1
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Rengifo Rojas C, Cercy J, Perillous S, Gonthier-Guéret C, Montibus B, Maupetit-Méhouas S, Espinadel A, Dupré M, Hong CC, Hata K, Nakabayashi K, Plagge A, Bouschet T, Arnaud P, Vaillant I, Court F. Biallelic non-productive enhancer-promoter interactions precede imprinted expression of Kcnk9 during mouse neural commitment. HGG ADVANCES 2024; 5:100271. [PMID: 38297831 PMCID: PMC10869267 DOI: 10.1016/j.xhgg.2024.100271] [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: 10/17/2023] [Revised: 12/18/2023] [Accepted: 01/23/2024] [Indexed: 02/02/2024] Open
Abstract
It is only partially understood how constitutive allelic methylation at imprinting control regions (ICRs) interacts with other regulation levels to drive timely parental allele-specific expression along large imprinted domains. The Peg13-Kcnk9 domain is an imprinted domain with important brain functions. To gain insights into its regulation during neural commitment, we performed an integrative analysis of its allele-specific epigenetic, transcriptomic, and cis-spatial organization using a mouse stem cell-based corticogenesis model that recapitulates the control of imprinted gene expression during neurodevelopment. We found that, despite an allelic higher-order chromatin structure associated with the paternally CTCF-bound Peg13 ICR, enhancer-Kcnk9 promoter contacts occurred on both alleles, although they were productive only on the maternal allele. This observation challenges the canonical model in which CTCF binding isolates the enhancer and its target gene on either side and suggests a more nuanced role for allelic CTCF binding at some ICRs.
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Affiliation(s)
- Cecilia Rengifo Rojas
- Genetics, Reproduction and Development Institute (iGReD), CNRS, INSERM, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Jil Cercy
- Genetics, Reproduction and Development Institute (iGReD), CNRS, INSERM, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Sophie Perillous
- Genetics, Reproduction and Development Institute (iGReD), CNRS, INSERM, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Céline Gonthier-Guéret
- Genetics, Reproduction and Development Institute (iGReD), CNRS, INSERM, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Bertille Montibus
- Genetics, Reproduction and Development Institute (iGReD), CNRS, INSERM, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Stéphanie Maupetit-Méhouas
- Genetics, Reproduction and Development Institute (iGReD), CNRS, INSERM, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Astrid Espinadel
- Genetics, Reproduction and Development Institute (iGReD), CNRS, INSERM, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Marylou Dupré
- Genetics, Reproduction and Development Institute (iGReD), CNRS, INSERM, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Charles C Hong
- Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Kenichiro Hata
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, 2-10-1 Okura, Setagaya, Tokyo 157-8535, Japan; Department of Human Molecular Genetics, Gunma University Graduate School of Medicine 3-39-22 Showa, Maebashi, Gunma 371-8511, Japan
| | - Kazuhiko Nakabayashi
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, 2-10-1 Okura, Setagaya, Tokyo 157-8535, Japan
| | - Antonius Plagge
- Department of Biochemistry, Cell and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - Tristan Bouschet
- Institut de Génomique Fonctionnelle, CNRS, INSERM, Université de Montpellier, Montpellier, France
| | - Philippe Arnaud
- Genetics, Reproduction and Development Institute (iGReD), CNRS, INSERM, Université Clermont Auvergne, Clermont-Ferrand, France.
| | - Isabelle Vaillant
- Genetics, Reproduction and Development Institute (iGReD), CNRS, INSERM, Université Clermont Auvergne, Clermont-Ferrand, France.
| | - Franck Court
- Genetics, Reproduction and Development Institute (iGReD), CNRS, INSERM, Université Clermont Auvergne, Clermont-Ferrand, France.
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2
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Bomsztyk K, Mar D, Denisenko O, Powell S, Vishnoi M, Delegard J, Patel A, Ellenbogen RG, Ramakrishna R, Rostomily R. Analysis of gliomas DNA methylation: Assessment of pre-analytical variables. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.26.586350. [PMID: 38586048 PMCID: PMC10996653 DOI: 10.1101/2024.03.26.586350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
Precision oncology is driven by molecular biomarkers. For glioblastoma multiforme (GBM), the most common malignant adult primary brain tumor, O6-methylguanine-DNA methyltransferase ( MGMT ) gene DNA promoter methylation is an important prognostic and treatment clinical biomarker. Time consuming pre-analytical steps such as biospecimen storage before fixing, sampling, and processing are major sources of errors and batch effects, that are further confounded by intra-tumor heterogeneity of MGMT promoter methylation. To assess the effect of pre-analytical variables on GBM DNA methylation, tissue storage/sampling (CryoGrid), sample preparation multi-sonicator (PIXUL) and 5-methylcytosine (5mC) DNA immunoprecipitation (Matrix MeDIP-qPCR/seq) platforms were used. MGMT promoter CpG methylation was examined in 173 surgical samples from 90 individuals, 50 of these were used for intra-tumor heterogeneity studies. MGMT promoter methylation levels in paired frozen and formalin fixed paraffin embedded (FFPE) samples were very close, confirming suitability of FFPE for MGMT promoter methylation analysis in clinical settings. Matrix MeDIP-qPCR yielded similar results to methylation specific PCR (MS-PCR). Warm ex-vivo ischemia (37°C up to 4hrs) and 3 cycles of repeated sample thawing and freezing did not alter 5mC levels at MGMT promoter, exon and upstream enhancer regions, demonstrating the resistance of DNA methylation to the most common variations in sample processing conditions that might be encountered in research and clinical settings. 20-30% of specimens exhibited intratumor heterogeneity in the MGMT DNA promoter methylation. Collectively these data demonstrate that variations in sample fixation, ischemia duration and temperature, and DNA methylation assay technique do not have significant impact on assessment of MGMT promoter methylation status. However, intratumor methylation heterogeneity underscores the need for histologic verification and value of multiple biopsies at different GBM geographic tumor sites in assessment of MGMT promoter methylation. Matrix-MeDIP-seq analysis revealed that MGMT promoter methylation status clustered with other differentially methylated genomic loci (e.g. HOXA and lncRNAs), that are likewise resilient to variation in above post-resection pre-analytical conditions. These MGMT -associated global DNA methylation patterns offer new opportunities to validate more granular data-based epigenetic GBM clinical biomarkers where the CryoGrid-PIXUL-Matrix toolbox could prove to be useful.
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3
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Hu X, Wang Y, Zhang X, Li C, Zhang X, Yang D, Liu Y, Li L. DNA methylation of HOX genes and its clinical implications in cancer. Exp Mol Pathol 2023; 134:104871. [PMID: 37696326 DOI: 10.1016/j.yexmp.2023.104871] [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: 03/29/2023] [Revised: 09/06/2023] [Accepted: 09/08/2023] [Indexed: 09/13/2023]
Abstract
Homeobox (HOX) genes encode highly conserved transcription factors that play vital roles in embryonic development. DNA methylation is a pivotal regulatory epigenetic signaling mark responsible for regulating gene expression. Abnormal DNA methylation is largely associated with the aberrant expression of HOX genes, which is implicated in a broad range of human diseases, including cancer. Numerous studies have clarified the mechanisms of DNA methylation in both physiological and pathological processes. In this review, we focus on how DNA methylation regulates HOX genes and briefly discuss drug development approaches targeting these mechanisms.
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Affiliation(s)
- Xin Hu
- Department of Immunology, School of Clinical and Basic Medical Sciences, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan 250117, Shandong, China
| | - Yong Wang
- Shandong Xinchuang Biotechnology Co., LTD, Jinan 250102, Shandong, China; Laboratory of Precision Medicine, Zhangqiu District People's Hospital of Jinan, Jinan 250200, Shandong, China
| | - Xiaoyu Zhang
- Department of Immunology, School of Clinical and Basic Medical Sciences, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan 250117, Shandong, China
| | - Chensheng Li
- Department of Gastrointestinal Surgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan 250021, Shandong, China
| | - Xikun Zhang
- Department of Minimally Invasive Interventional, The Third Affiliated Hospital of Shandong First Medical University, Jinan 250031, Shandong, China
| | - Dongxia Yang
- Shandong Xinchuang Biotechnology Co., LTD, Jinan 250102, Shandong, China
| | - Yuanyuan Liu
- Shandong Xinchuang Biotechnology Co., LTD, Jinan 250102, Shandong, China
| | - Lianlian Li
- Department of Oncology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan 250021, Shandong, China; Department of Immunology, School of Clinical and Basic Medical Sciences, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan 250117, Shandong, China.
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4
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Feng L, Chen X, Sheng G, Li Y, Li Y, Zhang Y, Yao K, Wu Z, Zhang R, Kiboku T, Kawasaki A, Horimoto K, Tang Y, Sun M, Han F, Chen D. Synthesis and Bioevaluation of 3-(Arylmethylene)indole Derivatives: Discovery of a Novel ALK Modulator with Antiglioblastoma Activities. J Med Chem 2023; 66:14609-14622. [PMID: 37861443 DOI: 10.1021/acs.jmedchem.3c01090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2023]
Abstract
Glioblastoma is the most common brain tumor, with high recurrence and low survival rates. An integrative bioinformatics analysis demonstrated that anaplastic lymphoma kinase (ALK) is a promising therapeutic target for glioblastoma. We designed and synthesized a series of 3-(arylmethylene)indole derivatives, which were further evaluated for antiproliferative activity using glioma cell lines. Among them, compound 4a significantly inhibited the viability of glioblastoma cells. With favorable pharmacokinetic characteristics and blood-brain barrier permeability, 4a improved the survival rate and inhibited the growth of orthotopic glioblastoma. The Phospho-Totum system revealed that ALK was a potential target for the antiglioblastoma activity of 4a. Further experiments indicated that 4a might be a novel ALK modulator, which interacted with the extracellular ligand-binding domain of ALK, thus selectively induced ERK-mediated autophagy and apoptosis. Our findings provide an alternative ALK-based targeting strategy and a new drug candidate for glioblastoma therapy.
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Affiliation(s)
- Lili Feng
- Medical Basic Research Innovation Center for Cardiovascular and Cerebrovascular Diseases, Ministry of Education, China, International Joint Laboratory for Drug Target of Critical Illnesses, School of Pharmacy, Nanjing Medical University, Nanjing 211166, China
| | - Xiang Chen
- Medical Basic Research Innovation Center for Cardiovascular and Cerebrovascular Diseases, Ministry of Education, China, International Joint Laboratory for Drug Target of Critical Illnesses, School of Pharmacy, Nanjing Medical University, Nanjing 211166, China
| | - Gang Sheng
- Medical Basic Research Innovation Center for Cardiovascular and Cerebrovascular Diseases, Ministry of Education, China, International Joint Laboratory for Drug Target of Critical Illnesses, School of Pharmacy, Nanjing Medical University, Nanjing 211166, China
| | - Yingchun Li
- Medical Basic Research Innovation Center for Cardiovascular and Cerebrovascular Diseases, Ministry of Education, China, International Joint Laboratory for Drug Target of Critical Illnesses, School of Pharmacy, Nanjing Medical University, Nanjing 211166, China
| | - Yingying Li
- Medical Basic Research Innovation Center for Cardiovascular and Cerebrovascular Diseases, Ministry of Education, China, International Joint Laboratory for Drug Target of Critical Illnesses, School of Pharmacy, Nanjing Medical University, Nanjing 211166, China
| | - Yixuan Zhang
- Gusu School, Nanjing Medical University, Suzhou Municipal Hospital, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou 215001, China
| | - Kun Yao
- Laboratory of Medicinal Chemical Biology, Department of Medicinal Chemistry, College of Pharmaceutical Sciences, Soochow University, Suzhou 215006, China
| | - Zhouyue Wu
- Medical Basic Research Innovation Center for Cardiovascular and Cerebrovascular Diseases, Ministry of Education, China, International Joint Laboratory for Drug Target of Critical Illnesses, School of Pharmacy, Nanjing Medical University, Nanjing 211166, China
| | - Rong Zhang
- Medical Basic Research Innovation Center for Cardiovascular and Cerebrovascular Diseases, Ministry of Education, China, International Joint Laboratory for Drug Target of Critical Illnesses, School of Pharmacy, Nanjing Medical University, Nanjing 211166, China
| | | | | | - Katsuhisa Horimoto
- Socium Inc., Tokyo 1350064, Japan
- Artificial Intelligence Research Center, National Institute of Advanced Industrial Science and Technology, Tokyo 1350064, Japan
| | - Yamin Tang
- Medical Basic Research Innovation Center for Cardiovascular and Cerebrovascular Diseases, Ministry of Education, China, International Joint Laboratory for Drug Target of Critical Illnesses, School of Pharmacy, Nanjing Medical University, Nanjing 211166, China
| | - Meiling Sun
- Department of Physiology, School of Basic Medical Sciences, Nanjing Medical University, Nanjing 211166, China
| | - Feng Han
- Medical Basic Research Innovation Center for Cardiovascular and Cerebrovascular Diseases, Ministry of Education, China, International Joint Laboratory for Drug Target of Critical Illnesses, School of Pharmacy, Nanjing Medical University, Nanjing 211166, China
- Gusu School, Nanjing Medical University, Suzhou Municipal Hospital, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou 215001, China
- Institute of Brain Science, The Affiliated Brain Hospital of Nanjing Medical University, Nanjing 210029, China
| | - Dongyin Chen
- Medical Basic Research Innovation Center for Cardiovascular and Cerebrovascular Diseases, Ministry of Education, China, International Joint Laboratory for Drug Target of Critical Illnesses, School of Pharmacy, Nanjing Medical University, Nanjing 211166, China
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5
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Mamatjan Y, Voisin MR, Nassiri F, Moraes FY, Bunda S, So J, Salih M, Shirahata M, Ono T, Shimizu H, Schrimpf D, von Deimling A, Aldape KD, Zadeh G. Integrated molecular analysis reveals hypermethylation and overexpression of HOX genes to be poor prognosticators in isocitrate dehydrogenase mutant glioma. Neuro Oncol 2023; 25:2028-2041. [PMID: 37474126 PMCID: PMC10628942 DOI: 10.1093/neuonc/noad126] [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: 02/02/2023] [Indexed: 07/22/2023] Open
Abstract
BACKGROUND Diffuse gliomas represent over 80% of malignant brain tumors ranging from low-grade to aggressive high-grade lesions. Within isocitrate dehydrogenase (IDH)-mutant gliomas, there is a high variability in survival and a need to more accurately predict outcome. METHODS To identify and characterize a predictive signature of outcome in gliomas, we utilized an integrative molecular analysis (using methylation, mRNA, copy number variation (CNV), and mutation data), analyzing a total of 729 IDH-mutant samples including a test set of 99 from University Health Network (UHN) and 2 validation cohorts including the German Cancer Research Center (DKFZ) and The Cancer Genome Atlas (TCGA). RESULTS Cox regression analysis of methylation data from the UHN cohort identified CpG-based signatures that split the glioma cohort into 2 prognostic groups strongly predicting survival that were validated using 2 independent cohorts from TCGA and DKFZ (all P-values < .0001). The methylation signatures that predicted poor outcomes also exhibited high CNV instability and hypermethylation of HOX gene probes. Integrated multi-platform analyses using mRNA and methylation (iRM) showed that parallel HOX gene overexpression and simultaneous hypermethylation were significantly associated with increased mutational load, high aneuploidy, and worse survival (P-value < .0001). A 7-HOX gene signature was developed and validated using the most significantly associated HOX genes with patient outcome in both 1p/19q codeleted and non-codeleted IDHmut gliomas. CONCLUSIONS HOX gene methylation and expression provide important prognostic information in IDH-mutant gliomas that are not captured by current molecular diagnostics. A 7-HOX gene signature of outcome shows significant survival differences in both 1p/19q codeleted and non-codeleted IDH-mutant gliomas.
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Affiliation(s)
- Yasin Mamatjan
- Princess Margaret Cancer Center and MacFeeters-Hamilton Center for Neuro-Oncology Research, University Health Network, Toronto, Ontario, Canada
- Faculty of Science, Thompson Rivers University, Kamloops, British Columbia, Canada
| | - Mathew R Voisin
- Princess Margaret Cancer Center and MacFeeters-Hamilton Center for Neuro-Oncology Research, University Health Network, Toronto, Ontario, Canada
| | - Farshad Nassiri
- Princess Margaret Cancer Center and MacFeeters-Hamilton Center for Neuro-Oncology Research, University Health Network, Toronto, Ontario, Canada
| | - Fabio Y Moraes
- Department of Oncology, Queens University, Kingston, Ontario, Canada
| | - Severa Bunda
- Princess Margaret Cancer Center and MacFeeters-Hamilton Center for Neuro-Oncology Research, University Health Network, Toronto, Ontario, Canada
| | - Jonathan So
- Department of Medicine, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Mira Salih
- Mount Sinai Hospital, New York, New York, USA
- Department of Neuro-Oncology/Neurosurgery, Saitama Medical University International Medical Center, Hidaka, Japan
| | - Mitsuaki Shirahata
- Department of Neuro-Oncology/Neurosurgery, Saitama Medical University International Medical Center, Hidaka, Japan
| | - Takahiro Ono
- Department of Neurosurgery, Akita University Graduate School of Medicine, Akita, Japan
| | - Hiroaki Shimizu
- Department of Neurosurgery, Akita University Graduate School of Medicine, Akita, Japan
| | - Daniel Schrimpf
- Department of Neuropathology, Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Andreas von Deimling
- Department of Neuropathology, Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Kenneth D Aldape
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA
| | - Gelareh Zadeh
- Princess Margaret Cancer Center and MacFeeters-Hamilton Center for Neuro-Oncology Research, University Health Network, Toronto, Ontario, Canada
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6
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Ajuyah P, Mayoh C, Lau LMS, Barahona P, Wong M, Chambers H, Valdes-Mora F, Senapati A, Gifford AJ, D'Arcy C, Hansford JR, Manoharan N, Nicholls W, Williams MM, Wood PJ, Cowley MJ, Tyrrell V, Haber M, Ekert PG, Ziegler DS, Khuong-Quang DA. Histone H3-wild type diffuse midline gliomas with H3K27me3 loss are a distinct entity with exclusive EGFR or ACVR1 mutation and differential methylation of homeobox genes. Sci Rep 2023; 13:3775. [PMID: 36882456 PMCID: PMC9992705 DOI: 10.1038/s41598-023-30395-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 02/22/2023] [Indexed: 03/09/2023] Open
Abstract
Diffuse midline gliomas (DMG) harbouring H3K27M mutation are paediatric tumours with a dismal outcome. Recently, a new subtype of midline gliomas has been described with similar features to DMG, including loss of H3K27 trimethylation, but lacking the canonical H3K27M mutation (H3-WT). Here, we report a cohort of five H3-WT tumours profiled by whole-genome sequencing, RNA sequencing and DNA methylation profiling and combine their analysis with previously published cases. We show that these tumours have recurrent and mutually exclusive mutations in either ACVR1 or EGFR and are characterised by high expression of EZHIP associated to its promoter hypomethylation. Affected patients share a similar poor prognosis as patients with H3K27M DMG. Global molecular analysis of H3-WT and H3K27M DMG reveal distinct transcriptome and methylome profiles including differential methylation of homeobox genes involved in development and cellular differentiation. Patients have distinct clinical features, with a trend demonstrating ACVR1 mutations occurring in H3-WT tumours at an older age. This in-depth exploration of H3-WT tumours further characterises this novel DMG, H3K27-altered sub-group, characterised by a specific immunohistochemistry profile with H3K27me3 loss, wild-type H3K27M and positive EZHIP. It also gives new insights into the possible mechanism and pathway regulation in these tumours, potentially opening new therapeutic avenues for these tumours which have no known effective treatment. This study has been retrospectively registered on clinicaltrial.gov on 8 November 2017 under the registration number NCT03336931 ( https://clinicaltrials.gov/ct2/show/NCT03336931 ).
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Affiliation(s)
- Pamela Ajuyah
- Lowy Cancer Research Centre, Children's Cancer Institute, UNSW Sydney, Kensington, NSW, Australia
| | - Chelsea Mayoh
- Lowy Cancer Research Centre, Children's Cancer Institute, UNSW Sydney, Kensington, NSW, Australia.,School of Clinical Medicine, UNSW Medicine & Health, UNSW Sydney, Kensington, NSW, Australia.,University of New South Wales Centre for Childhood Cancer Research, UNSW, Kensington, NSW, Australia
| | - Loretta M S Lau
- Lowy Cancer Research Centre, Children's Cancer Institute, UNSW Sydney, Kensington, NSW, Australia.,School of Clinical Medicine, UNSW Medicine & Health, UNSW Sydney, Kensington, NSW, Australia.,University of New South Wales Centre for Childhood Cancer Research, UNSW, Kensington, NSW, Australia.,Kids Cancer Centre, Sydney Children's Hospital, High Street, Randwick, NSW, 2031, Australia
| | - Paulette Barahona
- Lowy Cancer Research Centre, Children's Cancer Institute, UNSW Sydney, Kensington, NSW, Australia
| | - Marie Wong
- Lowy Cancer Research Centre, Children's Cancer Institute, UNSW Sydney, Kensington, NSW, Australia.,School of Clinical Medicine, UNSW Medicine & Health, UNSW Sydney, Kensington, NSW, Australia.,University of New South Wales Centre for Childhood Cancer Research, UNSW, Kensington, NSW, Australia
| | - Hazel Chambers
- Department of Anatomical Pathology, Royal Children's Hospital, University of Melbourne, Melbourne, VIC, Australia
| | - Fatima Valdes-Mora
- Lowy Cancer Research Centre, Children's Cancer Institute, UNSW Sydney, Kensington, NSW, Australia.,School of Clinical Medicine, UNSW Medicine & Health, UNSW Sydney, Kensington, NSW, Australia
| | - Akanksha Senapati
- Kids Cancer Centre, Sydney Children's Hospital, High Street, Randwick, NSW, 2031, Australia
| | - Andrew J Gifford
- Lowy Cancer Research Centre, Children's Cancer Institute, UNSW Sydney, Kensington, NSW, Australia.,School of Clinical Medicine, UNSW Medicine & Health, UNSW Sydney, Kensington, NSW, Australia.,Anatomical Pathology, NSW Health Pathology, Prince of Wales Hospital, Randwick, NSW, Australia
| | - Colleen D'Arcy
- Department of Anatomical Pathology, Royal Children's Hospital, University of Melbourne, Melbourne, VIC, Australia
| | - Jordan R Hansford
- Children's Cancer Centre, Royal Children's Hospital, 50 Flemington Road, Parkville, VIC, 3052, Australia.,Murdoch Children's Research Institute, Royal Children's Hospital, Parkville, VIC, Australia.,Department of Paediatrics, University of Melbourne, Parkville, VIC, Australia.,Michael Rice Cancer Centre, Women's and Children's Hospital, Adelaide, SA, Australia.,South Australia Health and Medical Research Institute, Adelaide, SA, Australia.,South Australia Immunogenomics Cancer Institute, Adelaide, SA, Australia.,University of Adelaide, Adelaide, SA, Australia
| | - Neevika Manoharan
- School of Clinical Medicine, UNSW Medicine & Health, UNSW Sydney, Kensington, NSW, Australia.,Kids Cancer Centre, Sydney Children's Hospital, High Street, Randwick, NSW, 2031, Australia
| | - Wayne Nicholls
- Oncology Service, Children's Health Queensland Hospital & Health Service, Brisbane, QLD, Australia
| | - Molly M Williams
- Children's Cancer Centre, Royal Children's Hospital, 50 Flemington Road, Parkville, VIC, 3052, Australia
| | - Paul J Wood
- Department of Paediatrics, School of Clinical Sciences at Monash Health, Monash University, Clayton, VIC, Australia
| | - Mark J Cowley
- Lowy Cancer Research Centre, Children's Cancer Institute, UNSW Sydney, Kensington, NSW, Australia.,School of Clinical Medicine, UNSW Medicine & Health, UNSW Sydney, Kensington, NSW, Australia.,University of New South Wales Centre for Childhood Cancer Research, UNSW, Kensington, NSW, Australia
| | - Vanessa Tyrrell
- Lowy Cancer Research Centre, Children's Cancer Institute, UNSW Sydney, Kensington, NSW, Australia.,School of Clinical Medicine, UNSW Medicine & Health, UNSW Sydney, Kensington, NSW, Australia
| | - Michelle Haber
- Lowy Cancer Research Centre, Children's Cancer Institute, UNSW Sydney, Kensington, NSW, Australia.,School of Clinical Medicine, UNSW Medicine & Health, UNSW Sydney, Kensington, NSW, Australia.,University of New South Wales Centre for Childhood Cancer Research, UNSW, Kensington, NSW, Australia
| | - Paul G Ekert
- Lowy Cancer Research Centre, Children's Cancer Institute, UNSW Sydney, Kensington, NSW, Australia.,School of Clinical Medicine, UNSW Medicine & Health, UNSW Sydney, Kensington, NSW, Australia.,University of New South Wales Centre for Childhood Cancer Research, UNSW, Kensington, NSW, Australia.,Cancer Immunology Program, Peter MacCallum Cancer Centre, Parkville, VIC, Australia.,The Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC, Australia
| | - David S Ziegler
- Lowy Cancer Research Centre, Children's Cancer Institute, UNSW Sydney, Kensington, NSW, Australia. .,School of Clinical Medicine, UNSW Medicine & Health, UNSW Sydney, Kensington, NSW, Australia. .,University of New South Wales Centre for Childhood Cancer Research, UNSW, Kensington, NSW, Australia. .,Kids Cancer Centre, Sydney Children's Hospital, High Street, Randwick, NSW, 2031, Australia.
| | - Dong-Anh Khuong-Quang
- Children's Cancer Centre, Royal Children's Hospital, 50 Flemington Road, Parkville, VIC, 3052, Australia. .,Murdoch Children's Research Institute, Royal Children's Hospital, Parkville, VIC, Australia.
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7
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Ervin EH, French R, Chang CH, Pauklin S. Inside the stemness engine: Mechanistic links between deregulated transcription factors and stemness in cancer. Semin Cancer Biol 2022; 87:48-83. [PMID: 36347438 DOI: 10.1016/j.semcancer.2022.11.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 10/22/2022] [Accepted: 11/03/2022] [Indexed: 11/07/2022]
Abstract
Cell identity is largely determined by its transcriptional profile. In tumour, deregulation of transcription factor expression and/or activity enables cancer cell to acquire a stem-like state characterised by capacity to self-renew, differentiate and form tumours in vivo. These stem-like cancer cells are highly metastatic and therapy resistant, thus warranting a more complete understanding of the molecular mechanisms downstream of the transcription factors that mediate the establishment of stemness state. Here, we review recent research findings that provide a mechanistic link between the commonly deregulated transcription factors and stemness in cancer. In particular, we describe the role of master transcription factors (SOX, OCT4, NANOG, KLF, BRACHYURY, SALL, HOX, FOX and RUNX), signalling-regulated transcription factors (SMAD, β-catenin, YAP, TAZ, AP-1, NOTCH, STAT, GLI, ETS and NF-κB) and unclassified transcription factors (c-MYC, HIF, EMT transcription factors and P53) across diverse tumour types, thereby yielding a comprehensive overview identifying shared downstream targets, highlighting unique mechanisms and discussing complexities.
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Affiliation(s)
- Egle-Helene Ervin
- Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Old Road, Headington, Oxford, OX3 7LD, United Kingdom.
| | - Rhiannon French
- Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Old Road, Headington, Oxford, OX3 7LD, United Kingdom.
| | - Chao-Hui Chang
- Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Old Road, Headington, Oxford, OX3 7LD, United Kingdom.
| | - Siim Pauklin
- Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Old Road, Headington, Oxford, OX3 7LD, United Kingdom.
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8
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K27M in canonical and noncanonical H3 variants occurs in distinct oligodendroglial cell lineages in brain midline gliomas. Nat Genet 2022; 54:1865-1880. [PMID: 36471070 PMCID: PMC9742294 DOI: 10.1038/s41588-022-01205-w] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Accepted: 09/16/2022] [Indexed: 12/12/2022]
Abstract
Canonical (H3.1/H3.2) and noncanonical (H3.3) histone 3 K27M-mutant gliomas have unique spatiotemporal distributions, partner alterations and molecular profiles. The contribution of the cell of origin to these differences has been challenging to uncouple from the oncogenic reprogramming induced by the mutation. Here, we perform an integrated analysis of 116 tumors, including single-cell transcriptome and chromatin accessibility, 3D chromatin architecture and epigenomic profiles, and show that K27M-mutant gliomas faithfully maintain chromatin configuration at developmental genes consistent with anatomically distinct oligodendrocyte precursor cells (OPCs). H3.3K27M thalamic gliomas map to prosomere 2-derived lineages. In turn, H3.1K27M ACVR1-mutant pontine gliomas uniformly mirror early ventral NKX6-1+/SHH-dependent brainstem OPCs, whereas H3.3K27M gliomas frequently resemble dorsal PAX3+/BMP-dependent progenitors. Our data suggest a context-specific vulnerability in H3.1K27M-mutant SHH-dependent ventral OPCs, which rely on acquisition of ACVR1 mutations to drive aberrant BMP signaling required for oncogenesis. The unifying action of K27M mutations is to restrict H3K27me3 at PRC2 landing sites, whereas other epigenetic changes are mainly contingent on the cell of origin chromatin state and cycling rate.
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9
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Hirtz A, Lebourdais N, Thomassin M, Rech F, Dumond H, Dubois-Pot-Schneider H. Identification of Gender- and Subtype-Specific Gene Expression Associated with Patient Survival in Low-Grade and Anaplastic Glioma in Connection with Steroid Signaling. Cancers (Basel) 2022; 14:cancers14174114. [PMID: 36077653 PMCID: PMC9454517 DOI: 10.3390/cancers14174114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 08/14/2022] [Accepted: 08/20/2022] [Indexed: 11/16/2022] Open
Abstract
Simple Summary Gliomas are primary brain tumors that are initially slow growing but progress to be more aggressive and, ultimately, fatal within a few years. They are more common in men than in women, suggesting a protective role for female hormones. By analyzing patient data collected in the public TGCA-LGG database, we have demonstrated a link between the expression level of key steroid biosynthesis enzymes or hormone receptors with patient survival, in ways that are dependent on gender and molecular subtype. We also determined the genes which expression associated with these actors of steroid signaling and the functions they perform, to decipher the mechanisms underlying gender-dependent differences. Together, these results establish, for the first time, the involvement of hormones in low-grade and anaplastic gliomas and provide clues for refining their classification and, thus, facilitating more personalized management of patients. Abstract Low-grade gliomas are rare primary brain tumors, which fatally evolve to anaplastic gliomas. The current treatment combines surgery, chemotherapy, and radiotherapy. If gender differences in the natural history of the disease were widely described, their underlying mechanisms remain to be determined for the identification of reliable markers of disease progression. We mined the transcriptomic and clinical data from the TCGA-LGG and CGGA databases to identify male-over-female differentially expressed genes and selected those associated with patient survival using univariate analysis, depending on molecular characteristics (IDH wild-type/mutated; 1p/19q codeleted/not) and grade. Then, the link between the expression levels (low or high) of the steroid biosynthesis enzyme or receptors of interest and survival was studied using the log-rank test. Finally, a functional analysis of gender-specific correlated genes was performed. HOX-related genes appeared to be differentially expressed between males and females in both grades, suggesting that a glioma could originate in perturbation of developmental signals. Moreover, aromatase, androgen, and estrogen receptor expressions were associated with patient survival and were mainly related to angiogenesis or immune response. Therefore, consideration of the tight control of steroid hormone production and signaling seems crucial for the understanding of glioma pathogenesis and emergence of future targeted therapies.
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Affiliation(s)
- Alex Hirtz
- Université de Lorraine, CNRS, CRAN, F-54000 Nancy, France
| | | | | | - Fabien Rech
- Université de Lorraine, CNRS, CRAN, F-54000 Nancy, France
- Université de Lorraine, CHRU-Nancy, Service de Neurochirurgie, F-54000 Nancy, France
| | - Hélène Dumond
- Université de Lorraine, CNRS, CRAN, F-54000 Nancy, France
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MEOX2 Regulates the Growth and Survival of Glioblastoma Stem Cells by Modulating Genes of the Glycolytic Pathway and Response to Hypoxia. Cancers (Basel) 2022; 14:cancers14092304. [PMID: 35565433 PMCID: PMC9099809 DOI: 10.3390/cancers14092304] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 05/03/2022] [Accepted: 05/04/2022] [Indexed: 02/04/2023] Open
Abstract
Simple Summary Glioblastoma is the most common incurable primary brain tumor in adults, typically leading to death within 15 months of diagnosis. Although there is an ongoing debate in the scientific community about the precise cellular origin of this tumor, glioblastoma stem cells (GSCs), which are able to self-renew, yield a full tumor mass, and determine chemo- and radio-resistance, are recognized to have a pivotal role. Our research aims to understand the role of the mesenchyme homeobox 2 (MEOX2) transcription factor in GSCs where it is strongly and specifically expressed. We have found that MEOX2 is indeed important for the survival of these cells. In fact, when we reduce its expression in two different GSC lines, they undergo a massive death accompanied by the inhibition of key genes of the glycolytic metabolism, the main source of energy for these cells. Our results reveal a novel function for MEOX2 in glioblastoma and suggest a mechanism through which GSCs may survive even in unfavorable conditions. Abstract The most widely accepted hypothesis for the development of glioblastoma suggests that glioblastoma stem-like cells (GSCs) are crucially involved in tumor initiation and recurrence as well as in the occurrence of chemo- and radio-resistance. Mesenchyme homeobox 2 (MEOX2) is a transcription factor overexpressed in glioblastoma, whose expression is negatively correlated with patient survival. Starting from our observation that MEOX2 expression is strongly enhanced in six GSC lines, we performed shRNA-mediated knock-down experiments in two different GSC lines and found that MEOX2 depletion resulted in the inhibition of cell growth and sphere-forming ability and an increase in apoptotic cell death. By a deep transcriptome analysis, we identified a core group of genes modulated in response to MEOX2 knock-down. Among these genes, the repressed ones are largely enriched in genes involved in the hypoxic response and glycolytic pathway, two strictly related pathways that contribute to the resistance of high-grade gliomas to therapies. An in silico study of the regulatory regions of genes differentially expressed by MEOX2 knock-down revealed that they mainly consisted of GC-rich regions enriched for Sp1 and Klf4 binding motifs, two main regulators of metabolism in glioblastoma. Our results show, for the first time, the involvement of MEOX2 in the regulation of genes of GSC metabolism, which is essential for the survival and growth of these cells.
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11
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Le Boiteux E, Guichet PO, Masliantsev K, Montibus B, Vaurs-Barriere C, Gonthier-Gueret C, Chautard E, Verrelle P, Karayan-Tapon L, Fogli A, Court F, Arnaud P. The Long Non-Coding RNA HOXA-AS2 Promotes Proliferation of Glioma Stem Cells and Modulates Their Inflammation Pathway Mainly through Post-Transcriptional Regulation. Int J Mol Sci 2022; 23:ijms23094743. [PMID: 35563134 PMCID: PMC9102906 DOI: 10.3390/ijms23094743] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 04/15/2022] [Accepted: 04/22/2022] [Indexed: 12/21/2022] Open
Abstract
Glioblastomas represent approximatively half of all gliomas and are the most deadly and aggressive form. Their therapeutic resistance and tumor relapse rely on a subpopulation of cells that are called Glioma Stem Cells (GSCs). Here, we investigated the role of the long non-coding RNA HOXA-AS2 in GSC biology using descriptive and functional analyses of glioma samples classified according to their isocitrate dehydrogenase (IDH) gene mutation status, and of GSC lines. We found that HOXA-AS2 is overexpressed only in aggressive (IDHwt) glioma and GSC lines. ShRNA-based depletion of HOXA-AS2 in GSCs decreased cell proliferation and altered the expression of several hundreds of genes. Integrative analysis revealed that these expression changes were not associated with changes in DNA methylation or chromatin signatures at the promoter of the majority of genes deregulated following HOXA-AS2 silencing in GSCs, suggesting a post-transcriptional regulation. In addition, transcription factor binding motif enrichment and correlation analyses indicated that HOXA-AS2 affects, directly or indirectly, the expression of key transcription factors implicated in GCS biology, including E2F8, E2F1, STAT1, and ATF3, thus contributing to GCS aggressiveness by promoting their proliferation and modulating the inflammation pathway.
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Affiliation(s)
- Elisa Le Boiteux
- Université Clermont Auvergne, CNRS, Inserm, GReD, F-63000 Clermont-Ferrand, France; (E.L.B.); (B.M.); (C.V.-B.); (C.G.-G.); (A.F.)
| | - Pierre-Olivier Guichet
- ProDiCeT UR 24144, Université de Poitiers, F-86000 Poitiers, France; (P.-O.G.); (K.M.); (L.K.-T.)
- Laboratoire de Cancérologie Biologique, CHU de Poitiers, F-86000 Poitiers, France
| | - Konstantin Masliantsev
- ProDiCeT UR 24144, Université de Poitiers, F-86000 Poitiers, France; (P.-O.G.); (K.M.); (L.K.-T.)
- Laboratoire de Cancérologie Biologique, CHU de Poitiers, F-86000 Poitiers, France
| | - Bertille Montibus
- Université Clermont Auvergne, CNRS, Inserm, GReD, F-63000 Clermont-Ferrand, France; (E.L.B.); (B.M.); (C.V.-B.); (C.G.-G.); (A.F.)
| | - Catherine Vaurs-Barriere
- Université Clermont Auvergne, CNRS, Inserm, GReD, F-63000 Clermont-Ferrand, France; (E.L.B.); (B.M.); (C.V.-B.); (C.G.-G.); (A.F.)
| | - Céline Gonthier-Gueret
- Université Clermont Auvergne, CNRS, Inserm, GReD, F-63000 Clermont-Ferrand, France; (E.L.B.); (B.M.); (C.V.-B.); (C.G.-G.); (A.F.)
| | - Emmanuel Chautard
- Pathology Department, Jean Perrin Center, F-63000 Clermont-Ferrand, France;
- INSERM, U1240 IMoST, Université Clermont Auvergne, F-63000 Clermont-Ferrand, France
| | - Pierre Verrelle
- CIMB, INSERM U1196 CNRS UMR9187, Curie Institute, F-91400 Orsay, France;
- Radiotherapy Department, Curie Institute, F-75248 Paris, France
- CNRS UMR 9187, INSERM U1196, Institut Curie, PSL Research University and Paris-Saclay University, F-91405 Orsay, France
| | - Lucie Karayan-Tapon
- ProDiCeT UR 24144, Université de Poitiers, F-86000 Poitiers, France; (P.-O.G.); (K.M.); (L.K.-T.)
- Laboratoire de Cancérologie Biologique, CHU de Poitiers, F-86000 Poitiers, France
| | - Anne Fogli
- Université Clermont Auvergne, CNRS, Inserm, GReD, F-63000 Clermont-Ferrand, France; (E.L.B.); (B.M.); (C.V.-B.); (C.G.-G.); (A.F.)
- Radiation Oncology Department, Institut Curie, F-75005 Paris, France
| | - Franck Court
- Université Clermont Auvergne, CNRS, Inserm, GReD, F-63000 Clermont-Ferrand, France; (E.L.B.); (B.M.); (C.V.-B.); (C.G.-G.); (A.F.)
- Correspondence: (F.C.); (P.A.)
| | - Philippe Arnaud
- Université Clermont Auvergne, CNRS, Inserm, GReD, F-63000 Clermont-Ferrand, France; (E.L.B.); (B.M.); (C.V.-B.); (C.G.-G.); (A.F.)
- Correspondence: (F.C.); (P.A.)
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12
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Pinson ME, Court F, Masson A, Renaud Y, Fantini A, Bacoeur-Ouzillou O, Barriere M, Pereira B, Guichet PO, Chautard E, Karayan-Tapon L, Verrelle P, Arnaud P, Vaurs-Barrière C. L1 chimeric transcripts are expressed in healthy brain and their deregulation in glioma follows that of their host locus. Hum Mol Genet 2022; 31:2606-2622. [PMID: 35298627 PMCID: PMC9396940 DOI: 10.1093/hmg/ddac056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 02/18/2022] [Accepted: 03/03/2022] [Indexed: 11/30/2022] Open
Abstract
Besides the consequences of retrotransposition, long interspersed element 1 (L1) retrotransposons can affect the host genome through their antisense promoter. In addition to the sense promoter, the evolutionarily recent L1 retrotransposons, which are present in several thousand copies, also possess an anti-sense promoter that can produce L1 chimeric transcripts (LCT) composed of the L1 5′ UTR followed by the adjacent genomic sequence. The full extent to which LCT expression occurs in a given tissue and whether disruption of the defense mechanisms that normally control L1 retrotransposons affects their expression and function in cancer cells, remain to be established. By using CLIFinder, a dedicated bioinformatics tool, we found that LCT expression was widespread in normal brain and aggressive glioma samples, and that approximately 17% of recent L1 retrotransposons, from the L1PA1 to L1PA7 subfamilies, were involved in their production. Importantly, the transcriptional activities of the L1 antisense promoters and of their host loci were coupled. Accordingly, we detected LCT-producing L1 retrotransposons mainly in transcriptionally active genes and genomic loci. Moreover, changes in the host genomic locus expression level in glioma were associated with a similar change in LCT expression level, regardless of the L1 promoter methylation status. Our findings support a model in which the host genomic locus transcriptional activity is the main driving force of LCT expression. We hypothesize that this model is more applicable when host gene and LCT are transcribed from the same strand.
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Affiliation(s)
- Marie-Elisa Pinson
- Université Clermont Auvergne, CNRS, Inserm, iGReD, F-63000 Clermont-Ferrand, France
| | - Franck Court
- Université Clermont Auvergne, CNRS, Inserm, iGReD, F-63000 Clermont-Ferrand, France
| | - Aymeric Masson
- Université Clermont Auvergne, CNRS, Inserm, iGReD, F-63000 Clermont-Ferrand, France
| | - Yoan Renaud
- Université Clermont Auvergne, CNRS, Inserm, iGReD, F-63000 Clermont-Ferrand, France
| | - Allison Fantini
- Université Clermont Auvergne, CNRS, Inserm, iGReD, F-63000 Clermont-Ferrand, France
| | | | - Marie Barriere
- Université Clermont Auvergne, CNRS, Inserm, iGReD, F-63000 Clermont-Ferrand, France
| | - Bruno Pereira
- Biostatistics Department, Délégation à la Recherche Clinique et à l'Innovation, Clermont-Ferrand Hospital, Clermont-Ferrand 63003, France
| | | | - Emmanuel Chautard
- Université Clermont Auvergne, INSERM, U1240 IMoST, Clermont-Ferrand 63011, France.,Pathology Department, Centre Jean PERRIN, Clermont-Ferrand 63011, France
| | - Lucie Karayan-Tapon
- Cancer Biology Department, CHU de Poitiers, Poitiers 86021, France.,INSERM, U1084, Poitiers 86021, France.,Université de Poitiers, Poitiers 86000, France
| | - Pierre Verrelle
- INSERM, U1196 CNRS UMR9187, Curie Institute, Orsay 91405, France.,Radiotherapy Department Curie Institute, Paris 75005, France.,Université Clermont Auvergne, Clermont-Ferrand 63000, France
| | - Philippe Arnaud
- Université Clermont Auvergne, CNRS, Inserm, iGReD, F-63000 Clermont-Ferrand, France
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Desaulniers D, Vasseur P, Jacobs A, Aguila MC, Ertych N, Jacobs MN. Integration of Epigenetic Mechanisms into Non-Genotoxic Carcinogenicity Hazard Assessment: Focus on DNA Methylation and Histone Modifications. Int J Mol Sci 2021; 22:10969. [PMID: 34681626 PMCID: PMC8535778 DOI: 10.3390/ijms222010969] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 09/30/2021] [Accepted: 10/04/2021] [Indexed: 12/15/2022] Open
Abstract
Epigenetics involves a series of mechanisms that entail histone and DNA covalent modifications and non-coding RNAs, and that collectively contribute to programing cell functions and differentiation. Epigenetic anomalies and DNA mutations are co-drivers of cellular dysfunctions, including carcinogenesis. Alterations of the epigenetic system occur in cancers whether the initial carcinogenic events are from genotoxic (GTxC) or non-genotoxic (NGTxC) carcinogens. NGTxC are not inherently DNA reactive, they do not have a unifying mode of action and as yet there are no regulatory test guidelines addressing mechanisms of NGTxC. To fil this gap, the Test Guideline Programme of the Organisation for Economic Cooperation and Development is developing a framework for an integrated approach for the testing and assessment (IATA) of NGTxC and is considering assays that address key events of cancer hallmarks. Here, with the intent of better understanding the applicability of epigenetic assays in chemical carcinogenicity assessment, we focus on DNA methylation and histone modifications and review: (1) epigenetic mechanisms contributing to carcinogenesis, (2) epigenetic mechanisms altered following exposure to arsenic, nickel, or phenobarbital in order to identify common carcinogen-specific mechanisms, (3) characteristics of a series of epigenetic assay types, and (4) epigenetic assay validation needs in the context of chemical hazard assessment. As a key component of numerous NGTxC mechanisms of action, epigenetic assays included in IATA assay combinations can contribute to improved chemical carcinogen identification for the better protection of public health.
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Affiliation(s)
- Daniel Desaulniers
- Environmental Health Sciences and Research Bureau, Hazard Identification Division, Health Canada, AL:2203B, Ottawa, ON K1A 0K9, Canada
| | - Paule Vasseur
- CNRS, LIEC, Université de Lorraine, 57070 Metz, France;
| | - Abigail Jacobs
- Independent at the Time of Publication, Previously US Food and Drug Administration, Rockville, MD 20852, USA;
| | - M. Cecilia Aguila
- Toxicology Team, Division of Human Food Safety, Center for Veterinary Medicine, US Food and Drug Administration, Department of Health and Human Services, Rockville, MD 20852, USA;
| | - Norman Ertych
- German Centre for the Protection of Laboratory Animals (Bf3R), German Federal Institute for Risk Assessment, Diedersdorfer Weg 1, 12277 Berlin, Germany;
| | - Miriam N. Jacobs
- Centre for Radiation, Chemical and Environmental Hazards, Public Health England, Chilton OX11 0RQ, UK;
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14
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Sun H, Wang Y, Wang Y, Ji F, Wang A, Yang M, He X, Li L. Bivalent Regulation and Related Mechanisms of H3K4/27/9me3 in Stem Cells. Stem Cell Rev Rep 2021; 18:165-178. [PMID: 34417934 DOI: 10.1007/s12015-021-10234-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/31/2021] [Indexed: 12/24/2022]
Abstract
The "bivalent domain" is a unique histone modification region consisting of two histone tri-methylation modifications. Over the years, it has been revealed that the maintenance and dynamic changes of the bivalent domains play a vital regulatory role in the differentiation of various stem cell systems, as well as in other cells, such as immunomodulation. Tri-methylation modifications involved in the formation of the bivalent domains are interrelated and mutually regulated, thus regulating many life processes of cells. Tri-methylation of histone H3 at lysine 4 (H3K4me3), tri-methylation of histone H3 at lysine 9 (H3K9me3) and tri-methylation of histone H3 at lysine 27 (H3K27me3) are the main tri-methylation modifications involved in the formation of bivalent domains. The three form different bivalent domains in pairs. Furthermore, it is equally clear that H3K4me3 is a positive regulator of transcription and that H3K9me3/H3K27me3 are negative regulators. Enzymes related to the regulation of histone methylation play a significant role in the "homeostasis" and "breaking homeostasis" of the bivalent domains. Bivalent domains regulate target genes, upstream transcription, downstream targeting regulation and related cytokines during the establishment and breakdown of homeostasis, and exert the specific regulation of stem cells. Indeed, a unified mechanism to explain the bivalent modification in all stem cells has been difficult to define, and whether the bivalent modification is antagonistic in inducing the differentiation of homologous stem cells is controversial. In this review, we focus on the different bivalent modifications in several key stem cells and explore the main mechanisms and effects of these modifications involved. Finally, we discussed the close relationship between bivalent domains and immune cells, and put forward the prospect of the application of bivalent domains in the field of stem cells.
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Affiliation(s)
- Han Sun
- The Key Laboratory of Pathobiology, Ministry of Education, College of Basic Medical Sciences, Jilin University, Changchun, 130021, China
| | - Yin Wang
- The Key Laboratory of Pathobiology, Ministry of Education, College of Basic Medical Sciences, Jilin University, Changchun, 130021, China
| | - Ying Wang
- The Key Laboratory of Pathobiology, Ministry of Education, College of Basic Medical Sciences, Jilin University, Changchun, 130021, China
| | - Feng Ji
- The Key Laboratory of Pathobiology, Ministry of Education, College of Basic Medical Sciences, Jilin University, Changchun, 130021, China
| | - An Wang
- The Key Laboratory of Pathobiology, Ministry of Education, College of Basic Medical Sciences, Jilin University, Changchun, 130021, China
| | - Ming Yang
- Department of Molecular Biology, College of Basic Medical Sciences, Jilin University, Changchun, 130021, China.
| | - Xu He
- The Key Laboratory of Pathobiology, Ministry of Education, College of Basic Medical Sciences, Jilin University, Changchun, 130021, China.
| | - Lisha Li
- The Key Laboratory of Pathobiology, Ministry of Education, College of Basic Medical Sciences, Jilin University, Changchun, 130021, China.
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15
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Bogeska R. HOX gene regulation in glioma stem cells, mediators of resistance in breast cancer, and paradoxical therapeutic interventions. Mol Oncol 2021; 15:1973-1974. [PMID: 34346179 PMCID: PMC8333774 DOI: 10.1002/1878-0261.13059] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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