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Nayarisseri A, Bandaru S, Khan A, Sharma K, Bhrdwaj A, Kaur M, Ghosh D, Chopra I, Panicker A, Kumar A, Saravanan P, Belapurkar P, Mendonça Junior FJB, Singh SK. Epigenetic dysregulation in cancers by isocitrate dehydrogenase 2 (IDH2). ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2024; 141:223-253. [PMID: 38960475 DOI: 10.1016/bs.apcsb.2023.12.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/05/2024]
Abstract
Recent advances in genome-wide studies have revealed numerous epigenetic regulations brought about by genes involved in cellular metabolism. Isocitrate dehydrogenase (IDH), an essential enzyme, that converts isocitrate into -ketoglutarate (KG) predominantly in the tricarboxylic acid (TCA) cycle, has gained particular importance due to its cardinal role in the metabolic pathway in cells. IDH1, IDH2, and IDH3 are the three isomeric IDH enzymes that have been shown to regulate cellular metabolism. Of particular importance, IDH2 genes are associated with several cancers, including gliomas, oligodendroglioma, and astrocytomas. These mutations lead to the production of oncometabolite D-2-hydroxyglutarate (D-2-HG), which accumulates in cells promoting tumor growth. The enhanced levels of D-2-HG competitively inhibit α-KG dependent enzymes, inhibiting cell TCA cycle, upregulating the cell growth and survival relevant HIF-1α pathway, promoting DNA hypermethylation related epigenetic activity, all of which synergistically contribute to carcinogenesis. The present review discusses epigenetic mechanisms inIDH2 regulation in cells and further its clinical implications.
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Affiliation(s)
- Anuraj Nayarisseri
- In silico Research Laboratory, Eminent Biosciences, Indore, Madhya Pradesh, India; Bioinformatics Research Laboratory, LeGene Biosciences Pvt Ltd, Indore, Madhya Pradesh, India.
| | - Srinivas Bandaru
- In silico Research Laboratory, Eminent Biosciences, Indore, Madhya Pradesh, India; Department of Biotechnology, Koneru Lakshmaiah Educational Foundation (KLEF), Green Fields, Vaddeswaram, Andhra Pradesh, India
| | - Arshiya Khan
- In silico Research Laboratory, Eminent Biosciences, Indore, Madhya Pradesh, India; Computer Aided Drug Designing and Molecular Modeling Lab, Department of Bioinformatics, Alagappa University, Karaikudi, Tamil Nadu, India
| | - Khushboo Sharma
- In silico Research Laboratory, Eminent Biosciences, Indore, Madhya Pradesh, India; Computer Aided Drug Designing and Molecular Modeling Lab, Department of Bioinformatics, Alagappa University, Karaikudi, Tamil Nadu, India
| | - Anushka Bhrdwaj
- In silico Research Laboratory, Eminent Biosciences, Indore, Madhya Pradesh, India; Computer Aided Drug Designing and Molecular Modeling Lab, Department of Bioinformatics, Alagappa University, Karaikudi, Tamil Nadu, India
| | - Manmeet Kaur
- In silico Research Laboratory, Eminent Biosciences, Indore, Madhya Pradesh, India
| | - Dipannita Ghosh
- In silico Research Laboratory, Eminent Biosciences, Indore, Madhya Pradesh, India
| | - Ishita Chopra
- In silico Research Laboratory, Eminent Biosciences, Indore, Madhya Pradesh, India; School of Medicine and Health Sciences, The George Washington University, Washington, DC, United States
| | - Aravind Panicker
- In silico Research Laboratory, Eminent Biosciences, Indore, Madhya Pradesh, India
| | - Abhishek Kumar
- In silico Research Laboratory, Eminent Biosciences, Indore, Madhya Pradesh, India; Department of Biosciences, Acropolis Institute, Indore, Madhya Pradesh, India
| | - Priyadevi Saravanan
- In silico Research Laboratory, Eminent Biosciences, Indore, Madhya Pradesh, India
| | - Pranoti Belapurkar
- Department of Biosciences, Acropolis Institute, Indore, Madhya Pradesh, India
| | | | - Sanjeev Kumar Singh
- Computer Aided Drug Designing and Molecular Modeling Lab, Department of Bioinformatics, Alagappa University, Karaikudi, Tamil Nadu, India
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Aljarrah D, Chalour N, Zorgani A, Nissan T, Pranjol MZI. Exploring the gut microbiota and its potential as a biomarker in gliomas. Biomed Pharmacother 2024; 173:116420. [PMID: 38471271 DOI: 10.1016/j.biopha.2024.116420] [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: 11/27/2023] [Revised: 02/24/2024] [Accepted: 03/07/2024] [Indexed: 03/14/2024] Open
Abstract
Gut microbiome alterations are associated with various cancers including brain tumours such as glioma and glioblastoma. The gut communicates with the brain via a bidirectional pathway known as the gut-brain axis (GBA) which is essential for maintaining homeostasis. The gut microbiota produces many metabolites including short chain fatty acids (SCFAs) and essential amino acids such as glutamate, glutamine, arginine and tryptophan. Through the modulation of these metabolites the gut microbiome is able to regulate several functions of brain cells, immune cells and tumour cells including DNA methylation, mitochondrial function, the aryl hydrocarbon receptor (AhR), T-cell proliferation, autophagy and even apoptosis. Here, we summarise current findings on gut microbiome with respect to brain cancers, an area of research that is widely overlooked. Several studies investigated the relationship between gut microbiota and brain tumours. However, it remains unclear whether the gut microbiome variation is a cause or product of cancer. Subsequently, a biomarker panel was constructed for use as a predictive, prognostic and diagnostic tool with respect to multiple cancers including glioma and glioblastoma multiforme (GBM). This review further presents the intratumoural microbiome, a fascinating microenvironment within the tumour as a possible treatment target that can be manipulated to maximise effectiveness of treatment via personalised therapy. Studies utilising the microbiome as a biomarker and therapeutic strategy are necessary to accurately assess the effectiveness of the gut microbiome as a clinical tool with respect to brain cancers.
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Affiliation(s)
- Dana Aljarrah
- Department of Chemistry, School of Life Sciences, University of Sussex, Brighton, UK.
| | - Naima Chalour
- Cognitive and Behavioural Neuroscience laboratory, Houari Boumediene University of Science and Technology, Bab Ezzouar, Algiers, Algeria; Faculty of Biological Sciences, Houari Boumediene University of Science and Technology, Bab Ezzouar, Algiers, Algeria.
| | - Amine Zorgani
- The Microbiome Mavericks, 60 rue Christian Lacouture, Bron 69500, France.
| | - Tracy Nissan
- Department of Molecular Biosciences, the Wenner-Gren Institute, Stockholm University, Stockholm, Sweden.
| | - Md Zahidul I Pranjol
- Department of Chemistry, School of Life Sciences, University of Sussex, Brighton, UK.
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Herrgott GA, Snyder JM, She R, Malta TM, Sabedot TS, Lee IY, Pawloski J, Podolsky-Gondim GG, Asmaro KP, Zhang J, Cannella CE, Nelson K, Thomas B, deCarvalho AC, Hasselbach LA, Tundo KM, Newaz R, Transou A, Morosini N, Francisco V, Poisson LM, Chitale D, Mukherjee A, Mosella MS, Robin AM, Walbert T, Rosenblum M, Mikkelsen T, Kalkanis S, Tirapelli DPC, Weisenberger DJ, Carlotti CG, Rock J, Castro AV, Noushmehr H. Detection of diagnostic and prognostic methylation-based signatures in liquid biopsy specimens from patients with meningiomas. Nat Commun 2023; 14:5669. [PMID: 37704607 PMCID: PMC10499807 DOI: 10.1038/s41467-023-41434-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Accepted: 08/31/2023] [Indexed: 09/15/2023] Open
Abstract
Recurrence of meningiomas is unpredictable by current invasive methods based on surgically removed specimens. Identification of patients likely to recur using noninvasive approaches could inform treatment strategy, whether intervention or monitoring. In this study, we analyze the DNA methylation levels in blood (serum and plasma) and tissue samples from 155 meningioma patients, compared to other central nervous system tumor and non-tumor entities. We discover DNA methylation markers unique to meningiomas and use artificial intelligence to create accurate and universal models for identifying and predicting meningioma recurrence, using either blood or tissue samples. Here we show that liquid biopsy is a potential noninvasive and reliable tool for diagnosing and predicting outcomes in meningioma patients. This approach can improve personalized management strategies for these patients.
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Affiliation(s)
- Grayson A Herrgott
- Department of Neurosurgery, Omics Laboratory, Hermelin Brain Tumor Center, Henry Ford Health, Detroit, MI, USA
| | - James M Snyder
- Department of Neurosurgery, Omics Laboratory, Hermelin Brain Tumor Center, Henry Ford Health, Detroit, MI, USA
| | - Ruicong She
- Department of Public Health, Biostatistics, Henry Ford Health, Detroit, MI, USA
| | - Tathiane M Malta
- Department of Neurosurgery, Omics Laboratory, Hermelin Brain Tumor Center, Henry Ford Health, Detroit, MI, USA
| | - Thais S Sabedot
- Department of Neurosurgery, Omics Laboratory, Hermelin Brain Tumor Center, Henry Ford Health, Detroit, MI, USA
| | - Ian Y Lee
- Department of Neurosurgery, Omics Laboratory, Hermelin Brain Tumor Center, Henry Ford Health, Detroit, MI, USA
| | - Jacob Pawloski
- Department of Neurosurgery, Omics Laboratory, Hermelin Brain Tumor Center, Henry Ford Health, Detroit, MI, USA
| | - Guilherme G Podolsky-Gondim
- Department of Neurosurgery, Ribeirao Preto Medical School, University of Sao Paulo, Ribeirao Preto, SP, Brazil
| | - Karam P Asmaro
- Department of Neurosurgery, Omics Laboratory, Hermelin Brain Tumor Center, Henry Ford Health, Detroit, MI, USA
| | - Jiaqi Zhang
- Department of Public Health, Biostatistics, Henry Ford Health, Detroit, MI, USA
| | - Cara E Cannella
- Department of Public Health, Biostatistics, Henry Ford Health, Detroit, MI, USA
| | - Kevin Nelson
- Department of Neurosurgery, Omics Laboratory, Hermelin Brain Tumor Center, Henry Ford Health, Detroit, MI, USA
| | - Bartow Thomas
- Department of Neurosurgery, Omics Laboratory, Hermelin Brain Tumor Center, Henry Ford Health, Detroit, MI, USA
| | - Ana C deCarvalho
- Department of Neurosurgery, Omics Laboratory, Hermelin Brain Tumor Center, Henry Ford Health, Detroit, MI, USA
| | - Laura A Hasselbach
- Department of Neurosurgery, Omics Laboratory, Hermelin Brain Tumor Center, Henry Ford Health, Detroit, MI, USA
| | - Kelly M Tundo
- Department of Neurosurgery, Omics Laboratory, Hermelin Brain Tumor Center, Henry Ford Health, Detroit, MI, USA
| | - Rehnuma Newaz
- Department of Neurosurgery, Omics Laboratory, Hermelin Brain Tumor Center, Henry Ford Health, Detroit, MI, USA
| | - Andrea Transou
- Department of Neurosurgery, Omics Laboratory, Hermelin Brain Tumor Center, Henry Ford Health, Detroit, MI, USA
| | - Natalia Morosini
- Department of Neurosurgery, Omics Laboratory, Hermelin Brain Tumor Center, Henry Ford Health, Detroit, MI, USA
| | - Victor Francisco
- Department of Neurosurgery, Omics Laboratory, Hermelin Brain Tumor Center, Henry Ford Health, Detroit, MI, USA
| | - Laila M Poisson
- Department of Neurosurgery, Omics Laboratory, Hermelin Brain Tumor Center, Henry Ford Health, Detroit, MI, USA
- Department of Public Health, Biostatistics, Henry Ford Health, Detroit, MI, USA
| | | | - Abir Mukherjee
- Department of Pathology, Henry Ford Health, Detroit, MI, USA
| | - Maritza S Mosella
- Department of Neurosurgery, Omics Laboratory, Hermelin Brain Tumor Center, Henry Ford Health, Detroit, MI, USA
| | - Adam M Robin
- Department of Neurosurgery, Omics Laboratory, Hermelin Brain Tumor Center, Henry Ford Health, Detroit, MI, USA
| | - Tobias Walbert
- Department of Neurosurgery, Omics Laboratory, Hermelin Brain Tumor Center, Henry Ford Health, Detroit, MI, USA
| | - Mark Rosenblum
- Department of Neurosurgery, Omics Laboratory, Hermelin Brain Tumor Center, Henry Ford Health, Detroit, MI, USA
| | - Tom Mikkelsen
- Department of Neurosurgery, Omics Laboratory, Hermelin Brain Tumor Center, Henry Ford Health, Detroit, MI, USA
| | - Steven Kalkanis
- Department of Neurosurgery, Omics Laboratory, Hermelin Brain Tumor Center, Henry Ford Health, Detroit, MI, USA
| | - Daniela P C Tirapelli
- Department of Neurosurgery, Ribeirao Preto Medical School, University of Sao Paulo, Ribeirao Preto, SP, Brazil
| | - Daniel J Weisenberger
- Department of Biochemistry and Molecular Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90033, USA
| | - Carlos G Carlotti
- Department of Neurosurgery, Ribeirao Preto Medical School, University of Sao Paulo, Ribeirao Preto, SP, Brazil
| | - Jack Rock
- Department of Neurosurgery, Omics Laboratory, Hermelin Brain Tumor Center, Henry Ford Health, Detroit, MI, USA
| | - Ana Valeria Castro
- Department of Neurosurgery, Omics Laboratory, Hermelin Brain Tumor Center, Henry Ford Health, Detroit, MI, USA.
- Department of Physiology, Michigan State University, E. Lansing, MI, USA.
| | - Houtan Noushmehr
- Department of Neurosurgery, Omics Laboratory, Hermelin Brain Tumor Center, Henry Ford Health, Detroit, MI, USA.
- Department of Physiology, Michigan State University, E. Lansing, MI, USA.
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