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Bernstein MN, Ma Z, Gleicher M, Dewey CN. CellO: comprehensive and hierarchical cell type classification of human cells with the Cell Ontology. iScience 2020; 24:101913. [PMID: 33364592 PMCID: PMC7753962 DOI: 10.1016/j.isci.2020.101913] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 10/28/2020] [Accepted: 12/02/2020] [Indexed: 12/15/2022] Open
Abstract
Cell type annotation is a fundamental task in the analysis of single-cell RNA-sequencing data. In this work, we present CellO, a machine learning-based tool for annotating human RNA-seq data with the Cell Ontology. CellO enables accurate and standardized cell type classification of cell clusters by considering the rich hierarchical structure of known cell types. Furthermore, CellO comes pre-trained on a comprehensive data set of human, healthy, untreated primary samples in the Sequence Read Archive. CellO's comprehensive training set enables it to run out of the box on diverse cell types and achieves competitive or even superior performance when compared to existing state-of-the-art methods. Lastly, CellO's linear models are easily interpreted, thereby enabling exploration of cell-type-specific expression signatures across the ontology. To this end, we also present the CellO Viewer: a web application for exploring CellO's models across the ontology.
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Affiliation(s)
| | - Zhongjie Ma
- Department of Computer Sciences, University of Wisconsin - Madison, Madison, WI 53706, USA
| | - Michael Gleicher
- Department of Computer Sciences, University of Wisconsin - Madison, Madison, WI 53706, USA
| | - Colin N Dewey
- Department of Computer Sciences, University of Wisconsin - Madison, Madison, WI 53706, USA.,Department of Biostatistics and Medical Informatics, University of Wisconsin - Madison, Madison, WI 53792, USA
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52
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Li T, Ortiz-Fernández L, Andrés-León E, Ciudad L, Javierre BM, López-Isac E, Guillén-Del-Castillo A, Simeón-Aznar CP, Ballestar E, Martin J. Epigenomics and transcriptomics of systemic sclerosis CD4+ T cells reveal long-range dysregulation of key inflammatory pathways mediated by disease-associated susceptibility loci. Genome Med 2020; 12:81. [PMID: 32977850 PMCID: PMC7519528 DOI: 10.1186/s13073-020-00779-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Accepted: 09/08/2020] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Systemic sclerosis (SSc) is a genetically complex autoimmune disease mediated by the interplay between genetic and epigenetic factors in a multitude of immune cells, with CD4+ T lymphocytes as one of the principle drivers of pathogenesis. METHODS DNA samples exacted from CD4+ T cells of 48 SSc patients and 16 healthy controls were hybridized on MethylationEPIC BeadChip array. In parallel, gene expression was interrogated by hybridizing total RNA on Clariom™ S array. Downstream bioinformatics analyses were performed to identify correlating differentially methylated CpG positions (DMPs) and differentially expressed genes (DEGs), which were then confirmed utilizing previously published promoter capture Hi-C (PCHi-C) data. RESULTS We identified 9112 and 3929 DMPs and DEGs, respectively. These DMPs and DEGs are enriched in functional categories related to inflammation and T cell biology. Furthermore, correlation analysis identified 17,500 possible DMP-DEG interaction pairs within a window of 5 Mb, and utilizing PCHi-C data, we observed that 212 CD4+ T cell-specific pairs of DMP-DEG also formed part of three-dimensional promoter-enhancer networks, potentially involving CTCF. Finally, combining PCHi-C data with SSc GWAS data, we identified four important SSc-associated susceptibility loci, TNIP1 (rs3792783), GSDMB (rs9303277), IL12RB1 (rs2305743), and CSK (rs1378942), that could potentially interact with DMP-DEG pairs cg17239269-ANXA6, cg19458020-CCR7, cg10808810-JUND, and cg11062629-ULK3, respectively. CONCLUSION Our study unveils a potential link between genetic, epigenetic, and transcriptional deregulation in CD4+ T cells of SSc patients, providing a novel integrated view of molecular components driving SSc pathogenesis.
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Affiliation(s)
- Tianlu Li
- Epigenetics and Immune Disease Group, Josep Carreras Research Institute (IJC), 08916, Badalona, Barcelona, Spain
| | - Lourdes Ortiz-Fernández
- Instituto de Parasitología y Biomedicina López-Neyra, Consejo Superior de Investigaciones Científicas (IPBLN-CSIC), Granada, Spain
| | - Eduardo Andrés-León
- Instituto de Parasitología y Biomedicina López-Neyra, Consejo Superior de Investigaciones Científicas (IPBLN-CSIC), Granada, Spain
| | - Laura Ciudad
- Epigenetics and Immune Disease Group, Josep Carreras Research Institute (IJC), 08916, Badalona, Barcelona, Spain
| | - Biola M Javierre
- 3D Chromatin Organization, Josep Carreras Research Institute (IJC), 08916, Badalona, Barcelona, Spain
| | - Elena López-Isac
- Instituto de Parasitología y Biomedicina López-Neyra, Consejo Superior de Investigaciones Científicas (IPBLN-CSIC), Granada, Spain
| | - Alfredo Guillén-Del-Castillo
- Unit of Systemic Autoimmunity Diseases, Department of Internal Medicine, Vall d'Hebron Hospital, Barcelona, Spain
| | - Carmen Pilar Simeón-Aznar
- Unit of Systemic Autoimmunity Diseases, Department of Internal Medicine, Vall d'Hebron Hospital, Barcelona, Spain
| | - Esteban Ballestar
- Epigenetics and Immune Disease Group, Josep Carreras Research Institute (IJC), 08916, Badalona, Barcelona, Spain.
| | - Javier Martin
- Instituto de Parasitología y Biomedicina López-Neyra, Consejo Superior de Investigaciones Científicas (IPBLN-CSIC), Granada, Spain.
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53
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Neuner SM, Tcw J, Goate AM. Genetic architecture of Alzheimer's disease. Neurobiol Dis 2020; 143:104976. [PMID: 32565066 PMCID: PMC7409822 DOI: 10.1016/j.nbd.2020.104976] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 05/30/2020] [Accepted: 06/13/2020] [Indexed: 02/06/2023] Open
Abstract
Advances in genetic and genomic technologies over the last thirty years have greatly enhanced our knowledge concerning the genetic architecture of Alzheimer's disease (AD). Several genes including APP, PSEN1, PSEN2, and APOE have been shown to exhibit large effects on disease susceptibility, with the remaining risk loci having much smaller effects on AD risk. Notably, common genetic variants impacting AD are not randomly distributed across the genome. Instead, these variants are enriched within regulatory elements active in human myeloid cells, and to a lesser extent liver cells, implicating these cell and tissue types as critical to disease etiology. Integrative approaches are emerging as highly effective for identifying the specific target genes through which AD risk variants act and will likely yield important insights related to potential therapeutic targets in the coming years. In the future, additional consideration of sex- and ethnicity-specific contributions to risk as well as the contribution of complex gene-gene and gene-environment interactions will likely be necessary to further improve our understanding of AD genetic architecture.
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Affiliation(s)
- Sarah M Neuner
- Nash Department of Neuroscience, Ronald M. Loeb Center for Alzheimer's Disease, Icahn School of Medicine at Mount Sinai, New York, USA
| | - Julia Tcw
- Nash Department of Neuroscience, Ronald M. Loeb Center for Alzheimer's Disease, Icahn School of Medicine at Mount Sinai, New York, USA
| | - Alison M Goate
- Nash Department of Neuroscience, Ronald M. Loeb Center for Alzheimer's Disease, Icahn School of Medicine at Mount Sinai, New York, USA; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, USA.
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54
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Abstract
B cells serve as a key weapon against infectious diseases. They also contribute to multiple autoimmune diseases, including multiple sclerosis (MS) where depletion of B cells is a highly effective therapy. We describe a comprehensive profile of central nervous system (CNS)-specific transcriptional B cell phenotypes in MS at single-cell resolution with paired immune repertoires. We reveal a polyclonal immunoglobulin M (IgM) and IgG1 cerebrospinal fluid B cell expansion polarized toward an inflammatory, memory and plasmablast/plasma cell phenotype, with differential up-regulation of specific proinflammatory pathways. We did not find evidence that CNS B cells harbor a neurotropic virus. These data support the targeting of activated resident B cells in the CNS as a potentially effective strategy for control of treatment-resistant chronic disease. Central nervous system B cells have several potential roles in multiple sclerosis (MS): secretors of proinflammatory cytokines and chemokines, presenters of autoantigens to T cells, producers of pathogenic antibodies, and reservoirs for viruses that trigger demyelination. To interrogate these roles, single-cell RNA sequencing (scRNA-Seq) was performed on paired cerebrospinal fluid (CSF) and blood from subjects with relapsing-remitting MS (RRMS; n = 12), other neurologic diseases (ONDs; n = 1), and healthy controls (HCs; n = 3). Single-cell immunoglobulin sequencing (scIg-Seq) was performed on a subset of these subjects and additional RRMS (n = 4), clinically isolated syndrome (n = 2), and OND (n = 2) subjects. Further, paired CSF and blood B cell subsets (RRMS; n = 7) were isolated using fluorescence activated cell sorting for bulk RNA sequencing (RNA-Seq). Independent analyses across technologies demonstrated that nuclear factor kappa B (NF-κB) and cholesterol biosynthesis pathways were activated, and specific cytokine and chemokine receptors were up-regulated in CSF memory B cells. Further, SMAD/TGF-β1 signaling was down-regulated in CSF plasmablasts/plasma cells. Clonally expanded, somatically hypermutated IgM+ and IgG1+ CSF B cells were associated with inflammation, blood–brain barrier breakdown, and intrathecal Ig synthesis. While we identified memory B cells and plasmablast/plasma cells with highly similar Ig heavy-chain sequences across MS subjects, similarities were also identified with ONDs and HCs. No viral transcripts, including from Epstein–Barr virus, were detected. Our findings support the hypothesis that in MS, CSF B cells are driven to an inflammatory and clonally expanded memory and plasmablast/plasma cell phenotype.
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55
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Liu Y, Fu L, Kaufmann K, Chen D, Chen M. A practical guide for DNase-seq data analysis: from data management to common applications. Brief Bioinform 2020; 20:1865-1877. [PMID: 30010713 DOI: 10.1093/bib/bby057] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Revised: 06/06/2018] [Accepted: 06/10/2018] [Indexed: 01/01/2023] Open
Abstract
Deoxyribonuclease I (DNase I)-hypersensitive site sequencing (DNase-seq) has been widely used to determine chromatin accessibility and its underlying regulatory lexicon. However, exploring DNase-seq data requires sophisticated downstream bioinformatics analyses. In this study, we first review computational methods for all of the major steps in DNase-seq data analysis, including experimental design, quality control, read alignment, peak calling, annotation of cis-regulatory elements, genomic footprinting and visualization. The challenges associated with each step are highlighted. Next, we provide a practical guideline and a computational pipeline for DNase-seq data analysis by integrating some of these tools. We also discuss the competing techniques and the potential applications of this pipeline for the analysis of analogous experimental data. Finally, we discuss the integration of DNase-seq with other functional genomics techniques.
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Affiliation(s)
- Yongjing Liu
- Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Liangyu Fu
- Department for Plant Cell and Molecular Biology, Institute for Biology, Humboldt-Universität zu Berlin, Berlin 10115, Germany
| | - Kerstin Kaufmann
- Department for Plant Cell and Molecular Biology, Institute for Biology, Humboldt-Universität zu Berlin, Berlin 10115, Germany
| | - Dijun Chen
- Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Ming Chen
- Department for Plant Cell and Molecular Biology, Institute for Biology, Humboldt-Universität zu Berlin, Berlin 10115, Germany
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56
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Hou R, Denisenko E, Forrest ARR. scMatch: a single-cell gene expression profile annotation tool using reference datasets. Bioinformatics 2020; 35:4688-4695. [PMID: 31028376 PMCID: PMC6853649 DOI: 10.1093/bioinformatics/btz292] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Revised: 03/28/2019] [Accepted: 04/21/2019] [Indexed: 12/17/2022] Open
Abstract
MOTIVATION Single-cell RNA sequencing (scRNA-seq) measures gene expression at the resolution of individual cells. Massively multiplexed single-cell profiling has enabled large-scale transcriptional analyses of thousands of cells in complex tissues. In most cases, the true identity of individual cells is unknown and needs to be inferred from the transcriptomic data. Existing methods typically cluster (group) cells based on similarities of their gene expression profiles and assign the same identity to all cells within each cluster using the averaged expression levels. However, scRNA-seq experiments typically produce low-coverage sequencing data for each cell, which hinders the clustering process. RESULTS We introduce scMatch, which directly annotates single cells by identifying their closest match in large reference datasets. We used this strategy to annotate various single-cell datasets and evaluated the impacts of sequencing depth, similarity metric and reference datasets. We found that scMatch can rapidly and robustly annotate single cells with comparable accuracy to another recent cell annotation tool (SingleR), but that it is quicker and can handle larger reference datasets. We demonstrate how scMatch can handle large customized reference gene expression profiles that combine data from multiple sources, thus empowering researchers to identify cell populations in any complex tissue with the desired precision. AVAILABILITY AND IMPLEMENTATION scMatch (Python code) and the FANTOM5 reference dataset are freely available to the research community here https://github.com/forrest-lab/scMatch. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Rui Hou
- Harry Perkins Institute of Medical Research, QEII Medical Centre and Centre for Medical Research, The University of Western Australia, Nedlands, Perth, WA 6009, Australia
| | - Elena Denisenko
- Harry Perkins Institute of Medical Research, QEII Medical Centre and Centre for Medical Research, The University of Western Australia, Nedlands, Perth, WA 6009, Australia
| | - Alistair R R Forrest
- Harry Perkins Institute of Medical Research, QEII Medical Centre and Centre for Medical Research, The University of Western Australia, Nedlands, Perth, WA 6009, Australia
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57
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Koyanagi KO. Inferring changes in histone modification during cell differentiation by ancestral state estimation based on phylogenetic trees of cell types: Human hematopoiesis as a model case. Gene 2020; 721S:100021. [PMID: 32550550 PMCID: PMC7286071 DOI: 10.1016/j.gene.2019.100021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Revised: 05/23/2019] [Accepted: 05/27/2019] [Indexed: 12/13/2022]
Abstract
Revealing the landscape of epigenetic changes in cells during differentiation is important for understanding the development of organisms. In this study, to infer such epigenetic changes during human hematopoiesis, ancestral state estimation based on a phylogenetic tree was applied to map the epigenomic changes in six kinds of histone modifications onto the hierarchical cell differentiation process of hematopoiesis using epigenomes of eight types of differentiated hematopoietic cells. The histone modification changes inferred during hematopoiesis showed that changes that occurred on the branches separating different cell types reflected the characteristics of hematopoiesis in terms of genomic position and gene function. These results suggested that ancestral state estimation based on phylogenetic analysis of histone modifications in differentiated hematopoietic cells could reconstruct an appropriate landscape of histone modification changes during hematopoiesis. Since integration of the inferred changes of different histone modifications could reveal genes with specific histone marks such as active histone marks and bivalent histone marks on each internal branch of cell-type trees, this approach could provide valuable information for understanding the cell differentiation steps of each cell lineage.
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Key Words
- Ancestral state estimation
- B, B cell
- BED, browser extensible data
- CRISPR, clustered regularly interspaced short palindromic repeat
- Cell lineage
- Cell-type tree
- ChIP-seq, chromatin immunoprecipitation sequencing
- DNA, deoxyribonucleic acid
- Eo, eosinophil
- Er, erythroblast
- H3K27ac, acetylation of histone H3 at lysine 27
- H3K27me3, trimethylations of histone H3 at lysine 27
- H3K36me3, trimethylation of histone H3 at lysine 36
- H3K4me1, monomethylation of histone H3 at lysine 4
- H3K4me3, trimethylation of histone H3 at lysine 4
- H3K9me3, trimethylations of histone H3 at lysine 9
- Histone modification
- KEGG, Kyoto encyclopedia of genes and genomes
- L, lymphoid lineage
- M, myeloid lineage
- Me, megakaryocyte
- Mo, monocyte
- Ne, neutrophil
- Nk, natural killer cell
- Phyloepigenetics
- T, T cell
- TSS, transcription start sites
- kb, kilobase(s)
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58
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Bernasconi A, Canakoglu A, Masseroli M, Ceri S. The road towards data integration in human genomics: players, steps and interactions. Brief Bioinform 2020; 22:30-44. [PMID: 32496509 DOI: 10.1093/bib/bbaa080] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Revised: 03/09/2020] [Accepted: 04/18/2020] [Indexed: 12/15/2022] Open
Abstract
Thousands of new experimental datasets are becoming available every day; in many cases, they are produced within the scope of large cooperative efforts, involving a variety of laboratories spread all over the world, and typically open for public use. Although the potential collective amount of available information is huge, the effective combination of such public sources is hindered by data heterogeneity, as the datasets exhibit a wide variety of notations and formats, concerning both experimental values and metadata. Thus, data integration is becoming a fundamental activity, to be performed prior to data analysis and biological knowledge discovery, consisting of subsequent steps of data extraction, normalization, matching and enrichment; once applied to heterogeneous data sources, it builds multiple perspectives over the genome, leading to the identification of meaningful relationships that could not be perceived by using incompatible data formats. In this paper, we first describe a technological pipeline from data production to data integration; we then propose a taxonomy of genomic data players (based on the distinction between contributors, repository hosts, consortia, integrators and consumers) and apply the taxonomy to describe about 30 important players in genomic data management. We specifically focus on the integrator players and analyse the issues in solving the genomic data integration challenges, as well as evaluate the computational environments that they provide to follow up data integration by means of visualization and analysis tools.
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59
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Bai X, Shi S, Ai B, Jiang Y, Liu Y, Han X, Xu M, Pan Q, Wang F, Wang Q, Zhang J, Li X, Feng C, Li Y, Wang Y, Song Y, Feng K, Li C. ENdb: a manually curated database of experimentally supported enhancers for human and mouse. Nucleic Acids Res 2020; 48:D51-D57. [PMID: 31665430 PMCID: PMC7145688 DOI: 10.1093/nar/gkz973] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Revised: 10/10/2019] [Accepted: 10/16/2019] [Indexed: 12/30/2022] Open
Abstract
Enhancers are a class of cis-regulatory elements that can increase gene transcription by forming loops in intergenic regions, introns and exons. Enhancers, as well as their associated target genes, and transcription factors (TFs) that bind to them, are highly associated with human disease and biological processes. Although some enhancer databases have been published, most only focus on enhancers identified by high-throughput experimental techniques. Therefore, it is highly desirable to construct a comprehensive resource of manually curated enhancers and their related information based on low-throughput experimental evidences. Here, we established a comprehensive manually-curated enhancer database for human and mouse, which provides a resource for experimentally supported enhancers, and to annotate the detailed information of enhancers. The current release of ENdb documents 737 experimentally validated enhancers and their related information, including 384 target genes, 263 TFs, 110 diseases and 153 functions in human and mouse. Moreover, the enhancer-related information was supported by experimental evidences, such as RNAi, in vitro knockdown, western blotting, qRT-PCR, luciferase reporter assay, chromatin conformation capture (3C) and chromosome conformation capture-on-chip (4C) assays. ENdb provides a user-friendly interface to query, browse and visualize the detailed information of enhancers. The database is available at http://www.licpathway.net/ENdb.
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Affiliation(s)
- Xuefeng Bai
- School of Medical Informatics, Daqing Campus, Harbin Medical University. Daqing 163319, China
| | - Shanshan Shi
- School of Medical Informatics, Daqing Campus, Harbin Medical University. Daqing 163319, China
| | - Bo Ai
- School of Medical Informatics, Daqing Campus, Harbin Medical University. Daqing 163319, China
| | - Yong Jiang
- School of Medical Informatics, Daqing Campus, Harbin Medical University. Daqing 163319, China
| | - Yuejuan Liu
- School of Medical Informatics, Daqing Campus, Harbin Medical University. Daqing 163319, China
| | - Xiaole Han
- School of Medical Informatics, Daqing Campus, Harbin Medical University. Daqing 163319, China
| | - Mingcong Xu
- School of Medical Informatics, Daqing Campus, Harbin Medical University. Daqing 163319, China
| | - Qi Pan
- School of Medical Informatics, Daqing Campus, Harbin Medical University. Daqing 163319, China
| | - Fan Wang
- School of Medical Informatics, Daqing Campus, Harbin Medical University. Daqing 163319, China
| | - Qiuyu Wang
- School of Medical Informatics, Daqing Campus, Harbin Medical University. Daqing 163319, China
| | - Jian Zhang
- School of Medical Informatics, Daqing Campus, Harbin Medical University. Daqing 163319, China
| | - Xuecang Li
- School of Medical Informatics, Daqing Campus, Harbin Medical University. Daqing 163319, China
| | - Chenchen Feng
- School of Medical Informatics, Daqing Campus, Harbin Medical University. Daqing 163319, China
| | - Yanyu Li
- School of Medical Informatics, Daqing Campus, Harbin Medical University. Daqing 163319, China
| | - Yuezhu Wang
- School of Medical Informatics, Daqing Campus, Harbin Medical University. Daqing 163319, China
| | - Yiwei Song
- School of Medical Informatics, Daqing Campus, Harbin Medical University. Daqing 163319, China
| | - Ke Feng
- School of Medical Informatics, Daqing Campus, Harbin Medical University. Daqing 163319, China
| | - Chunquan Li
- School of Medical Informatics, Daqing Campus, Harbin Medical University. Daqing 163319, China
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60
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Lee T, Sung MK, Lee S, Yang W, Oh J, Kim JY, Hwang S, Ban HJ, Choi JK. Convolutional neural network model to predict causal risk factors that share complex regulatory features. Nucleic Acids Res 2020; 47:e146. [PMID: 31598692 PMCID: PMC6902027 DOI: 10.1093/nar/gkz868] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Accepted: 10/01/2019] [Indexed: 11/18/2022] Open
Abstract
Major progress in disease genetics has been made through genome-wide association studies (GWASs). One of the key tasks for post-GWAS analyses is to identify causal noncoding variants with regulatory function. Here, on the basis of >2000 functional features, we developed a convolutional neural network framework for combinatorial, nonlinear modeling of complex patterns shared by risk variants scattered among multiple associated loci. When applied for major psychiatric disorders and autoimmune diseases, neural and immune features, respectively, exhibited high explanatory power while reflecting the pathophysiology of the relevant disease. The predicted causal variants were concentrated in active regulatory regions of relevant cell types and tended to be in physical contact with transcription factors while residing in evolutionarily conserved regions and resulting in expression changes of genes related to the given disease. We demonstrate some examples of novel candidate causal variants and associated genes. Our method is expected to contribute to the identification and functional interpretation of potential causal noncoding variants in post-GWAS analyses.
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Affiliation(s)
- Taeyeop Lee
- Graduate School of Medical Science and Engineering, KAIST, Daejeon 34141, Republic of Korea
| | - Min Kyung Sung
- Department of Bio and Brain Engineering, KAIST, Daejeon 34141, Republic of Korea.,MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Seulkee Lee
- Graduate School of Medical Science and Engineering, KAIST, Daejeon 34141, Republic of Korea.,Department of Bio and Brain Engineering, KAIST, Daejeon 34141, Republic of Korea.,Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul 06351, Republic of Korea
| | - Woojin Yang
- Department of Bio and Brain Engineering, KAIST, Daejeon 34141, Republic of Korea.,Korean Bioinformation Center (KOBIC), KRIBB, Daejeon 34141, Republic of Korea
| | - Jaeho Oh
- Department of Bio and Brain Engineering, KAIST, Daejeon 34141, Republic of Korea
| | - Jeong Yeon Kim
- Department of Bio and Brain Engineering, KAIST, Daejeon 34141, Republic of Korea
| | - Seongwon Hwang
- Seminar for Statistics, Eidgenössische Technische Hochschule (ETH) Zurich, CH-8092 Zurich, Switzerland
| | - Hyo-Jeong Ban
- Future Medicine Division, Korea Institute of Oriental Medicine, Daejeon 34054, Republic of Korea
| | - Jung Kyoon Choi
- Department of Bio and Brain Engineering, KAIST, Daejeon 34141, Republic of Korea
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61
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Bourges C, Groff AF, Burren OS, Gerhardinger C, Mattioli K, Hutchinson A, Hu T, Anand T, Epping MW, Wallace C, Smith KG, Rinn JL, Lee JC. Resolving mechanisms of immune-mediated disease in primary CD4 T cells. EMBO Mol Med 2020; 12:e12112. [PMID: 32239644 PMCID: PMC7207160 DOI: 10.15252/emmm.202012112] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2020] [Revised: 03/04/2020] [Accepted: 03/09/2020] [Indexed: 12/11/2022] Open
Abstract
Deriving mechanisms of immune-mediated disease from GWAS data remains a formidable challenge, with attempts to identify causal variants being frequently hampered by strong linkage disequilibrium. To determine whether causal variants could be identified from their functional effects, we adapted a massively parallel reporter assay for use in primary CD4 T cells, the cell type whose regulatory DNA is most enriched for immune-mediated disease SNPs. This enabled the effects of candidate SNPs to be examined in a relevant cellular context and generated testable hypotheses into disease mechanisms. To illustrate the power of this approach, we investigated a locus that has been linked to six immune-mediated diseases but cannot be fine-mapped. By studying the lead expression-modulating SNP, we uncovered an NF-κB-driven regulatory circuit which constrains T-cell activation through the dynamic formation of a super-enhancer that upregulates TNFAIP3 (A20), a key NF-κB inhibitor. In activated T cells, this feedback circuit is disrupted-and super-enhancer formation prevented-by the risk variant at the lead SNP, leading to unrestrained T-cell activation via a molecular mechanism that appears to broadly predispose to human autoimmunity.
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Affiliation(s)
- Christophe Bourges
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, University of Cambridge, Cambridge, UK
- Department of Medicine, University of Cambridge School of Clinical Medicine, Addenbrooke's Hospital, Cambridge, UK
| | - Abigail F Groff
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
| | - Oliver S Burren
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, University of Cambridge, Cambridge, UK
- Department of Medicine, University of Cambridge School of Clinical Medicine, Addenbrooke's Hospital, Cambridge, UK
| | - Chiara Gerhardinger
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
| | - Kaia Mattioli
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
| | - Anna Hutchinson
- MRC Biostatistics Unit, Cambridge Institute of Public Health, Cambridge, UK
| | - Theodore Hu
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, University of Cambridge, Cambridge, UK
- Department of Medicine, University of Cambridge School of Clinical Medicine, Addenbrooke's Hospital, Cambridge, UK
| | - Tanmay Anand
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, University of Cambridge, Cambridge, UK
- Department of Medicine, University of Cambridge School of Clinical Medicine, Addenbrooke's Hospital, Cambridge, UK
| | - Madeline W Epping
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, University of Cambridge, Cambridge, UK
- Department of Medicine, University of Cambridge School of Clinical Medicine, Addenbrooke's Hospital, Cambridge, UK
| | - Chris Wallace
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, University of Cambridge, Cambridge, UK
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
| | - Kenneth Gc Smith
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, University of Cambridge, Cambridge, UK
- Department of Medicine, University of Cambridge School of Clinical Medicine, Addenbrooke's Hospital, Cambridge, UK
| | - John L Rinn
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
- Department of Biochemistry, BioFrontiers Institute, University of Colorado, Boulder, CO, USA
| | - James C Lee
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, University of Cambridge, Cambridge, UK
- Department of Medicine, University of Cambridge School of Clinical Medicine, Addenbrooke's Hospital, Cambridge, UK
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
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62
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Choi J, Baldwin TM, Wong M, Bolden JE, Fairfax KA, Lucas EC, Cole R, Biben C, Morgan C, Ramsay KA, Ng AP, Kauppi M, Corcoran LM, Shi W, Wilson N, Wilson MJ, Alexander WS, Hilton DJ, de Graaf CA. Haemopedia RNA-seq: a database of gene expression during haematopoiesis in mice and humans. Nucleic Acids Res 2020; 47:D780-D785. [PMID: 30395284 PMCID: PMC6324085 DOI: 10.1093/nar/gky1020] [Citation(s) in RCA: 82] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Accepted: 10/12/2018] [Indexed: 11/24/2022] Open
Abstract
During haematopoiesis, haematopoietic stem cells differentiate into restricted potential progenitors before maturing into the many lineages required for oxygen transport, wound healing and immune response. We have updated Haemopedia, a database of gene-expression profiles from a broad spectrum of haematopoietic cells, to include RNA-seq gene-expression data from both mice and humans. The Haemopedia RNA-seq data set covers a wide range of lineages and progenitors, with 57 mouse blood cell types (flow sorted populations from healthy mice) and 12 human blood cell types. This data set has been made accessible for exploration and analysis, to researchers and clinicians with limited bioinformatics experience, on our online portal Haemosphere: https://www.haemosphere.org. Haemosphere also includes nine other publicly available high-quality data sets relevant to haematopoiesis. We have added the ability to compare gene expression across data sets and species by curating data sets with shared lineage designations or to view expression gene vs gene, with all plots available for download by the user.
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Affiliation(s)
- Jarny Choi
- Molecular Medicine Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia.,Centre for Stem Cell Systems, Anatomy and Neuroscience Department, The University of Melbourne, Parkville, Victoria, Australia
| | - Tracey M Baldwin
- Molecular Medicine Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
| | - Mae Wong
- CSL Limited, Parkville, Victoria, Australia
| | - Jessica E Bolden
- Molecular Medicine Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia.,Department of Medical Biology, The University of Melbourne, Parkville, Victoria, Australia
| | - Kirsten A Fairfax
- Molecular Medicine Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia.,Department of Medical Biology, The University of Melbourne, Parkville, Victoria, Australia
| | - Erin C Lucas
- Molecular Medicine Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
| | - Rebecca Cole
- Molecular Medicine Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
| | - Christine Biben
- Molecular Medicine Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia.,Department of Medical Biology, The University of Melbourne, Parkville, Victoria, Australia
| | - Clare Morgan
- Molecular Medicine Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia.,Department of Medical Biology, The University of Melbourne, Parkville, Victoria, Australia
| | - Kerry A Ramsay
- Molecular Medicine Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
| | - Ashley P Ng
- Department of Medical Biology, The University of Melbourne, Parkville, Victoria, Australia.,Cancer and Haematology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
| | - Maria Kauppi
- Department of Medical Biology, The University of Melbourne, Parkville, Victoria, Australia.,Cancer and Haematology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
| | - Lynn M Corcoran
- Department of Medical Biology, The University of Melbourne, Parkville, Victoria, Australia.,Molecular Immunology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
| | - Wei Shi
- Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia.,Department of Computing and Information Systems, The University of Melbourne, Parkville, Victoria, Australia
| | | | | | - Warren S Alexander
- Department of Medical Biology, The University of Melbourne, Parkville, Victoria, Australia.,Cancer and Haematology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
| | - Douglas J Hilton
- Molecular Medicine Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia.,Department of Medical Biology, The University of Melbourne, Parkville, Victoria, Australia
| | - Carolyn A de Graaf
- Molecular Medicine Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia.,Department of Medical Biology, The University of Melbourne, Parkville, Victoria, Australia
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63
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Dzobo K. Epigenomics-Guided Drug Development: Recent Advances in Solving the Cancer Treatment "jigsaw puzzle". OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2020; 23:70-85. [PMID: 30767728 DOI: 10.1089/omi.2018.0206] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The human epigenome plays a key role in determining cellular identity and eventually function. Drug discovery undertakings have focused mainly on the role of genomics in carcinogenesis, with the focus turning to the epigenome recently. Drugs targeting DNA and histone modifications are under development with some such as 5-azacytidine, decitabine, vorinostat, and panobinostat already approved by the Food and Drug Administration (FDA) and the European Medicines Agency (EMA). This expert review offers a critical analysis of the epigenomics-guided drug discovery and development and the opportunities and challenges for the next decade. Importantly, the coupling of epigenetic editing techniques, such as clustered regularly interspersed short palindromic repeat (CRISPR)-CRISPR-associated protein-9 (Cas9) and APOBEC-coupled epigenetic sequencing (ACE-seq) with epigenetic drug screens, will allow the identification of small-molecule inhibitors or drugs able to reverse epigenetic changes responsible for many diseases. In addition, concrete and sustainable innovation in cancer treatment ought to integrate epigenome targeting drugs with classic therapies such as chemotherapy and immunotherapy.
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Affiliation(s)
- Kevin Dzobo
- 1 International Centre for Genetic Engineering and Biotechnology (ICGEB), Cape Town Component, Cape Town, South Africa.,2 Division of Medical Biochemistry and Institute of Infectious Disease and Molecular Medicine, Department of Integrative Biomedical Sciences, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
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64
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Chung FFL, Herceg Z. The Promises and Challenges of Toxico-Epigenomics: Environmental Chemicals and Their Impacts on the Epigenome. ENVIRONMENTAL HEALTH PERSPECTIVES 2020; 128:15001. [PMID: 31950866 PMCID: PMC7015548 DOI: 10.1289/ehp6104] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Revised: 12/15/2019] [Accepted: 12/16/2019] [Indexed: 05/02/2023]
Abstract
BACKGROUND It has been estimated that a substantial portion of chronic and noncommunicable diseases can be caused or exacerbated by exposure to environmental chemicals. Multiple lines of evidence indicate that early life exposure to environmental chemicals at relatively low concentrations could have lasting effects on individual and population health. Although the potential adverse effects of environmental chemicals are known to the scientific community, regulatory agencies, and the public, little is known about the mechanistic basis by which these chemicals can induce long-term or transgenerational effects. To address this question, epigenetic mechanisms have emerged as the potential link between genetic and environmental factors of health and disease. OBJECTIVES We present an overview of epigenetic regulation and a summary of reported evidence of environmental toxicants as epigenetic disruptors. We also discuss the advantages and challenges of using epigenetic biomarkers as an indicator of toxicant exposure, using measures that can be taken to improve risk assessment, and our perspectives on the future role of epigenetics in toxicology. DISCUSSION Until recently, efforts to apply epigenomic data in toxicology and risk assessment were restricted by an incomplete understanding of epigenomic variability across tissue types and populations. This is poised to change with the development of new tools and concerted efforts by researchers across disciplines that have led to a better understanding of epigenetic mechanisms and comprehensive maps of epigenomic variation. With the foundations now in place, we foresee that unprecedented advancements will take place in the field in the coming years. https://doi.org/10.1289/EHP6104.
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Affiliation(s)
| | - Zdenko Herceg
- Epigenetics Group, International Agency for Research on Cancer (IARC), Lyon, France
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65
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A cell-free DNA metagenomic sequencing assay that integrates the host injury response to infection. Proc Natl Acad Sci U S A 2019; 116:18738-18744. [PMID: 31451660 DOI: 10.1073/pnas.1906320116] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
High-throughput metagenomic sequencing offers an unbiased approach to identify pathogens in clinical samples. Conventional metagenomic sequencing, however, does not integrate information about the host, which is often critical to distinguish infection from infectious disease, and to assess the severity of disease. Here, we explore the utility of high-throughput sequencing of cell-free DNA (cfDNA) after bisulfite conversion to map the tissue and cell types of origin of host-derived cfDNA, and to profile the bacterial and viral metagenome. We applied this assay to 51 urinary cfDNA isolates collected from a cohort of kidney transplant recipients with and without bacterial and viral infection of the urinary tract. We find that the cell and tissue types of origin of urinary cfDNA can be derived from its genome-wide profile of methylation marks, and strongly depend on infection status. We find evidence of kidney and bladder tissue damage due to viral and bacterial infection, respectively, and of the recruitment of neutrophils to the urinary tract during infection. Through direct comparison to conventional metagenomic sequencing as well as clinical tests of infection, we find this assay accurately captures the bacterial and viral composition of the sample. The assay presented here is straightforward to implement, offers a systems view into bacterial and viral infections of the urinary tract, and can find future use as a tool for the differential diagnosis of infection.
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66
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Zhang G, Shi J, Zhu S, Lan Y, Xu L, Yuan H, Liao G, Liu X, Zhang Y, Xiao Y, Li X. DiseaseEnhancer: a resource of human disease-associated enhancer catalog. Nucleic Acids Res 2019; 46:D78-D84. [PMID: 29059320 PMCID: PMC5753380 DOI: 10.1093/nar/gkx920] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2017] [Accepted: 10/01/2017] [Indexed: 01/09/2023] Open
Abstract
Large-scale sequencing studies discovered substantial genetic variants occurring in enhancers which regulate genes via long range chromatin interactions. Importantly, such variants could affect enhancer regulation by changing transcription factor bindings or enhancer hijacking, and in turn, make an essential contribution to disease progression. To facilitate better usage of published data and exploring enhancer deregulation in various human diseases, we created DiseaseEnhancer (http://biocc.hrbmu.edu.cn/DiseaseEnhancer/), a manually curated database for disease-associated enhancers. As of July 2017, DiseaseEnhancer includes 847 disease-associated enhancers in 143 human diseases. Database features include basic enhancer information (i.e. genomic location and target genes); disease types; associated variants on the enhancer and their mediated phenotypes (i.e. gain/loss of enhancer and the alterations of transcription factor bindings). We also include a feature on our website to export any query results into a file and download the full database. DiseaseEnhancer provides a promising avenue for researchers to facilitate the understanding of enhancer deregulation in disease pathogenesis, and identify new biomarkers for disease diagnosis and therapy.
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Affiliation(s)
- Guanxiong Zhang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150081, China
| | - Jian Shi
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150081, China
| | - Shiwei Zhu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150081, China
| | - Yujia Lan
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150081, China
| | - Liwen Xu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150081, China
| | - Huating Yuan
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150081, China
| | - Gaoming Liao
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150081, China
| | - Xiaoqin Liu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150081, China
| | - Yunpeng Zhang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150081, China
| | - Yun Xiao
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150081, China
| | - Xia Li
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150081, China
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67
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Madan N, Ghazi AR, Kong X, Chen ES, Shaw CA, Edelstein LC. Functionalization of CD36 cardiovascular disease and expression associated variants by interdisciplinary high throughput analysis. PLoS Genet 2019; 15:e1008287. [PMID: 31344026 PMCID: PMC6684090 DOI: 10.1371/journal.pgen.1008287] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Revised: 08/06/2019] [Accepted: 07/04/2019] [Indexed: 12/22/2022] Open
Abstract
CD36 is a platelet membrane glycoprotein whose engagement with oxidized low-density lipoprotein (oxLDL) results in platelet activation. The CD36 gene has been associated with platelet count, platelet volume, as well as lipid levels and CVD risk by genome-wide association studies. Platelet CD36 expression levels have been shown to be associated with both the platelet oxLDL response and an elevated risk of thrombo-embolism. Several genomic variants have been identified as associated with platelet CD36 levels, however none have been conclusively demonstrated to be causative. We screened 81 expression quantitative trait loci (eQTL) single nucleotide polymorphisms (SNPs) associated with platelet CD36 expression by a Massively Parallel Reporter Assay (MPRA) and analyzed the results with a novel Bayesian statistical method. Ten eQTLs located 13kb to 55kb upstream of the CD36 transcriptional start site of transcript ENST00000309881 and 49kb to 92kb upstream of transcript ENST00000447544, demonstrated significant transcription shifts between their minor and major allele in the MPRA assay. Of these, rs2366739 and rs1194196, separated by only 20bp, were confirmed by luciferase assay to alter transcriptional regulation. In addition, electromobility shift assays demonstrated differential DNA:protein complex formation between the two alleles of this locus. Furthermore, deletion of the genomic locus by CRISPR/Cas9 in K562 and Meg-01 cells results in upregulation of CD36 transcription. These data indicate that we have identified a variant that regulates expression of CD36, which in turn affects platelet function. To assess the clinical relevance of our findings we used the PhenoScanner tool, which aggregates large scale GWAS findings; the results reinforce the clinical relevance of our variants and the utility of the MPRA assay. The study demonstrates a generalizable paradigm for functional testing of genetic variants to inform mechanistic studies, support patient management and develop precision therapies. Platelets are anucleate cells that are best known as regulators of vascular hemostasis and thrombosis but also play important roles in cancer, angiogenesis, and inflammation. CD36 is a platelet surface marker that can activate platelet in response to oxidized low density lipoprotein (oxLDL). CD36 has been associated with numerous cardiovascular traits in human including blood lipid levels, platelet count, and cardiovascular disease prevalence in human genetic studies. Human variability in platelet CD36 levels are associated with the platelet response to oxLDL. However, the genetic mechanisms responsible for the variability of CD36 levels are unknown. We examined 81 genetic variants associated with CD36 levels for functionality using a high-throughput assay. Of the ten variants that were identified in that assay, one doublet, rs2366739 and rs1194196, were confirmed using additional molecular and cellular assays. Deletion of the genomic region containing rs2366739 and rs1194196 resulted in overexpression of CD36 in a cell culture system. This finding indicates a control locus which can serve as a potential target in modulating CD36 expression and altering platelet function in cardiovascular disease.
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Affiliation(s)
- Namrata Madan
- Cardeza Foundation for Hematologic Research/Department of Medicine, Sidney Kimmel Medical School, Thomas Jefferson University, Philadelphia, PA, United States of America
| | - Andrew R. Ghazi
- Department of Quantitative and Computational Biosciences, Baylor College of Medicine, Houston, TX, United States of America
| | - Xianguo Kong
- Cardeza Foundation for Hematologic Research/Department of Medicine, Sidney Kimmel Medical School, Thomas Jefferson University, Philadelphia, PA, United States of America
| | - Edward S. Chen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, United States of America
| | - Chad A. Shaw
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, United States of America
- Department of Statistics, Rice University, Houston, TX, United States of America
| | - Leonard C. Edelstein
- Cardeza Foundation for Hematologic Research/Department of Medicine, Sidney Kimmel Medical School, Thomas Jefferson University, Philadelphia, PA, United States of America
- * E-mail:
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68
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Kong X, Ma L, Chen E, Shaw CA, Edelstein LC. Identification of the Regulatory Elements and Target Genes of Megakaryopoietic Transcription Factor MEF2C. Thromb Haemost 2019; 119:716-725. [PMID: 30731491 PMCID: PMC6932631 DOI: 10.1055/s-0039-1678694] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Megakaryopoiesis produces specialized haematopoietic stem cells in the bone marrow that give rise to megakaryocytes which ultimately produce platelets. Defects in megakaryopoiesis can result in altered platelet counts and physiology, leading to dysfunctional haemostasis and thrombosis. Additionally, dysregulated megakaryopoiesis is also associated with myeloid pathologies. Transcription factors play critical roles in cell differentiation by regulating the temporal and spatial patterns of gene expression which ultimately decide cell fate. Several transcription factors have been described as regulating megakaryopoiesis including myocyte enhancer factor 2C (MEF2C); however, the genes regulated by MEF2C that influence megakaryopoiesis have not been reported. Using chromatin immunoprecipitation-sequencing and Gene Ontology data we identified five candidate genes that are bound by MEF2C and regulate megakaryopoiesis: MOV10, AGO3, HDAC1, RBBP5 and WASF2. To study expression of these genes, we silenced MEF2C gene expression in the Meg01 megakaryocytic cell line and in induced pluripotent stem cells by CRISPR/Cas9 editing. We also knocked down MEF2C expression in cord blood-derived haematopoietic stem cells by siRNA. We found that absent or reduced MEF2C expression resulted in defects in megakaryocytic differentiation and reduced levels of the candidate target genes. Luciferase assays confirmed that genomic sequences within the target genes are regulated by MEF2C levels. Finally, we demonstrate that small deletions linked to a platelet count-associated single nucleotide polymorphism alter transcriptional activity, suggesting a mechanism by which genetic variation in MEF2C alters platelet production. These data help elucidate the mechanism behind MEF2C regulation of megakaryopoiesis and genetic variation driving platelet production.
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Affiliation(s)
- Xianguo Kong
- Cardeza Foundation for Hematologic Research and Department of Medicine, Sidney Kimmel Medical School at Thomas Jefferson University, Philadelphia, PA
| | - Lin Ma
- Cardeza Foundation for Hematologic Research and Department of Medicine, Sidney Kimmel Medical School at Thomas Jefferson University, Philadelphia, PA
| | - Edward Chen
- Department of Human & Molecular Genetics, Baylor College of Medicine, Houston, TX
| | - Chad A. Shaw
- Department of Human & Molecular Genetics, Baylor College of Medicine, Houston, TX
- Department of Statistics, Rice University, Houston, TX
| | - Leonard C. Edelstein
- Cardeza Foundation for Hematologic Research and Department of Medicine, Sidney Kimmel Medical School at Thomas Jefferson University, Philadelphia, PA
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69
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Cirillo D, Valencia A. Big data analytics for personalized medicine. Curr Opin Biotechnol 2019; 58:161-167. [PMID: 30965188 DOI: 10.1016/j.copbio.2019.03.004] [Citation(s) in RCA: 71] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Revised: 02/22/2019] [Accepted: 03/01/2019] [Indexed: 01/06/2023]
Abstract
Big Data are radically changing biomedical research. The unprecedented advances in automated collection of large-scale molecular and clinical data pose major challenges to data analysis and interpretation, calling for the development of new computational approaches. The creation of powerful systems for the effective use of biomedical Big Data in Personalized Medicine (a.k.a. Precision Medicine) will require significant scientific and technical developments, including infrastructure, engineering, project and financial management. We review here how the evolution of data-driven methods offers the possibility to address many of these problems, guiding the formulation of hypotheses on systems functioning and the generation of mechanistic models, and facilitating the design of clinical procedures in Personalized Medicine.
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Affiliation(s)
- Davide Cirillo
- Barcelona Supercomputing Center (BSC), C/Jordi Girona 29, 08034, Barcelona, Spain.
| | - Alfonso Valencia
- Barcelona Supercomputing Center (BSC), C/Jordi Girona 29, 08034, Barcelona, Spain; ICREA, Pg. Lluís Companys 23, 08010, Barcelona, Spain
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70
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Wegner M, Diehl V, Bittl V, de Bruyn R, Wiechmann S, Matthess Y, Hebel M, Hayes MGB, Schaubeck S, Benner C, Heinz S, Bremm A, Dikic I, Ernst A, Kaulich M. Circular synthesized CRISPR/Cas gRNAs for functional interrogations in the coding and noncoding genome. eLife 2019; 8:e42549. [PMID: 30838976 PMCID: PMC6424562 DOI: 10.7554/elife.42549] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2018] [Accepted: 02/25/2019] [Indexed: 02/06/2023] Open
Abstract
Current technologies used to generate CRISPR/Cas gene perturbation reagents are labor intense and require multiple ligation and cloning steps. Furthermore, increasing gRNA sequence diversity negatively affects gRNA distribution, leading to libraries of heterogeneous quality. Here, we present a rapid and cloning-free mutagenesis technology that can efficiently generate covalently-closed-circular-synthesized (3Cs) CRISPR/Cas gRNA reagents and that uncouples sequence diversity from sequence distribution. We demonstrate the fidelity and performance of 3Cs reagents by tailored targeting of all human deubiquitinating enzymes (DUBs) and identify their essentiality for cell fitness. To explore high-content screening, we aimed to generate the largest up-to-date gRNA library that can be used to interrogate the coding and noncoding human genome and simultaneously to identify genes, predicted promoter flanking regions, transcription factors and CTCF binding sites that are linked to doxorubicin resistance. Our 3Cs technology enables fast and robust generation of bias-free gene perturbation libraries with yet unmatched diversities and should be considered an alternative to established technologies.
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Affiliation(s)
- Martin Wegner
- Institute of Biochemistry IIGoethe University Frankfurt - Medical Faculty, University HospitalFrankfurtGermany
| | - Valentina Diehl
- Institute of Biochemistry IIGoethe University Frankfurt - Medical Faculty, University HospitalFrankfurtGermany
| | - Verena Bittl
- Institute of Biochemistry IIGoethe University Frankfurt - Medical Faculty, University HospitalFrankfurtGermany
- Buchmann Institute for Molecular Life SciencesGoethe UniversityFrankfurtGermany
| | - Rahel de Bruyn
- Institute of Biochemistry IIGoethe University Frankfurt - Medical Faculty, University HospitalFrankfurtGermany
| | - Svenja Wiechmann
- Institute of Biochemistry IIGoethe University Frankfurt - Medical Faculty, University HospitalFrankfurtGermany
- Project Group Translational Medicine & Pharmacology TMPFraunhofer Institute for Molecular Biology and Applied Ecology IMEFrankfurtGermany
| | - Yves Matthess
- Institute of Biochemistry IIGoethe University Frankfurt - Medical Faculty, University HospitalFrankfurtGermany
| | - Marie Hebel
- Institute of Biochemistry IIGoethe University Frankfurt - Medical Faculty, University HospitalFrankfurtGermany
| | - Michael GB Hayes
- Department of MedicineUniversity of California, San DiegoSan DiegoUnited States
| | - Simone Schaubeck
- Institute of Biochemistry IIGoethe University Frankfurt - Medical Faculty, University HospitalFrankfurtGermany
| | - Christopher Benner
- Department of MedicineUniversity of California, San DiegoSan DiegoUnited States
| | - Sven Heinz
- Department of MedicineUniversity of California, San DiegoSan DiegoUnited States
| | - Anja Bremm
- Institute of Biochemistry IIGoethe University Frankfurt - Medical Faculty, University HospitalFrankfurtGermany
- Buchmann Institute for Molecular Life SciencesGoethe UniversityFrankfurtGermany
| | - Ivan Dikic
- Institute of Biochemistry IIGoethe University Frankfurt - Medical Faculty, University HospitalFrankfurtGermany
- Buchmann Institute for Molecular Life SciencesGoethe UniversityFrankfurtGermany
- Frankfurt Cancer InstituteFrankfurt am MainGermany
- Cardio-Pulmonary InstituteFrankfurt am MainGermany
| | - Andreas Ernst
- Institute of Biochemistry IIGoethe University Frankfurt - Medical Faculty, University HospitalFrankfurtGermany
- Project Group Translational Medicine & Pharmacology TMPFraunhofer Institute for Molecular Biology and Applied Ecology IMEFrankfurtGermany
| | - Manuel Kaulich
- Institute of Biochemistry IIGoethe University Frankfurt - Medical Faculty, University HospitalFrankfurtGermany
- Frankfurt Cancer InstituteFrankfurt am MainGermany
- Cardio-Pulmonary InstituteFrankfurt am MainGermany
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71
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Hecker M, Boxberger N, Illner N, Fitzner B, Schröder I, Winkelmann A, Dudesek A, Meister S, Koczan D, Lorenz P, Thiesen HJ, Zettl UK. A genetic variant associated with multiple sclerosis inversely affects the expression of CD58 and microRNA-548ac from the same gene. PLoS Genet 2019; 15:e1007961. [PMID: 30730892 PMCID: PMC6382214 DOI: 10.1371/journal.pgen.1007961] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Revised: 02/20/2019] [Accepted: 01/14/2019] [Indexed: 12/28/2022] Open
Abstract
Genome-wide association studies have identified more than 200 genetic variants to be associated with an increased risk of developing multiple sclerosis (MS). Still, little is known about the causal molecular mechanisms that underlie the genetic contribution to disease susceptibility. In this study, we investigated the role of the single-nucleotide polymorphism (SNP) rs1414273, which is located within the microRNA-548ac stem-loop sequence in the first intron of the CD58 gene. We conducted an expression quantitative trait locus (eQTL) analysis based on public RNA-sequencing and microarray data of blood-derived cells of more than 1000 subjects. Additionally, CD58 transcripts and mature hsa-miR-548ac molecules were measured using real-time PCR in peripheral blood samples of 32 MS patients. Cell culture experiments were performed to evaluate the efficiency of Drosha-mediated stem-loop processing dependent on genotype and to determine the target genes of this underexplored microRNA. Across different global populations and data sets, carriers of the MS risk allele showed reduced CD58 mRNA levels but increased hsa-miR-548ac levels. We provide evidence that the SNP rs1414273 might alter Drosha cleavage activity, thereby provoking partial uncoupling of CD58 gene expression and microRNA-548ac production from the shared primary transcript in immune cells. Moreover, the microRNA was found to regulate genes, which participate in inflammatory processes and in controlling the balance of protein folding and degradation. We thus uncovered new regulatory implications of the MS-associated haplotype of the CD58 gene locus, and we remind that paradoxical findings can be encountered in the analysis of eQTLs upon data aggregation. Our study illustrates that a better understanding of RNA processing events might help to establish the functional nature of genetic variants, which predispose to inflammatory and neurological diseases. More than 200 genetic loci have been associated with an increased risk of developing multiple sclerosis (MS). Here, we investigated the role of a single-nucleotide polymorphism (SNP), which is located within the microRNA-548ac stem-loop sequence in the first intron of the CD58 gene. We analyzed expression data of blood-derived cells of about 1000 subjects and observed that MS risk allele carriers have reduced CD58 mRNA levels but increased hsa-miR-548ac levels. Our findings suggest that Drosha cleavage activity is affected, perhaps attributable to the specific SNP. This may contribute to partial uncoupling of CD58 gene expression and hsa-miR-548ac production from the shared primary transcript in immune cells. We discovered that the mature microRNA downregulates genes involved in inflammatory processes and in controlling the balance of protein folding and degradation. Our study exemplifies that paradoxical findings can be encountered in the analysis of genetic variants regulating transcription and/or RNA processing.
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Affiliation(s)
- Michael Hecker
- University of Rostock, Department of Neurology, Division of Neuroimmunology, Rostock, Germany
- Steinbeis Transfer Center for Proteome Analysis, Rostock, Germany
- * E-mail:
| | - Nina Boxberger
- University of Rostock, Department of Neurology, Division of Neuroimmunology, Rostock, Germany
| | - Nicole Illner
- University of Rostock, Department of Neurology, Division of Neuroimmunology, Rostock, Germany
| | - Brit Fitzner
- University of Rostock, Department of Neurology, Division of Neuroimmunology, Rostock, Germany
- Steinbeis Transfer Center for Proteome Analysis, Rostock, Germany
| | - Ina Schröder
- University of Rostock, Department of Neurology, Division of Neuroimmunology, Rostock, Germany
| | - Alexander Winkelmann
- University of Rostock, Department of Neurology, Division of Neuroimmunology, Rostock, Germany
| | - Ales Dudesek
- University of Rostock, Department of Neurology, Division of Neuroimmunology, Rostock, Germany
| | - Stefanie Meister
- University of Rostock, Department of Neurology, Division of Neuroimmunology, Rostock, Germany
| | - Dirk Koczan
- University of Rostock, Institute of Immunology, Rostock, Germany
| | - Peter Lorenz
- University of Rostock, Institute of Immunology, Rostock, Germany
| | - Hans-Jürgen Thiesen
- Steinbeis Transfer Center for Proteome Analysis, Rostock, Germany
- University of Rostock, Institute of Immunology, Rostock, Germany
| | - Uwe Klaus Zettl
- University of Rostock, Department of Neurology, Division of Neuroimmunology, Rostock, Germany
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72
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Went M, Sud A, Speedy H, Sunter NJ, Försti A, Law PJ, Johnson DC, Mirabella F, Holroyd A, Li N, Orlando G, Weinhold N, van Duin M, Chen B, Mitchell JS, Mansouri L, Juliusson G, Smedby KE, Jayne S, Majid A, Dearden C, Allsup DJ, Bailey JR, Pratt G, Pepper C, Fegan C, Rosenquist R, Kuiper R, Stephens OW, Bertsch U, Broderick P, Einsele H, Gregory WM, Hillengass J, Hoffmann P, Jackson GH, Jöckel KH, Nickel J, Nöthen MM, da Silva Filho MI, Thomsen H, Walker BA, Broyl A, Davies FE, Hansson M, Goldschmidt H, Dyer MJS, Kaiser M, Sonneveld P, Morgan GJ, Hemminki K, Nilsson B, Catovsky D, Allan JM, Houlston RS. Genetic correlation between multiple myeloma and chronic lymphocytic leukaemia provides evidence for shared aetiology. Blood Cancer J 2018; 9:1. [PMID: 30602759 PMCID: PMC6315026 DOI: 10.1038/s41408-018-0162-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2018] [Accepted: 11/19/2018] [Indexed: 02/08/2023] Open
Abstract
The clustering of different types of B-cell malignancies in families raises the possibility of shared aetiology. To examine this, we performed cross-trait linkage disequilibrium (LD)-score regression of multiple myeloma (MM) and chronic lymphocytic leukaemia (CLL) genome-wide association study (GWAS) data sets, totalling 11,734 cases and 29,468 controls. A significant genetic correlation between these two B-cell malignancies was shown (Rg = 0.4, P = 0.0046). Furthermore, four of the 45 known CLL risk loci were shown to associate with MM risk and five of the 23 known MM risk loci associate with CLL risk. By integrating eQTL, Hi-C and ChIP-seq data, we show that these pleiotropic risk loci are enriched for B-cell regulatory elements and implicate B-cell developmental genes. These data identify shared biological pathways influencing the development of CLL and, MM and further our understanding of the aetiological basis of these B-cell malignancies.
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Affiliation(s)
- Molly Went
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, SW7 3RP, UK.
| | - Amit Sud
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, SW7 3RP, UK
| | - Helen Speedy
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, SW7 3RP, UK
| | - Nicola J Sunter
- Northern Institute for Cancer Research, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Asta Försti
- German Cancer Research Center, 69120, Heidelberg, Germany
- Center for Primary Health Care Research, Lund University, SE-205 02, Malmo, Sweden
| | - Philip J Law
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, SW7 3RP, UK
| | - David C Johnson
- Division of Molecular Pathology, The Institute of Cancer Research, London, SW7 3RP, UK
| | - Fabio Mirabella
- Division of Molecular Pathology, The Institute of Cancer Research, London, SW7 3RP, UK
| | - Amy Holroyd
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, SW7 3RP, UK
| | - Ni Li
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, SW7 3RP, UK
| | - Giulia Orlando
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, SW7 3RP, UK
| | - Niels Weinhold
- Myeloma Institute for Research and Therapy, University of Arkansas for Medical Sciences, Little Rock, AR, 72205, USA
- Department of Internal Medicine V, University of Heidelberg, 69117, Heidelberg, Germany
| | - Mark van Duin
- Department of Hematology, Erasmus MC Cancer Institute, 3075 EA, Rotterdam, The Netherlands
| | - Bowang Chen
- German Cancer Research Center, 69120, Heidelberg, Germany
| | - Jonathan S Mitchell
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, SW7 3RP, UK
| | - Larry Mansouri
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, 75105, Uppsala, Sweden
| | - Gunnar Juliusson
- Lund Strategic Research Center for Stem Cell Biology and Cell Therapy, Hematology and Transplantation, Lund University, Lund, Sweden
| | - Karin E Smedby
- Unit of Clinical Epidemiology, Department of Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Sandrine Jayne
- Ernest and Helen Scott Haematological Research Institute, Leicester University, Leicester, UK
| | - Aneela Majid
- Ernest and Helen Scott Haematological Research Institute, Leicester University, Leicester, UK
| | - Claire Dearden
- Division of Molecular Pathology, The Institute of Cancer Research, London, SW7 3RP, UK
| | - David J Allsup
- Department of Haematology, Hull Royal Infirmary, Hull, UK
| | - James R Bailey
- Hull York Medical School and University of Hull, Hull, UK
| | - Guy Pratt
- Department of Haematology, Birmingham Heartlands Hospital, Birmingham, UK
| | - Chris Pepper
- Department of Haematology, School of Medicine, Cardiff University, Cardiff, UK
| | - Chris Fegan
- Cardiff and Vale National Health Service Trust, Heath Park, Cardiff, UK
| | - Richard Rosenquist
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, 75105, Uppsala, Sweden
| | - Rowan Kuiper
- Department of Hematology, Erasmus MC Cancer Institute, 3075 EA, Rotterdam, The Netherlands
| | - Owen W Stephens
- Myeloma Institute for Research and Therapy, University of Arkansas for Medical Sciences, Little Rock, AR, 72205, USA
| | - Uta Bertsch
- German Cancer Research Center, 69120, Heidelberg, Germany
- National Centre of Tumor Diseases, 69120, Heidelberg, Germany
| | - Peter Broderick
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, SW7 3RP, UK
| | | | - Walter M Gregory
- Clinical Trials Research Unit, University of Leeds, Leeds, LS2 9PH, UK
| | - Jens Hillengass
- Department of Internal Medicine V, University of Heidelberg, 69117, Heidelberg, Germany
| | - Per Hoffmann
- Institute of Human Genetics, University of Bonn, D-53127, Bonn, Germany
- Division of Medical Genetics, Department of Biomedicine, University of Basel, 4003, Basel, Switzerland
| | | | - Karl-Heinz Jöckel
- Institute for Medical Informatics, Biometry and Epidemiology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Jolanta Nickel
- Department of Internal Medicine V, University of Heidelberg, 69117, Heidelberg, Germany
| | - Markus M Nöthen
- Institute of Human Genetics, University of Bonn, D-53127, Bonn, Germany
- Department of Genomics, Life and Brain Center, University of Bonn, D-53127, Bonn, Germany
| | | | - Hauke Thomsen
- German Cancer Research Center, 69120, Heidelberg, Germany
| | - Brian A Walker
- Myeloma Institute for Research and Therapy, University of Arkansas for Medical Sciences, Little Rock, AR, 72205, USA
| | - Annemiek Broyl
- Department of Hematology, Erasmus MC Cancer Institute, 3075 EA, Rotterdam, The Netherlands
| | - Faith E Davies
- Myeloma Institute for Research and Therapy, University of Arkansas for Medical Sciences, Little Rock, AR, 72205, USA
| | - Markus Hansson
- Center for Primary Health Care Research, Lund University, SE-205 02, Malmo, Sweden
- Hematology and Transfusion Medicine, Department of Laboratory Medicine, BMC B13, SE-221 84 Lund University, Lund, Sweden
| | - Hartmut Goldschmidt
- Department of Internal Medicine V, University of Heidelberg, 69117, Heidelberg, Germany
- National Centre of Tumor Diseases, 69120, Heidelberg, Germany
| | - Martin J S Dyer
- Ernest and Helen Scott Haematological Research Institute, Leicester University, Leicester, UK
| | - Martin Kaiser
- Division of Molecular Pathology, The Institute of Cancer Research, London, SW7 3RP, UK
| | - Pieter Sonneveld
- Department of Hematology, Erasmus MC Cancer Institute, 3075 EA, Rotterdam, The Netherlands
| | - Gareth J Morgan
- Myeloma Institute for Research and Therapy, University of Arkansas for Medical Sciences, Little Rock, AR, 72205, USA
| | - Kari Hemminki
- German Cancer Research Center, 69120, Heidelberg, Germany
- Center for Primary Health Care Research, Lund University, SE-205 02, Malmo, Sweden
| | - Björn Nilsson
- Hematology and Transfusion Medicine, Department of Laboratory Medicine, BMC B13, SE-221 84 Lund University, Lund, Sweden
- Broad Institute, 7 Cambridge Center, Cambridge, MA, 02142, USA
| | - Daniel Catovsky
- Division of Molecular Pathology, The Institute of Cancer Research, London, SW7 3RP, UK
| | - James M Allan
- Northern Institute for Cancer Research, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Richard S Houlston
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, SW7 3RP, UK
- Division of Molecular Pathology, The Institute of Cancer Research, London, SW7 3RP, UK
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73
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Pazos F, Garcia-Moreno A, Oliveros JC. Automatic detection of genomic regions with informative epigenetic patterns. BMC Genomics 2018; 19:847. [PMID: 30486775 PMCID: PMC6264639 DOI: 10.1186/s12864-018-5286-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Accepted: 11/20/2018] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Epigenetic phenomena are crucial for explaining the phenotypic plasticity seen in the cells of different tissues, developmental stages and diseases, all holding the same DNA sequence. As technology is allowing to retrieve epigenetic information in a genome-wide fashion, massive epigenomic datasets are being accumulated in public repositories. New approaches are required to mine those data to extract useful knowledge. We present here an automatic approach for detecting genomic regions with epigenetic variation patterns across samples related to a grouping of these samples, as a way of detecting regions functionally associated to the phenomenon behind the classification. RESULTS We show that the regions automatically detected by the method in the whole human genome associated to three different classifications of a set of epigenomes (cancer vs. healthy, brain vs. other organs, and fetal vs. adult tissues) are enriched in genes associated to these processes. CONCLUSIONS The method is fully automatic and can exhaustively scan the whole human genome at any resolution using large collections of epigenomes as input, although it also produces good results with small datasets. Consequently, it will be valuable for obtaining functional information from the incoming epigenomic information as it continues to accumulate.
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Affiliation(s)
- Florencio Pazos
- National Center for Biotechnology (CNB-CSIC), c/ Darwin, 3, 28049 Madrid, Spain
| | | | - Juan C. Oliveros
- National Center for Biotechnology (CNB-CSIC), c/ Darwin, 3, 28049 Madrid, Spain
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Harrison PW, Fan J, Richardson D, Clarke L, Zerbino D, Cochrane G, Archibald AL, Schmidt CJ, Flicek P. FAANG, establishing metadata standards, validation and best practices for the farmed and companion animal community. Anim Genet 2018; 49:520-526. [PMID: 30311252 PMCID: PMC6334167 DOI: 10.1111/age.12736] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/11/2018] [Indexed: 12/30/2022]
Abstract
The Functional Annotation of ANimal Genomes (FAANG) project aims, through a coordinated international effort, to provide high quality functional annotation of animal genomes with an initial focus on farmed and companion animals. A key goal of the initiative is to ensure high quality and rich supporting metadata to describe the project's animals, specimens, cell cultures and experimental assays. By defining rich sample and experimental metadata standards and promoting best practices in data descriptions, deposition and openness, FAANG champions higher quality and reusability of published datasets. FAANG has established a Data Coordination Centre, which sits at the heart of the Metadata and Data Sharing Committee. It continues to evolve the metadata standards, support submissions and, crucially, create powerful and accessible tools to support deposition and validation of metadata. FAANG conforms to the findable, accessible, interoperable, and reusable (FAIR) data principles, with high quality, open access and functionally interlinked data. In addition to data generated by FAANG members and specific FAANG projects, existing datasets that meet the main—or more permissive legacy—standards are incorporated into a central, focused, functional data resource portal for the entire farmed and companion animal community. Through clear and effective metadata standards, validation and conversion software, combined with promotion of best practices in metadata implementation, FAANG aims to maximise effectiveness and inter‐comparability of assay data. This supports the community to create a rich genome‐to‐phenotype resource and promotes continuing improvements in animal data standards as a whole.
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Affiliation(s)
- P W Harrison
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - J Fan
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - D Richardson
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - L Clarke
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - D Zerbino
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - G Cochrane
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - A L Archibald
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK
| | - C J Schmidt
- Department of Animal and Food Sciences, College of Agriculture and Natural Resources, University of Delaware, Newark, DE, 19716, USA
| | - P Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
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75
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Deconstructing and targeting the genomic architecture of human neurodegeneration. Nat Neurosci 2018; 21:1310-1317. [PMID: 30258235 DOI: 10.1038/s41593-018-0240-z] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2018] [Accepted: 08/23/2018] [Indexed: 01/17/2023]
Abstract
The field of neurodegenerative disease research has seen tremendous advances over the last two decades as new technologies and analytic methods have enabled well-powered human genomic studies. Driven first by genetic studies and more recently by transcriptomic and epigenomic studies of proper size, we have uncovered a large repertoire of loci, genes, and molecular features that are implicated in discrete, syndromically defined neurodegenerative conditions, such as Alzheimer's disease, amyotrophic lateral sclerosis, frontotemporal dementia, multiple sclerosis, and Parkinson's disease. As we begin to understand the impact of these genomic features in each disease, we also appreciate that many aging individuals accumulate each of these pathologies without fulfilling criteria for syndromic diagnoses, that other pathologies are common in individuals with a given diagnosis, and that there may be shared protective factors against central nervous system injury. Thus, we now need to bring these disparate observations together into a person-centered approach that considers all neurodegenerative and protective processes simultaneously to modulate the trajectory of cognitive and functional decline that comes with brain aging.
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76
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Went M, Sud A, Försti A, Halvarsson BM, Weinhold N, Kimber S, van Duin M, Thorleifsson G, Holroyd A, Johnson DC, Li N, Orlando G, Law PJ, Ali M, Chen B, Mitchell JS, Gudbjartsson DF, Kuiper R, Stephens OW, Bertsch U, Broderick P, Campo C, Bandapalli OR, Einsele H, Gregory WA, Gullberg U, Hillengass J, Hoffmann P, Jackson GH, Jöckel KH, Johnsson E, Kristinsson SY, Mellqvist UH, Nahi H, Easton D, Pharoah P, Dunning A, Peto J, Canzian F, Swerdlow A, Eeles RA, Kote-Jarai ZS, Muir K, Pashayan N, Nickel J, Nöthen MM, Rafnar T, Ross FM, da Silva Filho MI, Thomsen H, Turesson I, Vangsted A, Andersen NF, Waage A, Walker BA, Wihlborg AK, Broyl A, Davies FE, Thorsteinsdottir U, Langer C, Hansson M, Goldschmidt H, Kaiser M, Sonneveld P, Stefansson K, Morgan GJ, Hemminki K, Nilsson B, Houlston RS. Identification of multiple risk loci and regulatory mechanisms influencing susceptibility to multiple myeloma. Nat Commun 2018; 9:3707. [PMID: 30213928 PMCID: PMC6137048 DOI: 10.1038/s41467-018-04989-w] [Citation(s) in RCA: 78] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Accepted: 06/06/2018] [Indexed: 02/08/2023] Open
Abstract
Genome-wide association studies (GWAS) have transformed our understanding of susceptibility to multiple myeloma (MM), but much of the heritability remains unexplained. We report a new GWAS, a meta-analysis with previous GWAS and a replication series, totalling 9974 MM cases and 247,556 controls of European ancestry. Collectively, these data provide evidence for six new MM risk loci, bringing the total number to 23. Integration of information from gene expression, epigenetic profiling and in situ Hi-C data for the 23 risk loci implicate disruption of developmental transcriptional regulators as a basis of MM susceptibility, compatible with altered B-cell differentiation as a key mechanism. Dysregulation of autophagy/apoptosis and cell cycle signalling feature as recurrently perturbed pathways. Our findings provide further insight into the biological basis of MM.
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Affiliation(s)
- Molly Went
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, SW7 3RP, UK
| | - Amit Sud
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, SW7 3RP, UK
| | - Asta Försti
- German Cancer Research Center, 69120, Heidelberg, Germany
- Center for Primary Health Care Research, Lund University, SE-205 02, Malmo, Sweden
| | - Britt-Marie Halvarsson
- Hematology and Transfusion Medicine, Department of Laboratory Medicine, BMC B13, Lund University, SE-221 84, Lund, Sweden
| | - Niels Weinhold
- Myeloma Institute for Research and Therapy, University of Arkansas for Medical Sciences, Little Rock, AR, 72205, USA
- Department of Internal Medicine V, University of Heidelberg, 69117, Heidelberg, Germany
| | - Scott Kimber
- Division of Molecular Pathology, The Institute of Cancer Research, London, SW7 3RP, UK
| | - Mark van Duin
- Department of Hematology, Erasmus MC Cancer Institute, 3075 EA, Rotterdam, The Netherlands
| | | | - Amy Holroyd
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, SW7 3RP, UK
| | - David C Johnson
- Division of Molecular Pathology, The Institute of Cancer Research, London, SW7 3RP, UK
| | - Ni Li
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, SW7 3RP, UK
| | - Giulia Orlando
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, SW7 3RP, UK
| | - Philip J Law
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, SW7 3RP, UK
| | - Mina Ali
- Hematology and Transfusion Medicine, Department of Laboratory Medicine, BMC B13, Lund University, SE-221 84, Lund, Sweden
| | - Bowang Chen
- German Cancer Research Center, 69120, Heidelberg, Germany
| | - Jonathan S Mitchell
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, SW7 3RP, UK
| | - Daniel F Gudbjartsson
- deCODE Genetics, Sturlugata 8, IS-101, Reykjavik, Iceland
- School of Engineering and Natural Sciences, University of Iceland, IS-101, Reykjavik, Iceland
| | - Rowan Kuiper
- Department of Hematology, Erasmus MC Cancer Institute, 3075 EA, Rotterdam, The Netherlands
| | - Owen W Stephens
- Myeloma Institute for Research and Therapy, University of Arkansas for Medical Sciences, Little Rock, AR, 72205, USA
| | - Uta Bertsch
- German Cancer Research Center, 69120, Heidelberg, Germany
- National Centre of Tumor Diseases, 69120, Heidelberg, Germany
| | - Peter Broderick
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, SW7 3RP, UK
| | - Chiara Campo
- German Cancer Research Center, 69120, Heidelberg, Germany
| | | | | | - Walter A Gregory
- Clinical Trials Research Unit, University of Leeds, Leeds, LS2 9PH, UK
| | - Urban Gullberg
- Hematology and Transfusion Medicine, Department of Laboratory Medicine, BMC B13, Lund University, SE-221 84, Lund, Sweden
| | - Jens Hillengass
- Department of Internal Medicine V, University of Heidelberg, 69117, Heidelberg, Germany
| | - Per Hoffmann
- Institute of Human Genetics, University of Bonn, D-53127, Bonn, Germany
- Division of Medical Genetics, Department of Biomedicine, University of Basel, 4003, Basel, Switzerland
| | | | - Karl-Heinz Jöckel
- Institute for Medical Informatics, Biometry and Epidemiology, University Hospital Essen, University of Duisburg-Essen, Essen, D-45147, Germany
| | - Ellinor Johnsson
- Hematology and Transfusion Medicine, Department of Laboratory Medicine, BMC B13, Lund University, SE-221 84, Lund, Sweden
| | - Sigurður Y Kristinsson
- Department of Hematology, Landspitali, National University Hospital of Iceland, IS-101, Reykjavik, Iceland
| | - Ulf-Henrik Mellqvist
- Section of Hematology, Sahlgrenska University Hospital, Gothenburg, 413 45, Sweden
| | - Hareth Nahi
- Center for Hematology and Regenerative Medicine, SE-171 77, Stockholm, Sweden
| | - Douglas Easton
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, CB1 8RN, UK
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, CB1 8RN, UK
| | - Paul Pharoah
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, CB1 8RN, UK
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, CB1 8RN, UK
| | - Alison Dunning
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, CB1 8RN, UK
| | - Julian Peto
- Department of Non-Communicable Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, WC1E 7HT, UK
| | - Federico Canzian
- Genomic Epidemiology Group, German Cancer Research Center (DKFZ), Heidelberg, 69120, Germany
| | - Anthony Swerdlow
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, SW7 3RP, UK
- Division of Breast Cancer Research, The Institute of Cancer Research, London, SW7 3RP, UK
| | - Rosalind A Eeles
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, SW7 3RP, UK
- Royal Marsden NHS Foundation Trust, Fulham Road, London, SW3 6JJ, UK
| | - ZSofia Kote-Jarai
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, SW7 3RP, UK
| | - Kenneth Muir
- Institute of Population Health, University of Manchester, Manchester, M13 9PL, UK
- Warwick Medical School, University of Warwick, Coventry, CV4 7AL, UK
| | - Nora Pashayan
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, CB1 8RN, UK
- Department of Applied Health Research, University College London, London, WC1E 7HB, UK
| | - Jolanta Nickel
- Department of Internal Medicine V, University of Heidelberg, 69117, Heidelberg, Germany
| | - Markus M Nöthen
- Institute of Human Genetics, University of Bonn, D-53127, Bonn, Germany
- Department of Genomics, Life & Brain Center, University of Bonn, D-53127, Bonn, Germany
| | - Thorunn Rafnar
- deCODE Genetics, Sturlugata 8, IS-101, Reykjavik, Iceland
| | - Fiona M Ross
- Wessex Regional Genetics Laboratory, University of Southampton, Salisbury, SP2 8BJ, UK
| | | | - Hauke Thomsen
- German Cancer Research Center, 69120, Heidelberg, Germany
| | - Ingemar Turesson
- Hematology Clinic, Skåne University Hospital, SE-221 85, Lund, Sweden
| | - Annette Vangsted
- Department of Haematology, University Hospital of Copenhagen at Rigshospitalet, Blegdamsvej 9, DK-2100, Copenhagen, Denmark
| | - Niels Frost Andersen
- Department of Haematology, Aarhus University Hospital, Tage-Hansens Gade 2, DK-8000, Aarhus C, Denmark
| | - Anders Waage
- Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, Box 8905, N-7491, Trondheim, Norway
| | - Brian A Walker
- Myeloma Institute for Research and Therapy, University of Arkansas for Medical Sciences, Little Rock, AR, 72205, USA
| | - Anna-Karin Wihlborg
- Hematology and Transfusion Medicine, Department of Laboratory Medicine, BMC B13, Lund University, SE-221 84, Lund, Sweden
| | - Annemiek Broyl
- Department of Hematology, Erasmus MC Cancer Institute, 3075 EA, Rotterdam, The Netherlands
| | - Faith E Davies
- Myeloma Institute for Research and Therapy, University of Arkansas for Medical Sciences, Little Rock, AR, 72205, USA
| | - Unnur Thorsteinsdottir
- deCODE Genetics, Sturlugata 8, IS-101, Reykjavik, Iceland
- Faculty of Medicine, University of Iceland, IS-101, Reykjavik, Iceland
| | - Christian Langer
- Department of Internal Medicine III, University of Ulm, D-89081, Ulm, Germany
| | - Markus Hansson
- Hematology and Transfusion Medicine, Department of Laboratory Medicine, BMC B13, Lund University, SE-221 84, Lund, Sweden
- Hematology Clinic, Skåne University Hospital, SE-221 85, Lund, Sweden
| | - Hartmut Goldschmidt
- Department of Internal Medicine V, University of Heidelberg, 69117, Heidelberg, Germany
- National Centre of Tumor Diseases, 69120, Heidelberg, Germany
| | - Martin Kaiser
- Division of Molecular Pathology, The Institute of Cancer Research, London, SW7 3RP, UK
| | - Pieter Sonneveld
- Department of Hematology, Erasmus MC Cancer Institute, 3075 EA, Rotterdam, The Netherlands
| | | | - Gareth J Morgan
- Myeloma Institute for Research and Therapy, University of Arkansas for Medical Sciences, Little Rock, AR, 72205, USA
| | - Kari Hemminki
- German Cancer Research Center, 69120, Heidelberg, Germany.
- Center for Primary Health Care Research, Lund University, SE-205 02, Malmo, Sweden.
| | - Björn Nilsson
- Hematology and Transfusion Medicine, Department of Laboratory Medicine, BMC B13, Lund University, SE-221 84, Lund, Sweden.
- Broad Institute, 7 Cambridge Center, Cambridge, MA, 02142, USA.
| | - Richard S Houlston
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, SW7 3RP, UK.
- Division of Molecular Pathology, The Institute of Cancer Research, London, SW7 3RP, UK.
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77
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Peng Y, Zhang Y. Enhancer and super-enhancer: Positive regulators in gene transcription. Animal Model Exp Med 2018; 1:169-179. [PMID: 30891562 PMCID: PMC6388056 DOI: 10.1002/ame2.12032] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2018] [Revised: 07/19/2018] [Accepted: 07/31/2018] [Indexed: 12/23/2022] Open
Abstract
Enhancer is a positive regulator for spatiotemporal development in eukaryotes. As a cluster, super-enhancer is closely related to cell identity- and fate-determined processes. Both of them function tightly depending on their targeted transcription factors, cofactors, and genes through distal genomic interactions. They have been recognized as critical components and played positive roles in transcriptional regulatory network or factory. Recent advances of next-generation sequencing have dramatically expanded our ability and knowledge to interrogate the molecular mechanism of enhancer and super-enhancer for transcription. Here, we review the history, importance, advances and challenges on enhancer and super-enhancer field. This will benefit our understanding of their function mechanism for transcription underlying precise gene expression.
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Affiliation(s)
- Yanling Peng
- Animal Functional Genomics GroupAgricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhenChina
| | - Yubo Zhang
- Animal Functional Genomics GroupAgricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhenChina
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78
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Poller W, Dimmeler S, Heymans S, Zeller T, Haas J, Karakas M, Leistner DM, Jakob P, Nakagawa S, Blankenberg S, Engelhardt S, Thum T, Weber C, Meder B, Hajjar R, Landmesser U. Non-coding RNAs in cardiovascular diseases: diagnostic and therapeutic perspectives. Eur Heart J 2018; 39:2704-2716. [PMID: 28430919 PMCID: PMC6454570 DOI: 10.1093/eurheartj/ehx165] [Citation(s) in RCA: 273] [Impact Index Per Article: 45.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Revised: 01/14/2017] [Accepted: 03/15/2017] [Indexed: 02/06/2023] Open
Abstract
Recent research has demonstrated that the non-coding genome plays a key role in genetic programming and gene regulation during development as well as in health and cardiovascular disease. About 99% of the human genome do not encode proteins, but are transcriptionally active representing a broad spectrum of non-coding RNAs (ncRNAs) with important regulatory and structural functions. Non-coding RNAs have been identified as critical novel regulators of cardiovascular risk factors and cell functions and are thus important candidates to improve diagnostics and prognosis assessment. Beyond this, ncRNAs are rapidly emgerging as fundamentally novel therapeutics. On a first level, ncRNAs provide novel therapeutic targets some of which are entering assessment in clinical trials. On a second level, new therapeutic tools were developed from endogenous ncRNAs serving as blueprints. Particularly advanced is the development of RNA interference (RNAi) drugs which use recently discovered pathways of endogenous short interfering RNAs and are becoming versatile tools for efficient silencing of protein expression. Pioneering clinical studies include RNAi drugs targeting liver synthesis of PCSK9 resulting in highly significant lowering of LDL cholesterol or targeting liver transthyretin (TTR) synthesis for treatment of cardiac TTR amyloidosis. Further novel drugs mimicking actions of endogenous ncRNAs may arise from exploitation of molecular interactions not accessible to conventional pharmacology. We provide an update on recent developments and perspectives for diagnostic and therapeutic use of ncRNAs in cardiovascular diseases, including atherosclerosis/coronary disease, post-myocardial infarction remodelling, and heart failure.
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Affiliation(s)
- Wolfgang Poller
- Department of Cardiology, CBF, CC11, Charite Universitätsmedizin Berlin, Campus Benjamin Franklin, Charite Centrum 11 (Cardiovascular Medicine), Hindenburgdamm 20, Berlin, Germany
- German Center for Cardiovascular Research (DZHK), Site Berlin, Berlin, Germany
| | - Stefanie Dimmeler
- Institute for Cardiovascular Regeneration, Center of Molecular Medicine, Johann Wolfgang Goethe Universität, Theodor-Stern-Kai 7, Frankfurt am Main, Germany
- DZHK, Site Rhein-Main, Frankfurt, Germany
| | - Stephane Heymans
- Center for Heart Failure Research, Cardiovascular Research Institute Maastricht (CARIM), Maastricht University, Maastricht, Netherlands
| | - Tanja Zeller
- Clinic for General and Interventional Cardiology, University Heart Center Hamburg, Martinistrasse 52, Hamburg, Germany
- DZHK, Site Hamburg/Kiel/Lübeck, Hamburg, Germany
| | - Jan Haas
- Institute for Cardiomyopathies Heidelberg (ICH), Universitätsklinikum Heidelberg, Im Neuenheimer Feld 669, Heidelberg, Germany
- DZHK, Site Heidelberg/Mannheim, Heidelberg, Germany
| | - Mahir Karakas
- Clinic for General and Interventional Cardiology, University Heart Center Hamburg, Martinistrasse 52, Hamburg, Germany
- DZHK, Site Hamburg/Kiel/Lübeck, Hamburg, Germany
| | - David-Manuel Leistner
- Department of Cardiology, CBF, CC11, Charite Universitätsmedizin Berlin, Campus Benjamin Franklin, Charite Centrum 11 (Cardiovascular Medicine), Hindenburgdamm 20, Berlin, Germany
- German Center for Cardiovascular Research (DZHK), Site Berlin, Berlin, Germany
| | - Philipp Jakob
- Department of Cardiology, CBF, CC11, Charite Universitätsmedizin Berlin, Campus Benjamin Franklin, Charite Centrum 11 (Cardiovascular Medicine), Hindenburgdamm 20, Berlin, Germany
- German Center for Cardiovascular Research (DZHK), Site Berlin, Berlin, Germany
| | - Shinichi Nakagawa
- RNA Biology Laboratory, RIKEN Advanced Research Institute, Wako, Saitama, Japan
- RNA Biology Laboratory, Faculty of Pharmaceutical Sciences, Hokkaido University, Kita 12-jo Nishi 6-chome, Kita-ku, Sapporo, Japan
| | - Stefan Blankenberg
- Clinic for General and Interventional Cardiology, University Heart Center Hamburg, Martinistrasse 52, Hamburg, Germany
- DZHK, Site Hamburg/Kiel/Lübeck, Hamburg, Germany
| | - Stefan Engelhardt
- Institute for Pharmacology and Toxikology, Technische Universität München, Biedersteiner Strasse 29, München, Germany
- DZHK, Site Munich, Munich, Germany
| | - Thomas Thum
- Institute of Molecular and Translational Therapeutic Strategies (IMTTS), Hannover Medical School, Hannover, Germany
| | - Christian Weber
- DZHK, Site Munich, Munich, Germany
- Institute for Cardiovascular Prevention (IPEK), Ludwig-Maximilians-Universität, Pettenkoferstrasse 8a/9, Munich, Germany
| | - Benjamin Meder
- Institute for Cardiomyopathies Heidelberg (ICH), Universitätsklinikum Heidelberg, Im Neuenheimer Feld 669, Heidelberg, Germany
- DZHK, Site Heidelberg/Mannheim, Heidelberg, Germany
| | - Roger Hajjar
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ulf Landmesser
- Department of Cardiology, CBF, CC11, Charite Universitätsmedizin Berlin, Campus Benjamin Franklin, Charite Centrum 11 (Cardiovascular Medicine), Hindenburgdamm 20, Berlin, Germany
- German Center for Cardiovascular Research (DZHK), Site Berlin, Berlin, Germany
- Berlin Institute of Health, Kapelle-Ufer 2, Berlin, Germany
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79
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Klein HU, De Jager PL. How do we measure the epigenome(s)? Mult Scler 2018; 24:446-448. [PMID: 29722595 DOI: 10.1177/1352458517750772] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Affiliation(s)
- Hans-Ulrich Klein
- Center for Translational and Computational Neuro-immunology, Department of Neurology, Columbia University Medical Center, New York, NY, USA/Cell Circuits Program, Broad Institute, Cambridge, MA, USA
| | - Philip L De Jager
- Center for Translational and Computational Neuro-immunology, Department of Neurology, Columbia University Medical Center, New York, NY, USA/Cell Circuits Program, Broad Institute, Cambridge, MA, USA
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80
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Albrecht F, List M, Bock C, Lengauer T. DeepBlueR: large-scale epigenomic analysis in R. Bioinformatics 2018; 33:2063-2064. [PMID: 28334349 PMCID: PMC5870546 DOI: 10.1093/bioinformatics/btx099] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Accepted: 02/21/2017] [Indexed: 12/21/2022] Open
Abstract
Motivation While large amounts of epigenomic data are publicly available, their retrieval in a form suitable for downstream analysis is a bottleneck in current research. The DeepBlue Epigenomic Data Server provides a powerful interface and API for filtering, transforming, aggregating and downloading data from several epigenomic consortia. Results To make public epigenomic data conveniently available for analysis in R, we developed an R/Bioconductor package that connects to the DeepBlue Epigenomic Data Server, enabling users to quickly gather and transform epigenomic data from selected experiments for analysis in the Bioconductor ecosystem. Availability and Implementation http://deepblue.mpi-inf.mpg.de/R. Requirements R 3.3, Bioconductor 3.4. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Felipe Albrecht
- Max Planck Institute for Informatics.,Graduate School of Computer Science, Saarland Informatics Campus, 66123 Saarbrücken, Germany
| | | | - Christoph Bock
- Max Planck Institute for Informatics.,CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences.,Department of Laboratory Medicine, Medical University of Vienna, 1090 Vienna, Austria
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81
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Abstract
By exerting pro- and anti-tumorigenic actions, tumor-infiltrating immune cells can profoundly influence tumor progression, as well as the success of anti-cancer therapies. Therefore, the quantification of tumor-infiltrating immune cells holds the promise to unveil the multi-faceted role of the immune system in human cancers and its involvement in tumor escape mechanisms and response to therapy. Tumor-infiltrating immune cells can be quantified from RNA sequencing data of human tumors using bioinformatics approaches. In this review, we describe state-of-the-art computational methods for the quantification of immune cells from transcriptomics data and discuss the open challenges that must be addressed to accurately quantify immune infiltrates from RNA sequencing data of human bulk tumors.
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82
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Newman V, Moore B, Sparrow H, Perry E. The Ensembl Genome Browser: Strategies for Accessing Eukaryotic Genome Data. Methods Mol Biol 2018; 1757:115-139. [PMID: 29761458 DOI: 10.1007/978-1-4939-7737-6_6] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The Ensembl Genome Browser provides a wealth of freely available genomic data that can be accessed for many purposes by genetics, genomics, and molecular biology researchers. Herein we present two protocols for exploring different aspects of these data: a phenotype and its associated variants and genes, and a promoter and the epigenetic marks and protein-binding activity associated with it. These workflows illustrate a subset of the data types available through the Ensembl Browser, and can be considered a springboard for further exploration.
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Affiliation(s)
- Victoria Newman
- European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge, UK
| | - Benjamin Moore
- European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge, UK
| | - Helen Sparrow
- European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge, UK
| | - Emily Perry
- European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge, UK.
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83
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Carrillo-de-Santa-Pau E, Juan D, Pancaldi V, Were F, Martin-Subero I, Rico D, Valencia A. Automatic identification of informative regions with epigenomic changes associated to hematopoiesis. Nucleic Acids Res 2017; 45:9244-9259. [PMID: 28934481 PMCID: PMC5716146 DOI: 10.1093/nar/gkx618] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Accepted: 07/06/2017] [Indexed: 12/19/2022] Open
Abstract
Hematopoiesis is one of the best characterized biological systems but the connection between chromatin changes and lineage differentiation is not yet well understood. We have developed a bioinformatic workflow to generate a chromatin space that allows to classify 42 human healthy blood epigenomes from the BLUEPRINT, NIH ROADMAP and ENCODE consortia by their cell type. This approach let us to distinguish different cells types based on their epigenomic profiles, thus recapitulating important aspects of human hematopoiesis. The analysis of the orthogonal dimension of the chromatin space identify 32,662 chromatin determinant regions (CDRs), genomic regions with different epigenetic characteristics between the cell types. Functional analysis revealed that these regions are linked with cell identities. The inclusion of leukemia epigenomes in the healthy hematological chromatin sample space gives us insights on the healthy cell types that are more epigenetically similar to the disease samples. Further analysis of tumoral epigenetic alterations in hematopoietic CDRs points to sets of genes that are tightly regulated in leukemic transformations and commonly mutated in other tumors. Our method provides an analytical approach to study the relationship between epigenomic changes and cell lineage differentiation. Method availability: https://github.com/david-juan/ChromDet.
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Affiliation(s)
| | - David Juan
- Institut de Biologia Evolutiva, Consejo Superior de Investigaciones Científicas-Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, Barcelona, 08003, Spain
| | - Vera Pancaldi
- Barcelona Supercomputing Centre (BSC), Barcelona, 08034, Spain
| | - Felipe Were
- Structural Biology and BioComputing Programme, Spanish National Cancer Research Centre (CNIO), Madrid, 28029, Spain
| | - Ignacio Martin-Subero
- Institut d'Investigacions Biomédiques August Pi i Sunyer (IDIBAPS), Department of Anatomic Pathology, Pharmacology and Microbiology, University of Barcelona, Barcelona, 08036, Spain
| | - Daniel Rico
- Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Alfonso Valencia
- Barcelona Supercomputing Centre (BSC), Barcelona, 08034, Spain.,ICREA, Pg. Lluís Companys 23, Barcelona, 08010, Spain
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84
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van der Harst P, de Windt LJ, Chambers JC. Translational Perspective on Epigenetics in Cardiovascular Disease. J Am Coll Cardiol 2017; 70:590-606. [PMID: 28750703 PMCID: PMC5543329 DOI: 10.1016/j.jacc.2017.05.067] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Revised: 05/30/2017] [Accepted: 05/31/2017] [Indexed: 12/19/2022]
Abstract
A plethora of environmental and behavioral factors interact, resulting in changes in gene expression and providing a basis for the development and progression of cardiovascular diseases. Heterogeneity in gene expression responses among cells and individuals involves epigenetic mechanisms. Advancing technology allowing genome-scale interrogation of epigenetic marks provides a rapidly expanding view of the complexity and diversity of the epigenome. In this review, the authors discuss the expanding landscape of epigenetic modifications and highlight their importance for future understanding of disease. The epigenome provides a mechanistic link between environmental exposures and gene expression profiles ultimately leading to disease. The authors discuss the current evidence for transgenerational epigenetic inheritance and summarize the data linking epigenetics to cardiovascular disease. Furthermore, the potential targets provided by the epigenome for the development of future diagnostics, preventive strategies, and therapy for cardiovascular disease are reviewed. Finally, the authors provide some suggestions for future directions.
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Affiliation(s)
- Pim van der Harst
- Departments of Cardiology and Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands; Durrer Center for Cardiovascular Research, Netherlands Heart Institute, Utrecht, the Netherlands.
| | - Leon J de Windt
- Department of Cardiology, CARIM School for Cardiovascular Diseases, Maastricht University, Maastricht, the Netherlands
| | - John C Chambers
- Department of Epidemiology and Biostatistics, Imperial College London, London, United Kingdom; Ealing Hospital NHS Trust, Middlesex, United Kingdom
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85
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Ecker S, Beck S. Epigenetic variation taking center stage in immunological research. Epigenomics 2017; 9:375-378. [DOI: 10.2217/epi-2017-0006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Affiliation(s)
- Simone Ecker
- UCL Cancer Institute, University College London, 72 Huntley Street, London WC1E 6BT, UK
| | - Stephan Beck
- UCL Cancer Institute, University College London, 72 Huntley Street, London WC1E 6BT, UK
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86
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Li Y, Xu Q, Lv N, Wang L, Zhao H, Wang X, Guo J, Chen C, Li Y, Yu L. Clinical implications of genome-wide DNA methylation studies in acute myeloid leukemia. J Hematol Oncol 2017; 10:41. [PMID: 28153026 PMCID: PMC5290606 DOI: 10.1186/s13045-017-0409-z] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Accepted: 01/27/2017] [Indexed: 01/01/2023] Open
Abstract
Acute myeloid leukemia (AML) is the most common type of acute leukemia in adults. AML is a heterogeneous malignancy characterized by distinct genetic and epigenetic abnormalities. Recent genome-wide DNA methylation studies have highlighted an important role of dysregulated methylation signature in AML from biological and clinical standpoint. In this review, we will outline the recent advances in the methylome study of AML and overview the impacts of DNA methylation on AML diagnosis, treatment, and prognosis.
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Affiliation(s)
- Yan Li
- Department of Hematology and BMT center, Chinese PLA General Hospital, 28 Fuxing Road, Beijing, 100853, China.,Department of Hematology, Hainan Branch of Chinese PLA General Hospital, Sanya, 572013, Hainan Province, China
| | - Qingyu Xu
- Department of Hematology and BMT center, Chinese PLA General Hospital, 28 Fuxing Road, Beijing, 100853, China.,Medical school of Nankai University, 94 Weijin Road, Tianjin, 300071, China
| | - Na Lv
- Department of Hematology and BMT center, Chinese PLA General Hospital, 28 Fuxing Road, Beijing, 100853, China
| | - Lili Wang
- Department of Hematology and BMT center, Chinese PLA General Hospital, 28 Fuxing Road, Beijing, 100853, China
| | - Hongmei Zhao
- Annoroad Gene Technology Co. Ltd, Beijing, 100176, China
| | - Xiuli Wang
- Annoroad Gene Technology Co. Ltd, Beijing, 100176, China
| | - Jing Guo
- Annoroad Gene Technology Co. Ltd, Beijing, 100176, China
| | - Chongjian Chen
- Annoroad Gene Technology Co. Ltd, Beijing, 100176, China
| | - Yonghui Li
- Department of Hematology and BMT center, Chinese PLA General Hospital, 28 Fuxing Road, Beijing, 100853, China
| | - Li Yu
- Department of Hematology and BMT center, Chinese PLA General Hospital, 28 Fuxing Road, Beijing, 100853, China.
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