to get mechanistic insights of these genes in regulating the drug response and cancer progression which will likely to play pivotal role in cancer treatment and precision oncology.
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Affiliation(s)
- Chiranjib Bhowmick
- School of Medical Science and Technology, Indian Institute of Technology Kharagpur, West Medinipur, Kharagpur, West Bengal, 721302, India
| | - Motiur Rahaman
- School of Medical Science and Technology, Indian Institute of Technology Kharagpur, West Medinipur, Kharagpur, West Bengal, 721302, India
| | - Shatarupa Bhattacharya
- School of Medical Science and Technology, Indian Institute of Technology Kharagpur, West Medinipur, Kharagpur, West Bengal, 721302, India
| | - Mandrita Mukherjee
- School of Medical Science and Technology, Indian Institute of Technology Kharagpur, West Medinipur, Kharagpur, West Bengal, 721302, India
| | - Nishant Chakravorty
- School of Medical Science and Technology, Indian Institute of Technology Kharagpur, West Medinipur, Kharagpur, West Bengal, 721302, India
| | - Pranab Kumar Dutta
- Department of Electrical Engineering, Indian Institute of Technology Kharagpur, West Medinipur, Kharagpur, West Bengal, 721302, India
| | - Manjunatha Mahadevappa
- School of Medical Science and Technology, Indian Institute of Technology Kharagpur, West Medinipur, Kharagpur, West Bengal, 721302, India.
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3
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Sun Z, Chung D, Neelon B, Millar-Wilson A, Ethier SP, Xiao F, Zheng Y, Wallace K, Hardiman G. A Bayesian framework for pathway-guided identification of cancer subgroups by integrating multiple types of genomic data. Stat Med 2023; 42:5266-5284. [PMID: 37715500 DOI: 10.1002/sim.9911] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 07/15/2023] [Accepted: 09/05/2023] [Indexed: 09/17/2023]
Abstract
In recent years, comprehensive cancer genomics platforms, such as The Cancer Genome Atlas (TCGA), provide access to an enormous amount of high throughput genomic datasets for each patient, including gene expression, DNA copy number alterations, DNA methylation, and somatic mutation. While the integration of these multi-omics datasets has the potential to provide novel insights that can lead to personalized medicine, most existing approaches only focus on gene-level analysis and lack the ability to facilitate biological findings at the pathway-level. In this article, we propose Bayes-InGRiD (Bayesian Integrative Genomics Robust iDentification of cancer subgroups), a novel pathway-guided Bayesian sparse latent factor model for the simultaneous identification of cancer patient subgroups (clustering) and key molecular features (variable selection) within a unified framework, based on the joint analysis of continuous, binary, and count data. By utilizing pathway (gene set) information, Bayes-InGRiD does not only enhance the accuracy and robustness of cancer patient subgroup and key molecular feature identification, but also promotes biological understanding and interpretation. Finally, to facilitate an efficient posterior sampling, an alternative Gibbs sampler for logistic and negative binomial models is proposed using Pólya-Gamma mixtures of normal to represent latent variables for binary and count data, which yields a conditionally Gaussian representation of the posterior. The R package "INGRID" implementing the proposed approach is currently available in our research group GitHub webpage (https://dongjunchung.github.io/INGRID/).
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Affiliation(s)
- Zequn Sun
- Department of Preventive Medicine, Northwestern University, Chicago, Illinois
| | - Dongjun Chung
- Department of Biomedical Informatics, The Ohio State University, Columbus, Ohio
- The Pelotonia Institute for Immuno-Oncology, The Ohio State University Comprehensive Cancer Center, Columbus, Ohio
| | - Brian Neelon
- Department of Public Health Sciences, Medical University of South Carolina, Charleston, South Carolina
| | | | - Stephen P Ethier
- Department of Pathology and Laboratory Medicine, Medical University of South Carolina, Charleston, South Carolina
| | - Feifei Xiao
- Department of Biostatistics, University of Florida, Gainesville, Florida
| | - Yinan Zheng
- Department of Preventive Medicine, Northwestern University, Chicago, Illinois
| | - Kristin Wallace
- Department of Public Health Sciences, Medical University of South Carolina, Charleston, South Carolina
| | - Gary Hardiman
- Department of Public Health Sciences, Medical University of South Carolina, Charleston, South Carolina
- Faculty of Medicine, Health and Life Sciences, School of Biological Sciences and Institute for Global Food Security, Queen's University Belfast, Belfast, UK
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Chen H, Yang W, Ma L, Li Y, Ji Z. Machine-learning based integrating bulk and single-cell RNA sequencing reveals the SLC38A5-CCL5 signaling as a promising target for clear cell renal cell carcinoma treatment. Transl Oncol 2023; 38:101790. [PMID: 37722291 PMCID: PMC10518726 DOI: 10.1016/j.tranon.2023.101790] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 09/02/2023] [Accepted: 09/12/2023] [Indexed: 09/20/2023] Open
Abstract
Cancer-associated fibroblasts paly critical roles in regulating cancer cell biological properties by intricate and dynamic communication networks. But the mechanism of CAFs in clear cell renal cell carcinoma (ccRCC) is not clear. In our study, we identified CAFs and malignant cells from the integrated scRNA-seq datasets and establish a CAF-derived communication signature based on the highly activated regulons ETS1 and MEF2C. We stratified the ccRCC TME into two molecular subtypes with distinct prognoses, immune cell infiltration landscapes, and immune-related characteristics. The model derived from signature demonstrated high accuracy and robustness in predicting prognosis and ICIs therapy responses. Subsequently, the SLC38A5 of the model was found upregulated in CAFs and was related to decreased survival probabilities, inflamed TME, and upregulated inhibitory checkpoints. SLC38A5 inhibition could attenuate the pro-tumoral abilities of CAFs in terms of proliferation, migration, and invasion. Mechanically, CCL5 could restore these properties induced by SLC38A5 inhibition. In conclusion, our communication signature and its derived model enabled a more precise selection of ccRCC patients who were potential beneficiaries of ICIs. Besides, the SLC38A5-CCL5 axis may serve as a promising target for ccRCC treatment.
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Affiliation(s)
- Hualin Chen
- Department of Urology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, China
| | - Wenjie Yang
- Department of Urology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, China
| | - Lin Ma
- Department of Urology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, China
| | - Yingjie Li
- Department of Urology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, China
| | - Zhigang Ji
- Department of Urology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, China.
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Dawood H, Celik I, Ibrahim RS. Computational biology and in vitro studies for anticipating cancer-related molecular targets of sweet wormwood (Artemisia annua). BMC Complement Med Ther 2023; 23:312. [PMID: 37684586 PMCID: PMC10492370 DOI: 10.1186/s12906-023-04135-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 08/21/2023] [Indexed: 09/10/2023] Open
Abstract
BACKGROUND Cancer is one of the leading causes of death worldwide. Recently, it was shown that many natural extracts have positive effects against cancer, compared with chemotherapy or recent hormonal treatments. A. annua is an annual medicinal herb used in the traditional Chinese medicine. It has also been shown to inhibit the proliferation of various cancer cell lines. METHODS Multi-level modes of action of A. annua constituents in cancer therapy were investigated using an integrated approach of network pharmacology, molecular docking, dynamic simulations and in-vitro cytotoxicity testing on both healthy and cancer cells. RESULTS Network pharmacology-based analysis showed that the hit Artemisia annua constituents related to cancer targets were 3-(2-methylpropanoyl)-4-cadinene-3,11-diol, artemisinin G, O-(2-propenal) coniferaldehyde, (2-glyceryl)-O-coniferaldehyde and arteamisinin III, whereas the main cancer allied targets were NFKB1, MAP2K1 and AR. Sixty-eight significant signaling KEGG pathways with p < 0.01 were recognized, the most enriched of which were prostate cancer, breast cancer, melanoma and pancreatic cancer. Thirty-five biological processes were mainly regulated by cancer, involving cellular response to mechanical stimulus, positive regulation of gene expression and transcription. Molecular docking analysis of the top hit compounds against the most enriched target proteins showed that 3-(2-methylpropanoyl)-4-cadinene-3,11-diol and O-(2-propenal) coniferaldehyde exhibited the most stabilized interactions. Molecular dynamics simulations were performed to explain the stability of these two compounds in their protein-ligand complexes. Finally, confirmation of the potential anticancer activity was attained by in-vitro cytotoxicity testing of the extract on human prostate (PC-3), breast (MDA-MB-231), pancreatic (PANC-1) and melanoma (A375) cancerous cell lines. CONCLUSION This study presents deeper insights into A. annua molecular mechanisms of action in cancer for the first time using an integrated approaches verifying the herb's value.
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Affiliation(s)
- Hend Dawood
- Department of Pharmacognosy, Faculty of Pharmacy, Alexandria University, Alexandria, 21521, Egypt
| | - Ismail Celik
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Erciyes University, Kayseri, 38039, Turkey
| | - Reham S Ibrahim
- Department of Pharmacognosy, Faculty of Pharmacy, Alexandria University, Alexandria, 21521, Egypt.
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Huang Z, Wu C, Zhou W, Lu S, Tan Y, Wu Z, You R, Stalin A, Guo F, Zhang J, Liu P, Wang W, Duan X, You L, Wu J. Compound Kushen Injection inhibits epithelial-mesenchymal transition of gastric carcinoma by regulating VCAM1 induced by the TNF signaling pathway. PHYTOMEDICINE : INTERNATIONAL JOURNAL OF PHYTOTHERAPY AND PHYTOPHARMACOLOGY 2023; 118:154984. [PMID: 37487253 DOI: 10.1016/j.phymed.2023.154984] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 07/04/2023] [Accepted: 07/15/2023] [Indexed: 07/26/2023]
Abstract
BACKGROUND Gastric carcinoma (GC) treatment needs to be developed rapidly. Compound Kushen Injection (CKI), a formula from traditional Chinese medicine, has been used clinically in combination with chemotherapy to treat GC with satisfactory results. However, the molecular mechanism by which CKI acts to cure GC is still unclear. METHODS In the present study, in vivo and in vitro experiments were used to assess the efficacy of CKI. Using ceRNA microarray and TMT technologies, the molecular mechanism of CKI was further investigated at the transcriptional and protein levels, and a bioinformatics approach was employed to investigate and functionally validate key CKI targets in GC. RESULTS When combined with cisplatin (DDP), CKI significantly increased its efficacy in preventing the proliferation and metastasis of GC cells and malignant-looking tumors in mice. High-throughput sequencing data and bioinformatics analysis showed that CKI regulated the TNF signaling pathway, epithelial-mesenchymal transition (EMT), with VCAM1 as a key target. The transcription factors CEBPB, JUN, RELA, NFKB1, the EMT mesenchymal-like cell markers N-cadherin and vimentin, as well as the expression of VCAM1 and its upstream signaling driver TNF, were all downregulated by CKI. In contrast, the expression of the EMT epithelial-like cell marker E-cadherin was upregulated. CONCLUSION CKI can effectively inhibit GC growth and metastasis, improve body's immunity, and protect normal tissues from damage. The molecular mechanism by which CKI inhibits metastasis of GC is by regulating VCAM1 induced by the TNF signaling pathway to inhibit EMT of GC. Our results provide an important clue to clarify precisely the multi-scale molecular mechanism of CKI in the treatment of GC.
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Affiliation(s)
- Zhihong Huang
- Department of Clinical Pharmacology of Traditional Chinese Medicine, School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing 100029, China
| | - Chao Wu
- Department of Clinical Pharmacology of Traditional Chinese Medicine, School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing 100029, China
| | - Wei Zhou
- Department of pharmacy, China-Japan Friendship Hospital, Beijing 100029, China
| | - Shan Lu
- Department of Clinical Pharmacology of Traditional Chinese Medicine, School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing 100029, China
| | - Yingying Tan
- Department of Clinical Pharmacology of Traditional Chinese Medicine, School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing 100029, China
| | - Zhishan Wu
- Department of Clinical Pharmacology of Traditional Chinese Medicine, School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing 100029, China
| | - Rongli You
- Shanxi Zhendong Pharmaceutical Co., Ltd., Shanxi 47100, China
| | - Antony Stalin
- Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Fengying Guo
- School of Management, Beijing University of Chinese Medicine, Beijing 100029, China
| | - Jingyuan Zhang
- Department of Clinical Pharmacology of Traditional Chinese Medicine, School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing 100029, China
| | - Pengyun Liu
- Department of Clinical Pharmacology of Traditional Chinese Medicine, School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing 100029, China
| | - Wei Wang
- Shanxi Zhendong Pharmaceutical Co., Ltd., Shanxi 47100, China
| | - Xiaoxia Duan
- Beijing Zestbridge Medical Technology Co., Ltd., Beijing, 100176, China.
| | - Leiming You
- Department of Immunology and Microbiology, School of Life Science, Beijing University of Chinese Medicine, Beijing 102488, China.
| | - Jiarui Wu
- Department of Clinical Pharmacology of Traditional Chinese Medicine, School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing 100029, China.
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A Novel Defined Pyroptosis-Related Gene Signature for Predicting the Prognosis of Endometrial Cancer. DISEASE MARKERS 2022; 2022:7570494. [PMID: 36601599 PMCID: PMC9806687 DOI: 10.1155/2022/7570494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 10/15/2022] [Accepted: 11/24/2022] [Indexed: 12/23/2022]
Abstract
Endometrial carcinoma (EC) is the second major female genital malignancy. Genetic signatures may be an improved choice to predict the prognosis of EC patients. The relationship between pyroptosis and tumours has attracted much attention in recent years. Here, we constructed a new pyroptosis-related gene (PRG) signature for predicting the prognosis of EC. In this study, gene data and clinical information of EC patients were obtained from The Cancer Genome Atlas (TCGA). Following the identification of PRGs correlated with EC prognosis, we further investigate the bioinformatics functions of these PRGs by univariate Cox regression analysis and Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses. Then, we used the least absolute contraction and selection operator (LASSO) regression and multiple Cox regression analysis to construct a new PRG signature that contains seven PRGs (NFKB1, EEF2K, CTSV, MDM2, GZMB, PANX1, and PTEN) and performed the Kaplan-Meier (K-M) analysis, receiver operating characteristic curve (ROC) analysis, and principal component analysis (PCA) to evaluate the prognostic value of our novel PRG signature. Finally, we assessed the correlations between pyroptosis and immune cells/checkpoints through the CIBERSORT tool and single-sample gene set enrichment analysis (ssGSEA). The result suggested that our signature was powerful in predicting EC prognosis and may play a part in assessing response to immunotherapy in EC patients. In conclusion, our study established a novel PRG signature for EC, which can be used as an effective prognostic marker in clinical practice in the future.
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Understanding Molecular Mechanisms of Phenotype Switching and Crosstalk with TME to Reveal New Vulnerabilities of Melanoma. Cells 2022; 11:cells11071157. [PMID: 35406721 PMCID: PMC8997563 DOI: 10.3390/cells11071157] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 03/20/2022] [Accepted: 03/21/2022] [Indexed: 12/15/2022] Open
Abstract
Melanoma cells are notorious for their high plasticity and ability to switch back and forth between various melanoma cell states, enabling the adaptation to sub-optimal conditions and therapeutics. This phenotypic plasticity, which has gained more attention in cancer research, is proposed as a new paradigm for melanoma progression. In this review, we provide a detailed and deep comprehensive recapitulation of the complex spectrum of phenotype switching in melanoma, the key regulator factors, the various and new melanoma states, and corresponding signatures. We also present an extensive description of the role of epigenetic modifications (chromatin remodeling, methylation, and activities of long non-coding RNAs/miRNAs) and metabolic rewiring in the dynamic switch. Furthermore, we elucidate the main role of the crosstalk between the tumor microenvironment (TME) and oxidative stress in the regulation of the phenotype switching. Finally, we discuss in detail several rational therapeutic approaches, such as exploiting phenotype-specific and metabolic vulnerabilities and targeting components and signals of the TME, to improve the response of melanoma patients to treatments.
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LncRNA MAFG-AS1 promotes the malignant phenotype of ovarian cancer by upregulating NFKB1-dependent IGF1. Cancer Gene Ther 2022; 29:277-291. [PMID: 34035482 DOI: 10.1038/s41417-021-00306-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 01/24/2021] [Accepted: 02/03/2021] [Indexed: 02/04/2023]
Abstract
Long non-coding RNAs (lncRNAs) were recently recognized to vitally function in a variety of cancer cellular events, including epithelial-mesenchymal transition (EMT), invasion, and migration, particularly in ovarian cancer (OC). Herein, we sought to investigate the potential role of MAFG-AS1 in the malignant behaviors of OC cells. The binding affinity between MAFG-AS1, miR-339-5p, NFKB1 or IGF1 was characterized so as to identify the underlying mechanism of corresponding their interactions. We conducted MAFG-AS1 overexpression or knockdown along with NFKB1 and IGF1 silencing to examine their effects on the EMT, migration, and invasion of OC cells. Tumors were xenografted in nude mice to validate the in vitro findings. Our data showed significantly high expression pattern of MAFG-AS1 in the OC tissues and cells. Further mechanistic investigations revealed that MAFG-AS1 upregulated the IGF1 expression pattern through recruitment of NFKB1, whereas MAFG-AS1 upregulated the NFKB1 expression pattern through binding to miR-339-5p. Thus, MAFG-AS1 overexpression accelerated the EMT, invasion, and migration of OC cells, which could be annulled by silencing of IGF1 or NFKB1. Besides, our in vitro findings were successfully recapitulated in the xenograft mice. These results determined that MAFG-AS1 stimulated the OC malignant progression by upregulating the NFKB1-mediated IGF1 via miR-339-5p, thus highlighting a novel potential therapeutic target against OC.
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10
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Pan G, Zhang J, You F, Cui T, Luo P, Wang S, Li X, Yuan Q. ETS Proto-Oncogene 1-activated muskelin 1 antisense RNA drives the malignant progression of hepatocellular carcinoma by targeting miR-22-3p to upregulate ETS Proto-Oncogene 1. Bioengineered 2022; 13:1346-1358. [PMID: 34983308 PMCID: PMC8805956 DOI: 10.1080/21655979.2021.2017565] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Long noncoding RNA muskelin 1 antisense RNA (MKLN1-AS) acted as an oncogenic regulator in hepatocellular carcinoma (HCC). This study was performed to investigate the functional mechanism of MKLN1-AS. MKLN1-AS, microRNA-22-3p (miR-22-3p) and ETS Proto-Oncogene 1 (ETS1) levels were examined using reverse transcription-quantitative polymerase-chain reaction. Protein expression was detected by Western blot. The target relation was analyzed by dual-luciferase reporter assay, RNA immunoprecipitation assay and RNA pull-down assay. Cell proliferation ability was determined through cell counting kit-8 assay, colony formation assay and ethylenediurea assay. Angiogenesis was examined by tube formation assay. Cell migration and invasion were assessed via transwell assay. In vivo research was conducted by xenograft tumor model in nude mice. MKLN1-AS was upregulated in HCC tissues and cells. ETS1 promoted the ETS1 expression by binding to the 582–596 sites. Silence of MKLN1-AS suppressed cell growth, angiogenesis, migration, and invasion. MKLN1-AS interacted with miR-22-3p in HCC cells. The function of MKLN1-AS downregulation was relieved by miR-22-3p inhibition in HCC cells. ETS1 was validated as a target of miR-22-3p, and MKLN1-AS upregulated the ETS1 expression by sponging miR-22-3p. Overexpression of miR-22-3p retarded HCC progression by downregulating the level of ETS1. Tumor growth in vivo was also enhanced by MKLN1-AS through the regulation of miR-22-3p/ETS1 axis. These data demonstrated that ETS1-mediated MKLN1-AS contributed to the malignant phenotypes of HCC cells via depending on the miR-22-3p/ETS1 regulatory axis.
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Affiliation(s)
- Guozheng Pan
- Department of Hepatobiliary Sugery, Shengli Oilfield Central Hospital, Dongying, China
| | - Jian Zhang
- Department of Hepatobiliary Sugery, Shengli Oilfield Central Hospital, Dongying, China
| | - Faping You
- Department of Hepatobiliary Sugery, Shengli Oilfield Central Hospital, Dongying, China
| | - Tao Cui
- Department of Hepatobiliary Sugery, Shengli Oilfield Central Hospital, Dongying, China
| | - Peng Luo
- Department of Sales, Shanghai Topgen Biopharm Company Ltd, shanghai, china
| | - Shuling Wang
- Department of Hepatobiliary Sugery, Shengli Oilfield Central Hospital, Dongying, China
| | - Xiaomei Li
- Department of Medical Record, People Hospital of Dongying, Dongying, China
| | - Qingzhong Yuan
- Department of Hepatobiliary Sugery, Shengli Oilfield Central Hospital, Dongying, China
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Rohini M, Vairamani M, Selvamurugan N. TGF-β1-stimulation of NFATC2 and ATF3 proteins and their interaction for matrix metalloproteinase 13 expression in human breast cancer cells. Int J Biol Macromol 2021; 192:1325-1330. [PMID: 34687766 DOI: 10.1016/j.ijbiomac.2021.10.099] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2021] [Revised: 09/30/2021] [Accepted: 10/14/2021] [Indexed: 01/25/2023]
Abstract
Activating transcription factor 3 (ATF3), an inducible stress gene, is stimulated by transforming growth factor-beta1 (TGF-β1) in a protracted and relentless manner in human mammary cancer cells (hBC cells; MDA-MB231). The molecular mechanism behind this stable expression of ATF3 via TGF-β1 in MDA-MB231 cells is unknown. This study found that TGF-β1 stimulated the expression of the nuclear factor of activated T Cells 2 (NFATC2) in MDA-MB231 cells and provided evidence of its interaction with ATF3. The functional characterization of NFATC2 in association with ATF3 was determined by silencing of NFATC2 using siRNA. Knock-down of NFATC2 decreased the expression of both ATF3 and its target gene MMP13 (matrix metalloproteinase 13, a critical invasive gene) in hBC cells. Chromatin immunoprecipitation revealed that TGF-β1 promoted NFATC2 binding and NFATC2-ATF3 complex binding at the MMP13 promoter region, whereas silencing of NFATC2 decreased their binding in hBC cells. Thus, we uncovered the mechanism of interaction between NFATC2 and ATF3 regulated by TGF-β1, and NFATC2 acted as a pivotal factor in providing ATF3 stability and further drove MMP13 transcription. Targeting NFATC2 and blocking its association with ATF3 could therefore help to slow the progression of breast cancer.
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Affiliation(s)
- M Rohini
- Department of Biotechnology, College of Engineering and Technology, SRM Institute of Science and Technology, Kattankulathur, Tamil Nadu, India
| | - M Vairamani
- Department of Biotechnology, College of Engineering and Technology, SRM Institute of Science and Technology, Kattankulathur, Tamil Nadu, India
| | - N Selvamurugan
- Department of Biotechnology, College of Engineering and Technology, SRM Institute of Science and Technology, Kattankulathur, Tamil Nadu, India.
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12
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Lo Cascio C, McNamara JB, Melendez EL, Lewis EM, Dufault ME, Sanai N, Plaisier CL, Mehta S. Nonredundant, isoform-specific roles of HDAC1 in glioma stem cells. JCI Insight 2021; 6:e149232. [PMID: 34494550 PMCID: PMC8492336 DOI: 10.1172/jci.insight.149232] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 07/22/2021] [Indexed: 01/02/2023] Open
Abstract
Glioblastoma (GBM) is characterized by an aberrant yet druggable epigenetic landscape. One major family of epigenetic regulators, the histone deacetylases (HDACs), are considered promising therapeutic targets for GBM due to their repressive influences on transcription. Although HDACs share redundant functions and common substrates, the unique isoform-specific roles of different HDACs in GBM remain unclear. In neural stem cells, HDAC2 is the indispensable deacetylase to ensure normal brain development and survival in the absence of HDAC1. Surprisingly, we find that HDAC1 is the essential class I deacetylase in glioma stem cells, and its loss is not compensated for by HDAC2. Using cell-based and biochemical assays, transcriptomic analyses, and patient-derived xenograft models, we find that knockdown of HDAC1 alone has profound effects on the glioma stem cell phenotype in a p53-dependent manner. We demonstrate marked suppression in tumor growth upon targeting of HDAC1 and identify compensatory pathways that provide insights into combination therapies for GBM. Our study highlights the importance of HDAC1 in GBM and the need to develop isoform-specific drugs.
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Affiliation(s)
- Costanza Lo Cascio
- Ivy Brain Tumor Center, Barrow Neurological Institute, Phoenix, Arizona, USA.,Interdisciplinary Graduate Program in Neuroscience, School of Life Sciences, and
| | - James B McNamara
- Ivy Brain Tumor Center, Barrow Neurological Institute, Phoenix, Arizona, USA
| | - Ernesto L Melendez
- Ivy Brain Tumor Center, Barrow Neurological Institute, Phoenix, Arizona, USA
| | - Erika M Lewis
- School of Biological and Health Systems Engineering, Arizona State University, Tempe, Arizona, USA
| | - Matthew E Dufault
- Ivy Brain Tumor Center, Barrow Neurological Institute, Phoenix, Arizona, USA
| | - Nader Sanai
- Ivy Brain Tumor Center, Barrow Neurological Institute, Phoenix, Arizona, USA
| | - Christopher L Plaisier
- School of Biological and Health Systems Engineering, Arizona State University, Tempe, Arizona, USA
| | - Shwetal Mehta
- Ivy Brain Tumor Center, Barrow Neurological Institute, Phoenix, Arizona, USA
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13
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Integrative Bioinformatics Study of Tangeretin Potential Targets for Preventing Metastatic Breast Cancer. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE 2021; 2021:2234554. [PMID: 34335799 PMCID: PMC8294962 DOI: 10.1155/2021/2234554] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Accepted: 06/22/2021] [Indexed: 11/17/2022]
Abstract
Agents that target metastasis are important to improve treatment efficacy in patients with breast cancer. Tangeretin, a citrus flavonoid, exhibits antimetastatic effects on breast cancer cells, but its molecular mechanism remains unclear. Tangeretin targets were retrieved from PubChem, whereas metastatic breast cancer regulatory genes were downloaded from PubMed. In total, 58 genes were identified as potential therapeutic target genes of tangeretin (PTs). GO and KEGG pathway enrichment analyses of PTs were performed using WebGestalt (WEB-based Gene SeT AnaLysis Toolkit). The PPI network was analyzed using STRING-DB v11.0 and visualized by Cytoscape software. Hub genes were selected on the basis of the highest degree score as calculated by the CytoHubba plugin. Genetic alterations of the PTs were analyzed using cBioPortal. The prognostic values of the PTs were evaluated with the Kaplan-Meier plot. The expression of PTs across breast cancer samples was confirmed using GEPIA. The reliability of the PTs in metastatic breast cancer cells was validated using ONCOMINE. Molecular docking was performed to foresee the binding sites of tangeretin with PIK3Cα, MMP9, PTGS2, COX-2, and IKK. GO analysis showed that PTs participate in the biological process of stimulus response, are the cellular components of the nucleus and the membrane, and play molecular roles in enzyme regulation. KEGG pathway enrichment analysis revealed that PTs regulate the PI3K/Akt pathway. Genetic alterations for each target gene were MTOR (3%), NOTCH1 (4%), TP53 (42%), MMP9 (4%), NFKB1 (3%), PIK3CA (32%), PTGS2 (15%), and RELA (5%). The Kaplan-Meier plot showed that patients with low mRNA expression levels of MTOR, TP53, MMP9, NFKB1, PTGS2, and RELA and high expression of PIK3CA had a significantly better prognosis than their counterparts. Further validation of gene expression by using GEPIA revealed that the mRNA expression of MMP9 was significantly higher in breast cancer tissues than in normal tissues, whereas the mRNA expression of PTGS2 showed the opposite. Analysis with ONCOMINE demonstrated that the mRNA expression levels of MMP9 and NFKB1 were significantly higher in metastatic breast cancer cells than in normal tissues. The results of molecular docking analyses revealed the advantage of tangeretin as an inhibitor of PIK3CA, MMP9, PTGS2, and IKK. Tangeretin inhibits metastasis in breast cancer cells by targeting TP53, PTGS2, MMP9, and PIK3CA and regulating the PI3K/Akt signaling pathway. Further investigation is needed to validate the results of this study.
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14
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Zidane M, Truong T, Lesueur F, Xhaard C, Cordina-Duverger E, Boland A, Blanché H, Ory C, Chevillard S, Deleuze JF, Souchard V, Ren Y, Zemmache MZ, Canale S, Borson-Chazot F, Schvartz C, Mariné Barjoan E, Guizard AV, Laurent-Puig P, Mulot C, Guibon J, Karimi M, Schlumberger M, Adjadj E, Rubino C, Guenel P, Cazier JB, de Vathaire F. Role of DNA Repair Variants and Diagnostic Radiology Exams in Differentiated Thyroid Cancer Risk: A Pooled Analysis of Two Case-Control Studies. Cancer Epidemiol Biomarkers Prev 2021; 30:1208-1217. [PMID: 33827984 DOI: 10.1158/1055-9965.epi-20-1142] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 11/12/2020] [Accepted: 03/29/2021] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND Given the increased use and diversity of diagnostic procedures, it is important to understand genetic susceptibility to radiation-induced thyroid cancer. METHODS On the basis of self-declared diagnostic radiology examination records in addition to existing literature, we estimated the radiation dose delivered to the thyroid gland from diagnostic procedures during childhood and adulthood in two case-control studies conducted in France. A total of 1,071 differentiated thyroid cancer (DTC) cases and 1,188 controls from the combined studies were genotyped using a custom-made Illumina OncoArray DNA chip. We focused our analysis on variants in genes involved in DNA damage response and repair pathways, representing a total of 5,817 SNPs in 571 genes. We estimated the OR per milli-Gray (OR/mGy) of the radiation dose delivered to the thyroid gland using conditional logistic regression. We then used an unconditional logistic regression model to assess the association between DNA repair gene variants and DTC risk. We performed a meta-analysis of the two studies. RESULTS The OR/mGy was 1.02 (95% confidence interval, 1.00-1.03). We found significant associations between DTC and rs7164173 in CHD2 (P = 5.79 × 10-5), rs6067822 in NFATc2 (P = 9.26 × 10-5), rs1059394 and rs699517 both in ENOSF1/THYS, rs12702628 in RPA3, and an interaction between rs7068306 in MGMT and thyroid radiation doses (P = 3.40 × 10-4). CONCLUSIONS Our results suggest a role for variants in CDH2, NFATc2, ENOSF1/THYS, RPA3, and MGMT in DTC risk. IMPACT CDH2, NFATc2, ENOSF1/THYS, and RPA3 have not previously been shown to be associated with DTC risk.
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Affiliation(s)
- Monia Zidane
- INSERM, Centre for Research in Epidemiology and Population Health (CESP), 94800 Villejuif, France
- Université Paris-Sud Orsay, Villejuif, France
- Gustave Roussy, Villejuif, France
| | - Thérèse Truong
- INSERM, Centre for Research in Epidemiology and Population Health (CESP), 94800 Villejuif, France
- Université Paris-Sud Orsay, Villejuif, France
- Gustave Roussy, Villejuif, France
| | - Fabienne Lesueur
- Inserm, U900, Institut Curie, Université PSL, Mines ParisTech, Paris, France
| | - Constance Xhaard
- INSERM Centre d'Investigation Clinique CIC-P 1433, CHRU Nancy, France
- INSERM U1116, FCRIN INI-CRCT, Lorraine Université, Nancy, France
| | - Emilie Cordina-Duverger
- INSERM, Centre for Research in Epidemiology and Population Health (CESP), 94800 Villejuif, France
- Université Paris-Sud Orsay, Villejuif, France
- Gustave Roussy, Villejuif, France
| | - Anne Boland
- Université Paris-Saclay, CEA, Centre National de Recherche en Génomique Humaine, Evry, France
| | - Hélène Blanché
- Fondation Jean Dausset-CEPH (Centre Etude du Polymorphisme Humain), Paris, France
- Laboratory of Excellence GENMED (Medical Genomics)
| | - Catherine Ory
- CEA, Direction de la Recherche Fondamentale, Institut de Biologie François Jacob, iRCM, SREIT, Laboratoire de Cancérologie Expérimentale (LCE), Université Paris-Saclay, Fontenay-aux-Roses, France
| | - Sylvie Chevillard
- CEA, Direction de la Recherche Fondamentale, Institut de Biologie François Jacob, iRCM, SREIT, Laboratoire de Cancérologie Expérimentale (LCE), Université Paris-Saclay, Fontenay-aux-Roses, France
| | - Jean-François Deleuze
- Université Paris-Saclay, CEA, Centre National de Recherche en Génomique Humaine, Evry, France
- Fondation Jean Dausset-CEPH (Centre Etude du Polymorphisme Humain), Paris, France
- Laboratory of Excellence GENMED (Medical Genomics)
| | - Vincent Souchard
- INSERM, Centre for Research in Epidemiology and Population Health (CESP), 94800 Villejuif, France
- Université Paris-Sud Orsay, Villejuif, France
- Gustave Roussy, Villejuif, France
| | - Yan Ren
- INSERM, Centre for Research in Epidemiology and Population Health (CESP), 94800 Villejuif, France
- Université Paris-Sud Orsay, Villejuif, France
- Gustave Roussy, Villejuif, France
| | - Mohammed Zakarya Zemmache
- INSERM, Centre for Research in Epidemiology and Population Health (CESP), 94800 Villejuif, France
- Université Paris-Sud Orsay, Villejuif, France
- Gustave Roussy, Villejuif, France
| | | | - Françoise Borson-Chazot
- Rhône-Alpes Thyroid Cancer Registry, Cancer Research Center of Lyon (UMR INSERM 1052, CNRS 5286), RTH Laennec Faculty of Medicine, University of Lyon, Lyon
| | - Claire Schvartz
- Thyroid Cancer Registry of Champagne-Ardennes, Institut Jean Godinot, Reims, Cancer Registry of Isère, Meylan
| | | | - Anne-Valérie Guizard
- Registre Général des Tumeurs du Calvados, Centre François Baclesse, Caen, France
- U1086 INSERM-UCN "ANTICIPE," Caen, France
| | - Pierre Laurent-Puig
- Centre de Recherche des Cordeliers, INSERM, Sorbonne Université, USPC, Université Paris Descartes, Université Paris Diderot, EPIGENETEC, Paris, France
| | - Claire Mulot
- Centre de Recherche des Cordeliers, INSERM, Sorbonne Université, USPC, Université Paris Descartes, Université Paris Diderot, EPIGENETEC, Paris, France
| | - Julie Guibon
- INSERM, Centre for Research in Epidemiology and Population Health (CESP), 94800 Villejuif, France
- Université Paris-Sud Orsay, Villejuif, France
- Gustave Roussy, Villejuif, France
- Inserm, U900, Institut Curie, Université PSL, Mines ParisTech, Paris, France
| | - Mojgan Karimi
- INSERM, Centre for Research in Epidemiology and Population Health (CESP), 94800 Villejuif, France
- Université Paris-Sud Orsay, Villejuif, France
- Gustave Roussy, Villejuif, France
| | - Martin Schlumberger
- Université Paris-Sud Orsay, Villejuif, France
- Gustave Roussy, Villejuif, France
| | - Elizabeth Adjadj
- INSERM, Centre for Research in Epidemiology and Population Health (CESP), 94800 Villejuif, France
| | - Carole Rubino
- INSERM, Centre for Research in Epidemiology and Population Health (CESP), 94800 Villejuif, France
- Université Paris-Sud Orsay, Villejuif, France
- Gustave Roussy, Villejuif, France
| | - Pascal Guenel
- INSERM, Centre for Research in Epidemiology and Population Health (CESP), 94800 Villejuif, France
- Université Paris-Sud Orsay, Villejuif, France
- Gustave Roussy, Villejuif, France
| | - Jean-Baptiste Cazier
- Institute of Cancer and Genomic Sciences, Centre for Computational Biology, University of Birmingham, Birmingham, UK
| | - Florent de Vathaire
- INSERM, Centre for Research in Epidemiology and Population Health (CESP), 94800 Villejuif, France.
- Université Paris-Sud Orsay, Villejuif, France
- Gustave Roussy, Villejuif, France
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15
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Oh M, Kim K, Sun H. Covariance thresholding to detect differentially co-expressed genes from microarray gene expression data. J Bioinform Comput Biol 2021; 18:2050002. [PMID: 32336254 DOI: 10.1142/s021972002050002x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Gene set analysis aims to identify differentially expressed or co-expressed genes within a biological pathway between two experimental conditions, so that it can eventually reveal biological processes and pathways involved in disease development. In the last few decades, various statistical and computational methods have been proposed to improve statistical power of gene set analysis. In recent years, much attention has been paid to differentially co-expressed genes since they can be potentially disease-related genes without significant difference in average expression levels between two conditions. In this paper, we propose a new statistical method to identify differentially co-expressed genes from microarray gene expression data. The proposed method first estimates co-expression levels of paired genes using covariance regularization by thresholding, and then significance of difference in covariance estimation between two conditions is evaluated. We demonstrated that the proposed method is more powerful than the existing main-stream methods to detect co-expressed genes through extensive simulation studies. Also, we applied it to various microarray gene expression datasets related with mutant p53 transcriptional activity, and epithelium and stroma breast cancer.
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Affiliation(s)
- Mingyu Oh
- Department of Statistics, Pusan National University, Busan, 46241, Korea
| | - Kipoong Kim
- Department of Statistics, Pusan National University, Busan, 46241, Korea
| | - Hokeun Sun
- Department of Statistics, Pusan National University, Busan, 46241, Korea
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16
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Ma J, Du R, Huang Y, Zhong W, Gui H, Mao C, Song X, Lu J. Expression, Prognosis and Gene Regulation Network of NFAT Transcription Factors in Non-Small Cell Lung Cancer. Pathol Oncol Res 2021; 27:529240. [PMID: 34257525 PMCID: PMC8262184 DOI: 10.3389/pore.2021.529240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Accepted: 02/26/2021] [Indexed: 12/09/2022]
Abstract
Non-small cell lung cancer (NSCLC) is the leading cause of cancer-related death worldwide. The nuclear factor of activated T cells (NFAT) family is implicated in tumorigenesis and progression in various types of cancer. However, little is known about their expression patterns, distinct prognostic values, and potential regulatory networks in NSCLC. In this study, we comprehensively analyzed the distinct expression and prognostic value of NFATs in NSCLC through various large databases, including the Oncomine, UCSC Xena Browser, UALCAN databases, Kaplan–Meier Plotter, cBioPortal, and Enrichr. In lung adenocarcinoma (LUAD) and lung squamous cell carcinoma (LUSC), NFAT1/2/4/5 mRNA expression levels were significantly decreased and NFAT3 mRNA expression level was significantly increased. The cBioPortal database analysis showed that the mRNA dysregulation was one of the single most important factors for NFAT alteration in LUAD and LUSC and that both LUAD and LUSC cases with the alterations in the mRNA expression of NFATs had significantly better overall survival (OS). High expression levels of NFAT1/2/4/5 were significantly associated with better OS in LUAD, whereas high NFAT3 expression led to a worse OS. Overexpression of NFAT1/2 predicted better OS in LUSC, whereas high NFAT5 expression led to a worse OS. The networks for NFATs and the 50 most frequently altered neighbor genes in LUAD and LUSC were also constructed. NFATs and genes significantly associated with NFAT mRNA expression in LUAD and LUSC were significantly enriched in the cGMP-dependent protein kinase and Wnt signaling pathways. These results showed that the NFAT family members displayed varying degrees of abnormal expressions, suggesting that NFATs may be therapeutic targets for patients with NSCLC. Aberrant expression of NFATs was found to be associated with OS in the patients with NSCLC; among NFATs, NFAT3/4 may be new biomarkers for the prognosis of LUAD. However, further studies are required to validate our findings.
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Affiliation(s)
- Jin Ma
- Department of Pharmacy, Children's Hospital of Soochow University, Suzhou, China
| | - Rao Du
- Department of Pharmacy, Children's Hospital of Soochow University, Suzhou, China
| | - Yan Huang
- Department of Pharmacy, Children's Hospital of Soochow University, Suzhou, China
| | - Wen Zhong
- Department of Pharmacy, Children's Hospital of Soochow University, Suzhou, China
| | - Huan Gui
- Department of Pharmacy, Children's Hospital of Soochow University, Suzhou, China
| | - Chenmei Mao
- Department of Pharmacy, Children's Hospital of Soochow University, Suzhou, China
| | - Xiudao Song
- Clinical Pharmaceutical Laboratory of Traditional Chinese Medicine, Suzhou TCM Hospital Affiliated to Nanjing University of Chinese Medicine, Suzhou, China
| | - Jun Lu
- Department of Haematology, Children's Hospital of Soochow University, Suzhou, China
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17
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Integrative analysis of DNA methylation and gene expression profiles identified potential breast cancer-specific diagnostic markers. Biosci Rep 2021; 40:224161. [PMID: 32412047 PMCID: PMC7263199 DOI: 10.1042/bsr20201053] [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: 04/07/2020] [Revised: 05/13/2020] [Accepted: 05/14/2020] [Indexed: 12/14/2022] Open
Abstract
Breast cancer is a common malignant tumor among women whose prognosis is largely determined by the period and accuracy of diagnosis. We here propose to identify a robust DNA methylation-based breast cancer-specific diagnostic signature. Genome-wide DNA methylation and gene expression profiles of breast cancer patients along with their adjacent normal tissues from the Cancer Genome Atlas (TCGA) were obtained as the training set. CpGs that with significantly elevated methylation level in breast cancer than not only their adjacent normal tissues and the other ten common cancers from TCGA but also the healthy breast tissues from the Gene Expression Omnibus (GEO) were finally remained for logistic regression analysis. Another independent breast cancer DNA methylation dataset from GEO was used as the testing set. Lots of CpGs were hyper-methylated in breast cancer samples compared with adjacent normal tissues, which tend to be negatively correlated with gene expressions. Eight CpGs located at RIIAD1, ENPP2, ESPN, and ETS1, were finally retained. The diagnostic model was reliable in separating BRCA from normal samples. Besides, chromatin accessibility status of RIIAD1, ENPP2, ESPN and ETS1 showed great differences between MCF-7 and MDA-MB-231 cell lines. In conclusion, the present study should be helpful for breast cancer early and accurate diagnosis.
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18
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Pham VVH, Liu L, Bracken CP, Goodall GJ, Li J, Le TD. DriverGroup: a novel method for identifying driver gene groups. Bioinformatics 2021; 36:i583-i591. [PMID: 33381812 DOI: 10.1093/bioinformatics/btaa797] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
MOTIVATION Identifying cancer driver genes is a key task in cancer informatics. Most existing methods are focused on individual cancer drivers which regulate biological processes leading to cancer. However, the effect of a single gene may not be sufficient to drive cancer progression. Here, we hypothesize that there are driver gene groups that work in concert to regulate cancer, and we develop a novel computational method to detect those driver gene groups. RESULTS We develop a novel method named DriverGroup to detect driver gene groups by using gene expression and gene interaction data. The proposed method has three stages: (i) constructing the gene network, (ii) discovering critical nodes of the constructed network and (iii) identifying driver gene groups based on the discovered critical nodes. Before evaluating the performance of DriverGroup in detecting cancer driver groups, we firstly assess its performance in detecting the influence of gene groups, a key step of DriverGroup. The application of DriverGroup to DREAM4 data demonstrates that it is more effective than other methods in detecting the regulation of gene groups. We then apply DriverGroup to the BRCA dataset to identify driver groups for breast cancer. The identified driver groups are promising as several group members are confirmed to be related to cancer in literature. We further use the predicted driver groups in survival analysis and the results show that the survival curves of patient subpopulations classified using the predicted driver groups are significantly differentiated, indicating the usefulness of DriverGroup. AVAILABILITY AND IMPLEMENTATION DriverGroup is available at https://github.com/pvvhoang/DriverGroup. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Vu V H Pham
- UniSA STEM, University of South Australia, Mawson Lakes, SA, 5095, Australia
| | - Lin Liu
- UniSA STEM, University of South Australia, Mawson Lakes, SA, 5095, Australia
| | - Cameron P Bracken
- Centre for Cancer Biology, an alliance of SA Pathology and University of South Australia, Adelaide, SA, 5000, Australia.,Department of Medicine, The University of Adelaide, Adelaide, SA 5005, Australia
| | - Gregory J Goodall
- Centre for Cancer Biology, an alliance of SA Pathology and University of South Australia, Adelaide, SA, 5000, Australia.,Department of Medicine, The University of Adelaide, Adelaide, SA 5005, Australia
| | - Jiuyong Li
- UniSA STEM, University of South Australia, Mawson Lakes, SA, 5095, Australia
| | - Thuc D Le
- UniSA STEM, University of South Australia, Mawson Lakes, SA, 5095, Australia
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19
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Yu X, Guo J, Zhou Q, Huang W, Xu C, Long X. A novel immune-related prognostic index for predicting breast cancer overall survival. Breast Cancer 2021; 28:434-447. [PMID: 33146847 DOI: 10.1007/s12282-020-01175-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2020] [Accepted: 10/13/2020] [Indexed: 02/08/2023]
Abstract
PURPOSE To find immune-related genes with prognostic value in breast cancer, and construct a prognostic risk assessment model to make a more accurate assessment. Moreover, looking for potential immune markers for breast cancer immunotherapy. METHODS The breast cancer (BC) data were retrieved from The Cancer Genome Atlas (TCGA) database as a training set. Through the Weighted gene co-expression network analysis (WGCNA), Kaplan-Meier (KM) analysis, lasso regression analysis and stepwise backward Cox regression analysis, screening for prognosis-related immune genes, a prognostic index was built, and external validation with two data sets of Gene Expression Omnibus (GEO) database was performed. Transcription factor (TF) regulatory network was constructed to identify key transcription factors that regulate prognostic immune genes. Gene set enrichment analysis (GSEA) was used to explore the signal pathways differences between high and low-risk groups, estimate package and TIMER database were used to evaluate the relationship between risk score and tumor immune microenvironment. RESULTS We obtained 10 prognosis-related immune genes, and the index showed accurate prognostic value. We also identified 7 prognostic transcription factors. Multiple signaling pathways that inhibit tumor progression were enriched in the low-risk group, and risk score was significantly negatively related to the degree of immune infiltration and the expression level of immune checkpoint genes. CONCLUSION We successfully constructed an independent prognostic index, which not only has a stronger predictive ability than the tumor pathological stage, but also can reflect the immune infiltration of breast cancer patients.
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Affiliation(s)
- Xiaosi Yu
- Department of Labortory Medicine, Zhongnan Hospital of Wuhan University, 169 Donghu Road, Wuhan, 430071, China
| | - Juan Guo
- Department of Labortory Medicine, Zhongnan Hospital of Wuhan University, 169 Donghu Road, Wuhan, 430071, China
| | - Qian Zhou
- Department of Labortory Medicine, Zhongnan Hospital of Wuhan University, 169 Donghu Road, Wuhan, 430071, China
| | - Wenjie Huang
- Department of Labortory Medicine, Zhongnan Hospital of Wuhan University, 169 Donghu Road, Wuhan, 430071, China
| | - Chen Xu
- Department of Labortory Medicine, Zhongnan Hospital of Wuhan University, 169 Donghu Road, Wuhan, 430071, China
| | - Xinghua Long
- Department of Labortory Medicine, Zhongnan Hospital of Wuhan University, 169 Donghu Road, Wuhan, 430071, China.
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20
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Feng H, Song Z. Identification of core miRNAs and regulatory pathways in breast cancer by integrated bioinformatics analysis. Mol Omics 2021; 17:277-287. [PMID: 33462573 DOI: 10.1039/d0mo00171f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Breast cancer (BC) ranks first among malignancies in the female population due to its complicated pathological progression and poor prognosis. Hence, the aim of the present study was to identify potential molecular prognostic biomarkers able to predict the prognosis of BC patients. We integrated two microRNA (miRNA) expression microarrays and three gene microarrays related to BC from the NCBI Gene Expression Comprehensive (GEO) database to screen for differentially expressed miRNAs and identify their regulatory networks. The Kaplan-Meier plotter online analysis tool was used to assess the overall survival value of miRNAs expression in BC patients. The LinkedOmics online tool was used to analyze genes correlated with miRNAs expression. To clarify the upstream regulation mechanism of genes, we used ChIP-Atlas to identify and screen for transcription factors and visually verify them using the Integrative Genomics Viewer. To further analyze the downstream regulatory mechanism of miRNA in BC, we verified differentially expressed genes (DEGs) correlated to miRNAs in three GEO gene microarrays and the gene set predicted by miRWalk. The open access Metascape program allowed analysis of Gene Ontology (GO) processes, KEGG pathways and GO enrichment was performed on the DEGs. To further identify hub genes, Cytoscape software and its plug-in were applied to construct protein-protein interaction networks. In the present study, several possible molecules and related pathways related to miR-483 were identified by bioinformatics analysis. These molecules and pathways might represent key mechanisms involved in BC progression and development. This work provides a novel view and insight in the pathogenesis, treatment and prognosis for BC.
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Affiliation(s)
- Haizhou Feng
- Department of Veterinary Medicine, Southwest University, Chongqing 402460, China.
| | - Zhenhui Song
- Department of Veterinary Medicine, Southwest University, Chongqing 402460, China.
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21
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Pratt SJP, Hernández-Ochoa E, Martin SS. Calcium signaling: breast cancer's approach to manipulation of cellular circuitry. Biophys Rev 2020; 12:1343-1359. [PMID: 33569087 PMCID: PMC7755621 DOI: 10.1007/s12551-020-00771-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Accepted: 10/29/2020] [Indexed: 12/11/2022] Open
Abstract
Calcium is a versatile element that participates in cell signaling for a wide range of cell processes such as death, cell cycle, division, migration, invasion, metabolism, differentiation, autophagy, transcription, and others. Specificity of calcium in each of these processes is achieved through modulation of intracellular calcium concentrations by changing the characteristics (amplitude/frequency modulation) or location (spatial modulation) of the signal. Breast cancer utilizes calcium signaling as an advantage for survival and progression. This review integrates evidence showing that increases in expression of calcium channels, GPCRs, pumps, effectors, and enzymes, as well as resulting intracellular calcium signals, lead to high calcium and/or an elevated calcium- mobilizing capacity necessary for malignant functions such as migratory, invasive, proliferative, tumorigenic, or metastatic capacities.
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Affiliation(s)
- Stephen J P Pratt
- Program in Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD USA.,Department of Physiology, University of Maryland School of Medicine, Baltimore, MD USA.,Marlene and Stewart Greenebaum NCI Comprehensive Cancer Center, University of Maryland School of Medicine, 655 W. Baltimore Street, Bressler Research Building, Rm 10-020 D, Baltimore, MD 21201 USA
| | - Erick Hernández-Ochoa
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD USA
| | - Stuart S Martin
- Program in Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD USA.,Department of Physiology, University of Maryland School of Medicine, Baltimore, MD USA.,Marlene and Stewart Greenebaum NCI Comprehensive Cancer Center, University of Maryland School of Medicine, 655 W. Baltimore Street, Bressler Research Building, Rm 10-020 D, Baltimore, MD 21201 USA
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22
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Yu L, Peng F, Dong X, Chen Y, Sun D, Jiang S, Deng C. Sex-Determining Region Y Chromosome-Related High-Mobility-Group Box 10 in Cancer: A Potential Therapeutic Target. Front Cell Dev Biol 2020; 8:564740. [PMID: 33344444 PMCID: PMC7744619 DOI: 10.3389/fcell.2020.564740] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Accepted: 11/17/2020] [Indexed: 01/20/2023] Open
Abstract
Sex-determining region Y-related high mobility group-box 10 (SOX10), a member of the SOX family, has recently been highlighted as an essential transcriptional factor involved in developmental biology. Recently, the functionality of SOX 10 has been increasingly revealed by researchers worldwide. It has been reported that SOX10 significantly regulates the proliferation, migration, and apoptosis of tumors and is closely associated with the progression of cancer. In this review, we first introduce the basic background of the SOX family and SOX10 and then discuss the pathophysiological roles of SOX10 in cancer. Besides, we enumerate the application of SOX10 in the pathological diagnosis and therapeutic potential of cancer. Eventually, we summarize the potential directions and perspectives of SOX10 in neoplastic theranostics. The information compiled herein may assist in additional studies and increase the potential of SOX10 as a therapeutic target for cancer.
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Affiliation(s)
- Liming Yu
- Department of Cardiovascular Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China.,Department of Cardiovascular Surgery, General Hospital of Northern Theater Command, Shenyang, China
| | - Fan Peng
- Department of Cardiology, Xijing Hopspital, The Airforce Military Medical University, Xi'an, China
| | - Xue Dong
- Outpatient Department of Liaoning Military Region, General Hospital of Northern Theater Command, Shenyang, China
| | - Ying Chen
- Department of Hematology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Dongdong Sun
- Department of Cardiology, Xijing Hopspital, The Airforce Military Medical University, Xi'an, China
| | - Shuai Jiang
- Department of Cardiology, Xijing Hopspital, The Airforce Military Medical University, Xi'an, China
| | - Chao Deng
- Department of Cardiovascular Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
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23
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Nie L, Wang C, Li N, Feng X, Lee N, Su D, Tang M, Yao F, Chen J. Proteome-wide Analysis Reveals Substrates of E3 Ligase RNF146 Targeted for Degradation. Mol Cell Proteomics 2020; 19:2015-2030. [PMID: 32958691 PMCID: PMC7710139 DOI: 10.1074/mcp.ra120.002290] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Indexed: 12/28/2022] Open
Abstract
Specific E3 ligases target tumor suppressors for degradation. Inhibition of such E3 ligases may be an important approach to cancer treatment. RNF146 is a RING domain and PARylation-dependent E3 ligase that functions as an activator of the β-catenin/Wnt and YAP/Hippo pathways by targeting the degradation of several tumor suppressors. Tankyrases 1 and 2 (TNKS1/2) are the only known poly-ADP-ribosyltransferases that require RNF146 to degrade their substrates. However, systematic identification of RNF146 substrates have not yet been performed. To uncover substrates of RNF146 that are targeted for degradation, we generated RNF146 knockout cells and TNKS1/2-double knockout cells and performed proteome profiling with label-free quantification as well as transcriptome analysis. We identified 160 potential substrates of RNF146, which included many known substrates of RNF146 and TNKS1/2 and 122 potential TNKS-independent substrates of RNF146. In addition, we validated OTU domain-containing protein 5 and Protein mono-ADP-ribosyltransferase PARP10 as TNKS1/2-independent substrates of RNF146 and SARDH as a novel substrate of TNKS1/2 and RNF146. Our study is the first proteome-wide analysis of potential RNF146 substrates. Together, these findings not only demonstrate that proteome profiling can be a useful general approach for the systemic identification of substrates of E3 ligases but also reveal new substrates of RNF146, which provides a resource for further functional studies.
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Affiliation(s)
- Litong Nie
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Chao Wang
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Nan Li
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Xu Feng
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Namsoo Lee
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Dan Su
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Mengfan Tang
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Fan Yao
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Junjie Chen
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA.
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24
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Liu J, Li D, Zhang X, Li Y, Ou J. Histone Demethylase KDM3A Promotes Cervical Cancer Malignancy Through the ETS1/KIF14/Hedgehog Axis. Onco Targets Ther 2020; 13:11957-11973. [PMID: 33239895 PMCID: PMC7682655 DOI: 10.2147/ott.s276559] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Accepted: 10/22/2020] [Indexed: 12/17/2022] Open
Abstract
Background Lysine demethylase 3A (KDM3A) has been increasingly recognized as an important epigenetic regulator involved in cancer development. This study aims to explore the relevance of KDM3A to cervical cancer (CC) progression and the molecules involved. Materials and Methods Tumor and the adjacent tissues from CC patients were collected. KDM3A expression in tissues and CC cell lines and its correlation with the survival and prognosis of patients were determined. Malignant potentials of CC cells and the angiogenesis ability of HUVECs were measured to evaluate the function of KDM3A on CC progression. The interactions among KDM3A, H3K9me2 and ETS1, and the binding between ETS1 and KIF14 were validated through ChIP and luciferase assays. Altered expression of ETS1 and KIF14 was introduced to explore their roles in CC development. Results KDM3A was abundantly expressed in CC tissues and cells and linked to dismal prognosis of CC patients. Knockdown of KDM3A suppressed malignant behaviors of CC cells. KDM3A was found to increase ETS1 expression through the demethylation of H3K9me2. Overexpression of ETS1 blocked the inhibiting roles of sh-KDM3A. ETS1 could bind to the promoter region of KIF14 to trigger its transcription. Overexpression ofKIF14aggravated the malignant behaviors of CC cells and the angiogenesis ability of HUVECs, and it activated the Hedgehog signaling pathway. Artificial activation of Hedgehog by Sag1.5 diminished the effects of sh-KDM3A. These changes were reproduced in vivo. Conclusion This study evidenced that KDM3A promotes ETS1-mediated KIF14 transcription to promote CC progression with the involvement of the Hedgehog activation.
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Affiliation(s)
- Jinyu Liu
- Frist Department of Gynecologic Oncology, Jilin Cancer Hospital, Changchun 130012, Jilin, People's Republic of China
| | - Dongqing Li
- Second Department of Gynecologic Oncology, Jilin Cancer Hospital, Changchun 130012, Jilin, People's Republic of China
| | - Xin Zhang
- Department of Rheumatology and Immunology, China-Japan Union Hospital of Jilin University, Changchun 130033, Jilin, People's Republic of China
| | - Yanyan Li
- Frist Department of Gynecologic Oncology, Jilin Cancer Hospital, Changchun 130012, Jilin, People's Republic of China
| | - Jian Ou
- Department of Gynecological Oncology Radiotherapy, Jilin Cancer Hospital, Changchun 130012, Jilin, People's Republic of China
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25
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Perret R, Escuriol J, Velasco V, Mayeur L, Soubeyran I, Delfour C, Aubert S, Polivka M, Karanian M, Meurgey A, Le Guellec S, Weingertner N, Hoeller S, Coindre JM, Larousserie F, Pierron G, Tirode F, Le Loarer F. NFATc2-rearranged sarcomas: clinicopathologic, molecular, and cytogenetic study of 7 cases with evidence of AGGRECAN as a novel diagnostic marker. Mod Pathol 2020; 33:1930-1944. [PMID: 32327700 DOI: 10.1038/s41379-020-0542-z] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2019] [Revised: 03/26/2020] [Accepted: 03/26/2020] [Indexed: 12/19/2022]
Abstract
NFATc2-rearranged sarcomas (NFATc2-Sarcomas) are infrequent round cell tumors characterized by EWSR1-NFATc2 fusions and FUS-NFATc2 fusions. Although our knowledge on these neoplasms has increased recently, novel diagnostic tools and more comprehensive series are still needed. Here, we describe the features of a series of seven molecularly confirmed NFATc2-Sarcomas (EWSR1-NFATc2, n = 4; FUS-NFATc2, n = 3) and demonstrate the utility of AGGRECAN immunohistochemistry for their identification. Patients were four males and three females, ranging in age from 19 to 66 years (median: 33). All were primary bone tumors (femur, n = 4; tibia, n = 2; ilium, n = 1), frequently infiltrating the surrounding soft tissues. Treatment often consisted of neoadjuvant chemotherapy and surgery. Follow-up was available for six patients (median 18 months, range 5-102 months), three patients died of disease and four patients are currently alive. Histologically, tumors consisted of monotonous round cells growing in lobules and sheets in variable amounts of fibrous to myxoid stroma. Other findings included spindle cells, corded and trabecular architecture, nuclear pleomorphism, cartilaginous differentiation, and osteoid-like matrix. Histological response to neoadjuvant chemotherapy was poor in all resection specimens available for review (n = 4). Tumors were diffusely positive for AGGRECAN and CD99 (7/7), and a subset expressed Pan-Keratin (AE1-AE3; 3/6), S100 (2/6), BCOR (2/6), ETV-4 (2/5), WT1 (2/6), and ERG (2/5). Desmin, NKX3-1, and SATB2 were negative (0/6). Diffuse AGGRECAN staining was also seen in 8/129 round cell sarcomas used for comparison, including mesenchymal chondrosarcoma (7/26) and CIC-sarcoma (1/26). Array-CGH showed complex karyotypes with recurrent deletions of tumor suppressor genes (CDKN2A/B, TUSC7, and DMD) in three FUS-NFATC2 cases and a simpler profile without homozygous losses in one EWSR1-NFATc2 case. Segmental chromosomal gains covering the loci of the fusion genes were detected in both variants. Overall, our study confirms and expands previous observations on NFATc2-sarcomas and supports that AGGRECAN is a useful biomarker of these tumors.
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Affiliation(s)
- Raul Perret
- Department of Biopathology, Bergonie Institute, Bordeaux, France.
| | - Julien Escuriol
- Department of Biopathology, Bergonie Institute, Bordeaux, France.,Bordeaux University, Talence, France
| | - Valérie Velasco
- Department of Biopathology, Bergonie Institute, Bordeaux, France
| | - Laetitia Mayeur
- Department of Biopathology, Bergonie Institute, Bordeaux, France
| | - Isabelle Soubeyran
- Department of Biopathology, Bergonie Institute, Bordeaux, France.,INSERM U1218, ACTION Unit, Bordeaux, France
| | - Christophe Delfour
- Department of Pathology, Montpellier University Hospital, Montpellier, France
| | - Sébastien Aubert
- Department of Pathology, Institut de Pathologie, Univ. Lille, CHU Lille, F-59000, Lille, France
| | - Marc Polivka
- Department of Pathology, APHP, Hôpital Cochin, DMU Imagina, Université de Paris, F-75014, Paris, France
| | - Marie Karanian
- Department of Pathology, Leon Berard Center, Lyon, France.,Univ Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Centre Léon Bérard, Cancer Research Center of Lyon, Lyon, France
| | | | - Sophie Le Guellec
- Department of Pathology, Claudius Regaud Institute, Toulouse-Oncopole, Toulouse, France
| | - Noelle Weingertner
- Department of Pathology, Strasbourg Regional University Hospital (Hautepierre Hospital), Strasbourg, France
| | - Sylvia Hoeller
- Department of Pathology, Hospital of the University of Basel, Basel, Switzerland
| | - Jean-Michel Coindre
- Department of Biopathology, Bergonie Institute, Bordeaux, France.,Bordeaux University, Talence, France
| | | | - Gaëlle Pierron
- Department of Tumor Biology, Curie Institute, Paris, France
| | - Franck Tirode
- Univ Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Centre Léon Bérard, Cancer Research Center of Lyon, Lyon, France
| | - François Le Loarer
- Department of Biopathology, Bergonie Institute, Bordeaux, France. .,Bordeaux University, Talence, France. .,INSERM U1218, ACTION Unit, Bordeaux, France.
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26
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Min J, Pan X, Lv G. The circRNA circ_0000291 acts as a sponge of microRNA 326 to regulate E26 transformation-specific sequence-1 expression and promote breast cancer progression. Pathol Int 2020; 70:953-964. [PMID: 32869935 DOI: 10.1111/pin.13011] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Revised: 08/06/2020] [Accepted: 08/11/2020] [Indexed: 12/13/2022]
Abstract
Accumulating studies authenticate that circular RNAs (circRNAs) are involved in the progression of cancers. However, their role in breast cancer (BC) remains largely unknown. In this study, real-time polymerase chain reaction was employed to detect the circ_0000291 and miR-326 expressions in BC tissues and cells. The correlation between the expression level of circ_0000291 and clinicopathological parameters of BC patients was analyzed. Western blot was used to detect the expression of E26 transformation-specific sequence-1 (ETS1), E-cadherin, N-cadherin and Vimentin in BC cells. Cell proliferation was measured using the cell counting kit-8 assay and the bromodeoxyuridine assay. Cell migration and invasion were detected by Transwell assay. The interactions between circ_0000291 and miR-326, miR-326 and ETS1 were verified using bioinformatics prediction, the dual-luciferase reporter gene assay or/and RNA binding protein immunoprecipitation assay. We demonstrated that circ_0000291 was significantly upregulated in BC, and its high expression was positively correlated with T stage and local lymph node metastasis. Functional assays validated that circ_0000291 promoted BC cell proliferation, migration and invasion. The mechanism studies indicated that circ_0000291 could decoy miR-326 and in turn upregulate the expression of ETS1. In conclusion, circ_0000291 is the novel oncogenic circRNA and promotes BC progression via modulating the miR-326/ETS1 axis.
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Affiliation(s)
- Jie Min
- Department of Breast and Thyroid, Chongqing Hospital of Traditional Chinese Medicine, Chongqing, China
| | - Xue Pan
- Editorial Department of Chinese Journal of Endocrine Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Gang Lv
- Department of Breast and Thyroid, Chongqing Hospital of Traditional Chinese Medicine, Chongqing, China
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27
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Naringin Targets NFKB1 to Alleviate Oxygen-Glucose Deprivation/Reoxygenation-Induced Injury in PC12 Cells Via Modulating HIF-1α/AKT/mTOR-Signaling Pathway. J Mol Neurosci 2020; 71:101-111. [PMID: 32557145 DOI: 10.1007/s12031-020-01630-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2020] [Accepted: 06/08/2020] [Indexed: 12/24/2022]
Abstract
This study was designed to investigate the effect of naringin in oxygen-glucose deprivation/reoxygenation (OGD/R) model and its mechanism. The target gene of naringin and the enriched pathways of the gene were searched and identified using bioinformatics analysis. Then OGD/R model was built using PC12 cells, after which the cells were treated with different concentrations of naringin. Subsequently, cell proliferation and apoptosis were evaluated by cell counting kit-8 (CCK-8) and flow cytometry assays, respectively. Meanwhile, the expression of NFKB1 in PC12 cells underwent OGD/R-induced injury was detected by qRT-PCR, while apoptosis-related and pathway-related proteins were checked by Western blot. DCF-DA kit was utilized to measure the level of ROS. Our results revealed that NFKB1, which was upregulated in MACO rats and OGD/R-treated PC12 cells, was a target gene of naringin. Naringin could alleviate OGD/R-induced injury via promoting the proliferation, and repressing the apoptosis of PC12 cells through regulating the expression of NFKB1 and apoptosis-associated proteins and ROS level. Besides, the depletion of NFKB1 was positive to cell proliferation but negative to cell apoptosis. Moreover, the depletion of NFKB1 enhanced the influences of naringin on cell proliferation and apoptosis as well as the expression of apoptosis-related proteins and ROS level. Western blotting indicated that both naringin treatment and depletion of NFKB1 could increase the expression of HIF-1α, p-AKT, and p-mTOR compared with OGD/R group. What's more, treatment by naringin and si-NFKB1 together could significantly increase these effects. Nevertheless, the expression of AKT and mTOR among each group was almost not changed. In conclusion, naringin could prevent the OGD/R-induced injury in PC12 cells in vitro by targeting NFKB1 and regulating HIF-1α/AKT/mTOR-signaling pathway, which might provide novel ideas for the therapy of cerebral ischemia-reperfusion (I/R) injury.
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28
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Fan Z, Kong M, Li M, Hong W, Fan X, Xu Y. Brahma Related Gene 1 (Brg1) Regulates Cellular Cholesterol Synthesis by Acting as a Co-factor for SREBP2. Front Cell Dev Biol 2020; 8:259. [PMID: 32500071 PMCID: PMC7243037 DOI: 10.3389/fcell.2020.00259] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Accepted: 03/27/2020] [Indexed: 12/30/2022] Open
Abstract
Hepatocyte is a hub for cholesterol metabolism. Augmented synthesis of cholesterol in the liver is associated with hypercholesterolemia and contributes to the pathogenesis of a host of cardiovascular and metabolic diseases. Sterol response element binding protein 2 (SREBP2) regulates hepatic cholesterol metabolism by activating the transcription of rate-limiting enzymes in the cholesterol biosynthesis pathway. The underlying epigenetic mechanism is not well understood. We report here that mice with hepatocyte-specific knockout (CKO) of Brg1, a chromatin remodeling protein, exhibit reduced levels of hepatic cholesterol compared to the wild type (WT) littermates when placed on a high-fact diet (HFD) or a methionine-and-choline-deficient diet (MCD). Down-regulation of cholesterol levels as a result of BRG1 deficiency was accompanied by attenuation of cholesterogenic gene transcription. Likewise, BRG1 knockdown in hepatocytes markedly suppressed the induction of cholesterogenic genes by lipid depletion formulas. Brg1 interacted with SREBP2 and was recruited by SREBP2 to the cholesterogenic gene promoters. Reciprocally, Brg1 deficiency dampened the occupancies of SREBP2 on target promoters likely through modulating H3K9 methylation on the cholesterogenic gene promoters. Mechanistically, Brg1 recruited the H3K9 methyltransferase KDM3A to co-regulate pro-cholesterogenic transcription. KDM3A silencing dampened the cholesterogenic response in hepatocytes equivalent to Brg1 deficiency. In conclusion, our data demonstrate a novel epigenetic pathway that contributes to SREBP2-dependent cholesterol synthesis in hepatocytes.
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Affiliation(s)
- Zhiwen Fan
- Department of Pathology, Nanjing Drum Tower Hospital, Nanjing University Medical School, Nanjing, China
| | - Ming Kong
- Key Laboratory of Targeted Intervention of Cardiovascular Disease and Collaborative Innovation Center for Cardiovascular Translational Medicine, Department of Pathophysiology, Nanjing Medical University, Nanjing, China
| | - Min Li
- Department of Clinical Medicine and Laboratory Center for Experimental Medicine, Jiangsu Health Vocational College, Nanjing, China
| | - Wenxuan Hong
- Key Laboratory of Targeted Intervention of Cardiovascular Disease and Collaborative Innovation Center for Cardiovascular Translational Medicine, Department of Pathophysiology, Nanjing Medical University, Nanjing, China
| | - Xiangshan Fan
- Department of Pathology, Nanjing Drum Tower Hospital, Nanjing University Medical School, Nanjing, China
| | - Yong Xu
- Key Laboratory of Targeted Intervention of Cardiovascular Disease and Collaborative Innovation Center for Cardiovascular Translational Medicine, Department of Pathophysiology, Nanjing Medical University, Nanjing, China.,Institute of Biomedical Research, Liaocheng University, Liaocheng, China
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29
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Kim GC, Lee CG, Verma R, Rudra D, Kim T, Kang K, Nam JH, Kim Y, Im SH, Kwon HK. ETS1 Suppresses Tumorigenesis of Human Breast Cancer via Trans-Activation of Canonical Tumor Suppressor Genes. Front Oncol 2020; 10:642. [PMID: 32477936 PMCID: PMC7239993 DOI: 10.3389/fonc.2020.00642] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Accepted: 04/06/2020] [Indexed: 01/18/2023] Open
Abstract
ETS1 has shown dichotomous roles as an oncogene and a tumor suppressor gene in diverse cancers, but its functionality in breast cancer tumorigenesis still remains unclear. We utilized the Cancer Genome Atlas (TCGA) database to analyze comprehensive functions of ETS1 in human breast cancer (BRCA) patients by investigating its expression patterns and methylation status in relation to clinical prognosis. ETS1 expression was significantly diminished by hyper-methylation of the ETS1 promoter region in specimens from BRCA patients compared to a healthy control group. Moreover, ETS1high BRCA patients showed better prognosis and longer survival compared to ETS1low BRCA patients. Consistent with clinical evidence, comparative transcriptome analysis combined with CRISPR/Cas9 or shRNA based perturbation of ETS1 expression revealed direct as well as indirect mechanisms of ETS1 that hinder tumorigenesis of BRCA cells. Taken together, our study enlightens a novel function of ETS1 as a tumor suppressor in breast cancer cells.
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Affiliation(s)
- Gi-Cheon Kim
- Department of Microbiology and Immunology, Yonsei University College of Medicine, Seoul, South Korea.,Institute for Immunology and Immunological Diseases, Yonsei University College of Medicine, Seoul, South Korea
| | - Choong-Gu Lee
- Natural Product Informatics Research Center, Korea Institute of Science and Technology (KIST), Gangneung Institute of Natural Products, Gangneung, South Korea
| | - Ravi Verma
- Academy of Immunology and Microbiology (AIM), Institute for Basic Science (IBS), Pohang, South Korea
| | - Dipayan Rudra
- Academy of Immunology and Microbiology (AIM), Institute for Basic Science (IBS), Pohang, South Korea
| | - Taemook Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
| | - Keunsoo Kang
- Department of Microbiology, College of Natural Sciences, Dankook University, Cheonan, South Korea
| | - Jong Hee Nam
- Department of Pathology, Chonnam National University Medical School, Gwangju, South Korea
| | - Young Kim
- Department of Oral Pathology, School of Dentistry, Chonnam National University, Gwangju, South Korea
| | - Sin-Hyeog Im
- Academy of Immunology and Microbiology (AIM), Institute for Basic Science (IBS), Pohang, South Korea.,Division of Integrative Biosciences and Biotechnology, Department of Life Sciences, Pohang University of Science and Technology, Pohang, South Korea
| | - Ho-Keun Kwon
- Department of Microbiology and Immunology, Yonsei University College of Medicine, Seoul, South Korea.,Institute for Immunology and Immunological Diseases, Yonsei University College of Medicine, Seoul, South Korea.,Brain Korea 21 PLUS Project for Medical Sciences, Yonsei University College of Medicine, Seoul, South Korea
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30
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The pan-cancer landscape of netrin family reveals potential oncogenic biomarkers. Sci Rep 2020; 10:5224. [PMID: 32251318 PMCID: PMC7090012 DOI: 10.1038/s41598-020-62117-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Accepted: 03/09/2020] [Indexed: 02/02/2023] Open
Abstract
Recent cancer studies have found that the netrin family of proteins plays vital roles in the development of some cancers. However, the functions of the many variants of these proteins in cancer remain incompletely understood. In this work, we used the most comprehensive database available, including more than 10000 samples across more than 30 tumor types, to analyze the six members of the netrin family. We performed comprehensive analysis of genetic change and expression of the netrin genes and analyzed epigenetic and pathway relationships, as well as the correlation of expression of these proteins with drug sensitivity. Although the mutation rate of the netrin family is low in pan-cancer, among the tumor patients with netrin mutations, the highest number are Uterine Corpus Endometrial Carcinoma patients, accounting for 13.6% of cases (54 of 397). Interestingly, the highest mutation rate of a netrin family member is 38% for NTNG1 (152 of 397). Netrin proteins may participate in the development of endocrine-related tumors and sex hormone-targeting organ tumors. Additionally, the participation of NTNG1 and NTNG2 in various cancers shows their potential for use as new tumor markers and therapeutic targets. This analysis provides a broad molecular perspective of this protein family and suggests some new directions for the treatment of cancer.
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Semina EV, Rubina KA, Shmakova AA, Rysenkova KD, Klimovich PS, Aleksanrushkina NA, Sysoeva VY, Karagyaur MN, Tkachuk VA. Downregulation of uPAR promotes urokinase translocation into the nucleus and epithelial to mesenchymal transition in neuroblastoma. J Cell Physiol 2020; 235:6268-6286. [PMID: 31990070 PMCID: PMC7318179 DOI: 10.1002/jcp.29555] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Accepted: 01/13/2020] [Indexed: 12/16/2022]
Abstract
The urokinase system is involved in a variety of physiological processes, such as fibrinolysis, matrix remodeling, wound healing, and regeneration. Upon binding to its cognate receptor urokinase‐type plasminogen activator receptor (uPAR), urokinase‐type plasminogen activator (uPA) catalyzes the conversion of plasminogen to plasmin and the activation of matrix metalloproteases. Apart from this, uPA–uPAR interaction can lead to the activation of transcription factors, mitogen‐activated protein kinase signaling pathways and RTK cascades. Elevated expression of uPA and uPAR is markedly associated with cancer progression and metastasis and correlates with a poor prognosis in clinics. Targeting the urokinase system has proved to be effective in experimental models in vitro and in vivo, however, in clinics the inhibition of the uPA/uPAR system has fallen short of expectations, suggesting that the question of the functional relevance of uPA/uPAR system is far from being moot. Recently, using CRISPR/Cas9 technology, we have shown that uPAR knockout decreases the proliferation of neuroblastoma Neuro2a cells in vitro. In the present study we demonstrate that uPAR expression is essential for maintaining the epithelial phenotype in Neuro2a cells and that uPAR silencing promotes epithelial‐mesenchymal transition (EMT) and increased cell migration. Accordingly, uPAR knockout results in the downregulation of epithelial markers (E‐cadherin, occludin, and claudin‐5) and in the increase of mesenchymal markers (N‐cadherin, α‐smooth muscle actin, and interleukin‐6). In search of the molecular mechanism underlying these changes, we identified uPA as a key component. Two key insights emerged as a result of this work: in the absence of uPAR, uPA is translocated into the nucleus where it is presumably involved in the activation of transcription factors (nuclear factor κB and Snail) resulting in EMT. In uPAR‐expressing cells, uPAR functions as a uPA “trap” that binds uPA on the cell surface and promotes controlled uPA internalization and degradation in lysosomes.
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Affiliation(s)
- Ekaterina V Semina
- Department of Biochemistry and Molecular Medicine, Faculty of Medicine, Lomonosov Moscow State University, Moscow, Russia.,Laboratory of Molecular Endocrinology, Institute of Experimental Cardiology, Federal State Budgetary Organization National Cardiology Research Center Ministry of Health of the Russian Federation, Moscow, Russia
| | - Kseniya A Rubina
- Department of Biochemistry and Molecular Medicine, Faculty of Medicine, Lomonosov Moscow State University, Moscow, Russia.,Laboratory of Morohogenesis and Tissue Reparation, Faculty of Medicine, Lomonosov Moscow State University, Moscow, Russia
| | - Anna A Shmakova
- Department of Biochemistry and Molecular Medicine, Faculty of Medicine, Lomonosov Moscow State University, Moscow, Russia.,Laboratory of Molecular Endocrinology, Institute of Experimental Cardiology, Federal State Budgetary Organization National Cardiology Research Center Ministry of Health of the Russian Federation, Moscow, Russia
| | - Karina D Rysenkova
- Department of Biochemistry and Molecular Medicine, Faculty of Medicine, Lomonosov Moscow State University, Moscow, Russia.,Laboratory of Molecular Endocrinology, Institute of Experimental Cardiology, Federal State Budgetary Organization National Cardiology Research Center Ministry of Health of the Russian Federation, Moscow, Russia
| | - Polina S Klimovich
- Department of Biochemistry and Molecular Medicine, Faculty of Medicine, Lomonosov Moscow State University, Moscow, Russia.,Laboratory of Molecular Endocrinology, Institute of Experimental Cardiology, Federal State Budgetary Organization National Cardiology Research Center Ministry of Health of the Russian Federation, Moscow, Russia
| | - Natalya A Aleksanrushkina
- Department of Biochemistry and Molecular Medicine, Faculty of Medicine, Lomonosov Moscow State University, Moscow, Russia
| | - Veronika Y Sysoeva
- Department of Biochemistry and Molecular Medicine, Faculty of Medicine, Lomonosov Moscow State University, Moscow, Russia
| | - Maxim N Karagyaur
- Department of Biochemistry and Molecular Medicine, Faculty of Medicine, Lomonosov Moscow State University, Moscow, Russia
| | - Vsevolod A Tkachuk
- Department of Biochemistry and Molecular Medicine, Faculty of Medicine, Lomonosov Moscow State University, Moscow, Russia.,Laboratory of Molecular Endocrinology, Institute of Experimental Cardiology, Federal State Budgetary Organization National Cardiology Research Center Ministry of Health of the Russian Federation, Moscow, Russia
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Li W, Deng G, Zhang J, Hu E, He Y, Lv J, Sun X, Wang K, Chen L. Identification of breast cancer risk modules via an integrated strategy. Aging (Albany NY) 2019; 11:12131-12146. [PMID: 31860871 PMCID: PMC6949069 DOI: 10.18632/aging.102546] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Accepted: 11/19/2019] [Indexed: 12/17/2022]
Abstract
Breast cancer is one of the most common malignant cancers among females worldwide. This complex disease is not caused by a single gene, but resulted from multi-gene interactions, which could be represented by biological networks. Network modules are composed of genes with significant similarities in terms of expression, function and disease association. Therefore, the identification of disease risk modules could contribute to understanding the molecular mechanisms underlying breast cancer. In this paper, an integrated disease risk module identification strategy was proposed according to a multi-objective programming model for two similarity criteria as well as significance of permutation tests in Markov random field module score, function consistency score and Pearson correlation coefficient difference score. Three breast cancer risk modules were identified from a breast cancer-related interaction network. Genes in these risk modules were confirmed to play critical roles in breast cancer by literature review. These risk modules were enriched in breast cancer-related pathways or functions and could distinguish between breast tumor and normal samples with high accuracy for not only the microarray dataset used for breast cancer risk module identification, but also another two independent datasets. Our integrated strategy could be extended to other complex diseases to identify their risk modules and reveal their pathogenesis.
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Affiliation(s)
- Wan Li
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Gui Deng
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Ji Zhang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Erqiang Hu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Yuehan He
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Junjie Lv
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Xilin Sun
- Molecular Imaging Research Center (MIRC), Harbin Medical University, Harbin, China.,TOF-PET/CT/MR Center, the Fourth Hospital of Harbin Medical University, Harbin, China
| | - Kai Wang
- Molecular Imaging Research Center (MIRC), Harbin Medical University, Harbin, China.,TOF-PET/CT/MR Center, the Fourth Hospital of Harbin Medical University, Harbin, China
| | - Lina Chen
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
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