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Tong S, Ye L, Xu Y, Sun Q, Gao L, Cai J, Ye Z, Tian D, Chen Q. IRF2-ferroptosis related gene is associated with prognosis and EMT in gliomas. Transl Oncol 2022; 26:101544. [PMID: 36156371 PMCID: PMC9508157 DOI: 10.1016/j.tranon.2022.101544] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 07/20/2022] [Accepted: 09/11/2022] [Indexed: 11/30/2022] Open
Abstract
Ferroptosis is a new type of programmed cell death that has excellent anti-tumor potential in different tumors. However, the research on ferroptosis in glioma is still incomplete. In this study, we aimed to revealed the relationship between ferroptosis-related genes (FRGs) and glioma. We collected gene expression profiles of glioma patients from the TCGA and CGGA databases. All glioma samples were classified into five subtypes using the R software ConsensusClusterPlus. Subsequently, we performed single sample gene set enrichment analysis (ssGSEA) to explore the correlation between different subtypes and immune status and ferroptosis. Then co-expression modules were constructed via weighted gene co-expression network analysis (WGCNA). A Gene Ontology (GO) analysis was conducted to analyze the potential biological functions of the genes in the modules. Finally, we identified 10 hub genes using the PPI network. The in vitro experiments were used to validate our predictions. We found that the expression level of IRF2 is positively correlated with the grade of glioma. The overexpression of IRF2 could protect glioma cells from ferroptosis and enhance the invasive and migratory abilities. Silence of IRF2 had the opposite effect. In conclusion, we demonstrated a novel ferroptosis-related signature for predicting prognosis, and IRF2 could be a potential biomarker for diagnosis and treatment in glioma.
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Affiliation(s)
- Shiao Tong
- Department of Neurosurgery, Renmin Hospital of Wuhan University, Wuhan, Hubei, China
| | - Liguo Ye
- Department of Neurosurgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.
| | - Yang Xu
- Department of Neurosurgery, Renmin Hospital of Wuhan University, Wuhan, Hubei, China
| | - Qian Sun
- Department of Neurosurgery, Renmin Hospital of Wuhan University, Wuhan, Hubei, China
| | - Lun Gao
- Department of Neurosurgery, Renmin Hospital of Wuhan University, Wuhan, Hubei, China
| | - Jiayang Cai
- Department of Neurosurgery, Renmin Hospital of Wuhan University, Wuhan, Hubei, China
| | - Zhang Ye
- Department of Neurosurgery, Renmin Hospital of Wuhan University, Wuhan, Hubei, China
| | - Daofeng Tian
- Department of Neurosurgery, Renmin Hospital of Wuhan University, Wuhan, Hubei, China.
| | - Qianxue Chen
- Department of Neurosurgery, Renmin Hospital of Wuhan University, Wuhan, Hubei, China.
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Kashevarova AA, Nazarenko LP, Skryabin NA, Salyukova OA, Chechetkina NN, Tolmacheva EN, Sazhenova EA, Magini P, Graziano C, Romeo G, Kučinskas V, Lebedev IN. Array CGH analysis of a cohort of Russian patients with intellectual disability. Gene 2014; 536:145-50. [PMID: 24291026 DOI: 10.1016/j.gene.2013.11.029] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2013] [Revised: 10/30/2013] [Accepted: 11/01/2013] [Indexed: 12/20/2022]
Abstract
The use of array comparative genomic hybridization (array CGH) as a diagnostic tool in molecular genetics has facilitated the identification of many new microdeletion/microduplication syndromes (MMSs). Furthermore, this method has allowed for the identification of copy number variations (CNVs) whose pathogenic role has yet to be uncovered. Here, we report on our application of array CGH for the identification of pathogenic CNVs in 79 Russian children with intellectual disability (ID). Twenty-six pathogenic or likely pathogenic changes in copy number were detected in 22 patients (28%): 8 CNVs corresponded to known MMSs, and 17 were not associated with previously described syndromes. In this report, we describe our findings and comment on genes potentially associated with ID that are located within the CNV regions.
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Key Words
- ABLIM3
- ACAD10
- ADHD
- AFAP1L1
- AGA
- ASTN1
- Array comparative genomic hybridization (array CGH)
- CASP3
- CGH
- CHERISH
- CNS
- CNTN6
- CNV
- Copy number variation (CNV)
- DDX10
- DEAD (Asp-Glu-Ala-Asp) box polypeptide 10
- DECIPHER
- EEG
- EU
- European Union
- FJX1
- GLRA3
- HAND2
- HFE
- ID
- IFN
- IL17B
- ING2
- IQ
- IRF1
- IRF2
- Intellectual disability
- LDLRAD3
- METTL4
- MMP14
- MMSs
- MRI
- NDC80
- NDC80 kinetochore complex component
- NEIL3
- NO
- OMIM
- PCR
- PL CNS
- PON1
- PON2
- PON3
- SBF
- SCGN
- SCRG1
- SET domain binding factor
- SLC1A2
- SLC5A7
- SLC7A7
- SMCHD1
- SUFU
- SWAP switching B-cell complex 70kDa subunit
- SWAP70
- Ski-related novel protein N
- SnoN
- TGFβ
- TNR
- TRIM44
- WAGR
- Wilms tumor, aniridia, genitourinary anomalies and mental retardation syndrome
- actin binding LIM protein family, member 3
- actin filament associated protein 1-like 1
- acyl-CoA dehydrogenase family, member 10
- aspartylglucosaminidase
- astrotactin 1
- attention-deficit hyperactivity disorder
- caspase 3, apoptosis-related cysteine peptidase
- central nervous system
- comparative genomic hybridization
- contactin 6
- copy number variation
- database of chromosomal imbalance and phenotype in humans using ensembl resources
- electroencephalogram
- four jointed box 1 (Drosophila)
- glycine receptor, alpha 3
- grant of European Community's Seventh Framework Programme
- heart and neural crest derivatives expressed 2
- hemochromatosis
- inhibitor of growth family, member 2
- intellectual disability
- intelligence quotient
- interferon
- interferon regulatory factor 1
- interferon regulatory factor 2
- interleukin 17B
- low density lipoprotein receptor class A domain containing 3
- magnetic resonance imaging
- matrix metallopeptidase 14 (membrane-inserted)
- methyltransferase like 4
- microdeletion/microduplication syndromes
- nei endonuclease VIII-like 3 (E. coli)
- nitrogen oxide
- online mendelian inheritance in man
- paraoxonase 1
- paraoxonase 2
- paraoxonase 3
- perinatal lesion of central nervous system
- polymerase chain reaction
- qPCR
- quantitative PCR
- secretagogin, EF-hand calcium binding protein
- solute carrier family 1 (glial high affinity glutamate transporter), member 2
- solute carrier family 5 (sodium/choline cotransporter), member 7
- solute carrier family 7 (amino acid transporter light chain, y+L system), member 7
- stimulator of chondrogenesis 1
- structural maintenance of chromosomes flexible hinge domain containing 1
- suppressor of fused homolog (Drosophila)
- tenascin R
- transforming growth factor beta
- tripartite motif containing 44
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Vaidutis Kučinskas
- Vilnius University, Department of Human and Medical Genetics, Vilnius, Lithuania
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Tzoanopoulos D, Speletas M, Arvanitidis K, Veiopoulou C, Kyriaki S, Thyphronitis G, Sideras P, Kartalis G, Ritis K. Low expression of interferon regulatory factor-1 and identification of novel exons skipping in patients with chronic myeloid leukaemia. Br J Haematol 2002; 119:46-53. [PMID: 12358902 DOI: 10.1046/j.1365-2141.2002.03829.x] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Chronic myeloid leukaemia (CML) is a malignant clonal disorder of the haematopoietic stem cell. Treatment of CML patients with interferon alpha (IFN-alpha) has induced haematological and cytogenetic remission. Interferons transcriptionally activate target genes through the JAK-STAT and interferon regulated factors (IRFs) family pathways. Interferon regulated factor-1 (IRF-1) is a transcriptional activator of genes critical for cell growth, differentiation and apoptosis. The skipping of exons 2 or 2 and 3 of IRF-1 in patients with myelodysplastic syndromes and acute myelogenous leukaemia suggests that this factor may have a critical role in leukaemogenesis. The role of IRF-1 in CML is currently unknown. Therefore, mutational analysis of IRF-1 was performed and its expression pattern was also studied in CML patients. We studied IRF-1 in peripheral blood mononuclear cells of 21 patients in chronic phase CML. No point mutations were identified at the cDNA level. Surprisingly, fourfold reduction of full-length IRF-1 mRNA expression was established in 17/21 patients compared with normal individuals. Low expression of full-length IRF-1 was observed in conjunction with high levels of aberrantly spliced mRNAs, reported for the first time. In three patients who were also analysed during blastic transformation, further reduction of full-length IRF-1 mRNA was observed. These findings demonstrate that, in CML patients, IRF-1 can produce high levels of aberrant spliced mRNAs with subsequent reduction in the levels of full-length IRF-1 mRNA. This observation is consistent with the notion that exon skipping may constitute another mechanism of tumour suppressor gene inactivation in this disease.
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Affiliation(s)
- Dimitrios Tzoanopoulos
- First Division of Internal Medicine, Democritus University of Thrace, Regional Hospital of Alexandroupolis, Alexandroupolis, Greece
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Abstract
Interferon (IFN) regulatory factor-1 (IRF-1) was isolated by virtue of its affinity to specific DNA sequences in the IFN-beta promoter that mediate virus responsiveness. IRF-1 was the first factor identified of the IRF family and was most extensively characterized at the molecular level. Also, its physiologic role in host defense against pathogens, tumor prevention, and development of the immune system was investigated in detail. Even though some of the functions first associated with IRF-1 were later found to be mediated in part or predominantly by other activators of the IRF family of transcription factors, IRF-1 has remained a central paradigm in the transcriptional regulation of the IFN response.
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Affiliation(s)
- Andrea Kröger
- Department of Gene Regulation and Differentiation, GBF, Gesellschaft für Biotechnologische Forschung, D 38124 Braunschweig Mascheroder Weg 1, Germany
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Mamane Y, Heylbroeck C, Génin P, Algarté M, Servant MJ, LePage C, DeLuca C, Kwon H, Lin R, Hiscott J. Interferon regulatory factors: the next generation. Gene 1999; 237:1-14. [PMID: 10524230 DOI: 10.1016/s0378-1119(99)00262-0] [Citation(s) in RCA: 423] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Interferons are a large family of multifunctional secreted proteins involved in antiviral defense, cell growth regulation and immune activation. Viral infection induces transcription of multiple IFN genes, a response that is in part mediated by the interferon regulatory factors (IRFs). The initially characterized members IRF-1 and IRF-2 are now part of a growing family of transcriptional regulators that has expanded to nine members. The functions of the IRFs have also expanded to include distinct roles in biological processes such as pathogen response, cytokine signaling, cell growth regulation and hematopoietic development. The aim of this review is to provide an update on the novel discoveries in the area of IRF transcription factors and the important roles of the new generation of IRFs--particularly IRF-3, IRF-4 and IRF-7.
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Affiliation(s)
- Y Mamane
- Terry Fox Molecular Oncology Group, Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Canada
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Eason DD, Shepherd AT, Blanck G. Interferon regulatory factor 1 tryptophan 11 to arginine point mutation abolishes DNA binding. BIOCHIMICA ET BIOPHYSICA ACTA 1999; 1446:140-4. [PMID: 10395927 DOI: 10.1016/s0167-4781(99)00078-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Interferon regulatory factor-1 (IRF-1) is a transcriptional activator of genes induced by a variety of cytokines and growth factors. Defects in IRF-1 occur frequently in human cancers and may contribute to tumorigenesis. The IRF family of transcription factors share invariant tryptophan residues that have been proposed to function by orienting the DNA contacting residues of IRF-1 with the DNA core sequence of the IRF element. Here we describe a point mutation in IRF-1 that converts the tryptophan at codon 11 to arginine (W11R). The IRF-1 (W11R) mutation abolishes IRF-1 DNA binding and transactivating activities demonstrating the critical role of this invariant tryptophan in IRF-1 function.
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Affiliation(s)
- D D Eason
- Department of Biochemistry and Molecular Biology, University of South Florida, College of Medicine, MDC 7, 12901 Bruce B. Downs Blvd., Tampa, FL 33612, USA
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