1
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Huang Y, Zhao Z, Yi G, Zhang M. Importance of DNA nanotechnology for DNA methyltransferases in biosensing assays. J Mater Chem B 2024; 12:4063-4079. [PMID: 38572575 DOI: 10.1039/d3tb02947f] [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: 04/05/2024]
Abstract
DNA methylation is the process by which specific bases on a DNA sequence acquire methyl groups under the catalytic action of DNA methyltransferases (DNMT). Abnormal changes in the function of DNMT are important markers for cancers and other diseases; therefore, the detection of DNMT and the selection of its inhibitors are critical to biomedical research and clinical practice. DNA molecules can undergo intermolecular assembly to produce functional aggregates because of their inherently stable physical and chemical properties and unique structures. Conventional DNMT detection methods are cumbersome and complicated processes; therefore, it is necessary to develop biosensing technology based on the assembly of DNA nanostructures to achieve rapid analysis, simple operation, and high sensitivity. The design of the relevant program has been employed in life science, anticancer drug screening, and clinical diagnostics. In this review, we explore how DNA assembly, including 2D techniques like hybridization chain reaction (HCR), rolling circle amplification (RCA), catalytic hairpin assembly (CHA), and exponential isothermal amplified strand displacement reaction (EXPAR), as well as 3D structures such as DNA tetrahedra, G-quadruplexes, DNA hydrogels, and DNA origami, enhances DNMT detection. We highlight the benefits of these DNA nanostructure-based biosensing technologies for clinical use and critically examine the challenges of standardizing these methods. We aim to provide reference values for the application of these techniques in DNMT analysis and early cancer diagnosis and treatment, and to alert researchers to challenges in clinical application.
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Affiliation(s)
- Yuqi Huang
- Clinical Laboratory, Chongqing Jiulongpo District People's Hospital, Chongqing 400050, China.
| | - Zixin Zhao
- Key Laboratory of Medical Diagnostics of Ministry of Education, Department of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, P. R. China.
| | - Gang Yi
- Key Laboratory of Medical Diagnostics of Ministry of Education, Department of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, P. R. China.
| | - Mingjun Zhang
- Clinical Laboratory, Chongqing Jiulongpo District People's Hospital, Chongqing 400050, China.
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2
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Raj A, Petreaca RC, Mirzaei G. Multi-Omics Integration for Liver Cancer Using Regression Analysis. Curr Issues Mol Biol 2024; 46:3551-3562. [PMID: 38666952 PMCID: PMC11049490 DOI: 10.3390/cimb46040222] [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: 02/18/2024] [Revised: 04/11/2024] [Accepted: 04/16/2024] [Indexed: 04/28/2024] Open
Abstract
Genetic biomarkers have played a pivotal role in the classification, prognostication, and guidance of clinical cancer therapies. Large-scale and multi-dimensional analyses of entire cancer genomes, as exemplified by projects like The Cancer Genome Atlas (TCGA), have yielded an extensive repository of data that holds the potential to unveil the underlying biology of these malignancies. Mutations stand out as the principal catalysts of cellular transformation. Nonetheless, other global genomic processes, such as alterations in gene expression and chromosomal re-arrangements, also play crucial roles in conferring cellular immortality. The incorporation of multi-omics data specific to cancer has demonstrated the capacity to enhance our comprehension of the molecular mechanisms underpinning carcinogenesis. This report elucidates how the integration of comprehensive data on methylation, gene expression, and copy number variations can effectively facilitate the unsupervised clustering of cancer samples. We have identified regressors that can effectively classify tumor and normal samples with an optimal integration of RNA sequencing, DNA methylation, and copy number variation while also achieving significant p-values. Further, these regressors were trained using linear and logistic regression with k-means clustering. For comparison, we employed autoencoder- and stacking-based omics integration and computed silhouette scores to evaluate the clusters. The proof of concept is illustrated using liver cancer data. Our analysis serves to underscore the feasibility of unsupervised cancer classification by considering genetic markers beyond mutations, thereby emphasizing the clinical relevance of additional global cellular parameters that contribute to the transformative process in cells. This work is clinically relevant because changes in gene expression and genomic re-arrangements have been shown to be signatures of cellular transformation across cancers, as well as in liver cancers.
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Affiliation(s)
- Aditya Raj
- Department of Electrical and Computer Engineering, The Ohio State University, Columbus, OH 43210, USA;
| | - Ruben C. Petreaca
- Department of Molecular Genetics, The Ohio State University, Marion, OH 43302, USA;
- Cancer Biology Program, The Ohio State University James Comprehensive Cancer Center, Columbus, OH 43210, USA
| | - Golrokh Mirzaei
- Department of Computer Science and Engineering, The Ohio State University, Marion, OH 43302, USA
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3
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Gao J, Shi W, Wang J, Guan C, Dong Q, Sheng J, Zou X, Xu Z, Ge Y, Yang C, Li J, Bao H, Zhong X, Cui Y. Research progress and applications of epigenetic biomarkers in cancer. Front Pharmacol 2024; 15:1308309. [PMID: 38681199 PMCID: PMC11048075 DOI: 10.3389/fphar.2024.1308309] [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: 10/06/2023] [Accepted: 03/25/2024] [Indexed: 05/01/2024] Open
Abstract
Epigenetic changes are heritable changes in gene expression without changes in the nucleotide sequence of genes. Epigenetic changes play an important role in the development of cancer and in the process of malignancy metastasis. Previous studies have shown that abnormal epigenetic changes can be used as biomarkers for disease status and disease prediction. The reversibility and controllability of epigenetic modification changes also provide new strategies for early disease prevention and treatment. In addition, corresponding drug development has also reached the clinical stage. In this paper, we will discuss the recent progress and application status of tumor epigenetic biomarkers from three perspectives: DNA methylation, non-coding RNA, and histone modification, in order to provide new opportunities for additional tumor research and applications.
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Affiliation(s)
- Jianjun Gao
- Department of Hepatopancreatobiliary Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Wujiang Shi
- Department of Hepatopancreatobiliary Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Jiangang Wang
- Department of General Surgery, Tangdu Hospital, Air Force Medical University, Xi’an, China
| | - Canghai Guan
- Department of Hepatopancreatobiliary Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Qingfu Dong
- Department of Hepatopancreatobiliary Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Jialin Sheng
- Department of Hepatopancreatobiliary Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Xinlei Zou
- Department of Hepatopancreatobiliary Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Zhaoqiang Xu
- Department of Hepatopancreatobiliary Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Yifei Ge
- Department of Hepatopancreatobiliary Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Chengru Yang
- Department of Hepatopancreatobiliary Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Jiehan Li
- Department of Hepatopancreatobiliary Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Haolin Bao
- Department of Hepatopancreatobiliary Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Xiangyu Zhong
- Department of Hepatopancreatobiliary Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Yunfu Cui
- Department of Hepatopancreatobiliary Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
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4
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Soni N, Agarwal A, Ajmera P, Mehta P, Gupta V, Vibhute M, Gubbiotti M, Mark IT, Messina SA, Mohan S, Bathla G. High-Grade Astrocytoma with Piloid Features: A Dual Institutional Review of Imaging Findings of a Novel Entity. AJNR Am J Neuroradiol 2024; 45:468-474. [PMID: 38485198 DOI: 10.3174/ajnr.a8166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 12/21/2023] [Indexed: 04/10/2024]
Abstract
High-grade astrocytoma with piloid features (HGAP) is a recently identified brain tumor characterized by a distinct DNA methylation profile. Predominantly located in the posterior fossa of adults, HGAP is notably prevalent in individuals with neurofibromatosis type 1. We present an image-centric review of HGAP and explore the association between HGAP and neurofibromatosis type 1. Data were collected from 8 HGAP patients treated at two tertiary care institutions between January 2020 and October 2023. Demographic details, clinical records, management, and tumor molecular profiles were analyzed. Tumor characteristics, including location and imaging features on MR imaging, were reviewed. Clinical or imaging features suggestive of neurofibromatosis 1 or the presence of NF1 gene alteration were documented. The mean age at presentation was 45.5 years (male/female = 5:3). Tumors were midline, localized in the posterior fossa (n = 4), diencephalic/thalamic (n = 2), and spinal cord (n = 2). HGAP lesions were T1 hypointense, T2-hyperintense, mostly without diffusion restriction, predominantly peripheral irregular enhancement with central necrosis (n = 3) followed by mixed heterogeneous enhancement (n = 2). Two NF1 mutation carriers showed signs of neurofibromatosis type 1 before HGAP diagnosis, with one diagnosed during HGAP evaluation, strengthening the HGAP-NF1 link, particularly in patients with posterior fossa masses. All tumors were IDH1 wild-type, often with ATRX, CDKN2A/B, and NF1 gene alteration. Six patients underwent surgical resection followed by adjuvant chemoradiation. Six patients were alive, and two died during the last follow-up. Histone H3 mutations were not detected in our cohort, such as the common H3K27M typically seen in diffuse midline gliomas, linked to aggressive clinical behavior and poor prognosis. HGAP lesions may involve the brain or spine and tend to be midline or paramedian in location. Underlying neurofibromatosis type 1 diagnosis or imaging findings are important diagnostic cues.
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Affiliation(s)
- Neetu Soni
- From the Mayo Clinic (N.S., A.A., V.G.), Jacksonville, Florida
| | - Amit Agarwal
- From the Mayo Clinic (N.S., A.A., V.G.), Jacksonville, Florida
| | - Pranav Ajmera
- Mayo Clinic (P.A., P.M., I.T.M., S.A.M., G.B.), Rochester, Minnesota
| | - Parv Mehta
- Mayo Clinic (P.A., P.M., I.T.M., S.A.M., G.B.), Rochester, Minnesota
| | - Vivek Gupta
- From the Mayo Clinic (N.S., A.A., V.G.), Jacksonville, Florida
| | - Mukta Vibhute
- College of Medicine (M.V.), St. George's University, Grenada, West Indies
| | - Maria Gubbiotti
- MD Anderson Cancer Center (M.G.), University of Texas, Houston, Texas
| | - Ian T Mark
- Mayo Clinic (P.A., P.M., I.T.M., S.A.M., G.B.), Rochester, Minnesota
| | - Steven A Messina
- Mayo Clinic (P.A., P.M., I.T.M., S.A.M., G.B.), Rochester, Minnesota
| | - Suyash Mohan
- Perelman School of Medicine (S.M.), University of Pennsylvania, Philadelphia, Pennsylvania
| | - Girish Bathla
- Mayo Clinic (P.A., P.M., I.T.M., S.A.M., G.B.), Rochester, Minnesota
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Liang B, Wang Y, Huang J, Lin S, Mao G, Zhou Z, Yan W, Shan C, Wu H, Etcheverry A, He Y, Liu F, Kang H, Yin A, Zhang S. Genome-wide DNA methylation analysis identifies potent CpG signature for temzolomide response in non-G-CIMP glioblastomas with unmethylated MGMT promoter: MGMT-dependent roles of GPR81. CNS Neurosci Ther 2024; 30:e14465. [PMID: 37830163 PMCID: PMC11017469 DOI: 10.1111/cns.14465] [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: 08/09/2022] [Revised: 07/04/2023] [Accepted: 07/05/2023] [Indexed: 10/14/2023] Open
Abstract
PURPOSES To identify potent DNA methylation candidates that could predict response to temozolomide (TMZ) in glioblastomas (GBMs) that do not have glioma-CpGs island methylator phenotype (G-CIMP) but have an unmethylated promoter of O-6-methylguanine-DNA methyltransferase (unMGMT). METHODS The discovery-validation approach was planned incorporating a series of G-CIMP-/unMGMT GBM cohorts with DNA methylation microarray data and clinical information, to construct multi-CpG prediction models. Different bioinformatic and experimental analyses were performed for biological exploration. RESULTS By analyzing discovery sets with radiotherapy (RT) plus TMZ versus RT alone, we identified a panel of 64 TMZ efficacy-related CpGs, from which a 10-CpG risk signature was further constructed. Both the 64-CpG panel and the 10-CpG risk signature were validated showing significant correlations with overall survival of G-CIMP-/unMGMT GBMs when treated with RT/TMZ, rather than RT alone. The 10-CpG risk signature was further observed for aiding TMZ choice by distinguishing differential outcomes to RT/TMZ versus RT within each risk subgroup. Functional studies on GPR81, the gene harboring one of the 10 CpGs, indicated its distinct impacts on TMZ resistance in GBM cells, which may be dependent on the status of MGMT expression. CONCLUSIONS The 64 TMZ efficacy-related CpGs and in particular the 10-CpG risk signature may serve as promising predictive biomarker candidates for guiding optimal usage of TMZ in G-CIMP-/unMGMT GBMs.
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Affiliation(s)
- Bao‐Bao Liang
- Department of OncologyThe Second Affiliated Hospital of Xi'an Jiaotong UniversityXi'anShaanxiChina
| | - Yu‐Hong Wang
- The Emergency DepartmentThe Seventh Medical Center of Chinese PLA General HospitalBeijingChina
| | - Jing‐Jing Huang
- Department of Pediatric SurgeryThe Second Affiliated Hospital of Xi'an Jiaotong UniversityXi'anShaanxiChina
| | - Shuai Lin
- Department of OncologyThe Second Affiliated Hospital of Xi'an Jiaotong UniversityXi'anShaanxiChina
| | - Guo‐Chao Mao
- Department of OncologyThe Second Affiliated Hospital of Xi'an Jiaotong UniversityXi'anShaanxiChina
| | - Zhang‐Jian Zhou
- Department of OncologyThe Second Affiliated Hospital of Xi'an Jiaotong UniversityXi'anShaanxiChina
| | - Wan‐Jun Yan
- Department of OncologyThe Second Affiliated Hospital of Xi'an Jiaotong UniversityXi'anShaanxiChina
| | - Chang‐You Shan
- Department of OncologyThe Second Affiliated Hospital of Xi'an Jiaotong UniversityXi'anShaanxiChina
| | - Hui‐Zi Wu
- Department of OncologyThe Second Affiliated Hospital of Xi'an Jiaotong UniversityXi'anShaanxiChina
| | - Amandine Etcheverry
- CNRS, UMR 6290, Institut de Génétique et Développement de Rennes (IGdR)RennesFrance
| | - Ya‐Long He
- Department of Neurosurgery, Xijing HospitalAir Force Medical UniversityXi'anChina
| | - Fang‐Fang Liu
- Institute of Neurosciences, College of Basic MedicineAir Force Medical UniversityXi'anChina
| | - Hua‐Feng Kang
- Department of OncologyThe Second Affiliated Hospital of Xi'an Jiaotong UniversityXi'anShaanxiChina
| | - An‐An Yin
- Department of Biochemistry and Molecular BiologyAir Force Medical UniversityXi'anChina
- Department of Plastic and Reconstructive Surgery, Xijing HospitalAir Force Medical UniversityXi'anChina
| | - Shu‐Qun Zhang
- Department of OncologyThe Second Affiliated Hospital of Xi'an Jiaotong UniversityXi'anShaanxiChina
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6
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Wang T, Zhu G, Wang B, Hu M, Gong C, Tan K, Jiang L, Zhu X, Geng Y, Li L. Activation of Hypoxia Inducible Factor-1 Alpha-Mediated DNA Methylation Enzymes (DNMT3a and TET2) Under Hypoxic Conditions Regulates S100A6 Transcription to Promote Lung Cancer Cell Growth and Metastasis. Antioxid Redox Signal 2024. [PMID: 38299557 DOI: 10.1089/ars.2023.0397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/02/2024]
Abstract
Aims: This research was aimed at investigating the effects of hypoxia inducible factor-1 alpha (HIF-1α)-mediated DNA methylation enzymes (ten-eleven translocase-2 [TET2] and DNA methyltransferase-3a [DNMT3a]) under hypoxic conditions on S100A6 transcription, thereby promoting the growth and metastasis of lung cancer cells. Methods: The expression of HIF-1α or S100A6 in lung cancer cells was interfered with under normoxic and hypoxic conditions, and the cell proliferative, migratory, and invasive properties were assessed. The mechanism of HIF-1α-regulated TET2 and DNMT3 effects on S100A6 transcription under hypoxic conditions was further investigated. Results: Functionally, S100A6 over-expression promoted lung cancer cell proliferation and metastasis. S100A6 over-expression reversed the inhibitory effects of HIF-1α interference on the proliferation and metastasis of lung cancer cells. S100A6 was induced to express in an HIF-1α-dependent manner under hypoxic conditions, and silencing S100A6 or HIF-1α suppressed lung cancer cell proliferation and metastasis under hypoxic conditions. Further, The Cancer Genome Atlas-lung adenocarcinoma database analysis revealed that S100A6 mRNA levels had a negative correlation with methylation levels. Mechanistically, CpG hypomethylation status in the S100A6 promoter hypoxia response element had an association with HIF-1α induction. TET2 was enriched in S100A6 promoter region of lung cancer cells under hypoxic conditions, whereas DNMT3a enrichment was reduced in S100A6 promoter region. HIF-1α-mediated S100A6 activation was linked to DNMT3a-associated epigenetic inactivation and TET2 activation. Innovation: The activation of HIF-1α-mediated DNA methylation enzymes under hypoxic conditions regulated S100A6 transcription, thereby promoting lung cancer cell growth and metastasis. Conclusion: In lung cancer progression, hypoxia-induced factor HIF-1α combined with DNA methylation modifications co-regulates S100A6 transcriptional activation and promotes lung cancer cell growth and metastasis.
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Affiliation(s)
- Tengfei Wang
- The Department of Thoracic Surgery; Anhui Wanbei Coal-Electricity Group General Hospital, Suzhou, China
| | - Genbao Zhu
- General Clinical Research Center; Anhui Wanbei Coal-Electricity Group General Hospital, Suzhou, China
| | - Bo Wang
- The Department of Thoracic Surgery; Anhui Wanbei Coal-Electricity Group General Hospital, Suzhou, China
| | - Mengxue Hu
- General Clinical Research Center; Anhui Wanbei Coal-Electricity Group General Hospital, Suzhou, China
| | - Chen Gong
- General Clinical Research Center; Anhui Wanbei Coal-Electricity Group General Hospital, Suzhou, China
| | - Kemeng Tan
- General Clinical Research Center; Anhui Wanbei Coal-Electricity Group General Hospital, Suzhou, China
| | - La Jiang
- General Clinical Research Center; Anhui Wanbei Coal-Electricity Group General Hospital, Suzhou, China
| | - Xiaohong Zhu
- General Clinical Research Center; Anhui Wanbei Coal-Electricity Group General Hospital, Suzhou, China
| | - Yuliu Geng
- The Department of Thoracic Surgery; Anhui Wanbei Coal-Electricity Group General Hospital, Suzhou, China
| | - Lili Li
- General Clinical Research Center; Anhui Wanbei Coal-Electricity Group General Hospital, Suzhou, China
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7
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Flores-Fernández CN, Lin D, Robins K, O'Callaghan CA. DNA methylases for site-selective inhibition of type IIS restriction enzyme activity. Appl Microbiol Biotechnol 2024; 108:174. [PMID: 38270650 PMCID: PMC10810934 DOI: 10.1007/s00253-024-13015-7] [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: 01/08/2024] [Revised: 01/08/2024] [Accepted: 01/14/2024] [Indexed: 01/26/2024]
Abstract
DNA methylases of the restriction-modifications (R-M) systems are promising enzymes for the development of novel molecular and synthetic biology tools. Their use in vitro enables the deployment of independent and controlled catalytic reactions. This work aimed to produce recombinant DNA methylases belonging to the R-M systems, capable of in vitro inhibition of the type IIS restriction enzymes BsaI, BpiI, or LguI. Non-switchable methylases are those whose recognition sequences fully overlap the recognition sequences of their associated endonuclease. In switch methylases, the methylase and endonuclease recognition sequences only partially overlap, allowing sequence engineering to alter methylation without altering restriction. In this work, ten methylases from type I and II R-M systems were selected for cloning and expression in E. coli strains tolerant to methylation. Isopropyl β-D-1-thiogalactopyranoside (IPTG) concentrations and post-induction temperatures were tested to optimize the soluble methylases expression, which was achieved with 0.5 mM IPTG at 20 °C. The C-terminal His6-Tag versions showed better expression than the N-terminal tagged versions. DNA methylation was analyzed using purified methylases and custom test plasmids which, after the methylation reactions, were digested using the corresponding associated type IIS endonuclease. The non-switchable methylases M2.Eco31I, M2.BsaI, M2.HpyAII, and M1.MboII along with the switch methylases M.Osp807II and M2.NmeMC58II showed the best activity for site-selective inhibition of type IIS restriction enzyme activity. This work demonstrates that our recombinant methylases were able to block the activity of type IIS endonucleases in vitro, allowing them to be developed as valuable tools in synthetic biology and DNA assembly techniques. KEY POINTS: • Non-switchable methylases always inhibit the relevant type IIS endonuclease activity • Switch methylases inhibit the relevant type IIS endonuclease activity depending on the sequence engineering of their recognition site • Recombinant non-switchable and switch methylases were active in vitro and can be deployed as tools in synthetic biology and DNA assembly.
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Affiliation(s)
- Carol N Flores-Fernández
- Wellcome Trust Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford, OX3 7BN, UK
| | - Da Lin
- Wellcome Trust Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford, OX3 7BN, UK
- Current address: Triple Helix Biotechnology Ltd, Moneta Building (B280), Babraham Research Campus, Babraham, Cambridge, CB22 3AT, UK
| | - Katherine Robins
- Wellcome Trust Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford, OX3 7BN, UK
- Current address: Complete Regulatory, 19-20 King Edward Street, Macclesfield, SK10 1AQ, UK
| | - Chris A O'Callaghan
- Wellcome Trust Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford, OX3 7BN, UK.
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Schumann Y, Dottermusch M, Schweizer L, Krech M, Lempertz T, Schüller U, Neumann P, Neumann JE. Morphology-based molecular classification of spinal cord ependymomas using deep neural networks. Brain Pathol 2024:e13239. [PMID: 38205683 DOI: 10.1111/bpa.13239] [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: 09/07/2023] [Accepted: 12/31/2023] [Indexed: 01/12/2024] Open
Abstract
Based on DNA-methylation, ependymomas growing in the spinal cord comprise two major molecular types termed spinal (SP-EPN) and myxopapillary ependymomas (MPE(-A/B)), which differ with respect to their clinical features and prognosis. Due to the existing discrepancy between histomorphogical diagnoses and classification using methylation data, we asked whether deep neural networks can predict the DNA methylation class of spinal cord ependymomas from hematoxylin and eosin stained whole-slide images. Using explainable AI, we further aimed to prospectively improve the consistency of histology-based diagnoses with DNA methylation profiling by identifying and quantifying distinct morphological patterns of these molecular ependymoma types. We assembled a case series of 139 molecularly characterized spinal cord ependymomas (nMPE = 84, nSP-EPN = 55). Self-supervised and weakly-supervised neural networks were used for classification. We employed attention analysis and supervised machine-learning methods for the discovery and quantification of morphological features and their correlation to the diagnoses of experienced neuropathologists. Our best performing model predicted the DNA methylation class with 98% test accuracy and used self-supervised learning to outperform pretrained encoder-networks (86% test accuracy). In contrast, the diagnoses of neuropathologists matched the DNA methylation class in only 83% of cases. Domain-adaptation techniques improved model generalization to an external validation cohort by up to 22%. Statistically significant morphological features were identified per molecular type and quantitatively correlated to human diagnoses. The approach was extended to recently defined subtypes of myxopapillary ependymomas (MPE-(A/B), 80% test accuracy). In summary, we demonstrated the accurate prediction of the DNA methylation class of spinal cord ependymomas (SP-EPN, MPE(-A/B)) using hematoxylin and eosin stained whole-slide images. Our approach may prospectively serve as a supplementary resource for integrated diagnostics and may even help to establish a standardized, high-quality level of histology-based diagnostics across institutions-in particular in low-income countries, where expensive DNA-methylation analyses may not be readily available.
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Affiliation(s)
- Yannis Schumann
- Chair for High Performance Computing, Helmut-Schmidt-University Hamburg, Hamburg, Germany
| | - Matthias Dottermusch
- Center for Molecular Neurobiology (ZMNH), University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany
- Institute of Neuropathology, UKE, Hamburg, Germany
| | - Leonille Schweizer
- Institute of Neurology (Edinger Institute), University Hospital Frankfurt, Goethe University, Frankfurt am Main, Germany
- German Cancer Consortium (DKTK), Partner Site Frankfurt/Mainz, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Frankfurt Cancer Institute (FCI), Frankfurt am Main, Germany
| | - Maja Krech
- Institute for Neuropathology, Charité Berlin, Berlin, Germany
| | - Tasja Lempertz
- Center for Molecular Neurobiology (ZMNH), University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany
| | - Ulrich Schüller
- Institute of Neuropathology, UKE, Hamburg, Germany
- Research Institute Children's Cancer Center Hamburg, UKE, Hamburg, Germany
- Department of Pediatric Hematology and Oncology, UKE, Hamburg, Germany
| | - Philipp Neumann
- Chair for High Performance Computing, Helmut-Schmidt-University Hamburg, Hamburg, Germany
| | - Julia E Neumann
- Center for Molecular Neurobiology (ZMNH), University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany
- Institute of Neuropathology, UKE, Hamburg, Germany
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9
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Walker EN, Laws MT, Cozzi F, Quezado M, Brown DA, Burton EC. A case of disseminated spinal astroblastoma harboring a MAMLD1::BEND2 fusion. Neuropathology 2023. [PMID: 38129983 DOI: 10.1111/neup.12960] [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: 10/11/2023] [Revised: 12/01/2023] [Accepted: 12/06/2023] [Indexed: 12/23/2023]
Abstract
Astroblastoma, MN1-altered, is a rare neoplasm of the central nervous system (CNS). This malignancy shares similar histopathological features with other CNS tumors, including ependymomas, making it challenging to diagnose. DNA methylation profiling is a new and robust technique that may be used to overcome this diagnostic hurdle. We report the case of a now 25-year-old female diagnosed with what was initially called an ependymoma located in the cervical spine at the age of 2 years old. After initial resection, the tumor recurred multiple times and within 2 years of diagnosis had disseminated disease throughout the brain and spinal cord. She has now undergone over two decades of treatment, including multiple surgical resections, radiation therapy, and administration of numerous chemotherapeutic agents. In 2021, the patient presented to our institution with lumbosacral radicular symptoms due to enlarging lesions within the lumbosacral spine. Reexamination of formalin-fixed, paraffin-embedded material from the patient's tumor using genomic DNA methylation profiling resulted in a diagnostic change from grade III anaplastic ependymoma to astroblastoma, MN1-altered. This work describes another confirmed case of astroblastoma, MN1-altered, to the growing body of literature.
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Affiliation(s)
- Erin N Walker
- Neurosurgical Oncology Unit, Surgical Neurology Branch, National Institutes of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland, USA
- University of South Carolina School of Medicine Greenville, Greenville, South Carolina, USA
| | - Maxwell T Laws
- Neurosurgical Oncology Unit, Surgical Neurology Branch, National Institutes of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland, USA
| | - Francesca Cozzi
- Neurosurgical Oncology Unit, Surgical Neurology Branch, National Institutes of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland, USA
| | - Martha Quezado
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA
| | - Desmond A Brown
- Neurosurgical Oncology Unit, Surgical Neurology Branch, National Institutes of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland, USA
| | - Eric C Burton
- Neurosurgical Oncology Unit, Surgical Neurology Branch, National Institutes of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland, USA
- Neuro-Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
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10
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Singh J, Sahu S, Mohan T, Mahajan S, Sharma MC, Sarkar C, Suri V. Current status of DNA methylation profiling in neuro-oncology as a diagnostic support tool: A review. Neurooncol Pract 2023; 10:518-526. [PMID: 38009119 PMCID: PMC10666812 DOI: 10.1093/nop/npad040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2023] Open
Abstract
Over the last 2 decades, high throughput genome-wide molecular profiling has revealed characteristic genetic and epigenetic alterations associated with different types of central nervous system (CNS) tumors. DNA methylation profiling has emerged as an important molecular platform for CNS tumor classification with improved diagnostic accuracy and patient risk stratification in comparison to the standard of care histopathological analysis and any single molecular tests. The emergence of DNA methylation arrays have also played a crucial role in refining existing types and the discovery of new tumor types or subtypes. The adoption of methylation data into neuro-oncology has been greatly aided by the development of a freely accessible machine learning-based classifier. In this review, we discuss methylation workflow, address the utility of DNA methylation profiling in CNS tumors in a routine diagnostic setting, and provide an overview of the methylation-based tumor types and new types or subtypes identified with this platform.
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Affiliation(s)
- Jyotsna Singh
- Neuropathology Laboratory, Neurosciences Centre, All India Institute of Medical Sciences, New Delhi, India
| | - Saumya Sahu
- Neuropathology Laboratory, Neurosciences Centre, All India Institute of Medical Sciences, New Delhi, India
| | - Trishala Mohan
- Neuropathology Laboratory, Neurosciences Centre, All India Institute of Medical Sciences, New Delhi, India
| | - Swati Mahajan
- Neuropathology Laboratory, Neurosciences Centre, All India Institute of Medical Sciences, New Delhi, India
| | - Mehar C Sharma
- Neuropathology Laboratory, Neurosciences Centre, All India Institute of Medical Sciences, New Delhi, India
| | - Chitra Sarkar
- Department of Pathology, All India Institute of Medical Sciences, New Delhi, India
| | - Vaishali Suri
- Neuropathology Laboratory, Neurosciences Centre, All India Institute of Medical Sciences, New Delhi, India
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11
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Jia K, Duan J, Cheng G, Li H, Li S, Hu M. DNA Methylation is Involved in Sex Determination in Spinach. Biochem Genet 2023:10.1007/s10528-023-10524-4. [PMID: 37950843 DOI: 10.1007/s10528-023-10524-4] [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: 10/09/2022] [Accepted: 09/07/2023] [Indexed: 11/13/2023]
Abstract
DNA methylation plays a critical role in the modulation of gene expression. The role of DNA methylation in sex determination was investigated in spinach. The differentiated cytosine CpG methylation profiles of CCGG motifs were assessed with methylation sensitivity amplification polymorphism (MSAP) in spinach. Among 442 DNA fragments from four plants, 134 methylated fragments were found. Relative proportions of methylation sites were 28.8% in male plants and 31.8% in female plants. At the same time, cytosine methylation levels were higher in females than in males in CCGG motifs of genomes in the spinach. These findings suggest that methylation of CG islands is involved in sex determination and differentiation in spinach.
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Affiliation(s)
- Keli Jia
- School of Medical Laboratory, Sanquan College of Xinxiang Medical University, Xinxiang, China
| | - Jiaming Duan
- School of Medical Laboratory, Sanquan College of Xinxiang Medical University, Xinxiang, China
| | | | - Heng Li
- School of Medical Laboratory, Sanquan College of Xinxiang Medical University, Xinxiang, China
| | - Shufen Li
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, China.
| | - Miao Hu
- School of Medical Laboratory, Sanquan College of Xinxiang Medical University, Xinxiang, China.
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12
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Peng S, Zhang X, Wu Y. Potential applications of DNA methylation testing technology in female tumors and screening methods. Biochim Biophys Acta Rev Cancer 2023; 1878:188941. [PMID: 37329994 DOI: 10.1016/j.bbcan.2023.188941] [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: 04/21/2023] [Revised: 06/12/2023] [Accepted: 06/12/2023] [Indexed: 06/19/2023]
Abstract
DNA methylation is a common epigenetic modification, and the current commonly used methods for DNA methylation detection include methylation-specific PCR, methylation-sensitive restriction endonuclease-PCR, and methylation-specific sequencing. DNA methylation plays an important role in genomic and epigenomic studies, and combining DNA methylation with other epigenetic modifications, such as histone modifications, may lead to better DNA methylation. DNA methylation also plays an important role in the development of disease, and analyzing changes in individual DNA methylation patterns can provide individualized diagnostic and therapeutic solutions. Liquid biopsy techniques are also increasingly well established in clinical practice and may provide new methods for early cancer screening. It is important to find new screening methods that are easy to perform, minimally invasive, patient-friendly, and affordable. DNA methylation mechanisms are thought to have an important role in cancer and have potential applications in the diagnosis and treatment of female tumors. This review discussed early detection targets and screening methods for common female tumors such as breast, ovarian, and cervical cancers and discussed advances in the study of DNA methylation in these tumors. Although existing screening, diagnostic, and treatment modalities exist, the high morbidity and mortality rates of these tumors remain challenging.
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Affiliation(s)
- Shixuan Peng
- Graduate Collaborative Training Base of The First People's Hospital of Xiangtan City, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, China; Department of Pathology, The First People's Hospital of Xiangtan City, 100 Shuyuan Road, 411100 Xiangtan, Hunan Province, China
| | - Xinwen Zhang
- Graduate Collaborative Training Base of The First People's Hospital of Xiangtan City, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, China; Department of Pathology, The First People's Hospital of Xiangtan City, 100 Shuyuan Road, 411100 Xiangtan, Hunan Province, China
| | - Yongjun Wu
- Department of Pathology, The First People's Hospital of Xiangtan City, 100 Shuyuan Road, 411100 Xiangtan, Hunan Province, China.
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13
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Zhang H, Xiang G, Li J, He S, Wang Y, Deng A, Wang Y, Guo C. Promotion effect of FGF23 on osteopenia in congenital scoliosis through FGFr3/TNAP/OPN pathway. Chin Med J (Engl) 2023; 136:1468-1477. [PMID: 37192015 PMCID: PMC10278695 DOI: 10.1097/cm9.0000000000002690] [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: 11/09/2022] [Indexed: 05/18/2023] Open
Abstract
BACKGROUND Congenital scoliosis (CS) is a complex spinal malformation of unknown etiology with abnormal bone metabolism. Fibroblast growth factor 23 (FGF23), secreted by osteoblasts and osteocytes, can inhibit bone formation and mineralization. This research aims to investigate the relationship between CS and FGF23. METHODS We collected peripheral blood from two pairs of identical twins for methylation sequencing of the target region. FGF23 mRNA levels in the peripheral blood of CS patients and age-matched controls were measured. Receiver operator characteristic (ROC) curve analyses were conducted to evaluate the specificity and sensitivity of FGF23. The expression levels of FGF23 and its downstream factors fibroblast growth factor receptor 3 (FGFr3)/tissue non-specific alkaline phosphatase (TNAP)/osteopontin (OPN) in primary osteoblasts from CS patients (CS-Ob) and controls (CT-Ob) were detected. In addition, the osteogenic abilities of FGF23-knockdown or FGF23-overexpressing Ob were examined. RESULTS DNA methylation of the FGF23 gene in CS patients was decreased compared to that of their identical twins, accompanied by increased mRNA levels. CS patients had increased peripheral blood FGF23 mRNA levels and decreased computed tomography (CT) values compared with controls. The FGF23 mRNA levels were negatively correlated with the CT value of the spine, and ROCs of FGF23 mRNA levels showed high sensitivity and specificity for CS. Additionally, significantly increased levels of FGF23, FGFr3, OPN, impaired osteogenic mineralization and lower TNAP levels were observed in CS-Ob. Moreover, FGF23 overexpression in CT-Ob increased FGFr3 and OPN levels and decreased TNAP levels, while FGF23 knockdown induced downregulation of FGFr3 and OPN but upregulation of TNAP in CS-Ob. Mineralization of CS-Ob was rescued after FGF23 knockdown. CONCLUSIONS Our results suggested increased peripheral blood FGF23 levels, decreased bone mineral density in CS patients, and a good predictive ability of CS by peripheral blood FGF23 levels. FGF23 may contribute to osteopenia in CS patients through FGFr3/TNAP / OPN pathway.
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Affiliation(s)
- Hongqi Zhang
- Department of Spine Surgery and Orthopaedics, Xiangya Hospital, Central South University, Changsha, Hunan 410000, China
- National Clinical Research Center for Geriatric Disorder, Xiangya Hospital, Central South University, Changsha, Hunan 410000, China
| | - Gang Xiang
- Department of Spine Surgery and Orthopaedics, Xiangya Hospital, Central South University, Changsha, Hunan 410000, China
- National Clinical Research Center for Geriatric Disorder, Xiangya Hospital, Central South University, Changsha, Hunan 410000, China
| | - Jiong Li
- Department of Spine Surgery and Orthopaedics, Xiangya Hospital, Central South University, Changsha, Hunan 410000, China
- National Clinical Research Center for Geriatric Disorder, Xiangya Hospital, Central South University, Changsha, Hunan 410000, China
| | - Sihan He
- Department of Spine Surgery and Orthopaedics, Xiangya Hospital, Central South University, Changsha, Hunan 410000, China
- National Clinical Research Center for Geriatric Disorder, Xiangya Hospital, Central South University, Changsha, Hunan 410000, China
| | - Yunjia Wang
- Department of Spine Surgery and Orthopaedics, Xiangya Hospital, Central South University, Changsha, Hunan 410000, China
- National Clinical Research Center for Geriatric Disorder, Xiangya Hospital, Central South University, Changsha, Hunan 410000, China
| | - Ang Deng
- Department of Spine Surgery and Orthopaedics, Xiangya Hospital, Central South University, Changsha, Hunan 410000, China
- National Clinical Research Center for Geriatric Disorder, Xiangya Hospital, Central South University, Changsha, Hunan 410000, China
| | - Yuxiang Wang
- Department of Spine Surgery and Orthopaedics, Xiangya Hospital, Central South University, Changsha, Hunan 410000, China
- National Clinical Research Center for Geriatric Disorder, Xiangya Hospital, Central South University, Changsha, Hunan 410000, China
| | - Chaofeng Guo
- Department of Spine Surgery and Orthopaedics, Xiangya Hospital, Central South University, Changsha, Hunan 410000, China
- National Clinical Research Center for Geriatric Disorder, Xiangya Hospital, Central South University, Changsha, Hunan 410000, China
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14
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Lee K, Kim SI, Kim EE, Shim YM, Won JK, Park CK, Choi SH, Yun H, Lee H, Park SH. Genomic profiles of IDH-mutant gliomas: MYCN-amplified IDH-mutant astrocytoma had the worst prognosis. Sci Rep 2023; 13:6761. [PMID: 37185778 PMCID: PMC10130138 DOI: 10.1038/s41598-023-32153-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Accepted: 03/23/2023] [Indexed: 05/17/2023] Open
Abstract
This study aimed to find any ambiguous genetic outlier for "oligodendroglioma, IDH-mutant and 1p/19q-codeleted (O_IDH_mut)" and "astrocytoma, IDH-mutant (A_IDH_mut)" and to redefine the genetic landscape and prognostic factors of IDH-mutant gliomas. Next-generation sequencing (NGS) using a brain tumor-targeted gene panel, methylation profiles, and clinicopathological features were analyzed for O_IDH_mut (n = 74) in 70 patients and for A_IDH_mut (n = 95) in 90 patients. 97.3% of O_IDH_mut and 98.9% of A_IDH_mut displayed a classic genomic landscape. Combined CIC (75.7%) and/or FUBP1 (45.9%) mutations were detected in 93.2% and MGMTp methylation in 95.9% of O_IDH_mut patients. In A_IDH_mut, TP53 mutations were found in 86.3% and combined ATRX (82.1%) and TERTp (6.3%) mutations in 88.4%. Although there were 3 confusing cases, NOS (not otherwise specified) category, based on genetic profiles, but they were clearly classified by combining histopathology and DKFZ methylation classifier algorithms. The patients with MYCN amplification and/or CDKN2A/2B homozygous deletion in the A_IDH_mut category had a worse prognosis than those without these gene alterations and MYCN-amplified A_IDH_mut showed the worst prognosis. However, there was no prognostic genetic marker in O_IDH_mut. In histopathologically or genetically ambiguous cases, methylation profiles can be used as an objective tool to avoid a diagnosis of NOS or NEC (not elsewhere classified), as well as for tumor classification. The authors have not encountered a case of true mixed oligoastrocytoma using an integrated diagnosis of histopathological, genetic and methylation profiles. MYCN amplification, in addition to CDKN2A/2B homozygous deletion, should be included in the genetic criteria for CNS WHO grade 4 A_IDH_mut.
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Affiliation(s)
- Kwanghoon Lee
- Department of Pathology, College of Medicine, Seoul National University Hospital, Seoul, Republic of Korea
| | - Seong-Ik Kim
- Department of Pathology, College of Medicine, Seoul National University Hospital, Seoul, Republic of Korea
| | - Eric Eunshik Kim
- Department of Pathology, College of Medicine, Seoul National University Hospital, Seoul, Republic of Korea
| | - Yu-Mi Shim
- Department of Pathology, College of Medicine, Seoul National University Hospital, Seoul, Republic of Korea
| | - Jae-Kyung Won
- Department of Pathology, College of Medicine, Seoul National University Hospital, Seoul, Republic of Korea
| | - Chul-Kee Park
- Department of Neurosurgery, College of Medicine, Seoul National University Hospital, Seoul, Republic of Korea
| | - Seung Hong Choi
- Department of Radiology, College of Medicine, Seoul National University Hospital, Seoul, Republic of Korea
| | - Hongseok Yun
- Department of Genomic Medicine, College of Medicine, Seoul National University Hospital, Seoul, Republic of Korea
| | - Hyunju Lee
- School of Electrical Engineering and Computer Science, Gwangju Institute of Science and Technology, Gwangju, 61005, Republic of Korea
- Artificial Intelligence Graduate School, Gwangju Institute of Science and Technology, Gwangju, 61005, Republic of Korea
| | - Sung-Hye Park
- Department of Pathology, College of Medicine, Seoul National University Hospital, Seoul, Republic of Korea.
- Neuroscience Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea.
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15
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Davidson C. Histopathologic and Molecular Evaluation of Meningioma. Neurosurg Clin N Am 2023; 34:311-318. [DOI: 10.1016/j.nec.2023.02.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/07/2023]
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16
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Wang J, Zhang M, Liu YF, Yao Y, Ji YS, Etcheverry A, Chen K, Song BQ, Lin W, Yin A, He YL. Potent predictive CpG signature for temozolomide response in non-glioma-CpG island methylator phenotype glioblastomas with methylated MGMT promoter. Epigenomics 2022; 14:1233-1247. [DOI: 10.2217/epi-2022-0344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Aim: We aimed to identify potent CpG signatures predicting temozolomide (TMZ) response in glioblastomas (GBMs) that do not have the glioma-CpG island methylator phenotype (G-CIMP) but have a methylated promoter of MGMT (me MGMT). Materials & methods: Different datasets of non-G-CIMP me MGMT GBMs with molecular and clinical data were analyzed. Results: A panel of 77 TMZ efficacy-related CpGs and a seven-CpG risk signature were identified and validated for distinguishing differential outcomes to radiotherapy plus TMZ versus radiotherapy alone in non-G-CIMP me MGMT GBMs. An integrated classification scheme was also proposed for refining a MGMT-based TMZ-guiding approach in all G-CIMP-GBMs. Conclusion: The CpG signatures may serve as promising predictive biomarker candidates for guiding optimal TMZ usage in non-G-CIMP me MGMT GBMs.
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Affiliation(s)
- Jiu Wang
- Department of Neurosurgery, Xijing Institute of Clinical Neuroscience, Xijing Hospital, Fourth Military Medical University, Xi’an, 710032, China
| | - Meng Zhang
- Department of Pharmacology, School of Pharmacy, Fourth Military Medical University, Xi’an, 710032, Shaanxi
| | - Yi-feng Liu
- Department of Biochemistry & Molecular Biology, Fourth Military Medical University, Xi’an, 710032, China
| | - Yan Yao
- Department of Biochemistry & Molecular Biology, Fourth Military Medical University, Xi’an, 710032, China
| | - Yu-sha Ji
- Department of Biochemistry & Molecular Biology, Fourth Military Medical University, Xi’an, 710032, China
| | - Amandine Etcheverry
- CNRS, UMR 6290, Institut de Génétique et Développement de Rennes (IGdR), Rennes F-35043, France
| | - Kun Chen
- Department of Anatomy, Histology & Embryology & K.K. Leung, Brain Research Centre, School of Basic Medicine, Fourth Military Medical University, Xi’an, 710032, China
| | - Bao-qiang Song
- Department of Plastic & Reconstructive Surgery, Xijing Hospital, Fourth Military Medical University, Xi’an, 710032, China
| | - Wei Lin
- Department of Neurosurgery, Xijing Institute of Clinical Neuroscience, Xijing Hospital, Fourth Military Medical University, Xi’an, 710032, China
| | - Anan Yin
- Department of Neurosurgery, Xijing Institute of Clinical Neuroscience, Xijing Hospital, Fourth Military Medical University, Xi’an, 710032, China
- Department of Biochemistry & Molecular Biology, Fourth Military Medical University, Xi’an, 710032, China
- Department of Plastic & Reconstructive Surgery, Xijing Hospital, Fourth Military Medical University, Xi’an, 710032, China
| | - Ya-long He
- Department of Neurosurgery, Xijing Institute of Clinical Neuroscience, Xijing Hospital, Fourth Military Medical University, Xi’an, 710032, China
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17
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Wang S, Ding B, Wang S, Yan W, Xia Q, Meng D, Xie S, Shen S, Yu B, Liu H, Hu J, Zhang X. Gene signature of m 6A RNA regulators in diagnosis, prognosis, treatment, and immune microenvironment for cervical cancer. Sci Rep 2022; 12:17667. [PMID: 36271283 PMCID: PMC9587246 DOI: 10.1038/s41598-022-22211-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Accepted: 10/11/2022] [Indexed: 01/18/2023] Open
Abstract
Continuing studies imply that m6A RNA modification is involved in the development of cervical cancer (CC), but lack strong support on recurrence and diagnosis prediction. In this research, a comprehensive analysis of 33 m6A regulators was performed to fulfill them. Here, we performed diagnostic and prognosis models and identified key regulators, respectively. Then the CC patients were separated into two clusters in accordance with 33 regulators, and participants in the cluster 1 had a worse prognosis. Subsequently, the m6AScore was calculated to quantify the m6A modification pattern based on regulators and we found that patients in cluster 1 had higher m6AScore. Afterwards, immune microenvironment, cell infiltration, escape analyses and tumor burden mutation analyses were executed, and results showed that m6AScore was correlated with them, but to a limited extent. Interestingly, HLAs and immune checkpoint expression, and immunophenoscore in patients with high-m6AScores were significantly lower than those in the low-m6AScore group. These suggested the m6AScores might be used to predict the feasibility of immunotherapy in patients. Results provided a distinctive perspective on m6A modification and theoretical basis for CC diagnosis, prognosis, clinical treatment strategies, and potential mechanism exploration.
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Affiliation(s)
- Shizhi Wang
- grid.263826.b0000 0004 1761 0489Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, 87 Dingjiaqiao, Gulou District, Nanjing, 210009 China
| | - Bo Ding
- grid.263826.b0000 0004 1761 0489Department of Gynecology and Obstetrics, School of Medicine, Zhongda Hospital, Southeast University, Nanjing, China
| | - Shiyuan Wang
- grid.263826.b0000 0004 1761 0489Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, 87 Dingjiaqiao, Gulou District, Nanjing, 210009 China
| | - Wenjing Yan
- grid.263826.b0000 0004 1761 0489Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, 87 Dingjiaqiao, Gulou District, Nanjing, 210009 China
| | - Qianqian Xia
- grid.263826.b0000 0004 1761 0489Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, 87 Dingjiaqiao, Gulou District, Nanjing, 210009 China
| | - Dan Meng
- grid.263826.b0000 0004 1761 0489Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, 87 Dingjiaqiao, Gulou District, Nanjing, 210009 China
| | - Shuqian Xie
- grid.263826.b0000 0004 1761 0489Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, 87 Dingjiaqiao, Gulou District, Nanjing, 210009 China
| | - Siyuan Shen
- grid.263826.b0000 0004 1761 0489Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, 87 Dingjiaqiao, Gulou District, Nanjing, 210009 China
| | - Bingjia Yu
- grid.263826.b0000 0004 1761 0489Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, 87 Dingjiaqiao, Gulou District, Nanjing, 210009 China
| | - Haohan Liu
- grid.263826.b0000 0004 1761 0489Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, 87 Dingjiaqiao, Gulou District, Nanjing, 210009 China
| | - Jing Hu
- grid.263826.b0000 0004 1761 0489Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, 87 Dingjiaqiao, Gulou District, Nanjing, 210009 China
| | - Xing Zhang
- grid.263826.b0000 0004 1761 0489Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, 87 Dingjiaqiao, Gulou District, Nanjing, 210009 China
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18
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Richardson TE, Walker JM, Abdullah KG, McBrayer SK, Viapiano MS, Mussa ZM, Tsankova NM, Snuderl M, Hatanpaa KJ. Chromosomal instability in adult-type diffuse gliomas. Acta Neuropathol Commun 2022; 10:115. [PMID: 35978439 PMCID: PMC9386991 DOI: 10.1186/s40478-022-01420-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 08/04/2022] [Indexed: 11/14/2022] Open
Abstract
Chromosomal instability (CIN) is a fundamental property of cancer and a key underlying mechanism of tumorigenesis and malignant progression, and has been documented in a wide variety of cancers, including colorectal carcinoma with mutations in genes such as APC. Recent reports have demonstrated that CIN, driven in part by mutations in genes maintaining overall genomic stability, is found in subsets of adult-type diffusely infiltrating gliomas of all histologic and molecular grades, with resulting elevated overall copy number burden, chromothripsis, and poor clinical outcome. Still, relatively few studies have examined the effect of this process, due in part to the difficulty of routinely measuring CIN clinically. Herein, we review the underlying mechanisms of CIN, the relationship between chromosomal instability and malignancy, the prognostic significance and treatment potential in various cancers, systemic disease, and more specifically, in diffusely infiltrating glioma subtypes. While still in the early stages of discovery compared to other solid tumor types in which CIN is a known driver of malignancy, the presence of CIN as an early factor in gliomas may in part explain the ability of these tumors to develop resistance to standard therapy, while also providing a potential molecular target for future therapies.
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Affiliation(s)
- Timothy E. Richardson
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, Annenberg Building, 15th Floor, 1468 Madison Avenue, New York, NY 10029 USA
| | - Jamie M. Walker
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, Annenberg Building, 15th Floor, 1468 Madison Avenue, New York, NY 10029 USA
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029 USA
| | - Kalil G. Abdullah
- Department of Neurosurgery, University of Pittsburgh School of Medicine, 200 Lothrop St, Pittsburgh, PA 15213 USA
- Hillman Comprehensive Cancer Center, University of Pittsburgh Medical Center, 5115 Centre Ave, Pittsburgh, PA 15232 USA
| | - Samuel K. McBrayer
- Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX 75390 USA
- Children’s Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390 USA
| | - Mariano S. Viapiano
- Department of Neuroscience and Physiology, State University of New York, Upstate Medical University, Syracuse, NY 13210 USA
- Department of Neurosurgery, State University of New York, Upstate Medical University, Syracuse, NY 13210 USA
| | - Zarmeen M. Mussa
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, Annenberg Building, 15th Floor, 1468 Madison Avenue, New York, NY 10029 USA
| | - Nadejda M. Tsankova
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, Annenberg Building, 15th Floor, 1468 Madison Avenue, New York, NY 10029 USA
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029 USA
| | - Matija Snuderl
- Department of Pathology, New York University Langone Health, New York City, NY 10016 USA
| | - Kimmo J. Hatanpaa
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX 75390 USA
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19
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Shen Y, Lian D, Shi K, Gao Y, Hu X, Yu K, Zhao Q, Feng C. Cancer Risk and Mutational Patterns Following Organ Transplantation. Front Cell Dev Biol 2022; 10:956334. [PMID: 35837331 PMCID: PMC9274140 DOI: 10.3389/fcell.2022.956334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Accepted: 06/13/2022] [Indexed: 12/24/2022] Open
Abstract
The rapid development of medical technology and widespread application of immunosuppressive drugs have improved the success rate of organ transplantation significantly. However, the use of immunosuppressive agents increases the frequency of malignancy greatly. With the prospect of “precision medicine” for tumors and development of next-generation sequencing technology, more attention has been paid to the application of high-throughput sequencing technology in clinical oncology research, which is mainly applied to the early diagnosis of tumors and analysis of tumor-related genes. All generations of cancers carry somatic mutations, meanwhile, significant differences were observed in mutational signatures across tumors. Systematic sequencing of cancer genomes from patients after organ transplantation can reveal DNA damage and repair processes in exposed cancer cells and their precursors. In this review, we summarize the application of high-throughput sequencing and organoids in the field of organ transplantation, the mutational patterns of cancer genomes, and propose a new research strategy for understanding the mechanism of cancer following organ transplantation.
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Affiliation(s)
- Yangyang Shen
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Di Lian
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Kai Shi
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Yuefeng Gao
- College of Applied Engineering, Henan University of Science and Technology, Sanmenxia, China
- Sanmenxia Polytechnic, Sanmenxia, China
| | - Xiaoxiang Hu
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Kun Yu
- College of Animal Science and Technology, China Agricultural University, Beijing, China
- *Correspondence: Kun Yu, ; Qian Zhao, ; Chungang Feng,
| | - Qian Zhao
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
- *Correspondence: Kun Yu, ; Qian Zhao, ; Chungang Feng,
| | - Chungang Feng
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
- *Correspondence: Kun Yu, ; Qian Zhao, ; Chungang Feng,
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