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Zeng Y, Mao Y, Chen Y, Wang Y, Xu S. DNA methylation induces subtle mechanical alteration but significant chiral selectivity. Chem Commun (Camb) 2023; 59:14855-14858. [PMID: 38015496 PMCID: PMC10794036 DOI: 10.1039/d3cc05211g] [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] [Indexed: 11/29/2023]
Abstract
DNA methylation is a major epigenetic modification that is closely related to human health. Many experimental techniques as well as theoretical methods have been used to detect the modified nucleotides and identify their effects on molecular binding. It remains challenging to resolve the effect of few methylations of nucleic acids. Using super-resolution force spectroscopy, we firstly revealed that single cytosine methylation increases the mechanical stability of the DNA duplex by 1.9 ± 0.3 pN. Methylation also induces significant chiral selectivity towards drug molecules such as d,l-tetrahydropalmatine. Our results precisely quantify the mechanical effect of methylation and suggest that drug design should take methylation into consideration for enhanced selectivity.
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Affiliation(s)
- Yi Zeng
- Department of Chemistry, University of Houston, Houston, TX 77204, USA.
| | - Yujia Mao
- Department of Chemistry, University of Houston, Houston, TX 77204, USA.
| | - Yanjun Chen
- Department of Chemistry, University of Houston, Houston, TX 77204, USA.
| | - Yuhong Wang
- Department of Biology and Biochemistry, University of Houston, TX 77204, USA.
| | - Shoujun Xu
- Department of Chemistry, University of Houston, Houston, TX 77204, USA.
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2
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Lees J, Pèrtille F, Løtvedt P, Jensen P, Bosagna CG. The mitoepigenome responds to stress, suggesting novel mito-nuclear interactions in vertebrates. BMC Genomics 2023; 24:561. [PMID: 37736707 PMCID: PMC10515078 DOI: 10.1186/s12864-023-09668-9] [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: 03/28/2023] [Accepted: 09/11/2023] [Indexed: 09/23/2023] Open
Abstract
The mitochondria are central in the cellular response to changing environmental conditions resulting from disease states, environmental exposures or normal physiological processes. Although the influences of environmental stressors upon the nuclear epigenome are well characterized, the existence and role of the mitochondrial epigenome remains contentious. Here, by quantifying the mitochondrial epigenomic response of pineal gland cells to circadian stress, we confirm the presence of extensive cytosine methylation within the mitochondrial genome. Furthermore, we identify distinct epigenetically plastic regions (mtDMRs) which vary in cytosinic methylation, primarily in a non CpG context, in response to stress and in a sex-specific manner. Motifs enriched in mtDMRs contain recognition sites for nuclear-derived DNA-binding factors (ATF4, HNF4A) important in the cellular metabolic stress response, which we found to be conserved across diverse vertebrate taxa. Together, these findings suggest a new layer of mito-nuclear interaction in which the nuclear metabolic stress response could alter mitochondrial transcriptional dynamics through the binding of nuclear-derived transcription factors in a methylation-dependent context.
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Affiliation(s)
- John Lees
- Evolutionsbiologiskt Centrum (EBC), Uppsala University, Uppsala, 75236, Sweden
| | - Fábio Pèrtille
- Evolutionsbiologiskt Centrum (EBC), Uppsala University, Uppsala, 75236, Sweden
| | - Pia Løtvedt
- Institutionen För Fysik, Kemi Och Biologi (IFM), Linköping University, Linköping, 58330, Sweden
| | - Per Jensen
- Institutionen För Fysik, Kemi Och Biologi (IFM), Linköping University, Linköping, 58330, Sweden
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3
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Wang Z, Wang P, Zhang J, Gong H, Zhang X, Song J, Nie L, Peng Y, Li Y, Peng H, Cui Y, Li H, Hu B, Mi J, Liang L, Liu H, Zhang J, Ye M, Yazdanbakhsh K, Mohandas N, An X, Han X, Liu J. The novel GATA1-interacting protein HES6 is an essential transcriptional cofactor for human erythropoiesis. Nucleic Acids Res 2023; 51:4774-4790. [PMID: 36929421 PMCID: PMC10250228 DOI: 10.1093/nar/gkad167] [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: 10/08/2022] [Revised: 02/21/2023] [Accepted: 03/15/2023] [Indexed: 03/18/2023] Open
Abstract
Normal erythropoiesis requires the precise regulation of gene expression patterns, and transcription cofactors play a vital role in this process. Deregulation of cofactors has emerged as a key mechanism contributing to erythroid disorders. Through gene expression profiling, we found HES6 as an abundant cofactor expressed at gene level during human erythropoiesis. HES6 physically interacted with GATA1 and influenced the interaction of GATA1 with FOG1. Knockdown of HES6 impaired human erythropoiesis by decreasing GATA1 expression. Chromatin immunoprecipitation and RNA sequencing revealed a rich set of HES6- and GATA1-co-regulated genes involved in erythroid-related pathways. We also discovered a positive feedback loop composed of HES6, GATA1 and STAT1 in the regulation of erythropoiesis. Notably, erythropoietin (EPO) stimulation led to up-regulation of these loop components. Increased expression levels of loop components were observed in CD34+ cells of polycythemia vera patients. Interference by either HES6 knockdown or inhibition of STAT1 activity suppressed proliferation of erythroid cells with the JAK2V617F mutation. We further explored the impact of HES6 on polycythemia vera phenotypes in mice. The identification of the HES6-GATA1 regulatory loop and its regulation by EPO provides novel insights into human erythropoiesis regulated by EPO/EPOR and a potential therapeutic target for the management of polycythemia vera.
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Affiliation(s)
- Zi Wang
- Department of Hematology, The Second Xiangya Hospital of Central South University; Molecular Biology Research Center, Center for Medical Genetics, School of Life Sciences; Hunan Province Key Laboratory of Basic and Applied Hematology, Central South University, Changsha 410011, China
| | - Pan Wang
- Department of Hematology, The Second Xiangya Hospital of Central South University; Molecular Biology Research Center, Center for Medical Genetics, School of Life Sciences; Hunan Province Key Laboratory of Basic and Applied Hematology, Central South University, Changsha 410011, China
| | - Jieying Zhang
- Department of Hematology, The Second Xiangya Hospital of Central South University; Molecular Biology Research Center, Center for Medical Genetics, School of Life Sciences; Hunan Province Key Laboratory of Basic and Applied Hematology, Central South University, Changsha 410011, China
- Basic Medical Institute; Hongqiao International Institute of Medicine, Tongren Hospital; Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Han Gong
- Department of Hematology, The Second Xiangya Hospital of Central South University; Molecular Biology Research Center, Center for Medical Genetics, School of Life Sciences; Hunan Province Key Laboratory of Basic and Applied Hematology, Central South University, Changsha 410011, China
| | - Xuchao Zhang
- Department of Hematology, The Second Xiangya Hospital of Central South University; Molecular Biology Research Center, Center for Medical Genetics, School of Life Sciences; Hunan Province Key Laboratory of Basic and Applied Hematology, Central South University, Changsha 410011, China
| | - Jianhui Song
- Xiangya Hospital, Central South University, Changsha 410008, China
| | - Ling Nie
- Xiangya Hospital, Central South University, Changsha 410008, China
| | - Yuanliang Peng
- Department of Hematology, The Second Xiangya Hospital of Central South University; Molecular Biology Research Center, Center for Medical Genetics, School of Life Sciences; Hunan Province Key Laboratory of Basic and Applied Hematology, Central South University, Changsha 410011, China
| | - Yanan Li
- Department of Hematology, The Second Xiangya Hospital of Central South University; Molecular Biology Research Center, Center for Medical Genetics, School of Life Sciences; Hunan Province Key Laboratory of Basic and Applied Hematology, Central South University, Changsha 410011, China
| | - Hongling Peng
- Department of Hematology, The Second Xiangya Hospital of Central South University; Molecular Biology Research Center, Center for Medical Genetics, School of Life Sciences; Hunan Province Key Laboratory of Basic and Applied Hematology, Central South University, Changsha 410011, China
| | - Yajuan Cui
- Department of Hematology, The Second Xiangya Hospital of Central South University; Molecular Biology Research Center, Center for Medical Genetics, School of Life Sciences; Hunan Province Key Laboratory of Basic and Applied Hematology, Central South University, Changsha 410011, China
| | - Heng Li
- Department of Hematology, The Second Xiangya Hospital of Central South University; Molecular Biology Research Center, Center for Medical Genetics, School of Life Sciences; Hunan Province Key Laboratory of Basic and Applied Hematology, Central South University, Changsha 410011, China
| | - Bin Hu
- Department of Hematology, The Second Xiangya Hospital of Central South University; Molecular Biology Research Center, Center for Medical Genetics, School of Life Sciences; Hunan Province Key Laboratory of Basic and Applied Hematology, Central South University, Changsha 410011, China
| | - Jun Mi
- Basic Medical Institute; Hongqiao International Institute of Medicine, Tongren Hospital; Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Long Liang
- Department of Hematology, The Second Xiangya Hospital of Central South University; Molecular Biology Research Center, Center for Medical Genetics, School of Life Sciences; Hunan Province Key Laboratory of Basic and Applied Hematology, Central South University, Changsha 410011, China
| | - Hong Liu
- Xiangya Hospital, Central South University, Changsha 410008, China
| | - Ji Zhang
- Department of Clinical Laboratory, the First Affiliated Hospital, University of South China, Hengyang 421001, China
| | - Mao Ye
- Molecular Science and Biomedicine Laboratory, State Key Laboratory for Chemo/Biosensing and Chemometrics; College of Biology; College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | | | - Narla Mohandas
- Red Cell Physiology Laboratory, NY Blood Center, NY 10065, USA
| | - Xiuli An
- Laboratory of Membrane Biology, NY Blood Center, NY 10065, USA
| | - Xu Han
- Department of Hematology, The Second Xiangya Hospital of Central South University; Molecular Biology Research Center, Center for Medical Genetics, School of Life Sciences; Hunan Province Key Laboratory of Basic and Applied Hematology, Central South University, Changsha 410011, China
| | - Jing Liu
- Department of Hematology, The Second Xiangya Hospital of Central South University; Molecular Biology Research Center, Center for Medical Genetics, School of Life Sciences; Hunan Province Key Laboratory of Basic and Applied Hematology, Central South University, Changsha 410011, China
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4
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Wei A, Wu H. Mammalian DNA methylome dynamics: mechanisms, functions and new frontiers. Development 2022; 149:dev182683. [PMID: 36519514 PMCID: PMC10108609 DOI: 10.1242/dev.182683] [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] [Indexed: 12/23/2022]
Abstract
DNA methylation is a highly conserved epigenetic modification that plays essential roles in mammalian gene regulation, genome stability and development. Despite being primarily considered a stable and heritable epigenetic silencing mechanism at heterochromatic and repetitive regions, whole genome methylome analysis reveals that DNA methylation can be highly cell-type specific and dynamic within proximal and distal gene regulatory elements during early embryonic development, stem cell differentiation and reprogramming, and tissue maturation. In this Review, we focus on the mechanisms and functions of regulated DNA methylation and demethylation, highlighting how these dynamics, together with crosstalk between DNA methylation and histone modifications at distinct regulatory regions, contribute to mammalian development and tissue maturation. We also discuss how recent technological advances in single-cell and long-read methylome sequencing, along with targeted epigenome-editing, are enabling unprecedented high-resolution and mechanistic dissection of DNA methylome dynamics.
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Affiliation(s)
- Alex Wei
- Department of Genetics, University of Pennsylvania, Philadelphia, PA 19104, USA
- Penn Epigenetics Institute, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Hao Wu
- Department of Genetics, University of Pennsylvania, Philadelphia, PA 19104, USA
- Penn Epigenetics Institute, University of Pennsylvania, Philadelphia, PA 19104, USA
- Penn Institute of Regenerative Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
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5
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Sapozhnikov DM, Szyf M. Enzyme-free targeted DNA demethylation using CRISPR-dCas9-based steric hindrance to identify DNA methylation marks causal to altered gene expression. Nat Protoc 2022; 17:2840-2881. [PMID: 36207463 DOI: 10.1038/s41596-022-00741-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 06/22/2022] [Indexed: 11/09/2022]
Abstract
DNA methylation involves the enzymatic addition of a methyl group primarily to cytosine residues in DNA. This protocol describes how to produce complete and minimally confounded DNA demethylation of specific sites in the genome of cultured cells by clustered regularly interspaced short palindromic repeats (CRISPR)-dCas9 and without the involvement of an epigenetic-modifying enzyme, the purpose of which is the evaluation of the functional (i.e., gene expression or phenotypic) consequences of DNA demethylation of specific sites that have been previously implicated in particular pathological or physiological contexts. This protocol maximizes the ability of the easily reprogrammable CRISPR-dCas9 system to assess the impact of DNA methylation from a causal rather than correlational perspective: alternative protocols for CRISPR-dCas9-based site-specific DNA methylation or demethylation rely on the recruitment of epigenetic enzymes that exhibit additional nonspecific activities at both the targeted site and throughout the genome, confounding conclusions of causality of DNA methylation. Inhibition or loss of DNA methylation is accomplished by three consecutive lentiviral transductions. The first two lentiviruses establish stable expression of dCas9 and a guide RNA, which will physically obstruct either maintenance or de novo DNA methyltransferase activity at the guide RNA target site. A third lentivirus introduces Cre recombinase to delete the dCas9 transgene, which leads to loss of dCas9 from the target site, allowing transcription factors and/or the transcription machinery to interact with the demethylated target site. This protocol requires 3-8 months to complete owing to prolonged cell passaging times, but there is little hands-on time, and no specific skills beyond basic molecular biology techniques are necessary.
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Affiliation(s)
- Daniel M Sapozhnikov
- Department of Pharmacology and Therapeutics, Faculty of Medicine, McGill University, Montreal, Quebec, Canada
| | - Moshe Szyf
- Department of Pharmacology and Therapeutics, Faculty of Medicine, McGill University, Montreal, Quebec, Canada.
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6
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Gong X, Jensen E, Bucerius S, Parniske M. A CCaMK/Cyclops response element in the promoter of Lotus japonicus calcium-binding protein 1 (CBP1) mediates transcriptional activation in root symbioses. THE NEW PHYTOLOGIST 2022; 235:1196-1211. [PMID: 35318667 DOI: 10.1111/nph.18112] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 12/24/2021] [Indexed: 06/14/2023]
Abstract
Early gene expression in arbuscular mycorrhiza (AM) and the nitrogen-fixing root nodule symbiosis (RNS) is governed by a shared regulatory complex. Yet many symbiosis-induced genes are specifically activated in only one of the two symbioses. The Lotus japonicus T-DNA insertion line T90, carrying a promoterless uidA (GUS) gene in the promoter of Calcium Binding Protein 1 (CBP1) is exceptional as it exhibits GUS activity in both root endosymbioses. To identify the responsible cis- and trans-acting factors, we subjected deletion/modification series of CBP1 promoter : reporter fusions to transactivation and spatio-temporal expression analysis and screened ethyl methanesulphonate (EMS)-mutagenized T90 populations for aberrant GUS expression. We identified one cis-regulatory element required for GUS expression in the epidermis and a second element, necessary and sufficient for transactivation by the calcium and calmodulin-dependent protein kinase (CCaMK) in combination with the transcription factor Cyclops and conferring gene expression during both AM and RNS. Lack of GUS expression in T90 white mutants could be traced to DNA hypermethylation detected in and around this element. We concluded that the CCaMK/Cyclops complex can contribute to at least three distinct gene expression patterns on its direct target promoters NIN (RNS), RAM1 (AM), and CBP1 (AM and RNS), calling for yet-to-be identified specificity-conferring factors.
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Affiliation(s)
- Xiaoyun Gong
- Genetics, Faculty of Biology, LMU Munich, Grosshaderner Str. 2-4, D-82152, Martinsried, Germany
| | - Elaine Jensen
- The Sainsbury Laboratory, Colney Lane, Norwich, NR4 7UH, UK
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, Wales, Ceredigion, SY23 3EB, UK
| | - Simone Bucerius
- Genetics, Faculty of Biology, LMU Munich, Grosshaderner Str. 2-4, D-82152, Martinsried, Germany
| | - Martin Parniske
- Genetics, Faculty of Biology, LMU Munich, Grosshaderner Str. 2-4, D-82152, Martinsried, Germany
- The Sainsbury Laboratory, Colney Lane, Norwich, NR4 7UH, UK
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7
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Habano W, Miura T, Terashima J, Ozawa S. Aryl hydrocarbon receptor as a DNA methylation reader in the stress response pathway. Toxicology 2022; 470:153154. [PMID: 35301058 DOI: 10.1016/j.tox.2022.153154] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 01/31/2022] [Accepted: 03/10/2022] [Indexed: 10/18/2022]
Abstract
The aryl hydrocarbon receptor (AhR) mediates various cellular responses upon exposure to exogenous and endogenous stress factors. In these responses, AhR plays a dual role as a stress sensor for detecting various AhR ligands and as a transcription factor that upregulates the expression of downstream effector genes, such as those encoding drug-metabolizing enzymes. As a transcription factor, it selectively binds to the unmethylated form of a specific sequence called the xenobiotic responsive element (XRE). We suggest that AhR is a novel DNA methylation reader, unlike classical methylation readers, such as methyl-CpG-binding protein 2, which binds to methylated sequences. Under physiological conditions of continuous exposure to endogenous AhR ligands, such as kynurenine, methylation states of the individual target XREs must be strictly regulated to select and coordinate the expression of downstream genes responsible for maintaining homeostasis in the body. In contrast, long-term exposure to AhR ligands frequently leads to changes in the methylation patterns around the XRE sequence. These data indicate that AhR may contribute to the adaptive cellular response to various stresses by modulating DNA methylation. Thus, the DNA methylation profile of AhR target genes should be dynamically controlled through a balance between robustness and flexibility under both physiological and stress conditions. AhR is a pivotal player in the regulation of stress response as it shows versatility by functioning as a stress sensor, methylation reader, and putative methylation modulator.
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Affiliation(s)
- Wataru Habano
- Division of Pharmacodynamics and Molecular Genetics, Department of Clinical Pharmaceutical Sciences, School of Pharmacy, Iwate Medical University, Shiwa 028-3694, Iwate, Japan.
| | - Toshitaka Miura
- Division of Pharmacodynamics and Molecular Genetics, Department of Clinical Pharmaceutical Sciences, School of Pharmacy, Iwate Medical University, Shiwa 028-3694, Iwate, Japan
| | - Jun Terashima
- Division of Pharmacodynamics and Molecular Genetics, Department of Clinical Pharmaceutical Sciences, School of Pharmacy, Iwate Medical University, Shiwa 028-3694, Iwate, Japan
| | - Shogo Ozawa
- Division of Pharmacodynamics and Molecular Genetics, Department of Clinical Pharmaceutical Sciences, School of Pharmacy, Iwate Medical University, Shiwa 028-3694, Iwate, Japan
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8
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Zhang L, Rong W, Ma J, Li H, Tang X, Xu S, Wang L, Wan L, Zhu Q, Jiang B, Su F, Cui H. Comprehensive Analysis of DNA 5-Methylcytosine and N6-Adenine Methylation by Nanopore Sequencing in Hepatocellular Carcinoma. Front Cell Dev Biol 2022; 10:827391. [PMID: 35321246 PMCID: PMC8937020 DOI: 10.3389/fcell.2022.827391] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 02/10/2022] [Indexed: 12/13/2022] Open
Abstract
DNA methylation is a widespread epigenetic signal in human genome. With Nanopore technology, differential methylation modifications including 5-methylcytosine (5mC) and 6-methyladenine (6mA) can be identified. 5mC is the most important modification in mammals, although 6mA may also function in growth and development as well as in pathogenesis. While the role of 5mC at CpG islands in promoter regions associated with transcriptional regulation has been well studied, but the relationship between 6mA and transcription is still unclear. Thus, we collected two pairs of tumor tissues and adjacent normal tissues from hepatocellular carcinoma (HCC) surgical samples for Nanopore sequencing and transcriptome sequencing. It was found that 2,373 genes had both 5mC and 6mA, along with up- and down-regulated methylation sites. These genes were regarded as unstable methylation genes. Compared with 6mA, 5mC had more inclined distribution of unstable methylation sites. Chi-square test showed that the levels of 5mC were consistent with both up- and down-regulated genes, but 6mA was not significant. Moreover, the top three unstable methylation genes, TBC1D3H, CSMD1, and ROBO2, were all related to cancer. Transcriptome and survival analyses revealed four potential tumor suppressor genes including KCNIP4, CACNA1C, PACRG, and ST6GALNAC3. In this study, we firstly proposed to combine 5mC and 6mA methylation sites to explore functional genes, and further research found top of these unstable methylation genes might be functional and some of them could serve as potential tumor suppressor genes. Our study provided a new solution for epigenetic regulation research and therapy of HCC.
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Affiliation(s)
- Lili Zhang
- Clinical Biobank, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
- Department of General Surgery, Department of Hepato-Bilio-Pancreatic Surgery, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
| | - Weiqi Rong
- Department of Hepatobiliary Surgery, National Cancer Center, National Clinical Research Center for Cancer, Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jie Ma
- Department of Hepatopancreatobiliary Surgery, Affiliated Hospital of Qinghai University, Qinghai, China
| | - Hexin Li
- Clinical Biobank, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
| | - Xiaokun Tang
- Clinical Biobank, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
| | - Siyuan Xu
- Clinical Biobank, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
| | - Luyao Wang
- Clinical Biobank, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
| | - Li Wan
- Clinical Biobank, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
| | - Qing Zhu
- Department of Hepatopancreatobiliary Surgery, Affiliated Hospital of Qinghai University, Qinghai, China
| | - Boyue Jiang
- Department of General Surgery, Department of Hepato-Bilio-Pancreatic Surgery, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
| | - Fei Su
- Clinical Biobank, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
| | - Hongyuan Cui
- Department of General Surgery, Department of Hepato-Bilio-Pancreatic Surgery, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
- Department of Hepatopancreatobiliary Surgery, Affiliated Hospital of Qinghai University, Qinghai, China
- *Correspondence: Hongyuan Cui,
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9
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Wada K, Misaka T, Yokokawa T, Kimishima Y, Kaneshiro T, Oikawa M, Yoshihisa A, Takeishi Y. Blood-Based Epigenetic Markers of FKBP5 Gene Methylation in Patients With Dilated Cardiomyopathy. J Am Heart Assoc 2021; 10:e021101. [PMID: 34713710 PMCID: PMC8751844 DOI: 10.1161/jaha.121.021101] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Background Blood‐based DNA methylation patterns are linked to types of diseases. FKBP prolyl isomerase 5 (FKBP5), a protein cochaperone, is known to be associated with the inflammatory response, but the regulatory mechanisms by leukocyte FKBP5 DNA methylation in patients with dilated cardiomyopathy (DCM) remain unclear. Methods and Results The present study enrolled patients with DCM (n=31) and age‐matched and sex‐matched control participants (n=43). We assessed FKBP5 CpG (cytosine‐phosphate‐guanine) methylation of CpG islands at the 5′ side as well as putative promoter regions by methylation‐specific quantitative polymerase chain reaction using leukocyte DNA isolated from the peripheral blood. FKBP5 CpG methylation levels at the CpG island of the gene body and the promoter regions were significantly decreased in patients with DCM. Leukocyte FKBP5 and IL‐1β (interleukin 1β) mRNA expression levels were significantly higher in patients with DCM than in controls. The protein expressions of DNMT1 (DNA methyltransferase 1) and DNMT3A (DNA methyltransferase 3A) in leukocytes were significantly reduced in patients with DCM. In vitro methylation assay revealed that FKBP5 promoter activity was inhibited at the methylated conditions in response to immune stimulation, suggesting that the decreased FKBP5 CpG methylation was functionally associated with elevation of FKBP5 mRNA expressions. Histological analysis using a mouse model with pressure overload showed that FKBP5‐expressing cells were substantially infiltrated in the myocardial interstitium in the failing hearts, indicating a possible role of FKBP5 expressions of immune cells in the cardiac remodeling. Conclusions Our findings demonstrate a link between specific CpG hypomethylation of leukocyte FKBP5 and DCM. Blood‐based epigenetic modification in FKBP5 may be a novel molecular mechanism that contributes to the pathogenesis of DCM.
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Affiliation(s)
- Kento Wada
- Department of Cardiovascular Medicine Fukushima Medical University Fukushima Japan
| | - Tomofumi Misaka
- Department of Cardiovascular Medicine Fukushima Medical University Fukushima Japan
| | - Tetsuro Yokokawa
- Department of Cardiovascular Medicine Fukushima Medical University Fukushima Japan
| | - Yusuke Kimishima
- Department of Cardiovascular Medicine Fukushima Medical University Fukushima Japan
| | - Takashi Kaneshiro
- Department of Cardiovascular Medicine Fukushima Medical University Fukushima Japan.,Department of Arrhythmia and Cardiac Pacing Fukushima Medical University Fukushima Japan
| | - Masayoshi Oikawa
- Department of Cardiovascular Medicine Fukushima Medical University Fukushima Japan
| | - Akiomi Yoshihisa
- Department of Cardiovascular Medicine Fukushima Medical University Fukushima Japan.,Department of Clinical Laboratory Sciences Fukushima Medical University School of Health Science Fukushima Japan
| | - Yasuchika Takeishi
- Department of Cardiovascular Medicine Fukushima Medical University Fukushima Japan
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10
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Activation of γ-globin gene expression by GATA1 and NF-Y in hereditary persistence of fetal hemoglobin. Nat Genet 2021; 53:1177-1186. [PMID: 34341563 PMCID: PMC8610173 DOI: 10.1038/s41588-021-00904-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2020] [Accepted: 06/25/2021] [Indexed: 11/30/2022]
Abstract
Hereditary persistence of fetal hemoglobin (HPFH) ameliorates β-hemoglobinopathies by inhibiting the developmental switch from γ-globin (HBG1/HBG2) to β-globin (HBB) gene expression. Some forms of HPFH are associated with γ-globin promoter variants that either disrupt binding motifs for transcriptional repressors or create new motifs for transcriptional activators. How these variants sustain γ-globin gene expression postnatally remains undefined. We mapped γ-globin promoter sequences functionally in erythroid cells harboring different HPFH variants. Those that disrupt a BCL11A repressor binding element induce γ-globin expression by facilitating the recruitment of transcription factors NF-Y to a nearby proximal CCAAT box and GATA1 to an upstream motif. The proximal CCAAT element becomes dispensable for HPFH variants that generate new binding motifs for activators NF-Y or KLF1, but GATA1 recruitment remains essential. Our findings define distinct mechanisms through which transcription factors and their cis-regulatory elements activate γ-globin expression in different forms of HPFH, some of which are being recreated by therapeutic genome editing.
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11
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Abstract
Malignancies of the erythroid lineage are rare but aggressive diseases. Notably, the first insights into their biology emerged over half a century ago from avian and murine tumor viruses-induced erythroleukemia models providing the rationale for several transgenic mouse models that unraveled the transforming potential of signaling effectors and transcription factors in the erythroid lineage. More recently, genetic roadmaps have fueled efforts to establish models that are based on the epigenomic lesions observed in patients with erythroid malignancies. These models, together with often unexpected erythroid phenotypes in genetically modified mice, provided further insights into the molecular mechanisms of disease initiation and maintenance. Here, we review how the increasing knowledge of human erythroleukemia genetics combined with those from various mouse models indicate that the pathogenesis of the disease is based on the interplay between signaling mutations, impaired TP53 function, and altered chromatin organization. These alterations lead to aberrant activity of erythroid transcriptional master regulators like GATA1, indicating that erythroleukemia will most likely require combinatorial targeting for efficient therapeutic interventions.
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Genome-wide identification and function characterization of GATA transcription factors during development and in response to abiotic stresses and hormone treatments in pepper. J Appl Genet 2021; 62:265-280. [PMID: 33624251 DOI: 10.1007/s13353-021-00618-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 01/29/2021] [Accepted: 02/05/2021] [Indexed: 01/03/2023]
Abstract
Pepper (Capsicum annuum L.) is an economically important vegetable crop whose production and quality are severely reduced under adverse environmental stress conditions. The GATA transcription factors belonging to type IV zinc-finger proteins, play a significant role in regulating light morphogenesis, nitrate assimilation, and organ development in plants. However, the functional characteristics of GATA gene family during development and in response to environmental stresses have not yet been investigated in pepper. In this study, a total of 28 pepper GATA (CaGATA) genes were identified. To gain an overview of the CaGATAs, we analyzed their chromosomal distribution, gene structure, conservative domains, cis-elements, phylogeny, and evolutionary relationship. We divided 28 CaGATAs into four groups distributed on 10 chromosomes, and identified 7 paralogs in CaGATA family of pepper and 35 orthologous gene pairs between CaGATAs and Arabidopsis GATAs (AtGATAs). The results of promoter cis-element analysis and the quantitative real-time PCR (qRT-PCR) analysis revealed that CaGATA genes were involved in regulating the plant growth and development and the responses to various abiotic stresses and hormone treatments in pepper. Tissue-specific expression analysis showed that most CaGATA genes were preferentially expressed in flower buds, flowers, and leaves. Several CaGATA genes, especially CaGATA14, were significantly regulated under multiple abiotic stresses, and CaGATA21 and CaGATA27 were highly responsive to phytohormone treatments. Taken together, our results lay a foundation for the biological function analysis of GATA gene family in pepper.
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13
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Greville G, Llop E, Howard J, Madden SF, Perry AS, Peracaula R, Rudd PM, McCann A, Saldova R. 5-AZA-dC induces epigenetic changes associated with modified glycosylation of secreted glycoproteins and increased EMT and migration in chemo-sensitive cancer cells. Clin Epigenetics 2021; 13:34. [PMID: 33579350 PMCID: PMC7881483 DOI: 10.1186/s13148-021-01015-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Accepted: 01/18/2021] [Indexed: 12/16/2022] Open
Abstract
Background Glycosylation, one of the most fundamental post-translational modifications, is altered in cancer and is subject in part, to epigenetic regulation. As there are many epigenetic-targeted therapies currently in clinical trials for the treatment of a variety of cancers, it is important to understand the impact epi-therapeutics have on glycosylation. Results Ovarian and triple negative breast cancer cells were treated with the DNA methyltransferase inhibitor, 5-AZA-2-deoxycytidine (5-AZA-dC). Branching and sialylation were increased on secreted N-glycans from chemo-sensitive/non-metastatic cell lines following treatment with 5-AZA-dC. These changes correlated with increased mRNA expression levels in MGAT5 and ST3GAL4 transcripts in ovarian cancer cell lines. Using siRNA transient knock down of GATA2 and GATA3 transcription factors, we show that these regulate the glycosyltransferases ST3GAL4 and MGAT5, respectively. Moreover, 5-AZA-dC-treated cells displayed an increase in migration, with a greater effect seen in chemo-sensitive cell lines. Western blots showed an increase in apoptotic and senescence (p21) markers in all 5-AZA-dC-treated cells. The alterations seen in N-glycans from secreted glycoproteins in 5-AZA-dC-treated breast and ovarian cancer cells were similar to the N-glycans previously known to potentiate tumour cell survival. Conclusions While the FDA has approved epi-therapeutics for some cancer treatments, their global effect is still not fully understood. This study gives insight into the effects that epigenetic alterations have on cancer cell glycosylation, and how this potentially impacts on the overall fate of those cells. Graphic abstract ![]()
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Affiliation(s)
- Gordon Greville
- GlycoScience Group, the National Institute for Bioprocessing, Research and Training (NIBRT), Fosters Avenue, Mount Merrion, Blackrock, Co Dublin, Ireland.,College of Health and Agricultural Science (CHAS), UCD School of Medicine, University College Dublin (UCD), Belfield, Dublin 4, Ireland
| | - Esther Llop
- Biochemistry and Molecular Biology Unit, Department of Biology, University of Girona, Girona, Spain.,Girona Biomedical Research Institute (IDIBGI), Girona, Spain
| | - Jane Howard
- College of Health and Agricultural Science (CHAS), UCD School of Medicine, University College Dublin (UCD), Belfield, Dublin 4, Ireland.,UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin (UCD), Belfield, Dublin 4, Ireland
| | - Stephen F Madden
- Data Science Centre, Royal College of Surgeons in Ireland (RCSI), Dublin 2, Ireland
| | - Antoinette S Perry
- UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin (UCD), Belfield, Dublin 4, Ireland.,School of Biology and Environmental Science, University College Dublin (UCD), Belfield, Dublin 4, Ireland
| | - Rosa Peracaula
- Biochemistry and Molecular Biology Unit, Department of Biology, University of Girona, Girona, Spain.,Girona Biomedical Research Institute (IDIBGI), Girona, Spain
| | - Pauline M Rudd
- GlycoScience Group, the National Institute for Bioprocessing, Research and Training (NIBRT), Fosters Avenue, Mount Merrion, Blackrock, Co Dublin, Ireland.,UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin (UCD), Belfield, Dublin 4, Ireland
| | - Amanda McCann
- College of Health and Agricultural Science (CHAS), UCD School of Medicine, University College Dublin (UCD), Belfield, Dublin 4, Ireland.,UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin (UCD), Belfield, Dublin 4, Ireland
| | - Radka Saldova
- GlycoScience Group, the National Institute for Bioprocessing, Research and Training (NIBRT), Fosters Avenue, Mount Merrion, Blackrock, Co Dublin, Ireland. .,College of Health and Agricultural Science (CHAS), UCD School of Medicine, University College Dublin (UCD), Belfield, Dublin 4, Ireland.
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14
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Su W, Zuo T, Peterson T. Ectopic Expression of a Maize Gene Is Induced by Composite Insertions Generated Through Alternative Transposition. Genetics 2020; 216:1039-1049. [PMID: 32988986 PMCID: PMC7768264 DOI: 10.1534/genetics.120.303592] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2020] [Accepted: 09/23/2020] [Indexed: 12/25/2022] Open
Abstract
Transposable elements (TEs) are DNA sequences that can mobilize and proliferate throughout eukaryotic genomes. Previous studies have shown that in plant genomes, TEs can influence gene expression in various ways, such as inserting in introns or exons to alter transcript structure and content, and providing novel promoters and regulatory elements to generate new regulatory patterns. Furthermore, TEs can also regulate gene expression at the epigenetic level by modifying chromatin structure, changing DNA methylation status, and generating small RNAs. In this study, we demonstrated that Ac/fractured Ac (fAc) TEs are able to induce ectopic gene expression by duplicating and shuffling enhancer elements. Ac/fAc elements belong to the hAT family of class II TEs. They can undergo standard transposition events, which involve the two termini of a single transposon, or alternative transposition events that involve the termini of two different nearby elements. Our previous studies have shown that alternative transposition can generate various genome rearrangements such as deletions, duplications, inversions, translocations, and composite insertions (CIs). We identified >50 independent cases of CIs generated by Ac/fAc alternative transposition and analyzed 10 of them in detail. We show that these CIs induced ectopic expression of the maize pericarp color 2 (p2) gene, which encodes a Myb-related protein. All the CIs analyzed contain sequences including a transcriptional enhancer derived from the nearby p1 gene, suggesting that the CI-induced activation of p2 is affected by mobilization of the p1 enhancer. This is further supported by analysis of a mutant in which the CI is excised and p2 expression is lost. These results show that alternative transposition events are not only able to induce genome rearrangements, but also generate CIs that can control gene expression.
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Affiliation(s)
- Weijia Su
- Department of Genetics, Development, and Cell Biology, Iowa State University, Ames, Iowa 50011-3260
| | - Tao Zuo
- Department of Genetics, Development, and Cell Biology, Iowa State University, Ames, Iowa 50011-3260
| | - Thomas Peterson
- Department of Genetics, Development, and Cell Biology, Iowa State University, Ames, Iowa 50011-3260
- Department of Agronomy, Iowa State University, Ames, Iowa 50011-3260
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Gómez-Martín C, Aparicio-Puerta E, Medina JM, Barturen G, Oliver JL, Hackenberg M. geno 5mC: A Database to Explore the Association between Genetic Variation (SNPs) and CpG Methylation in the Human Genome. J Mol Biol 2020; 433:166709. [PMID: 33188782 DOI: 10.1016/j.jmb.2020.11.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 10/15/2020] [Accepted: 11/06/2020] [Indexed: 01/23/2023]
Abstract
Genetic variation, gene expression and DNA methylation influence each other in a complex way. To study the impact of sequence variation and DNA methylation on gene expression, we generated geno5mC, a database that contains statistically significant SNP-CpG associations that are biologically classified either through co-localization with known regulatory regions (promoters and enhancers), or through known correlations with the expression levels of nearby genes. The SNP rs727563 can be used to illustrate the usefulness of this approach. This SNP has been associated with inflammatory bowel disease through GWAS, but it is not located near any gene related to this phenotype. However, geno5mC reveals that rs727563 is associated with the methylation state of several CpGs located in promoter regions of genes reported to be involved in inflammatory processes. This case exemplifies how geno5mC can be used to infer relevant and previously unknown interactions between described disease-associated SNPs and their functional targets.
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Affiliation(s)
- C Gómez-Martín
- Dpto. de Genética, Facultad de Ciencias, Universidad de Granada, Campus de Fuentenueva s/n, 18071 Granada, Spain; Lab. de Bioinformática, Instituto de Biotecnología, Centro de Investigación Biomédica, PTS, Avda. del Conocimiento s/n, 18100 Granada, Spain
| | - E Aparicio-Puerta
- Dpto. de Genética, Facultad de Ciencias, Universidad de Granada, Campus de Fuentenueva s/n, 18071 Granada, Spain; Lab. de Bioinformática, Instituto de Biotecnología, Centro de Investigación Biomédica, PTS, Avda. del Conocimiento s/n, 18100 Granada, Spain; Instituto de Investigación Biosanitaria (IBS) Granada, University Hospitals of Granada-University, Granada, Spain, Conocimiento s/n, 18100 Granada, Spain; Excellence Research Unit "Modeling Nature" (MNat), University of Granada, 18071 Granada, Spain
| | - J M Medina
- Dpto. de Genética, Facultad de Ciencias, Universidad de Granada, Campus de Fuentenueva s/n, 18071 Granada, Spain; Lab. de Bioinformática, Instituto de Biotecnología, Centro de Investigación Biomédica, PTS, Avda. del Conocimiento s/n, 18100 Granada, Spain
| | - Guillermo Barturen
- Centro Pfizer-Universidad de Granada-Junta de Andalucía de Genómica e Investigación Oncológica, Genetics of Complex Diseases, 18016 Granada, Spain
| | - J L Oliver
- Dpto. de Genética, Facultad de Ciencias, Universidad de Granada, Campus de Fuentenueva s/n, 18071 Granada, Spain; Lab. de Bioinformática, Instituto de Biotecnología, Centro de Investigación Biomédica, PTS, Avda. del Conocimiento s/n, 18100 Granada, Spain
| | - M Hackenberg
- Dpto. de Genética, Facultad de Ciencias, Universidad de Granada, Campus de Fuentenueva s/n, 18071 Granada, Spain; Lab. de Bioinformática, Instituto de Biotecnología, Centro de Investigación Biomédica, PTS, Avda. del Conocimiento s/n, 18100 Granada, Spain; Instituto de Investigación Biosanitaria (IBS) Granada, University Hospitals of Granada-University, Granada, Spain, Conocimiento s/n, 18100 Granada, Spain; Excellence Research Unit "Modeling Nature" (MNat), University of Granada, 18071 Granada, Spain.
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Abstract
We have uncovered a novel role for the nuclear receptor-binding SET domain protein 1 (NSD1) in human and murine erythroid differentiation. Mechanistically, we found that the histone methyltransferase activity of NSD1 is essential for chromatin binding, protein interactions and target gene activation of the erythroid transcriptional master regulator GATA1.
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Affiliation(s)
- Samantha Tauchmann
- University Children's Hospital Basel (UKBB), Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Marwa Almosailleakh
- University Children's Hospital Basel (UKBB), Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Juerg Schwaller
- University Children's Hospital Basel (UKBB), Department of Biomedicine, University of Basel, Basel, Switzerland
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