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Yao J, Yao P, Li Y, He K, Ma X, Yang Q, Jia J, Chen Z, Yu S, Gu S, Chen K, Zhao Y, Li W, Wang G, Guo M. Integration of multi-omics data revealed the orphan CpG islands and enhancer-dominated c is-regulatory network in glioma. iScience 2024; 27:110946. [PMID: 39391717 PMCID: PMC11465130 DOI: 10.1016/j.isci.2024.110946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Revised: 07/12/2024] [Accepted: 09/10/2024] [Indexed: 10/12/2024] Open
Abstract
The complex transcriptional regulatory network leads to the poor prognosis of glioma. The role of orphan CpG islands (oCGIs) in the transcriptional regulatory network has been overlooked. We conducted a comprehensive exploration of the cis-regulatory roles of oCGIs and enhancers by integrating multi-omics data. Direct regulation of target genes by oCGIs or enhancers is of great importance in the cis-regulatory network. Furthermore, based on single-cell multi-omics data, we found that the highly activated cis-regulatory network in cluster 2 (C2) sustains the high proliferative potential of glioma cells. The upregulation of oCGIs and enhancers related genes in C2 results in glioma patients exhibiting resistance to radiotherapy and chemotherapy. These findings were further validated through glioma cell line related experiments. Our study offers insight into the pathogenesis of glioma and provides a strategy to treat this challenging disease.
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Affiliation(s)
- Jiawei Yao
- Department of Neurosurgery, The Second Affiliated Hospital of Harbin Medical University, Harbin 150086, China
| | - Penglei Yao
- Department of Neurosurgery, The Second Affiliated Hospital of Harbin Medical University, Harbin 150086, China
| | - Yang Li
- Department of Neurosurgery, The Second Affiliated Hospital of Harbin Medical University, Harbin 150086, China
| | - Ke He
- Department of Neurosurgery, The Second Affiliated Hospital of Harbin Medical University, Harbin 150086, China
| | - Xinqi Ma
- Department of Neurosurgery, The Second Affiliated Hospital of Harbin Medical University, Harbin 150086, China
| | - Qingsong Yang
- Department of Neurosurgery, The Second Affiliated Hospital of Harbin Medical University, Harbin 150086, China
| | - Junming Jia
- Department of Neurosurgery, The Second Affiliated Hospital of Harbin Medical University, Harbin 150086, China
| | - Zeren Chen
- Department of Neurosurgery, The Second Affiliated Hospital of Harbin Medical University, Harbin 150086, China
| | - Shan Yu
- Department of Pathology, The Second Affiliated Hospital of Harbin Medical University, Harbin 150086, China
| | - Shuqing Gu
- Department of Neurosurgery, The First Hospital of Qiqihar, Qiqihar 161005, China
| | - Kunliang Chen
- Department of Neurosurgery, People’s Hospital of the Daxing’an Mountain Range, Daxing’an Mountain Range 165300, China
| | - Yan Zhao
- Department of Neurosurgery, The Second Affiliated Hospital of Harbin Medical University, Harbin 150086, China
| | - Weihua Li
- Medical Imaging Department, Shenzhen Second People’s Hospital, the First Affiliated Hospital of Shenzhen University Health Science Center, Shenzhen 518035, China
| | - Guangzhi Wang
- Department of Neurosurgery, The Second Affiliated Hospital of Harbin Medical University, Harbin 150086, China
| | - Mian Guo
- Department of Neurosurgery, The Second Affiliated Hospital of Harbin Medical University, Harbin 150086, China
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2
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Mayfield JM, Hitefield NL, Czajewski I, Vanhye L, Holden L, Morava E, van Aalten DMF, Wells L. O-GlcNAc transferase congenital disorder of glycosylation (OGT-CDG): Potential mechanistic targets revealed by evaluating the OGT interactome. J Biol Chem 2024; 300:107599. [PMID: 39059494 PMCID: PMC11381892 DOI: 10.1016/j.jbc.2024.107599] [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: 10/25/2023] [Revised: 07/10/2024] [Accepted: 07/11/2024] [Indexed: 07/28/2024] Open
Abstract
O-GlcNAc transferase (OGT) is the sole enzyme responsible for the post-translational modification of O-GlcNAc on thousands of target nucleocytoplasmic proteins. To date, nine variants of OGT that segregate with OGT Congenital Disorder of Glycosylation (OGT-CDG) have been reported and characterized. Numerous additional variants have been associated with OGT-CDG, some of which are currently undergoing investigation. This disorder primarily presents with global developmental delay and intellectual disability (ID), alongside other variable neurological features and subtle facial dysmorphisms in patients. Several hypotheses aim to explain the etiology of OGT-CDG, with a prominent hypothesis attributing the pathophysiology of OGT-CDG to mutations segregating with this disorder disrupting the OGT interactome. The OGT interactome consists of thousands of proteins, including substrates as well as interactors that require noncatalytic functions of OGT. A key aim in the field is to identify which interactors and substrates contribute to the primarily neural-specific phenotype of OGT-CDG. In this review, we will discuss the heterogenous phenotypic features of OGT-CDG seen clinically, the variable biochemical effects of mutations associated with OGT-CDG, and the use of animal models to understand this disorder. Furthermore, we will discuss how previously identified OGT interactors causal for ID provide mechanistic targets for investigation that could explain the dysregulated gene expression seen in OGT-CDG models. Identifying shared or unique altered pathways impacted in OGT-CDG patients will provide a better understanding of the disorder as well as potential therapeutic targets.
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Affiliation(s)
- Johnathan M Mayfield
- Department of Biochemistry and Molecular Biology, Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia, USA
| | - Naomi L Hitefield
- Department of Biochemistry and Molecular Biology, Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia, USA
| | | | - Lotte Vanhye
- Department of Clinical Genomics and Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Laura Holden
- Department of Biochemistry and Molecular Biology, Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia, USA
| | - Eva Morava
- Department of Clinical Genomics and Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Daan M F van Aalten
- School of Life Sciences, University of Dundee, Dundee, UK; Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark.
| | - Lance Wells
- Department of Biochemistry and Molecular Biology, Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia, USA.
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3
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Cowell LM, King M, West H, Broadsmith M, Genever P, Pownall ME, Isaacs HV. Regulation of gene expression downstream of a novel Fgf/Erk pathway during Xenopus development. PLoS One 2023; 18:e0286040. [PMID: 37856433 PMCID: PMC10586617 DOI: 10.1371/journal.pone.0286040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 05/08/2023] [Indexed: 10/21/2023] Open
Abstract
Activation of Map kinase/Erk signalling downstream of fibroblast growth factor (Fgf) tyrosine kinase receptors regulates gene expression required for mesoderm induction and patterning of the anteroposterior axis during Xenopus development. We have proposed that a subset of Fgf target genes are activated in the embyo in response to inhibition of a transcriptional repressor. Here we investigate the hypothesis that Cic (Capicua), which was originally identified as a transcriptional repressor negatively regulated by receptor tyrosine kinase/Erk signalling in Drosophila, is involved in regulating Fgf target gene expression in Xenopus. We characterise Xenopus Cic and show that it is widely expressed in the embryo. Fgf overexpression or ectodermal wounding, both of which potently activate Erk, reduce Cic protein levels in embryonic cells. In keeping with our hypothesis, we show that Cic knockdown and Fgf overexpression have overlapping effects on embryo development and gene expression. Transcriptomic analysis identifies a cohort of genes that are up-regulated by Fgf overexpression and Cic knockdown. We investigate two of these genes as putative targets of the proposed Fgf/Erk/Cic axis: fos and rasl11b, which encode a leucine zipper transcription factor and a ras family GTPase, respectively. We identify Cic consensus binding sites in a highly conserved region of intron 1 in the fos gene and Cic sites in the upstream regions of several other Fgf/Cic co-regulated genes, including rasl11b. We show that expression of fos and rasl11b is blocked in the early mesoderm when Fgf and Erk signalling is inhibited. In addition, we show that fos and rasl11b expression is associated with the Fgf independent activation of Erk at the site of ectodermal wounding. Our data support a role for a Fgf/Erk/Cic axis in regulating a subset of Fgf target genes during gastrulation and is suggestive that Erk signalling is involved in regulating Cic target genes at the site of ectodermal wounding.
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Affiliation(s)
- Laura M. Cowell
- Department of Biology, University of York, Heslington, York, United Kingdom
| | - Michael King
- Department of Biology, University of York, Heslington, York, United Kingdom
| | - Helena West
- Department of Biology, University of York, Heslington, York, United Kingdom
| | - Matthew Broadsmith
- Department of Biology, University of York, Heslington, York, United Kingdom
| | - Paul Genever
- Department of Biology, University of York, Heslington, York, United Kingdom
| | | | - Harry V. Isaacs
- Department of Biology, University of York, Heslington, York, United Kingdom
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4
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Venneker S, Bovée JVMG. IDH Mutations in Chondrosarcoma: Case Closed or Not? Cancers (Basel) 2023; 15:3603. [PMID: 37509266 PMCID: PMC10377514 DOI: 10.3390/cancers15143603] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 06/29/2023] [Accepted: 07/10/2023] [Indexed: 07/30/2023] Open
Abstract
Chondrosarcomas are malignant cartilage-producing tumours that frequently harbour isocitrate dehydrogenase 1 and -2 (IDH) gene mutations. Several studies have confirmed that these mutations are key players in the early stages of cartilage tumour development, but their role in later stages remains ambiguous. The prognostic value of IDH mutations remains unclear and preclinical studies have not identified effective treatment modalities (in)directly targeting these mutations. In contrast, the IDH mutation status is a prognostic factor in other cancers, and IDH mutant inhibitors as well as therapeutic strategies targeting the underlying vulnerabilities induced by IDH mutations seem effective in these tumour types. This discrepancy in findings might be ascribed to a difference in tumour type, elevated D-2-hydroxyglutarate levels, and the type of in vitro model (endogenous vs. genetically modified) used in preclinical studies. Moreover, recent studies suggest that the (epi)genetic landscape in which the IDH mutation functions is an important factor to consider when investigating potential therapeutic strategies or patient outcomes. These findings imply that the dichotomy between IDH wildtype and mutant is too simplistic and additional subgroups indeed exist within chondrosarcoma. Future studies should focus on the identification, characterisation, and tailoring of treatments towards these biological subgroups within IDH wildtype and mutant chondrosarcoma.
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Affiliation(s)
- Sanne Venneker
- Department of Pathology, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
| | - Judith V M G Bovée
- Department of Pathology, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
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5
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Takemon Y, LeBlanc VG, Song J, Chan SY, Lee SD, Trinh DL, Ahmad ST, Brothers WR, Corbett RD, Gagliardi A, Moradian A, Cairncross JG, Yip S, Aparicio SAJR, Chan JA, Hughes CS, Morin GB, Gorski SM, Chittaranjan S, Marra MA. Multi-Omic Analysis of CIC's Functional Networks Reveals Novel Interaction Partners and a Potential Role in Mitotic Fidelity. Cancers (Basel) 2023; 15:2805. [PMID: 37345142 PMCID: PMC10216487 DOI: 10.3390/cancers15102805] [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: 04/07/2023] [Revised: 05/11/2023] [Accepted: 05/15/2023] [Indexed: 06/23/2023] Open
Abstract
CIC encodes a transcriptional repressor and MAPK signalling effector that is inactivated by loss-of-function mutations in several cancer types, consistent with a role as a tumour suppressor. Here, we used bioinformatic, genomic, and proteomic approaches to investigate CIC's interaction networks. We observed both previously identified and novel candidate interactions between CIC and SWI/SNF complex members, as well as novel interactions between CIC and cell cycle regulators and RNA processing factors. We found that CIC loss is associated with an increased frequency of mitotic defects in human cell lines and an in vivo mouse model and with dysregulated expression of mitotic regulators. We also observed aberrant splicing in CIC-deficient cell lines, predominantly at 3' and 5' untranslated regions of genes, including genes involved in MAPK signalling, DNA repair, and cell cycle regulation. Our study thus characterises the complexity of CIC's functional network and describes the effect of its loss on cell cycle regulation, mitotic integrity, and transcriptional splicing, thereby expanding our understanding of CIC's potential roles in cancer. In addition, our work exemplifies how multi-omic, network-based analyses can be used to uncover novel insights into the interconnected functions of pleiotropic genes/proteins across cellular contexts.
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Affiliation(s)
- Yuka Takemon
- Genome Science and Technology Graduate Program, University of British Columbia, Vancouver, BC V5Z 4S6, Canada;
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer Research Institute, Vancouver, BC V5Z 1L3, Canada; (V.G.L.); (A.M.); (S.M.G.)
| | - Véronique G. LeBlanc
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer Research Institute, Vancouver, BC V5Z 1L3, Canada; (V.G.L.); (A.M.); (S.M.G.)
| | - Jungeun Song
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer Research Institute, Vancouver, BC V5Z 1L3, Canada; (V.G.L.); (A.M.); (S.M.G.)
| | - Susanna Y. Chan
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer Research Institute, Vancouver, BC V5Z 1L3, Canada; (V.G.L.); (A.M.); (S.M.G.)
| | - Stephen Dongsoo Lee
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer Research Institute, Vancouver, BC V5Z 1L3, Canada; (V.G.L.); (A.M.); (S.M.G.)
| | - Diane L. Trinh
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer Research Institute, Vancouver, BC V5Z 1L3, Canada; (V.G.L.); (A.M.); (S.M.G.)
| | - Shiekh Tanveer Ahmad
- Department of Pathology & Laboratory Medicine, University of Calgary, Calgary, AB T2N 1N4, Canada
- Arnie Charbonneau Cancer Institute, University of Calgary, Calgary, AB T2N 4Z6, Canada
- Alberta Children’s Hospital Research Institute, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - William R. Brothers
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer Research Institute, Vancouver, BC V5Z 1L3, Canada; (V.G.L.); (A.M.); (S.M.G.)
| | - Richard D. Corbett
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer Research Institute, Vancouver, BC V5Z 1L3, Canada; (V.G.L.); (A.M.); (S.M.G.)
| | - Alessia Gagliardi
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer Research Institute, Vancouver, BC V5Z 1L3, Canada; (V.G.L.); (A.M.); (S.M.G.)
| | - Annie Moradian
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer Research Institute, Vancouver, BC V5Z 1L3, Canada; (V.G.L.); (A.M.); (S.M.G.)
| | - J. Gregory Cairncross
- Arnie Charbonneau Cancer Institute, University of Calgary, Calgary, AB T2N 4Z6, Canada
- Department of Clinical Neurosciences, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - Stephen Yip
- Department of Molecular Oncology, BC Cancer Research Institute, Vancouver, BC V5Z 1L3, Canada; (S.Y.); (S.A.J.R.A.); (C.S.H.)
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC V6T 1Z7, Canada
| | - Samuel A. J. R. Aparicio
- Department of Molecular Oncology, BC Cancer Research Institute, Vancouver, BC V5Z 1L3, Canada; (S.Y.); (S.A.J.R.A.); (C.S.H.)
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC V6T 1Z7, Canada
| | - Jennifer A. Chan
- Department of Pathology & Laboratory Medicine, University of Calgary, Calgary, AB T2N 1N4, Canada
- Arnie Charbonneau Cancer Institute, University of Calgary, Calgary, AB T2N 4Z6, Canada
- Alberta Children’s Hospital Research Institute, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Christopher S. Hughes
- Department of Molecular Oncology, BC Cancer Research Institute, Vancouver, BC V5Z 1L3, Canada; (S.Y.); (S.A.J.R.A.); (C.S.H.)
| | - Gregg B. Morin
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer Research Institute, Vancouver, BC V5Z 1L3, Canada; (V.G.L.); (A.M.); (S.M.G.)
- Department of Medical Genetics, University of British Columbia, Vancouver, BC V6H 3N1, Canada
| | - Sharon M. Gorski
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer Research Institute, Vancouver, BC V5Z 1L3, Canada; (V.G.L.); (A.M.); (S.M.G.)
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
| | - Suganthi Chittaranjan
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer Research Institute, Vancouver, BC V5Z 1L3, Canada; (V.G.L.); (A.M.); (S.M.G.)
| | - Marco A. Marra
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer Research Institute, Vancouver, BC V5Z 1L3, Canada; (V.G.L.); (A.M.); (S.M.G.)
- Department of Medical Genetics, University of British Columbia, Vancouver, BC V6H 3N1, Canada
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