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Bi Z, Zhou J, Ma Y, Guo Q, Ju B, Zou H, Zhan Z, Yang F, Du H, Gan X, Song E. Integrative analysis and risk model construction for super‑enhancer‑related immune genes in clear cell renal cell carcinoma. Oncol Lett 2024; 27:190. [PMID: 38495834 PMCID: PMC10941079 DOI: 10.3892/ol.2024.14323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 02/09/2024] [Indexed: 03/19/2024] Open
Abstract
Clear cell renal cell carcinoma (ccRCC) is the most common type of kidney cancer associated with poor prognosis, and accounts for the majority of RCC-related deaths. The lack of comprehensive diagnostic and prognostic biomarkers has limited further understanding of the pathophysiology of ccRCC. Super-enhancers (SEs) are congregated enhancer clusters that have a key role in tumor processes such as epithelial-mesenchymal transition, metabolic reprogramming, immune escape and resistance to apoptosis. RCC may also be immunogenic and sensitive to immunotherapy. In the present study, an Arraystar human SE-long non-coding RNA (lncRNA) microarray was first employed to profile the differentially expressed SE-lncRNAs and mRNAs in 5 paired ccRCC and peritumoral tissues and to identify SE-related genes. The overlap of these genes with immune genes was then determined to identify SE-related immune genes. A model for predicting clinical prognosis and response to immunotherapy was built following the comprehensive analysis of a ccRCC gene expression dataset from The Cancer Genome Atlas (TCGA) database. The patients from TCGA were divided into high- and low-risk groups based on the median score derived from the risk model, and the Kaplan-Meier survival analysis showed that the low-risk group had a higher survival probability. In addition, according to the receiver operating characteristic curve analysis, the risk model had more advantages than other clinical factors in predicting the overall survival (OS) rate of patients with ccRCC. Using this model, it was demonstrated that the high-risk group had a more robust immune response. Furthermore, 61 potential drugs with half-maximal inhibitory concentration values that differed significantly between the two patient groups were screened to investigate potential drug treatment of ccRCC. In summary, the present study provided a novel index for predicting the survival probability of patients with ccRCC and may provide some insights into the mechanisms through which SE-related immune genes influence the diagnosis, prognosis and potential treatment drugs of ccRCC.
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Affiliation(s)
- Zhenyu Bi
- Department of Urology, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang 150000, P.R. China
| | - Jinghao Zhou
- Department of Oncology, The Second Affiliated Hospital of Shandong First Medical University, Taian, Shandong 271000, P.R. China
| | - Yan Ma
- Department of Urology, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang 150000, P.R. China
| | - Qingxin Guo
- Department of Urology, Hongqi Hospital Affiliated to Mudanjiang Medical College, Mudanjiang, Heilongjiang 157009, P.R. China
| | - Boyang Ju
- Department of Urology, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang 150000, P.R. China
| | - Haoran Zou
- Department of Urology, Zhumadian Central Hospital, Zhumadian, Henan 463000, P.R. China
| | - Zuhao Zhan
- Department of Urology, The First Hospital of Zibo, Zibo, Shandong 255200, P.R. China
| | - Feihong Yang
- Department of Urology, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang 150000, P.R. China
| | - Han Du
- Department of Urology, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang 150000, P.R. China
| | - Xiuguo Gan
- Department of Urology, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang 150000, P.R. China
| | - Erlin Song
- Department of Urology, Affiliated Hospital of Guilin Medical University, Guilin, Guangxi Zhuang Autonomous Region 541001, P.R. China
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Lavaud M, Tesfaye R, Lassous L, Brounais B, Baud'huin M, Verrecchia F, Lamoureux F, Georges S, Ory B. Super-enhancers: drivers of cells' identities and cells' debacles. Epigenomics 2024. [PMID: 38587919 DOI: 10.2217/epi-2023-0409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/10/2024] Open
Abstract
Precise spatiotemporal regulations of gene expression are essential for determining cells' fates and functions. Enhancers are cis-acting DNA elements that act as periodic transcriptional thrusters and their activities are cell type specific. Clusters of enhancers, called super-enhancers, are more densely occupied by transcriptional activators than enhancers, driving stronger expression of their target genes, which have prominent roles in establishing and maintaining cellular identities. Here we review the current knowledge on the composition and structure of super-enhancers to understand how they robustly stimulate the expression of cellular identity genes. We also review their involvement in the development of various cell types and both noncancerous and cancerous disorders, implying the therapeutic interest of targeting them to fight against various diseases.
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Affiliation(s)
- Mélanie Lavaud
- CRCI2NA, INSERM UMR 1307, CNRS UMR 6075, Nantes University & Angers University, Medical School, Nantes, 44035, France
| | - Robel Tesfaye
- CRCI2NA, INSERM UMR 1307, CNRS UMR 6075, Nantes University & Angers University, Medical School, Nantes, 44035, France
- Cancéropôle Grand-Ouest, Réseau Épigénétique, Medical School, Nantes, 44035, France
- EpiSAVMEN, Epigenetic consortium Pays de la Loire, France
| | - Léa Lassous
- CRCI2NA, INSERM UMR 1307, CNRS UMR 6075, Nantes University & Angers University, Medical School, Nantes, 44035, France
| | - Bénédicte Brounais
- CRCI2NA, INSERM UMR 1307, CNRS UMR 6075, Nantes University & Angers University, Medical School, Nantes, 44035, France
| | - Marc Baud'huin
- CRCI2NA, INSERM UMR 1307, CNRS UMR 6075, Nantes University & Angers University, Medical School, Nantes, 44035, France
| | - Franck Verrecchia
- CRCI2NA, INSERM UMR 1307, CNRS UMR 6075, Nantes University & Angers University, Medical School, Nantes, 44035, France
| | - François Lamoureux
- CRCI2NA, INSERM UMR 1307, CNRS UMR 6075, Nantes University & Angers University, Medical School, Nantes, 44035, France
| | - Steven Georges
- CRCI2NA, INSERM UMR 1307, CNRS UMR 6075, Nantes University & Angers University, Medical School, Nantes, 44035, France
| | - Benjamin Ory
- CRCI2NA, INSERM UMR 1307, CNRS UMR 6075, Nantes University & Angers University, Medical School, Nantes, 44035, France
- Cancéropôle Grand-Ouest, Réseau Épigénétique, Medical School, Nantes, 44035, France
- EpiSAVMEN, Epigenetic consortium Pays de la Loire, France
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Kim M, Wang P, Clow PA, Chien I(E, Wang X, Peng J, Chai H, Liu X, Lee B, Ngan CY, Yue F, Milenkovic O, Chuang JH, Wei CL, Casellas R, Cheng AW, Ruan Y. Multifaceted roles of cohesin in regulating transcriptional loops. bioRxiv 2024:2024.03.25.586715. [PMID: 38585764 PMCID: PMC10996690 DOI: 10.1101/2024.03.25.586715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
Cohesin is required for chromatin loop formation. However, its precise role in regulating gene transcription remains largely unknown. We investigated the relationship between cohesin and RNA Polymerase II (RNAPII) using single-molecule mapping and live-cell imaging methods in human cells. Cohesin-mediated transcriptional loops were highly correlated with those of RNAPII and followed the direction of gene transcription. Depleting RAD21, a subunit of cohesin, resulted in the loss of long-range (>100 kb) loops between distal (super-)enhancers and promoters of cell-type-specific genes. By contrast, the short-range (<50 kb) loops were insensitive to RAD21 depletion and connected genes that are mostly housekeeping. This result explains why only a small fraction of genes are affected by the loss of long-range chromatin interactions due to cohesin depletion. Remarkably, RAD21 depletion appeared to up-regulate genes located in early initiation zones (EIZ) of DNA replication, and the EIZ signals were amplified drastically without RAD21. Our results revealed new mechanistic insights of cohesin's multifaceted roles in establishing transcriptional loops, preserving long-range chromatin interactions for cell-specific genes, and maintaining timely order of DNA replication.
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Affiliation(s)
- Minji Kim
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, USA
- Present address: Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, 48109, USA
- Equal contributions
| | - Ping Wang
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, USA
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Evanston, IL, 60201, USA
- Equal contributions
| | - Patricia A. Clow
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, USA
- Equal contributions
| | - I (Eli) Chien
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61820, USA
| | - Xiaotao Wang
- Obstetrics and Gynecology Hospital, Institute of Reproduction and Development, Fudan University, Shanghai, China
- Shanghai Key Laboratory of Reproduction and Development, Shanghai, China
| | - Jianhao Peng
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61820, USA
| | - Haoxi Chai
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, USA
| | - Xiyuan Liu
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, USA
- State Key Laboratory of Ophthalmology, Optometry and Vision Science, Eye hospital and School of Ophthalmology and Optometry, Wenzhou Medical University, Wenzhou, Zhejiang, 325027, P.R. China
| | - Byoungkoo Lee
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, USA
| | - Chew Yee Ngan
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, USA
| | - Feng Yue
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Evanston, IL, 60201, USA
- Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
| | - Olgica Milenkovic
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61820, USA
| | - Jeffrey H. Chuang
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, USA
- Department of Genetics and Genome Sciences, UConn Health, Farmington, CT, 06030, USA
| | - Chia-Lin Wei
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, USA
| | - Rafael Casellas
- Hematopoietic Biology and Malignancy, MD Anderson Cancer Center, Houston, TX, 77054, USA
| | - Albert W. Cheng
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, USA
- School of Biological and Health Systems Engineering, Arizona State University, Tempe, AZ, 85281, USA
| | - Yijun Ruan
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, USA
- Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang Province, 310058, P.R. China
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Blayney JW, Francis H, Rampasekova A, Camellato B, Mitchell L, Stolper R, Cornell L, Babbs C, Boeke JD, Higgs DR, Kassouf M. Super-enhancers include classical enhancers and facilitators to fully activate gene expression. Cell 2023; 186:5826-5839.e18. [PMID: 38101409 PMCID: PMC10858684 DOI: 10.1016/j.cell.2023.11.030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 07/06/2023] [Accepted: 11/27/2023] [Indexed: 12/17/2023]
Abstract
Super-enhancers are compound regulatory elements that control expression of key cell identity genes. They recruit high levels of tissue-specific transcription factors and co-activators such as the Mediator complex and contact target gene promoters with high frequency. Most super-enhancers contain multiple constituent regulatory elements, but it is unclear whether these elements have distinct roles in activating target gene expression. Here, by rebuilding the endogenous multipartite α-globin super-enhancer, we show that it contains bioinformatically equivalent but functionally distinct element types: classical enhancers and facilitator elements. Facilitators have no intrinsic enhancer activity, yet in their absence, classical enhancers are unable to fully upregulate their target genes. Without facilitators, classical enhancers exhibit reduced Mediator recruitment, enhancer RNA transcription, and enhancer-promoter interactions. Facilitators are interchangeable but display functional hierarchy based on their position within a multipartite enhancer. Facilitators thus play an important role in potentiating the activity of classical enhancers and ensuring robust activation of target genes.
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Affiliation(s)
- Joseph W Blayney
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Headington, Oxford OX3 9DS, UK
| | - Helena Francis
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Headington, Oxford OX3 9DS, UK
| | - Alexandra Rampasekova
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Headington, Oxford OX3 9DS, UK
| | - Brendan Camellato
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY 10016, USA
| | - Leslie Mitchell
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY 10016, USA
| | - Rosa Stolper
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Headington, Oxford OX3 9DS, UK
| | - Lucy Cornell
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Headington, Oxford OX3 9DS, UK
| | - Christian Babbs
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Headington, Oxford OX3 9DS, UK
| | - Jef D Boeke
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY 10016, USA; Department of Biomedical Engineering, NYU Tandon School of Engineering, Brooklyn, NY 11201, USA.
| | - Douglas R Higgs
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Headington, Oxford OX3 9DS, UK; Chinese Academy of Medical Sciences Oxford Institute, Oxford OX3 7BN, UK.
| | - Mira Kassouf
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Headington, Oxford OX3 9DS, UK.
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Abstract
Transcription Factor (TF) condensates are a heterogenous mix of RNA, DNA, and multiple co-factor proteins capable of modulating the transcriptional response of the cell. The dynamic nature and the spatial location of TF-condensates in the 3D nuclear space is believed to provide a fast response, which is on the same pace as the signaling cascade and yet ever-so-specific in the crowded environment of the nucleus. However, the current understanding of how TF-condensates can achieve these feet so quickly and efficiently is still unclear. In this review, we draw parallels with other protein condensates and share our speculations on how the nucleus uses these TF-condensates to achieve high transcriptional specificity and fidelity. We discuss the various constituents of TF-condensates, their properties, and the known and unknown functions of TF-condensates with a particular focus on steroid signaling-induced transcriptional programs.
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Affiliation(s)
- Rajat Mann
- National Centre for Biological Sciences, TIFR, Bangalore, India
| | - Dimple Notani
- National Centre for Biological Sciences, TIFR, Bangalore, India
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Yang Y, Li X, Meng Z, Liu Y, Qian K, Chu M, Pan Z. A body map of super-enhancers and their function in pig. Front Vet Sci 2023; 10:1239965. [PMID: 37869495 PMCID: PMC10587440 DOI: 10.3389/fvets.2023.1239965] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 09/26/2023] [Indexed: 10/24/2023] Open
Abstract
Introduction Super-enhancers (SEs) are clusters of enhancers that act synergistically to drive the high-level expression of genes involved in cell identity and function. Although SEs have been extensively investigated in humans and mice, they have not been well characterized in pigs. Methods Here, we identified 42,380 SEs in 14 pig tissues using chromatin immunoprecipitation sequencing, and statistics of its overall situation, studied the composition and characteristics of SE, and explored the influence of SEs characteristics on gene expression. Results We observed that approximately 40% of normal enhancers (NEs) form SEs. Compared to NEs, we found that SEs were more likely to be enriched with an activated enhancer and show activated functions. Interestingly, SEs showed X chromosome depletion and short interspersed nuclear element enrichment, implying that SEs play an important role in sex traits and repeat evolution. Additionally, SE-associated genes exhibited higher expression levels and stronger conservation than NE-associated genes. However, genes with the largest SEs had higher expression levels than those with the smallest SEs, indicating that SE size may influence gene expression. Moreover, we observed a negative correlation between SE gene distance and gene expression, indicating that the proximity of SEs can affect gene activity. Gene ontology enrichment and motif analysis revealed that SEs have strong tissue-specific activity. For example, the CORO2B gene with a brain-specific SE shows strong brain-specific expression, and the phenylalanine hydroxylase gene with liver-specific SEs shows strong liver-specific expression. Discussion In this study, we illustrated a body map of SEs and explored their functions in pigs, providing information on the composition and tissue-specific patterns of SEs. This study can serve as a valuable resource of gene regulatory and comparative analyses to the scientific community and provides a theoretical reference for genetic control mechanisms of important traits in pigs.
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Affiliation(s)
- Youbing Yang
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang, China
| | - Xinyue Li
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang, China
- Key Laboratory of Animal Genetics and Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zhu Meng
- Key Laboratory of Animal Genetics and Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yongjian Liu
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang, China
| | - Kaifeng Qian
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang, China
| | - Mingxing Chu
- Key Laboratory of Animal Genetics and Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zhangyuan Pan
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang, China
- Key Laboratory of Animal Genetics and Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
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Nayak S, Jiang K, Hope E, Cross M, Overmiller A, Naz F, Worrell S, Bajpai D, Hasneen K, Brooks SR, Dell'Orso S, Morasso MI. Chromatin Landscape Governing Murine Epidermal Differentiation. J Invest Dermatol 2023; 143:1220-1232.e9. [PMID: 36708949 PMCID: PMC10293054 DOI: 10.1016/j.jid.2022.12.020] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 11/16/2022] [Accepted: 12/12/2022] [Indexed: 01/27/2023]
Abstract
Chromatin landscape and regulatory networks are determinants in lineage specification and differentiation. To define the temporospatial differentiation axis in murine epidermal cells in vivo, we generated datasets profiling expression dynamics (RNA sequencing), chromatin accessibility (assay for transposase-accessible chromatin using sequencing), architecture (Hi-C), and histone modifications (chromatin immunoprecipitation followed by sequencing) in the epidermis. We show that many differentially regulated genes are suppressed during the differentiation process, with superenhancers controlling differentiation-specific epigenomic changes. Our data shows the relevance of the Dlx/Klf/Grhl combinatorial regulatory network in maintaining correct temporospatial gene expression during epidermal differentiation. We determined differential open compartments, topologically associating domain score, and looping in the basal cell and suprabasal cell epidermal fractions, with the evolutionarily conserved epidermal differentiation complex region showing distinct suprabasal cell-specific topologically associating domain and loop formation that coincided with superenhancer sites. Overall, our study provides a global genome-wide resource of chromatin dynamics that define unrecognized regulatory networks and the epigenetic control of Dlx3-bound superenhancer elements during epidermal differentiation.
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Affiliation(s)
- Subhashree Nayak
- Laboratory of Skin Biology, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Kan Jiang
- Biodata Mining and Discovery Section, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Emma Hope
- Laboratory of Skin Biology, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Michael Cross
- Laboratory of Skin Biology, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Andrew Overmiller
- Laboratory of Skin Biology, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Faiza Naz
- Genomic Technology Section, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Stephen Worrell
- Laboratory of Skin Biology, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Deepti Bajpai
- Laboratory of Skin Biology, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Kowser Hasneen
- Laboratory of Skin Biology, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Stephen R Brooks
- Biodata Mining and Discovery Section, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Stefania Dell'Orso
- Genomic Technology Section, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Maria I Morasso
- Laboratory of Skin Biology, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, Maryland, USA.
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Deforzh E, Kharel P, Karelin A, Ivanov P, Krichevsky AM. HOXDeRNA activates a cancerous transcription program and super-enhancers genome-wide. bioRxiv 2023:2023.06.30.547275. [PMID: 37425921 PMCID: PMC10327164 DOI: 10.1101/2023.06.30.547275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
Background The origin and genesis of highly malignant and heterogenous glioblastoma brain tumors remain unknown. We previously identified an enhancer-associated long non-coding RNA, LINC01116 (named HOXDeRNA here), that is absent in the normal brain but is commonly expressed in malignant glioma. HOXDeRNA has a unique capacity to transform human astrocytes into glioma-like cells. This work aimed to investigate molecular events underlying the genome-wide function of this lncRNA in glial cell fate and transformation. Results Using a combination of RNA-Seq, ChIRP-Seq, and ChIP-Seq, we now demonstrate that HOXDeRNA binds in trans to the promoters of genes encoding 44 glioma-specific transcription factors distributed throughout the genome and derepresses them by removing the Polycomb repressive complex 2 (PRC2). Among the activated transcription factors are the core neurodevelopmental regulators SOX2, OLIG2, POU3F2, and SALL2. This process requires an RNA quadruplex structure of HOXDeRNA that interacts with EZH2. Moreover, HOXDeRNA-induced astrocyte transformation is accompanied by the activation of multiple oncogenes such as EGFR, PDGFR, BRAF, and miR-21, and glioma-specific super-enhancers enriched for binding sites of glioma master transcription factors SOX2 and OLIG2. Conclusions Our results demonstrate that HOXDeRNA overrides PRC2 repression of glioma core regulatory circuitry with RNA quadruplex structure. These findings help reconstruct the sequence of events underlying the process of astrocyte transformation and suggest a driving role for HOXDeRNA and a unifying RNA-dependent mechanism of gliomagenesis.
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Affiliation(s)
- Evgeny Deforzh
- Department of Neurology, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Prakash Kharel
- Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Anton Karelin
- Department of Neurology, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Pavel Ivanov
- Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Anna M. Krichevsky
- Department of Neurology, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115, USA
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9
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Hong D, Lin H, Liu L, Shu M, Dai J, Lu F, Tong M, Huang J. Complexity of enhancer networks predicts cell identity and disease genes revealed by single-cell multi-omics analysis. Brief Bioinform 2023; 24:6868525. [PMID: 36464486 DOI: 10.1093/bib/bbac508] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 10/21/2022] [Accepted: 10/24/2022] [Indexed: 12/09/2022] Open
Abstract
Many enhancers exist as clusters in the genome and control cell identity and disease genes; however, the underlying mechanism remains largely unknown. Here, we introduce an algorithm, eNet, to build enhancer networks by integrating single-cell chromatin accessibility and gene expression profiles. The complexity of enhancer networks is assessed by two metrics: the number of enhancers and the frequency of predicted enhancer interactions (PEIs) based on chromatin co-accessibility. We apply eNet algorithm to a human blood dataset and find cell identity and disease genes tend to be regulated by complex enhancer networks. The network hub enhancers (enhancers with frequent PEIs) are the most functionally important. Compared with super-enhancers, enhancer networks show better performance in predicting cell identity and disease genes. eNet is robust and widely applicable in various human or mouse tissues datasets. Thus, we propose a model of enhancer networks containing three modes: Simple, Multiple and Complex, which are distinguished by their complexity in regulating gene expression. Taken together, our work provides an unsupervised approach to simultaneously identify key cell identity and disease genes and explore the underlying regulatory relationships among enhancers in single cells.
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Affiliation(s)
- Danni Hong
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, Fujian 361102, China
| | - Hongli Lin
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, Fujian 361102, China
| | - Lifang Liu
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, Fujian 361102, China
| | - Muya Shu
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Jianwu Dai
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Falong Lu
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Mengsha Tong
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, Fujian 361102, China.,National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, Fujian 361102, China
| | - Jialiang Huang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, Fujian 361102, China.,National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, Fujian 361102, China
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10
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Zhang Y, Zhang J, Wang C, Dai H, Du X, Li Q, Pan Z. The super-enhancer repertoire in porcine liver. J Anim Sci 2023; 101:skad056. [PMID: 36800318 PMCID: PMC10024791 DOI: 10.1093/jas/skad056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Accepted: 02/16/2023] [Indexed: 02/18/2023] Open
Abstract
The transcriptional initiation of genes is inextricably bound with the functions of cis-regulatory sequences. The pig is one of the most important livestock species and an ideal animal model for biomedical studies. At the same time, the liver is a critical organ with diverse and complex metabolic functions. Here, we performed Cleavage Under Targets and Tagmentation (CUT&Tag) coupled with high-throughput sequencing to profile the chromatin landscape of histone H3 lysine 27 acetylation (H3K27ac), histone H3 lysine 4 monomethylation (H3K4me1), and CCAAT enhancer-binding protein β (C-EBPβ) in the 70-d-old porcine liver, compared the different profiles among the three markers and their associated stitched-enhancers by stitching and sorting the peaks within 12.5 kb (Pott and Lieb, 2015) and generated the porcine liver-specific super-enhancers (SEs) by the combination of three markers. Compared to typical enhancers (TEs) and other stitched-enhancers, liver-specific SEs showed a higher density of cis-motifs and SNPs, which may recruit more tissue-specific vital TFs. The expression profiles in fetal and 70-d-old pigs proved that a large proportion of SE-associated genes were up-regulated and were more related to hepatic metabolisms and detoxification pathways. Our results illustrated the difference and connection among promoter and enhancer markers, identified the features of liver SEs and their associated genes, and provided novel insight into cis-element identification, function, and liver transcriptional regulation.
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Affiliation(s)
- Yi Zhang
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Jinbi Zhang
- College of Animal Science and Technology, Jinling Institute of Technology, Nanjing 211169, China
| | - Caixia Wang
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Hongjian Dai
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Xing Du
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Qifa Li
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Zengxiang Pan
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
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11
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Bae S, Kim K, Kang K, Kim H, Lee M, Oh B, Kaneko K, Ma S, Choi JH, Kwak H, Lee EY, Park SH, Park-Min KH. RANKL-responsive epigenetic mechanism reprograms macrophages into bone-resorbing osteoclasts. Cell Mol Immunol 2023; 20:94-109. [PMID: 36513810 PMCID: PMC9794822 DOI: 10.1038/s41423-022-00959-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Accepted: 11/03/2022] [Indexed: 12/15/2022] Open
Abstract
Monocyte/macrophage lineage cells are highly plastic and can differentiate into various cells under different environmental stimuli. Bone-resorbing osteoclasts are derived from the monocyte/macrophage lineage in response to receptor activator of NF-κB ligand (RANKL). However, the epigenetic signature contributing to the fate commitment of monocyte/macrophage lineage differentiation into human osteoclasts is largely unknown. In this study, we identified RANKL-responsive human osteoclast-specific superenhancers (SEs) and SE-associated enhancer RNAs (SE-eRNAs) by integrating data obtained from ChIP-seq, ATAC-seq, nuclear RNA-seq and PRO-seq analyses. RANKL induced the formation of 200 SEs, which are large clusters of enhancers, while suppressing 148 SEs in macrophages. RANKL-responsive SEs were strongly correlated with genes in the osteoclastogenic program and were selectively increased in human osteoclasts but marginally presented in osteoblasts, CD4+ T cells, and CD34+ cells. In addition to the major transcription factors identified in osteoclasts, we found that BATF binding motifs were highly enriched in RANKL-responsive SEs. The depletion of BATF1/3 inhibited RANKL-induced osteoclast differentiation. Furthermore, we found increased chromatin accessibility in SE regions, where RNA polymerase II was significantly recruited to induce the extragenic transcription of SE-eRNAs, in human osteoclasts. Knocking down SE-eRNAs in the vicinity of the NFATc1 gene diminished the expression of NFATc1, a major regulator of osteoclasts, and osteoclast differentiation. Inhibiting BET proteins suppressed the formation of some RANKL-responsive SEs and NFATc1-associated SEs, and the expression of SE-eRNA:NFATc1. Moreover, SE-eRNA:NFATc1 was highly expressed in the synovial macrophages of rheumatoid arthritis patients exhibiting high-osteoclastogenic potential. Our genome-wide analysis revealed RANKL-inducible SEs and SE-eRNAs as osteoclast-specific signatures, which may contribute to the development of osteoclast-specific therapeutic interventions.
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Affiliation(s)
- Seyeon Bae
- Arthritis and Tissue Degeneration Program, David Z. Rosensweig Genomics Research Center, Hospital for Special Surgery, New York, NY, 10021, USA
- Department of Medicine, Weill Cornell Medical College, New York, NY, 10065, USA
| | - Kibyeong Kim
- Department of Biological Science, Ulsan National Institute of Science & Technology (UNIST), Ulsan, 44919, Republic of Korea
- Department of Life Science, College of Natural Sciences, Research Institute for Natural Sciences, Hanyang University, Seoul, Korea
| | - Keunsoo Kang
- Department of Microbiology, Dankook University, Cheonan, 3116, Republic of Korea
| | - Haemin Kim
- Arthritis and Tissue Degeneration Program, David Z. Rosensweig Genomics Research Center, Hospital for Special Surgery, New York, NY, 10021, USA
- Department of Medicine, Weill Cornell Medical College, New York, NY, 10065, USA
| | - Minjoon Lee
- Arthritis and Tissue Degeneration Program, David Z. Rosensweig Genomics Research Center, Hospital for Special Surgery, New York, NY, 10021, USA
| | - Brian Oh
- Arthritis and Tissue Degeneration Program, David Z. Rosensweig Genomics Research Center, Hospital for Special Surgery, New York, NY, 10021, USA
| | - Kaichi Kaneko
- Arthritis and Tissue Degeneration Program, David Z. Rosensweig Genomics Research Center, Hospital for Special Surgery, New York, NY, 10021, USA
| | - Sungkook Ma
- Department of Biological Science, Ulsan National Institute of Science & Technology (UNIST), Ulsan, 44919, Republic of Korea
| | - Jae Hoon Choi
- Department of Life Science, College of Natural Sciences, Research Institute for Natural Sciences, Hanyang University, Seoul, Korea
| | - Hojoong Kwak
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, USA
| | - Eun Young Lee
- Division of Rheumatology, Department of Internal Medicine, Seoul National University College of Medicine, Seoul, Korea.
| | - Sung Ho Park
- Department of Biological Science, Ulsan National Institute of Science & Technology (UNIST), Ulsan, 44919, Republic of Korea.
| | - Kyung-Hyun Park-Min
- Arthritis and Tissue Degeneration Program, David Z. Rosensweig Genomics Research Center, Hospital for Special Surgery, New York, NY, 10021, USA.
- Department of Medicine, Weill Cornell Medical College, New York, NY, 10065, USA.
- BCMB Allied Program, Weill Cornell Graduate School of Medical Sciences, New York, NY, 10021, USA.
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12
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Lakhia R, Mishra A, Biggers L, Malladi V, Cobo-Stark P, Hajarnis S, Patel V. Enhancer and super-enhancer landscape in polycystic kidney disease. Kidney Int 2023; 103:87-99. [PMID: 36283570 PMCID: PMC9841439 DOI: 10.1016/j.kint.2022.08.039] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 06/15/2022] [Accepted: 08/19/2022] [Indexed: 11/07/2022]
Abstract
Widespread aberrant gene expression is a pathological hallmark of polycystic kidney disease (PKD). Numerous pathogenic signaling cascades, including c-Myc, Fos, and Jun, are transactivated. However, the underlying epigenetic regulators are poorly defined. Here we show that H3K27ac, an acetylated modification of DNA packing protein histone H3 that marks active enhancers, is elevated in mouse and human samples of autosomal dominant PKD. Using comparative H3K27ac ChIP-Seq analysis, we mapped over 16000 active intronic and intergenic enhancer elements in Pkd1-mutant mouse kidneys. We found that the cystic kidney epigenetic landscape resembles that of a developing kidney, and over 90% of upregulated genes in Pkd1-mutant kidneys are co-housed with activated enhancers in the same topologically associated domains. Furthermore, we identified an evolutionarily conserved enhancer cluster downstream of the c-Myc gene and super-enhancers flanking both Jun and Fos loci in mouse and human models of autosomal dominant PKD. Deleting these regulatory elements reduced c-Myc, Jun, or Fos abundance and suppressed proliferation and 3D cyst growth of Pkd1-mutant cells. Finally, inhibiting glycolysis and glutaminolysis or activating Ppara in Pkd1-mutant cells lowerd global H3K27ac levels and its abundance on c-Myc enhancers. Thus, our work suggests that epigenetic rewiring mediates the transcriptomic dysregulation in PKD, and the regulatory elements can be targeted to slow cyst growth.
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Affiliation(s)
- Ronak Lakhia
- Department of Internal Medicine, Nephrology, UT Southwestern Medical Center, Dallas, Texas, USA.
| | - Abheepsa Mishra
- Department of Internal Medicine, Nephrology, UT Southwestern Medical Center, Dallas, Texas, USA
| | - Laurence Biggers
- Department of Internal Medicine, Nephrology, UT Southwestern Medical Center, Dallas, Texas, USA
| | - Venkat Malladi
- Lyda Hill Department of Bioinformatics, UT Southwestern Medical Center, Dallas, Texas, USA
| | - Patricia Cobo-Stark
- Department of Internal Medicine, Nephrology, UT Southwestern Medical Center, Dallas, Texas, USA
| | - Sachin Hajarnis
- Department of Internal Medicine, Nephrology, UT Southwestern Medical Center, Dallas, Texas, USA
| | - Vishal Patel
- Department of Internal Medicine, Nephrology, UT Southwestern Medical Center, Dallas, Texas, USA
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13
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Orton SM, Sangha A, Gupta M, Martens K, Metz LM, de Koning APJ, Pfeffer G. Expression of risk genes linked to vitamin D receptor super-enhancer regions and their association with phenotype severity in multiple sclerosis. Front Neurol 2022; 13:1064008. [PMID: 36644209 PMCID: PMC9832371 DOI: 10.3389/fneur.2022.1064008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Accepted: 12/05/2022] [Indexed: 12/29/2022] Open
Abstract
Multiple sclerosis (MS) is a chronic debilitating neurological condition with a wide range of phenotype variability. A complex interplay of genetic and environmental factors contributes to disease onset and progression in MS patients. Vitamin D deficiency is a known susceptibility factor for MS, however the underlying mechanism of vitamin D-gene interactions in MS etiology is still poorly understood. Vitamin D receptor super-enhancers (VSEs) are enriched in MS risk variants and may modulate these environment-gene interactions. mRNA expression in total of 64 patients with contrasting MS severity was quantified in select genes. First, RNA-seq was performed on a discovery cohort (10 mild, 10 severe MS phenotype) and ten genes regulated by VSEs that have been linked to MS risk were analyzed. Four candidates showed a significant positive association (GRINA, PLEC, PARP10, and LRG1) in the discovery cohort and were then quantified using digital droplet PCR (ddPCR) in a validation cohort (33 mild, 11 severe MS phenotype). A significant differential expression persisted in the validation cohort for three of the VSE-MS genes: GRINA (p = 0.0138), LRG1 (p = 0.0157), and PLEC (p = 0.0391). In summary, genes regulated by VSE regions that contain known MS risk variants were shown to have differential expression based on disease severity (p<0.05). The findings implicate a role for vitamin D super-enhancers in modulating disease activity. In addition, expression levels may have some utility as prognostic biomarkers in the future.
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Affiliation(s)
- Sarah M. Orton
- Faculty of Science and Technology, Mount Royal University, Calgary, AB, Canada,*Correspondence: Sarah M. Orton ✉
| | - Amarpreet Sangha
- Faculty of Science and Technology, Mount Royal University, Calgary, AB, Canada
| | - Mehul Gupta
- Department of Clinical Neurosciences, Cumming School of Medicine, Hotchkiss Brain Institute, University of Calgary, Calgary, AB, Canada
| | - Kristina Martens
- Department of Clinical Neurosciences, Cumming School of Medicine, Hotchkiss Brain Institute, University of Calgary, Calgary, AB, Canada
| | - Luanne M. Metz
- Department of Clinical Neurosciences, Cumming School of Medicine, Hotchkiss Brain Institute, University of Calgary, Calgary, AB, Canada
| | - A. P. J. de Koning
- Department of Medical Genetics, Alberta Child Health Research Institute, Cumming of Medicine, University of Calgary, Calgary, AB, Canada
| | - Gerald Pfeffer
- Department of Clinical Neurosciences, Cumming School of Medicine, Hotchkiss Brain Institute, University of Calgary, Calgary, AB, Canada,Department of Medical Genetics, Alberta Child Health Research Institute, Cumming of Medicine, University of Calgary, Calgary, AB, Canada
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14
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Tian SZ, Li G, Ning D, Jing K, Xu Y, Yang Y, Fullwood MJ, Yin P, Huang G, Plewczynski D, Zhai J, Dai Z, Chen W, Zheng M. MCIBox: a toolkit for single-molecule multi-way chromatin interaction visualization and micro-domains identification. Brief Bioinform 2022; 23:6696142. [PMID: 36094071 DOI: 10.1093/bib/bbac380] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2022] [Revised: 08/05/2022] [Accepted: 08/09/2022] [Indexed: 12/14/2022] Open
Abstract
The emerging ligation-free three-dimensional (3D) genome mapping technologies can identify multiplex chromatin interactions with single-molecule precision. These technologies not only offer new insight into high-dimensional chromatin organization and gene regulation, but also introduce new challenges in data visualization and analysis. To overcome these challenges, we developed MCIBox, a toolkit for multi-way chromatin interaction (MCI) analysis, including a visualization tool and a platform for identifying micro-domains with clustered single-molecule chromatin complexes. MCIBox is based on various clustering algorithms integrated with dimensionality reduction methods that can display multiplex chromatin interactions at single-molecule level, allowing users to explore chromatin extrusion patterns and super-enhancers regulation modes in transcription, and to identify single-molecule chromatin complexes that are clustered into micro-domains. Furthermore, MCIBox incorporates a two-dimensional kernel density estimation algorithm to identify micro-domains boundaries automatically. These micro-domains were stratified with distinctive signatures of transcription activity and contained different cell-cycle-associated genes. Taken together, MCIBox represents an invaluable tool for the study of multiple chromatin interactions and inaugurates a previously unappreciated view of 3D genome structure.
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Affiliation(s)
- Simon Zhongyuan Tian
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, Department of Biology, School of Life Sciences, Southern University of Science and Technology, 1088 Xueyuan Rd, Nanshan District, Shenzhen, 518055, Guangdong, China
| | - Guoliang Li
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, No.1 Shizishan Street, Hongshan District, Wuhan, 430070, Hubei, China.,Agricultural Bioinformatics Key Laboratory of Hubei Province, Hubei Engineering Technology Research Center of Agricultural Big Data, 3D Genomics Research Center, College of Informatics, Huazhong Agricultural University, No.1, Shizishan Street, Hongshan District, Wuhan, 430070, Hubei, China
| | - Duo Ning
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, Department of Biology, School of Life Sciences, Southern University of Science and Technology, 1088 Xueyuan Rd, Nanshan District, Shenzhen, 518055, Guangdong, China
| | - Kai Jing
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, Department of Biology, School of Life Sciences, Southern University of Science and Technology, 1088 Xueyuan Rd, Nanshan District, Shenzhen, 518055, Guangdong, China
| | - Yewen Xu
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, Department of Biology, School of Life Sciences, Southern University of Science and Technology, 1088 Xueyuan Rd, Nanshan District, Shenzhen, 518055, Guangdong, China
| | - Yang Yang
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, Department of Biology, School of Life Sciences, Southern University of Science and Technology, 1088 Xueyuan Rd, Nanshan District, Shenzhen, 518055, Guangdong, China
| | - Melissa J Fullwood
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Dr, 637551, Singapore.,Cancer Science Institute of Singapore, National University of Singapore, 14 Medical Dr, 117599, Singapore.,Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), 61 Biopolis Dr, 138673, Singapore
| | - Pengfei Yin
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, Department of Biology, School of Life Sciences, Southern University of Science and Technology, 1088 Xueyuan Rd, Nanshan District, Shenzhen, 518055, Guangdong, China
| | - Guangyu Huang
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, Department of Biology, School of Life Sciences, Southern University of Science and Technology, 1088 Xueyuan Rd, Nanshan District, Shenzhen, 518055, Guangdong, China
| | - Dariusz Plewczynski
- Laboratory of Bioinformatics and Computational Genomics, Faculty of Mathematics and Information Science, Warsaw University of Technology, Pl. Politechniki 1, 00-661, Warsaw, Poland.,Laboratory of Functional and Structural Genomics, Centre of New Technologies, University of Warsaw, S. Banacha 2c, 00-927, Warsaw, Poland
| | - Jixian Zhai
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, Department of Biology, School of Life Sciences, Southern University of Science and Technology, 1088 Xueyuan Rd, Nanshan District, Shenzhen, 518055, Guangdong, China.,Institute of Plant and Food Science, Southern University of Science and Technology, Southern University of Science and Technology, 1088, Xueyuan Rd, Nanshan District, Shenzhen, 518055, Guangdong, China.,Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Southern University of Science and Technology, 1088 Xueyuan Rd, Nanshan District, Shenzhen, 518055, Guangdong, China
| | - Ziwei Dai
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, Department of Biology, School of Life Sciences, Southern University of Science and Technology, 1088 Xueyuan Rd, Nanshan District, Shenzhen, 518055, Guangdong, China
| | - Wei Chen
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, Department of Biology, School of Life Sciences, Southern University of Science and Technology, 1088 Xueyuan Rd, Nanshan District, Shenzhen, 518055, Guangdong, China
| | - Meizhen Zheng
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, Department of Biology, School of Life Sciences, Southern University of Science and Technology, 1088 Xueyuan Rd, Nanshan District, Shenzhen, 518055, Guangdong, China
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15
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Zhang Y, Zhang J, Wang C, Qin X, Zhang Y, Liu J, Pan Z. Effective Quality Breeding Directions-Comparison and Conservative Analysis of Hepatic Super-Enhancers between Chinese and Western Pig Breeds. Biology (Basel) 2022; 11:1631. [PMID: 36358332 PMCID: PMC9687233 DOI: 10.3390/biology11111631] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 11/03/2022] [Accepted: 11/04/2022] [Indexed: 10/24/2023]
Abstract
The transcriptional initiation of genes is closely bound to the functions of cis-regulatory elements, including promoters, typical enhancers (TEs), and recently-identified super-enhancers (SEs). In this study, we identified these cis-regulatory elements in the livers of two Chinese (Meishan and Enshi Black) and two Western (Duroc and Large White) pig breeds using ChIP-seq data, then explored their similarities and differences. In addition, we analyzed the conservation of SEs among different tissues and species (pig, human, and mouse). We observed that SEs were more significantly enriched by transcriptional initiation regions, TF binding sites, and SNPs than other cis-elements. Western breeds included fewer SEs in number, while more growth-related QTLs were associated with these SEs. Additionally, the SEs were highly tissue-specific, and were conserved in the liver among humans, pigs, and mice. We concluded that intense selection could concentrate functional SEs; thus, SEs could be applied as effective detection regions in genomic selection breeding.
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Affiliation(s)
- Yi Zhang
- Laboratory of Statistical Genetics and Epigenetics, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Jinbi Zhang
- College of Animal Science and Technology, Jinling Institute of Technology, Nanjing 211169, China
| | - Caixia Wang
- Laboratory of Statistical Genetics and Epigenetics, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Xinxin Qin
- Laboratory of Statistical Genetics and Epigenetics, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Yuge Zhang
- Laboratory of Statistical Genetics and Epigenetics, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Jingge Liu
- College of Animal Science and Technology, Jinling Institute of Technology, Nanjing 211169, China
| | - Zengxiang Pan
- Laboratory of Statistical Genetics and Epigenetics, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
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16
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Dai W, Wu J, Peng X, Hou W, Huang H, Cheng Q, Liu Z, Luyten W, Schoofs L, Zhou J, Liu S. CDK12 orchestrates super-enhancer-associated CCDC137 transcription to direct hepatic metastasis in colorectal cancer. Clin Transl Med 2022; 12:e1087. [PMID: 36254394 PMCID: PMC9577262 DOI: 10.1002/ctm2.1087] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 09/22/2022] [Accepted: 09/29/2022] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Hepatic metastasis is the primary and direct cause of death in individuals with colorectal cancer (CRC) attribute to lack of effective therapeutic targets. The present study aimed to identify potential druggable candidate targets for patients with liver metastatic CRC. METHODS The transcriptional profiles of super-enhancers (SEs) in primary and liver metastatic CRC were evaluated in publicly accessible CRC datasets. Immunohistochemistry of human CRC tissues was conducted to determine the expression level of CDK12. Cellular proliferation, survival and stemness were examined upon CDK12 inhibition by shCDK12 or a selective CDK12 inhibitor named SR-4835 with multiple in vitro and in vivo assays. RNA sequencing and bioinformatics analyses were carried out to investigate the mechanisms of CDK12 inhibition in CRC cells. RESULTS We identified CDK12 as a driver gene for direct hepatic metastasis in CRC. Suppression of CDK12 led to robust inhibition of proliferation, survival and stemness. Mechanistically, CDK12 intervention preferentially repressed the transcription of SE-associated genes. Integration of the SE landscape and RNA sequencing, BCL2L1 and CCDC137 were identified as SE-associated oncogenic genes to strengthen the abilities of cellular survival, proliferation and stemness, eventually increasing liver metastasis of CRC. CONCLUSIONS Our data highlight the potential of CDK12 and SE-associated oncogenic transcripts as therapeutic targets for patients with liver metastatic CRC.
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Affiliation(s)
- Wei Dai
- School of PharmacyGannan Medical UniversityGanzhouJiangxiChina
| | - Junhong Wu
- School of PharmacyGannan Medical UniversityGanzhouJiangxiChina
| | - Xiaopeng Peng
- School of PharmacyGannan Medical UniversityGanzhouJiangxiChina
| | - Wen Hou
- School of PharmacyGannan Medical UniversityGanzhouJiangxiChina
| | - Hao Huang
- School of PharmacyGannan Medical UniversityGanzhouJiangxiChina
| | - Qilai Cheng
- School of PharmacyGannan Medical UniversityGanzhouJiangxiChina
| | - Zhiping Liu
- Center for ImmunologyGannan Medical UniversityGanzhouJiangxiChina
| | | | | | - Jingfeng Zhou
- Department of Hematology and OncologyInternational Cancer CenterShenzhen Key LaboratoryShenzhen University General HospitalShenzhen University Clinical Medical AcademyShenzhen University Health Science CenterShenzhenChina
| | - Shenglan Liu
- School of PharmacyGannan Medical UniversityGanzhouJiangxiChina
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17
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Nguyen DT, Yang W, Renganathan A, Weimholt C, Angappulige DH, Nguyen T, Sprung RW, Andriole GL, Kim EH, Mahajan NP, Mahajan K. Acetylated HOXB13 Regulated Super Enhancer Genes Define Therapeutic Vulnerabilities of Castration-Resistant Prostate Cancer. Clin Cancer Res 2022; 28:4131-4145. [PMID: 35849143 PMCID: PMC9481728 DOI: 10.1158/1078-0432.ccr-21-3603] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 04/01/2022] [Accepted: 07/13/2022] [Indexed: 12/24/2022]
Abstract
PURPOSE Androgen receptor (AR) antagonism is exacerbated by HOXB13 in castration-resistant prostate cancers (CRPC). However, it is unclear when and how HOXB13 primes CRPCs for AR antagonism. By mass-spectrometry analysis of CRPC extract, we uncovered a novel lysine 13 (K13) acetylation in HOXB13 mediated by CBP/p300. To determine whether acetylated K13-HOXB13 is a clinical biomarker of CRPC development, we characterized its role in prostate cancer biology. EXPERIMENTAL DESIGN We identified tumor-specific acK13-HOXB13 signal enriched super enhancer (SE)-regulated targets. We analyzed the effect of loss of HOXB13K13-acetylation on chromatin binding, SE proximal target gene expression, self-renewal, enzalutamide sensitivity, and CRPC tumor growth by employing isogenic parental and HOXB13K13A mutants. Finally, using primary human prostate organoids, we evaluated whether inhibiting an acK13-HOXB13 target, ACK1, with a selective inhibitor (R)-9b is superior to AR antagonists in inhibiting CRPC growth. RESULTS acK13-HOXB13 promotes increased expression of lineage (AR, HOXB13), prostate cancer diagnostic (FOLH1), CRPC-promoting (ACK1), and angiogenesis (VEGFA, Angiopoietins) genes early in prostate cancer development by establishing tumor-specific SEs. acK13-HOXB13 recruitment to key SE-regulated targets is insensitive to enzalutamide. ACK1 expression is significantly reduced in the loss of function HOXB13K13A mutant CRPCs. Consequently, HOXB13K13A mutants display reduced self-renewal, increased sensitivity to enzalutamide, and impaired xenograft tumor growth. Primary human prostate tumor organoids expressing HOXB13 are significantly resistant to AR antagonists but sensitive to (R)-9b. CONCLUSIONS In summary, acetylated HOXB13 is a biomarker of clinically significant prostate cancer. Importantly, PSMA-targeting agents and (R)-9b could be new therapeutic modalities to target HOXB13-ACK1 axis regulated prostate cancers.
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Affiliation(s)
- Duy T Nguyen
- Division of Urologic Surgery, Washington University in St. Louis, St. Louis, Missouri.,Department of Surgery, Washington University in St. Louis, St. Louis, Missouri.,Mayo Clinic Graduate School of Biomedical Science, College of Medicine & Science, Rochester, Minnesota
| | - Wei Yang
- Genome Technology Access Center, Department of Genetics, Washington University in St. Louis, St. Louis, Missouri
| | - Arun Renganathan
- Division of Urologic Surgery, Washington University in St. Louis, St. Louis, Missouri.,Department of Surgery, Washington University in St. Louis, St. Louis, Missouri
| | - Cody Weimholt
- Department of Pathology and Immunology, Washington University in St. Louis, St. Louis, Missouri
| | - Duminduni H Angappulige
- Division of Urologic Surgery, Washington University in St. Louis, St. Louis, Missouri.,Department of Surgery, Washington University in St. Louis, St. Louis, Missouri
| | - Thanh Nguyen
- Division of Urologic Surgery, Washington University in St. Louis, St. Louis, Missouri.,Department of Surgery, Washington University in St. Louis, St. Louis, Missouri.,Cancer and Cell Biology Graduate Program, Baylor College of Medicine, Houston, Texas
| | - Robert W Sprung
- Division of Endocrinology, Metabolism and Lipid Research, Washington University School of Medicine, St. Louis, Missouri
| | - Gerald L Andriole
- Division of Urologic Surgery, Washington University in St. Louis, St. Louis, Missouri.,Department of Surgery, Washington University in St. Louis, St. Louis, Missouri.,National Capital Region, Johns Hopkins Medicine, Sibley Memorial Hospital, Washington, District of Columbia.,Siteman Cancer Center, Washington University in St. Louis, St. Louis, Missouri
| | - Eric H Kim
- Division of Urologic Surgery, Washington University in St. Louis, St. Louis, Missouri.,Department of Surgery, Washington University in St. Louis, St. Louis, Missouri.,Siteman Cancer Center, Washington University in St. Louis, St. Louis, Missouri
| | - Nupam P Mahajan
- Division of Urologic Surgery, Washington University in St. Louis, St. Louis, Missouri.,Department of Surgery, Washington University in St. Louis, St. Louis, Missouri.,Siteman Cancer Center, Washington University in St. Louis, St. Louis, Missouri
| | - Kiran Mahajan
- Division of Urologic Surgery, Washington University in St. Louis, St. Louis, Missouri.,Department of Surgery, Washington University in St. Louis, St. Louis, Missouri.,Siteman Cancer Center, Washington University in St. Louis, St. Louis, Missouri
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18
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Tang SC, Vijayakumar U, Zhang Y, Fullwood MJ. Super-Enhancers, Phase-Separated Condensates, and 3D Genome Organization in Cancer. Cancers (Basel) 2022; 14:2866. [PMID: 35740532 DOI: 10.3390/cancers14122866] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2022] [Revised: 06/08/2022] [Accepted: 06/08/2022] [Indexed: 01/27/2023] Open
Abstract
3D chromatin organization plays an important role in transcription regulation and gene expression. The 3D genome is highly maintained by several architectural proteins, such as CTCF, Yin Yang 1, and cohesin complex. This structural organization brings regulatory DNA elements in close proximity to their target promoters. In this review, we discuss the 3D chromatin organization of super-enhancers and their relationship to phase-separated condensates. Super-enhancers are large clusters of DNA elements. They can physically contact with their target promoters by chromatin looping during transcription. Multiple transcription factors can bind to enhancer and promoter sequences and recruit a complex array of transcriptional co-activators and RNA polymerase II to effect transcriptional activation. Phase-separated condensates of transcription factors and transcriptional co-activators have been implicated in assembling the transcription machinery at particular enhancers. Cancer cells can hijack super-enhancers to drive oncogenic transcription to promote cell survival and proliferation. These dysregulated transcriptional programs can cause cancer cells to become highly dependent on transcriptional regulators, such as Mediator and BRD4. Moreover, the expression of oncogenes that are driven by super-enhancers is sensitive to transcriptional perturbation and often occurs in phase-separated condensates, supporting therapeutic rationales of targeting SE components, 3D genome organization, or dysregulated condensates in cancer.
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19
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Jiang X, Qin N, Hua T, Wei X, Li Y, Chen C, Gong L, Liu S, Wang C, Yin R, Jiang Y, Dai J, Xu L, Shen H, Ma H. Functional characterization and clinical significance of super-enhancers in lung adenocarcinoma. Mol Carcinog 2022; 61:776-786. [PMID: 35596703 DOI: 10.1002/mc.23419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 04/10/2022] [Accepted: 05/03/2022] [Indexed: 11/06/2022]
Abstract
Super-enhancers (SEs) are important transcriptional regulators in tumorigenesis; however, the functional characterization and clinical significance of SEs in lung adenocarcinoma (LUAD) remain unclear. By using H3K27ac ChIP-seq data of two LUAD cell lines and eight lung tissues, we detected 1045 cancer-specific and 5032 normal-specific SEs. Compared to normal-specific SEs, cancer-specific SEs have different regulatory mechanisms where associated target genes were enriched in critical tumor-related pathways and tended to be regulated by transcription factors of Fos Proto-Oncogene, AP-1 Transcription Factor Subunit and Jun Proto-Oncogene, AP-1 Transcription Factor Subunit families. By using expression data of 513 LUAD and 57 adjacent samples from The Cancer Genome Atlas and 80 tumor-normal paired LUAD samples from the Nanjing Lung Cancer Cohort study, we performed differential expression analysis of target genes for SEs and defined 243 crucial SEs. Unsupervised clustering of crucial SEs revealed two subtypes with different levels of genomic aberrations (i.e., mutation and copy number alteration) and clinical outcomes (progression-free interval: p = 0.030; disease-free interval: p = 0.047). In addition, patients with adverse clinical outcomes were more sensitive to three small molecule inhibitors (bortezomib, doxorubicin, and etoposide), and their targets (PSMB5 and TOP2A) also have elevated expression levels among these patients. Taken together, our findings provided a comprehensive characterization of SEs in LUAD and emphasized their clinical significance in LUAD therapy.
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Affiliation(s)
- Xiangxiang Jiang
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Na Qin
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China.,Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China
| | - Tingting Hua
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Xiaoxia Wei
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Yuancheng Li
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Congcong Chen
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Linnan Gong
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Su Liu
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Cheng Wang
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China.,Department of Bioinformatics, School of Biomedical Engineering and Informatics, Nanjing Medical University, Nanjing, China
| | - Rong Yin
- Jiangsu Key Laboratory of Molecular and Translational Cancer Research, Department of Thoracic Surgery, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, China
| | - Yue Jiang
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China.,Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China
| | - Juncheng Dai
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China.,Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China
| | - Lin Xu
- Jiangsu Key Laboratory of Molecular and Translational Cancer Research, Department of Thoracic Surgery, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, China
| | - Hongbing Shen
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China.,Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China.,Research Units of Cohort Study on Cardiovascular Diseases and Cancers, Chinese Academy of Medical Sciences, Beijing, China
| | - Hongxia Ma
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China.,Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China.,Research Units of Cohort Study on Cardiovascular Diseases and Cancers, Chinese Academy of Medical Sciences, Beijing, China
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20
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Abstract
Hematological malignancies affecting either the lymphoid or the myeloid lineages involve epigenetic mutations or dysregulation in the majority of cases. These epigenetic abnormalities can affect regulatory elements in the genome and, particularly, enhancers. Recently, large regulatory elements known as super-enhancers, initially identified for their critical roles in cell-type specific expression regulation of genes controlling cell identity, have been shown to also be involved in tumorigenesis in many cancer types and hematological malignancies via the regulation of numerous oncogenes, including MYC. In this review, we highlight the existing links between super-enhancers and hematological malignancies, with a particular focus on acute myeloid leukemia, a clonal hematopoietic neoplasm with dismal outcomes, resulting in an uncontrolled proliferation of myeloblasts, abnormally blocked during differentiation and accumulating within the patient's bone marrow. We report recent works, performed during the last few years, treating this subject and consider the possibility of targeting oncogenic regulatory elements, as well as the effectiveness and limitations reported so far for such strategies.
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Affiliation(s)
| | - Camille Lobry
- INSERM U944, CNRS UMR7212, Institut de Recherche Saint Louis, Université de Paris, 75010 Paris, France;
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21
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Gomez RL, Woods LM, Ramachandran R, Abou Tayoun AN, Philpott A, Ali FR. Super-enhancer associated core regulatory circuits mediate susceptibility to retinoic acid in neuroblastoma cells. Front Cell Dev Biol 2022; 10:943924. [PMID: 36147741 PMCID: PMC9485839 DOI: 10.3389/fcell.2022.943924] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2022] [Accepted: 08/08/2022] [Indexed: 11/25/2022] Open
Abstract
Neuroblastoma is a pediatric tumour that accounts for more than 15% of cancer-related deaths in children. High-risk tumours are often difficult to treat, and patients' survival chances are less than 50%. Retinoic acid treatment is part of the maintenance therapy given to neuroblastoma patients; however, not all tumours differentiate in response to retinoic acid. Within neuroblastoma tumors, two phenotypically distinct cell types have been identified based on their super-enhancer landscape and transcriptional core regulatory circuitries: adrenergic (ADRN) and mesenchymal (MES). We hypothesized that the distinct super-enhancers in these different tumour cells mediate differential response to retinoic acid. To this end, three different neuroblastoma cell lines, ADRN (MYCN amplified and non-amplified) and MES cells, were treated with retinoic acid, and changes in the super-enhancer landscape upon treatment and after subsequent removal of retinoic acid was studied. Using ChIP-seq for the active histone mark H3K27ac, paired with RNA-seq, we compared the super-enhancer landscape in cells that undergo neuronal differentiation in response to retinoic acid versus those that fail to differentiate and identified unique super-enhancers associated with neuronal differentiation. Among the ADRN cells that respond to treatment, MYCN-amplified cells remain differentiated upon removal of retinoic acid, whereas MYCN non-amplified cells revert to an undifferentiated state, allowing for the identification of super-enhancers responsible for maintaining differentiation. This study identifies key super-enhancers that are crucial for retinoic acid-mediated differentiation.
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Affiliation(s)
- Roshna Lawrence Gomez
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates
| | - Laura M Woods
- Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Center, Cambridge Biomedical Campus, Cambridge, United Kingdom.,Department of Oncology, University of Cambridge, Cambridge, United Kingdom
| | - Revathy Ramachandran
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates
| | - Ahmad N Abou Tayoun
- Center for Genomic Discovery, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates.,Al Jalila Genomics Center, Al Jalila Children's Hospital, Dubai, United Arab Emirates
| | - Anna Philpott
- Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Center, Cambridge Biomedical Campus, Cambridge, United Kingdom.,Department of Oncology, University of Cambridge, Cambridge, United Kingdom
| | - Fahad R Ali
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates.,Center for Genomic Discovery, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates
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22
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Gu W, Jiang X, Wang W, Mujagond P, Liu J, Mai Z, Tang H, li S, Xiao H, Zhao J. Super-Enhancer-Associated Long Non-Coding RNA LINC01485 Promotes Osteogenic Differentiation of Human Bone Marrow Mesenchymal Stem Cells by Regulating MiR-619-5p/RUNX2 Axis. Front Endocrinol (Lausanne) 2022; 13:846154. [PMID: 35663324 PMCID: PMC9161675 DOI: 10.3389/fendo.2022.846154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Accepted: 04/05/2022] [Indexed: 11/13/2022] Open
Abstract
OBJECTIVE To investigate the mechanisms of super-enhancer-associated LINC01485/miR-619-5p/RUNX2 signaling axis involvement in osteogenic differentiation of human bone marrow mesenchymal stem cells (hBMSCs). METHODS Osteogenic differentiation of hBMSCs was induced in vitro. The expression levels of LINC01485 and miR-619-5p during osteogenesis were measured using quantitative real-time polymerase chain reaction (qRT-PCR). Osteogenic differentiation was examined by qRT-PCR, western blot, alkaline phosphatase (ALP) staining, ALP activity measurement, and Alizarin Red S (ARS) staining assays. Thereafter, the effects of LINC01485 and miR-619-5p on osteogenic differentiation of hBMSCs were evaluated by performing loss- and gain-of-function experiments. Subsequently, a fluorescence in situ hybridization (FISH) assay was employed to determine the cellular localization of LINC01485. Bioinformatics analysis, RNA antisense purification (RAP) assay, and dual-luciferase reporter assays were conducted to analyze the interactions of LINC01485, miR-619-5p, and RUNX2. Rescue experiments were performed to further delineate the role of the competitive endogenous RNA (ceRNA) signaling axis consisting of LINC01485/miR-619-5p/RUNX2 in osteogenic differentiation of hBMSCs. RESULTS The expression of LINC01485 was up-regulated during osteogenic differentiation of hBMSCs. The overexpression of LINC01485 promoted osteogenic differentiation of hBMSCs by up-regulating the expression of osteogenesis-related genes [e.g., runt-related transcription factor 2 (RUNX2), osterix (OSX), collagen type 1 alpha 1 (COL1A1), osteocalcin (OCN), and osteopontin (OPN)], and increasing the activity of ALP. ALP staining and ARS staining were also found to be increased upon overexpression of LINC01485. The opposing results were obtained upon LINC01485 interference in hBMSCs. miR-619-5p was found to inhibit osteogenic differentiation. FISH assay displayed that LINC01485 was mainly localized in the cytoplasm. RAP assay results showed that LINC01485 bound to miR-619-5p, and dual-luciferase reporter assay verified that LINC01485 bound to miR-619-5p, while miR-619-5p and RUNX2 bound to each other. Rescue experiments illustrated that LINC01485 could promote osteogenesis by increasing RUNX2 expression by sponging miR-619-5p. CONCLUSION LINC01485 could influence RUNX2 expression by acting as a ceRNA of miR-619-5p, thereby promoting osteogenic differentiation of hBMSCs. The LINC01485/miR-619-5p/RUNX2 axis might comprise a novel target in the bone tissue engineering field.
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Affiliation(s)
- Wenli Gu
- Stomatological Hospital, Southern Medical University, Guangzhou, China
| | - Xiao Jiang
- Stomatological Hospital, Southern Medical University, Guangzhou, China
| | - Wei Wang
- Stomatological Hospital, Southern Medical University, Guangzhou, China
| | | | - Jingpeng Liu
- Stomatological Hospital, Southern Medical University, Guangzhou, China
| | - Zhaoyi Mai
- Stomatological Hospital, Southern Medical University, Guangzhou, China
| | - Hai Tang
- Stomatological Hospital, Southern Medical University, Guangzhou, China
| | - Simin li
- Stomatological Hospital, Southern Medical University, Guangzhou, China
| | - Hui Xiao
- Stomatological Hospital, Southern Medical University, Guangzhou, China
- *Correspondence: Hui Xiao, ; Jianjiang Zhao,
| | - Jianjiang Zhao
- Shenzhen Stomatological Hospital, Southern Medical University, Shenzhen, China
- *Correspondence: Hui Xiao, ; Jianjiang Zhao,
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23
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Peng Y, Kang H, Luo J, Zhang Y. A Comparative Analysis of Super-Enhancers and Broad H3K4me3 Domains in Pig, Human, and Mouse Tissues. Front Genet 2021; 12:701049. [PMID: 34899824 PMCID: PMC8652260 DOI: 10.3389/fgene.2021.701049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 10/29/2021] [Indexed: 11/13/2022] Open
Abstract
Super-enhancers (SEs) and broad H3K4me3 domains (BDs) are crucial regulators in the control of tissue identity in human and mouse. However, their features in pig remain largely unknown. In this study, by integrative computational analyses of epigenomic and transcriptomic data, we have characterized SEs and BDs in six pig tissues and analyzed their conservation in comparison with human and mouse tissues. Similar to human and mouse, pig SEs and BDs display higher tissue specificity than their typical counterparts. Genes proximal to SEs and BDs are associated with tissue identity in most tissues. About 55-182 SEs (5-17% in total) and 99-309 BDs (8-16% in total) across pig tissues are considered as functionally conserved elements because they have orthologous SEs and BDs in human and mouse. However, these elements do not necessarily exhibit sequence conservation. The functionally conserved SEs are correlated to tissue identity in majority of pig tissues, while those conserved BDs are linked to tissue identity in a few tissues. Our study provides resources for future gene regulatory studies in pig. It highlights that SEs are more effective in defining tissue identity than BDs, which is contrasting to a previous study. It also provides novel insights on understanding the sequence features of functionally conserved elements.
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Affiliation(s)
- Yanling Peng
- Animal Functional Genomics Group, 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, China
| | - Huifang Kang
- Animal Functional Genomics Group, 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, China
| | - Jing Luo
- Animal Functional Genomics Group, 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, China
| | - Yubo Zhang
- Animal Functional Genomics Group, 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, China
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24
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Kainth AS, Chowdhary S, Pincus D, Gross DS. Primordial super-enhancers: heat shock-induced chromatin organization in yeast. Trends Cell Biol 2021; 31:801-813. [PMID: 34001402 PMCID: PMC8448919 DOI: 10.1016/j.tcb.2021.04.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 03/30/2021] [Accepted: 04/09/2021] [Indexed: 01/29/2023]
Abstract
Specialized mechanisms ensure proper expression of critically important genes such as those specifying cell identity or conferring protection from environmental stress. Investigations of the heat shock response have been critical in elucidating basic concepts of transcriptional control. Recent studies demonstrate that in response to thermal stress, heat shock-responsive genes associate with high levels of transcriptional activators and coactivators and those in yeast intensely interact across and between chromosomes, coalescing into condensates. In mammalian cells, cell identity genes that are regulated by super-enhancers (SEs) are also densely occupied by transcriptional machinery that form phase-separated condensates. We suggest that the stress-remodeled yeast nucleome bears functional and structural resemblance to mammalian SEs, and will reveal fundamental mechanisms of gene control by transcriptional condensates.
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Affiliation(s)
- Amoldeep S Kainth
- Department of Biochemistry and Molecular Biology, Louisiana State University Health Sciences Center, Shreveport, LA 71130, USA; Department of Molecular Genetics and Cell Biology, The University of Chicago, Chicago, IL 60637, USA
| | - Surabhi Chowdhary
- Department of Biochemistry and Molecular Biology, Louisiana State University Health Sciences Center, Shreveport, LA 71130, USA; Department of Molecular Genetics and Cell Biology, The University of Chicago, Chicago, IL 60637, USA
| | - David Pincus
- Department of Molecular Genetics and Cell Biology, The University of Chicago, Chicago, IL 60637, USA.
| | - David S Gross
- Department of Biochemistry and Molecular Biology, Louisiana State University Health Sciences Center, Shreveport, LA 71130, USA.
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25
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Abstract
The regulation of gene expression has been studied for decades, but the underlying mechanisms are still not fully understood. As well as local and distant regulation, there are specific mechanisms of regulation during development and physiological modulation of gene activity in differentiated cells. Current research strongly supports a role for the 3D chromosomal structure in the regulation of gene expression. However, it is not known whether the genome structure reflects the formation of active or repressed chromosomal domains or if these structures play a primary role in the regulation of gene expression. During early development, heterochromatinization of ribosomal DNA (rDNA) is coupled with silencing or activation of the expression of different sets of genes. Although the mechanisms behind this type of regulation are not known, rDNA clusters shape frequent inter-chromosomal contacts with a large group of genes controlling development. This review aims to shed light on the involvement of clusters of ribosomal genes in the global regulation of gene expression. We also discuss the possible role of RNA-mediated and phase-separation mechanisms in the global regulation of gene expression by nucleoli.
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Affiliation(s)
- Nickolai A Tchurikov
- Engelhardt Institute of Molecular Biology Russian Academy of Sciences, Moscow, Russia
| | - Yuri V Kravatsky
- Engelhardt Institute of Molecular Biology Russian Academy of Sciences, Moscow, Russia
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26
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Lee Z, Raabe M, Hu WS. Epigenomic features revealed by ATAC-seq impact transgene expression in CHO cells. Biotechnol Bioeng 2021; 118:1851-1861. [PMID: 33521928 DOI: 10.1002/bit.27701] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 01/14/2021] [Accepted: 01/25/2021] [Indexed: 12/15/2022]
Abstract
Different regions of a mammalian genome have different accessibilities to transcriptional machinery. The integration site of a transgene affects how actively it is transcribed. Highly accessible genomic regions called super-enhancers have been recently described as strong regulatory elements that shape cell identity. Super-enhancers have been identified in Chinese hamster ovary (CHO) cells using the Assay for Transposase-Accessible Chromatin Sequencing (ATAC-seq). Genes near super-enhancer regions had high transcript levels and were enriched for oncogenic signaling and proliferation functions, consistent with an immortalized phenotype. Inaccessible regions in the genome with low ATAC signal also had low transcriptional activity. Genes in inaccessible regions were enriched for remote tissue functions such as taste, smell, and neuronal activation. A lentiviral reporter integration assay showed integration into super-enhancer regions conferred higher reporter expression than insertion into inaccessible regions. Targeted integration of an IgG vector into the Plec super-enhancer region yielded clones that expressed the immunoglobulin light chain gene mostly in the top 20% of all transcripts with the majority in the top 5%. The results suggest the epigenomic landscape of CHO cells can guide the selection of integration sites in the development of cell lines for therapeutic protein production.
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Affiliation(s)
- Zion Lee
- Department of Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, Minnesota, USA
| | - Marina Raabe
- Department of Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, Minnesota, USA
| | - Wei-Shou Hu
- Department of Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, Minnesota, USA
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27
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Chandra S, Ehrlich KC, Lacey M, Baribault C, Ehrlich M. Epigenetics and expression of key genes associated with cardiac fibrosis: NLRP3, MMP2, MMP9, CCN2/CTGF and AGT. Epigenomics 2021; 13:219-234. [PMID: 33538177 PMCID: PMC7907962 DOI: 10.2217/epi-2020-0446] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Aims: Excessive inflammatory signaling and pathological remodeling of the extracellular matrix drive cardiac fibrosis and require changes in gene expression. Materials and methods: Using bioinformatics, both tissue-specific expression profiles and epigenomic profiles of some genes critical for cardiac fibrosis were examined, namely, NLRP3, MMP2, MMP9, CCN2/CTGF, AGT (encodes angiotensin II precursors) and hsa-mir-223 (post-transcriptionally regulates NLRP3). Results: In monocytes, neutrophils, fibroblasts, venous cells, liver and brain, enhancers or super-enhancers were found that correlate with high expression of these genes. One enhancer extended into a silent gene neighbor. These enhancers harbored tissue-specific foci of DNA hypomethylation, open chromatin and transcription factor binding. Conclusions: This study identified previously undescribed enhancers containing hypomethylated transcription factor binding subregions that are predicted to regulate expression of these cardiac fibrosis-inducing genes.
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Affiliation(s)
- Sruti Chandra
- Tulane Research Innovation for Arrhythmia Discoveries, Tulane University School of Medicine, New Orleans, LA, 70112, USA
| | - Kenneth C Ehrlich
- Tulane Center for Biomedical Informatics & Genomics, Tulane University Health Sciences Center, New Orleans, LA, 70112, USA
| | - Michelle Lacey
- Department of Mathematics, Tulane University, New Orleans, LA, 70112, USA.,Tulane Cancer Center, Tulane University Health Sciences Center, New Orleans, LA, 70112, USA
| | - Carl Baribault
- Center for Research & Scientific Computing, Tulane University Information Technology, New Orleans, LA, 70112, USA
| | - Melanie Ehrlich
- Tulane Center for Biomedical Informatics & Genomics, Tulane University Health Sciences Center, New Orleans, LA, 70112, USA.,Tulane Cancer Center, Tulane University Health Sciences Center, New Orleans, LA, 70112, USA.,Hayward Genetics Center, Tulane University Health Sciences Center, New Orleans, LA, 70112, USA
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28
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Zhang C, Lu X, Huang J, He H, Chen L, Liu Y, Wang H, Xu Y, Xing S, Ruan X, Yang X, Chen L, Xu D. Epigenome screening highlights that JMJD6 confers an epigenetic vulnerability and mediates sunitinib sensitivity in renal cell carcinoma. Clin Transl Med 2021; 11:e328. [PMID: 33634984 PMCID: PMC7882098 DOI: 10.1002/ctm2.328] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 01/30/2021] [Accepted: 01/31/2021] [Indexed: 12/12/2022] Open
Abstract
Aberrant epigenetic reprogramming represents a hallmark of renal cell carcinoma (RCC) tumorigenesis and progression. Whether there existed other epigenetic vulnerabilities that could serve as therapeutic targets remained unclear and promising. Here, we combined the clustered regularly interspaced short palindromic repeats functional screening results and multiple RCC datasets to identify JMJD6 as the potent target in RCC. JMJD6 expression correlated with poor survival outcomes of RCC patients and promoted RCC progression in vitro and in vivo. Mechanistically, aberrant p300 led to high JMJD6 expression, which activated a series of oncogenic crosstalk. Particularly, high-throughput sequencing data revealed that JMJD6 could assemble super-enhancers to drive a list of identity genes in kidney cancer, including VEGFA, β-catenin, and SRC. Moreover, this JMJD6-mediated oncogenic effect could be suppressed by a novel JMJD6 inhibitor (SKLB325), which was further demonstrated in RCC cells, patient-derived organoid models, and in vivo. Given the probable overlapped crosstalk between JMJD6 signature and tyrosine kinase inhibitors downstream targets, targeting JMJD6 sensitized RCC to sunitinib and was synergistic when they were combined together. Collectively, this study indicated that targeting JMJD6 was an effective approach to treat RCC patients.
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Affiliation(s)
- Chuanjie Zhang
- Department of Urology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xuan Lu
- Department of Pharmacology, Basic Medical College, Anhui Medical University, Hefei, China
| | - Jingyi Huang
- Department of Urology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Hongchao He
- Department of Urology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Li Chen
- Department of Pharmacy, Shanghai Xuhui District Central Hospital, Xuhui Hospital of Zhongshan Hospital Affiliated to Fudan University, Shanghai, China
| | - Yihan Liu
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, China
- Department of Pathology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Haofei Wang
- Department of Urology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yang Xu
- Department of Urology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Siwei Xing
- Department of Urology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xiaohao Ruan
- Department of Urology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xiaoqun Yang
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, China
- Department of Pathology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Lu Chen
- Department of Urology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Danfeng Xu
- Department of Urology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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Zhang C, Chen L, Liu Y, Huang J, Liu A, Xu Y, Shen Y, He H, Xu D. Downregulated METTL14 accumulates BPTF that reinforces super-enhancers and distal lung metastasis via glycolytic reprogramming in renal cell carcinoma. Am J Cancer Res 2021; 11:3676-3693. [PMID: 33664855 PMCID: PMC7914369 DOI: 10.7150/thno.55424] [Citation(s) in RCA: 57] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Accepted: 01/04/2021] [Indexed: 12/16/2022] Open
Abstract
Background: Methyltransferase-like 14 (METTL14) participates in tumorigenesis in several malignancies, but how METTL14 mediates the metastasis of renal cell carcinoma (RCC) has never been reported. Methods: Western blotting, quantitative real-time PCR, and immunohistochemistry were used to determine the mRNA and protein levels of relevant genes. Methylated RNA immunoprecipitation sequencing and RNA sequencing were utilized to screen potential targets of METTL14. Chromatin immunoprecipitation sequencing and assay for transposase-accessible chromatin sequencing were performed to investigate epigenetic alterations. The biological roles and mechanisms of METTL14/BPTF in promoting lung metastasis were confirmed in vitro and in vivo using cell lines, patient samples, xenograft models, and organoids. Results: Utilizing the TCGA-KIRC and Ruijin-RCC datasets, we found low expression of METTL14 in mRCC samples, which predicted poor prognosis. METTL14 deficiency promoted RCC metastasis in vitro and in vivo. Mechanistically, METTL14-mediated m6A modification negatively regulated the mRNA stability of bromodomain PHD finger transcription factor (BPTF) and depended on BPTF to drive lung metastasis. Accumulated BPTF in METTL14-deficient cells remodeled the enhancer landscape to reinforce several oncogenic crosstalk. Particularly, BPTF constituted super-enhancers that activate downstream targets like enolase 2 and SRC proto-oncogene nonreceptor tyrosine kinase, leading to glycolytic reprogramming of METTL14-/- cells. Finally, we determined the efficacy of the BPTF inhibitor AU1 in suppressing mRCC of patient-derived cells, mRCC-derived organoids (MDOs), and orthotopic xenograft models. Conclusions: Our study is the first to investigate the essential role of m6A modification and the METTL14/BPTF axis in the epigenetic and metabolic remodeling of mRCC, highlighting AU1 as a vital therapeutic candidate.
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Bruter AV, Rodionova MD, Varlamova EA, Shtil AA. Super-Enhancers in the Regulation of Gene Transcription: General Aspects and Antitumor Targets. Acta Naturae 2021; 13:4-15. [PMID: 33959383 PMCID: PMC8084300 DOI: 10.32607/actanaturae.11067] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 09/07/2020] [Indexed: 01/18/2023] Open
Abstract
Super-enhancers (genome elements that activate gene transcription) are DNA regions with an elevated concentration of transcriptional complexes. These multiprotein structures contain, among other components, the cyclin-dependent kinases 8 and 19. These and other transcriptional protein kinases are regarded as novel targets for pharmacological inhibition by antitumor drug candidates.
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Affiliation(s)
- A. V. Bruter
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334 Russia
- Blokhin National Medical Research Center of Oncology, Moscow, 115478 Russia
| | | | - E. A. Varlamova
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334 Russia
- Blokhin National Medical Research Center of Oncology, Moscow, 115478 Russia
| | - A. A. Shtil
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334 Russia
- Blokhin National Medical Research Center of Oncology, Moscow, 115478 Russia
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31
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Agrawal P, Blinka S, Pulakanti K, Reimer MH, Stelloh C, Meyer AE, Rao S. Genome editing demonstrates that the -5 kb Nanog enhancer regulates Nanog expression by modulating RNAPII initiation and/or recruitment. J Biol Chem 2020; 296:100189. [PMID: 33334884 PMCID: PMC7948488 DOI: 10.1074/jbc.ra120.015152] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 12/07/2020] [Accepted: 12/15/2020] [Indexed: 12/30/2022] Open
Abstract
Transcriptional enhancers have been defined by their ability to operate independent of distance and orientation in plasmid-based reporter assays of gene expression. At present, histone marks are used to identify and define enhancers but do not consider the endogenous role of an enhancer in the context of native chromatin. We employed a combination of genomic editing, single cell analyses, and sequencing approaches to investigate a Nanog-associated cis-regulatory element, which has been reported by others to be either an alternative promoter or a super-enhancer. We first demonstrate both distance and orientation independence in native chromatin, eliminating the issues raised with plasmid-based approaches. We next demonstrate that the dominant super-enhancer modulates Nanog globally and operates by recruiting and/or initiating RNA Polymerase II. Our studies have important implications to how transcriptional enhancers are defined and how they regulate gene expression.
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Affiliation(s)
- Puja Agrawal
- Department of Cell Biology, Neurobiology, and Anatomy, Medical College of Wisconsin, Milwaukee, Wisconsin, USA; Blood Research Institute, Versiti, Milwaukee, Wisconsin, USA
| | - Steven Blinka
- Department of Cell Biology, Neurobiology, and Anatomy, Medical College of Wisconsin, Milwaukee, Wisconsin, USA; Blood Research Institute, Versiti, Milwaukee, Wisconsin, USA
| | | | | | - Cary Stelloh
- Blood Research Institute, Versiti, Milwaukee, Wisconsin, USA
| | - Alison E Meyer
- Blood Research Institute, Versiti, Milwaukee, Wisconsin, USA
| | - Sridhar Rao
- Department of Cell Biology, Neurobiology, and Anatomy, Medical College of Wisconsin, Milwaukee, Wisconsin, USA; Blood Research Institute, Versiti, Milwaukee, Wisconsin, USA; Department of Pediatrics, Medical College of Wisconsin, Milwaukee, Wisconsin, USA.
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32
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Abstract
Selective gene expression is crucial in maintaining the self-renewing and multipotent properties of stem cells. Mediator is a large, evolutionarily conserved, multi-subunit protein complex that modulates gene expression by relaying signals from cell type-specific transcription factors to RNA polymerase II. In humans, this complex consists of 30 subunits arranged in four modules. One critical module of the Mediator complex is the kinase module consisting of four subunits: MED12, MED13, CDK8, and CCNC. The kinase module exists in variable association with the 26-subunit Mediator core and affects transcription through phosphorylation of transcription factors and by controlling Mediator structure and function. Many studies have shown the kinase module to be a key player in the maintenance of stem cells that is distinct from a general role in transcription. Genetic studies have revealed that dysregulation of this kinase subunit contributes to the development of many human diseases. In this review, we discuss the importance of the Mediator kinase module by examining how this module functions with the more recently identified transcriptional super-enhancers, how changes in the kinase module and its activity can lead to the development of human disease, and the role of this unique module in directing and maintaining cell state. As we look to use stem cells to understand human development and treat human disease through both cell-based therapies and tissue engineering, we need to remain aware of the on-going research and address critical gaps in knowledge related to the molecular mechanisms that control cell fate.
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Affiliation(s)
- Joseph Straub
- School of Biological Sciences, Louisiana Tech University, Ruston, Louisiana, USA
| | - Sree Venigalla
- School of Biological Sciences, Louisiana Tech University, Ruston, Louisiana, USA
| | - Jamie J Newman
- School of Biological Sciences, Louisiana Tech University, Ruston, Louisiana, USA
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33
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Ehrlich KC, Baribault C, Ehrlich M. Epigenetics of Muscle- and Brain-Specific Expression of KLHL Family Genes. Int J Mol Sci 2020; 21:E8394. [PMID: 33182325 PMCID: PMC7672584 DOI: 10.3390/ijms21218394] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 11/02/2020] [Accepted: 11/06/2020] [Indexed: 02/07/2023] Open
Abstract
KLHL and the related KBTBD genes encode components of the Cullin-E3 ubiquitin ligase complex and typically target tissue-specific proteins for degradation, thereby affecting differentiation, homeostasis, metabolism, cell signaling, and the oxidative stress response. Despite their importance in cell function and disease (especially, KLHL40, KLHL41, KBTBD13, KEAP1, and ENC1), previous studies of epigenetic factors that affect transcription were predominantly limited to promoter DNA methylation. Using diverse tissue and cell culture whole-genome profiles, we examined 17 KLHL or KBTBD genes preferentially expressed in skeletal muscle or brain to identify tissue-specific enhancer and promoter chromatin, open chromatin (DNaseI hypersensitivity), and DNA hypomethylation. Sixteen of the 17 genes displayed muscle- or brain-specific enhancer chromatin in their gene bodies, and most exhibited specific intergenic enhancer chromatin as well. Seven genes were embedded in super-enhancers (particularly strong, tissue-specific clusters of enhancers). The enhancer chromatin regions typically displayed foci of DNA hypomethylation at peaks of open chromatin. In addition, we found evidence for an intragenic enhancer in one gene upregulating expression of its neighboring gene, specifically for KLHL40/HHATL and KLHL38/FBXO32 gene pairs. Many KLHL/KBTBD genes had tissue-specific promoter chromatin at their 5' ends, but surprisingly, two (KBTBD11 and KLHL31) had constitutively unmethylated promoter chromatin in their 3' exons that overlaps a retrotransposed KLHL gene. Our findings demonstrate the importance of expanding epigenetic analyses beyond the 5' ends of genes in studies of normal and abnormal gene regulation.
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Affiliation(s)
- Kenneth C. Ehrlich
- Center for Biomedical Informatics and Genomics, Tulane University Health Sciences Center, New Orleans, LA 70112, USA;
| | - Carl Baribault
- Center for Research and Scientific Computing (CRSC), Tulane University Information Technology, Tulane University, New Orleans, LA 70112, USA;
| | - Melanie Ehrlich
- Center for Biomedical Informatics and Genomics, Tulane Cancer Center, Hayward Genetics Program, Tulane University Health Sciences Center, New Orleans, LA 70112, USA
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34
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Sciumè G, Mikami Y, Jankovic D, Nagashima H, Villarino AV, Morrison T, Yao C, Signorella S, Sun HW, Brooks SR, Fang D, Sartorelli V, Nakayamada S, Hirahara K, Zitti B, Davis FP, Kanno Y, O'Shea JJ, Shih HY. Rapid Enhancer Remodeling and Transcription Factor Repurposing Enable High Magnitude Gene Induction upon Acute Activation of NK Cells. Immunity 2020; 53:745-758.e4. [PMID: 33010223 DOI: 10.1016/j.immuni.2020.09.008] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Revised: 05/08/2020] [Accepted: 09/11/2020] [Indexed: 12/24/2022]
Abstract
Innate immune responses rely on rapid and precise gene regulation mediated by accessibility of regulatory regions to transcription factors (TFs). In natural killer (NK) cells and other innate lymphoid cells, competent enhancers are primed during lineage acquisition, and formation of de novo enhancers characterizes the acquisition of innate memory in activated NK cells and macrophages. Here, we investigated how primed and de novo enhancers coordinate to facilitate high-magnitude gene induction during acute activation. Epigenomic and transcriptomic analyses of regions near highly induced genes (HIGs) in NK cells both in vitro and in a model of Toxoplasma gondii infection revealed de novo chromatin accessibility and enhancer remodeling controlled by signal-regulated TFs STATs. Acute NK cell activation redeployed the lineage-determining TF T-bet to de novo enhancers, independent of DNA-sequence-specific motif recognition. Thus, acute stimulation reshapes enhancer function through the combinatorial usage and repurposing of both lineage-determining and signal-regulated TFs to ensure an effective response.
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35
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Aiello G, Ballabio C, Ruggeri R, Fagnocchi L, Anderle M, Morassut I, Caron D, Garilli F, Gianno F, Giangaspero F, Piazza S, Romanel A, Zippo A, Tiberi L. Truncated BRPF1 Cooperates with Smoothened to Promote Adult Shh Medulloblastoma. Cell Rep 2020; 29:4036-4052.e10. [PMID: 31851932 DOI: 10.1016/j.celrep.2019.11.046] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Revised: 05/14/2019] [Accepted: 11/12/2019] [Indexed: 12/12/2022] Open
Abstract
The transition of neural progenitors to differentiated postmitotic neurons is mainly considered irreversible in physiological conditions. In the present work, we show that Shh pathway activation through SmoM2 expression promotes postmitotic neurons dedifferentiation, re-entering in the cell cycle and originating medulloblastoma in vivo. Notably, human adult patients present inactivating mutations of the chromatin reader BRPF1 that are associated with SMO mutations and absent in pediatric and adolescent patients. Here, we found that truncated BRPF1 protein, as found in human adult patients, is able to induce medulloblastoma in adult mice upon SmoM2 activation. Indeed, postmitotic neurons re-entered the cell cycle and proliferated as a result of chromatin remodeling of neurons by BRPF1. Our model of brain cancer explains the onset of a subset of human medulloblastoma in adult individuals where granule neuron progenitors are no longer present.
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Affiliation(s)
- Giuseppe Aiello
- Armenise-Harvard Laboratory of Brain Disorders and Cancer, CIBIO, University of Trento, Via Sommarive 9, 38123 Trento, Italy
| | - Claudio Ballabio
- Armenise-Harvard Laboratory of Brain Disorders and Cancer, CIBIO, University of Trento, Via Sommarive 9, 38123 Trento, Italy
| | - Riccardo Ruggeri
- Armenise-Harvard Laboratory of Brain Disorders and Cancer, CIBIO, University of Trento, Via Sommarive 9, 38123 Trento, Italy
| | - Luca Fagnocchi
- Laboratory of Chromatin Biology & Epigenetics, CIBIO, University of Trento, Via Sommarive 9, 38123 Trento, Italy
| | - Marica Anderle
- Armenise-Harvard Laboratory of Brain Disorders and Cancer, CIBIO, University of Trento, Via Sommarive 9, 38123 Trento, Italy
| | - Ilaria Morassut
- Armenise-Harvard Laboratory of Brain Disorders and Cancer, CIBIO, University of Trento, Via Sommarive 9, 38123 Trento, Italy
| | - Davide Caron
- Armenise-Harvard Laboratory of Brain Disorders and Cancer, CIBIO, University of Trento, Via Sommarive 9, 38123 Trento, Italy
| | - Francesca Garilli
- Armenise-Harvard Laboratory of Brain Disorders and Cancer, CIBIO, University of Trento, Via Sommarive 9, 38123 Trento, Italy
| | - Francesca Gianno
- Department of Radiologic, Oncologic and Anatomo Pathological Sciences, University Sapienza of Rome, Rome, Italy; IRCCS Neuromed, Pozzilli, Isernia, Italy
| | - Felice Giangaspero
- Department of Radiologic, Oncologic and Anatomo Pathological Sciences, University Sapienza of Rome, Rome, Italy; IRCCS Neuromed, Pozzilli, Isernia, Italy
| | - Silvano Piazza
- Bioinformatics Core Facility, CIBIO, University of Trento, Via Sommarive 9, 38123 Trento, Italy
| | - Alessandro Romanel
- Laboratory of Bioinformatics and Computational Genomics, CIBIO, University of Trento, Via Sommarive 9, 38123 Trento, Italy
| | - Alessio Zippo
- Laboratory of Chromatin Biology & Epigenetics, CIBIO, University of Trento, Via Sommarive 9, 38123 Trento, Italy
| | - Luca Tiberi
- Armenise-Harvard Laboratory of Brain Disorders and Cancer, CIBIO, University of Trento, Via Sommarive 9, 38123 Trento, Italy.
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36
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Xu Y, Wu Y, Zhang S, Ma P, Jin X, Wang Z, Yao M, Zhang E, Tao B, Qin Y, Chen H, Liu A, Chen M, Xiao M, Lu C, Mao R, Fan Y. A Tumor-Specific Super-Enhancer Drives Immune Evasion by Guiding Synchronous Expression of PD-L1 and PD-L2. Cell Rep 2020; 29:3435-3447.e4. [PMID: 31825827 DOI: 10.1016/j.celrep.2019.10.093] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Revised: 08/10/2019] [Accepted: 10/22/2019] [Indexed: 12/12/2022] Open
Abstract
PD-L1 and PD-L2 are important targets for immune checkpoint blockade, but how tumor cells achieve their expression remains to be addressed. Here, we find that PD-L1 and PD-L2 are co-expressed in cancer cell lines and tissues across different cancer types. In breast cancer, MDA-MB-231 and SUM-159 cells show high expression of both PD-L1 and PD-L2. The expression of both PD-L1 and PD-L2 is greatly reduced upon treatment of inhibitors of super-enhancers. Bioinformatic analysis identifies a potential super-enhancer (PD-L1L2-SE) that is located between the CD274 and CD273 genes. Genetic deletion of PD-L1L2-SE profoundly reduces the expression of PD-L1 and PD-L2. PD-L1L2-SE-deficient cancer cells fail to generate immune evasion and are sensitive to T cell-mediated killing. Notably, epigenetic activation of such a region (PD-L1L2-SE) is correlated with PD-L1 and PD-L2. Taken together, we identify a super-enhancer (PD-L1L2-SE) that is responsible for the overexpression of PD-L1 and PD-L2 as well as immune evasion in cancer.
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Affiliation(s)
- Yuanpei Xu
- Department of Immunology, School of Medicine, Nantong University, Jiangsu 226001, China
| | - Yingcheng Wu
- Laboratory of Medical Science, School of Medicine, Nantong University, Jiangsu 226001, China; Department of Pathophysiology, School of Medicine, Nantong University, Jiangsu 226001, China
| | - Siliang Zhang
- The Department of Radiation Oncology, Harbin Medical University Cancer Hospital, Heilongjiang 150086, China
| | - Panpan Ma
- Department of Immunology, School of Medicine, Nantong University, Jiangsu 226001, China
| | - Xinxin Jin
- Department of Immunology, School of Medicine, Nantong University, Jiangsu 226001, China
| | - Zhou Wang
- School of Life Sciences, Nantong University, Jiangsu 226001, China
| | - Min Yao
- Department of Immunology, School of Medicine, Nantong University, Jiangsu 226001, China
| | - Erhao Zhang
- Laboratory of Medical Science, School of Medicine, Nantong University, Jiangsu 226001, China
| | - Baorui Tao
- Department of Pathophysiology, School of Medicine, Nantong University, Jiangsu 226001, China
| | - Yongwei Qin
- Department of Pathogenic Biology, School of Medicine, Nantong University, Jiangsu 226001, China
| | - Hao Chen
- Department of Gastroenterology, Affiliated Hospital of Nantong University, Jiangsu 226001, China
| | - Aifen Liu
- Laboratory of Medical Science, School of Medicine, Nantong University, Jiangsu 226001, China
| | - Miaomiao Chen
- Laboratory of Medical Science, School of Medicine, Nantong University, Jiangsu 226001, China
| | - Mingbing Xiao
- Department of Gastroenterology, Affiliated Hospital of Nantong University, Jiangsu 226001, China
| | - Cuihua Lu
- Department of Gastroenterology, Affiliated Hospital of Nantong University, Jiangsu 226001, China
| | - Renfang Mao
- Department of Pathophysiology, School of Medicine, Nantong University, Jiangsu 226001, China.
| | - Yihui Fan
- Department of Immunology, School of Medicine, Nantong University, Jiangsu 226001, China; Laboratory of Medical Science, School of Medicine, Nantong University, Jiangsu 226001, China; Department of Pathogenic Biology, School of Medicine, Nantong University, Jiangsu 226001, China; Department of Gastroenterology, Affiliated Hospital of Nantong University, Jiangsu 226001, China.
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37
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Theisen ER, Selich-Anderson J, Miller KR, Tanner JM, Taslim C, Pishas KI, Sharma S, Lessnick SL. Chromatin profiling reveals relocalization of lysine-specific demethylase 1 by an oncogenic fusion protein. Epigenetics 2020; 16:405-424. [PMID: 32842875 PMCID: PMC7993145 DOI: 10.1080/15592294.2020.1805678] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Paediatric cancers commonly harbour quiet mutational landscapes and are instead characterized by single driver events such as the mutation of critical chromatin regulators, expression of oncohistones, or expression of oncogenic fusion proteins. These events ultimately promote malignancy through disruption of normal gene regulation and development. The driver protein in Ewing sarcoma, EWS/FLI, is an oncogenic fusion and transcription factor that reshapes the enhancer landscape, resulting in widespread transcriptional dysregulation. Lysine-specific demethylase 1 (LSD1) is a critical functional partner for EWS/FLI as inhibition of LSD1 reverses the transcriptional activity of EWS/FLI. However, how LSD1 participates in fusion-directed epigenomic regulation and aberrant gene activation is unknown. We now show EWS/FLI causes dynamic rearrangement of LSD1 and we uncover a role for LSD1 in gene activation through colocalization at EWS/FLI binding sites throughout the genome. LSD1 is integral to the establishment of Ewing sarcoma super-enhancers at GGAA-microsatellites, which ubiquitously overlap non-microsatellite loci bound by EWS/FLI. Together, we show that EWS/FLI induces widespread changes to LSD1 distribution in a process that impacts the enhancer landscape throughout the genome.
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Affiliation(s)
- Emily R Theisen
- Center for Childhood Cancer and Blood Diseases, The Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, OH, USA
| | - Julia Selich-Anderson
- Center for Childhood Cancer and Blood Diseases, The Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, OH, USA
| | - Kyle R Miller
- Center for Childhood Cancer and Blood Diseases, The Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, OH, USA
| | - Jason M Tanner
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Cenny Taslim
- Center for Childhood Cancer and Blood Diseases, The Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, OH, USA
| | - Kathleen I Pishas
- Center for Childhood Cancer and Blood Diseases, The Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, OH, USA.,Cancer Genomics and Genetics, Peter MacCallum Cancer Centre, Melbourne, VIC, USA
| | - Sunil Sharma
- Applied Cancer Research and Drug Discovery, Translational Genomics Research Institute (Tgen), Phoenix, AX, USA
| | - Stephen L Lessnick
- Center for Childhood Cancer and Blood Diseases, The Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, OH, USA.,Division of Pediatric Hematology/Oncology/Blood and Marrow Transplant, The Ohio State University, Columbus, OH, USA
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38
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Paraiso KD, Blitz IL, Coley M, Cheung J, Sudou N, Taira M, Cho KWY. Endodermal Maternal Transcription Factors Establish Super-Enhancers during Zygotic Genome Activation. Cell Rep 2020; 27:2962-2977.e5. [PMID: 31167141 PMCID: PMC6610736 DOI: 10.1016/j.celrep.2019.05.013] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Revised: 03/30/2019] [Accepted: 05/01/2019] [Indexed: 01/06/2023] Open
Abstract
Elucidation of the sequence of events underlying the dynamic interaction
between transcription factors and chromatin states is essential. Maternal
transcription factors function at the top of the regulatory hierarchy to specify
the primary germ layers at the onset of zygotic genome activation (ZGA). We
focus on the formation of endoderm progenitor cells and examine the interactions
between maternal transcription factors and chromatin state changes underlying
the cell specification process. Endoderm-specific factors Otx1 and Vegt together
with Foxh1 orchestrate endoderm formation by coordinated binding to select
regulatory regions. These interactions occur before the deposition of enhancer
histone marks around the regulatory regions, and these TFs recruit RNA
polymerase II, regulate enhancer activity, and establish super-enhancers
associated with important endodermal genes. Therefore, maternal transcription
factors Otx1, Vegt, and Foxh1 combinatorially regulate the activity of
super-enhancers, which in turn activate key lineage-specifying genes during
ZGA. How do maternal transcription factors interact with chromatin regions to
coordinate the endodermal gene regulatory program? Paraiso et al. demonstrate
that combinatorial binding of maternal Otx1, Vegt, and Foxh1 to select enhancers
and super-enhancers in the genome controls endodermal cell fate specification
during zygotic gene activation.
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Affiliation(s)
- Kitt D Paraiso
- Department of Developmental and Cell Biology, University of California, Irvine, CA, USA; Center for Complex Biological Systems, University of California, Irvine, CA, USA
| | - Ira L Blitz
- Department of Developmental and Cell Biology, University of California, Irvine, CA, USA
| | - Masani Coley
- Department of Developmental and Cell Biology, University of California, Irvine, CA, USA
| | - Jessica Cheung
- Department of Developmental and Cell Biology, University of California, Irvine, CA, USA
| | - Norihiro Sudou
- Department of Anatomy, Tokyo Women's Medical University, Tokyo, Japan
| | - Masanori Taira
- Department of Biological Sciences, Chuo University, Tokyo, Japan
| | - Ken W Y Cho
- Department of Developmental and Cell Biology, University of California, Irvine, CA, USA; Center for Complex Biological Systems, University of California, Irvine, CA, USA.
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39
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Qu J, Ouyang Z, Wu W, Li G, Wang J, Lu Q, Li Z. Functions and Clinical Significance of Super-Enhancers in Bone-Related Diseases. Front Cell Dev Biol 2020; 8:534. [PMID: 32714929 PMCID: PMC7344144 DOI: 10.3389/fcell.2020.00534] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Accepted: 06/08/2020] [Indexed: 12/14/2022] Open
Abstract
Super-enhancers (SEs) are a large cluster of cis-regulatory DNA elements that contain many binding motifs, which master transcription factors and cofactors bind to with high density. SEs usually regulate the expression of genes that can control the cell identity and fate, and SEs can be used to explain the patterns of the expression of cell-specific genes. Hence, it shows great potential for application in the treatment of diseases like cancer. At present, the clinical treatments for osteosarcoma, Ewing sarcoma, and other bone-related diseases remain challenging. The poor prognosis and difficult treatment of these diseases imposes heavy economic burden on patients and society. In recent years, research on SEs with respect to bone-related diseases has attracted increasing attention. In this paper, we first review the identification and functional mechanisms of SEs. Then, we integrate the findings of the emerging studies on SEs in bone-related diseases. Finally, we summarize recent strategies for targeting SEs for the treatment of bone-related diseases. This review aims to provide comprehensive insights into the roles of SEs in bone-related diseases.
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Affiliation(s)
- Jian Qu
- Department of Pharmacy, The Second Xiangya Hospital, Central South University, Changsha, China.,Hunan Key Laboratory of Tumor Models and Individualized Medicine, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Zhanbo Ouyang
- Department of Pharmacy, The Second Xiangya Hospital, Central South University, Changsha, China.,Hunan Key Laboratory of Tumor Models and Individualized Medicine, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Wenqiang Wu
- Mathematical Engineering Academy of Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Guohua Li
- Department of Pharmacy, The Second Xiangya Hospital, Central South University, Changsha, China.,Hunan Key Laboratory of Tumor Models and Individualized Medicine, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Jiaojiao Wang
- Department of Pharmacy, The Second Xiangya Hospital, Central South University, Changsha, China.,Hunan Key Laboratory of Tumor Models and Individualized Medicine, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Qiong Lu
- Department of Pharmacy, The Second Xiangya Hospital, Central South University, Changsha, China.,Hunan Key Laboratory of Tumor Models and Individualized Medicine, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Zhihong Li
- Hunan Key Laboratory of Tumor Models and Individualized Medicine, The Second Xiangya Hospital, Central South University, Changsha, China.,Department of Orthopedics, The Second Xiangya Hospital, Central South University, Changsha, China
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40
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Jahangiri L, Tsaprouni L, Trigg RM, Williams JA, Gkoutos GV, Turner SD, Pereira J. Core regulatory circuitries in defining cancer cell identity across the malignant spectrum. Open Biol 2020; 10:200121. [PMID: 32634370 PMCID: PMC7574545 DOI: 10.1098/rsob.200121] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Gene expression programmes driving cell identity are established by tightly regulated transcription factors that auto- and cross-regulate in a feed-forward manner, forming core regulatory circuitries (CRCs). CRC transcription factors create and engage super-enhancers by recruiting acetylation writers depositing permissive H3K27ac chromatin marks. These super-enhancers are largely associated with BET proteins, including BRD4, that influence higher-order chromatin structure. The orchestration of these events triggers accessibility of RNA polymerase machinery and the imposition of lineage-specific gene expression. In cancers, CRCs drive cell identity by superimposing developmental programmes on a background of genetic alterations. Further, the establishment and maintenance of oncogenic states are reliant on CRCs that drive factors involved in tumour development. Hence, the molecular dissection of CRC components driving cell identity and cancer state can contribute to elucidating mechanisms of diversion from pre-determined developmental programmes and highlight cancer dependencies. These insights can provide valuable opportunities for identifying and re-purposing drug targets. In this article, we review the current understanding of CRCs across solid and liquid malignancies and avenues of investigation for drug development efforts. We also review techniques used to understand CRCs and elaborate the indication of discussed CRC transcription factors in the wider context of cancer CRC models.
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Affiliation(s)
- Leila Jahangiri
- Department of Life Sciences, Birmingham City University, Birmingham, UK.,Division of Cellular and Molecular Pathology, Addenbrooke's Hospital, University of Cambridge, Cambridge, UK
| | - Loukia Tsaprouni
- Department of Life Sciences, Birmingham City University, Birmingham, UK
| | - Ricky M Trigg
- Division of Cellular and Molecular Pathology, Addenbrooke's Hospital, University of Cambridge, Cambridge, UK.,Department of Functional Genomics, GlaxoSmithKline, Stevenage, UK
| | - John A Williams
- Institute of Translational Medicine, University Hospitals Birmingham NHS Foundation Trust, Birmingham, UK.,Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK.,Mammalian Genetics Unit, Medical Research Council Harwell Institute, Oxfordshire, UK
| | - Georgios V Gkoutos
- Institute of Translational Medicine, University Hospitals Birmingham NHS Foundation Trust, Birmingham, UK.,Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK.,MRC Health Data Research, UK.,NIHR Experimental Cancer Medicine Centre, Birmingham, UK.,NIHR Surgical Reconstruction and Microbiology Research Centre, Birmingham, UK.,NIHR Biomedical Research Centre, Birmingham, UK
| | - Suzanne D Turner
- Division of Cellular and Molecular Pathology, Addenbrooke's Hospital, University of Cambridge, Cambridge, UK
| | - Joao Pereira
- Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Charlestown, USA
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41
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Dubois-Chevalier J, Dubois V, Staels B, Lefebvre P, Eeckhoute J. Perspectives on the use of super-enhancers as a defining feature of cell/tissue-identity genes. Epigenomics 2020; 12:715-723. [PMID: 32396464 DOI: 10.2217/epi-2019-0290] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Super-enhancers (SE) have become a popular concept and are widely used as a feature defining key identity genes. Here, we provide perspectives on the use of SE to define and identify cell/tissue-identity genes. By mining SE and their associated genes using murine functional genomics data, we highlight and discuss current limitations and open questions regarding both the sensitivity and specificity of identity genes/transcription factors predicted by SE. In this context, we point to cell/tissue-specific promoters as an important additional level of information, which we propose to combine with SE when aiming to define potential identity genes.
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Affiliation(s)
- Julie Dubois-Chevalier
- University of Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1011-EGID, Lille F-59000 Lille, France
| | - Vanessa Dubois
- University of Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1011-EGID, Lille F-59000 Lille, France
| | - Bart Staels
- University of Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1011-EGID, Lille F-59000 Lille, France
| | - Philippe Lefebvre
- University of Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1011-EGID, Lille F-59000 Lille, France
| | - Jérôme Eeckhoute
- University of Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1011-EGID, Lille F-59000 Lille, France
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42
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Guo T, Zambo KDA, Zamuner FT, Ou T, Hopkins C, Kelley DZ, Wulf HA, Winkler E, Erbe R, Danilova L, Considine M, Sidransky D, Favorov A, Florea L, Fertig EJ, Gaykalova DA. Chromatin structure regulates cancer-specific alternative splicing events in primary HPV-related oropharyngeal squamous cell carcinoma. Epigenetics 2020; 15:959-971. [PMID: 32164487 DOI: 10.1080/15592294.2020.1741757] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Human papillomavirus-related oropharyngeal squamous cell carcinoma (HPV+ OPSCC) represents a unique disease entity within head and neck cancer with rising incidence. Previous work has shown that alternative splicing events (ASEs) are prevalent in HPV+ OPSCC, but further validation is needed to understand the regulation of this process and its role in these tumours. In this study, eleven ASEs (GIT2, CTNNB1, MKNK2, MRPL33, SIPA1L3, SNHG6, SYCP2, TPRG1, ZHX2, ZNF331, and ELOVL1) were selected for validation from 109 previously published candidate ASEs to elucidate the post-transcriptional mechanisms of oncogenesis in HPV+ disease. In vitro qRT-PCR confirmed differential expression of 9 of 11 ASE candidates, and in silico analysis within the TCGA cohort confirmed 8 of 11 candidates. Six ASEs (MRPL33, SIPA1L3, SNHG6, TPRG1, ZHX2, and ELOVL1) showed significant differential expression across both methods. Further evaluation of chromatin modification revealed that ASEs strongly correlated with cancer-specific distribution of acetylated lysine 27 of histone 3 (H3K27ac). Subsequent epigenetic treatment of HPV+ HNSCC cell lines (UM-SCC-047 and UPCI-SCC-090) with JQ1 not only induced downregulation of cancer-specific ASE isoforms, but also growth inhibition in both cell lines. The UPCI-SCC-090 cell line, with greater ASE expression, also showed more significant growth inhibition after JQ1 treatment. This study confirms several novel cancer-specific ASEs in HPV+OPSCC and provides evidence for the role of chromatin modifications in regulation of alternative splicing in HPV+OPSCC. This highlights the role of epigenetic changes in the oncogenesis of HPV+OPSCC, which represents a unique, unexplored target for therapeutics that can alter the global post-transcriptional landscape.
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Affiliation(s)
- Theresa Guo
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins University School of Medicine , Baltimore, MD, USA
| | - Kristina Diana A Zambo
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins University School of Medicine , Baltimore, MD, USA
| | - Fernando T Zamuner
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins University School of Medicine , Baltimore, MD, USA
| | - Tingting Ou
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins University School of Medicine , Baltimore, MD, USA
| | - Christopher Hopkins
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins University School of Medicine , Baltimore, MD, USA
| | - Dylan Z Kelley
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins University School of Medicine , Baltimore, MD, USA
| | - Hildegard A Wulf
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins University School of Medicine , Baltimore, MD, USA
| | - Eli Winkler
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins University School of Medicine , Baltimore, MD, USA
| | - Rossin Erbe
- Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine , Baltimore, MD, USA
| | - Ludmila Danilova
- Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine , Baltimore, MD, USA.,Laboratory of Systems Biology and Computational Genetics, Vavilov Institute of General Genetics, Russian Academy of Sciences , Moscow, Russia
| | - Michael Considine
- Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine , Baltimore, MD, USA
| | - David Sidransky
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins University School of Medicine , Baltimore, MD, USA.,Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine , Baltimore, MD, USA
| | - Alexander Favorov
- Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine , Baltimore, MD, USA.,Laboratory of Systems Biology and Computational Genetics, Vavilov Institute of General Genetics, Russian Academy of Sciences , Moscow, Russia
| | - Liliana Florea
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University , Baltimore, MD, USA
| | - Elana J Fertig
- Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine , Baltimore, MD, USA.,Department of Applied Mathematics and Statistics, Johns Hopkins University , Baltimore, MD, USA.,Department of Biomedical Engineering, Johns Hopkins University School of Medicine , MD, Baltimore, USA
| | - Daria A Gaykalova
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins University School of Medicine , Baltimore, MD, USA.,Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine , Baltimore, MD, USA
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43
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Ehrlich KC, Lacey M, Ehrlich M. Epigenetics of Skeletal Muscle-Associated Genes in the ASB, LRRC, TMEM, and OSBPL Gene Families. Epigenomes 2020; 4:1. [PMID: 34968235 PMCID: PMC8594701 DOI: 10.3390/epigenomes4010001] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2019] [Revised: 01/21/2020] [Accepted: 01/28/2020] [Indexed: 02/07/2023] Open
Abstract
Much remains to be discovered about the intersection of tissue-specific transcription control and the epigenetics of skeletal muscle (SkM), a very complex and dynamic organ. From four gene families, Leucine-Rich Repeat Containing (LRRC), Oxysterol Binding Protein Like (OSBPL), Ankyrin Repeat and Socs Box (ASB), and Transmembrane Protein (TMEM), we chose 21 genes that are preferentially expressed in human SkM relative to 52 other tissue types and analyzed relationships between their tissue-specific epigenetics and expression. We also compared their genetics, proteomics, and descriptions in the literature. For this study, we identified genes with little or no previous descriptions of SkM functionality (ASB4, ASB8, ASB10, ASB12, ASB16, LRRC14B, LRRC20, LRRC30, TMEM52, TMEM233, OSBPL6/ORP6, and OSBPL11/ORP11) and included genes whose SkM functions had been previously addressed (ASB2, ASB5, ASB11, ASB15, LRRC2, LRRC38, LRRC39, TMEM38A/TRIC-A, and TMEM38B/TRIC-B). Some of these genes have associations with SkM or heart disease, cancer, bone disease, or other diseases. Among the transcription-related SkM epigenetic features that we identified were: super-enhancers, promoter DNA hypomethylation, lengthening of constitutive low-methylated promoter regions, and SkM-related enhancers for one gene embedded in a neighboring gene (e.g., ASB8-PFKM, LRRC39-DBT, and LRRC14B-PLEKHG4B gene-pairs). In addition, highly or lowly co-expressed long non-coding RNA (lncRNA) genes probably regulate several of these genes. Our findings give insights into tissue-specific epigenetic patterns and functionality of related genes in a gene family and can elucidate normal and disease-related regulation of gene expression in SkM.
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Affiliation(s)
- Kenneth C. Ehrlich
- Center for Bioinformatics and Genomics, Tulane University Health Sciences Center, New Orleans, LA 70112, USA;
| | - Michelle Lacey
- Department of Mathematics, Tulane University, New Orleans, LA 70118, USA;
- Tulane Cancer Center, Tulane University Health Sciences Center, New Orleans, LA 70112, USA
| | - Melanie Ehrlich
- Center for Bioinformatics and Genomics, Tulane University Health Sciences Center, New Orleans, LA 70112, USA;
- Tulane Cancer Center, Tulane University Health Sciences Center, New Orleans, LA 70112, USA
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44
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Fulciniti M, Lin CY, Samur MK, Lopez MA, Singh I, Lawlor MA, Szalat RE, Ott CJ, Avet-Loiseau H, Anderson KC, Young RA, Bradner JE, Munshi NC. Non-overlapping Control of Transcriptome by Promoter- and Super-Enhancer-Associated Dependencies in Multiple Myeloma. Cell Rep 2018; 25:3693-3705.e6. [PMID: 30590042 DOI: 10.1016/j.celrep.2018.12.016] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2016] [Revised: 10/04/2018] [Accepted: 12/03/2018] [Indexed: 12/22/2022] Open
Abstract
The relationship between promoter proximal transcription
factor-associated gene expression and super-enhancer-driven transcriptional
programs are not well defined. However, their distinct genomic occupancy
suggests a mechanism for specific and separable gene control. We explored the
transcriptional and functional interrelationship between E2F transcription
factors and BET transcriptional co-activators in multiple myeloma. We found that
the transcription factor E2F1 and its heterodimerization partner DP1 represent a
dependency in multiple myeloma cells. Global chromatin analysis reveals distinct
regulatory axes for E2F and BETs, with E2F predominantly localized to active
gene promoters of growth and/or proliferation genes and BETs disproportionately
at enhancer-regulated tissue-specific genes. These two separate gene regulatory
axes can be simultaneously targeted to impair the myeloma proliferative program,
providing an important molecular mechanism for combination therapy. This study
therefore suggests a sequestered cellular functional control that may be
perturbed in cancer with potential for development of a promising therapeutic
strategy. Uncontrolled proliferation is a hallmark of tumorigenesis and is
associated with perturbed transcriptomic profile. Fulciniti et al. explored the
interrelationship between E2F transcription factors and BET transcriptional
co-activators in multiple myeloma, reporting the existence of two distinct
regulatory axes that can be synergistically targeted to impact myeloma growth
and survival.
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45
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Williams RM, Candido-Ferreira I, Repapi E, Gavriouchkina D, Senanayake U, Ling ITC, Telenius J, Taylor S, Hughes J, Sauka-Spengler T. Reconstruction of the Global Neural Crest Gene Regulatory Network In Vivo. Dev Cell 2019; 51:255-276.e7. [PMID: 31639368 PMCID: PMC6838682 DOI: 10.1016/j.devcel.2019.10.003] [Citation(s) in RCA: 74] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2019] [Revised: 05/31/2019] [Accepted: 10/01/2019] [Indexed: 02/07/2023]
Abstract
Precise control of developmental processes is encoded in the genome in the form of gene regulatory networks (GRNs). Such multi-factorial systems are difficult to decode in vertebrates owing to their complex gene hierarchies and dynamic molecular interactions. Here we present a genome-wide in vivo reconstruction of the GRN underlying development of the multipotent neural crest (NC) embryonic cell population. By coupling NC-specific epigenomic and transcriptional profiling at population and single-cell levels with genome/epigenome engineering in vivo, we identify multiple regulatory layers governing NC ontogeny, including NC-specific enhancers and super-enhancers, novel trans-factors, and cis-signatures allowing reverse engineering of the NC-GRN at unprecedented resolution. Furthermore, identification and dissection of divergent upstream combinatorial regulatory codes has afforded new insights into opposing gene circuits that define canonical and neural NC fates early during NC ontogeny. Our integrated approach, allowing dissection of cell-type-specific regulatory circuits in vivo, has broad implications for GRN discovery and investigation.
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Affiliation(s)
- Ruth M Williams
- University of Oxford, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, Oxford OX3 9DS, UK
| | - Ivan Candido-Ferreira
- University of Oxford, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, Oxford OX3 9DS, UK
| | - Emmanouela Repapi
- University of Oxford, MRC Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine, Oxford OX3 9DS, UK
| | - Daria Gavriouchkina
- University of Oxford, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, Oxford OX3 9DS, UK
| | - Upeka Senanayake
- University of Oxford, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, Oxford OX3 9DS, UK
| | - Irving T C Ling
- University of Oxford, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, Oxford OX3 9DS, UK; University of Oxford, Department of Paediatric Surgery, Children's Hospital Oxford, Oxford, UK
| | - Jelena Telenius
- University of Oxford, MRC Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine, Oxford OX3 9DS, UK; University of Oxford, MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, Oxford OX3 9DS, UK
| | - Stephen Taylor
- University of Oxford, MRC Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine, Oxford OX3 9DS, UK
| | - Jim Hughes
- University of Oxford, MRC Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine, Oxford OX3 9DS, UK; University of Oxford, MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, Oxford OX3 9DS, UK
| | - Tatjana Sauka-Spengler
- University of Oxford, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, Oxford OX3 9DS, UK.
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46
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Schuijers J, Manteiga JC, Weintraub AS, Day DS, Zamudio AV, Hnisz D, Lee TI, Young RA. Transcriptional Dysregulation of MYC Reveals Common Enhancer-Docking Mechanism. Cell Rep 2018; 23:349-60. [PMID: 29641996 DOI: 10.1016/j.celrep.2018.03.056] [Citation(s) in RCA: 112] [Impact Index Per Article: 22.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Revised: 02/09/2018] [Accepted: 03/14/2018] [Indexed: 12/11/2022] Open
Abstract
Transcriptional dysregulation of the MYC oncogene is among the most frequent events in aggressive tumor cells, and this is generally accomplished by acquisition of a super-enhancer somewhere within the 2.8 Mb TAD where MYC resides. We find that these diverse cancer-specific super-enhancers, differing in size and location, interact with the MYC gene through a common and conserved CTCF binding site located 2 kb upstream of the MYC promoter. Genetic perturbation of this enhancer-docking site in tumor cells reduces CTCF binding, super-enhancer interaction, MYC gene expression, and cell proliferation. CTCF binding is highly sensitive to DNA methylation, and this enhancer-docking site, which is hypomethylated in diverse cancers, can be inactivated through epigenetic editing with dCas9-DNMT. Similar enhancer-docking sites occur at other genes, including genes with prominent roles in multiple cancers, suggesting a mechanism by which tumor cell oncogenes can generally hijack enhancers. These results provide insights into mechanisms that allow a single target gene to be regulated by diverse enhancer elements in different cell types.
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47
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Song Y, van den Berg PR, Markoulaki S, Soldner F, Dall'Agnese A, Henninger JE, Drotar J, Rosenau N, Cohen MA, Young RA, Semrau S, Stelzer Y, Jaenisch R. Dynamic Enhancer DNA Methylation as Basis for Transcriptional and Cellular Heterogeneity of ESCs. Mol Cell 2019; 75:905-920.e6. [PMID: 31422875 DOI: 10.1016/j.molcel.2019.06.045] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Revised: 05/06/2019] [Accepted: 06/26/2019] [Indexed: 12/18/2022]
Abstract
Variable levels of DNA methylation have been reported at tissue-specific differential methylation regions (DMRs) overlapping enhancers, including super-enhancers (SEs) associated with key cell identity genes, but the mechanisms responsible for this intriguing behavior are not well understood. We used allele-specific reporters at the endogenous Sox2 and Mir290 SEs in embryonic stem cells and found that the allelic DNA methylation state is dynamically switching, resulting in cell-to-cell heterogeneity. Dynamic DNA methylation is driven by the balance between DNA methyltransferases and transcription factor binding on one side and co-regulated with the Mediator complex recruitment and H3K27ac level changes at regulatory elements on the other side. DNA methylation at the Sox2 and the Mir290 SEs is independently regulated and has distinct consequences on the cellular differentiation state. Dynamic allele-specific DNA methylation at the two SEs was also seen at different stages in preimplantation embryos, revealing that methylation heterogeneity occurs in vivo.
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Affiliation(s)
- Yuelin Song
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Biology Department, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | | | | | - Frank Soldner
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | | | | | - Jesse Drotar
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Nicholas Rosenau
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Malkiel A Cohen
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Richard A Young
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Biology Department, Massachusetts Institute of Technology, Cambridge, MA 02142, USA.
| | - Stefan Semrau
- Leiden Institute of Physics, Leiden University, 2300 RA Leiden, the Netherlands.
| | - Yonatan Stelzer
- Department of Molecular Cell Biology, Weizmann Institute of Science, 76100 Rehovot, Israel.
| | - Rudolf Jaenisch
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Biology Department, Massachusetts Institute of Technology, Cambridge, MA 02142, USA.
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48
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Natsume A, Hirano M, Ranjit M, Aoki K, Wakabayashi T. Aberrant Transcriptional Regulation of Super-enhancers by RET Finger Protein-histone Deacetylase 1 Complex in Glioblastoma: Chemoresistance to Temozolomide. Neurol Med Chir (Tokyo) 2019; 59:293-298. [PMID: 31178471 PMCID: PMC6694022 DOI: 10.2176/nmc.ra.2019-0049] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Glioblastoma (GBM), the most common primary brain tumor, is the most aggressive human cancers, with a median survival rate of only 14.6 months. Temozolomide (TMZ) is the frontline chemotherapeutic drug in GBM. Drug resistance is the predominant obstacle in TMZ therapy. Drug resistance occurs via multiple pathways such as DNA mismatch repair and base excision repair systems, by which glioma cells acquire chemoresistance to some extent (5% and 95%, respectively). Histone3 Lysin27 residue-acetylation (H3K27ac) status regulates cis-regulatory elements, which increases the likelihood of gene transcription. Histone deacetylase (HDAC) complex deacetylate lysine residues on core histones, leading to a decrease in gene transcription. In cis-regulatory element regions, complexes with HDAC repress histones by H3K27ac deacetylation. The cis-regulating and three-dimensional transcriptional mechanism is called "super-enhancer". RET finger protein (RFP) is a protein that is expressed in many kinds of cancer. RFP forms a protein complex with HDAC1. The disruption of the RFP-HDAC1 complex has resulted in increased drug sensitivity in other cancers. We conclude that the downregulation of RFP or the disruption of the RFP/HDAC1 complex leads to an increase in TMZ efficacy in glioblastoma by changing histone modifications which lead to changes in cell division, cell cycle and apoptosis.
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Affiliation(s)
- Atsushi Natsume
- Department of Neurosurgery, Nagoya University School of Medicine
| | - Masaki Hirano
- Department of Neurosurgery, Nagoya University School of Medicine
| | - Melissa Ranjit
- Department of Neurosurgery, Nagoya University School of Medicine
| | - Kosuke Aoki
- Department of Neurosurgery, Nagoya University School of Medicine
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49
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Abstract
The spreading of epigenetic domains has emerged as a distinguishing epigenomic phenotype for diverse cell types. In particular, clusters of H3K27ac- and H3K4me3-marked elements, referred to as super-enhancers, and broad H3K4me3 domains, respectively, have been linked to cell identity and disease states. Here, we characterized the broad domains from different pancreatic ductal adenocarcinoma (PDAC) cell lines that represent distinct histological grades. Our integrative genomic analysis found that human derived cell line models for distinct PDAC grades exhibit characteristic broad epigenetic features associated with gene expression patterns that are predictive of patient prognosis and provide insight into pancreatic cancer cell identity. In particular, we find that genes marked by overlapping Low-Grade broad domains correspond to an epithelial phenotype and hold potential as markers for patient stratification. We further utilize ChIP-seq to compare the effects of histone acetyltransferase (HAT) inhibitors to detect global changes in histone acetylation and methylation levels. We found that HAT inhibitors impact certain broad domains of pancreatic cancer cells. Overall, our results reveal potential roles for broad domains in cells from distinct PDAC grades and demonstrate the plasticity of particular broad epigenomic domains to epigenetic inhibitors.
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50
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Ghosh C, Paul S, Dandawate P, Gunewardena SS, Subramaniam D, West C, Anant S, Dhar A. Super-enhancers: novel target for pancreatic ductal adenocarcinoma. Oncotarget 2019; 10:1554-71. [PMID: 30899425 DOI: 10.18632/oncotarget.26704] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Accepted: 02/01/2019] [Indexed: 01/02/2023] Open
Abstract
Super-enhancers (SEs) are unique areas of the genome which drive high-level of transcription and play a pivotal role in the cell physiology. Previous studies have established several important genes in cancer as SE-driven oncogenes. It is likely that oncogenes may hack the resident tissue regenerative program and interfere with SE-driven repair networks, leading to the specific pancreatic ductal adenocarcinoma (PDAC) phenotype. Here, we used ChIP-Seq to identify the presence of SE in PDAC cell lines. Differential H3K27AC marks were identified at enhancer regions of genes including c-MYC, MED1, OCT-4, NANOG, and SOX2 that can act as SE in non-cancerous, cancerous and metastatic PDAC cell lines. GZ17-6.02 affects acetylation of the genes, reduces transcription of major transcription factors, sonic hedgehog pathway proteins, and stem cell markers. In accordance with the decrease in Oct-4 expression, ChIP-Seq revealed a significant decrease in the occupancy of OCT-4 in the entire genome after GZ17-6.02 treatment suggesting the possible inhibitory effect of GZ17-6.02 on PDAC. Hence, SE genes are associated with PDAC and targeting their regulation with GZ17-6.02 offers a novel approach for treatment.
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