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O'Donnell E, Muñoz M, Davis R, Randall RL, Tepper C, Carr-Ascher J. Genetic and Epigenetic Characterization of Sarcoma Stem Cells Across Subtypes Identifies EZH2 as a Therapeutic Target. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.14.594060. [PMID: 38798385 PMCID: PMC11118861 DOI: 10.1101/2024.05.14.594060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
High-grade complex karyotype soft tissue sarcomas (STS) are a heterogeneous and aggressive set of cancers that share a common treatment strategy. Disease progression and failure to respond to anthracycline based chemotherapy, standard first-line treatment, is associated with poor patient outcomes. To address this, we investigated the contribution of STS cancer stem cells (STS-CSCs) to doxorubicin resistance. We identified a positive correlation between CSC abundance and doxorubicin IC 50 in resistant cell lines. We investigated if a common genetic signature across STS-CSCs could be targeted. Utilizing patient derived samples from five sarcoma subtypes we identified Enhancer of Zeste homolog 2 (EZH2), a member of the polycomb repressive complex 2 (PRC2) responsible for H3K27 methylation as being enriched in the CSC population. EZH2 activity and a shared epigenetic profile was observed across subtypes. Targeting of EZH2 using Tazemetostat, an FDA approved inhibitor specifically ablated the STS-CSC population. Treatment of doxorubicin resistant cell lines with tazemetostat resulted in a decrease in the STS-CSC population. Further, co-treatment was not only synergistic in the parent cell lines, but restored chemosensitivity in doxorubicin resistant lines. These data confirm the presence of shared genetic programs across distinct subtypes of CSC-STS that can be therapeutically targeted.
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Xue G, Li X, Kalim M, Fang J, Jiang Z, Zheng N, Wang Z, Li X, Abdelrahim M, He Z, Nikiforov M, Jin G, Lu Y. Clinical drug screening reveals clofazimine potentiates the efficacy while reducing the toxicity of anti-PD-1 and CTLA-4 immunotherapy. Cancer Cell 2024; 42:780-796.e6. [PMID: 38518774 DOI: 10.1016/j.ccell.2024.03.001] [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: 06/05/2023] [Revised: 01/17/2024] [Accepted: 03/01/2024] [Indexed: 03/24/2024]
Abstract
Emerging as the most potent and durable combinational immunotherapy, dual anti-PD-1 and CTLA-4 immune checkpoint blockade (ICB) therapy notoriously increases grade 3-5 immune-related adverse events (irAEs) in patients. Accordingly, attempts to improve the antitumor potency of anti-PD-1+CTLA-4 ICB by including additional therapeutics have been largely discouraged due to concerns of further increasing fatal toxicity. Here, we screened ∼3,000 Food and Drug Administration (FDA)-approved drugs and identified clofazimine as a potential third agent to optimize anti-PD-1+CTLA-4 ICB. Remarkably, clofazimine outperforms ICB dose reduction or steroid treatment in reversing lethality of irAEs, but unlike the detrimental effect of steroids on antitumor efficacy, clofazimine potentiates curative responses in anti-PD-1+CTLA-4 ICB. Mechanistically, clofazimine promotes E2F1 activation in CD8+ T cells to overcome resistance and counteracts pathogenic Th17 cells to abolish irAEs. Collectively, clofazimine potentiates the antitumor efficacy of anti-PD-1+CTLA-4 ICB, curbs intractable irAEs, and may fill a desperate clinical need to improve patient survival.
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Affiliation(s)
- Gang Xue
- Comprehensive Cancer Center, Wake Forest Baptist Health, Winston-Salem, NC 27157, USA.
| | - Xin Li
- Houston Methodist Cancer Center/Weill Cornell Medicine, Houston, TX 77030, USA
| | - Muhammad Kalim
- Houston Methodist Cancer Center/Weill Cornell Medicine, Houston, TX 77030, USA
| | - Jing Fang
- Houston Methodist Cancer Center/Weill Cornell Medicine, Houston, TX 77030, USA
| | - Zhiwu Jiang
- Houston Methodist Cancer Center/Weill Cornell Medicine, Houston, TX 77030, USA
| | - Ningbo Zheng
- Houston Methodist Cancer Center/Weill Cornell Medicine, Houston, TX 77030, USA
| | - Ziyu Wang
- Houston Methodist Cancer Center/Weill Cornell Medicine, Houston, TX 77030, USA
| | - Xiaoyin Li
- Department of Mathematics and Statistics, St. Cloud State University, St Cloud, MN 56301, USA
| | - Maen Abdelrahim
- Houston Methodist Cancer Center/Weill Cornell Medicine, Houston, TX 77030, USA
| | - Zhiheng He
- Department of Molecular Microbiology and Immunology, University of Southern California, Los Angeles, CA 90033, USA.
| | | | - Guangxu Jin
- Comprehensive Cancer Center, Wake Forest Baptist Health, Winston-Salem, NC 27157, USA.
| | - Yong Lu
- Houston Methodist Cancer Center/Weill Cornell Medicine, Houston, TX 77030, USA.
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Ai G, He C, Bi S, Zhou Z, Liu A, Hu X, Liu Y, Jin L, Zhou J, Zhang H, Du D, Chen H, Gong X, Saeed S, Su H, Lan C, Chen W, Li Q, Mao H, Li L, Liu H, Chen D, Kaufmann K, Alazab KF, Yan W. Dissecting the molecular basis of spike traits by integrating gene regulatory networks and genetic variation in wheat. PLANT COMMUNICATIONS 2024; 5:100879. [PMID: 38486454 PMCID: PMC11121755 DOI: 10.1016/j.xplc.2024.100879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 02/25/2024] [Accepted: 03/11/2024] [Indexed: 04/30/2024]
Abstract
Spike architecture influences both grain weight and grain number per spike, which are the two major components of grain yield in bread wheat (Triticum aestivum L.). However, the complex wheat genome and the influence of various environmental factors pose challenges in mapping the causal genes that affect spike traits. Here, we systematically identified genes involved in spike trait formation by integrating information on genomic variation and gene regulatory networks controlling young spike development in wheat. We identified 170 loci that are responsible for variations in spike length, spikelet number per spike, and grain number per spike through genome-wide association study and meta-QTL analyses. We constructed gene regulatory networks for young inflorescences at the double ridge stage and the floret primordium stage, in which the spikelet meristem and the floret meristem are predominant, respectively, by integrating transcriptome, histone modification, chromatin accessibility, eQTL, and protein-protein interactome data. From these networks, we identified 169 hub genes located in 76 of the 170 QTL regions whose polymorphisms are significantly associated with variation in spike traits. The functions of TaZF-B1, VRT-B2, and TaSPL15-A/D in establishment of wheat spike architecture were verified. This study provides valuable molecular resources for understanding spike traits and demonstrates that combining genetic analysis and developmental regulatory networks is a robust approach for dissection of complex traits.
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Affiliation(s)
- Guo Ai
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China; College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Chao He
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China; College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Siteng Bi
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China; College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Ziru Zhou
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China; College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Ankui Liu
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China; College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Xin Hu
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China; College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Yanyan Liu
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China; College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Liujie Jin
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China; College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - JiaCheng Zhou
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China; College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Heping Zhang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China; College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Dengxiang Du
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China; College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Hao Chen
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China; College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Xin Gong
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China; College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Sulaiman Saeed
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China; College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Handong Su
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China; College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Caixia Lan
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China; College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Wei Chen
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China; College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Qiang Li
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China; College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Hailiang Mao
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China; College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Lin Li
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China; College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Wuhan 430070, China; Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome, Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Hao Liu
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Dijun Chen
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Kerstin Kaufmann
- Department for Plant Cell and Molecular Biology, Institute for Biology, Humboldt-Universität Zu Berlin, 10115 Berlin, Germany
| | - Khaled F Alazab
- Plant Research Department, Nuclear Research Center, Egyptian Atomic Energy Authority, Cairo 13759, Egypt
| | - Wenhao Yan
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China; College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China.
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Sunitha Kumary VUN, Venters BJ, Raman K, Sen S, Estève PO, Cowles MW, Keogh MC, Pradhan S. Emerging Approaches to Profile Accessible Chromatin from Formalin-Fixed Paraffin-Embedded Sections. EPIGENOMES 2024; 8:20. [PMID: 38804369 PMCID: PMC11130958 DOI: 10.3390/epigenomes8020020] [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: 04/16/2024] [Accepted: 05/06/2024] [Indexed: 05/29/2024] Open
Abstract
Nucleosomes are non-uniformly distributed across eukaryotic genomes, with stretches of 'open' chromatin strongly associated with transcriptionally active promoters and enhancers. Understanding chromatin accessibility patterns in normal tissue and how they are altered in pathologies can provide critical insights to development and disease. With the advent of high-throughput sequencing, a variety of strategies have been devised to identify open regions across the genome, including DNase-seq, MNase-seq, FAIRE-seq, ATAC-seq, and NicE-seq. However, the broad application of such methods to FFPE (formalin-fixed paraffin-embedded) tissues has been curtailed by the major technical challenges imposed by highly fixed and often damaged genomic material. Here, we review the most common approaches for mapping open chromatin regions, recent optimizations to overcome the challenges of working with FFPE tissue, and a brief overview of a typical data pipeline with analysis considerations.
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Affiliation(s)
| | - Bryan J. Venters
- EpiCypher Inc., Durham, NC 27709, USA; (V.U.N.S.K.); (B.J.V.); (M.W.C.)
| | - Karthikeyan Raman
- Genome Biology Division, New England Biolabs, Ipswich, MA 01983, USA; (K.R.); (S.S.); (P.-O.E.)
| | - Sagnik Sen
- Genome Biology Division, New England Biolabs, Ipswich, MA 01983, USA; (K.R.); (S.S.); (P.-O.E.)
| | - Pierre-Olivier Estève
- Genome Biology Division, New England Biolabs, Ipswich, MA 01983, USA; (K.R.); (S.S.); (P.-O.E.)
| | - Martis W. Cowles
- EpiCypher Inc., Durham, NC 27709, USA; (V.U.N.S.K.); (B.J.V.); (M.W.C.)
| | | | - Sriharsa Pradhan
- Genome Biology Division, New England Biolabs, Ipswich, MA 01983, USA; (K.R.); (S.S.); (P.-O.E.)
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205
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Garbutt TA, Wang Z, Wang H, Ma H, Ruan H, Dong Y, Xie Y, Tan L, Phookan R, Stouffer J, Vedantham V, Yang Y, Qian L, Liu J. Epigenetic Regulation of Cardiomyocyte Maturation by Arginine Methyltransferase CARM1. Circulation 2024; 149:1501-1515. [PMID: 38223978 PMCID: PMC11073921 DOI: 10.1161/circulationaha.121.055738] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Accepted: 12/19/2023] [Indexed: 01/16/2024]
Abstract
BACKGROUND During the neonatal stage, the cardiomyocyte undergoes a constellation of molecular, cytoarchitectural, and functional changes known collectively as cardiomyocyte maturation to increase myocardial contractility and cardiac output. Despite the importance of cardiomyocyte maturation, the molecular mechanisms governing this critical process remain largely unexplored. METHODS We leveraged an in vivo mosaic knockout system to characterize the role of Carm1, the founding member of protein arginine methyltransferase, in cardiomyocyte maturation. Using a battery of assays, including immunohistochemistry, immuno-electron microscopy imaging, and action potential recording, we assessed the effect of loss of Carm1 function on cardiomyocyte cell growth, myofibril expansion, T-tubule formation, and electrophysiological maturation. Genome-wide transcriptome profiling, H3R17me2a chromatin immunoprecipitation followed by sequencing, and assay for transposase-accessible chromatin with high-throughput sequencing were used to investigate the mechanisms by which CARM1 (coactivator-associated arginine methyltransferase 1) regulates cardiomyocyte maturation. Finally, we interrogated the human syntenic region to the H3R17me2a chromatin immunoprecipitation followed by sequencing peaks for single-nucleotide polymorphisms associated with human heart diseases. RESULTS We report that mosaic ablation of Carm1 disrupts multiple aspects of cardiomyocyte maturation cell autonomously, leading to reduced cardiomyocyte size and sarcomere thickness, severe loss and disorganization of T tubules, and compromised electrophysiological maturation. Genomics study demonstrates that CARM1 directly activates genes that underlie cardiomyocyte cytoarchitectural and electrophysiological maturation. Moreover, our study reveals significant enrichment of human heart disease-associated single-nucleotide polymorphisms in the human genomic region syntenic to the H3R17me2a chromatin immunoprecipitation followed by sequencing peaks. CONCLUSIONS This study establishes a critical and multifaceted role for CARM1 in regulating cardiomyocyte maturation and demonstrates that deregulation of CARM1-dependent cardiomyocyte maturation gene expression may contribute to human heart diseases.
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Affiliation(s)
- Tiffany A. Garbutt
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, NC 27599, USA
- McAllister Heart Institute, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Zhenhua Wang
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, NC 27599, USA
- McAllister Heart Institute, University of North Carolina, Chapel Hill, NC 27599, USA
- Department of Cardiovascular Surgery, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Haofei Wang
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, NC 27599, USA
- McAllister Heart Institute, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Hong Ma
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, NC 27599, USA
- McAllister Heart Institute, University of North Carolina, Chapel Hill, NC 27599, USA
- Present address: Department of Cardiology, 2 Affiliated Hospital, School of Medicine, Zhejiang University. Hangzhou 310009, China
| | - Hongmei Ruan
- Department of Medicine and Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Yanhan Dong
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, NC 27599, USA
- McAllister Heart Institute, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Yifang Xie
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, NC 27599, USA
- McAllister Heart Institute, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Lianmei Tan
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, NC 27599, USA
- McAllister Heart Institute, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Ranan Phookan
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, NC 27599, USA
- McAllister Heart Institute, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Joy Stouffer
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, NC 27599, USA
- McAllister Heart Institute, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Vasanth Vedantham
- Department of Medicine and Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Yuchen Yang
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, NC 27599, USA
- McAllister Heart Institute, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Li Qian
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, NC 27599, USA
- McAllister Heart Institute, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Jiandong Liu
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, NC 27599, USA
- McAllister Heart Institute, University of North Carolina, Chapel Hill, NC 27599, USA
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206
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Rosean S, Sosa EA, O'Shea D, Raj SM, Seoighe C, Greally JM. Regulatory landscape enrichment analysis (RLEA): a computational toolkit for non-coding variant enrichment and cell type prioritization. BMC Bioinformatics 2024; 25:179. [PMID: 38714913 PMCID: PMC11075237 DOI: 10.1186/s12859-024-05794-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Accepted: 04/22/2024] [Indexed: 05/12/2024] Open
Abstract
BACKGROUND As genomic studies continue to implicate non-coding sequences in disease, testing the roles of these variants requires insights into the cell type(s) in which they are likely to be mediating their effects. Prior methods for associating non-coding variants with cell types have involved approaches using linkage disequilibrium or ontological associations, incurring significant processing requirements. GaiaAssociation is a freely available, open-source software that enables thousands of genomic loci implicated in a phenotype to be tested for enrichment at regulatory loci of multiple cell types in minutes, permitting insights into the cell type(s) mediating the studied phenotype. RESULTS In this work, we present Regulatory Landscape Enrichment Analysis (RLEA) by GaiaAssociation and demonstrate its capability to test the enrichment of 12,133 variants across the cis-regulatory regions of 44 cell types. This analysis was completed in 134.0 ± 2.3 s, highlighting the efficient processing provided by GaiaAssociation. The intuitive interface requires only four inputs, offers a collection of customizable functions, and visualizes variant enrichment in cell-type regulatory regions through a heatmap matrix. GaiaAssociation is available on PyPi for download as a command line tool or Python package and the source code can also be installed from GitHub at https://github.com/GreallyLab/gaiaAssociation . CONCLUSIONS GaiaAssociation is a novel package that provides an intuitive and efficient resource to understand the enrichment of non-coding variants across the cis-regulatory regions of different cells, empowering studies seeking to identify disease-mediating cell types.
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Affiliation(s)
- Samuel Rosean
- Department of Systems and Computational Biology, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Eric A Sosa
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Dónal O'Shea
- School of Mathematics, Statistics & Applied Mathematics, National University of Ireland Galway, Galway, H91 TK33, Ireland
| | - Srilakshmi M Raj
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Cathal Seoighe
- School of Mathematics, Statistics & Applied Mathematics, National University of Ireland Galway, Galway, H91 TK33, Ireland
| | - John M Greally
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, 10461, USA.
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207
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Marinov GK, Chen X, Swaffer MP, Xiang T, Grossman AR, Greenleaf WJ. Genome-wide distribution of 5-hydroxymethyluracil and chromatin accessibility in the Breviolum minutum genome. Genome Biol 2024; 25:115. [PMID: 38711126 PMCID: PMC11071213 DOI: 10.1186/s13059-024-03261-3] [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: 09/23/2023] [Accepted: 04/28/2024] [Indexed: 05/08/2024] Open
Abstract
BACKGROUND In dinoflagellates, a unique and extremely divergent genomic and nuclear organization has evolved. The highly unusual features of dinoflagellate nuclei and genomes include permanently condensed liquid crystalline chromosomes, primarily packaged by proteins other than histones, genes organized in very long unidirectional gene arrays, a general absence of transcriptional regulation, high abundance of the otherwise very rare DNA modification 5-hydroxymethyluracil (5-hmU), and many others. While most of these fascinating properties are originally identified in the 1970s and 1980s, they have not yet been investigated using modern genomic tools. RESULTS In this work, we address some of the outstanding questions regarding dinoflagellate genome organization by mapping the genome-wide distribution of 5-hmU (using both immunoprecipitation-based and basepair-resolution chemical mapping approaches) and of chromatin accessibility in the genome of the Symbiodiniaceae dinoflagellate Breviolum minutum. We find that the 5-hmU modification is preferentially enriched over certain classes of repetitive elements, often coincides with the boundaries between gene arrays, and is generally correlated with decreased chromatin accessibility, the latter otherwise being largely uniform along the genome. We discuss the potential roles of 5-hmU in the functional organization of dinoflagellate genomes and its relationship to the transcriptional landscape of gene arrays. CONCLUSIONS Our results provide the first window into the 5-hmU and chromatin accessibility landscapes in dinoflagellates.
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Affiliation(s)
- Georgi K Marinov
- Department of Genetics, Stanford University, Stanford, CA, 94305, USA.
| | - Xinyi Chen
- Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA
| | - Matthew P Swaffer
- Department of Biology, Stanford University, Stanford, CA, 94305, USA
| | - Tingting Xiang
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, 94305, USA
| | - Arthur R Grossman
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, 94305, USA
| | - William J Greenleaf
- Department of Genetics, Stanford University, Stanford, CA, 94305, USA.
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, 94305, USA.
- Department of Applied Physics, Stanford University, Stanford, CA, 94305, USA.
- Chan Zuckerberg Biohub, San Francisco, CA, USA.
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208
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Shen J, Wang Y, Luo J. CD-Loop: a chromatin loop detection method based on the diffusion model. Front Genet 2024; 15:1393406. [PMID: 38770419 PMCID: PMC11102972 DOI: 10.3389/fgene.2024.1393406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Accepted: 04/11/2024] [Indexed: 05/22/2024] Open
Abstract
Motivation In recent years, there have been significant advances in various chromatin conformation capture techniques, and annotating the topological structure from Hi-C contact maps has become crucial for studying the three-dimensional structure of chromosomes. However, the structure and function of chromatin loops are highly dynamic and diverse, influenced by multiple factors. Therefore, obtaining the three-dimensional structure of the genome remains a challenging task. Among many chromatin loop prediction methods, it is difficult to fully extract features from the contact map and make accurate predictions at low sequencing depths. Results In this study, we put forward a deep learning framework based on the diffusion model called CD-Loop for predicting accurate chromatin loops. First, by pre-training the input data, we obtain prior probabilities for predicting the classification of the Hi-C contact map. Then, by combining the denoising process based on the diffusion model and the prior probability obtained by pre-training, candidate loops were predicted from the input Hi-C contact map. Finally, CD-Loop uses a density-based clustering algorithm to cluster the candidate chromatin loops and predict the final chromatin loops. We compared CD-Loop with the currently popular methods, such as Peakachu, Chromosight, and Mustache, and found that in different cell types, species, and sequencing depths, CD-Loop outperforms other methods in loop annotation. We conclude that CD-Loop can accurately predict chromatin loops and reveal cell-type specificity. The code is available at https://github.com/wangyang199897/CD-Loop.
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Affiliation(s)
| | | | - Junwei Luo
- School of Software, Henan Polytechnic University, Jiaozuo, China
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209
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Guo S, Hu X, Cotton JL, Ma L, Li Q, Cui J, Wang Y, Thakare RP, Tao Z, Ip YT, Wu X, Wang J, Mao J. VGLL2 and TEAD1 fusion proteins drive YAP/TAZ-independent transcription and tumorigenesis by engaging p300. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.01.592016. [PMID: 38746415 PMCID: PMC11092657 DOI: 10.1101/2024.05.01.592016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Studies on Hippo pathway regulation of tumorigenesis largely center on YAP and TAZ, the transcriptional co-regulators of TEAD. Here, we present an oncogenic mechanism involving VGLL and TEAD fusions that is Hippo pathway-related but YAP/TAZ-independent. We characterize two recurrent fusions, VGLL2-NCOA2 and TEAD1-NCOA2, recently identified in spindle cell rhabdomyosarcoma. We demonstrate that, in contrast to VGLL2 and TEAD1, the fusion proteins are strong activators of TEAD-dependent transcription, and their function does not require YAP/TAZ. Furthermore, we identify that VGLL2 and TEAD1 fusions engage specific epigenetic regulation by recruiting histone acetyltransferase p300 to control TEAD-mediated transcriptional and epigenetic landscapes. We showed that small molecule p300 inhibition can suppress fusion proteins-induced oncogenic transformation both in vitro and in vivo. Overall, our study reveals a molecular basis for VGLL involvement in cancer and provides a framework for targeting tumors carrying VGLL, TEAD, or NCOA translocations.
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Affiliation(s)
- Susu Guo
- Department of Clinical Laboratory, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, No 241, West Huaihai Road, Shanghai, P. R., 200030, China
| | - Xiaodi Hu
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, Massachusetts, 01605, USA
| | - Jennifer L. Cotton
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, Massachusetts, 01605, USA
| | - Lifang Ma
- Department of Clinical Laboratory, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, No 241, West Huaihai Road, Shanghai, P. R., 200030, China
| | - Qi Li
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, Massachusetts, 01605, USA
- Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, Massachusetts, 01605, USA
| | - Jiangtao Cui
- Department of Clinical Laboratory, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, No 241, West Huaihai Road, Shanghai, P. R., 200030, China
| | - Yongjie Wang
- Department of Clinical Laboratory, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, No 241, West Huaihai Road, Shanghai, P. R., 200030, China
| | - Ritesh P. Thakare
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, Massachusetts, 01605, USA
| | - Zhipeng Tao
- Cutaneous Biology Research Center, Massachusetts General Hospital, Harvard Medical School, Charlestown, Massachusetts, 01605, USA
| | - Y. Tony Ip
- Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, Massachusetts, 01605, USA
| | - Xu Wu
- Cutaneous Biology Research Center, Massachusetts General Hospital, Harvard Medical School, Charlestown, Massachusetts, 01605, USA
| | - Jiayi Wang
- Department of Clinical Laboratory, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, No 241, West Huaihai Road, Shanghai, P. R., 200030, China
| | - Junhao Mao
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, Massachusetts, 01605, USA
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210
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Saldana-Guerrero IM, Montano-Gutierrez LF, Boswell K, Hafemeister C, Poon E, Shaw LE, Stavish D, Lea RA, Wernig-Zorc S, Bozsaky E, Fetahu IS, Zoescher P, Pötschger U, Bernkopf M, Wenninger-Weinzierl A, Sturtzel C, Souilhol C, Tarelli S, Shoeb MR, Bozatzi P, Rados M, Guarini M, Buri MC, Weninger W, Putz EM, Huang M, Ladenstein R, Andrews PW, Barbaric I, Cresswell GD, Bryant HE, Distel M, Chesler L, Taschner-Mandl S, Farlik M, Tsakiridis A, Halbritter F. A human neural crest model reveals the developmental impact of neuroblastoma-associated chromosomal aberrations. Nat Commun 2024; 15:3745. [PMID: 38702304 PMCID: PMC11068915 DOI: 10.1038/s41467-024-47945-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Accepted: 04/15/2024] [Indexed: 05/06/2024] Open
Abstract
Early childhood tumours arise from transformed embryonic cells, which often carry large copy number alterations (CNA). However, it remains unclear how CNAs contribute to embryonic tumourigenesis due to a lack of suitable models. Here we employ female human embryonic stem cell (hESC) differentiation and single-cell transcriptome and epigenome analysis to assess the effects of chromosome 17q/1q gains, which are prevalent in the embryonal tumour neuroblastoma (NB). We show that CNAs impair the specification of trunk neural crest (NC) cells and their sympathoadrenal derivatives, the putative cells-of-origin of NB. This effect is exacerbated upon overexpression of MYCN, whose amplification co-occurs with CNAs in NB. Moreover, CNAs potentiate the pro-tumourigenic effects of MYCN and mutant NC cells resemble NB cells in tumours. These changes correlate with a stepwise aberration of developmental transcription factor networks. Together, our results sketch a mechanistic framework for the CNA-driven initiation of embryonal tumours.
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Affiliation(s)
- Ingrid M Saldana-Guerrero
- Centre for Stem Cell Biology, School of Biosciences, The University of Sheffield, Sheffield, UK
- Neuroscience Institute, The University of Sheffield, Sheffield, UK
- Sheffield Institute for Nucleic Acids (SInFoNiA), School of Medicine and Population Health, The University of Sheffield, Sheffield, UK
| | | | - Katy Boswell
- Centre for Stem Cell Biology, School of Biosciences, The University of Sheffield, Sheffield, UK
- Neuroscience Institute, The University of Sheffield, Sheffield, UK
| | | | - Evon Poon
- Division of Clinical Studies, The Institute of Cancer Research (ICR) & Royal Marsden NHS Trust, London, UK
| | - Lisa E Shaw
- Department of Dermatology, Medical University of Vienna, Vienna, Austria
| | - Dylan Stavish
- Centre for Stem Cell Biology, School of Biosciences, The University of Sheffield, Sheffield, UK
- Neuroscience Institute, The University of Sheffield, Sheffield, UK
| | - Rebecca A Lea
- Centre for Stem Cell Biology, School of Biosciences, The University of Sheffield, Sheffield, UK
- Neuroscience Institute, The University of Sheffield, Sheffield, UK
| | - Sara Wernig-Zorc
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria
| | - Eva Bozsaky
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria
| | - Irfete S Fetahu
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria
- Medical University of Vienna, Department of Neurology, Division of Neuropathology and Neurochemistry, Vienna, Austria
| | - Peter Zoescher
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria
| | - Ulrike Pötschger
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria
| | - Marie Bernkopf
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria
- Labdia Labordiagnostik GmbH, Vienna, Austria
| | | | - Caterina Sturtzel
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria
| | - Celine Souilhol
- Centre for Stem Cell Biology, School of Biosciences, The University of Sheffield, Sheffield, UK
- Neuroscience Institute, The University of Sheffield, Sheffield, UK
- Biomolecular Sciences Research Centre, Department of Biosciences and Chemistry, Sheffield Hallam University, Sheffield, UK
| | - Sophia Tarelli
- Centre for Stem Cell Biology, School of Biosciences, The University of Sheffield, Sheffield, UK
- Neuroscience Institute, The University of Sheffield, Sheffield, UK
| | - Mohamed R Shoeb
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria
| | - Polyxeni Bozatzi
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria
| | - Magdalena Rados
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria
| | - Maria Guarini
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Michelle C Buri
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria
| | - Wolfgang Weninger
- Department of Dermatology, Medical University of Vienna, Vienna, Austria
| | - Eva M Putz
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria
| | - Miller Huang
- Children's Hospital Los Angeles, Cancer and Blood Disease Institutes, and The Saban Research Institute, Los Angeles, CA, USA
- Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Ruth Ladenstein
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria
| | - Peter W Andrews
- Centre for Stem Cell Biology, School of Biosciences, The University of Sheffield, Sheffield, UK
| | - Ivana Barbaric
- Centre for Stem Cell Biology, School of Biosciences, The University of Sheffield, Sheffield, UK
- Neuroscience Institute, The University of Sheffield, Sheffield, UK
| | | | - Helen E Bryant
- Sheffield Institute for Nucleic Acids (SInFoNiA), School of Medicine and Population Health, The University of Sheffield, Sheffield, UK
| | - Martin Distel
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria
| | - Louis Chesler
- Division of Clinical Studies, The Institute of Cancer Research (ICR) & Royal Marsden NHS Trust, London, UK
| | | | - Matthias Farlik
- Department of Dermatology, Medical University of Vienna, Vienna, Austria
| | - Anestis Tsakiridis
- Centre for Stem Cell Biology, School of Biosciences, The University of Sheffield, Sheffield, UK.
- Neuroscience Institute, The University of Sheffield, Sheffield, UK.
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211
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Hu G, Grover CE, Vera DL, Lung PY, Girimurugan SB, Miller ER, Conover JL, Ou S, Xiong X, Zhu D, Li D, Gallagher JP, Udall JA, Sui X, Zhang J, Bass HW, Wendel JF. Evolutionary Dynamics of Chromatin Structure and Duplicate Gene Expression in Diploid and Allopolyploid Cotton. Mol Biol Evol 2024; 41:msae095. [PMID: 38758089 PMCID: PMC11140268 DOI: 10.1093/molbev/msae095] [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: 11/02/2023] [Revised: 04/10/2024] [Accepted: 05/10/2024] [Indexed: 05/18/2024] Open
Abstract
Polyploidy is a prominent mechanism of plant speciation and adaptation, yet the mechanistic understandings of duplicated gene regulation remain elusive. Chromatin structure dynamics are suggested to govern gene regulatory control. Here, we characterized genome-wide nucleosome organization and chromatin accessibility in allotetraploid cotton, Gossypium hirsutum (AADD, 2n = 4X = 52), relative to its two diploid parents (AA or DD genome) and their synthetic diploid hybrid (AD), using DNS-seq. The larger A-genome exhibited wider average nucleosome spacing in diploids, and this intergenomic difference diminished in the allopolyploid but not hybrid. Allopolyploidization also exhibited increased accessibility at promoters genome-wide and synchronized cis-regulatory motifs between subgenomes. A prominent cis-acting control was inferred for chromatin dynamics and demonstrated by transposable element removal from promoters. Linking accessibility to gene expression patterns, we found distinct regulatory effects for hybridization and later allopolyploid stages, including nuanced establishment of homoeolog expression bias and expression level dominance. Histone gene expression and nucleosome organization are coordinated through chromatin accessibility. Our study demonstrates the capability to track high-resolution chromatin structure dynamics and reveals their role in the evolution of cis-regulatory landscapes and duplicate gene expression in polyploids, illuminating regulatory ties to subgenomic asymmetry and dominance.
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Affiliation(s)
- Guanjing Hu
- State Key Laboratory of Cotton Bio-breeding and Integrated, Chinese Academy of Agricultural Sciences, Institute of Cotton Research, Anyang 455000, China
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Chinese Academy of Agricultural Sciences, Agricultural Genomics Institute at Shenzhen, Shenzhen 518120, China
| | - Corrinne E Grover
- Department of Ecology, Evolution and Organismal Biology, Iowa State University, Ames, IA 50011, USA
| | - Daniel L Vera
- Department of Biological Science, Florida State University, Tallahassee, FL 32306, USA
| | - Pei-Yau Lung
- Department of Statistics, Florida State University, Tallahassee, FL 32306, USA
| | | | - Emma R Miller
- Department of Ecology, Evolution and Organismal Biology, Iowa State University, Ames, IA 50011, USA
| | - Justin L Conover
- Department of Ecology, Evolution and Organismal Biology, Iowa State University, Ames, IA 50011, USA
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, AZ 85721, USA
| | - Shujun Ou
- Department of Molecular Genetics, Ohio State University, Columbus, OH 43210, USA
| | - Xianpeng Xiong
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Chinese Academy of Agricultural Sciences, Agricultural Genomics Institute at Shenzhen, Shenzhen 518120, China
| | - De Zhu
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Chinese Academy of Agricultural Sciences, Agricultural Genomics Institute at Shenzhen, Shenzhen 518120, China
| | - Dongming Li
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Chinese Academy of Agricultural Sciences, Agricultural Genomics Institute at Shenzhen, Shenzhen 518120, China
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450000, China
| | - Joseph P Gallagher
- Forage Seed and Cereal Research Unit, USDA/Agricultural Research Service, Corvallis, OR 97331, USA
| | - Joshua A Udall
- Crop Germplasm Research Unit, USDA/Agricultural Research Service, College Station, TX 77845, USA
| | - Xin Sui
- Department of Statistics, Florida State University, Tallahassee, FL 32306, USA
| | - Jinfeng Zhang
- Department of Statistics, Florida State University, Tallahassee, FL 32306, USA
| | - Hank W Bass
- Department of Biological Science, Florida State University, Tallahassee, FL 32306, USA
| | - Jonathan F Wendel
- Department of Ecology, Evolution and Organismal Biology, Iowa State University, Ames, IA 50011, USA
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212
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Garcia IS, Silva-Vignato B, Cesar ASM, Petrini J, da Silva VH, Morosini NS, Goes CP, Afonso J, da Silva TR, Lima BD, Clemente LG, Regitano LCDA, Mourão GB, Coutinho LL. Novel putative causal mutations associated with fat traits in Nellore cattle uncovered by eQTLs located in open chromatin regions. Sci Rep 2024; 14:10094. [PMID: 38698200 PMCID: PMC11066111 DOI: 10.1038/s41598-024-60703-5] [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: 10/19/2023] [Accepted: 04/26/2024] [Indexed: 05/05/2024] Open
Abstract
Intramuscular fat (IMF) and backfat thickness (BFT) are critical economic traits impacting meat quality. However, the genetic variants controlling these traits need to be better understood. To advance knowledge in this area, we integrated RNA-seq and single nucleotide polymorphisms (SNPs) identified in genomic and transcriptomic data to generate a linkage disequilibrium filtered panel of 553,581 variants. Expression quantitative trait loci (eQTL) analysis revealed 36,916 cis-eQTLs and 14,408 trans-eQTLs. Association analysis resulted in three eQTLs associated with BFT and 24 with IMF. Functional enrichment analysis of genes regulated by these 27 eQTLs revealed noteworthy pathways that can play a fundamental role in lipid metabolism and fat deposition, such as immune response, cytoskeleton remodeling, iron transport, and phospholipid metabolism. We next used ATAC-Seq assay to identify and overlap eQTL and open chromatin regions. Six eQTLs were in regulatory regions, four in predicted insulators and possible CCCTC-binding factor DNA binding sites, one in an active enhancer region, and the last in a low signal region. Our results provided novel insights into the transcriptional regulation of IMF and BFT, unraveling putative regulatory variants.
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Affiliation(s)
- Ingrid Soares Garcia
- Department of Animal Science, College of Agriculture "Luiz de Queiroz", University of São Paulo, Piracicaba, SP, Brazil
| | - Bárbara Silva-Vignato
- Department of Animal Science, College of Agriculture "Luiz de Queiroz", University of São Paulo, Piracicaba, SP, Brazil
| | - Aline Silva Mello Cesar
- Department of Agroindustry, Food and Nutrition, College of Agriculture "Luiz de Queiroz", University of São Paulo, Piracicaba, SP, Brazil
| | - Juliana Petrini
- Department of Animal Science, College of Agriculture "Luiz de Queiroz", University of São Paulo, Piracicaba, SP, Brazil
| | - Vinicius Henrique da Silva
- Department of Animal Science, College of Agriculture "Luiz de Queiroz", University of São Paulo, Piracicaba, SP, Brazil
| | - Natália Silva Morosini
- Department of Animal Science, College of Agriculture "Luiz de Queiroz", University of São Paulo, Piracicaba, SP, Brazil
| | - Carolina Purcell Goes
- Department of Animal Science, College of Agriculture "Luiz de Queiroz", University of São Paulo, Piracicaba, SP, Brazil
| | | | - Thaís Ribeiro da Silva
- Department of Animal Science, College of Agriculture "Luiz de Queiroz", University of São Paulo, Piracicaba, SP, Brazil
| | - Beatriz Delcarme Lima
- Department of Animal Science, College of Agriculture "Luiz de Queiroz", University of São Paulo, Piracicaba, SP, Brazil
| | - Luan Gaspar Clemente
- Department of Animal Science, College of Agriculture "Luiz de Queiroz", University of São Paulo, Piracicaba, SP, Brazil
| | | | - Gerson Barreto Mourão
- Department of Animal Science, College of Agriculture "Luiz de Queiroz", University of São Paulo, Piracicaba, SP, Brazil
| | - Luiz Lehmann Coutinho
- Department of Animal Science, College of Agriculture "Luiz de Queiroz", University of São Paulo, Piracicaba, SP, Brazil.
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213
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Han X, Xing L, Hong Y, Zhang X, Hao B, Lu JY, Huang M, Wang Z, Ma S, Zhan G, Li T, Hao X, Tao Y, Li G, Zhou S, Zheng Z, Shao W, Zeng Y, Ma D, Zhang W, Xie Z, Deng H, Yan J, Deng W, Shen X. Nuclear RNA homeostasis promotes systems-level coordination of cell fate and senescence. Cell Stem Cell 2024; 31:694-716.e11. [PMID: 38631356 DOI: 10.1016/j.stem.2024.03.015] [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: 09/22/2023] [Revised: 02/01/2024] [Accepted: 03/26/2024] [Indexed: 04/19/2024]
Abstract
Understanding cellular coordination remains a challenge despite knowledge of individual pathways. The RNA exosome, targeting a wide range of RNA substrates, is often downregulated in cellular senescence. Utilizing an auxin-inducible system, we observed that RNA exosome depletion in embryonic stem cells significantly affects the transcriptome and proteome, causing pluripotency loss and pre-senescence onset. Mechanistically, exosome depletion triggers acute nuclear RNA aggregation, disrupting nuclear RNA-protein equilibrium. This disturbance limits nuclear protein availability and hinders polymerase initiation and engagement, reducing gene transcription. Concurrently, it promptly disrupts nucleolar transcription, ribosomal processes, and nuclear exporting, resulting in a translational shutdown. Prolonged exosome depletion induces nuclear structural changes resembling senescent cells, including aberrant chromatin compaction, chromocenter disassembly, and intensified heterochromatic foci. These effects suggest that the dynamic turnover of nuclear RNA orchestrates crosstalk between essential processes to optimize cellular function. Disruptions in nuclear RNA homeostasis result in systemic functional decline, altering the cell state and promoting senescence.
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Affiliation(s)
- Xue Han
- State Key Laboratory of Membrane Biology, Beijing Frontier Research Center for Biological Structure, Tsinghua-Peking Joint Center for Life Sciences, School of Basic Medical Sciences, Tsinghua University, Beijing 100084, China
| | - Linqing Xing
- State Key Laboratory of Membrane Biology, Beijing Frontier Research Center for Biological Structure, Tsinghua-Peking Joint Center for Life Sciences, School of Basic Medical Sciences, Tsinghua University, Beijing 100084, China
| | - Yantao Hong
- State Key Laboratory of Membrane Biology, Beijing Frontier Research Center for Biological Structure, Tsinghua-Peking Joint Center for Life Sciences, School of Basic Medical Sciences, Tsinghua University, Beijing 100084, China
| | - Xuechun Zhang
- State Key Laboratory of Membrane Biology, Beijing Frontier Research Center for Biological Structure, Tsinghua-Peking Joint Center for Life Sciences, School of Basic Medical Sciences, Tsinghua University, Beijing 100084, China
| | - Bo Hao
- SXMU-Tsinghua Collaborative Innovation Center for Frontier Medicine, Shanxi Medical University, Taiyuan, Shanxi 030001, China
| | - J Yuyang Lu
- State Key Laboratory of Membrane Biology, Beijing Frontier Research Center for Biological Structure, Tsinghua-Peking Joint Center for Life Sciences, School of Basic Medical Sciences, Tsinghua University, Beijing 100084, China
| | - Mengyuan Huang
- State Key Laboratory of Membrane Biology, Beijing Frontier Research Center for Biological Structure, Tsinghua-Peking Joint Center for Life Sciences, School of Basic Medical Sciences, Tsinghua University, Beijing 100084, China
| | - Zuhui Wang
- Biomedical Pioneering Innovation Center (BIOPIC), Beijing Advanced Innovation Center for Genomics (ICG), Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Shaoqian Ma
- State Key Laboratory of Membrane Biology, Beijing Frontier Research Center for Biological Structure, Tsinghua-Peking Joint Center for Life Sciences, School of Basic Medical Sciences, Tsinghua University, Beijing 100084, China
| | - Ge Zhan
- State Key Laboratory of Membrane Biology, Beijing Frontier Research Center for Biological Structure, Tsinghua-Peking Joint Center for Life Sciences, School of Basic Medical Sciences, Tsinghua University, Beijing 100084, China
| | - Tong Li
- State Key Laboratory of Membrane Biology, Beijing Frontier Research Center for Biological Structure, Tsinghua-Peking Joint Center for Life Sciences, School of Basic Medical Sciences, Tsinghua University, Beijing 100084, China
| | - Xiaowen Hao
- State Key Laboratory of Membrane Biology, Beijing Frontier Research Center for Biological Structure, Tsinghua-Peking Joint Center for Life Sciences, School of Basic Medical Sciences, Tsinghua University, Beijing 100084, China
| | - Yibing Tao
- State Key Laboratory of Membrane Biology, Beijing Frontier Research Center for Biological Structure, Tsinghua-Peking Joint Center for Life Sciences, School of Basic Medical Sciences, Tsinghua University, Beijing 100084, China
| | - Guanwen Li
- State Key Laboratory of Membrane Biology, Beijing Frontier Research Center for Biological Structure, Tsinghua-Peking Joint Center for Life Sciences, School of Basic Medical Sciences, Tsinghua University, Beijing 100084, China
| | - Shuqin Zhou
- State Key Laboratory of Membrane Biology, Beijing Frontier Research Center for Biological Structure, Tsinghua-Peking Joint Center for Life Sciences, School of Basic Medical Sciences, Tsinghua University, Beijing 100084, China
| | - Zheng Zheng
- State Key Laboratory of Membrane Biology, Beijing Frontier Research Center for Biological Structure, Tsinghua-Peking Joint Center for Life Sciences, School of Basic Medical Sciences, Tsinghua University, Beijing 100084, China
| | - Wen Shao
- State Key Laboratory of Membrane Biology, Beijing Frontier Research Center for Biological Structure, Tsinghua-Peking Joint Center for Life Sciences, School of Basic Medical Sciences, Tsinghua University, Beijing 100084, China
| | - Yitian Zeng
- State Key Laboratory of Membrane Biology, Beijing Frontier Research Center for Biological Structure, Tsinghua-Peking Joint Center for Life Sciences, School of Basic Medical Sciences, Tsinghua University, Beijing 100084, China
| | - Dacheng Ma
- MOE Key Laboratory of Bioinformatics and Bioinformatics Division, Center for Synthetic and Systems Biology, Department of Automation, Beijing National Research Center for Information Science and Technology, Tsinghua University, Beijing 100084, China
| | - Wenhao Zhang
- MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Zhen Xie
- MOE Key Laboratory of Bioinformatics and Bioinformatics Division, Center for Synthetic and Systems Biology, Department of Automation, Beijing National Research Center for Information Science and Technology, Tsinghua University, Beijing 100084, China
| | - Haiteng Deng
- MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Jiangwei Yan
- SXMU-Tsinghua Collaborative Innovation Center for Frontier Medicine, Shanxi Medical University, Taiyuan, Shanxi 030001, China
| | - Wulan Deng
- Biomedical Pioneering Innovation Center (BIOPIC), Beijing Advanced Innovation Center for Genomics (ICG), Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Xiaohua Shen
- State Key Laboratory of Membrane Biology, Beijing Frontier Research Center for Biological Structure, Tsinghua-Peking Joint Center for Life Sciences, School of Basic Medical Sciences, Tsinghua University, Beijing 100084, China; SXMU-Tsinghua Collaborative Innovation Center for Frontier Medicine, Shanxi Medical University, Taiyuan, Shanxi 030001, China.
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214
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Tu K, Li X, Zhang Q, Huang W, Xie D. A data-adaptive methods in detecting exogenous methyltransferase accessible chromatin in human genome using nanopore sequencing. Bioinformatics 2024; 40:btae206. [PMID: 38613848 PMCID: PMC11256936 DOI: 10.1093/bioinformatics/btae206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2023] [Revised: 03/15/2024] [Accepted: 04/12/2024] [Indexed: 04/15/2024] Open
Abstract
MOTIVATION Identifying chromatin accessibility is one of the key steps in studying the regulation of eukaryotic genomes. The combination of exogenous methyltransferase and nanopore sequencing provides an strategy to identify open chromatin over long genomic ranges at the single-molecule scale. However, endogenous methylation, non-open-chromatin-specific exogenous methylation and base-calling errors limit the accuracy and hinders its application to complex genomes. RESULTS We systematically evaluated the impact of these three influence factors, and developed a model-based computational method, methyltransferase accessible genome region finder (MAGNIFIER), to address the issues. By incorporating control data, MAGNIFIER attenuates the three influence factors with data-adaptive comparison strategy. We demonstrate that MAGNIFIER is not only sensitive to identify the open chromatin with much improved accuracy, but also able to detect the chromatin accessibility of repetitive regions that are missed by NGS-based methods. By incorporating long-read RNA-seq data, we revealed the association between the accessible Alu elements and non-classic gene isoforms. AVAILABILITY AND IMPLEMENTATION Freely available on web at https://github.com/Goatofmountain/MAGNIFIER.
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Affiliation(s)
- Kailing Tu
- National Frontier Center of Disease Molecular Network, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610000, China
| | - Xuemei Li
- National Frontier Center of Disease Molecular Network, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610000, China
| | - Qilin Zhang
- National Frontier Center of Disease Molecular Network, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610000, China
| | - Wei Huang
- School of Mathematics and Statistics, Key Laboratory for Applied Statistics of the Ministry of Education, Northeast Normal University, Changchun 130024, China
| | - Dan Xie
- National Frontier Center of Disease Molecular Network, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610000, China
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215
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Ramírez-Cuéllar J, Ferrari R, Sanz RT, Valverde-Santiago M, García-García J, Nacht AS, Castillo D, Le Dily F, Neguembor MV, Malatesta M, Bonnin S, Marti-Renom MA, Beato M, Vicent GP. LATS1 controls CTCF chromatin occupancy and hormonal response of 3D-grown breast cancer cells. EMBO J 2024; 43:1770-1798. [PMID: 38565950 PMCID: PMC11066098 DOI: 10.1038/s44318-024-00080-x] [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: 05/15/2023] [Revised: 02/05/2024] [Accepted: 02/27/2024] [Indexed: 04/04/2024] Open
Abstract
The cancer epigenome has been studied in cells cultured in two-dimensional (2D) monolayers, but recent studies highlight the impact of the extracellular matrix and the three-dimensional (3D) environment on multiple cellular functions. Here, we report the physical, biochemical, and genomic differences between T47D breast cancer cells cultured in 2D and as 3D spheroids. Cells within 3D spheroids exhibit a rounder nucleus with less accessible, more compacted chromatin, as well as altered expression of ~2000 genes, the majority of which become repressed. Hi-C analysis reveals that cells in 3D are enriched for regions belonging to the B compartment, have decreased chromatin-bound CTCF and increased fusion of topologically associating domains (TADs). Upregulation of the Hippo pathway in 3D spheroids results in the activation of the LATS1 kinase, which promotes phosphorylation and displacement of CTCF from DNA, thereby likely causing the observed TAD fusions. 3D cells show higher chromatin binding of progesterone receptor (PR), leading to an increase in the number of hormone-regulated genes. This effect is in part mediated by LATS1 activation, which favors cytoplasmic retention of YAP and CTCF removal.
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Affiliation(s)
- Julieta Ramírez-Cuéllar
- Center for Genomic Regulation (CRG), Barcelona Institute for Science and Technology (BIST) Barcelona, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Roberto Ferrari
- Center for Genomic Regulation (CRG), Barcelona Institute for Science and Technology (BIST) Barcelona, Barcelona, Spain
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Rosario T Sanz
- Molecular Biology Institute of Barcelona, Consejo Superior de Investigaciones Científicas (IBMB-CSIC), C/ Baldiri Reixac, 4-8, 08028, Barcelona, Spain
| | - Marta Valverde-Santiago
- Molecular Biology Institute of Barcelona, Consejo Superior de Investigaciones Científicas (IBMB-CSIC), C/ Baldiri Reixac, 4-8, 08028, Barcelona, Spain
| | - Judith García-García
- Molecular Biology Institute of Barcelona, Consejo Superior de Investigaciones Científicas (IBMB-CSIC), C/ Baldiri Reixac, 4-8, 08028, Barcelona, Spain
| | - A Silvina Nacht
- Center for Genomic Regulation (CRG), Barcelona Institute for Science and Technology (BIST) Barcelona, Barcelona, Spain
| | - David Castillo
- CNAG-CRG, Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, Baldiri Reixac 4, Barcelona, 08028, Spain
| | - Francois Le Dily
- Center for Genomic Regulation (CRG), Barcelona Institute for Science and Technology (BIST) Barcelona, Barcelona, Spain
| | - Maria Victoria Neguembor
- Center for Genomic Regulation (CRG), Barcelona Institute for Science and Technology (BIST) Barcelona, Barcelona, Spain
| | - Marco Malatesta
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Sarah Bonnin
- Center for Genomic Regulation (CRG), Barcelona Institute for Science and Technology (BIST) Barcelona, Barcelona, Spain
| | - Marc A Marti-Renom
- Center for Genomic Regulation (CRG), Barcelona Institute for Science and Technology (BIST) Barcelona, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- CNAG-CRG, Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, Baldiri Reixac 4, Barcelona, 08028, Spain
- ICREA, Barcelona, Spain
| | - Miguel Beato
- Center for Genomic Regulation (CRG), Barcelona Institute for Science and Technology (BIST) Barcelona, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Guillermo P Vicent
- Center for Genomic Regulation (CRG), Barcelona Institute for Science and Technology (BIST) Barcelona, Barcelona, Spain.
- Molecular Biology Institute of Barcelona, Consejo Superior de Investigaciones Científicas (IBMB-CSIC), C/ Baldiri Reixac, 4-8, 08028, Barcelona, Spain.
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216
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Bian X, Wang W, Abudurexiti M, Zhang X, Ma W, Shi G, Du L, Xu M, Wang X, Tan C, Sun H, He X, Zhang C, Zhu Y, Zhang M, Ye D, Wang J. Integration Analysis of Single-Cell Multi-Omics Reveals Prostate Cancer Heterogeneity. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2305724. [PMID: 38483933 PMCID: PMC11095148 DOI: 10.1002/advs.202305724] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 02/25/2024] [Indexed: 05/16/2024]
Abstract
Prostate cancer (PCa) is an extensive heterogeneous disease with a complex cellular ecosystem in the tumor microenvironment (TME). However, the manner in which heterogeneity is shaped by tumors and stromal cells, or vice versa, remains poorly understood. In this study, single-cell RNA sequencing, spatial transcriptomics, and bulk ATAC-sequence are integrated from a series of patients with PCa and healthy controls. A stemness subset of club cells marked with SOX9highARlow expression is identified, which is markedly enriched after neoadjuvant androgen-deprivation therapy (ADT). Furthermore, a subset of CD8+CXCR6+ T cells that function as effector T cells is markedly reduced in patients with malignant PCa. For spatial transcriptome analysis, machine learning and computational intelligence are comprehensively utilized to identify the cellular diversity of prostate cancer cells and cell-cell communication in situ. Macrophage and neutrophil state transitions along the trajectory of cancer progression are also examined. Finally, the immunosuppressive microenvironment in advanced PCa is found to be associated with the infiltration of regulatory T cells (Tregs), potentially induced by an FAP+ fibroblast subset. In summary, the cellular heterogeneity is delineated in the stage-specific PCa microenvironment at single-cell resolution, uncovering their reciprocal crosstalk with disease progression, which can be helpful in promoting PCa diagnosis and therapy.
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Affiliation(s)
- Xiaojie Bian
- Department of UrologyFudan University Shanghai Cancer CenterDepartment of OncologyShanghai Medical CollegeFudan UniversityShanghai200032China
- Cancer InstituteShanghai Urological Cancer InstituteFudan University Shanghai Cancer CenterDepartment of OncologyShanghai Medical CollegeFudan UniversityShanghai200032China
| | - Wenfeng Wang
- Cancer InstituteShanghai Urological Cancer InstituteFudan University Shanghai Cancer CenterDepartment of OncologyShanghai Medical CollegeFudan UniversityShanghai200032China
| | - Mierxiati Abudurexiti
- Cancer InstituteShanghai Urological Cancer InstituteFudan University Shanghai Cancer CenterDepartment of OncologyShanghai Medical CollegeFudan UniversityShanghai200032China
- Department of UrologyShanghai Pudong New Area Gongli HospitalShanghai200135China
| | - Xingming Zhang
- Cancer InstituteShanghai Urological Cancer InstituteFudan University Shanghai Cancer CenterDepartment of OncologyShanghai Medical CollegeFudan UniversityShanghai200032China
| | - Weiwei Ma
- Department of UrologyFudan University Shanghai Cancer CenterDepartment of OncologyShanghai Medical CollegeFudan UniversityShanghai200032China
- Cancer InstituteShanghai Urological Cancer InstituteFudan University Shanghai Cancer CenterDepartment of OncologyShanghai Medical CollegeFudan UniversityShanghai200032China
| | - Guohai Shi
- Department of UrologyFudan University Shanghai Cancer CenterDepartment of OncologyShanghai Medical CollegeFudan UniversityShanghai200032China
| | - Leilei Du
- Cancer InstituteShanghai Urological Cancer InstituteFudan University Shanghai Cancer CenterDepartment of OncologyShanghai Medical CollegeFudan UniversityShanghai200032China
| | - Midie Xu
- Department of PathologyFudan University Shanghai Cancer CenterShanghai200032China
| | - Xin Wang
- Department of PathologyFudan University Shanghai Cancer CenterShanghai200032China
| | - Cong Tan
- Department of PathologyFudan University Shanghai Cancer CenterShanghai200032China
| | - Hui Sun
- Department of PathologyFudan University Shanghai Cancer CenterShanghai200032China
| | - Xiadi He
- Department of Cancer BiologyDana‐Farber Cancer InstituteBostonMA02215USA
- Department of Biological Chemistry and Molecular PharmacologyHarvard Medical SchoolBostonMA02115USA
| | - Chenyue Zhang
- Department of Integrated TherapyFudan University Shanghai Cancer CenterShanghai200032China
| | - Yao Zhu
- Department of UrologyFudan University Shanghai Cancer CenterDepartment of OncologyShanghai Medical CollegeFudan UniversityShanghai200032China
- Cancer InstituteShanghai Urological Cancer InstituteFudan University Shanghai Cancer CenterDepartment of OncologyShanghai Medical CollegeFudan UniversityShanghai200032China
| | - Min Zhang
- Pediatric Translational Medicine Institute and Pediatric Congenital Heart Disease InstituteShanghai Children's Medical CenterShanghai Jiao Tong University School of MedicineShanghai200127China
| | - Dingwei Ye
- Department of UrologyFudan University Shanghai Cancer CenterDepartment of OncologyShanghai Medical CollegeFudan UniversityShanghai200032China
- Cancer InstituteShanghai Urological Cancer InstituteFudan University Shanghai Cancer CenterDepartment of OncologyShanghai Medical CollegeFudan UniversityShanghai200032China
| | - Jianhua Wang
- Cancer InstituteShanghai Urological Cancer InstituteFudan University Shanghai Cancer CenterDepartment of OncologyShanghai Medical CollegeFudan UniversityShanghai200032China
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217
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Alvarez-Martinez M, Cox LS, Pearson CF, Branchett WJ, Chakravarty P, Wu X, Slawinski H, Al-Dibouni A, Samelis VA, Gabryšová L, Priestnall SL, Suárez-Bonnet A, Mikolajczak A, Briscoe J, Powrie F, O'Garra A. Blimp-1 and c-Maf regulate immune gene networks to protect against distinct pathways of pathobiont-induced colitis. Nat Immunol 2024; 25:886-901. [PMID: 38609547 PMCID: PMC11065689 DOI: 10.1038/s41590-024-01814-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: 02/07/2022] [Accepted: 03/13/2024] [Indexed: 04/14/2024]
Abstract
Intestinal immune responses to microbes are controlled by the cytokine IL-10 to avoid immune pathology. Here, we use single-cell RNA sequencing of colon lamina propria leukocytes (LPLs) along with RNA-seq and ATAC-seq of purified CD4+ T cells to show that the transcription factors Blimp-1 (encoded by Prdm1) and c-Maf co-dominantly regulate Il10 while negatively regulating proinflammatory cytokines in effector T cells. Double-deficient Prdm1fl/flMaffl/flCd4Cre mice infected with Helicobacter hepaticus developed severe colitis with an increase in TH1/NK/ILC1 effector genes in LPLs, while Prdm1fl/flCd4Cre and Maffl/flCd4Cre mice exhibited moderate pathology and a less-marked type 1 effector response. LPLs from infected Maffl/flCd4Cre mice had increased type 17 responses with increased Il17a and Il22 expression and an increase in granulocytes and myeloid cell numbers, resulting in increased T cell-myeloid-neutrophil interactions. Genes over-expressed in human inflammatory bowel disease showed differential expression in LPLs from infected mice in the absence of Prdm1 or Maf, revealing potential mechanisms of human disease.
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Affiliation(s)
| | - Luke S Cox
- Immunoregulation and Infection Laboratory, The Francis Crick Institute, London, UK
| | - Claire F Pearson
- Kennedy Institute of Rheumatology, University of Oxford, Oxford, UK
| | - William J Branchett
- Immunoregulation and Infection Laboratory, The Francis Crick Institute, London, UK
| | - Probir Chakravarty
- Computational Biology Laboratory, The Francis Crick Institute, London, UK
| | - Xuemei Wu
- Immunoregulation and Infection Laboratory, The Francis Crick Institute, London, UK
| | - Hubert Slawinski
- Advanced Sequencing Facility, The Francis Crick Institute, London, UK
| | - Alaa Al-Dibouni
- Immunoregulation and Infection Laboratory, The Francis Crick Institute, London, UK
| | - Vasileios A Samelis
- Immunoregulation and Infection Laboratory, The Francis Crick Institute, London, UK
| | - Leona Gabryšová
- Immunoregulation and Infection Laboratory, The Francis Crick Institute, London, UK
| | - Simon L Priestnall
- Department of Pathobiology and Population Sciences, Royal Veterinary College, London, UK
- Experimental Histopathology, The Francis Crick Institute, London, UK
| | - Alejandro Suárez-Bonnet
- Department of Pathobiology and Population Sciences, Royal Veterinary College, London, UK
- Experimental Histopathology, The Francis Crick Institute, London, UK
| | - Anna Mikolajczak
- Experimental Histopathology, The Francis Crick Institute, London, UK
| | - James Briscoe
- Developmental Dynamics Laboratory, The Francis Crick Institute, London, UK
| | - Fiona Powrie
- Kennedy Institute of Rheumatology, University of Oxford, Oxford, UK
| | - Anne O'Garra
- Immunoregulation and Infection Laboratory, The Francis Crick Institute, London, UK.
- National Heart and Lung Institute, Imperial College London, London, UK.
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218
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Bowness JS, Almeida M, Nesterova TB, Brockdorff N. YY1 binding is a gene-intrinsic barrier to Xist-mediated gene silencing. EMBO Rep 2024; 25:2258-2277. [PMID: 38654121 PMCID: PMC11094009 DOI: 10.1038/s44319-024-00136-3] [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: 02/23/2024] [Revised: 03/26/2024] [Accepted: 04/03/2024] [Indexed: 04/25/2024] Open
Abstract
X chromosome inactivation (XCI) in mammals is mediated by Xist RNA which functions in cis to silence genes on a single X chromosome in XX female cells, thereby equalising levels of X-linked gene expression relative to XY males. XCI progresses over a period of several days, with some X-linked genes silencing faster than others. The chromosomal location of a gene is an important determinant of silencing rate, but uncharacterised gene-intrinsic features also mediate resistance or susceptibility to silencing. In this study, we examine mouse embryonic stem cell lines with an inducible Xist allele (iXist-ChrX mESCs) and integrate allele-specific data of gene silencing and decreasing inactive X (Xi) chromatin accessibility over time courses of Xist induction with cellular differentiation. Our analysis reveals that motifs bound by the transcription factor YY1 are associated with persistently accessible regulatory elements, including many promoters and enhancers of slow-silencing genes. We further show that YY1 is evicted relatively slowly from target sites on Xi, and that silencing of X-linked genes is increased upon YY1 degradation. Together our results suggest that YY1 acts as a barrier to Xist-mediated silencing until the late stages of the XCI process.
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Affiliation(s)
- Joseph S Bowness
- Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003, Barcelona, Spain
| | - Mafalda Almeida
- Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK
| | | | - Neil Brockdorff
- Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK.
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219
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Geens B, Goossens S, Li J, Van de Peer Y, Vanden Broeck J. Untangling the gordian knot: The intertwining interactions between developmental hormone signaling and epigenetic mechanisms in insects. Mol Cell Endocrinol 2024; 585:112178. [PMID: 38342134 DOI: 10.1016/j.mce.2024.112178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 01/30/2024] [Accepted: 02/04/2024] [Indexed: 02/13/2024]
Abstract
Hormones control developmental and physiological processes, often by regulating the expression of multiple genes simultaneously or sequentially. Crosstalk between hormones and epigenetics is pivotal to dynamically coordinate this process. Hormonal signals can guide the addition and removal of epigenetic marks, steering gene expression. Conversely, DNA methylation, histone modifications and non-coding RNAs can modulate regional chromatin structure and accessibility and regulate the expression of numerous (hormone-related) genes. Here, we provide a review of the interplay between the classical insect hormones, ecdysteroids and juvenile hormones, and epigenetics. We summarize the mode-of-action and roles of these hormones in post-embryonic development, and provide a general overview of epigenetic mechanisms. We then highlight recent advances on the interactions between these hormonal pathways and epigenetics, and their involvement in development. Furthermore, we give an overview of several 'omics techniques employed in the field. Finally, we discuss which questions remain unanswered and possible avenues for future research.
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Affiliation(s)
- Bart Geens
- Molecular Developmental Physiology and Signal Transduction, KU Leuven, Naamsestraat 59 box 2465, B-3000 Leuven, Belgium.
| | - Stijn Goossens
- Molecular Developmental Physiology and Signal Transduction, KU Leuven, Naamsestraat 59 box 2465, B-3000 Leuven, Belgium.
| | - Jia Li
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium; VIB Center for Plant Systems Biology, VIB, Ghent, Belgium.
| | - Yves Van de Peer
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium; VIB Center for Plant Systems Biology, VIB, Ghent, Belgium.
| | - Jozef Vanden Broeck
- Molecular Developmental Physiology and Signal Transduction, KU Leuven, Naamsestraat 59 box 2465, B-3000 Leuven, Belgium.
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220
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Scholz R, Brösamle D, Yuan X, Beyer M, Neher JJ. Epigenetic control of microglial immune responses. Immunol Rev 2024; 323:209-226. [PMID: 38491845 DOI: 10.1111/imr.13317] [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: 12/18/2023] [Accepted: 03/02/2024] [Indexed: 03/18/2024]
Abstract
Microglia, the major population of brain-resident macrophages, are now recognized as a heterogeneous population comprising several cell subtypes with different (so far mostly supposed) functions in health and disease. A number of studies have performed molecular characterization of these different microglial activation states over the last years making use of "omics" technologies, that is transcriptomics, proteomics and, less frequently, epigenomics profiling. These approaches offer the possibility to identify disease mechanisms, discover novel diagnostic biomarkers, and develop new therapeutic strategies. Here, we focus on epigenetic profiling as a means to understand microglial immune responses beyond what other omics methods can offer, that is, revealing past and present molecular responses, gene regulatory networks and potential future response trajectories, and defining cell subtype-specific disease relevance through mapping non-coding genetic variants. We review the current knowledge in the field regarding epigenetic regulation of microglial identity and function, provide an exemplary analysis that demonstrates the advantages of performing joint transcriptomic and epigenomic profiling of single microglial cells and discuss how comprehensive epigenetic analyses may enhance our understanding of microglial pathophysiology.
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Affiliation(s)
- Rebekka Scholz
- Immunogenomics & Neurodegeneration, German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
- Systems Medicine, German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
| | - Desirée Brösamle
- Biomedical Center (BMC), Biochemistry, Faculty of Medicine, LMU Munich, Munich, Germany
- Neuroimmunology and Neurodegenerative Diseases, German Center for Neurodegenerative Diseases (DZNE), Munich, Germany
- Department of Cellular Neurology, Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany
- Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
| | - Xidi Yuan
- Biomedical Center (BMC), Biochemistry, Faculty of Medicine, LMU Munich, Munich, Germany
- Neuroimmunology and Neurodegenerative Diseases, German Center for Neurodegenerative Diseases (DZNE), Munich, Germany
- Department of Cellular Neurology, Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany
- Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
| | - Marc Beyer
- Immunogenomics & Neurodegeneration, German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
- Systems Medicine, German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
- Platform for Single Cell Genomics and Epigenomics, German Center for Neurodegenerative Diseases (DZNE) and University of Bonn and West German Genome Center, Bonn, Germany
| | - Jonas J Neher
- Biomedical Center (BMC), Biochemistry, Faculty of Medicine, LMU Munich, Munich, Germany
- Neuroimmunology and Neurodegenerative Diseases, German Center for Neurodegenerative Diseases (DZNE), Munich, Germany
- Department of Cellular Neurology, Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany
- Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
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221
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Fortelny N, Farlik M, Fife V, Gorki AD, Lassnig C, Maurer B, Meissl K, Dolezal M, Boccuni L, Ravi Sundar Jose Geetha A, Akagha MJ, Karjalainen A, Shoebridge S, Farhat A, Mann U, Jain R, Tikoo S, Zila N, Esser-Skala W, Krausgruber T, Sitnik K, Penz T, Hladik A, Suske T, Zahalka S, Senekowitsch M, Barreca D, Halbritter F, Macho-Maschler S, Weninger W, Neubauer HA, Moriggl R, Knapp S, Sexl V, Strobl B, Decker T, Müller M, Bock C. JAK-STAT signaling maintains homeostasis in T cells and macrophages. Nat Immunol 2024; 25:847-859. [PMID: 38658806 PMCID: PMC11065702 DOI: 10.1038/s41590-024-01804-1] [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: 07/22/2022] [Accepted: 03/07/2024] [Indexed: 04/26/2024]
Abstract
Immune cells need to sustain a state of constant alertness over a lifetime. Yet, little is known about the regulatory processes that control the fluent and fragile balance that is called homeostasis. Here we demonstrate that JAK-STAT signaling, beyond its role in immune responses, is a major regulator of immune cell homeostasis. We investigated JAK-STAT-mediated transcription and chromatin accessibility across 12 mouse models, including knockouts of all STAT transcription factors and of the TYK2 kinase. Baseline JAK-STAT signaling was detected in CD8+ T cells and macrophages of unperturbed mice-but abrogated in the knockouts and in unstimulated immune cells deprived of their normal tissue context. We observed diverse gene-regulatory programs, including effects of STAT2 and IRF9 that were independent of STAT1. In summary, our large-scale dataset and integrative analysis of JAK-STAT mutant and wild-type mice uncovered a crucial role of JAK-STAT signaling in unstimulated immune cells, where it contributes to a poised epigenetic and transcriptional state and helps prepare these cells for rapid response to immune stimuli.
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Affiliation(s)
- Nikolaus Fortelny
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
- Center for Tumor Biology and Immunology, Department of Biosciences and Medical Biology, Paris-Lodron University Salzburg, Salzburg, Austria
| | - Matthias Farlik
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria.
- Department of Dermatology, Medical University of Vienna, Vienna, Austria.
| | - Victoria Fife
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Anna-Dorothea Gorki
- Research Division of Infection Biology, Department of Medicine I, Medical University of Vienna, Vienna, Austria
| | - Caroline Lassnig
- Animal Breeding and Genetics and VetBiomodels, Department of Biological Sciences and Pathobiology, University of Veterinary Medicine, Vienna, Austria
| | - Barbara Maurer
- Pharmacology and Toxicology, Department of Biological Sciences and Pathobiology, University of Veterinary Medicine, Vienna, Austria
| | - Katrin Meissl
- Animal Breeding and Genetics and VetBiomodels, Department of Biological Sciences and Pathobiology, University of Veterinary Medicine, Vienna, Austria
| | - Marlies Dolezal
- Platform for Bioinformatics and Biostatistics, Department of Biological Sciences and Pathobiology, University of Veterinary Medicine, Vienna, Austria
| | - Laura Boccuni
- Max Perutz Labs, University of Vienna, Vienna, Austria
| | | | - Mojoyinola Joanna Akagha
- Animal Breeding and Genetics and VetBiomodels, Department of Biological Sciences and Pathobiology, University of Veterinary Medicine, Vienna, Austria
| | - Anzhelika Karjalainen
- Animal Breeding and Genetics and VetBiomodels, Department of Biological Sciences and Pathobiology, University of Veterinary Medicine, Vienna, Austria
| | - Stephen Shoebridge
- Animal Breeding and Genetics and VetBiomodels, Department of Biological Sciences and Pathobiology, University of Veterinary Medicine, Vienna, Austria
| | - Asma Farhat
- Research Division of Infection Biology, Department of Medicine I, Medical University of Vienna, Vienna, Austria
| | - Ulrike Mann
- Department of Dermatology, Medical University of Vienna, Vienna, Austria
| | - Rohit Jain
- Department of Dermatology, Medical University of Vienna, Vienna, Austria
| | - Shweta Tikoo
- Department of Dermatology, Medical University of Vienna, Vienna, Austria
| | - Nina Zila
- Department of Dermatology, Medical University of Vienna, Vienna, Austria
| | - Wolfgang Esser-Skala
- Center for Tumor Biology and Immunology, Department of Biosciences and Medical Biology, Paris-Lodron University Salzburg, Salzburg, Austria
| | - Thomas Krausgruber
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
- Institute of Artificial Intelligence, Center for Medical Data Science, Medical University of Vienna, Vienna, Austria
| | - Katarzyna Sitnik
- Animal Breeding and Genetics and VetBiomodels, Department of Biological Sciences and Pathobiology, University of Veterinary Medicine, Vienna, Austria
| | - Thomas Penz
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Anastasiya Hladik
- Research Division of Infection Biology, Department of Medicine I, Medical University of Vienna, Vienna, Austria
| | - Tobias Suske
- Animal Breeding and Genetics and VetBiomodels, Department of Biological Sciences and Pathobiology, University of Veterinary Medicine, Vienna, Austria
| | - Sophie Zahalka
- Research Division of Infection Biology, Department of Medicine I, Medical University of Vienna, Vienna, Austria
| | - Martin Senekowitsch
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Daniele Barreca
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Florian Halbritter
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Sabine Macho-Maschler
- Animal Breeding and Genetics and VetBiomodels, Department of Biological Sciences and Pathobiology, University of Veterinary Medicine, Vienna, Austria
| | - Wolfgang Weninger
- Department of Dermatology, Medical University of Vienna, Vienna, Austria
| | - Heidi A Neubauer
- Animal Breeding and Genetics and VetBiomodels, Department of Biological Sciences and Pathobiology, University of Veterinary Medicine, Vienna, Austria
| | - Richard Moriggl
- Animal Breeding and Genetics and VetBiomodels, Department of Biological Sciences and Pathobiology, University of Veterinary Medicine, Vienna, Austria
| | - Sylvia Knapp
- Research Division of Infection Biology, Department of Medicine I, Medical University of Vienna, Vienna, Austria
| | - Veronika Sexl
- Pharmacology and Toxicology, Department of Biological Sciences and Pathobiology, University of Veterinary Medicine, Vienna, Austria
- University of Innsbruck, Innsbruck, Austria
| | - Birgit Strobl
- Animal Breeding and Genetics and VetBiomodels, Department of Biological Sciences and Pathobiology, University of Veterinary Medicine, Vienna, Austria
| | - Thomas Decker
- Max Perutz Labs, University of Vienna, Vienna, Austria
| | - Mathias Müller
- Animal Breeding and Genetics and VetBiomodels, Department of Biological Sciences and Pathobiology, University of Veterinary Medicine, Vienna, Austria
| | - Christoph Bock
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria.
- Institute of Artificial Intelligence, Center for Medical Data Science, Medical University of Vienna, Vienna, Austria.
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222
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Su Y, He S, Chen Q, Zhang H, Huang C, Zhao Q, Pu Y, He X, Jiang L, Ma Y, Zhao Q. Integrative ATAC-seq and RNA-seq analysis of myogenic differentiation of ovine skeletal muscle satellite cell. Genomics 2024; 116:110851. [PMID: 38692440 DOI: 10.1016/j.ygeno.2024.110851] [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: 01/29/2024] [Revised: 04/01/2024] [Accepted: 04/28/2024] [Indexed: 05/03/2024]
Abstract
Skeletal muscle satellite cells (SMSCs) play an important role in regulating muscle growth and regeneration. Chromatin accessibility allows physical interactions that synergistically regulate gene expression through enhancers, promoters, insulators, and chromatin binding factors. However, the chromatin accessibility altas and its regulatory role in ovine myoblast differentiation is still unclear. Therefore, ATAC-seq and RNA-seq analysis were performed on ovine SMSCs at the proliferation stage (SCG) and differentiation stage (SCD). 17,460 DARs (differential accessibility regions) and 3732 DEGs (differentially expressed genes) were identified. Based on joint analysis of ATAC-seq and RNA-seq, we revealed that PI3K-Akt, TGF-β and other signaling pathways regulated SMSCs differentiation. We identified two novel candidate genes, FZD5 and MAP2K6, which may affect the proliferation and differentiation of SMSCs. Our data identify potential cis regulatory elements of ovine SMSCs. This study can provide a reference for exploring the mechanisms of the differentiation and regeneration of SMSCs in the future.
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Affiliation(s)
- Yingxiao Su
- Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193,China
| | - Siqi He
- Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193,China; College of Animal Science, Shanxi Agricultural University, Taigu 030801, China
| | - Qian Chen
- Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193,China; College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, China
| | - Hechun Zhang
- Chaoyang Chaomu Breeding Farm Co., LTD, Chaoyang, Liaoning 122629, China
| | - Chang Huang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193,China; College of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China
| | - Qian Zhao
- Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193,China; College of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China
| | - Yabin Pu
- Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193,China
| | - Xiaohong He
- Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193,China
| | - Lin Jiang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193,China
| | - Yuehui Ma
- Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193,China
| | - Qianjun Zhao
- Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193,China.
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Lee KH, Kim J, Kim JH. 3D epigenomics and 3D epigenopathies. BMB Rep 2024; 57:216-231. [PMID: 38627948 PMCID: PMC11139681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 01/15/2024] [Accepted: 03/18/2024] [Indexed: 05/25/2024] Open
Abstract
Mammalian genomes are intricately compacted to form sophisticated 3-dimensional structures within the tiny nucleus, so called 3D genome folding. Despite their shapes reminiscent of an entangled yarn, the rapid development of molecular and next-generation sequencing technologies (NGS) has revealed that mammalian genomes are highly organized in a hierarchical order that delicately affects transcription activities. An increasing amount of evidence suggests that 3D genome folding is implicated in diseases, giving us a clue on how to identify novel therapeutic approaches. In this review, we will study what 3D genome folding means in epigenetics, what types of 3D genome structures there are, how they are formed, and how the technologies have developed to explore them. We will also discuss the pathological implications of 3D genome folding. Finally, we will discuss how to leverage 3D genome folding and engineering for future studies. [BMB Reports 2024; 57(5): 216-231].
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Affiliation(s)
- Kyung-Hwan Lee
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology, Daejeon 34141, Korea
| | - Jungyu Kim
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology, Daejeon 34141, Korea
| | - Ji Hun Kim
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology, Daejeon 34141, Korea
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224
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Lv Z, Fan H, Gao M, Zhang X, Li G, Fan Y, Ning Z, Guo Y. The accessible chromatin landscape of lipopolysaccharide-induced systemic inflammatory response identifying epigenome signatures and transcription regulatory networks in chickens. Int J Biol Macromol 2024; 266:131136. [PMID: 38547952 DOI: 10.1016/j.ijbiomac.2024.131136] [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: 02/04/2024] [Revised: 03/11/2024] [Accepted: 03/23/2024] [Indexed: 04/01/2024]
Abstract
Lipopolysaccharide (LPS) can induce systemic inflammatory response (SIR) in animals. Understanding the regulatory mechanism of SIR and therapies to ensure healthy growth is urgently needed. Chromatin remodeling plays a crucial role in the expression of genes involved in immune diseases. In the present study, the ATAC-seq analysis revealed 3491 differential open chromatin sites in the spleen of chicks with SIR induced by LPS challenge, and we presented the motifs on these sites and the associated transcription factors. The regulatory network was presented by combining the differential open chromatin data with the mRNAs and exploded cytokines. Interestingly, the LPS challenge could regulate the mRNA expression of 202 genes through chromatin reprogramming, including critical genes such as TLE1 and JUN, which regulate signaling pathways such as I-κB kinase/NF-κB, Toll-like receptor, and downstream cytokine genes. Furthermore, dietary daidzein could inhibit DNA topoisomerase II, which reprograms the spatial conformation of chromatin in the inflammatory response and attenuates SIR. In conclusion, we successfully identified key genes directly regulated by chromatin reprogramming in SIR and demonstrated the chromatin epigenome signatures and transcriptional regulatory network, which provides an important reference for further research on avian epigenetics. There is great potential for alleviating SIR using dietary daidzein.
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Affiliation(s)
- Zengpeng Lv
- State Key Laboratory of Animal Nutrition and Feeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, PR China.
| | - Hao Fan
- State Key Laboratory of Animal Nutrition and Feeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, PR China; Section of Hematology and Oncology, Department of Medicine, The University of Chicago, Chicago, IL 60637, USA
| | - Mingkun Gao
- State Key Laboratory of Animal Nutrition and Feeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, PR China
| | - Xiaodan Zhang
- State Key Laboratory of Animal Nutrition and Feeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, PR China
| | - Guang Li
- State Key Laboratory of Animal Nutrition and Feeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, PR China
| | - Yuyang Fan
- Xi'an Jiaotong-Liverpool University, Suzhou 215123, PR China
| | - Zhonghua Ning
- State Key Laboratory of Animal Nutrition and Feeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, PR China
| | - Yuming Guo
- State Key Laboratory of Animal Nutrition and Feeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, PR China.
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225
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Yuan Y, Chen Q, Brovkina M, Clowney EJ, Yadlapalli S. Clock-dependent chromatin accessibility rhythms regulate circadian transcription. PLoS Genet 2024; 20:e1011278. [PMID: 38805552 PMCID: PMC11161047 DOI: 10.1371/journal.pgen.1011278] [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: 09/22/2023] [Revised: 06/07/2024] [Accepted: 04/29/2024] [Indexed: 05/30/2024] Open
Abstract
Chromatin organization plays a crucial role in gene regulation by controlling the accessibility of DNA to transcription machinery. While significant progress has been made in understanding the regulatory role of clock proteins in circadian rhythms, how chromatin organization affects circadian rhythms remains poorly understood. Here, we employed ATAC-seq (Assay for Transposase-Accessible Chromatin with Sequencing) on FAC-sorted Drosophila clock neurons to assess genome-wide chromatin accessibility at dawn and dusk over the circadian cycle. We observed significant oscillations in chromatin accessibility at promoter and enhancer regions of hundreds of genes, with enhanced accessibility either at dusk or dawn, which correlated with their peak transcriptional activity. Notably, genes with enhanced accessibility at dusk were enriched with E-box motifs, while those more accessible at dawn were enriched with VRI/PDP1-box motifs, indicating that they are regulated by the core circadian feedback loops, PER/CLK and VRI/PDP1, respectively. Further, we observed a complete loss of chromatin accessibility rhythms in per01 null mutants, with chromatin consistently accessible at both dawn and dusk, underscoring the critical role of Period protein in driving chromatin compaction during the repression phase at dawn. Together, this study demonstrates the significant role of chromatin organization in circadian regulation, revealing how the interplay between clock proteins and chromatin structure orchestrates the precise timing of biological processes throughout the day. This work further implies that variations in chromatin accessibility might play a central role in the generation of diverse circadian gene expression patterns in clock neurons.
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Affiliation(s)
- Ye Yuan
- Cellular and Molecular Biology Program, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Qianqian Chen
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Margarita Brovkina
- Cellular and Molecular Biology Program, University of Michigan, Ann Arbor, Michigan, United States of America
| | - E Josephine Clowney
- Cellular and Molecular Biology Program, University of Michigan, Ann Arbor, Michigan, United States of America
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, Michigan, United States of America
- Michigan Neuroscience Institute, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Swathi Yadlapalli
- Cellular and Molecular Biology Program, University of Michigan, Ann Arbor, Michigan, United States of America
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, Michigan, United States of America
- Michigan Neuroscience Institute, University of Michigan, Ann Arbor, Michigan, United States of America
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226
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Bhattarai KR, Mobley RJ, Barnett KR, Ferguson DC, Hansen BS, Diedrich JD, Bergeron BP, Yoshimura S, Yang W, Crews KR, Manring CS, Jabbour E, Paietta E, Litzow MR, Kornblau SM, Stock W, Inaba H, Jeha S, Pui CH, Cheng C, Pruett-Miller SM, Relling MV, Yang JJ, Evans WE, Savic D. Investigation of inherited noncoding genetic variation impacting the pharmacogenomics of childhood acute lymphoblastic leukemia treatment. Nat Commun 2024; 15:3681. [PMID: 38693155 PMCID: PMC11063049 DOI: 10.1038/s41467-024-48124-4] [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: 02/10/2023] [Accepted: 04/18/2024] [Indexed: 05/03/2024] Open
Abstract
Defining genetic factors impacting chemotherapy failure can help to better predict response and identify drug resistance mechanisms. However, there is limited understanding of the contribution of inherited noncoding genetic variation on inter-individual differences in chemotherapy response in childhood acute lymphoblastic leukemia (ALL). Here we map inherited noncoding variants associated with treatment outcome and/or chemotherapeutic drug resistance to ALL cis-regulatory elements and investigate their gene regulatory potential and target gene connectivity using massively parallel reporter assays and three-dimensional chromatin looping assays, respectively. We identify 54 variants with transcriptional effects and high-confidence gene connectivity. Additionally, functional interrogation of the top variant, rs1247117, reveals changes in chromatin accessibility, PU.1 binding affinity and gene expression, and deletion of the genomic interval containing rs1247117 sensitizes cells to vincristine. Together, these data demonstrate that noncoding regulatory variants associated with diverse pharmacological traits harbor significant effects on allele-specific transcriptional activity and impact sensitivity to antileukemic agents.
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Affiliation(s)
- Kashi Raj Bhattarai
- Hematological Malignancies Program, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Robert J Mobley
- Hematological Malignancies Program, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Kelly R Barnett
- Hematological Malignancies Program, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Daniel C Ferguson
- Hematological Malignancies Program, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Baranda S Hansen
- Center for Advanced Genome Engineering, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
- Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Jonathan D Diedrich
- Hematological Malignancies Program, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Brennan P Bergeron
- Hematological Malignancies Program, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
- Graduate School of Biomedical Sciences, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Satoshi Yoshimura
- Hematological Malignancies Program, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
- Department of Advanced Pediatric Medicine, Tohoku University School of Medicine, Tokyo, Japan
| | - Wenjian Yang
- Hematological Malignancies Program, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Kristine R Crews
- Hematological Malignancies Program, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Christopher S Manring
- Alliance Hematologic Malignancy Biorepository; Clara D. Bloomfield Center for Leukemia Outcomes Research, Columbus, OH, 43210, USA
| | - Elias Jabbour
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | | | - Mark R Litzow
- Division of Hematology, Department of Medicine, Mayo Clinic, Rochester, MN, 55905, USA
| | - Steven M Kornblau
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Wendy Stock
- Comprehensive Cancer Center, University of Chicago Medicine, Chicago, IL, USA
| | - Hiroto Inaba
- Hematological Malignancies Program, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Sima Jeha
- Hematological Malignancies Program, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Ching-Hon Pui
- Hematological Malignancies Program, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Cheng Cheng
- Department of Biostatistics, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Shondra M Pruett-Miller
- Center for Advanced Genome Engineering, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
- Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Mary V Relling
- Hematological Malignancies Program, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Jun J Yang
- Hematological Malignancies Program, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
- Graduate School of Biomedical Sciences, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
- Integrated Biomedical Sciences Program, University of Tennessee Health Science Center, Memphis, TN, 38163, USA
| | - William E Evans
- Hematological Malignancies Program, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Daniel Savic
- Hematological Malignancies Program, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA.
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA.
- Graduate School of Biomedical Sciences, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA.
- Integrated Biomedical Sciences Program, University of Tennessee Health Science Center, Memphis, TN, 38163, USA.
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227
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Qiu X, Zhang S, Zhang Y, Cai L, Li D, Lu Y. Reduction of ETV1 is Identified as a Prominent Feature of Age-Related Cataract. Curr Eye Res 2024; 49:496-504. [PMID: 38200696 DOI: 10.1080/02713683.2024.2302545] [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: 12/25/2022] [Accepted: 01/01/2024] [Indexed: 01/12/2024]
Abstract
PURPOSE To identify the inactive genes in cataract lenses and explore their function in lens epithelial cells (LECs). METHODS Lens epithelium samples obtained from both age-related cataract (ARC) patients and normal donors were subjected to two forms of histone H3 immunoprecipitation: H3K9ac and H3K27me3 chromatin immunoprecipitation (ChIP), followed by ChIP-seq. The intersection set of "active genes in normal controls" and "repressed genes in cataract lenses" was identified. To validate the role of a specific gene, ETV1, within this set, quantitative polymerase chain reaction (qPCR), western blot, and immunofluorescence were performed using clinical lens epithelium samples. Small interference RNA (siRNA) was utilized to reduce the mRNA level of ETV1 in cultured LECs. Following this, transwell assay and western blot was performed to examine the migration ability of the cells. Furthermore, RNA-seq analysis was conducted on both cell samples with ETV1 knockdown and control cells. Additionally, the expression level of ETV1 in LECs was examined using qPCR under H2O2 treatment. RESULTS Six genes were identified in the intersection set of "active genes in normal controls" and "repressed genes in ARC lenses". Among these genes, ETV1 showed the most significant fold-change decrease in the cataract samples compared to the control samples. After ETV1 knockdown by siRNA in cultured LECs, reduced cell migration was observed, along with a decrease in the expression of β-Catenin and Vimentin, two specific genes associated with cell migration. In addition, under the oxidative stress induced by H2O2 treatment, the expression level of ETV1 in LECs significantly decreased. CONCLUSIONS Based on the findings of this study, it can be concluded that ETV1 is significantly reduced in human ARC lenses. The repression of ETV1 in ARC lenses appears to contribute to the disrupted differentiation of lens epithelium, which is likely caused by the inhibition of both cell differentiation and migration processes.
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Affiliation(s)
- Xiaodi Qiu
- Eye Institute, Eye & ENT Hospital of Fudan University, Shanghai, China
- Shanghai Key Laboratory of Visual Impairment and Restoration, Shanghai, China
- NHC Key Laboratory of Myopia, Fudan University, Shanghai, China
- Laboratory of Myopia, Chinese Academy of Medical Sciences, Shanghai, China
| | - Shaohua Zhang
- Eye Institute, Eye & ENT Hospital of Fudan University, Shanghai, China
- Shanghai Key Laboratory of Visual Impairment and Restoration, Shanghai, China
- NHC Key Laboratory of Myopia, Fudan University, Shanghai, China
- Laboratory of Myopia, Chinese Academy of Medical Sciences, Shanghai, China
| | - Youmeng Zhang
- Department of Stomatology, Eye & ENT Hospital of Fudan University, Shanghai, China
| | - Lei Cai
- Eye Institute, Eye & ENT Hospital of Fudan University, Shanghai, China
- Shanghai Key Laboratory of Visual Impairment and Restoration, Shanghai, China
- NHC Key Laboratory of Myopia, Fudan University, Shanghai, China
- Laboratory of Myopia, Chinese Academy of Medical Sciences, Shanghai, China
| | - Dan Li
- Eye Institute, Eye & ENT Hospital of Fudan University, Shanghai, China
- Shanghai Key Laboratory of Visual Impairment and Restoration, Shanghai, China
- NHC Key Laboratory of Myopia, Fudan University, Shanghai, China
- Laboratory of Myopia, Chinese Academy of Medical Sciences, Shanghai, China
| | - Yi Lu
- Eye Institute, Eye & ENT Hospital of Fudan University, Shanghai, China
- Shanghai Key Laboratory of Visual Impairment and Restoration, Shanghai, China
- NHC Key Laboratory of Myopia, Fudan University, Shanghai, China
- Laboratory of Myopia, Chinese Academy of Medical Sciences, Shanghai, China
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228
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Sun H, Chang Z, Li H, Tang Y, Liu Y, Qiao L, Feng G, Huang R, Han D, Yin DT. Multi-omics analysis-based macrophage differentiation-associated papillary thyroid cancer patient classifier. Transl Oncol 2024; 43:101889. [PMID: 38382228 PMCID: PMC10900934 DOI: 10.1016/j.tranon.2024.101889] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 01/02/2024] [Accepted: 01/21/2024] [Indexed: 02/23/2024] Open
Abstract
BACKGROUND The reclassification of Papillary Thyroid Carcinoma (PTC) is an area of research that warrants attention. The connection between thyroid cancer, inflammation, and immune responses necessitates considering the mechanisms of differential prognosis of thyroid tumors from an immunological perspective. Given the high adaptability of macrophages to environmental stimuli, focusing on the differentiation characteristics of macrophages might offer a novel approach to address the issues related to PTC subtyping. METHODS Single-cell RNA sequencing data of medullary cells infiltrated by papillary thyroid carcinoma obtained from public databases was subjected to dimensionality reduction clustering analysis. The RunUMAP and FindAllMarkers functions were utilized to identify the gene expression matrix of different clusters. Cell differentiation trajectory analysis was conducted using the Monocle R package. A complex regulatory network for the classification of Immune status and Macrophage differentiation-associated Papillary Thyroid Cancer Classification (IMPTCC) was constructed through quantitative multi-omics analysis. Immunohistochemistry (IHC) staining was utilized for pathological histology validation. RESULTS Through the integration of single-cell RNA and bulk sequencing data combined with multi-omics analysis, we identified crucial transcription factors, immune cells/immune functions, and signaling pathways. Based on this, regulatory networks for three IMPTCC clusters were established. CONCLUSION Based on the co-expression network analysis results, we identified three subtypes of IMPTCC: Immune-Suppressive Macrophage differentiation-associated Papillary Thyroid Carcinoma Classification (ISMPTCC), Immune-Neutral Macrophage differentiation-associated Papillary Thyroid Carcinoma Classification (INMPTCC), and Immune-Activated Macrophage differentiation-associated Papillary Thyroid Carcinoma Classification (IAMPTCC). Each subtype exhibits distinct metabolic, immune, and regulatory characteristics corresponding to different states of macrophage differentiation.
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Affiliation(s)
- Hanlin Sun
- Department of Thyroid Surgery, the First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, Henan, PR China
| | - Zhengyan Chang
- Department of Pathology, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, PR China
| | - Hongqiang Li
- Department of Thyroid Surgery, the First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, Henan, PR China
| | - Yifeng Tang
- Department of Thyroid Surgery, the First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, Henan, PR China
| | - Yihao Liu
- Department of Thyroid Surgery, the First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, Henan, PR China
| | - Lixue Qiao
- Department of Thyroid Surgery, the First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, Henan, PR China
| | - Guicheng Feng
- Department of Thyroid Surgery, the First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, Henan, PR China
| | - Runzhi Huang
- Department of Burn Surgery, the First Affiliated Hospital of Naval Medical University, Shanghai 200433, PR China.
| | - Dongyan Han
- Department of Pathology, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, PR China.
| | - De-Tao Yin
- Department of Thyroid Surgery, the First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, Henan, PR China; Engineering Research Center of Multidisciplinary Diagnosis and Treatment of Thyroid Cancer of Henan Province, Zhengzhou 450052, Henan, PR China; Key Medicine Laboratory of Thyroid Cancer of Henan Province, Zhengzhou 450052, Henan, PR China.
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229
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Gamble N, Bradu A, Caldwell JA, McKeever J, Bolonduro O, Ermis E, Kaiser C, Kim Y, Parks B, Klemm S, Greenleaf WJ, Crabtree GR, Koh AS. PU.1 and BCL11B sequentially cooperate with RUNX1 to anchor mSWI/SNF to poise the T cell effector landscape. Nat Immunol 2024; 25:860-872. [PMID: 38632339 PMCID: PMC11089574 DOI: 10.1038/s41590-024-01807-y] [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: 06/27/2023] [Accepted: 03/11/2024] [Indexed: 04/19/2024]
Abstract
Adaptive immunity relies on specialized effector functions elicited by lymphocytes, yet how antigen recognition activates appropriate effector responses through nonspecific signaling intermediates is unclear. Here we examined the role of chromatin priming in specifying the functional outputs of effector T cells and found that most of the cis-regulatory landscape active in effector T cells was poised early in development before the expression of the T cell antigen receptor. We identified two principal mechanisms underpinning this poised landscape: the recruitment of the nucleosome remodeler mammalian SWItch/Sucrose Non-Fermentable (mSWI/SNF) by the transcription factors RUNX1 and PU.1 to establish chromatin accessibility at T effector loci; and a 'relay' whereby the transcription factor BCL11B succeeded PU.1 to maintain occupancy of the chromatin remodeling complex mSWI/SNF together with RUNX1, after PU.1 silencing during lineage commitment. These mechanisms define modes by which T cells acquire the potential to elicit specialized effector functions early in their ontogeny and underscore the importance of integrating extrinsic cues to the developmentally specified intrinsic program.
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Affiliation(s)
- Noah Gamble
- Department of Pathology, University of Chicago, Chicago, IL, USA
- Graduate Program in Biophysical Sciences, University of Chicago, Chicago, IL, USA
| | - Alexandra Bradu
- Department of Pathology, University of Chicago, Chicago, IL, USA
| | - Jason A Caldwell
- Department of Pathology, University of Chicago, Chicago, IL, USA
| | - Joshua McKeever
- Department of Pathology, University of Chicago, Chicago, IL, USA
- Committee on Molecular Metabolism and Nutrition, University of Chicago, Chicago, IL, USA
| | - Olubusayo Bolonduro
- Department of Pathology, University of Chicago, Chicago, IL, USA
- Committee on Genetics, Genomics, Systems Biology, University of Chicago, Chicago, IL, USA
| | - Ebru Ermis
- Department of Pathology, University of Chicago, Chicago, IL, USA
| | - Caroline Kaiser
- Department of Pathology, University of Chicago, Chicago, IL, USA
- Department of Human Genetics, University of Chicago, Chicago, IL, USA
| | - YeEun Kim
- Immunology Program, Stanford University, Stanford, CA, USA
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Benjamin Parks
- Department of Genetics, Stanford University, Stanford, CA, USA
- Department of Computer Science, Stanford University, Stanford, CA, USA
| | - Sandy Klemm
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - William J Greenleaf
- Department of Computer Science, Stanford University, Stanford, CA, USA
- Department of Applied Physics, Stanford University, Stanford, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Gerald R Crabtree
- Department of Pathology, Stanford University, Stanford, CA, USA
- Department of Developmental Biology, Stanford University, Stanford, CA, USA
| | - Andrew S Koh
- Department of Pathology, University of Chicago, Chicago, IL, USA.
- Institute for Biophysical Dynamics, University of Chicago, Chicago, IL, USA.
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230
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Moreno-Oñate M, Gallardo-Fuentes L, Martínez-García PM, Naranjo S, Jiménez-Gancedo S, Tena JJ, Santos-Pereira JM. Rewiring of the epigenome and chromatin architecture by exogenously induced retinoic acid signaling during zebrafish embryonic development. Nucleic Acids Res 2024; 52:3682-3701. [PMID: 38321954 PMCID: PMC11040003 DOI: 10.1093/nar/gkae065] [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: 06/27/2023] [Revised: 01/15/2024] [Accepted: 01/24/2024] [Indexed: 02/08/2024] Open
Abstract
Retinoic acid (RA) is the ligand of RA receptors (RARs), transcription factors that bind to RA response elements. RA signaling is required for multiple processes during embryonic development, including body axis extension, hindbrain antero-posterior patterning and forelimb bud initiation. Although some RA target genes have been identified, little is known about the genome-wide effects of RA signaling during in vivo embryonic development. Here, we stimulate the RA pathway by treating zebrafish embryos with all-trans-RA (atRA) and use a combination of RNA-seq, ATAC-seq, ChIP-seq and HiChIP to gain insight into the molecular mechanisms by which exogenously induced RA signaling controls gene expression. We find that RA signaling is involved in anterior/posterior patterning, central nervous system development, and the transition from pluripotency to differentiation. AtRA treatment also alters chromatin accessibility during early development and promotes chromatin binding of RARαa and the RA targets Hoxb1b, Meis2b and Sox3, which cooperate in central nervous system development. Finally, we show that exogenous RA induces a rewiring of chromatin architecture, with alterations in chromatin 3D interactions involving target genes. Altogether, our findings identify genome-wide targets of RA signaling and provide a molecular mechanism by which developmental signaling pathways regulate target gene expression by altering chromatin topology.
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Affiliation(s)
- Marta Moreno-Oñate
- Centro Andaluz de Biología del Desarrollo (CABD), Consejo Superior de Investigaciones Científicas/Universidad Pablo de Olavide, 41013 Sevilla, Spain
| | - Lourdes Gallardo-Fuentes
- Centro Andaluz de Biología del Desarrollo (CABD), Consejo Superior de Investigaciones Científicas/Universidad Pablo de Olavide, 41013 Sevilla, Spain
| | - Pedro M Martínez-García
- Centro Andaluz de Biología del Desarrollo (CABD), Consejo Superior de Investigaciones Científicas/Universidad Pablo de Olavide, 41013 Sevilla, Spain
| | - Silvia Naranjo
- Centro Andaluz de Biología del Desarrollo (CABD), Consejo Superior de Investigaciones Científicas/Universidad Pablo de Olavide, 41013 Sevilla, Spain
| | - Sandra Jiménez-Gancedo
- Centro Andaluz de Biología del Desarrollo (CABD), Consejo Superior de Investigaciones Científicas/Universidad Pablo de Olavide, 41013 Sevilla, Spain
| | - Juan J Tena
- Centro Andaluz de Biología del Desarrollo (CABD), Consejo Superior de Investigaciones Científicas/Universidad Pablo de Olavide, 41013 Sevilla, Spain
| | - José M Santos-Pereira
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, 41013 Sevilla, Spain
- Departamento de Biología Celular, Facultad de Biología, Universidad de Sevilla, 41012 Sevilla, Spain
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Saotome M, Poduval D, Grimm SA, Nagornyuk A, Gunarathna S, Shimbo T, Wade P, Takaku M. Genomic transcription factor binding site selection is edited by the chromatin remodeling factor CHD4. Nucleic Acids Res 2024; 52:3607-3622. [PMID: 38281186 PMCID: PMC11039999 DOI: 10.1093/nar/gkae025] [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: 05/27/2023] [Revised: 12/19/2023] [Accepted: 01/04/2024] [Indexed: 01/30/2024] Open
Abstract
Biologically precise enhancer licensing by lineage-determining transcription factors enables activation of transcripts appropriate to biological demand and prevents deleterious gene activation. This essential process is challenged by the millions of matches to most transcription factor binding motifs present in many eukaryotic genomes, leading to questions about how transcription factors achieve the exquisite specificity required. The importance of chromatin remodeling factors to enhancer activation is highlighted by their frequent mutation in developmental disorders and in cancer. Here, we determine the roles of CHD4 in enhancer licensing and maintenance in breast cancer cells and during cellular reprogramming. In unchallenged basal breast cancer cells, CHD4 modulates chromatin accessibility. Its depletion leads to redistribution of transcription factors to previously unoccupied sites. During cellular reprogramming induced by the pioneer factor GATA3, CHD4 activity is necessary to prevent inappropriate chromatin opening. Mechanistically, CHD4 promotes nucleosome positioning over GATA3 binding motifs to compete with transcription factor-DNA interaction. We propose that CHD4 acts as a chromatin proof-reading enzyme that prevents unnecessary gene expression by editing chromatin binding activities of transcription factors.
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Affiliation(s)
- Mika Saotome
- Department of Biomedical Sciences, University of North Dakota School of Medicine and Health Sciences, Grand Forks, ND 58202, USA
| | - Deepak B Poduval
- Department of Biomedical Sciences, University of North Dakota School of Medicine and Health Sciences, Grand Forks, ND 58202, USA
| | - Sara A Grimm
- Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
| | - Aerica Nagornyuk
- Department of Biomedical Sciences, University of North Dakota School of Medicine and Health Sciences, Grand Forks, ND 58202, USA
| | - Sakuntha Gunarathna
- Department of Biomedical Sciences, University of North Dakota School of Medicine and Health Sciences, Grand Forks, ND 58202, USA
| | - Takashi Shimbo
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
| | - Paul A Wade
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
| | - Motoki Takaku
- Department of Biomedical Sciences, University of North Dakota School of Medicine and Health Sciences, Grand Forks, ND 58202, USA
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Wang Y, Wang S, Meng Z, Liu XM, Mao Y. Determinant of m6A regional preference by transcriptional dynamics. Nucleic Acids Res 2024; 52:3510-3521. [PMID: 38452220 DOI: 10.1093/nar/gkae169] [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: 01/28/2023] [Revised: 02/21/2024] [Accepted: 02/27/2024] [Indexed: 03/09/2024] Open
Abstract
N6-Methyladenosine (m6A) is the most abundant chemical modification occurring on eukaryotic mRNAs, and has been reported to be involved in almost all stages of mRNA metabolism. The distribution of m6A sites is notably asymmetric along mRNAs, with a strong preference toward the 3' terminus of the transcript. How m6A regional preference is shaped remains incompletely understood. In this study, by performing m6A-seq on chromatin-associated RNAs, we found that m6A regional preference arises during transcription. Nucleosome occupancy is remarkedly increased in the region downstream of m6A sites, suggesting an intricate interplay between m6A methylation and nucleosome-mediated transcriptional dynamics. Notably, we found a remarkable slowdown of Pol-II movement around m6A sites. In addition, inhibiting Pol-II movement increases nearby m6A methylation levels. By analyzing massively parallel assays for m6A, we found that RNA secondary structures inhibit m6A methylation. Remarkably, the m6A sites associated with Pol-II pausing tend to be embedded within RNA secondary structures. These results suggest that Pol-II pausing could affect the accessibility of m6A motifs to the methyltransferase complex and subsequent m6A methylation by mediating RNA secondary structure. Overall, our study reveals a crucial role of transcriptional dynamics in the formation of m6A regional preference.
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Affiliation(s)
- Yalan Wang
- Department of Neurology of The Second Affiliated Hospital & Liangzhu Laboratory, Zhejiang University School of Medicine, Hangzhou, China
- Shanghai Key Laboratory of Metabolic Remodeling and Health, Institute of Metabolism and Integrative Biology, Institute of Reproduction and Development, Fudan University, Shanghai, China
| | - Shen Wang
- School of Life Science and Technology, China Pharmaceutical University, Nanjing, China
| | - Zhen Meng
- Department of Neurology of The Second Affiliated Hospital & Liangzhu Laboratory, Zhejiang University School of Medicine, Hangzhou, China
| | - Xiao-Min Liu
- School of Life Science and Technology, China Pharmaceutical University, Nanjing, China
| | - Yuanhui Mao
- Department of Neurology of The Second Affiliated Hospital & Liangzhu Laboratory, Zhejiang University School of Medicine, Hangzhou, China
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Zhu M, Han Y, Gu T, Wang R, Si X, Kong D, Zhao P, Wang X, Li J, Zhai X, Yu Z, Lu H, Li J, Huang H, Qian P. Class I HDAC inhibitors enhance antitumor efficacy and persistence of CAR-T cells by activation of the Wnt pathway. Cell Rep 2024; 43:114065. [PMID: 38578828 DOI: 10.1016/j.celrep.2024.114065] [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: 09/11/2023] [Revised: 01/18/2024] [Accepted: 03/21/2024] [Indexed: 04/07/2024] Open
Abstract
Epigenetic modification shapes differentiation trajectory and regulates the exhaustion state of chimeric antigen receptor T (CAR-T) cells. Limited efficacy induced by terminal exhaustion closely ties with intrinsic transcriptional regulation. However, the comprehensive regulatory mechanisms remain largely elusive. Here, we identify class I histone deacetylase inhibitors (HDACi) as boosters of CAR-T cell function by high-throughput screening of chromatin-modifying drugs, in which M344 and chidamide enhance memory maintenance and resistance to exhaustion of CAR-T cells that induce sustained antitumor efficacy both in vitro and in vivo. Mechanistically, HDACi decrease HDAC1 expression and enhance H3K27ac activity. Multi-omics analyses from RNA-seq, ATAC-seq, and H3K27ac CUT&Tag-seq show that HDACi upregulate expression of TCF4, LEF1, and CTNNB1, which subsequently activate the canonical Wnt/β-catenin pathway. Collectively, our findings elucidate the functional roles of class I HDACi in enhancing CAR-T cell function, which provides the basis and therapeutic targets for synergic combination of CAR-T cell therapy and HDACi treatment.
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Affiliation(s)
- Meng Zhu
- Center for Stem Cell and Regenerative Medicine and Bone Marrow Transplantation Center, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China; Liangzhu Laboratory, Zhejiang University, 1369 West Wenyi Road, Hangzhou 311121, China; Institute of Hematology, Zhejiang University & Zhejiang Province Engineering Laboratory for Stem Cell and Immunity Therapy, Hangzhou 310058, China
| | - Yingli Han
- Center for Stem Cell and Regenerative Medicine and Bone Marrow Transplantation Center, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China; Liangzhu Laboratory, Zhejiang University, 1369 West Wenyi Road, Hangzhou 311121, China; Institute of Hematology, Zhejiang University & Zhejiang Province Engineering Laboratory for Stem Cell and Immunity Therapy, Hangzhou 310058, China
| | - Tianning Gu
- Center for Stem Cell and Regenerative Medicine and Bone Marrow Transplantation Center, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China; Liangzhu Laboratory, Zhejiang University, 1369 West Wenyi Road, Hangzhou 311121, China; Institute of Hematology, Zhejiang University & Zhejiang Province Engineering Laboratory for Stem Cell and Immunity Therapy, Hangzhou 310058, China; Bone Marrow Transplantation Center, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Rui Wang
- Center for Stem Cell and Regenerative Medicine and Bone Marrow Transplantation Center, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China; Liangzhu Laboratory, Zhejiang University, 1369 West Wenyi Road, Hangzhou 311121, China; Institute of Hematology, Zhejiang University & Zhejiang Province Engineering Laboratory for Stem Cell and Immunity Therapy, Hangzhou 310058, China
| | - Xiaohui Si
- Center for Stem Cell and Regenerative Medicine and Bone Marrow Transplantation Center, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China; Liangzhu Laboratory, Zhejiang University, 1369 West Wenyi Road, Hangzhou 311121, China; Institute of Hematology, Zhejiang University & Zhejiang Province Engineering Laboratory for Stem Cell and Immunity Therapy, Hangzhou 310058, China; Bone Marrow Transplantation Center, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Delin Kong
- Center for Stem Cell and Regenerative Medicine and Bone Marrow Transplantation Center, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China; Liangzhu Laboratory, Zhejiang University, 1369 West Wenyi Road, Hangzhou 311121, China; Institute of Hematology, Zhejiang University & Zhejiang Province Engineering Laboratory for Stem Cell and Immunity Therapy, Hangzhou 310058, China; Bone Marrow Transplantation Center, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Peng Zhao
- Center for Stem Cell and Regenerative Medicine and Bone Marrow Transplantation Center, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China; Liangzhu Laboratory, Zhejiang University, 1369 West Wenyi Road, Hangzhou 311121, China; Institute of Hematology, Zhejiang University & Zhejiang Province Engineering Laboratory for Stem Cell and Immunity Therapy, Hangzhou 310058, China
| | - Xiujian Wang
- Center for Stem Cell and Regenerative Medicine and Bone Marrow Transplantation Center, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China; Liangzhu Laboratory, Zhejiang University, 1369 West Wenyi Road, Hangzhou 311121, China; Institute of Hematology, Zhejiang University & Zhejiang Province Engineering Laboratory for Stem Cell and Immunity Therapy, Hangzhou 310058, China; Bone Marrow Transplantation Center, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Jinxin Li
- Center for Stem Cell and Regenerative Medicine and Bone Marrow Transplantation Center, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China; Liangzhu Laboratory, Zhejiang University, 1369 West Wenyi Road, Hangzhou 311121, China; Institute of Hematology, Zhejiang University & Zhejiang Province Engineering Laboratory for Stem Cell and Immunity Therapy, Hangzhou 310058, China
| | - Xingyuan Zhai
- Center for Stem Cell and Regenerative Medicine and Bone Marrow Transplantation Center, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China; Liangzhu Laboratory, Zhejiang University, 1369 West Wenyi Road, Hangzhou 311121, China; Institute of Hematology, Zhejiang University & Zhejiang Province Engineering Laboratory for Stem Cell and Immunity Therapy, Hangzhou 310058, China; Bone Marrow Transplantation Center, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Zebin Yu
- Center for Stem Cell and Regenerative Medicine and Bone Marrow Transplantation Center, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China; Liangzhu Laboratory, Zhejiang University, 1369 West Wenyi Road, Hangzhou 311121, China; Institute of Hematology, Zhejiang University & Zhejiang Province Engineering Laboratory for Stem Cell and Immunity Therapy, Hangzhou 310058, China
| | - Huan Lu
- Center for Stem Cell and Regenerative Medicine and Bone Marrow Transplantation Center, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China; Liangzhu Laboratory, Zhejiang University, 1369 West Wenyi Road, Hangzhou 311121, China; Institute of Hematology, Zhejiang University & Zhejiang Province Engineering Laboratory for Stem Cell and Immunity Therapy, Hangzhou 310058, China
| | - Jingyi Li
- Center for Stem Cell and Regenerative Medicine and Bone Marrow Transplantation Center, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China; Liangzhu Laboratory, Zhejiang University, 1369 West Wenyi Road, Hangzhou 311121, China; Institute of Hematology, Zhejiang University & Zhejiang Province Engineering Laboratory for Stem Cell and Immunity Therapy, Hangzhou 310058, China
| | - He Huang
- Center for Stem Cell and Regenerative Medicine and Bone Marrow Transplantation Center, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China; Liangzhu Laboratory, Zhejiang University, 1369 West Wenyi Road, Hangzhou 311121, China; Institute of Hematology, Zhejiang University & Zhejiang Province Engineering Laboratory for Stem Cell and Immunity Therapy, Hangzhou 310058, China; Bone Marrow Transplantation Center, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.
| | - Pengxu Qian
- Center for Stem Cell and Regenerative Medicine and Bone Marrow Transplantation Center, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China; Liangzhu Laboratory, Zhejiang University, 1369 West Wenyi Road, Hangzhou 311121, China; Institute of Hematology, Zhejiang University & Zhejiang Province Engineering Laboratory for Stem Cell and Immunity Therapy, Hangzhou 310058, China.
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Kosicki M, Cintrón DL, Page NF, Georgakopoulos-Soares I, Akiyama JA, Plajzer-Frick I, Novak CS, Kato M, Hunter RD, von Maydell K, Barton S, Godfrey P, Beckman E, Sanders SJ, Pennacchio LA, Ahituv N. Massively parallel reporter assays and mouse transgenic assays provide complementary information about neuronal enhancer activity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.22.590634. [PMID: 38712228 PMCID: PMC11071441 DOI: 10.1101/2024.04.22.590634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
Genetic studies find hundreds of thousands of noncoding variants associated with psychiatric disorders. Massively parallel reporter assays (MPRAs) and in vivo transgenic mouse assays can be used to assay the impact of these variants. However, the relevance of MPRAs to in vivo function is unknown and transgenic assays suffer from low throughput. Here, we studied the utility of combining the two assays to study the impact of non-coding variants. We carried out an MPRA on over 50,000 sequences derived from enhancers validated in transgenic mouse assays and from multiple fetal neuronal ATAC-seq datasets. We also tested over 20,000 variants, including synthetic mutations in highly active neuronal enhancers and 177 common variants associated with psychiatric disorders. Variants with a high impact on MPRA activity were further tested in mice. We found a strong and specific correlation between MPRA and mouse neuronal enhancer activity including changes in neuronal enhancer activity in mouse embryos for variants with strong MPRA effects. Mouse assays also revealed pleiotropic variant effects that could not be observed in MPRA. Our work provides a large catalog of functional neuronal enhancers and variant effects and highlights the effectiveness of combining MPRAs and mouse transgenic assays.
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Affiliation(s)
- Michael Kosicki
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Dianne Laboy Cintrón
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA 94158, USA
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA 94158, USA
| | - Nicholas F. Page
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA 94158, USA
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA 94158, USA
- Department of Psychiatry and Behavioral Sciences, Kavli Institute for Fundamental Neuroscience, Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | - Ilias Georgakopoulos-Soares
- Institute for Personalized Medicine, Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA 17033, USA
| | - Jennifer A. Akiyama
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Ingrid Plajzer-Frick
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Catherine S. Novak
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Momoe Kato
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Riana D. Hunter
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Kianna von Maydell
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Sarah Barton
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Patrick Godfrey
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Erik Beckman
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Stephan J. Sanders
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA 94158, USA
- Department of Psychiatry and Behavioral Sciences, Kavli Institute for Fundamental Neuroscience, Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
- Institute of Developmental and Regenerative Medicine, Department of Paediatrics, University of Oxford, Oxford, OX3 16 7TY, UK
| | - Len A. Pennacchio
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Nadav Ahituv
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA 94158, USA
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA 94158, USA
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235
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Xu Q, Yang Z, Jia Y, Wang R, Zhang Q, Gai R, Wu Y, Yang Q, He G, Wu JH, Ming F. PeNAC67-PeKAN2-PeSCL23 and B-class MADS-box transcription factors synergistically regulate the specialization process from petal to lip in Phalaenopsis equestris. MOLECULAR HORTICULTURE 2024; 4:15. [PMID: 38649966 PMCID: PMC11036780 DOI: 10.1186/s43897-023-00079-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Accepted: 12/26/2023] [Indexed: 04/25/2024]
Abstract
The molecular basis of orchid flower development involves a specific regulatory program in which MADS-box transcription factors play a central role. The recent 'perianth code' model hypothesizes that two types of higher-order heterotetrameric complexes, namely SP complex and L complex, play pivotal roles in the orchid perianth organ formation. Therefore, we explored their roles and searched for other components of the regulatory network.Through the combined analysis for transposase-accessible chromatin with high-throughput sequencing and RNA sequencing of the lip-like petal and lip from Phalaenopsis equestris var.trilip, transcription factor-(TF) genes involved in lip development were revealed. PeNAC67 encoding a NAC-type TF and PeSCL23 encoding a GRAS-type TF were differentially expressed between the lip-like petal and the lip. PeNAC67 interacted with and stabilized PeMADS3, which positively regulated the development of lip-like petal to lip. PeSCL23 and PeNAC67 competitively bound with PeKAN2 and positively regulated the development of lip-like petal to petal by affecting the level of PeMADS3. PeKAN2 as an important TF that interacts with PeMADS3 and PeMADS9 can promote lip development. These results extend the 'perianth code' model and shed light on the complex regulation of orchid flower development.
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Affiliation(s)
- Qingyu Xu
- Development Centre of Plant Germplasm Resources, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Zhenyu Yang
- Development Centre of Plant Germplasm Resources, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Yupeng Jia
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, China
| | - Rui Wang
- Development Centre of Plant Germplasm Resources, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Qiyu Zhang
- Development Centre of Plant Germplasm Resources, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Ruonan Gai
- Development Centre of Plant Germplasm Resources, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Yiding Wu
- Development Centre of Plant Germplasm Resources, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Qingyong Yang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, China
| | - Guoren He
- Development Centre of Plant Germplasm Resources, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Ju Hua Wu
- Development Centre of Plant Germplasm Resources, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Feng Ming
- Development Centre of Plant Germplasm Resources, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China.
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China.
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236
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Harvey TN, Gillard GB, Røsæg LL, Grammes F, Monsen Ø, Vik JO, Hvidsten TR, Sandve SR. The genome regulatory landscape of Atlantic salmon liver through smoltification. PLoS One 2024; 19:e0302388. [PMID: 38648207 PMCID: PMC11034671 DOI: 10.1371/journal.pone.0302388] [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: 09/28/2023] [Accepted: 04/02/2024] [Indexed: 04/25/2024] Open
Abstract
The anadromous Atlantic salmon undergo a preparatory physiological transformation before seawater entry, referred to as smoltification. Key molecular developmental processes involved in this life stage transition, such as remodeling of gill functions, are known to be synchronized and modulated by environmental cues like photoperiod. However, little is known about the photoperiod influence and genome regulatory processes driving other canonical aspects of smoltification such as the large-scale changes in lipid metabolism and energy homeostasis in the developing smolt liver. Here we generate transcriptome, DNA methylation, and chromatin accessibility data from salmon livers across smoltification under different photoperiod regimes. We find a systematic reduction of expression levels of genes with a metabolic function, such as lipid metabolism, and increased expression of energy related genes such as oxidative phosphorylation, during smolt development in freshwater. However, in contrast to similar studies of the gill, smolt liver gene expression prior to seawater transfer was not impacted by photoperiodic history. Integrated analyses of gene expression, chromatin accessibility, and transcription factor (TF) binding signatures highlight chromatin remodeling and TF dynamics underlying smolt gene regulatory changes. Differential peak accessibility patterns largely matched differential gene expression patterns during smoltification and we infer that ZNF682, KLFs, and NFY TFs are important in driving a liver metabolic shift from synthesis to break down of organic compounds in freshwater. Overall, chromatin accessibility and TFBS occupancy were highly correlated to changes in gene expression. On the other hand, we identified numerous differential methylation patterns across the genome, but associated genes were not functionally enriched or correlated to observed gene expression changes across smolt development. Taken together, this work highlights the relative importance of chromatin remodeling during smoltification and demonstrates that metabolic remodeling occurs as a preadaptation to life at sea that is not to a large extent driven by photoperiod history.
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Affiliation(s)
- Thomas N. Harvey
- Centre for Integrative Genetics (CIGENE), Department of Animal and Aquacultural Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, Ås, Norway
| | - Gareth B. Gillard
- Centre for Integrative Genetics (CIGENE), Department of Animal and Aquacultural Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, Ås, Norway
| | - Line L. Røsæg
- Centre for Integrative Genetics (CIGENE), Department of Animal and Aquacultural Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, Ås, Norway
| | | | - Øystein Monsen
- Michael Sars Centre, University of Bergen, Bergen, Norway
| | - Jon Olav Vik
- Faculty of Chemistry, Biotechnology and Food Sciences, Norwegian University of Life Sciences, Ås, Norway
| | - Torgeir R. Hvidsten
- Faculty of Chemistry, Biotechnology and Food Sciences, Norwegian University of Life Sciences, Ås, Norway
| | - Simen R. Sandve
- Centre for Integrative Genetics (CIGENE), Department of Animal and Aquacultural Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, Ås, Norway
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237
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Hao T, Song Z, Zhang M, Zhang L. Signaling Transduction Pathways and G-Protein-Coupled Receptors in Different Stages of the Embryonic Diapause Termination Process in Artemia. Curr Issues Mol Biol 2024; 46:3676-3693. [PMID: 38666959 PMCID: PMC11049050 DOI: 10.3390/cimb46040229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2024] [Revised: 04/02/2024] [Accepted: 04/17/2024] [Indexed: 04/28/2024] Open
Abstract
Artemia is a widely distributed small aquatic crustacean, renowned for its ability to enter a state of embryonic diapause. The embryonic diapause termination (EDT) is closely linked to environmental cues, but the precise underlying mechanisms remain elusive. In this study, ATAC-seq and RNA-seq sequencing techniques were employed to explore the gene expression profiles in Artemia cysts 30 min after EDT. These profiles were compared with those during diapause and 5 h after EDT. The regulatory mechanisms governing the EDT process were analyzed through Gene Ontology (GO) enrichment analysis of differentially expressed genes. Furthermore, the active G-protein-coupled receptors (GPCRs) were identified through structural analysis. The results unveiled that the signaling transduction during EDT primarily hinges on GPCRs and the cell surface receptor signaling pathway, but distinct genes are involved across different stages. Hormone-mediated signaling pathways and the tachykinin receptor signaling pathway exhibited heightened activity in the '0-30 min' group, whereas the Wnt signaling pathway manifested its function solely in the '30 min-5 h' group. These results imply a complete divergence in the mechanisms of signal regulation during these two stages. Moreover, through structural analysis, five GPCRs operating at different stages of EDT were identified. These findings provide valuable insights into the signal regulation mechanisms governing Artemia diapause.
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Affiliation(s)
- Tong Hao
- Tianjin Key Laboratory of Animal and Plant Resistance, College of Life Sciences, Tianjin Normal University, Tianjin 300387, China; (Z.S.); (M.Z.); (L.Z.)
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238
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Wallis M, Xu Q, Krawczyk M, Skowronska-Krawczyk D. Evolution of the enhancer-rich regulatory region of the gene for the cell-type specific transcription factor POU1F1. Heliyon 2024; 10:e28640. [PMID: 38590853 PMCID: PMC10999999 DOI: 10.1016/j.heliyon.2024.e28640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2023] [Revised: 03/14/2024] [Accepted: 03/21/2024] [Indexed: 04/10/2024] Open
Abstract
Precise spatio-temporal expression of genes in organogenesis is regulated by the coordinated interplay of DNA elements such as promoter and enhancers present in the regulatory region of a given locus. POU1F1 transcription factor plays a crucial role in the development of somatotrophs, lactotrophs and thyrotrophs in the anterior pituitary gland, and in maintaining high expression of growth hormone, prolactin and TSH. In mouse, expression of POU1F1 is controlled by a region fenced by two CTCF sites, containing 5 upstream enhancer elements, designated E-A (5' to 3'). Elements C, B and A correspond to elements shown previously to play a role in pituitary development and hormonal expression; functional roles for elements E and D have not been reported. We performed comparative sequence analysis of this regulatory region and discovered that three elements, B, C and E, are present in all vertebrate groups except Agnatha. One very long (>2 kb) element (A) is unique to mammals suggesting a specific change in regulation of the gene in this group. Using DNA accessibility assay (ATAC-seq) we showed that conserved elements in anterior pituitary of four non-mammals are open, suggesting functionality as regulatory elements. We showed that, in many non-mammalian vertebrates, an additional upstream exon closely follows element E, leading to alternatively spliced transcripts. Here, element E functions as an alternative promoter, but in mammals this feature is lost, suggesting conversion of alternative promoter to enhancer. Our work shows that regulation of POU1F1 changed markedly during the course of vertebrate evolution, use of a low number of enhancer elements combined with alternative promoters in non-mammalian vertebrates being replaced by use of a unique combination of regulatory units in mammals. Most importantly, our work suggests that evolutionary conversion of alternate promoter to enhancer could be one of the evolutionary mechanisms of enhancer birth.
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Affiliation(s)
- Michael Wallis
- Department of Biochemistry and Biomedicine, School of Life Sciences, University of Sussex, Brighton BN1 9QG, UK
| | - Qianlan Xu
- Department of Physiology and Biophysics, Department of Ophthalmology, Center for Translational Vision Research, School of Medicine, University of California, Irvine, CA, USA
| | - Michal Krawczyk
- 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
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239
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Casey C, Fullard JF, Sleator RD. Unravelling the genetic basis of Schizophrenia. Gene 2024; 902:148198. [PMID: 38266791 DOI: 10.1016/j.gene.2024.148198] [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: 09/01/2023] [Revised: 12/07/2023] [Accepted: 01/19/2024] [Indexed: 01/26/2024]
Abstract
Neuronal development is a highly regulated mechanism that is central to organismal function in animals. In humans, disruptions to this process can lead to a range of neurodevelopmental phenotypes, including Schizophrenia (SCZ). SCZ has a significant genetic component, whereby an individual with an SCZ affected family member is eight times more likely to develop the disease than someone with no family history of SCZ. By examining a combination of genomic, transcriptomic and epigenomic datasets, large-scale 'omics' studies aim to delineate the relationship between genetic variation and abnormal cellular activity in the SCZ brain. Herein, we provide a brief overview of some of the key omics methods currently being used in SCZ research, including RNA-seq, the assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-seq) and high-throughput chromosome conformation capture (3C) approaches (e.g., Hi-C), as well as single-cell/nuclei iterations of these methods. We also discuss how these techniques are being employed to further our understanding of the genetic basis of SCZ, and to identify associated molecular pathways, biomarkers, and candidate drug targets.
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Affiliation(s)
- Clara Casey
- Department of Biological Sciences, Munster Technological University, Bishopstown, Cork, Ireland; Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, United States; Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, United States; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, United States
| | - John F Fullard
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, United States; Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, United States; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, United States
| | - Roy D Sleator
- Department of Biological Sciences, Munster Technological University, Bishopstown, Cork, Ireland.
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240
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Yuan Q, Duren Z. Inferring gene regulatory networks from single-cell multiome data using atlas-scale external data. Nat Biotechnol 2024:10.1038/s41587-024-02182-7. [PMID: 38609714 DOI: 10.1038/s41587-024-02182-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 02/26/2024] [Indexed: 04/14/2024]
Abstract
Existing methods for gene regulatory network (GRN) inference rely on gene expression data alone or on lower resolution bulk data. Despite the recent integration of chromatin accessibility and RNA sequencing data, learning complex mechanisms from limited independent data points still presents a daunting challenge. Here we present LINGER (Lifelong neural network for gene regulation), a machine-learning method to infer GRNs from single-cell paired gene expression and chromatin accessibility data. LINGER incorporates atlas-scale external bulk data across diverse cellular contexts and prior knowledge of transcription factor motifs as a manifold regularization. LINGER achieves a fourfold to sevenfold relative increase in accuracy over existing methods and reveals a complex regulatory landscape of genome-wide association studies, enabling enhanced interpretation of disease-associated variants and genes. Following the GRN inference from reference single-cell multiome data, LINGER enables the estimation of transcription factor activity solely from bulk or single-cell gene expression data, leveraging the abundance of available gene expression data to identify driver regulators from case-control studies.
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Affiliation(s)
- Qiuyue Yuan
- Center for Human Genetics, Department of Genetics and Biochemistry, Clemson University, Greenwood, SC, USA
| | - Zhana Duren
- Center for Human Genetics, Department of Genetics and Biochemistry, Clemson University, Greenwood, SC, USA.
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241
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Mononen J, Taipale M, Malinen M, Velidendla B, Niskanen E, Levonen AL, Ruotsalainen AK, Heikkinen S. Genetic variation is a key determinant of chromatin accessibility and drives differences in the regulatory landscape of C57BL/6J and 129S1/SvImJ mice. Nucleic Acids Res 2024; 52:2904-2923. [PMID: 38153160 PMCID: PMC11014276 DOI: 10.1093/nar/gkad1225] [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: 05/23/2022] [Revised: 11/09/2023] [Accepted: 12/12/2023] [Indexed: 12/29/2023] Open
Abstract
Most common genetic variants associated with disease are located in non-coding regions of the genome. One mechanism by which they function is through altering transcription factor (TF) binding. In this study, we explore how genetic variation is connected to differences in the regulatory landscape of livers from C57BL/6J and 129S1/SvImJ mice fed either chow or a high-fat diet. To identify sites where regulatory variation affects TF binding and nearby gene expression, we employed an integrative analysis of H3K27ac ChIP-seq (active enhancers), ATAC-seq (chromatin accessibility) and RNA-seq (gene expression). We show that, across all these assays, the genetically driven (i.e. strain-specific) differences in the regulatory landscape are more pronounced than those modified by diet. Most notably, our analysis revealed that differentially accessible regions (DARs, N = 29635, FDR < 0.01 and fold change > 50%) are almost always strain-specific and enriched with genetic variation. Moreover, proximal DARs are highly correlated with differentially expressed genes. We also show that TF binding is affected by genetic variation, which we validate experimentally using ChIP-seq for TCF7L2 and CTCF. This study provides detailed insights into how non-coding genetic variation alters the gene regulatory landscape, and demonstrates how this can be used to study the regulatory variation influencing TF binding.
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Affiliation(s)
- Juho Mononen
- Institute of Biomedicine, Faculty of Health Sciences, University of Eastern Finland, Kuopio FI-70211, Finland
| | - Mari Taipale
- A.I. Virtanen Institute, Faculty of Health Sciences, University of Eastern Finland, Kuopio FI-70211, Finland
| | - Marjo Malinen
- Department of Environmental and Biological Sciences, Faculty of Science and Forestry, University of Eastern Finland, Joensuu FI- 80101, Finland
- Department of Forestry and Environmental Engineering, South-Eastern Finland University of Applied Sciences, Kouvola FI-45100, Finland
| | - Bharadwaja Velidendla
- Institute of Biomedicine, Faculty of Health Sciences, University of Eastern Finland, Kuopio FI-70211, Finland
| | - Einari Niskanen
- Institute of Biomedicine, Faculty of Health Sciences, University of Eastern Finland, Kuopio FI-70211, Finland
| | - Anna-Liisa Levonen
- A.I. Virtanen Institute, Faculty of Health Sciences, University of Eastern Finland, Kuopio FI-70211, Finland
| | - Anna-Kaisa Ruotsalainen
- A.I. Virtanen Institute, Faculty of Health Sciences, University of Eastern Finland, Kuopio FI-70211, Finland
| | - Sami Heikkinen
- Institute of Biomedicine, Faculty of Health Sciences, University of Eastern Finland, Kuopio FI-70211, Finland
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242
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Zhang X, Marand AP, Yan H, Schmitz RJ. scifi-ATAC-seq: massive-scale single-cell chromatin accessibility sequencing using combinatorial fluidic indexing. Genome Biol 2024; 25:90. [PMID: 38589969 PMCID: PMC11003106 DOI: 10.1186/s13059-024-03235-5] [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: 09/28/2023] [Accepted: 04/01/2024] [Indexed: 04/10/2024] Open
Abstract
Single-cell ATAC-seq has emerged as a powerful approach for revealing candidate cis-regulatory elements genome-wide at cell-type resolution. However, current single-cell methods suffer from limited throughput and high costs. Here, we present a novel technique called scifi-ATAC-seq, single-cell combinatorial fluidic indexing ATAC-sequencing, which combines a barcoded Tn5 pre-indexing step with droplet-based single-cell ATAC-seq using the 10X Genomics platform. With scifi-ATAC-seq, up to 200,000 nuclei across multiple samples can be indexed in a single emulsion reaction, representing an approximately 20-fold increase in throughput compared to the standard 10X Genomics workflow.
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Affiliation(s)
- Xuan Zhang
- Department of Genetics, University of Georgia, Athens, GA, USA
| | - Alexandre P Marand
- Department of Genetics, University of Georgia, Athens, GA, USA
- Current address: Department of Molecular, Cellular, and Development Biology, University of Michigan, Ann Arbor, MI, USA
| | - Haidong Yan
- Department of Genetics, University of Georgia, Athens, GA, USA
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243
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Peng QY, An Y, Jiang ZZ, Xu Y. The Role of Immune Cells in DKD: Mechanisms and Targeted Therapies. J Inflamm Res 2024; 17:2103-2118. [PMID: 38601771 PMCID: PMC11005934 DOI: 10.2147/jir.s457526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Accepted: 03/19/2024] [Indexed: 04/12/2024] Open
Abstract
Diabetic kidney disease (DKD), is a common microvascular complication and a major cause of death in patients with diabetes. Disorders of immune cells and immune cytokines can accelerate DKD development of in a number of ways. As the kidney is composed of complex and highly differentiated cells, the interactions among different cell types and immune cells play important regulatory roles in disease development. Here, we summarize the latest research into the molecular mechanisms underlying the interactions among various immune and renal cells in DKD. In addition, we discuss the most recent studies related to single cell technology and bioinformatics analysis in the field of DKD. The aims of our review were to explore immune cells as potential therapeutic targets in DKD and provide some guidance for future clinical treatments.
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Affiliation(s)
- Qiu-Yue Peng
- Department of Endocrinology and Metabolism, the Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, People’s Republic of China
- Metabolic Vascular Disease Key Laboratory of Sichuan Province, Sichuan, People’s Republic of China
- Sichuan Clinical Research Center for Nephropathy, Luzhou, Sichuan, People’s Republic of China
| | - Ying An
- Department of Endocrinology and Metabolism, the Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, People’s Republic of China
- Metabolic Vascular Disease Key Laboratory of Sichuan Province, Sichuan, People’s Republic of China
- Sichuan Clinical Research Center for Nephropathy, Luzhou, Sichuan, People’s Republic of China
| | - Zong-Zhe Jiang
- Department of Endocrinology and Metabolism, the Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, People’s Republic of China
- Metabolic Vascular Disease Key Laboratory of Sichuan Province, Sichuan, People’s Republic of China
- Sichuan Clinical Research Center for Nephropathy, Luzhou, Sichuan, People’s Republic of China
| | - Yong Xu
- Department of Endocrinology and Metabolism, the Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, People’s Republic of China
- Metabolic Vascular Disease Key Laboratory of Sichuan Province, Sichuan, People’s Republic of China
- Sichuan Clinical Research Center for Nephropathy, Luzhou, Sichuan, People’s Republic of China
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244
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Bister J, Filipovic I, Sun D, Crona-Guterstam Y, Cornillet M, Ponzetta A, Michaëlsson J, Gidlöf S, Ivarsson MA, Strunz B, Björkström NK. Tissue-specific nonheritable influences drive endometrial immune system variation. Sci Immunol 2024; 9:eadj7168. [PMID: 38579017 DOI: 10.1126/sciimmunol.adj7168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 03/11/2024] [Indexed: 04/07/2024]
Abstract
Although human twin studies have revealed the combined contribution of heritable and environmental factors in shaping immune system variability in blood, the contribution of these factors to immune system variability in tissues remains unexplored. The human uterus undergoes constant regeneration and is exposed to distinct environmental factors. To assess uterine immune system variation, we performed a system-level analysis of endometrial and peripheral blood immune cells in monozygotic twins. Although most immune cell phenotypes in peripheral blood showed high genetic heritability, more variation was found in endometrial immune cells, indicating a stronger influence by environmental factors. Cytomegalovirus infection was identified to influence peripheral blood immune cell variability but had limited effect on endometrial immune cells. Instead, hormonal contraception shaped the local endometrial milieu and immune cell composition with minor influence on the systemic immune system. These results highlight that the magnitude of human immune system variation and factors influencing it can be tissue specific.
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Affiliation(s)
- Jonna Bister
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Iva Filipovic
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Dan Sun
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Ylva Crona-Guterstam
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
- Division of Obstetrics and Gynecology, Department of Clinical Science, Intervention and Technology, Karolinska Institutet, Stockholm, Sweden
- Department of Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden
| | - Martin Cornillet
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Andrea Ponzetta
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Jakob Michaëlsson
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Sebastian Gidlöf
- Division of Obstetrics and Gynecology, Department of Clinical Science, Intervention and Technology, Karolinska Institutet, Stockholm, Sweden
- Department of Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden
- Department of Gynecology and Reproductive Medicine, Karolinska University Hospital, Stockholm, Sweden
| | - Martin A Ivarsson
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Benedikt Strunz
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Niklas K Björkström
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
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245
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Holkom M, Yang X, Li R, Chen Y, Zhao H, Shang Z. Fibroblast regulates angiogenesis in assembled oral cancer organoid: A possible role of NNMT. Oral Dis 2024. [PMID: 38566601 DOI: 10.1111/odi.14945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 12/27/2023] [Accepted: 03/20/2024] [Indexed: 04/04/2024]
Abstract
OBJECTIVE Tumour angiogenesis is affected by various cell types in the tumour microenvironment (TME), including cancer cells and cancer-associated fibroblasts (CAFs). Here, an assembled organoid model was generated to investigate the mechanism by which the TME regulates angiogenesis in oral squamous cell carcinoma (OSCC). MATERIALS AND METHODS Secretion of vascular endothelial growth factor-A (VEGFA) was analysed to compare the proangiogenic properties of OSCC cells and corresponding CAFs. Cell aggregates consisting of endothelial cells (ECs), CAFs and cancer cells were generated to construct assembled organoids. Nicotinamide N-methyltransferase (NNMT) was pharmacologically or genetically inhibited to block the activation of CAFs. ATAC-seq was employed to test the transcriptional network of fibroblasts overexpressing NNMT. RESULTS Compared with cancer cells, CAFs secreted more VEGFA. Coculture with CAFs more effectively promoted the sprouting of ECs. Blockade of CAF activation via inhibition of NNMT drastically reduced the expression of CD31 in the assembled organoids. Overexpression of NNMT enhanced the transcription of genes related to angiogenesis in fibroblasts. Specifically, NNMT orchestrated the enrichment of the transcription factor JUNB at the promoter of VEGFA. CONCLUSIONS We clarify that stromal NNMT enables the steady reproduction of angiogenesis in assembled oral cancer organoids, providing a novel target for exploiting antiangiogenic therapy.
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Affiliation(s)
- Mohammed Holkom
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, Key Laboratory of Oral Biomedicine Ministry of Education, Hubei Key Laboratory of Stomatology, School & Hospital of Stomatology, Wuhan University, Wuhan, China
| | - Xiao Yang
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, Key Laboratory of Oral Biomedicine Ministry of Education, Hubei Key Laboratory of Stomatology, School & Hospital of Stomatology, Wuhan University, Wuhan, China
| | - Rui Li
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, Key Laboratory of Oral Biomedicine Ministry of Education, Hubei Key Laboratory of Stomatology, School & Hospital of Stomatology, Wuhan University, Wuhan, China
| | - Yang Chen
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, Key Laboratory of Oral Biomedicine Ministry of Education, Hubei Key Laboratory of Stomatology, School & Hospital of Stomatology, Wuhan University, Wuhan, China
| | - Hui Zhao
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, Key Laboratory of Oral Biomedicine Ministry of Education, Hubei Key Laboratory of Stomatology, School & Hospital of Stomatology, Wuhan University, Wuhan, China
- Department of Oral and Maxillofacial-Head and Neck Oncology, School of Stomatology-Hospital of Stomatology, Wuhan University, Wuhan, China
| | - Zhengjun Shang
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, Key Laboratory of Oral Biomedicine Ministry of Education, Hubei Key Laboratory of Stomatology, School & Hospital of Stomatology, Wuhan University, Wuhan, China
- Department of Oral and Maxillofacial-Head and Neck Oncology, School of Stomatology-Hospital of Stomatology, Wuhan University, Wuhan, China
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246
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Nava AA, Arboleda VA. The omics era: a nexus of untapped potential for Mendelian chromatinopathies. Hum Genet 2024; 143:475-495. [PMID: 37115317 PMCID: PMC11078811 DOI: 10.1007/s00439-023-02560-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2022] [Accepted: 04/10/2023] [Indexed: 04/29/2023]
Abstract
The OMICs cascade describes the hierarchical flow of information through biological systems. The epigenome sits at the apex of the cascade, thereby regulating the RNA and protein expression of the human genome and governs cellular identity and function. Genes that regulate the epigenome, termed epigenes, orchestrate complex biological signaling programs that drive human development. The broad expression patterns of epigenes during human development mean that pathogenic germline mutations in epigenes can lead to clinically significant multi-system malformations, developmental delay, intellectual disabilities, and stem cell dysfunction. In this review, we refer to germline developmental disorders caused by epigene mutation as "chromatinopathies". We curated the largest number of human chromatinopathies to date and our expanded approach more than doubled the number of established chromatinopathies to 179 disorders caused by 148 epigenes. Our study revealed that 20.6% (148/720) of epigenes cause at least one chromatinopathy. In this review, we highlight key examples in which OMICs approaches have been applied to chromatinopathy patient biospecimens to identify underlying disease pathogenesis. The rapidly evolving OMICs technologies that couple molecular biology with high-throughput sequencing or proteomics allow us to dissect out the causal mechanisms driving temporal-, cellular-, and tissue-specific expression. Using the full repertoire of data generated by the OMICs cascade to study chromatinopathies will provide invaluable insight into the developmental impact of these epigenes and point toward future precision targets for these rare disorders.
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Affiliation(s)
- Aileen A Nava
- Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
- Department of Pathology & Laboratory Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
- Department of Computational Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
- Broad Stem Cell Research Center, University of California, Los Angeles, CA, USA
| | - Valerie A Arboleda
- Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA.
- Department of Pathology & Laboratory Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA.
- Department of Computational Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA.
- Broad Stem Cell Research Center, University of California, Los Angeles, CA, USA.
- Molecular Biology Institute, University of California, Los Angeles, CA, USA.
- Jonsson Comprehensive Cancer Center, University of California, Los Angeles, CA, USA.
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247
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Jin K, McCoy BM, Goldman EA, Usova V, Tkachev V, Chitsazan AD, Kakebeen A, Jeffery U, Creevy KE, Wills A, Snyder‐Mackler N, Promislow DEL. DNA methylation and chromatin accessibility predict age in the domestic dog. Aging Cell 2024; 23:e14079. [PMID: 38263575 PMCID: PMC11019125 DOI: 10.1111/acel.14079] [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: 11/10/2021] [Revised: 12/11/2023] [Accepted: 12/12/2023] [Indexed: 01/25/2024] Open
Abstract
Across mammals, the epigenome is highly predictive of chronological age. These "epigenetic clocks," most of which have been built using DNA methylation (DNAm) profiles, have gained traction as biomarkers of aging and organismal health. While the ability of DNAm to predict chronological age has been repeatedly demonstrated, the ability of other epigenetic features to predict age remains unclear. Here, we use two types of epigenetic information-DNAm, and chromatin accessibility as measured by ATAC-seq-to develop age predictors in peripheral blood mononuclear cells sampled from a population of domesticated dogs. We measured DNAm and ATAC-seq profiles for 71 dogs, building separate predictive clocks from each, as well as the combined dataset. We also use fluorescence-assisted cell sorting to quantify major lymphoid populations for each sample. We found that chromatin accessibility can accurately predict chronological age (R2 ATAC = 26%), though less accurately than the DNAm clock (R2 DNAm = 33%), and the clock built from the combined datasets was comparable to both (R2 combined = 29%). We also observed various populations of CD62L+ T cells significantly correlated with dog age. Finally, we found that all three clocks selected features that were in or near at least two protein-coding genes: BAIAP2 and SCARF2, both previously implicated in processes related to cognitive or neurological impairment. Taken together, these results highlight the potential of chromatin accessibility as a complementary epigenetic resource for modeling and investigating biologic age.
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Affiliation(s)
- Kelly Jin
- Department of Laboratory Medicine & PathologyUniversity of WashingtonSeattleWashingtonUSA
| | - Brianah M. McCoy
- Center for Evolution and MedicineArizona State UniversityTempeArizonaUSA
- School of Life SciencesArizona State UniversityTempeArizonaUSA
| | | | - Viktoria Usova
- Department of Laboratory Medicine & PathologyUniversity of WashingtonSeattleWashingtonUSA
| | - Victor Tkachev
- Division of Pediatric Hematology/OncologyBoston Children's HospitalBostonMassachusettsUSA
- Dana Farber Cancer InstituteBostonMassachusettsUSA
- Harvard Medical SchoolBostonMassachusettsUSA
| | - Alex D. Chitsazan
- Department of BiochemistryUniversity of WashingtonSeattleWashingtonUSA
| | - Anneke Kakebeen
- Department of BiochemistryUniversity of WashingtonSeattleWashingtonUSA
| | - Unity Jeffery
- College of Veterinary MedicineTexas A & M UniversityCollege StationTexasUSA
| | - Kate E. Creevy
- College of Veterinary MedicineTexas A & M UniversityCollege StationTexasUSA
| | - Andrea Wills
- Department of BiochemistryUniversity of WashingtonSeattleWashingtonUSA
| | - Noah Snyder‐Mackler
- Center for Evolution and MedicineArizona State UniversityTempeArizonaUSA
- School of Life SciencesArizona State UniversityTempeArizonaUSA
| | - Daniel E. L. Promislow
- Department of Laboratory Medicine & PathologyUniversity of WashingtonSeattleWashingtonUSA
- Department of BiologyUniversity of WashingtonSeattleWashingtonUSA
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248
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Li NN, Lun DX, Gong N, Meng G, Du XY, Wang H, Bao X, Li XY, Song JW, Hu K, Li L, Li SY, Liu W, Zhu W, Zhang Y, Li J, Yao T, Mou L, Han X, Hao F, Hu Y, Liu L, Zhu H, Wu Y, Liu B. Targeting the chromatin structural changes of antitumor immunity. J Pharm Anal 2024; 14:100905. [PMID: 38665224 PMCID: PMC11043877 DOI: 10.1016/j.jpha.2023.11.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 09/28/2023] [Accepted: 11/21/2023] [Indexed: 04/28/2024] Open
Abstract
Epigenomic imbalance drives abnormal transcriptional processes, promoting the onset and progression of cancer. Although defective gene regulation generally affects carcinogenesis and tumor suppression networks, tumor immunogenicity and immune cells involved in antitumor responses may also be affected by epigenomic changes, which may have significant implications for the development and application of epigenetic therapy, cancer immunotherapy, and their combinations. Herein, we focus on the impact of epigenetic regulation on tumor immune cell function and the role of key abnormal epigenetic processes, DNA methylation, histone post-translational modification, and chromatin structure in tumor immunogenicity, and introduce these epigenetic research methods. We emphasize the value of small-molecule inhibitors of epigenetic modulators in enhancing antitumor immune responses and discuss the challenges of developing treatment plans that combine epigenetic therapy and immunotherapy through the complex interaction between cancer epigenetics and cancer immunology.
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Affiliation(s)
- Nian-nian Li
- Weifang People's Hospital, Weifang, Shandong, 261000, China
- School of Life Sciences, Nankai University, Tianjin, 300071, China
| | - Deng-xing Lun
- Weifang People's Hospital, Weifang, Shandong, 261000, China
| | - Ningning Gong
- Weifang Traditional Chinese Medicine Hospital, Weifang, Shandong, 261000, China
| | - Gang Meng
- Shaanxi Key Laboratory of Sericulture, Ankang University, Ankang, Shaanxi, 725000, China
| | - Xin-ying Du
- Weifang People's Hospital, Weifang, Shandong, 261000, China
| | - He Wang
- Weifang People's Hospital, Weifang, Shandong, 261000, China
| | - Xiangxiang Bao
- Weifang People's Hospital, Weifang, Shandong, 261000, China
| | - Xin-yang Li
- Guizhou Education University, Guiyang, 550018, China
| | - Ji-wu Song
- Weifang People's Hospital, Weifang, Shandong, 261000, China
| | - Kewei Hu
- Weifang Traditional Chinese Medicine Hospital, Weifang, Shandong, 261000, China
| | - Lala Li
- Guizhou Normal University, Guiyang, 550025, China
| | - Si-ying Li
- Weifang People's Hospital, Weifang, Shandong, 261000, China
| | - Wenbo Liu
- Weifang People's Hospital, Weifang, Shandong, 261000, China
| | - Wanping Zhu
- Weifang People's Hospital, Weifang, Shandong, 261000, China
| | - Yunlong Zhang
- School of Medical Imaging, Weifang Medical University, Weifang, Shandong, 261053, China
| | - Jikai Li
- Department of Bone and Soft Tissue Oncology, Tianjin Hospital, Tianjin, 300299, China
| | - Ting Yao
- School of Life Sciences, Nankai University, Tianjin, 300071, China
- Teda Institute of Biological Sciences & Biotechnology, Nankai University, Tianjin, 300457, China
| | - Leming Mou
- Weifang People's Hospital, Weifang, Shandong, 261000, China
| | - Xiaoqing Han
- Weifang People's Hospital, Weifang, Shandong, 261000, China
| | - Furong Hao
- Weifang People's Hospital, Weifang, Shandong, 261000, China
| | - Yongcheng Hu
- Weifang People's Hospital, Weifang, Shandong, 261000, China
| | - Lin Liu
- School of Life Sciences, Nankai University, Tianjin, 300071, China
| | - Hongguang Zhu
- Weifang People's Hospital, Weifang, Shandong, 261000, China
| | - Yuyun Wu
- Xinqiao Hospital of Army Military Medical University, Chongqing, 400038, China
| | - Bin Liu
- Weifang People's Hospital, Weifang, Shandong, 261000, China
- School of Life Sciences, Nankai University, Tianjin, 300071, China
- Teda Institute of Biological Sciences & Biotechnology, Nankai University, Tianjin, 300457, China
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249
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Ren L, Huang D, Liu H, Ning L, Cai P, Yu X, Zhang Y, Luo N, Lin H, Su J, Zhang Y. Applications of single‑cell omics and spatial transcriptomics technologies in gastric cancer (Review). Oncol Lett 2024; 27:152. [PMID: 38406595 PMCID: PMC10885005 DOI: 10.3892/ol.2024.14285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Accepted: 01/19/2024] [Indexed: 02/27/2024] Open
Abstract
Gastric cancer (GC) is a prominent contributor to global cancer-related mortalities, and a deeper understanding of its molecular characteristics and tumor heterogeneity is required. Single-cell omics and spatial transcriptomics (ST) technologies have revolutionized cancer research by enabling the exploration of cellular heterogeneity and molecular landscapes at the single-cell level. In the present review, an overview of the advancements in single-cell omics and ST technologies and their applications in GC research is provided. Firstly, multiple single-cell omics and ST methods are discussed, highlighting their ability to offer unique insights into gene expression, genetic alterations, epigenomic modifications, protein expression patterns and cellular location in tissues. Furthermore, a summary is provided of key findings from previous research on single-cell omics and ST methods used in GC, which have provided valuable insights into genetic alterations, tumor diagnosis and prognosis, tumor microenvironment analysis, and treatment response. In summary, the application of single-cell omics and ST technologies has revealed the levels of cellular heterogeneity and the molecular characteristics of GC, and holds promise for improving diagnostics, personalized treatments and patient outcomes in GC.
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Affiliation(s)
- Liping Ren
- School of Healthcare Technology, Chengdu Neusoft University, Chengdu, Sichuan 611844, P.R. China
| | - Danni Huang
- Department of Radiology, Central South University Xiangya School of Medicine Affiliated Haikou People's Hospital, Haikou, Hainan 570208, P.R. China
| | - Hongjiang Liu
- School of Computer Science and Technology, Aba Teachers College, Aba, Sichuan 624099, P.R. China
| | - Lin Ning
- School of Healthcare Technology, Chengdu Neusoft University, Chengdu, Sichuan 611844, P.R. China
| | - Peiling Cai
- School of Basic Medical Sciences, Chengdu University, Chengdu, Sichuan 610106, P.R. China
| | - Xiaolong Yu
- Hainan Yazhou Bay Seed Laboratory, Sanya Nanfan Research Institute, Material Science and Engineering Institute of Hainan University, Sanya, Hainan 572025, P.R. China
| | - Yang Zhang
- Innovative Institute of Chinese Medicine and Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan 611137, P.R. China
| | - Nanchao Luo
- School of Computer Science and Technology, Aba Teachers College, Aba, Sichuan 624099, P.R. China
| | - Hao Lin
- Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, Sichuan 611731, P.R. China
| | - Jinsong Su
- Research Institute of Integrated Traditional Chinese Medicine and Western Medicine, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan 611137, P.R. China
| | - Yinghui Zhang
- School of Healthcare Technology, Chengdu Neusoft University, Chengdu, Sichuan 611844, P.R. China
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250
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Chan S, Wang Y, Luo Y, Zheng M, Xie F, Xue M, Yang X, Xue P, Zha C, Fang M. Differential Regulation of Male-Hormones-Related Enhancers Revealed by Chromatin Accessibility and Transcriptional Profiles in Pig Liver. Biomolecules 2024; 14:427. [PMID: 38672444 PMCID: PMC11048672 DOI: 10.3390/biom14040427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Revised: 03/22/2024] [Accepted: 03/25/2024] [Indexed: 04/28/2024] Open
Abstract
Surgical castration can effectively avoid boar taint and improve pork quality by removing the synthesis of androstenone in the testis, thereby reducing its deposition in adipose tissue. The expression of genes involved in testis-derived hormone metabolism was altered following surgical castration, but the upstream regulatory factors and underlying mechanism remain unclear. In this study, we systematically profiled chromatin accessibility and transcriptional dynamics in liver tissue of castrated and intact full-sibling Yorkshire pigs. First, we identified 897 differentially expressed genes and 6864 differential accessible regions (DARs) using RNA- and ATAC-seq. By integrating the RNA- and ATAC-seq results, 227 genes were identified, and a significant positive correlation was revealed between differential gene expression and the ATAC-seq signal. We constructed a transcription factor regulatory network after motif analysis of DARs and identified a candidate transcription factor (TF) SP1 that targeted the HSD3B1 gene, which was responsible for the metabolism of androstenone. Subsequently, we annotated DARs by incorporating H3K27ac ChIP-seq data, marking 2234 typical enhancers and 245 super enhancers involved in the regulation of all testis-derived hormones. Among these, four typical enhancers associated with HSD3B1 were identified. Furthermore, an in-depth investigation was conducted on the androstenone-related enhancers, and an androstenone-related mutation was identified in a newfound candidatetypical enhancer (andEN) with dual-luciferase assays. These findings provide further insights into how enhancers function as links between phenotypic and non-coding area variations. The discovery of upstream TF and enhancers of HSD3B1 contributes to understanding the regulatory networks of androstenone metabolism and provides an important foundation for improving pork quality.
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Affiliation(s)
- Shuheng Chan
- Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, MOA Key Laboratory of Animal Genetics and Breeding, Beijing Key Laboratory for Animal Genetic Improvement, State Key Laboratory of Animal Biotech Breeding, Frontiers Science Center for Molecular Design Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China; (S.C.); (Y.L.); (P.X.)
| | - Yubei Wang
- Sanya Institute of China Agricultural University, Sanya 572025, China
| | - Yabiao Luo
- Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, MOA Key Laboratory of Animal Genetics and Breeding, Beijing Key Laboratory for Animal Genetic Improvement, State Key Laboratory of Animal Biotech Breeding, Frontiers Science Center for Molecular Design Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China; (S.C.); (Y.L.); (P.X.)
| | - Meili Zheng
- Beijing General Station of Animal Husbandry, Beijing 100107, China
| | - Fuyin Xie
- Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, MOA Key Laboratory of Animal Genetics and Breeding, Beijing Key Laboratory for Animal Genetic Improvement, State Key Laboratory of Animal Biotech Breeding, Frontiers Science Center for Molecular Design Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China; (S.C.); (Y.L.); (P.X.)
| | - Mingming Xue
- Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, MOA Key Laboratory of Animal Genetics and Breeding, Beijing Key Laboratory for Animal Genetic Improvement, State Key Laboratory of Animal Biotech Breeding, Frontiers Science Center for Molecular Design Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China; (S.C.); (Y.L.); (P.X.)
| | - Xiaoyang Yang
- Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, MOA Key Laboratory of Animal Genetics and Breeding, Beijing Key Laboratory for Animal Genetic Improvement, State Key Laboratory of Animal Biotech Breeding, Frontiers Science Center for Molecular Design Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China; (S.C.); (Y.L.); (P.X.)
| | - Pengxiang Xue
- Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, MOA Key Laboratory of Animal Genetics and Breeding, Beijing Key Laboratory for Animal Genetic Improvement, State Key Laboratory of Animal Biotech Breeding, Frontiers Science Center for Molecular Design Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China; (S.C.); (Y.L.); (P.X.)
| | - Chengwan Zha
- Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, MOA Key Laboratory of Animal Genetics and Breeding, Beijing Key Laboratory for Animal Genetic Improvement, State Key Laboratory of Animal Biotech Breeding, Frontiers Science Center for Molecular Design Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China; (S.C.); (Y.L.); (P.X.)
| | - Meiying Fang
- Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, MOA Key Laboratory of Animal Genetics and Breeding, Beijing Key Laboratory for Animal Genetic Improvement, State Key Laboratory of Animal Biotech Breeding, Frontiers Science Center for Molecular Design Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China; (S.C.); (Y.L.); (P.X.)
- Sanya Institute of China Agricultural University, Sanya 572025, China
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