1
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Lu X, Zhang W, Zhang J, Ren D, Zhao P, Ying Y. EPAS1, a hypoxia- and ferroptosis-related gene, promotes malignant behaviour of cervical cancer by ceRNA and super-enhancer. J Cell Mol Med 2024; 28:e18361. [PMID: 38722283 PMCID: PMC11081013 DOI: 10.1111/jcmm.18361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Revised: 03/12/2024] [Accepted: 04/11/2024] [Indexed: 05/12/2024] Open
Abstract
Hypoxia and Ferroptosis are associated with the malignant behaviour of cervical cancer. Endothelial PAS domain-containing protein 1 (EPAS1) contributes to the progression of cervical cancer. EPAS1 plays important roles in hypoxia and ferroptosis. Using the GEO dataset, machine-learning algorithms were used to screen for hypoxia- and ferroptosis-related genes (HFRGs) in cervical cancer. EPAS1 was identified as the hub gene. qPCR and WB were used to investigate the expression of EPAS1 in normal and cervical cancer tissues. The proliferation, invasion and migration of EPAS1 cells in HeLa and SiHa cell lines were detected using CCK8, transwell and wound healing assays, respectively. Apoptosis was detected by flow cytometry. A dual-luciferase assay was used to analyse the MALAT1-miR-182-5P-EPAS1 mRNA axis and core promoter elements of the super-enhancer. EPAS1 was significantly overexpressed in cervical cancer tissues. EPAS1 could increase the proliferation, invasion, migration of HeLa and SiHa cells and reduce the apoptosis of HeLa and SiHa cell. According to the double-luciferase assay, EPAS1 expression was regulated by the MALAT1-Mir-182-5p-EPAS1 mRNA axis. EPAS1 is associated with super-enhancers. Double-luciferase assay showed that the core elements of the super-enhancer were E1 and E3. EPAS1, an HFRG, is significantly overexpressed in cervical cancer. EPAS1 promotes malignant behaviour of cervical cancer cells. EPAS1 expression is regulated by super-enhancers and the MALAT1-miR-182-5P- EPAS1 mRNA axis. EPAS1 may be a target for the diagnosis and treatment of cervical cancer.
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Affiliation(s)
- Xiaoqin Lu
- Department of Obstetrics and GynecologyThe Second Affiliated Hospital of Zhengzhou UniversityZhengzhouChina
| | - Wenyi Zhang
- Department of Obstetrics and GynecologyThe Second Affiliated Hospital of Zhengzhou UniversityZhengzhouChina
| | - Jingyan Zhang
- Department of Obstetrics and GynecologyThe Second Affiliated Hospital of Zhengzhou UniversityZhengzhouChina
| | - Dan Ren
- Department of Obstetrics and GynecologyThe Second Affiliated Hospital of Zhengzhou UniversityZhengzhouChina
| | - Panpan Zhao
- Department of Obstetrics and GynecologyThe Second Affiliated Hospital of Zhengzhou UniversityZhengzhouChina
| | - Yanqi Ying
- Department of Obstetrics and GynecologyThe Second Affiliated Hospital of Zhengzhou UniversityZhengzhouChina
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2
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Zhang T, Ambrodji A, Huang H, Bouchonville KJ, Etheridge AS, Schmidt RE, Bembenek BM, Temesgen ZB, Wang Z, Innocenti F, Stroka D, Diasio RB, Largiadèr CR, Offer SM. Germline cis variant determines epigenetic regulation of the anti-cancer drug metabolism gene dihydropyrimidine dehydrogenase ( DPYD). eLife 2024; 13:RP94075. [PMID: 38686795 PMCID: PMC11060711 DOI: 10.7554/elife.94075] [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] [Indexed: 05/02/2024] Open
Abstract
Enhancers are critical for regulating tissue-specific gene expression, and genetic variants within enhancer regions have been suggested to contribute to various cancer-related processes, including therapeutic resistance. However, the precise mechanisms remain elusive. Using a well-defined drug-gene pair, we identified an enhancer region for dihydropyrimidine dehydrogenase (DPD, DPYD gene) expression that is relevant to the metabolism of the anti-cancer drug 5-fluorouracil (5-FU). Using reporter systems, CRISPR genome-edited cell models, and human liver specimens, we demonstrated in vitro and vivo that genotype status for the common germline variant (rs4294451; 27% global minor allele frequency) located within this novel enhancer controls DPYD transcription and alters resistance to 5-FU. The variant genotype increases recruitment of the transcription factor CEBPB to the enhancer and alters the level of direct interactions between the enhancer and DPYD promoter. Our data provide insight into the regulatory mechanisms controlling sensitivity and resistance to 5-FU.
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Affiliation(s)
- Ting Zhang
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo ClinicRochesterUnited States
| | - Alisa Ambrodji
- Department of Clinical Chemistry, Inselspital, Bern University Hospital, University of BernBernSwitzerland
- Graduate School for Cellular and Biomedical Sciences, University of BernBernSwitzerland
| | - Huixing Huang
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo ClinicRochesterUnited States
| | - Kelly J Bouchonville
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo ClinicRochesterUnited States
| | - Amy S Etheridge
- Eshelman School of Pharmacy, Division of Pharmacotherapy and Experimental Therapeutics, University of North Carolina at Chapel HillChapel HillUnited States
| | - Remington E Schmidt
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo ClinicRochesterUnited States
| | - Brianna M Bembenek
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo ClinicRochesterUnited States
| | - Zoey B Temesgen
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo ClinicRochesterUnited States
| | - Zhiquan Wang
- Division of Hematology, Department of Medicine, Mayo ClinicRochesterUnited States
| | - Federico Innocenti
- Eshelman School of Pharmacy, Division of Pharmacotherapy and Experimental Therapeutics, University of North Carolina at Chapel HillChapel HillUnited States
| | - Deborah Stroka
- Department of Visceral Surgery and Medicine, Inselspital, Bern University Hospital, University of BernBernSwitzerland
| | - Robert B Diasio
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo ClinicRochesterUnited States
| | - Carlo R Largiadèr
- Department of Clinical Chemistry, Inselspital, Bern University Hospital, University of BernBernSwitzerland
| | - Steven M Offer
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo ClinicRochesterUnited States
- Department of Pathology, University of Iowa Carver College of Medicine, University of IowaIowa CityUnited States
- Holden Comprehensive Cancer Center, University of Iowa Carver College of Medicine, University of IowaIowa CityUnited States
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3
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Feng Y, Mahdi H, Piekarz R, Beumer JH, Synold TW. An LC-MS/MS method for determination of the bromodomain inhibitor ZEN-3694 and its metabolite ZEN-3791 in human plasma. Bioanalysis 2024. [PMID: 38497709 DOI: 10.4155/bio-2023-0252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/19/2024] Open
Abstract
We have developed and validated a novel LC-MS/MS method for the simultaneous quantification of ZEN-3694 and its active metabolite ZEN-3791 in human plasma after protein precipitation. Stable isotope-labeled versions were used as internal standards. Chromatographic separation was achieved on a Kinetex C18 column using 0.1% formic acid in H2O and 0.1% formic acid in MeOH as mobile phases. Detection was performed via positive electrospray ionization mode with multiple reaction monitoring. The assay exhibited linearity in the concentration range of 5-5000 ng/ml for both analytes. Intra- and inter-assay precision and accuracy were within ±11%. ZEN-3694 and ZEN-3791 recoveries were between 93 and 105%. This LC-MS/MS assay is an essential tool to study ZEN-3694 in an ongoing clinical trial (NCT04840589).
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Affiliation(s)
- Ye Feng
- Department of Medical Oncology & Therapeutics Research, City of Hope, Duarte, CA 91010, USA
| | - Haider Mahdi
- Department of Obstetrics, Gynecology & Reproductive Sciences & Magee Women's Research Institute, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Richard Piekarz
- Investigational Drug Branch, Cancer Therapy Evaluation Program, National Cancer Institute, Bethesda, MD 20892, USA
| | - Jan H Beumer
- UPMC Hillman Cancer Center, Hillman Research Pavilion, Pittsburgh, PA 15232, USA
| | - Timothy W Synold
- Department of Medical Oncology & Therapeutics Research, City of Hope, Duarte, CA 91010, USA
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4
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Zhang T, Ambrodji A, Huang H, Bouchonville KJ, Etheridge AS, Schmidt RE, Bembenek BM, Temesgen ZB, Wang Z, Innocenti F, Stroka D, Diasio RB, Largiadèr CR, Offer SM. Germline cis variant determines epigenetic regulation of the anti-cancer drug metabolism gene dihydropyrimidine dehydrogenase ( DPYD). BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.11.01.565230. [PMID: 37961517 PMCID: PMC10635067 DOI: 10.1101/2023.11.01.565230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Enhancers are critical for regulating tissue-specific gene expression, and genetic variants within enhancer regions have been suggested to contribute to various cancer-related processes, including therapeutic resistance. However, the precise mechanisms remain elusive. Using a well-defined drug-gene pair, we identified an enhancer region for dihydropyrimidine dehydrogenase (DPD, DPYD gene) expression that is relevant to the metabolism of the anti-cancer drug 5-fluorouracil (5-FU). Using reporter systems, CRISPR genome edited cell models, and human liver specimens, we demonstrated in vitro and vivo that genotype status for the common germline variant (rs4294451; 27% global minor allele frequency) located within this novel enhancer controls DPYD transcription and alters resistance to 5-FU. The variant genotype increases recruitment of the transcription factor CEBPB to the enhancer and alters the level of direct interactions between the enhancer and DPYD promoter. Our data provide insight into the regulatory mechanisms controlling sensitivity and resistance to 5-FU.
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Affiliation(s)
- Ting Zhang
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN 55905, USA
| | - Alisa Ambrodji
- Department of Clinical Chemistry, Inselspital, Bern University Hospital, University of Bern, CH-3010 Bern, Switzerland
- Graduate School for Cellular and Biomedical Sciences, University of Bern, Freiestrasse 1, CH-3010 Bern, Switzerland
| | - Huixing Huang
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN 55905, USA
| | - Kelly J. Bouchonville
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN 55905, USA
| | - Amy S. Etheridge
- Eshelman School of Pharmacy, Division of Pharmacotherapy and Experimental Therapeutics, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Remington E. Schmidt
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN 55905, USA
| | - Brianna M. Bembenek
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN 55905, USA
| | - Zoey B. Temesgen
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN 55905, USA
| | - Zhiquan Wang
- Division of Hematology, Department of Medicine, Mayo Clinic, Rochester, MN 55905 USA
| | - Federico Innocenti
- Eshelman School of Pharmacy, Division of Pharmacotherapy and Experimental Therapeutics, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Deborah Stroka
- Department of Visceral Surgery and Medicine, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Robert B. Diasio
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN 55905, USA
| | - Carlo R. Largiadèr
- Department of Clinical Chemistry, Inselspital, Bern University Hospital, University of Bern, CH-3010 Bern, Switzerland
| | - Steven M. Offer
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN 55905, USA
- Department of Pathology, University of Iowa Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
- Holden Comprehensive Cancer Center, University of Iowa Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
- Lead contact
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5
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Chen Y, Tan J, Yang C, Ling Z, Xu J, Sun D, Luo F. Dynamic chromatin accessibility landscapes of osteoblast differentiation and mineralization. Biochim Biophys Acta Mol Basis Dis 2024; 1870:166938. [PMID: 37931716 DOI: 10.1016/j.bbadis.2023.166938] [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: 04/05/2023] [Revised: 10/12/2023] [Accepted: 10/29/2023] [Indexed: 11/08/2023]
Abstract
Bone acts as a self-healing organ, which undergoes continuous regeneration process that is tightly regulated by the cooperation of osteoclasts with the capability of bone resorption and osteoblasts with the capability of bone formation. Generally, bone marrow derived mesenchymal stem cells (BMSCs) differentiated to final osteoblasts have been considered as critical role in bone remodeling. In this regard, several transcription factors (TFs) whose binding sites are initially hidden deep within accessible chromatin that participate in modulating osteoblast differentiation and bone matrix mineralization. Then, it is necessary to explore further the dynamic changes about the epigenetic transcription machinery during osteoblastogenesis. Here, we performed the chromatin accessibility and transcriptomic landscape of osteoblast differentiation and mineralization by using transposase-accessible chromatin sequencing (ATAC-seq) and RNA sequencing (RNA-Seq). Our data found that global chromatin accessibility during osteoblastogenesis was extensively improved. Above this, it is shown that key target genes including Col6a3, Serpina3n, Ms4a4d, Lyz2, Phf11b and Grin3a were enriched in differential loci RNA-seq and ATAC-Seq peaks with continuous changed tendency during osteoblasts differentiation and mineralization. In addition, Analysis of Motif Enrichment (AME) was used to elucidate TFs which modulated these target genes. In this study, it was shown for the first time that these important TFs including MEF2A, PRRX1, Shox2 and HOXB13 could alter promoter accessibility of target genes during osteoblastogenesis. This helps us understand how TF binding motif accessibility influences osteoblast differentiation. In addition, it also suggests that modulating the chromatin accessibility of osteogenesis could be developed as the promising strategies to regulate bone regeneration.
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Affiliation(s)
- Yueqi Chen
- Department of Orthopedics, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, People's Republic of China; Department of Orthopedics, 76nd Group Army Hospital, Xining, People's Republic of China.
| | - Jiulin Tan
- Department of Orthopedics, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, People's Republic of China
| | - Chuan Yang
- Department of Biomedical Materials Science, Third Military Medical University (Army Medical University), Chongqing, People's Republic of China
| | - Zhiguo Ling
- Institute of Immunology, Third Military Medical University (Army Medical University), Chongqing, People's Republic of China
| | - Jianzhong Xu
- Department of Orthopedics, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, People's Republic of China
| | - Dong Sun
- Department of Orthopedics, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, People's Republic of China.
| | - Fei Luo
- Department of Orthopedics, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, People's Republic of China.
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6
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Tracy KM, Prior S, Trowbridge WT, Boyd JR, Ghule PN, Frietze S, Stein JL, Stein GS, Lian JB. Bromodomain Proteins Epigenetically Regulate the Mitotically Associated lncRNA MANCR in Triple Negative Breast Cancer Cells. Crit Rev Eukaryot Gene Expr 2024; 34:61-71. [PMID: 38073442 PMCID: PMC11023627 DOI: 10.1615/critreveukaryotgeneexpr.2023050109] [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] [Indexed: 12/18/2023]
Abstract
Long non-coding RNA (lncRNA)-mediated control of gene expression contributes to regulation of biological processes that include proliferation and phenotype, as well as compromised expression of genes that are functionally linked to cancer initiation and tumor progression. lncRNAs have emerged as novel targets and biomarkers in breast cancer. We have shown that mitotically associated lncRNA MANCR is expressed in triple-negative breast cancer (TNBC) cells and that it serves a critical role in promoting genome stability and survival in aggressive breast cancer cells. Using an siRNA strategy, we selectively depleted BRD2, BRD3, and BRD4, singly and in combination, to establish which bromodomain proteins regulate MANCR expression in TNBC cells. Our findings were confirmed by using in situ hybridization combined with immunofluorescence analysis that revealed BRD4, either alone or with BRD2 and BRD3, can support MANCR regulation of TNBC cells. Here we provide evidence for MANCR-responsive epigenetic control of super enhancers by histone modifications that are required for gene transcription to support cell survival and expression of the epithelial tumor phenotype in triple negative breast cancer cells.
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Affiliation(s)
- Kirsten M. Tracy
- Department of Biochemistry, University of Vermont Larner College of Medicine, Burlington, VT 05405
| | - Shannon Prior
- Department of Biomedical and Health Sciences, University of Vermont College of Nursing and Health Sciences, Burlington, VT 05405
| | - Willem T. Trowbridge
- Department of Biochemistry, University of Vermont Larner College of Medicine, Burlington, VT 05405
| | - Joseph R. Boyd
- Department of Biomedical and Health Sciences, University of Vermont College of Nursing and Health Sciences, Burlington, VT 05405
| | - Prachi N. Ghule
- Department of Biochemistry, University of Vermont Larner College of Medicine, Burlington, VT 05405
- Department of Biomedical and Health Sciences, University of Vermont College of Nursing and Health Sciences, Burlington, VT 05405
| | - Seth Frietze
- Department of Biochemistry, University of Vermont Larner College of Medicine, Burlington, VT 05405
- Department of Biomedical and Health Sciences, University of Vermont College of Nursing and Health Sciences, Burlington, VT 05405
- University of Vermont Cancer Center, University of Vermont Larner College of Medicine, Burlington, VT 05405
| | - Janet L. Stein
- Department of Biochemistry, University of Vermont Larner College of Medicine, Burlington, VT 05405
- University of Vermont Cancer Center, University of Vermont Larner College of Medicine, Burlington, VT 05405
| | - Gary S. Stein
- Department of Biochemistry, University of Vermont Larner College of Medicine, Burlington, VT 05405
- University of Vermont Cancer Center, University of Vermont Larner College of Medicine, Burlington, VT 05405
| | - Jane B. Lian
- Department of Biochemistry, University of Vermont Larner College of Medicine, Burlington, VT 05405
- University of Vermont Cancer Center, University of Vermont Larner College of Medicine, Burlington, VT 05405
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7
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Pouliou M, Koutsi MA, Champezou L, Giannopoulou AI, Vatsellas G, Piperi C, Agelopoulos M. MYCN Amplifications and Metabolic Rewiring in Neuroblastoma. Cancers (Basel) 2023; 15:4803. [PMID: 37835497 PMCID: PMC10571721 DOI: 10.3390/cancers15194803] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 09/20/2023] [Accepted: 09/27/2023] [Indexed: 10/15/2023] Open
Abstract
Cancer is a disease caused by (epi)genomic and gene expression abnormalities and characterized by metabolic phenotypes that are substantially different from the normal phenotypes of the tissues of origin. Metabolic reprogramming is one of the key features of tumors, including those established in the human nervous system. In this work, we emphasize a well-known cancerous genomic alteration: the amplification of MYCN and its downstream effects in neuroblastoma phenotype evolution. Herein, we extend our previous computational biology investigations by conducting an integrative workflow applied to published genomics datasets and comprehensively assess the impact of MYCN amplification in the upregulation of metabolism-related transcription factor (TF)-encoding genes in neuroblastoma cells. The results obtained first emphasized overexpressed TFs, and subsequently those committed in metabolic cellular processes, as validated by gene ontology analyses (GOs) and literature curation. Several genes encoding for those TFs were investigated at the mechanistic and regulatory levels by conducting further omics-based computational biology assessments applied on published ChIP-seq datasets retrieved from MYCN-amplified- and MYCN-enforced-overexpression within in vivo systems of study. Hence, we approached the mechanistic interrelationship between amplified MYCN and overexpression of metabolism-related TFs in neuroblastoma and showed that many are direct targets of MYCN in an amplification-inducible fashion. These results illuminate how MYCN executes its regulatory underpinnings on metabolic processes in neuroblastoma.
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Affiliation(s)
- Marialena Pouliou
- Center of Basic Research, Biomedical Research Foundation, Academy of Athens, 4 Soranou Ephessiou St., 11527 Athens, Greece; (M.P.); (M.A.K.); (L.C.); (G.V.)
| | - Marianna A. Koutsi
- Center of Basic Research, Biomedical Research Foundation, Academy of Athens, 4 Soranou Ephessiou St., 11527 Athens, Greece; (M.P.); (M.A.K.); (L.C.); (G.V.)
| | - Lydia Champezou
- Center of Basic Research, Biomedical Research Foundation, Academy of Athens, 4 Soranou Ephessiou St., 11527 Athens, Greece; (M.P.); (M.A.K.); (L.C.); (G.V.)
| | - Angeliki-Ioanna Giannopoulou
- Department of Biological Chemistry, Medical School, National and Kapodistrian University of Athens, 75 M. Asias Street Bldg 16, 11527 Athens, Greece;
| | - Giannis Vatsellas
- Center of Basic Research, Biomedical Research Foundation, Academy of Athens, 4 Soranou Ephessiou St., 11527 Athens, Greece; (M.P.); (M.A.K.); (L.C.); (G.V.)
| | - Christina Piperi
- Department of Biological Chemistry, Medical School, National and Kapodistrian University of Athens, 75 M. Asias Street Bldg 16, 11527 Athens, Greece;
| | - Marios Agelopoulos
- Center of Basic Research, Biomedical Research Foundation, Academy of Athens, 4 Soranou Ephessiou St., 11527 Athens, Greece; (M.P.); (M.A.K.); (L.C.); (G.V.)
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8
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Guijarro LG, Justo Bermejo FJ, Boaru DL, De Castro-Martinez P, De Leon-Oliva D, Fraile-Martínez O, Garcia-Montero C, Alvarez-Mon M, Toledo-Lobo MDV, Ortega MA. Is Insulin Receptor Substrate4 (IRS4) a Platform Involved in the Activation of Several Oncogenes? Cancers (Basel) 2023; 15:4651. [PMID: 37760618 PMCID: PMC10526421 DOI: 10.3390/cancers15184651] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2023] [Revised: 09/06/2023] [Accepted: 09/13/2023] [Indexed: 09/29/2023] Open
Abstract
The IRS (insulin receptor substrate) family of scaffold proteins includes insulin receptor substrate-4 (IRS4), which is expressed only in a few cell lines, including human kidney, brain, liver, and thymus and some cell lines. Its N-terminus carries a phosphotyrosine-binding (PTB) domain and a pleckstrin homology domain (PH), which distinguishes it as a member of this family. In this paper, we collected data about the molecular mechanisms that explain the relevance of IRS4 in the development of cancer and identify IRS4 differences that distinguish it from IRS1 and IRS2. Search engines and different databases, such as PubMed, UniProt, ENSEMBL and SCANSITE 4.0, were used. We used the name of the protein that it encodes "(IRS-4 or IRS4)", or the combination of these terms with the word "(cancer)" or "(human)", for searches. Terms related to specific tumor pathologies ("breast", "ovary", "colon", "lung", "lymphoma", etc.) were also used. Despite the lack of knowledge on IRS4, it has been reported that some cancers and benign tumors are characterized by high levels of IRS-4 expression. Specifically, the role of IRS-4 in different types of digestive tract neoplasms, gynecological tumors, lung cancers, melanomas, hematological tumors, and other less common types of cancers has been shown. IRS4 differs from IRS1 and IRS2 in that can activate several oncogenes that regulate the PI3K/Akt cascade, such as BRK and FER, which are characterized by tyrosine kinase-like activity without regulation via extracellular ligands. In addition, IRS4 can activate the CRKL oncogene, which is an adapter protein that regulates the MAP kinase cascade. Knowledge of the role played by IRS4 in cancers at the molecular level, specifically as a platform for oncogenes, may enable the identification and validation of new therapeutic targets.
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Affiliation(s)
- Luis G. Guijarro
- Unit of Biochemistry and Molecular Biology, Department of System Biology (CIBEREHD), University of Alcalá, 28801 Alcala de Henares, Spain
- Ramón y Cajal Institute of Sanitary Research (IRYCIS), 28034 Madrid, Spain; (D.L.B.); (D.D.L.-O.); (O.F.-M.); (C.G.-M.); (M.A.-M.); (M.A.O.)
| | | | - Diego Liviu Boaru
- Ramón y Cajal Institute of Sanitary Research (IRYCIS), 28034 Madrid, Spain; (D.L.B.); (D.D.L.-O.); (O.F.-M.); (C.G.-M.); (M.A.-M.); (M.A.O.)
- Department of Medicine and Medical Specialities, Faculty of Medicine and Health Sciences, University of Alcalá, 28801 Alcala de Henares, Spain;
| | - Patricia De Castro-Martinez
- Department of Medicine and Medical Specialities, Faculty of Medicine and Health Sciences, University of Alcalá, 28801 Alcala de Henares, Spain;
| | - Diego De Leon-Oliva
- Ramón y Cajal Institute of Sanitary Research (IRYCIS), 28034 Madrid, Spain; (D.L.B.); (D.D.L.-O.); (O.F.-M.); (C.G.-M.); (M.A.-M.); (M.A.O.)
- Department of Medicine and Medical Specialities, Faculty of Medicine and Health Sciences, University of Alcalá, 28801 Alcala de Henares, Spain;
| | - Oscar Fraile-Martínez
- Ramón y Cajal Institute of Sanitary Research (IRYCIS), 28034 Madrid, Spain; (D.L.B.); (D.D.L.-O.); (O.F.-M.); (C.G.-M.); (M.A.-M.); (M.A.O.)
- Department of Medicine and Medical Specialities, Faculty of Medicine and Health Sciences, University of Alcalá, 28801 Alcala de Henares, Spain;
| | - Cielo Garcia-Montero
- Ramón y Cajal Institute of Sanitary Research (IRYCIS), 28034 Madrid, Spain; (D.L.B.); (D.D.L.-O.); (O.F.-M.); (C.G.-M.); (M.A.-M.); (M.A.O.)
- Department of Medicine and Medical Specialities, Faculty of Medicine and Health Sciences, University of Alcalá, 28801 Alcala de Henares, Spain;
| | - Melchor Alvarez-Mon
- Ramón y Cajal Institute of Sanitary Research (IRYCIS), 28034 Madrid, Spain; (D.L.B.); (D.D.L.-O.); (O.F.-M.); (C.G.-M.); (M.A.-M.); (M.A.O.)
- Department of Medicine and Medical Specialities, Faculty of Medicine and Health Sciences, University of Alcalá, 28801 Alcala de Henares, Spain;
- Immune System Diseases-Rheumatology, Oncology Service and Internal Medicine (CIBEREHD), University Hospital Príncipe de Asturias, 28806 Alcala de Henares, Spain
| | - María del Val Toledo-Lobo
- Ramón y Cajal Institute of Sanitary Research (IRYCIS), 28034 Madrid, Spain; (D.L.B.); (D.D.L.-O.); (O.F.-M.); (C.G.-M.); (M.A.-M.); (M.A.O.)
- Department of Biomedicine and Biotechnology, University of Alcalá, 28801 Alcala de Henares, Spain;
| | - Miguel A. Ortega
- Ramón y Cajal Institute of Sanitary Research (IRYCIS), 28034 Madrid, Spain; (D.L.B.); (D.D.L.-O.); (O.F.-M.); (C.G.-M.); (M.A.-M.); (M.A.O.)
- Department of Medicine and Medical Specialities, Faculty of Medicine and Health Sciences, University of Alcalá, 28801 Alcala de Henares, Spain;
- Cancer Registry and Pathology Department, Principe de Asturias University Hospital, 28806 Alcala de Henares, Spain
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9
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Wu Q, Tao X, Luo Y, Zheng S, Lin N, Xie X. A novel super-enhancer-related gene signature predicts prognosis and immune microenvironment for breast cancer. BMC Cancer 2023; 23:776. [PMID: 37596527 PMCID: PMC10439574 DOI: 10.1186/s12885-023-11241-2] [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: 01/27/2023] [Accepted: 07/31/2023] [Indexed: 08/20/2023] Open
Abstract
BACKGROUND This study targeted at developing a robust, prognostic signature based on super-enhancer-related genes (SERGs) to reveal survival prognosis and immune microenvironment of breast cancer. METHODS RNA-sequencing data of breast cancer were retrieved from The Cancer Genome Atlas (TCGA), 1069 patients of which were randomly assigned into training or testing set in 1:1 ratio. SERGs were downloaded from Super-Enhancer Database (SEdb). After which, a SERGs signature was established based on the training set, with its prognostic value further validated in the testing set. Subsequently, we identified the potential function enrichment and tumor immune infiltration of the model. Moreover, in vitro experiments were completed to further explore the biological functions of ZIC2 gene (one of the risk genes in the prognostic model) in breast cancer. RESULTS A risk score system of prognostic value was constructed with 6 SERGs (ZIC2, NFE2, FOXJ1, KLF15, POU3F2 and SPIB) to find patients in high-risk group with significantly worse prognosis in both training and testing sets. In addition, a multivariate regression was established via integrating the 6 genes with age and N stage, indicating well performance by calibration, time-dependent receiver operating characteristic (ROC) analysis and decision curve analysis (DCA). Further analysis demonstrated that tumor-associated pathological processes and pathways were significantly enriched in the high-risk group. In general, the novel SERGs signature could be applied to screen breast cancer with immunosuppressive microenvironment for the risk score was negatively correlated with ESTIMATE score, tumor-infiltration lymphocytes (such as CD4 + and CD8 + T cell), immune checkpoints and chemotactic factors. Furthermore, down-regulation of ZIC2 gene expression inhibited the cell viability, cellular migration and cell cycle of breast cancer cells. CONCLUSIONS The novel SERGs signature could predict the prognosis of breast cancer; and SERGs might serve as potential therapeutic targets for breast cancer.
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Affiliation(s)
- Qing Wu
- Department of Oncology, Molecular Oncology Research Institute, The First Affiliated Hospital of Fujian Medical University, No. 20 Chazhong Road, Fuzhou, 350005, China
- Department of Oncology, National Regional Medical Center, Binhai Campus of The First Affiliated Hospital, Fujian Medical University, Fuzhou, 350212, China
| | - Xuan Tao
- Department of Pathology, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China
| | - Yang Luo
- Department of Oncology, Molecular Oncology Research Institute, The First Affiliated Hospital of Fujian Medical University, No. 20 Chazhong Road, Fuzhou, 350005, China
| | - Shiyao Zheng
- College of Clinical Medicine for Oncology, Fujian Medical University, Fuzhou, Fujian, China
| | - Nan Lin
- Fuzong Clinical Medical College of Fujian Medical University, Fuzhou, Fujian, China
- Department of Gastrointestinal Surgery, The 900th Hospital of Joint Logistics Support Forces of Chinese PLA, Fuzhou, Fujian, China
| | - Xianhe Xie
- Department of Oncology, Molecular Oncology Research Institute, The First Affiliated Hospital of Fujian Medical University, No. 20 Chazhong Road, Fuzhou, 350005, China.
- Department of Oncology, National Regional Medical Center, Binhai Campus of The First Affiliated Hospital, Fujian Medical University, Fuzhou, 350212, China.
- Fujian Key Laboratory of Precision Medicine for Cancer, The First Affiliated Hospital, Fujian Medical University, Fuzhou, 350005, China.
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