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Volnitskiy A, Shabalin K, Pantina R, Varfolomeeva E, Kovalev R, Burdakov V, Emelianova S, Garaeva L, Yakimov A, Sogoyan M, Filatov M, Konevega AL, Shtam T. OCT4 Expression in Gliomas Is Dependent on Cell Metabolism. Curr Issues Mol Biol 2024; 46:1107-1120. [PMID: 38392188 PMCID: PMC10887564 DOI: 10.3390/cimb46020070] [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: 11/28/2023] [Revised: 01/16/2024] [Accepted: 01/21/2024] [Indexed: 02/24/2024] Open
Abstract
The OCT4 transcription factor is necessary to maintain cell stemness in the early stages of embryogenesis and is involved in the formation of induced pluripotent stem cells, but its role in oncogenesis is not yet entirely clear. In this work, OCT4 expression was investigated in malignant gliomas. Twenty glioma cell lines and a sample of normal adult brain tissue were used. OCT4 expression was found in all studied glioma cell lines but was not detected in normal adult brain tissue. For one of these lines, OCT4 knockdown caused tumor cell death. By varying the culture conditions of these cells, we unexpectedly found that OCT4 expression increased when cells were incubated in serum-free medium, and this effect was significantly enhanced in serum-free and L-glutamine-free medium. L-glutamine and the Krebs cycle, which is slowed down in serum-free medium according to our NMR data, are sources of α-KG. Thus, our data indicate that OCT4 expression in gliomas may be regulated by the α-KG-dependent metabolic reprogramming of cells.
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Affiliation(s)
- Andrey Volnitskiy
- Petersburg Nuclear Physics Institute Named by B.P. Konstantinov of National Research Centre "Kurchatov Institute", Orlova Roscha 1, 188300 Gatchina, Russia
| | - Konstantin Shabalin
- Petersburg Nuclear Physics Institute Named by B.P. Konstantinov of National Research Centre "Kurchatov Institute", Orlova Roscha 1, 188300 Gatchina, Russia
| | - Rimma Pantina
- Petersburg Nuclear Physics Institute Named by B.P. Konstantinov of National Research Centre "Kurchatov Institute", Orlova Roscha 1, 188300 Gatchina, Russia
| | - Elena Varfolomeeva
- Petersburg Nuclear Physics Institute Named by B.P. Konstantinov of National Research Centre "Kurchatov Institute", Orlova Roscha 1, 188300 Gatchina, Russia
| | - Roman Kovalev
- Petersburg Nuclear Physics Institute Named by B.P. Konstantinov of National Research Centre "Kurchatov Institute", Orlova Roscha 1, 188300 Gatchina, Russia
| | - Vladimir Burdakov
- Petersburg Nuclear Physics Institute Named by B.P. Konstantinov of National Research Centre "Kurchatov Institute", Orlova Roscha 1, 188300 Gatchina, Russia
| | - Svetlana Emelianova
- Petersburg Nuclear Physics Institute Named by B.P. Konstantinov of National Research Centre "Kurchatov Institute", Orlova Roscha 1, 188300 Gatchina, Russia
| | - Luiza Garaeva
- Petersburg Nuclear Physics Institute Named by B.P. Konstantinov of National Research Centre "Kurchatov Institute", Orlova Roscha 1, 188300 Gatchina, Russia
| | - Alexander Yakimov
- Petersburg Nuclear Physics Institute Named by B.P. Konstantinov of National Research Centre "Kurchatov Institute", Orlova Roscha 1, 188300 Gatchina, Russia
- Institute of Biomedical Systems and Biotechnologies, Peter the Great St. Petersburg Polytechnic University, Politehnicheskaya 29, 195251 St. Petersburg, Russia
| | - Marina Sogoyan
- H.Turner National Medical Research Center for Children's Orthopedics and Trauma Surgery of the Ministry of Health of the Russian Federation, Parkovaya 64-68, Pushkin, 196603 St. Petersburg, Russia
| | - Michael Filatov
- Petersburg Nuclear Physics Institute Named by B.P. Konstantinov of National Research Centre "Kurchatov Institute", Orlova Roscha 1, 188300 Gatchina, Russia
| | - Andrey L Konevega
- Petersburg Nuclear Physics Institute Named by B.P. Konstantinov of National Research Centre "Kurchatov Institute", Orlova Roscha 1, 188300 Gatchina, Russia
- Institute of Biomedical Systems and Biotechnologies, Peter the Great St. Petersburg Polytechnic University, Politehnicheskaya 29, 195251 St. Petersburg, Russia
- National Research Center "Kurchatov Institute", Akademika Kurchatova pl. 1, 123182 Moscow, Russia
| | - Tatiana Shtam
- Petersburg Nuclear Physics Institute Named by B.P. Konstantinov of National Research Centre "Kurchatov Institute", Orlova Roscha 1, 188300 Gatchina, Russia
- National Research Center "Kurchatov Institute", Akademika Kurchatova pl. 1, 123182 Moscow, Russia
- Institute of Cytology, Russian Academy of Sciences, Tikhoretsky Ave. 4, 194064 St. Petersburg, Russia
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Luo J, Huang R, Xiao P, Xu A, Dong Z, Zhang L, Wu R, Qiu Y, Zhu L, Zhang R, Tang L. Construction of hub transcription factor-microRNAs-messenger RNA regulatory network in recurrent implantation failure. J Assist Reprod Genet 2024; 41:3-13. [PMID: 37878219 PMCID: PMC10789703 DOI: 10.1007/s10815-023-02947-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Accepted: 09/14/2023] [Indexed: 10/26/2023] Open
Abstract
PURPOSE Recurrent implantation failure (RIF) affects up to 10% of in vitro fertilization (IVF) patients worldwide. However, the pathogenesis of RIF remains unclear. This study was aimed at identifying hub transcription factors (TFs) of RIF in bioinformatics approaches. METHODS The GSE111974 (mRNA), GSE71332 (miRNA), and GSE103465 (mRNA) datasets were downloaded from the Gene Expression Omnibus database from human endometrial tissue using R version 4.2.1 and used to identify differentially expressed TFs (DETFs), differentially expressed miRNAs, and differentially expressed genes for RIF, respectively. DETFs were subjected to functional enrichment analysis and the protein-protein interaction network analysis using the Search Tool for the Retrieval of Interacting Genes (version 11.5) database. Hub TFs were identified using the cytoHubb plug-in, after which a hub TF-miRNA-mRNA network was constructed using Cytoscape v3.8.2. RESULTS Fifty-seven DETFs were identified, in which Gene Ontology analysis revealed to be mainly involved in the regulation of transcription. Kyoto Encyclopedia of Genes and Genomes pathway analysis suggested that DETFs were enriched in transcriptional misregulation in cancer, aldosterone synthesis and secretion, AMPK signaling pathway, and cGMP-PKG signaling pathway. EOMES, NKX2-1, and POU5F1 were identified as hub TFs, and a hub TF-miRNA-mRNA regulatory network was constructed using these three hub TFs, four miRNAs, and four genes. CONCLUSION Collectively, we identified three promising molecular biomarkers for the diagnosis of RIF, which may further be potential therapeutic targets. This study provides novel insights into the molecular mechanisms underlying RIF. However, further experiments are required to verify these results.
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Affiliation(s)
- Jiahuan Luo
- Department of Reproductive Genetics, The First Affiliated Hospital of Kunming Medical University, No. 295, Xichang Road, Wuhua District, Kunming, China
- Department of Reproductive Medicine, The First Affiliated Hospital of Dali University, Dali, China
- Innovation Team in Reproductive Medicine, Dali University, No. 32, Carlsberg Avenue, Dali, Yunnan, China
- First Clinical Medical College, Kunming Medical University, Kunming, China
| | - Rongxia Huang
- Department of Gynecology, Kunming Maternal and Child Health Hospital, Kunming, China
| | - Pengying Xiao
- Reproductive Medicine Center, Dongguan Songshan Lake Central Hospital, Dongguan, 523429, China
| | - Anli Xu
- Department of Reproductive Medicine, The First Affiliated Hospital of Dali University, Dali, China
- Innovation Team in Reproductive Medicine, Dali University, No. 32, Carlsberg Avenue, Dali, Yunnan, China
- Reproductive Medicine Center, Kunming Maternal and Child Health Hospital, No. 43, Huashan West Road, Huashan Street, Wuhua District, Kunming, China
| | - Zhaomei Dong
- Department of Reproductive Medicine, The First Affiliated Hospital of Dali University, Dali, China
- Innovation Team in Reproductive Medicine, Dali University, No. 32, Carlsberg Avenue, Dali, Yunnan, China
- Reproductive Medicine Center, Kunming Maternal and Child Health Hospital, No. 43, Huashan West Road, Huashan Street, Wuhua District, Kunming, China
| | - Lirong Zhang
- Department of Reproductive Medicine, The First Affiliated Hospital of Dali University, Dali, China
- Innovation Team in Reproductive Medicine, Dali University, No. 32, Carlsberg Avenue, Dali, Yunnan, China
- Reproductive Medicine Center, Kunming Maternal and Child Health Hospital, No. 43, Huashan West Road, Huashan Street, Wuhua District, Kunming, China
| | - Rui Wu
- Department of Reproductive Medicine, The First Affiliated Hospital of Dali University, Dali, China
- Reproductive Medicine Center, Kunming Maternal and Child Health Hospital, No. 43, Huashan West Road, Huashan Street, Wuhua District, Kunming, China
| | - Yunlin Qiu
- Department of Reproductive Medicine, The First Affiliated Hospital of Dali University, Dali, China
- Reproductive Medicine Center, Kunming Maternal and Child Health Hospital, No. 43, Huashan West Road, Huashan Street, Wuhua District, Kunming, China
| | - Li Zhu
- Department of Reproductive Medicine, The First Affiliated Hospital of Dali University, Dali, China.
- Innovation Team in Reproductive Medicine, Dali University, No. 32, Carlsberg Avenue, Dali, Yunnan, China.
- Reproductive Medicine Center, Kunming Maternal and Child Health Hospital, No. 43, Huashan West Road, Huashan Street, Wuhua District, Kunming, China.
| | - Ruopeng Zhang
- Reproductive Medicine Center, Dongguan Songshan Lake Central Hospital, Dongguan, 523429, China.
- Reproductive Medicine Center, Kunming Maternal and Child Health Hospital, No. 43, Huashan West Road, Huashan Street, Wuhua District, Kunming, China.
| | - Li Tang
- Department of Reproductive Genetics, The First Affiliated Hospital of Kunming Medical University, No. 295, Xichang Road, Wuhua District, Kunming, China.
- First Clinical Medical College, Kunming Medical University, Kunming, China.
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Chandra O, Sharma M, Pandey N, Jha IP, Mishra S, Kong SL, Kumar V. Patterns of transcription factor binding and epigenome at promoters allow interpretable predictability of multiple functions of non-coding and coding genes. Comput Struct Biotechnol J 2023; 21:3590-3603. [PMID: 37520281 PMCID: PMC10371796 DOI: 10.1016/j.csbj.2023.07.014] [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: 01/25/2023] [Revised: 07/05/2023] [Accepted: 07/11/2023] [Indexed: 08/01/2023] Open
Abstract
Understanding the biological roles of all genes only through experimental methods is challenging. A computational approach with reliable interpretability is needed to infer the function of genes, particularly for non-coding RNAs. We have analyzed genomic features that are present across both coding and non-coding genes like transcription factor (TF) and cofactor ChIP-seq (823), histone modifications ChIP-seq (n = 621), cap analysis gene expression (CAGE) tags (n = 255), and DNase hypersensitivity profiles (n = 255) to predict ontology-based functions of genes. Our approach for gene function prediction was reliable (>90% balanced accuracy) for 486 gene-sets. PubMed abstract mining and CRISPR screens supported the inferred association of genes with biological functions, for which our method had high accuracy. Further analysis revealed that TF-binding patterns at promoters have high predictive strength for multiple functions. TF-binding patterns at the promoter add an unexplored dimension of explainable regulatory aspects of genes and their functions. Therefore, we performed a comprehensive analysis for the functional-specificity of TF-binding patterns at promoters and used them for clustering functions to reveal many latent groups of gene-sets involved in common major cellular processes. We also showed how our approach could be used to infer the functions of non-coding genes using the CRISPR screens of coding genes, which were validated using a long non-coding RNA CRISPR screen. Thus our results demonstrated the generality of our approach by using gene-sets from CRISPR screens. Overall, our approach opens an avenue for predicting the involvement of non-coding genes in various functions.
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Affiliation(s)
- Omkar Chandra
- Department of Computational Biology, Indraprastha Institute of Information Technology, Okhla Ph-III, New Delhi, India
| | - Madhu Sharma
- Department of Computational Biology, Indraprastha Institute of Information Technology, Okhla Ph-III, New Delhi, India
| | - Neetesh Pandey
- Department of Computational Biology, Indraprastha Institute of Information Technology, Okhla Ph-III, New Delhi, India
| | - Indra Prakash Jha
- Department of Computational Biology, Indraprastha Institute of Information Technology, Okhla Ph-III, New Delhi, India
| | - Shreya Mishra
- Department of Computational Biology, Indraprastha Institute of Information Technology, Okhla Ph-III, New Delhi, India
| | - Say Li Kong
- Genome Institute of Singapore, Agency for Science Technology and Research, Singapore, Singapore
| | - Vibhor Kumar
- Department of Computational Biology, Indraprastha Institute of Information Technology, Okhla Ph-III, New Delhi, India
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Abstract
POUV is a relatively newly emerged class of POU transcription factors present in jawed vertebrates (Gnathostomata). The function of POUV-class proteins is inextricably linked to zygotic genome activation (ZGA). A large body of evidence now extends the role of these proteins to subsequent developmental stages. While some functions resemble those of other POU-class proteins and are related to neuroectoderm development, others have emerged de novo. The most notable of the latter functions is pluripotency control by Oct4 in mammals. In this review, we focus on these de novo functions in the best-studied species harbouring POUV proteins-zebrafish, Xenopus (anamniotes) and mammals (amniotes). Despite the broad diversity of their biological functions in vertebrates, POUV proteins exert a common feature related to their role in safeguarding the undifferentiated state of cells. Here we summarize numerous pieces of evidence for these specific functions of the POUV-class proteins and recap available loss-of-function data.
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Affiliation(s)
- Evgeny I. Bakhmet
- Laboratory of the Molecular Biology of Stem Cells, Institute of Cytology, Russian Academy of Sciences, St Petersburg, Russia
| | - Alexey N. Tomilin
- Laboratory of the Molecular Biology of Stem Cells, Institute of Cytology, Russian Academy of Sciences, St Petersburg, Russia
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