1
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Zhao C. Genome wide association study gateway-transitioning variants from association to causality in complex diseases. Sleep 2024; 47:zsae116. [PMID: 38752386 DOI: 10.1093/sleep/zsae116] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/12/2024] Open
Affiliation(s)
- Chen Zhao
- Institute of Human Genetics, TUM School of Medicine and Health, Technical University of Munich, Munich, Germany
- Neurogenetic Systems Analysis Group, Institute of Neurogenomics, Helmholtz Munich, Germany
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2
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Zhang J, Wang Q, Qi S, Duan Y, Liu Z, Liu J, Zhang Z, Li C. An oncogenic enhancer promotes melanoma progression via regulating ETV4 expression. J Transl Med 2024; 22:547. [PMID: 38849954 PMCID: PMC11157841 DOI: 10.1186/s12967-024-05356-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2024] [Accepted: 05/29/2024] [Indexed: 06/09/2024] Open
Abstract
BACKGROUND Enhancers are important gene regulatory elements that promote the expression of critical genes in development and disease. Aberrant enhancer can modulate cancer risk and activate oncogenes that lead to the occurrence of various cancers. However, the underlying mechanism of most enhancers in cancer remains unclear. Here, we aim to explore the function and mechanism of a crucial enhancer in melanoma. METHODS Multi-omics data were applied to identify an enhancer (enh17) involved in melanoma progression. To evaluate the function of enh17, CRISPR/Cas9 technology were applied to knockout enh17 in melanoma cell line A375. RNA-seq, ChIP-seq and Hi-C data analysis integrated with luciferase reporter assay were performed to identify the potential target gene of enh17. Functional experiments were conducted to further validate the function of the target gene ETV4. Multi-omics data integrated with CUT&Tag sequencing were performed to validate the binding profile of the inferred transcription factor STAT3. RESULTS An enhancer, named enh17 here, was found to be aberrantly activated and involved in melanoma progression. CRISPR/Cas9-mediated deletion of enh17 inhibited cell proliferation, migration, and tumor growth of melanoma both in vitro and in vivo. Mechanistically, we identified ETV4 as a target gene regulated by enh17, and functional experiments further support ETV4 as a target gene that is involved in cancer-associated phenotypes. In addition, STAT3 acts as a transcription factor binding with enh17 to regulate the transcription of ETV4. CONCLUSIONS Our findings revealed that enh17 plays an oncogenic role and promotes tumor progression in melanoma, and its transcriptional regulatory mechanisms were fully elucidated, which may open a promising window for melanoma prevention and treatment.
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Affiliation(s)
- Junyou Zhang
- School of Engineering Medicine, Beihang University, Beijing, 100191, China
- Key Laboratory of Big Data-Based Precision Medicine (Ministry of Industry and Information Technology), Beihang University, Beijing, 100191, China
- School of Biological Science and Medical Engineering, Beihang University, Beijing, 100191, China
| | - Qilin Wang
- School of Engineering Medicine, Beihang University, Beijing, 100191, China
- Key Laboratory of Big Data-Based Precision Medicine (Ministry of Industry and Information Technology), Beihang University, Beijing, 100191, China
- School of Biological Science and Medical Engineering, Beihang University, Beijing, 100191, China
| | - Sihan Qi
- School of Engineering Medicine, Beihang University, Beijing, 100191, China
- Key Laboratory of Big Data-Based Precision Medicine (Ministry of Industry and Information Technology), Beihang University, Beijing, 100191, China
- School of Biological Science and Medical Engineering, Beihang University, Beijing, 100191, China
| | - Yingying Duan
- School of Engineering Medicine, Beihang University, Beijing, 100191, China
- Key Laboratory of Big Data-Based Precision Medicine (Ministry of Industry and Information Technology), Beihang University, Beijing, 100191, China
- School of Biological Science and Medical Engineering, Beihang University, Beijing, 100191, China
| | - Zhaoshuo Liu
- School of Engineering Medicine, Beihang University, Beijing, 100191, China
- Key Laboratory of Big Data-Based Precision Medicine (Ministry of Industry and Information Technology), Beihang University, Beijing, 100191, China
- School of Biological Science and Medical Engineering, Beihang University, Beijing, 100191, China
| | - Jiaxin Liu
- School of Engineering Medicine, Beihang University, Beijing, 100191, China
- Key Laboratory of Big Data-Based Precision Medicine (Ministry of Industry and Information Technology), Beihang University, Beijing, 100191, China
- School of Biological Science and Medical Engineering, Beihang University, Beijing, 100191, China
| | - Ziyi Zhang
- School of Engineering Medicine, Beihang University, Beijing, 100191, China
- Key Laboratory of Big Data-Based Precision Medicine (Ministry of Industry and Information Technology), Beihang University, Beijing, 100191, China
- School of Biological Science and Medical Engineering, Beihang University, Beijing, 100191, China
| | - Chunyan Li
- School of Engineering Medicine, Beihang University, Beijing, 100191, China.
- Key Laboratory of Big Data-Based Precision Medicine (Ministry of Industry and Information Technology), Beihang University, Beijing, 100191, China.
- School of Biological Science and Medical Engineering, Beihang University, Beijing, 100191, China.
- Beijing Advanced Innovation Center for Big Data-Based Precision Medicine, Beihang University, Beijing, 100191, China.
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3
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Mowery CT, Freimer JW, Chen Z, Casaní-Galdón S, Umhoefer JM, Arce MM, Gjoni K, Daniel B, Sandor K, Gowen BG, Nguyen V, Simeonov DR, Garrido CM, Curie GL, Schmidt R, Steinhart Z, Satpathy AT, Pollard KS, Corn JE, Bernstein BE, Ye CJ, Marson A. Systematic decoding of cis gene regulation defines context-dependent control of the multi-gene costimulatory receptor locus in human T cells. Nat Genet 2024; 56:1156-1167. [PMID: 38811842 PMCID: PMC11176074 DOI: 10.1038/s41588-024-01743-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 04/04/2024] [Indexed: 05/31/2024]
Abstract
Cis-regulatory elements (CREs) interact with trans regulators to orchestrate gene expression, but how transcriptional regulation is coordinated in multi-gene loci has not been experimentally defined. We sought to characterize the CREs controlling dynamic expression of the adjacent costimulatory genes CD28, CTLA4 and ICOS, encoding regulators of T cell-mediated immunity. Tiling CRISPR interference (CRISPRi) screens in primary human T cells, both conventional and regulatory subsets, uncovered gene-, cell subset- and stimulation-specific CREs. Integration with CRISPR knockout screens and assay for transposase-accessible chromatin with sequencing (ATAC-seq) profiling identified trans regulators influencing chromatin states at specific CRISPRi-responsive elements to control costimulatory gene expression. We then discovered a critical CCCTC-binding factor (CTCF) boundary that reinforces CRE interaction with CTLA4 while also preventing promiscuous activation of CD28. By systematically mapping CREs and associated trans regulators directly in primary human T cell subsets, this work overcomes longstanding experimental limitations to decode context-dependent gene regulatory programs in a complex, multi-gene locus critical to immune homeostasis.
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Grants
- P30 DK063720 NIDDK NIH HHS
- R01 HG008140 NHGRI NIH HHS
- T32 GM007618 NIGMS NIH HHS
- S10 OD028511 NIH HHS
- F99 CA234842 NCI NIH HHS
- S10 OD021822 NIH HHS
- K00 CA234842 NCI NIH HHS
- P01 AI138962 NIAID NIH HHS
- U01 HL157989 NHLBI NIH HHS
- R01 DK129364 NIDDK NIH HHS
- T32 DK007418 NIDDK NIH HHS
- R01 AI136972 NIAID NIH HHS
- F30 AI157167 NIAID NIH HHS
- R01 HG011239 NHGRI NIH HHS
- NIH grants 1R01DK129364-01A1, P01AI138962, and R01HG008140; the Larry L. Hillblom Foundation (grant no. 2020-D-002-NET); and Northern California JDRF Center of Excellence. A.M. is a member of the Parker Institute for Cancer Immunotherapy (PICI), and has received funding from the Arc Institute, Chan Zuckerberg Biohub, Innovative Genomics Institute (IGI), Cancer Research Institute (CRI) Lloyd J. Old STAR award, a gift from the Jordan Family, a gift from the Byers family and a gift from B. Bakar.
- UCSF ImmunoX Computational Immunology Fellow, is supported by NIH grant F30AI157167, and has received support from NIH grants T32DK007418 and T32GM007618
- NIH grant R01HG008140
- Career Award for Medical Scientists from the Burroughs Wellcome Fund, a Lloyd J. Old STAR Award from the Cancer Research Institute, and the Parker Institute for Cancer Immunotherapy
- NIH grant U01HL157989
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Affiliation(s)
- Cody T Mowery
- Medical Scientist Training Program, University of California, San Francisco, San Francisco, CA, USA
- Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, CA, USA
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA
| | - Jacob W Freimer
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Zeyu Chen
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Departments of Cell Biology and Pathology, Harvard Medical School, Boston, MA, USA
| | - Salvador Casaní-Galdón
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Departments of Cell Biology and Pathology, Harvard Medical School, Boston, MA, USA
| | - Jennifer M Umhoefer
- Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, CA, USA
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA
| | - Maya M Arce
- Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, CA, USA
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Ketrin Gjoni
- Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, USA
| | - Bence Daniel
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
- Department of Pathology, Stanford University, Stanford, CA, USA
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA
- Department of Microchemistry, Proteomics, Lipidomics and Next Generation Sequencing, Genentech, South San Francisco, CA, USA
| | - Katalin Sandor
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Benjamin G Gowen
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Vinh Nguyen
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA
- Diabetes Center, University of California, San Francisco, San Francisco, CA, USA
- Department of Surgery, University of California, San Francisco, San Francisco, CA, USA
- UCSF CoLabs, University of California, San Francisco, San Francisco, CA, USA
| | - Dimitre R Simeonov
- Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, CA, USA
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA
| | - Christian M Garrido
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA
| | - Gemma L Curie
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Ralf Schmidt
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA
- Department of Laboratory Medicine, Medical University of Vienna, Vienna, Austria
| | - Zachary Steinhart
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA
| | - Ansuman T Satpathy
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
- Department of Pathology, Stanford University, Stanford, CA, USA
- Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA
- Program in Immunology, Stanford University, Stanford, CA, USA
| | - Katherine S Pollard
- Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, USA
- Chan Zuckerberg Biohub SF, San Francisco, CA, USA
| | - Jacob E Corn
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
- Department of Biology, ETH Zürich, Zürich, Switzerland
| | - Bradley E Bernstein
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Departments of Cell Biology and Pathology, Harvard Medical School, Boston, MA, USA
| | - Chun Jimmie Ye
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA.
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, USA.
- Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA.
- Chan Zuckerberg Biohub SF, San Francisco, CA, USA.
- Rosalind Russell/Ephraim P. Engleman Rheumatology Research Center, University of California, San Francisco, San Francisco, CA, USA.
- Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA, USA.
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA.
| | - Alexander Marson
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA.
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA.
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA.
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA.
- Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA.
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA.
- UCSF Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA.
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4
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Kernohan KD, Boycott KM. The expanding diagnostic toolbox for rare genetic diseases. Nat Rev Genet 2024; 25:401-415. [PMID: 38238519 DOI: 10.1038/s41576-023-00683-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/22/2023] [Indexed: 05/23/2024]
Abstract
Genomic technologies, such as targeted, exome and short-read genome sequencing approaches, have revolutionized the care of patients with rare genetic diseases. However, more than half of patients remain without a diagnosis. Emerging approaches from research-based settings such as long-read genome sequencing and optical genome mapping hold promise for improving the identification of disease-causal genetic variants. In addition, new omic technologies that measure the transcriptome, epigenome, proteome or metabolome are showing great potential for variant interpretation. As genetic testing options rapidly expand, the clinical community needs to be mindful of their individual strengths and limitations, as well as remaining challenges, to select the appropriate diagnostic test, correctly interpret results and drive innovation to address insufficiencies. If used effectively - through truly integrative multi-omics approaches and data sharing - the resulting large quantities of data from these established and emerging technologies will greatly improve the interpretative power of genetic and genomic diagnostics for rare diseases.
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Affiliation(s)
- Kristin D Kernohan
- CHEO Research Institute, University of Ottawa, Ottawa, ON, Canada
- Newborn Screening Ontario, CHEO, Ottawa, ON, Canada
| | - Kym M Boycott
- CHEO Research Institute, University of Ottawa, Ottawa, ON, Canada.
- Department of Genetics, CHEO, Ottawa, ON, Canada.
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5
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Bower G, Hollingsworth EW, Jacinto S, Clock B, Cao K, Liu M, Dziulko A, Alcaina-Caro A, Xu Q, Skowronska-Krawczyk D, Lopez-Rios J, Dickel DE, Bardet AF, Pennacchio LA, Visel A, Kvon EZ. Conserved Cis-Acting Range Extender Element Mediates Extreme Long-Range Enhancer Activity in Mammals. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.26.595809. [PMID: 38826394 PMCID: PMC11142232 DOI: 10.1101/2024.05.26.595809] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
While most mammalian enhancers regulate their cognate promoters over moderate distances of tens of kilobases (kb), some enhancers act over distances in the megabase range. The sequence features enabling such extreme-distance enhancer-promoter interactions remain elusive. Here, we used in vivo enhancer replacement experiments in mice to show that short- and medium-range enhancers cannot initiate gene expression at extreme-distance range. We uncover a novel conserved cis-acting element, Range EXtender (REX), that confers extreme-distance regulatory activity and is located next to a long-range enhancer of Sall1. The REX element itself has no endogenous enhancer activity. However, addition of the REX to other short- and mid-range enhancers substantially increases their genomic interaction range. In the most extreme example observed, addition of the REX increased the range of an enhancer by an order of magnitude, from its native 71kb to 840kb. The REX element contains highly conserved [C/T]AATTA homeodomain motifs. These motifs are enriched around long-range limb enhancers genome-wide, including the ZRS, a benchmark long-range limb enhancer of Shh. Mutating the [C/T]AATTA motifs within the ZRS does not affect its limb-specific enhancer activity at short range, but selectively abolishes its long-range activity, resulting in severe limb reduction in knock-in mice. In summary, we identify a sequence signature globally associated with long-range enhancer-promoter interactions and describe a prototypical REX element that is necessary and sufficient to confer extreme-distance gene activation by remote enhancers.
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Affiliation(s)
- Grace Bower
- Department of Developmental and Cell Biology, University of California, Irvine, CA 92967, USA
| | - Ethan W. Hollingsworth
- Department of Developmental and Cell Biology, University of California, Irvine, CA 92967, USA
- Medical Scientist Training Program, University of California, Irvine, CA 92967, USA
| | - Sandra Jacinto
- Department of Developmental and Cell Biology, University of California, Irvine, CA 92967, USA
| | - Benjamin Clock
- Department of Developmental and Cell Biology, University of California, Irvine, CA 92967, USA
| | - Kaitlyn Cao
- Department of Developmental and Cell Biology, University of California, Irvine, CA 92967, USA
| | - Mandy Liu
- Department of Developmental and Cell Biology, University of California, Irvine, CA 92967, USA
| | - Adam Dziulko
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Ana Alcaina-Caro
- Centro Andaluz de Biología del Desarrollo (CABD), CSIC-Universidad Pablo de Olavide-Junta de Andalucía, Seville, 41013, Spain
| | - Qianlan Xu
- Department of Physiology and Biophysics, Department of Ophthalmology, Center for Translational Vision Research, School of Medicine, University of California, Irvine, CA, USA
| | - Dorota Skowronska-Krawczyk
- Department of Physiology and Biophysics, Department of Ophthalmology, Center for Translational Vision Research, School of Medicine, University of California, Irvine, CA, USA
| | - Javier Lopez-Rios
- Centro Andaluz de Biología del Desarrollo (CABD), CSIC-Universidad Pablo de Olavide-Junta de Andalucía, Seville, 41013, Spain
| | - Diane E. Dickel
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Anaïs F. Bardet
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Université de Strasbourg, CNRS UMR7104, INSERM U1258, 67400 Illkirch, France
| | - Len A. Pennacchio
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- U.S. Department of Energy Joint Genome Institute, Walnut Creek, CA 94598, USA
- Comparative Biochemistry Program, University of California, Berkeley, CA 94720, USA
| | - Axel Visel
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- U.S. Department of Energy Joint Genome Institute, Walnut Creek, CA 94598, USA
- School of Natural Sciences, University of California, Merced, CA 95343, USA
| | - Evgeny Z. Kvon
- Department of Developmental and Cell Biology, University of California, Irvine, CA 92967, USA
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6
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Han MH, Park J, Park M. Advances in the multimodal analysis of the 3D chromatin structure and gene regulation. Exp Mol Med 2024; 56:763-771. [PMID: 38658704 PMCID: PMC11059362 DOI: 10.1038/s12276-024-01246-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 04/03/2024] [Accepted: 04/08/2024] [Indexed: 04/26/2024] Open
Abstract
Recent studies have demonstrated that the three-dimensional conformation of the chromatin plays a crucial role in gene regulation, with aberrations potentially leading to various diseases. Advanced methodologies have revealed a link between the chromatin conformation and biological function. This review divides these methodologies into sequencing-based and imaging-based methodologies, tracing their development over time. We particularly highlight innovative techniques that facilitate the simultaneous mapping of RNAs, histone modifications, and proteins within the context of the 3D architecture of chromatin. This multimodal integration substantially improves our ability to establish a robust connection between the spatial arrangement of molecular components in the nucleus and their functional roles. Achieving a comprehensive understanding of gene regulation requires capturing diverse data modalities within individual cells, enabling the direct inference of functional relationships between these components. In this context, imaging-based technologies have emerged as an especially promising approach for gathering spatial information across multiple components in the same cell.
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Affiliation(s)
- Man-Hyuk Han
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
| | - Jihyun Park
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
| | - Minhee Park
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea.
- Graduate School of Engineering Biology, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea.
- KAIST Institute for BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea.
- KAIST Stem Cell Center, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea.
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7
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Chen Z, Snetkova V, Bower G, Jacinto S, Clock B, Dizehchi A, Barozzi I, Mannion BJ, Alcaina-Caro A, Lopez-Rios J, Dickel DE, Visel A, Pennacchio LA, Kvon EZ. Increased enhancer-promoter interactions during developmental enhancer activation in mammals. Nat Genet 2024; 56:675-685. [PMID: 38509385 PMCID: PMC11203181 DOI: 10.1038/s41588-024-01681-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2022] [Accepted: 02/06/2024] [Indexed: 03/22/2024]
Abstract
Remote enhancers are thought to interact with their target promoters via physical proximity, yet the importance of this proximity for enhancer function remains unclear. Here we investigate the three-dimensional (3D) conformation of enhancers during mammalian development by generating high-resolution tissue-resolved contact maps for nearly a thousand enhancers with characterized in vivo activities in ten murine embryonic tissues. Sixty-one percent of developmental enhancers bypass their neighboring genes, which are often marked by promoter CpG methylation. The majority of enhancers display tissue-specific 3D conformations, and both enhancer-promoter and enhancer-enhancer interactions are moderately but consistently increased upon enhancer activation in vivo. Less than 14% of enhancer-promoter interactions form stably across tissues; however, these invariant interactions form in the absence of the enhancer and are likely mediated by adjacent CTCF binding. Our results highlight the general importance of enhancer-promoter physical proximity for developmental gene activation in mammals.
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Affiliation(s)
- Zhuoxin Chen
- Department of Developmental and Cell Biology, School of the Biological Sciences, University of California, Irvine, CA, USA
| | - Valentina Snetkova
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Grace Bower
- Department of Developmental and Cell Biology, School of the Biological Sciences, University of California, Irvine, CA, USA
| | - Sandra Jacinto
- Department of Developmental and Cell Biology, School of the Biological Sciences, University of California, Irvine, CA, USA
| | - Benjamin Clock
- Department of Developmental and Cell Biology, School of the Biological Sciences, University of California, Irvine, CA, USA
| | - Atrin Dizehchi
- Department of Developmental and Cell Biology, School of the Biological Sciences, University of California, Irvine, CA, USA
| | - Iros Barozzi
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Center for Cancer Research, Medical University of Vienna, Vienna, Austria
| | - Brandon J Mannion
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Comparative Biochemistry Program, University of California, Berkeley, CA, USA
| | - Ana Alcaina-Caro
- Centro Andaluz de Biología del Desarrollo, CSIC, Universidad Pablo de Olavide, Junta de Andalucía, Seville, Spain
| | - Javier Lopez-Rios
- Centro Andaluz de Biología del Desarrollo, CSIC, Universidad Pablo de Olavide, Junta de Andalucía, Seville, Spain
- School of Health Sciences, Universidad Loyola Andalucía, Seville, Spain
| | - Diane E Dickel
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Octant, Inc, Emeryville, CA, USA
| | - Axel Visel
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- U.S. Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
- School of Natural Sciences, University of California, Merced, CA, USA
| | - Len A Pennacchio
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Comparative Biochemistry Program, University of California, Berkeley, CA, USA
- U.S. Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - Evgeny Z Kvon
- Department of Developmental and Cell Biology, School of the Biological Sciences, University of California, Irvine, CA, USA.
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8
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Dong P, Voloudakis G, Fullard JF, Hoffman GE, Roussos P. Convergence of the dysregulated regulome in schizophrenia with polygenic risk and evolutionarily constrained enhancers. Mol Psychiatry 2024; 29:782-792. [PMID: 38145985 PMCID: PMC11153027 DOI: 10.1038/s41380-023-02370-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 12/06/2023] [Accepted: 12/07/2023] [Indexed: 12/27/2023]
Abstract
Enhancers play an essential role in the etiology of schizophrenia; however, the dysregulation of enhancer activity and its impact on the regulome in schizophrenia remains understudied. To address this gap in our knowledge, we assessed enhancer and gene expression in 1,382 brain samples comprising cases with schizophrenia and unaffected controls. Dysregulation of enhancer expression was concordant with changes in gene expression, and was more closely associated with schizophrenia polygenic risk, suggesting that enhancer dysregulation is proximal to the genetic etiology of the disease. Modeling the shared variance of cis-coordinated genes and enhancers revealed a gene regulatory program that was highly associated with genetic vulnerability to schizophrenia. By integrating coordinated factors with evolutionary constraints, we found that enhancers acquired during human evolution are more likely to regulate genes that are implicated in neuropsychiatric disorders and, thus, hold potential as therapeutic targets. Our analysis provides a systematic view of regulome dysregulation in schizophrenia and highlights its convergence with schizophrenia polygenic risk and human-gained enhancers.
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Affiliation(s)
- Pengfei Dong
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
- Department of Genetics and Genomic Science, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
| | - Georgios Voloudakis
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Genetics and Genomic Science, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Mental Illness Research Education and Clinical Center (MIRECC), James J. Peters VA Medical Center, Bronx, NY, 10468, USA
- Center for Precision Medicine and Translational Therapeutics, James J. Peters VA Medical Center, Bronx, NY, 10468, USA
| | - John F Fullard
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Genetics and Genomic Science, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Gabriel E Hoffman
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Genetics and Genomic Science, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Panos Roussos
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
- Department of Genetics and Genomic Science, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
- Mental Illness Research Education and Clinical Center (MIRECC), James J. Peters VA Medical Center, Bronx, NY, 10468, USA.
- Center for Precision Medicine and Translational Therapeutics, James J. Peters VA Medical Center, Bronx, NY, 10468, USA.
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9
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Zhigulev A, Norberg Z, Cordier J, Spalinskas R, Bassereh H, Björn N, Pradhananga S, Gréen H, Sahlén P. Enhancer mutations modulate the severity of chemotherapy-induced myelosuppression. Life Sci Alliance 2024; 7:e202302244. [PMID: 38228368 PMCID: PMC10796589 DOI: 10.26508/lsa.202302244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 12/19/2023] [Accepted: 12/21/2023] [Indexed: 01/18/2024] Open
Abstract
Non-small cell lung cancer is often diagnosed at advanced stages, and many patients are still treated with classical chemotherapy. The unselective nature of chemotherapy often results in severe myelosuppression. Previous studies showed that protein-coding mutations could not fully explain the predisposition to myelosuppression. Here, we investigate the possible role of enhancer mutations in myelosuppression susceptibility. We produced transcriptome and promoter-interaction maps (using HiCap) of three blood stem-like cell lines treated with carboplatin or gemcitabine. Taking advantage of publicly available enhancer datasets, we validated HiCap results in silico and in living cells using epigenetic CRISPR technology. We also developed a network approach for interactome analysis and detection of differentially interacting genes. Differential interaction analysis provided additional information on relevant genes and pathways for myelosuppression compared with differential gene expression analysis at the bulk level. Moreover, we showed that enhancers of differentially interacting genes are highly enriched for variants associated with differing levels of myelosuppression. Altogether, our work represents a prominent example of integrative transcriptome and gene regulatory datasets analysis for the functional annotation of noncoding mutations.
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Affiliation(s)
- Artemy Zhigulev
- https://ror.org/026vcq606 Royal Institute of Technology - KTH, School of Chemistry, Biotechnology and Health, Science for Life Laboratory, Stockholm, Sweden
| | - Zandra Norberg
- https://ror.org/026vcq606 Royal Institute of Technology - KTH, School of Chemistry, Biotechnology and Health, Science for Life Laboratory, Stockholm, Sweden
| | - Julie Cordier
- https://ror.org/026vcq606 Royal Institute of Technology - KTH, School of Chemistry, Biotechnology and Health, Science for Life Laboratory, Stockholm, Sweden
| | - Rapolas Spalinskas
- https://ror.org/026vcq606 Royal Institute of Technology - KTH, School of Chemistry, Biotechnology and Health, Science for Life Laboratory, Stockholm, Sweden
| | - Hassan Bassereh
- https://ror.org/026vcq606 Royal Institute of Technology - KTH, School of Chemistry, Biotechnology and Health, Science for Life Laboratory, Stockholm, Sweden
| | - Niclas Björn
- Division of Clinical Chemistry and Pharmacology, Department of Biomedical and Clinical Sciences, Faculty of Medicine and Health Sciences, Linköping University, Linköping, Sweden
| | - Sailendra Pradhananga
- https://ror.org/026vcq606 Royal Institute of Technology - KTH, School of Chemistry, Biotechnology and Health, Science for Life Laboratory, Stockholm, Sweden
| | - Henrik Gréen
- Division of Clinical Chemistry and Pharmacology, Department of Biomedical and Clinical Sciences, Faculty of Medicine and Health Sciences, Linköping University, Linköping, Sweden
- Department of Forensic Genetics and Forensic Toxicology, National Board of Forensic Medicine, Linköping, Sweden
| | - Pelin Sahlén
- https://ror.org/026vcq606 Royal Institute of Technology - KTH, School of Chemistry, Biotechnology and Health, Science for Life Laboratory, Stockholm, Sweden
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10
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Sui JY, Eichenfield DZ, Sun BK. The role of enhancers in psoriasis and atopic dermatitis. Br J Dermatol 2023; 190:10-19. [PMID: 37658835 DOI: 10.1093/bjd/ljad321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 08/25/2023] [Accepted: 08/27/2023] [Indexed: 09/05/2023]
Abstract
Regulatory elements, particularly enhancers, play a crucial role in disease susceptibility and progression. Enhancers are DNA sequences that activate gene expression and can be affected by epigenetic modifications, interactions with transcription factors (TFs) or changes to the enhancer DNA sequence itself. Altered enhancer activity impacts gene expression and contributes to disease. In this review, we define enhancers and the experimental techniques used to identify and characterize them. We also discuss recent studies that examine how enhancers contribute to atopic dermatitis (AD) and psoriasis. Articles in the PubMed database were identified (from 1 January 2010 to 28 February 2023) that were relevant to enhancer variants, enhancer-associated TFs and enhancer histone modifications in psoriasis or AD. Most enhancers associated with these conditions regulate genes affecting epidermal homeostasis or immune function. These discoveries present potential therapeutic targets to complement existing treatment options for AD and psoriasis.
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Affiliation(s)
- Jennifer Y Sui
- Department of Dermatology, University of California San Diego School of Medicine, CA, USA
- Division of Pediatric and Adolescent Dermatology, Rady Children's Hospital of San Diego, CA, USA
| | - Dawn Z Eichenfield
- Department of Dermatology, University of California San Diego School of Medicine, CA, USA
- Division of Pediatric and Adolescent Dermatology, Rady Children's Hospital of San Diego, CA, USA
| | - Bryan K Sun
- Department of Dermatology, University of California San Diego School of Medicine, CA, USA
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11
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Gschwind AR, Mualim KS, Karbalayghareh A, Sheth MU, Dey KK, Jagoda E, Nurtdinov RN, Xi W, Tan AS, Jones H, Ma XR, Yao D, Nasser J, Avsec Ž, James BT, Shamim MS, Durand NC, Rao SSP, Mahajan R, Doughty BR, Andreeva K, Ulirsch JC, Fan K, Perez EM, Nguyen TC, Kelley DR, Finucane HK, Moore JE, Weng Z, Kellis M, Bassik MC, Price AL, Beer MA, Guigó R, Stamatoyannopoulos JA, Lieberman Aiden E, Greenleaf WJ, Leslie CS, Steinmetz LM, Kundaje A, Engreitz JM. An encyclopedia of enhancer-gene regulatory interactions in the human genome. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.09.563812. [PMID: 38014075 PMCID: PMC10680627 DOI: 10.1101/2023.11.09.563812] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
Identifying transcriptional enhancers and their target genes is essential for understanding gene regulation and the impact of human genetic variation on disease1-6. Here we create and evaluate a resource of >13 million enhancer-gene regulatory interactions across 352 cell types and tissues, by integrating predictive models, measurements of chromatin state and 3D contacts, and largescale genetic perturbations generated by the ENCODE Consortium7. We first create a systematic benchmarking pipeline to compare predictive models, assembling a dataset of 10,411 elementgene pairs measured in CRISPR perturbation experiments, >30,000 fine-mapped eQTLs, and 569 fine-mapped GWAS variants linked to a likely causal gene. Using this framework, we develop a new predictive model, ENCODE-rE2G, that achieves state-of-the-art performance across multiple prediction tasks, demonstrating a strategy involving iterative perturbations and supervised machine learning to build increasingly accurate predictive models of enhancer regulation. Using the ENCODE-rE2G model, we build an encyclopedia of enhancer-gene regulatory interactions in the human genome, which reveals global properties of enhancer networks, identifies differences in the functions of genes that have more or less complex regulatory landscapes, and improves analyses to link noncoding variants to target genes and cell types for common, complex diseases. By interpreting the model, we find evidence that, beyond enhancer activity and 3D enhancer-promoter contacts, additional features guide enhancerpromoter communication including promoter class and enhancer-enhancer synergy. Altogether, these genome-wide maps of enhancer-gene regulatory interactions, benchmarking software, predictive models, and insights about enhancer function provide a valuable resource for future studies of gene regulation and human genetics.
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Affiliation(s)
- Andreas R. Gschwind
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
- Basic Sciences and Engineering Initiative, Betty Irene Moore Children’s Heart Center, Lucile Packard Children’s Hospital, Stanford, CA, USA
| | - Kristy S. Mualim
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
- Department of Plant Biology, Carnegie Institute of Science, Stanford, CA, USA
| | - Alireza Karbalayghareh
- Computational and Systems Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Maya U. Sheth
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
- Basic Sciences and Engineering Initiative, Betty Irene Moore Children’s Heart Center, Lucile Packard Children’s Hospital, Stanford, CA, USA
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Kushal K. Dey
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Evelyn Jagoda
- The Novo Nordisk Foundation Center for Genomic Mechanisms of Disease, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Ramil N. Nurtdinov
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Catalonia, Spain
| | - Wang Xi
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Anthony S. Tan
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
- Basic Sciences and Engineering Initiative, Betty Irene Moore Children’s Heart Center, Lucile Packard Children’s Hospital, Stanford, CA, USA
| | - Hank Jones
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
- Basic Sciences and Engineering Initiative, Betty Irene Moore Children’s Heart Center, Lucile Packard Children’s Hospital, Stanford, CA, USA
| | - X. Rosa Ma
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
- Basic Sciences and Engineering Initiative, Betty Irene Moore Children’s Heart Center, Lucile Packard Children’s Hospital, Stanford, CA, USA
| | - David Yao
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Joseph Nasser
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Present Address: Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | | | - Benjamin T. James
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Muhammad S. Shamim
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Center for Theoretical Biological Physics, Rice University, Houston, TX, USA
- Department of Bioengineering, Rice University, Houston, TX, USA
- Medical Scientist Training Program, Baylor College of Medicine, Houston, Texas, USA
| | - Neva C. Durand
- Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Center for Theoretical Biological Physics, Rice University, Houston, TX, USA
- Department of Computer Science, Rice University, Houston, TX, USA
| | - Suhas S. P. Rao
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
- Department of Structural Biology, Stanford University, Stanford, CA, USA
| | - Ragini Mahajan
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Center for Theoretical Biological Physics, Rice University, Houston, TX, USA
- Department of Biosciences, Rice University, Houston, TX, USA
| | - Benjamin R. Doughty
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Kalina Andreeva
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Jacob C. Ulirsch
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Present Address: Artificial Intelligence Laboratory, Illumina, Inc., San Diego, CA, USA
| | - Kaili Fan
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
- Present Address: Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
| | | | - Tri C. Nguyen
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
- Basic Sciences and Engineering Initiative, Betty Irene Moore Children’s Heart Center, Lucile Packard Children’s Hospital, Stanford, CA, USA
| | | | - Hilary K. Finucane
- Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Jill E. Moore
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Zhiping Weng
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Manolis Kellis
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Michael C. Bassik
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Alkes L. Price
- Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Michael A. Beer
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Roderic Guigó
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Catalonia, Spain
| | - John A. Stamatoyannopoulos
- Altius Institute for Biomedical Sciences, Seattle, WA, USA
- Clinical Research Division, Fred Hutch Cancer Center, Seattle, WA, USA
| | - Erez Lieberman Aiden
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Center for Theoretical Biological Physics, Rice University, Houston, TX, USA
- Department of Computer Science, Rice University, Houston, TX, USA
| | - William J. Greenleaf
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
- Department of Applied Physics, Stanford University, Stanford, CA, USA
| | | | - Lars M. Steinmetz
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
- Stanford Genome Technology Center, Palo Alto, CA, USA
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany
| | - Anshul Kundaje
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
- Department of Computer Science, Stanford University, Stanford, CA, USA
| | - Jesse M. Engreitz
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
- Basic Sciences and Engineering Initiative, Betty Irene Moore Children’s Heart Center, Lucile Packard Children’s Hospital, Stanford, CA, USA
- The Novo Nordisk Foundation Center for Genomic Mechanisms of Disease, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Stanford Cardiovascular Institute, Stanford University, Stanford, CA, USA
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12
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West RR, Bauer TR, Tuschong LM, Embree LJ, Calvo KR, Tillo D, Davis J, Holland SM, Hickstein DD. A novel GATA2 distal enhancer mutation results in MonoMAC syndrome in 2 second cousins. Blood Adv 2023; 7:6351-6363. [PMID: 37595058 PMCID: PMC10587712 DOI: 10.1182/bloodadvances.2023010458] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 07/24/2023] [Accepted: 08/12/2023] [Indexed: 08/20/2023] Open
Abstract
Mutations in the transcription factor GATA2 can cause MonoMAC syndrome, a GATA2 deficiency disease characterized by several findings, including disseminated nontuberculous mycobacterial infections, severe deficiencies of monocytes, natural killer cells, and B lymphocytes, and myelodysplastic syndrome. GATA2 mutations are found in ∼90% of patients with a GATA2 deficiency phenotype and are largely missense mutations in the conserved second zinc-finger domain. Mutations in an intron 5 regulatory enhancer element are also well described in GATA2 deficiency. Here, we present a multigeneration kindred with the clinical features of GATA2 deficiency but lacking an apparent GATA2 mutation. Whole genome sequencing revealed a unique adenine-to-thymine variant in the GATA2 -110 enhancer 116,855 bp upstream of the GATA2 ATG start site. The mutation creates a new E-box consensus in position with an existing GATA-box to generate a new hematopoietic regulatory composite element. The mutation segregates with the disease in several generations of the family. Cell type-specific allelic imbalance of GATA2 expression was observed in the bone marrow of a patient with higher expression from the mutant-linked allele. Allele-specific overexpression of GATA2 was observed in CRISPR/Cas9-modified HL-60 cells and in luciferase assays with the enhancer mutation. This study demonstrates overexpression of GATA2 resulting from a single nucleotide change in an upstream enhancer element in patients with MonoMAC syndrome. Patients in this study were enrolled in the National Institute of Allergy and Infectious Diseases clinical trial and the National Cancer Institute clinical trial (both trials were registered at www.clinicaltrials.gov as #NCT01905826 and #NCT01861106, respectively).
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Affiliation(s)
- Robert R. West
- Immune Deficiency–Cellular Therapy Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Thomas R. Bauer
- Immune Deficiency–Cellular Therapy Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Laura M. Tuschong
- Immune Deficiency–Cellular Therapy Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Lisa J. Embree
- Immune Deficiency–Cellular Therapy Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Katherine R. Calvo
- Department of Laboratory Medicine, National Institutes of Health Clinical Center, Bethesda, MD
| | - Desiree Tillo
- Genomics Core, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Joie Davis
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | - Steven M. Holland
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | - Dennis D. Hickstein
- Immune Deficiency–Cellular Therapy Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD
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13
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Vincent CA, Nissen I, Dakhel S, Hörnblad A, Remeseiro S. Epigenomic perturbation of novel EGFR enhancers reduces the proliferative and invasive capacity of glioblastoma and increases sensitivity to temozolomide. BMC Cancer 2023; 23:945. [PMID: 37803333 PMCID: PMC10557167 DOI: 10.1186/s12885-023-11418-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 09/18/2023] [Indexed: 10/08/2023] Open
Abstract
BACKGROUND Glioblastoma (GB) is the most aggressive of all primary brain tumours and due to its highly invasive nature, surgical resection is nearly impossible. Patients typically rely on radiotherapy with concurrent temozolomide (TMZ) treatment and face a median survival of ~ 14 months. Alterations in the Epidermal Growth Factor Receptor gene (EGFR) are common in GB tumours, but therapies targeting EGFR have not shown significant clinical efficacy. METHODS Here, we investigated the influence of the EGFR regulatory genome on GB cells and identified novel EGFR enhancers located near the GB-associated SNP rs723527. We used CRISPR/Cas9-based approaches to target the EGFR enhancer regions, generating multiple modified GB cell lines, which enabled us to study the functional response to enhancer perturbation. RESULTS Epigenomic perturbation of the EGFR regulatory region decreases EGFR expression and reduces the proliferative and invasive capacity of glioblastoma cells, which also undergo a metabolic reprogramming in favour of mitochondrial respiration and present increased apoptosis. Moreover, EGFR enhancer-perturbation increases the sensitivity of GB cells to TMZ, the first-choice chemotherapeutic agent to treat glioblastoma. CONCLUSIONS Our findings demonstrate how epigenomic perturbation of EGFR enhancers can ameliorate the aggressiveness of glioblastoma cells and enhance the efficacy of TMZ treatment. This study demonstrates how CRISPR/Cas9-based perturbation of enhancers can be used to modulate the expression of key cancer genes, which can help improve the effectiveness of existing cancer treatments and potentially the prognosis of difficult-to-treat cancers such as glioblastoma.
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Affiliation(s)
- Craig A Vincent
- Umeå Centre for Molecular Medicine (UCMM), Umeå University, Umeå, Sweden
- Wallenberg Centre for Molecular Medicine (WCMM), Umeå University, Umeå, Sweden
| | - Itzel Nissen
- Umeå Centre for Molecular Medicine (UCMM), Umeå University, Umeå, Sweden
- Wallenberg Centre for Molecular Medicine (WCMM), Umeå University, Umeå, Sweden
| | - Soran Dakhel
- Umeå Centre for Molecular Medicine (UCMM), Umeå University, Umeå, Sweden
- Wallenberg Centre for Molecular Medicine (WCMM), Umeå University, Umeå, Sweden
| | - Andreas Hörnblad
- Umeå Centre for Molecular Medicine (UCMM), Umeå University, Umeå, Sweden
| | - Silvia Remeseiro
- Umeå Centre for Molecular Medicine (UCMM), Umeå University, Umeå, Sweden.
- Wallenberg Centre for Molecular Medicine (WCMM), Umeå University, Umeå, Sweden.
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14
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Yang Y, Li X, Meng Z, Liu Y, Qian K, Chu M, Pan Z. A body map of super-enhancers and their function in pig. Front Vet Sci 2023; 10:1239965. [PMID: 37869495 PMCID: PMC10587440 DOI: 10.3389/fvets.2023.1239965] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 09/26/2023] [Indexed: 10/24/2023] Open
Abstract
Introduction Super-enhancers (SEs) are clusters of enhancers that act synergistically to drive the high-level expression of genes involved in cell identity and function. Although SEs have been extensively investigated in humans and mice, they have not been well characterized in pigs. Methods Here, we identified 42,380 SEs in 14 pig tissues using chromatin immunoprecipitation sequencing, and statistics of its overall situation, studied the composition and characteristics of SE, and explored the influence of SEs characteristics on gene expression. Results We observed that approximately 40% of normal enhancers (NEs) form SEs. Compared to NEs, we found that SEs were more likely to be enriched with an activated enhancer and show activated functions. Interestingly, SEs showed X chromosome depletion and short interspersed nuclear element enrichment, implying that SEs play an important role in sex traits and repeat evolution. Additionally, SE-associated genes exhibited higher expression levels and stronger conservation than NE-associated genes. However, genes with the largest SEs had higher expression levels than those with the smallest SEs, indicating that SE size may influence gene expression. Moreover, we observed a negative correlation between SE gene distance and gene expression, indicating that the proximity of SEs can affect gene activity. Gene ontology enrichment and motif analysis revealed that SEs have strong tissue-specific activity. For example, the CORO2B gene with a brain-specific SE shows strong brain-specific expression, and the phenylalanine hydroxylase gene with liver-specific SEs shows strong liver-specific expression. Discussion In this study, we illustrated a body map of SEs and explored their functions in pigs, providing information on the composition and tissue-specific patterns of SEs. This study can serve as a valuable resource of gene regulatory and comparative analyses to the scientific community and provides a theoretical reference for genetic control mechanisms of important traits in pigs.
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Affiliation(s)
- Youbing Yang
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang, China
| | - Xinyue Li
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang, China
- Key Laboratory of Animal Genetics and Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zhu Meng
- Key Laboratory of Animal Genetics and Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yongjian Liu
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang, China
| | - Kaifeng Qian
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang, China
| | - Mingxing Chu
- Key Laboratory of Animal Genetics and Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zhangyuan Pan
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang, China
- Key Laboratory of Animal Genetics and Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
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15
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Malfait J, Wan J, Spicuglia S. Epromoters are new players in the regulatory landscape with potential pleiotropic roles. Bioessays 2023; 45:e2300012. [PMID: 37246247 DOI: 10.1002/bies.202300012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 05/11/2023] [Accepted: 05/15/2023] [Indexed: 05/30/2023]
Abstract
Precise spatiotemporal control of gene expression during normal development and cell differentiation is achieved by the combined action of proximal (promoters) and distal (enhancers) cis-regulatory elements. Recent studies have reported that a subset of promoters, termed Epromoters, works also as enhancers to regulate distal genes. This new paradigm opened novel questions regarding the complexity of our genome and raises the possibility that genetic variation within Epromoters has pleiotropic effects on various physiological and pathological traits by differentially impacting multiple proximal and distal genes. Here, we discuss the different observations pointing to an important role of Epromoters in the regulatory landscape and summarize the evidence supporting a pleiotropic impact of these elements in disease. We further hypothesize that Epromoter might represent a major contributor to phenotypic variation and disease.
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Affiliation(s)
- Juliette Malfait
- Aix-Marseille University, Inserm, TAGC, UMR1090, Marseille, France
- Equipe Labélisée Ligue Contre le Cancer, LIGUE, Marseille, France
| | - Jing Wan
- Aix-Marseille University, Inserm, TAGC, UMR1090, Marseille, France
- Equipe Labélisée Ligue Contre le Cancer, LIGUE, Marseille, France
| | - Salvatore Spicuglia
- Aix-Marseille University, Inserm, TAGC, UMR1090, Marseille, France
- Equipe Labélisée Ligue Contre le Cancer, LIGUE, Marseille, France
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16
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Lillo A, Serrano-Marín J, Lillo J, Raïch I, Navarro G, Franco R. Differential Gene Expression in Activated Microglia Treated with Adenosine A 2A Receptor Antagonists Highlights Olfactory Receptor 56 and T-Cell Activation GTPase-Activating Protein 1 as Potential Biomarkers of the Polarization of Activated Microglia. Cells 2023; 12:2213. [PMID: 37759436 PMCID: PMC10526142 DOI: 10.3390/cells12182213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 08/26/2023] [Accepted: 08/29/2023] [Indexed: 09/29/2023] Open
Abstract
Microglial activation often accompanies the plastic changes occurring in the brain of patients with neurodegenerative diseases. A2A and A3 adenosine receptors have been proposed as therapeutic targets to combat neurodegeneration. RNAseq was performed using samples isolated from lipopolysaccharide/interferon-γ activated microglia treated with SCH 58261, a selective A2A receptor antagonist, and with both SCH 58261 and 2-Cl-IB-MECA, a selective A3 receptor agonist. None of the treatments led to any clear microglial phenotype when gene expression for classical biomarkers of microglial polarization was assessed. However, many of the downregulated genes were directly or indirectly related to immune system-related events. Searching for genes whose expression was both significantly and synergistically affected when treated with the two adenosine receptor ligands, the AC122413.1 and Olfr56 were selected among those that were, respectively, upregulated and downregulated. We therefore propose that the products of these genes, olfactory receptor 56 and T-cell activation GTPase-activating protein 1, deserve attention as potential biomarkers of phenotypes that occur upon microglial activation.
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Affiliation(s)
- Alejandro Lillo
- Department of Biochemistry and Physiology, School of Pharmacy and Food Science, Universitat de Barcelona, 08007 Barcelona, Spain; (A.L.); (J.L.); (I.R.); (G.N.)
- CiberNed, Network Center for Neurodegenerative Diseases, National Spanish Health Institute Carlos III, 28029 Madrid, Spain
| | - Joan Serrano-Marín
- Molecular Neurobiology Laboratory, Department of Biochemistry and Molecular Biomedicine, Faculty of Biology, Universitat de Barcelona, 08028 Barcelona, Spain;
| | - Jaume Lillo
- Department of Biochemistry and Physiology, School of Pharmacy and Food Science, Universitat de Barcelona, 08007 Barcelona, Spain; (A.L.); (J.L.); (I.R.); (G.N.)
- Molecular Neurobiology Laboratory, Department of Biochemistry and Molecular Biomedicine, Faculty of Biology, Universitat de Barcelona, 08028 Barcelona, Spain;
| | - Iu Raïch
- Department of Biochemistry and Physiology, School of Pharmacy and Food Science, Universitat de Barcelona, 08007 Barcelona, Spain; (A.L.); (J.L.); (I.R.); (G.N.)
- Molecular Neurobiology Laboratory, Department of Biochemistry and Molecular Biomedicine, Faculty of Biology, Universitat de Barcelona, 08028 Barcelona, Spain;
| | - Gemma Navarro
- Department of Biochemistry and Physiology, School of Pharmacy and Food Science, Universitat de Barcelona, 08007 Barcelona, Spain; (A.L.); (J.L.); (I.R.); (G.N.)
- CiberNed, Network Center for Neurodegenerative Diseases, National Spanish Health Institute Carlos III, 28029 Madrid, Spain
- Institute of Neurosciences, Universitat de Barcelona, 08007 Barcelona, Spain
| | - Rafael Franco
- CiberNed, Network Center for Neurodegenerative Diseases, National Spanish Health Institute Carlos III, 28029 Madrid, Spain
- Molecular Neurobiology Laboratory, Department of Biochemistry and Molecular Biomedicine, Faculty of Biology, Universitat de Barcelona, 08028 Barcelona, Spain;
- School of Chemistry, Universitat de Barcelona, 08028 Barcelona, Spain
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17
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Bravo González-Blas C, De Winter S, Hulselmans G, Hecker N, Matetovici I, Christiaens V, Poovathingal S, Wouters J, Aibar S, Aerts S. SCENIC+: single-cell multiomic inference of enhancers and gene regulatory networks. Nat Methods 2023; 20:1355-1367. [PMID: 37443338 PMCID: PMC10482700 DOI: 10.1038/s41592-023-01938-4] [Citation(s) in RCA: 85] [Impact Index Per Article: 85.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Accepted: 06/06/2023] [Indexed: 07/15/2023]
Abstract
Joint profiling of chromatin accessibility and gene expression in individual cells provides an opportunity to decipher enhancer-driven gene regulatory networks (GRNs). Here we present a method for the inference of enhancer-driven GRNs, called SCENIC+. SCENIC+ predicts genomic enhancers along with candidate upstream transcription factors (TFs) and links these enhancers to candidate target genes. To improve both recall and precision of TF identification, we curated and clustered a motif collection with more than 30,000 motifs. We benchmarked SCENIC+ on diverse datasets from different species, including human peripheral blood mononuclear cells, ENCODE cell lines, melanoma cell states and Drosophila retinal development. Next, we exploit SCENIC+ predictions to study conserved TFs, enhancers and GRNs between human and mouse cell types in the cerebral cortex. Finally, we use SCENIC+ to study the dynamics of gene regulation along differentiation trajectories and the effect of TF perturbations on cell state. SCENIC+ is available at scenicplus.readthedocs.io .
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Affiliation(s)
- Carmen Bravo González-Blas
- VIB Center for Brain & Disease Research, Leuven, Belgium
- Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Seppe De Winter
- VIB Center for Brain & Disease Research, Leuven, Belgium
- Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Gert Hulselmans
- VIB Center for Brain & Disease Research, Leuven, Belgium
- Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Nikolai Hecker
- VIB Center for Brain & Disease Research, Leuven, Belgium
- Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Irina Matetovici
- VIB Center for Brain & Disease Research, Leuven, Belgium
- VIB Tech Watch, VIB Headquarters, Ghent, Belgium
| | - Valerie Christiaens
- VIB Center for Brain & Disease Research, Leuven, Belgium
- Department of Human Genetics, KU Leuven, Leuven, Belgium
| | | | - Jasper Wouters
- VIB Center for Brain & Disease Research, Leuven, Belgium
- Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Sara Aibar
- VIB Center for Brain & Disease Research, Leuven, Belgium
- Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Stein Aerts
- VIB Center for Brain & Disease Research, Leuven, Belgium.
- Department of Human Genetics, KU Leuven, Leuven, Belgium.
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18
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Blotas C, Férec C, Moisan S. Tissue-Specific Regulation of CFTR Gene Expression. Int J Mol Sci 2023; 24:10678. [PMID: 37445855 DOI: 10.3390/ijms241310678] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 06/21/2023] [Accepted: 06/23/2023] [Indexed: 07/15/2023] Open
Abstract
More than 2000 variations are described within the CFTR (Cystic Fibrosis Transmembrane Regulator) gene and related to large clinical issues from cystic fibrosis to mono-organ diseases. Although these CFTR-associated diseases have been well documented, a large phenotype spectrum is observed and correlations between phenotypes and genotypes are still not well established. To address this issue, we present several regulatory elements that can modulate CFTR gene expression in a tissue-specific manner. Among them, cis-regulatory elements act through chromatin loopings and take part in three-dimensional structured organization. With tissue-specific transcription factors, they form chromatin modules and can regulate gene expression. Alterations of specific regulations can impact and modulate disease expressions. Understanding all those mechanisms highlights the need to expand research outside the gene to enhance our knowledge.
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Affiliation(s)
- Clara Blotas
- Univ Brest, Inserm, EFS, UMR 1078, GGB, F-29200 Brest, France
| | - Claude Férec
- Univ Brest, Inserm, EFS, UMR 1078, GGB, F-29200 Brest, France
| | - Stéphanie Moisan
- Univ Brest, Inserm, EFS, UMR 1078, GGB, F-29200 Brest, France
- Laboratoire de Génétique Moléculaire et d'Histocompatibilité, CHU Brest, F-29200 Brest, France
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19
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Liang Q, Cheng X, Wang J, Owen L, Shakoor A, Lillvis JL, Zhang C, Farkas M, Kim IK, Li Y, DeAngelis M, Chen R. A multi-omics atlas of the human retina at single-cell resolution. CELL GENOMICS 2023; 3:100298. [PMID: 37388908 PMCID: PMC10300490 DOI: 10.1016/j.xgen.2023.100298] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 02/22/2023] [Accepted: 03/17/2023] [Indexed: 07/01/2023]
Abstract
Cell classes in the human retina are highly heterogeneous with their abundance varying by several orders of magnitude. Here, we generated and integrated a multi-omics single-cell atlas of the adult human retina, including more than 250,000 nuclei for single-nuclei RNA-seq and 137,000 nuclei for single-nuclei ATAC-seq. Cross-species comparison of the retina atlas among human, monkey, mice, and chicken revealed relatively conserved and non-conserved types. Interestingly, the overall cell heterogeneity in primate retina decreases compared with that of rodent and chicken retina. Through integrative analysis, we identified 35,000 distal cis-element-gene pairs, constructed transcription factor (TF)-target regulons for more than 200 TFs, and partitioned the TFs into distinct co-active modules. We also revealed the heterogeneity of the cis-element-gene relationships in different cell types, even from the same class. Taken together, we present a comprehensive single-cell multi-omics atlas of the human retina as a resource that enables systematic molecular characterization at individual cell-type resolution.
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Affiliation(s)
- Qingnan Liang
- HGSC, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Xuesen Cheng
- HGSC, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jun Wang
- HGSC, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Leah Owen
- Department of Ophthalmology and Visual Sciences, University of Utah, Salt Lake City, UT 84132, USA
- Department of Population Health Sciences, University of Utah, Salt Lake City, UT 84132, USA
- Department of Ophthalmology, Jacobs School of Medicine and Biomedical Engineering, University at Buffalo SUNY, Buffalo, NY 14203, USA
| | - Akbar Shakoor
- Department of Ophthalmology, Jacobs School of Medicine and Biomedical Engineering, University at Buffalo SUNY, Buffalo, NY 14203, USA
| | - John L. Lillvis
- Department of Ophthalmology, Jacobs School of Medicine and Biomedical Engineering, University at Buffalo SUNY, Buffalo, NY 14203, USA
- VA Western New York Healthcare System, Buffalo, NY 14215, USA
| | - Charles Zhang
- Department of Ophthalmology, Jacobs School of Medicine and Biomedical Engineering, University at Buffalo SUNY, Buffalo, NY 14203, USA
| | - Michael Farkas
- Department of Ophthalmology, Jacobs School of Medicine and Biomedical Engineering, University at Buffalo SUNY, Buffalo, NY 14203, USA
- VA Western New York Healthcare System, Buffalo, NY 14215, USA
| | - Ivana K. Kim
- Retina Service, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, MA 02114, USA
| | - Yumei Li
- HGSC, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Margaret DeAngelis
- Department of Ophthalmology and Visual Sciences, University of Utah, Salt Lake City, UT 84132, USA
- Department of Population Health Sciences, University of Utah, Salt Lake City, UT 84132, USA
- Department of Ophthalmology, Jacobs School of Medicine and Biomedical Engineering, University at Buffalo SUNY, Buffalo, NY 14203, USA
- VA Western New York Healthcare System, Buffalo, NY 14215, USA
| | - Rui Chen
- HGSC, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
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20
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McAllan L, Baranasic D, Villicaña S, Brown S, Zhang W, Lehne B, Adamo M, Jenkinson A, Elkalaawy M, Mohammadi B, Hashemi M, Fernandes N, Lambie N, Williams R, Christiansen C, Yang Y, Zudina L, Lagou V, Tan S, Castillo-Fernandez J, King JWD, Soong R, Elliott P, Scott J, Prokopenko I, Cebola I, Loh M, Lenhard B, Batterham RL, Bell JT, Chambers JC, Kooner JS, Scott WR. Integrative genomic analyses in adipocytes implicate DNA methylation in human obesity and diabetes. Nat Commun 2023; 14:2784. [PMID: 37188674 PMCID: PMC10185556 DOI: 10.1038/s41467-023-38439-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 05/03/2023] [Indexed: 05/17/2023] Open
Abstract
DNA methylation variations are prevalent in human obesity but evidence of a causative role in disease pathogenesis is limited. Here, we combine epigenome-wide association and integrative genomics to investigate the impact of adipocyte DNA methylation variations in human obesity. We discover extensive DNA methylation changes that are robustly associated with obesity (N = 190 samples, 691 loci in subcutaneous and 173 loci in visceral adipocytes, P < 1 × 10-7). We connect obesity-associated methylation variations to transcriptomic changes at >500 target genes, and identify putative methylation-transcription factor interactions. Through Mendelian Randomisation, we infer causal effects of methylation on obesity and obesity-induced metabolic disturbances at 59 independent loci. Targeted methylation sequencing, CRISPR-activation and gene silencing in adipocytes, further identifies regional methylation variations, underlying regulatory elements and novel cellular metabolic effects. Our results indicate DNA methylation is an important determinant of human obesity and its metabolic complications, and reveal mechanisms through which altered methylation may impact adipocyte functions.
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Affiliation(s)
- Liam McAllan
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, W12 0NN, UK
- MRC London Institute of Medical Sciences, London, W12 0NN, UK
| | - Damir Baranasic
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, W12 0NN, UK
- MRC London Institute of Medical Sciences, London, W12 0NN, UK
| | - Sergio Villicaña
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Scarlett Brown
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, W12 0NN, UK
- MRC London Institute of Medical Sciences, London, W12 0NN, UK
| | - Weihua Zhang
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, W2 1PG, UK
- Department of Cardiology, Ealing Hospital, London North West University Healthcare NHS Trust, Middlesex, UB1 3HW, UK
| | - Benjamin Lehne
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, W2 1PG, UK
| | - Marco Adamo
- UCLH Bariatric Centre for Weight Loss, Weight Management and Metabolic and Endocrine Surgery, University College London Hospitals, Ground Floor West Wing, 250 Euston Road, London, NW1 2PG, UK
| | - Andrew Jenkinson
- UCLH Bariatric Centre for Weight Loss, Weight Management and Metabolic and Endocrine Surgery, University College London Hospitals, Ground Floor West Wing, 250 Euston Road, London, NW1 2PG, UK
| | - Mohamed Elkalaawy
- UCLH Bariatric Centre for Weight Loss, Weight Management and Metabolic and Endocrine Surgery, University College London Hospitals, Ground Floor West Wing, 250 Euston Road, London, NW1 2PG, UK
| | - Borzoueh Mohammadi
- UCLH Bariatric Centre for Weight Loss, Weight Management and Metabolic and Endocrine Surgery, University College London Hospitals, Ground Floor West Wing, 250 Euston Road, London, NW1 2PG, UK
| | - Majid Hashemi
- UCLH Bariatric Centre for Weight Loss, Weight Management and Metabolic and Endocrine Surgery, University College London Hospitals, Ground Floor West Wing, 250 Euston Road, London, NW1 2PG, UK
| | - Nadia Fernandes
- Imperial BRC Genomics Facility, Faculty of Medicine, Imperial College London, London, W12 0NN, UK
| | - Nathalie Lambie
- Imperial BRC Genomics Facility, Faculty of Medicine, Imperial College London, London, W12 0NN, UK
| | - Richard Williams
- Imperial BRC Genomics Facility, Faculty of Medicine, Imperial College London, London, W12 0NN, UK
| | - Colette Christiansen
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
- School of Mathematics and Statistics, Faculty of Science, Technology, Engineering and Mathematics, The Open University, Milton Keynes, UK
| | - Youwen Yang
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, W2 1PG, UK
- School of Cardiovascular and Metabolic Medicine and Sciences, James Black Centre, King's College London British Heart Foundation Centre of Excellence, 125 Coldharbour Lane, London, SE5 9NU, UK
| | - Liudmila Zudina
- Department of Clinical & Experimental Medicine, University of Surrey, Guildford, UK
| | - Vasiliki Lagou
- Department of Microbiology and Immunology, Laboratory of Adaptive Immunity, KU Leuven, Leuven, Belgium
- VIB-KU Leuven Center for Brain and Disease Research, Leuven, Belgium
| | - Sili Tan
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | | | - James W D King
- MRC London Institute of Medical Sciences, London, W12 0NN, UK
| | - Richie Soong
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
- Department of Pathology, National University Hospital, Singapore, Singapore
| | - Paul Elliott
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, W2 1PG, UK
- MRC Centre for Environment and Health, School of Public Health, Imperial College London, London, UK
- National Institute for Health Research Biomedical Research Centre, Imperial College London, London, UK
| | - James Scott
- National Heart and Lung Institute, Imperial College London, London, W12 0NN, UK
- Imperial College Healthcare NHS Trust, London, W12 0HS, UK
| | - Inga Prokopenko
- Department of Clinical & Experimental Medicine, University of Surrey, Guildford, UK
- People-Centred Artificial Intelligence Institute, University of Surrey, Guildford, UK
- Institute of Biochemistry and Genetics, Ufa Federal Research Centre Russian Academy of Sciences, Ufa, Russian Federation
| | - Inês Cebola
- Section of Genetics and Genomics, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
| | - Marie Loh
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, W2 1PG, UK
- Translational Laboratory in Genetic Medicine (TLGM), Agency for Science, Technology and Research (A*STAR), 8A Biomedical Grove, Immunos, Level 5, Singapore, 138648, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
| | - Boris Lenhard
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, W12 0NN, UK
- MRC London Institute of Medical Sciences, London, W12 0NN, UK
| | - Rachel L Batterham
- UCLH Bariatric Centre for Weight Loss, Weight Management and Metabolic and Endocrine Surgery, University College London Hospitals, Ground Floor West Wing, 250 Euston Road, London, NW1 2PG, UK
- Centre for Obesity Research, Rayne Institute, Department of Medicine, University College, London, WC1E 6JJ, UK
- National Institute of Health Research University College London Hospitals Biomedical Research Centre, London, W1T 7DN, UK
| | - Jordana T Bell
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - John C Chambers
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, W2 1PG, UK
- Department of Cardiology, Ealing Hospital, London North West University Healthcare NHS Trust, Middlesex, UB1 3HW, UK
- MRC Centre for Environment and Health, School of Public Health, Imperial College London, London, UK
- Imperial College Healthcare NHS Trust, London, W12 0HS, UK
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
| | - Jaspal S Kooner
- Department of Cardiology, Ealing Hospital, London North West University Healthcare NHS Trust, Middlesex, UB1 3HW, UK
- MRC Centre for Environment and Health, School of Public Health, Imperial College London, London, UK
- National Heart and Lung Institute, Imperial College London, London, W12 0NN, UK
- Imperial College Healthcare NHS Trust, London, W12 0HS, UK
| | - William R Scott
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, W12 0NN, UK.
- MRC London Institute of Medical Sciences, London, W12 0NN, UK.
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, W2 1PG, UK.
- Imperial College Healthcare NHS Trust, London, W12 0HS, UK.
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21
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Salvatore M, Horlacher M, Marsico A, Winther O, Andersson R. Transfer learning identifies sequence determinants of cell-type specific regulatory element accessibility. NAR Genom Bioinform 2023; 5:lqad026. [PMID: 37007588 PMCID: PMC10052367 DOI: 10.1093/nargab/lqad026] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 03/01/2023] [Accepted: 03/07/2023] [Indexed: 04/03/2023] Open
Abstract
Dysfunction of regulatory elements through genetic variants is a central mechanism in the pathogenesis of disease. To better understand disease etiology, there is consequently a need to understand how DNA encodes regulatory activity. Deep learning methods show great promise for modeling of biomolecular data from DNA sequence but are limited to large input data for training. Here, we develop ChromTransfer, a transfer learning method that uses a pre-trained, cell-type agnostic model of open chromatin regions as a basis for fine-tuning on regulatory sequences. We demonstrate superior performances with ChromTransfer for learning cell-type specific chromatin accessibility from sequence compared to models not informed by a pre-trained model. Importantly, ChromTransfer enables fine-tuning on small input data with minimal decrease in accuracy. We show that ChromTransfer uses sequence features matching binding site sequences of key transcription factors for prediction. Together, these results demonstrate ChromTransfer as a promising tool for learning the regulatory code.
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Affiliation(s)
| | | | - Annalisa Marsico
- Computational Health Center, Helmholtz Center Munich, Munich, Germany
| | - Ole Winther
- Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, 2200, Copenhagen, Denmark
- Section for Cognitive Systems, DTU Compute, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
- Department of Genomic medicine, Rigshospitalet, 2100 Copenhagen, Denmark
| | - Robin Andersson
- To whom correspondence should be addressed. Tel: +45 35330245;
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22
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Santosa EK, Lau CM, Sahin M, Leslie CS, Sun JC. 3D Chromatin Dynamics during Innate and Adaptive Immune Memory Acquisition. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.16.524322. [PMID: 36711541 PMCID: PMC9882143 DOI: 10.1101/2023.01.16.524322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Immune cells responding to pathogens undergo molecular changes that are intimately linked to genome organization. Recent work has demonstrated that natural killer (NK) and CD8 + T cells experience substantial transcriptomic and epigenetic rewiring during their differentiation from naïve to effector to memory cells. Whether these molecular adaptations are accompanied by changes in three-dimensional (3D) chromatin architecture is unknown. In this study, we combine histone profiling, ATAC-seq, RNA-seq and high-throughput chromatin capture (HiC) assay to investigate the dynamics of one-dimensional (1D) and 3D chromatin during the differentiation of innate and adaptive lymphocytes. To this end, we discovered a coordinated 1D and 3D epigenetic remodeling during innate immune memory differentiation, and demonstrate that effector CD8 + T cells adopt an NK-like architectural program that is maintained in memory cells. Altogether, our study reveals the dynamic nature of the 1D and 3D genome during the formation of innate and adaptive immunological memory.
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