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Zhao A, Xu W, Han R, Wei J, Yu Q, Wang M, Li H, Li M, Chi G. Role of histone modifications in neurogenesis and neurodegenerative disease development. Ageing Res Rev 2024; 98:102324. [PMID: 38762100 DOI: 10.1016/j.arr.2024.102324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2023] [Revised: 04/30/2024] [Accepted: 05/05/2024] [Indexed: 05/20/2024]
Abstract
Progressive neuronal dysfunction and death are key features of neurodegenerative diseases; therefore, promoting neurogenesis in neurodegenerative diseases is crucial. With advancements in proteomics and high-throughput sequencing technology, it has been demonstrated that histone post-transcriptional modifications (PTMs) are often altered during neurogenesis when the brain is affected by disease or external stimuli and that the degree of histone modification is closely associated with the development of neurodegenerative diseases. This review aimed to show the regulatory role of histone modifications in neurogenesis and neurodegenerative diseases by discussing the changing patterns and functional significance of histone modifications, including histone methylation, acetylation, ubiquitination, phosphorylation, and lactylation. Finally, we explored the control of neurogenesis and the development of neurodegenerative diseases by artificially modulating histone modifications.
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Affiliation(s)
- Anqi Zhao
- The Key Laboratory of Pathobiology, Ministry of Education, Jilin University, Changchun 130021, China
| | - Wenhong Xu
- The Key Laboratory of Pathobiology, Ministry of Education, Jilin University, Changchun 130021, China
| | - Rui Han
- Department of Neurovascular Surgery, First Hospital of Jilin University, Changchun, 130021, China
| | - Junyuan Wei
- The Key Laboratory of Pathobiology, Ministry of Education, Jilin University, Changchun 130021, China
| | - Qi Yu
- The Key Laboratory of Pathobiology, Ministry of Education, Jilin University, Changchun 130021, China
| | - Miaomiao Wang
- The Key Laboratory of Pathobiology, Ministry of Education, Jilin University, Changchun 130021, China
| | - Haokun Li
- The Key Laboratory of Pathobiology, Ministry of Education, Jilin University, Changchun 130021, China
| | - Meiying Li
- The Key Laboratory of Pathobiology, Ministry of Education, Jilin University, Changchun 130021, China.
| | - Guangfan Chi
- The Key Laboratory of Pathobiology, Ministry of Education, Jilin University, Changchun 130021, China.
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2
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Pinto TS, Feltran GDS, Fernandes CJDC, de Camargo Andrade AF, Coque ADC, Silva SL, Abuderman AA, Zambuzzi WF, Foganholi da Silva RA. Epigenetic changes in shear-stressed endothelial cells. Cell Biol Int 2024; 48:665-681. [PMID: 38420868 DOI: 10.1002/cbin.12138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2023] [Revised: 01/18/2024] [Accepted: 01/28/2024] [Indexed: 03/02/2024]
Abstract
Epigenetic changes, particularly histone compaction modifications, have emerged as critical regulators in the epigenetic pathway driving endothelial cell phenotype under constant exposure to laminar forces induced by blood flow. However, the underlying epigenetic mechanisms governing endothelial cell behavior in this context remain poorly understood. To address this knowledge gap, we conducted in vitro experiments using human umbilical vein endothelial cells subjected to various tensional forces simulating pathophysiological blood flow shear stress conditions, ranging from normotensive to hypertensive forces. Our study uncovers a noteworthy observation wherein endothelial cells exposed to high shear stress demonstrate a decrease in the epigenetic marks H3K4ac and H3K27ac, accompanied by significant alterations in the levels of HDAC (histone deacetylase) proteins. Moreover, we demonstrate a negative regulatory effect of increased shear stress on HOXA13 gene expression and a concomitant increase in the expression of the long noncoding RNA, HOTTIP, suggesting a direct association with the suppression of HOXA13. Collectively, these findings represent the first evidence of the role of histone-related epigenetic modifications in modulating chromatin compaction during mechanosignaling of endothelial cells in response to elevated shear stress forces. Additionally, our results highlight the importance of understanding the physiological role of HOXA13 in vascular biology and hypertensive patients, emphasizing the potential for developing small molecules to modulate its activity. These findings warrant further preclinical investigations and open new avenues for therapeutic interventions targeting epigenetic mechanisms in hypertensive conditions.
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Affiliation(s)
- Thaís Silva Pinto
- Lab. of Bioassays and Cellular Dynamics, Department of Chemical and Biological Sciences, Institute of Biosciences, Paulista State University-UNESP, Botucatu, São Paulo, Brazil
| | - Geórgia da Silva Feltran
- Lab. of Bioassays and Cellular Dynamics, Department of Chemical and Biological Sciences, Institute of Biosciences, Paulista State University-UNESP, Botucatu, São Paulo, Brazil
| | - Célio Júnior da C Fernandes
- Lab. of Bioassays and Cellular Dynamics, Department of Chemical and Biological Sciences, Institute of Biosciences, Paulista State University-UNESP, Botucatu, São Paulo, Brazil
| | - Amanda Fantini de Camargo Andrade
- Lab. of Bioassays and Cellular Dynamics, Department of Chemical and Biological Sciences, Institute of Biosciences, Paulista State University-UNESP, Botucatu, São Paulo, Brazil
| | - Alex de Camargo Coque
- Epigenetic Study Center and Gene Regulation-CEEpiRG, Program in Environmental and Experimental Pathology, Paulista University, São Paulo, São Paulo, Brazil
| | - Simone L Silva
- School of Dentistry, University of Taubaté, Taubaté, São Paulo, Brazil
| | - Abdulwahab A Abuderman
- Department of Basic Medical Sciences, College of Medicine, Prince Sattam bin Abdulaziz University, Riyadh, Saudi Arabia
| | - Willian F Zambuzzi
- Lab. of Bioassays and Cellular Dynamics, Department of Chemical and Biological Sciences, Institute of Biosciences, Paulista State University-UNESP, Botucatu, São Paulo, Brazil
| | - Rodrigo A Foganholi da Silva
- Epigenetic Study Center and Gene Regulation-CEEpiRG, Program in Environmental and Experimental Pathology, Paulista University, São Paulo, São Paulo, Brazil
- School of Dentistry, University of Taubaté, Taubaté, São Paulo, Brazil
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3
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Ma W, Zhang J, Chen W, Liu N, Wu T. The histone lysine acetyltransferase KAT2B inhibits cholangiocarcinoma growth: evidence for interaction with SP1 to regulate NF2-YAP signaling. J Exp Clin Cancer Res 2024; 43:117. [PMID: 38641672 PMCID: PMC11027350 DOI: 10.1186/s13046-024-03036-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Accepted: 04/02/2024] [Indexed: 04/21/2024] Open
Abstract
BACKGROUND Cholangiocarcinoma (CCA) is a highly malignant cancer of the biliary tract with poor prognosis. Further mechanistic insights into the molecular mechanisms of CCA are needed to develop more effective target therapy. METHODS The expression of the histone lysine acetyltransferase KAT2B in human CCA was analyzed in human CCA tissues. CCA xenograft was developed by inoculation of human CCA cells with or without KAT2B overexpression into SCID mice. Western blotting, ChIP-qPCR, qRT-PCR, protein immunoprecipitation, GST pull-down and RNA-seq were performed to delineate KAT2B mechanisms of action in CCA. RESULTS We identified KAT2B as a frequently downregulated histone acetyltransferase in human CCA. Downregulation of KAT2B was significantly associated with CCA disease progression and poor prognosis of CCA patients. The reduction of KAT2B expression in human CCA was attributed to gene copy number loss. In experimental systems, we demonstrated that overexpression of KAT2B suppressed CCA cell proliferation and colony formation in vitro and inhibits CCA growth in mice. Mechanistically, forced overexpression of KAT2B enhanced the expression of the tumor suppressor gene NF2, which is independent of its histone acetyltransferase activity. We showed that KAT2B was recruited to the promoter region of the NF2 gene via interaction with the transcription factor SP1, which led to enhanced transcription of the NF2 gene. KAT2B-induced NF2 resulted in subsequent inhibition of YAP activity, as reflected by reduced nuclear accumulation of oncogenic YAP and inhibition of YAP downstream genes. Depletion of NF2 was able to reverse KAT2B-induced reduction of nuclear YAP and subvert KAT2B-induced inhibition of CCA cell growth. CONCLUSIONS This study provides the first evidence for an important tumor inhibitory effect of KAT2B in CCA through regulation of NF2-YAP signaling and suggests that this signaling cascade may be therapeutically targeted for CCA treatment.
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Affiliation(s)
- Wenbo Ma
- Department of Pathology and Laboratory Medicine, Tulane University School of Medicine, 1430 Tulane Avenue, SL-79, New Orleans, LA, 70112, USA
| | - Jinqiang Zhang
- Department of Pathology and Laboratory Medicine, Tulane University School of Medicine, 1430 Tulane Avenue, SL-79, New Orleans, LA, 70112, USA
| | - Weina Chen
- Department of Pathology and Laboratory Medicine, Tulane University School of Medicine, 1430 Tulane Avenue, SL-79, New Orleans, LA, 70112, USA
| | - Nianli Liu
- Department of Pathology and Laboratory Medicine, Tulane University School of Medicine, 1430 Tulane Avenue, SL-79, New Orleans, LA, 70112, USA
| | - Tong Wu
- Department of Pathology and Laboratory Medicine, Tulane University School of Medicine, 1430 Tulane Avenue, SL-79, New Orleans, LA, 70112, USA.
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4
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Kim H, Lee YJ, Kwon Y, Kim J. Efficient generation of brain organoids using magnetized gold nanoparticles. Sci Rep 2023; 13:21240. [PMID: 38040919 PMCID: PMC10692130 DOI: 10.1038/s41598-023-48655-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 11/29/2023] [Indexed: 12/03/2023] Open
Abstract
Brain organoids, which are three-dimensional cell culture models, have the ability to mimic certain structural and functional aspects of the human brain. However, creating these organoids can be a complicated and difficult process due to various technological hurdles. This study presents a method for effectively generating cerebral organoids from human induced pluripotent stem cells (hiPSCs) using electromagnetic gold nanoparticles (AuNPs). By exposing mature cerebral organoids to magnetized AuNPs, we were able to cultivate them in less than 3 weeks. The initial differentiation and neural induction of the neurosphere occurred within the first week, followed by maturation, including regional patterning and the formation of complex networks, during the subsequent 2 weeks under the influence of magnetized AuNPs. Furthermore, we observed a significant enhancement in neurogenic maturation in the brain organoids, as evidenced by increased histone acetylation in the presence of electromagnetic AuNPs. Consequently, electromagnetic AuNPs offer a promising in vitro system for efficiently generating more advanced human brain organoids that closely resemble the complexity of the human brain.
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Affiliation(s)
- Hongwon Kim
- Laboratory of Stem Cells & Gene Editing, Department of Chemistry, Dongguk University, Pildong-Ro 1-Gil 30, Jung-Gu, Seoul, 04620, Republic of Korea
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, NJ, 08854, USA
| | - Yoo-Jung Lee
- Laboratory of Stem Cells & Gene Editing, Department of Chemistry, Dongguk University, Pildong-Ro 1-Gil 30, Jung-Gu, Seoul, 04620, Republic of Korea
| | - Youngeun Kwon
- Laboratory of Protein Engineering, Department of Biomedical Engineering, Dongguk University, Seoul, 04620, Republic of Korea
| | - Jongpil Kim
- Laboratory of Stem Cells & Gene Editing, Department of Chemistry, Dongguk University, Pildong-Ro 1-Gil 30, Jung-Gu, Seoul, 04620, Republic of Korea.
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5
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Zheng W, Wang L, He W, Hu X, Zhu Q, Gu L, Jiang C. Transcriptome profiles and chromatin states in mouse androgenetic haploid embryonic stem cells. Cell Prolif 2023; 56:e13436. [PMID: 36855927 PMCID: PMC10472531 DOI: 10.1111/cpr.13436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 02/12/2023] [Accepted: 02/17/2023] [Indexed: 03/02/2023] Open
Abstract
Haploid embryonic stem cells (haESCs) are derived from the inner cell mass of the haploid blastocyst, containing only one set of chromosomes. Extensive and accurate chromatin remodelling occurs during haESC derivation, but the intrinsic transcriptome profiles and chromatin structure of haESCs have not been fully explored. We profiled the transcriptomes, nucleosome positioning, and key histone modifications of four mouse haESC lines, and compared these profiles with those of other closely-related stem cell lines, MII oocytes, round spermatids, sperm, and mouse embryonic fibroblasts. haESCs had transcriptome profiles closer to those of naïve pluripotent stem cells. Consistent with the one X chromosome in haESCs, Xist was repressed, indicating no X chromosome inactivation. haESCs and ESCs shared a similar global chromatin structure. However, a nucleosome depletion region was identified in 2056 promoters in ESCs, which was absent in haESCs. Furthermore, three characteristic spatial relationships were formed between transcription factor motifs and nucleosomes in both haESCs and ESCs, specifically in the linker region, on the nucleosome central surface, and nucleosome borders. Furthermore, the chromatin state of 4259 enhancers was off in haESCs but active in ESCs. Functional annotation of these enhancers revealed enrichment in regulation of the cell cycle, a predominantly reported mechanism of haESC self-diploidization. Notably, the transcriptome profiles and chromatin structure of haESCs were highly preserved during passaging but different from those of differentiated cell types.
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Affiliation(s)
- Weisheng Zheng
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Orthopaedic Department of Tongji Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and TechnologyTongji UniversityShanghaiChina
| | - Liping Wang
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Orthopaedic Department of Tongji Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and TechnologyTongji UniversityShanghaiChina
| | - Wenteng He
- Institute for Regenerative Medicine, Shanghai East Hospital, School of Life Sciences and TechnologyTongji UniversityShanghaiChina
| | - Xinjie Hu
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Orthopaedic Department of Tongji Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and TechnologyTongji UniversityShanghaiChina
| | - Qianshu Zhu
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Orthopaedic Department of Tongji Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and TechnologyTongji UniversityShanghaiChina
| | - Liang Gu
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Orthopaedic Department of Tongji Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and TechnologyTongji UniversityShanghaiChina
| | - Cizhong Jiang
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Orthopaedic Department of Tongji Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and TechnologyTongji UniversityShanghaiChina
- Frontier Science Center for Stem Cell ResearchTongji UniversityShanghaiChina
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6
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Kar S, Niharika, Roy A, Patra SK. Overexpression of SOX2 Gene by Histone Modifications: SOX2 Enhances Human Prostate and Breast Cancer Progression by Prevention of Apoptosis and Enhancing Cell Proliferation. Oncology 2023; 101:591-608. [PMID: 37549026 DOI: 10.1159/000531195] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 05/02/2023] [Indexed: 08/09/2023]
Abstract
INTRODUCTION SOX2 plays a crucial role in tumor development, cancer stem cell maintenance, and cancer progression. Mechanisms of SOX2 gene regulation in human breast and prostate cancers are not established yet. METHODS SOX2 expression in prostate and breast cancer tissues and cell lines was determined by qRT-PCR, Western blot, and immunochemistry, followed by the investigation of pro-tumorigenic properties like cell proliferation, migration, and apoptosis by gene knockdown and treatment with epigenetic modulators and ChIP. RESULTS Prostate and breast cancer tissues showed very high expression of SOX2. All cancer cell lines DU145 and PC3 (prostate) and MCF7 and MDA-MB-231 (breast) exhibited high expression of SOX2. Inhibition of SOX2 drastically decreased cell proliferation and migration. Epigenetic modulators enhanced SOX2 gene expression in both cancer types. DNA methylation pattern in SOX2 promoter could not be appreciably counted for SOX2 overexpression. Activation of SOX2 gene promoter was due to very high deposition of H3K4me3 and H3K9acS10p and drastic decrease of H3K9me3 and H3K27me3. CONCLUSION Histone modification is crucial for the overexpression of SOX2 during tumor development and cancer progression. These findings show the avenue of co-targeting SOX2 and its active epigenetic modifier enzymes to effectively treat aggressive prostate and breast cancers.
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Affiliation(s)
- Swayamsiddha Kar
- Epigenetics and Cancer Research Laboratory, Biochemistry and Molecular Biology Group, Department of Life Science, National Institute of Technology, Rourkela, India
| | - Niharika
- Epigenetics and Cancer Research Laboratory, Biochemistry and Molecular Biology Group, Department of Life Science, National Institute of Technology, Rourkela, India
| | - Ankan Roy
- Epigenetics and Cancer Research Laboratory, Biochemistry and Molecular Biology Group, Department of Life Science, National Institute of Technology, Rourkela, India
| | - Samir Kumar Patra
- Epigenetics and Cancer Research Laboratory, Biochemistry and Molecular Biology Group, Department of Life Science, National Institute of Technology, Rourkela, India
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Liu X, Guo C, Leng T, Fan Z, Mai J, Chen J, Xu J, Li Q, Jiang B, Sai K, Yang W, Gu J, Wang J, Sun S, Chen Z, Zhong Y, Liang X, Chen C, Cai J, Lin Y, Liang J, Hu J, Yan G, Zhu W, Yin W. Differential regulation of H3K9/H3K14 acetylation by small molecules drives neuron-fate-induction of glioma cell. Cell Death Dis 2023; 14:142. [PMID: 36805688 PMCID: PMC9941105 DOI: 10.1038/s41419-023-05611-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 01/20/2023] [Accepted: 01/23/2023] [Indexed: 02/22/2023]
Abstract
Differentiation therapy using small molecules is a promising strategy for improving the prognosis of glioblastoma (GBM). Histone acetylation plays an important role in cell fate determination. Nevertheless, whether histone acetylation in specific sites determines GBM cells fate remains to be explored. Through screening from a 349 small molecule-library, we identified that histone deacetylase inhibitor (HDACi) MS-275 synergized with 8-CPT-cAMP was able to transdifferentiate U87MG GBM cells into neuron-like cells, which were characterized by cell cycle arrest, rich neuron biomarkers, and typical neuron electrophysiology. Intriguingly, acetylation tags of histone 3 at lysine 9 (H3K9ac) were decreased in the promoter of multiple oncogenes and cell cycle genes, while ones of H3K9ac and histone 3 at lysine 14 (H3K14ac) were increased in the promoter of neuron-specific genes. We then compiled a list of genes controlled by H3K9ac and H3K14ac, and proved that it is a good predictive power for pathologic grading and survival prediction. Moreover, cAMP agonist combined with HDACi also induced glioma stem cells (GSCs) to differentiate into neuron-like cells through the regulation of H3K9ac/K14ac, indicating that combined induction has the potential for recurrence-preventive application. Furthermore, the combination of cAMP activator plus HDACi significantly repressed the tumor growth in a subcutaneous GSC-derived tumor model, and temozolomide cooperated with the differentiation-inducing combination to prolong the survival in an orthotopic GSC-derived tumor model. These findings highlight epigenetic reprogramming through H3K9ac and H3K14ac as a novel approach for driving neuron-fate-induction of GBM cells.
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Affiliation(s)
- Xincheng Liu
- grid.12981.330000 0001 2360 039XDepartment of Pharmacology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080 P. R. China ,grid.284723.80000 0000 8877 7471Department of Emergency Medicine, Guangdong Cardiovascular Institute, Guangdong Provincial People’s Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, 510080 P. R. China
| | - Cui Guo
- grid.12981.330000 0001 2360 039XDepartment of Pharmacology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080 P. R. China
| | - Tiandong Leng
- grid.9001.80000 0001 2228 775XDepartment of Neuroscience, Morehouse School of Medicine, Atlanta, GA 30310 USA
| | - Zhen Fan
- grid.12981.330000 0001 2360 039XDepartment of Pharmacology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080 P. R. China
| | - Jialuo Mai
- grid.12981.330000 0001 2360 039XDepartment of Pharmacology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080 P. R. China
| | - Jiehong Chen
- grid.12981.330000 0001 2360 039XDepartment of Pharmacology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080 P. R. China
| | - Jinhai Xu
- grid.12981.330000 0001 2360 039XGuangdong Province Key Laboratory of Brain Function and Disease, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080 P. R. China
| | - Qianyi Li
- grid.12981.330000 0001 2360 039XGuangdong Province Key Laboratory of Brain Function and Disease, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080 P. R. China
| | - Bin Jiang
- grid.12981.330000 0001 2360 039XGuangdong Province Key Laboratory of Brain Function and Disease, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080 P. R. China
| | - Ke Sai
- grid.488530.20000 0004 1803 6191Department of Neurosurgery/Neuro-oncology, Sun Yat-sen University Cancer Center, Guangzhou, 510060 P. R. China ,grid.488530.20000 0004 1803 6191State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, 510060 P. R. China
| | - Wenzhuo Yang
- grid.488530.20000 0004 1803 6191Department of Neurosurgery/Neuro-oncology, Sun Yat-sen University Cancer Center, Guangzhou, 510060 P. R. China ,grid.488530.20000 0004 1803 6191State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, 510060 P. R. China
| | - Jiayu Gu
- grid.12981.330000 0001 2360 039XDepartment of Pharmacology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080 P. R. China
| | - Jingyi Wang
- grid.12981.330000 0001 2360 039XDepartment of Pharmacology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080 P. R. China
| | - Shuxin Sun
- grid.488530.20000 0004 1803 6191Department of Neurosurgery/Neuro-oncology, Sun Yat-sen University Cancer Center, Guangzhou, 510060 P. R. China ,grid.488530.20000 0004 1803 6191State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, 510060 P. R. China
| | - Zhijie Chen
- grid.488530.20000 0004 1803 6191Department of Neurosurgery/Neuro-oncology, Sun Yat-sen University Cancer Center, Guangzhou, 510060 P. R. China ,grid.488530.20000 0004 1803 6191State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, 510060 P. R. China
| | - Yingqian Zhong
- grid.12981.330000 0001 2360 039XDepartment of Pharmacology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080 P. R. China
| | - Xuanming Liang
- grid.12981.330000 0001 2360 039XDepartment of Pharmacology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080 P. R. China
| | - Chaoxin Chen
- grid.12981.330000 0001 2360 039XDepartment of Pharmacology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080 P. R. China
| | - Jing Cai
- grid.12981.330000 0001 2360 039XDepartment of Pharmacology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080 P. R. China
| | - Yuan Lin
- grid.12981.330000 0001 2360 039XDepartment of Pharmacology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080 P. R. China
| | - Jiankai Liang
- grid.12981.330000 0001 2360 039XDepartment of Pharmacology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080 P. R. China
| | - Jun Hu
- grid.12981.330000 0001 2360 039XDepartment of Pharmacology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080 P. R. China
| | - Guangmei Yan
- grid.12981.330000 0001 2360 039XDepartment of Pharmacology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080 P. R. China
| | - Wenbo Zhu
- Department of Pharmacology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, P. R. China.
| | - Wei Yin
- Department of Biochemistry and Molecular Biology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, P. R. China.
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Princová J, Salat-Canela C, Daněk P, Marešová A, de Cubas L, Bähler J, Ayté J, Hidalgo E, Převorovský M. Perturbed fatty-acid metabolism is linked to localized chromatin hyperacetylation, increased stress-response gene expression and resistance to oxidative stress. PLoS Genet 2023; 19:e1010582. [PMID: 36626368 PMCID: PMC9870116 DOI: 10.1371/journal.pgen.1010582] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 01/23/2023] [Accepted: 12/19/2022] [Indexed: 01/11/2023] Open
Abstract
Oxidative stress is associated with cardiovascular and neurodegenerative diseases, diabetes, cancer, psychiatric disorders and aging. In order to counteract, eliminate and/or adapt to the sources of stress, cells possess elaborate stress-response mechanisms, which also operate at the level of regulating transcription. Interestingly, it is becoming apparent that the metabolic state of the cell and certain metabolites can directly control the epigenetic information and gene expression. In the fission yeast Schizosaccharomyces pombe, the conserved Sty1 stress-activated protein kinase cascade is the main pathway responding to most types of stresses, and regulates the transcription of hundreds of genes via the Atf1 transcription factor. Here we report that fission yeast cells defective in fatty acid synthesis (cbf11, mga2 and ACC/cut6 mutants; FAS inhibition) show increased expression of a subset of stress-response genes. This altered gene expression depends on Sty1-Atf1, the Pap1 transcription factor, and the Gcn5 and Mst1 histone acetyltransferases, is associated with increased acetylation of histone H3 at lysine 9 in the corresponding gene promoters, and results in increased cellular resistance to oxidative stress. We propose that changes in lipid metabolism can regulate the chromatin and transcription of specific stress-response genes, which in turn might help cells to maintain redox homeostasis.
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Affiliation(s)
- Jarmila Princová
- Laboratory of Microbial Genomics, Department of Cell Biology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Clàudia Salat-Canela
- Oxidative Stress and Cell Cycle Group, Universitat Pompeu Fabra, C/Dr. Aiguader, Barcelona, Spain
| | - Petr Daněk
- Laboratory of Microbial Genomics, Department of Cell Biology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Anna Marešová
- Laboratory of Microbial Genomics, Department of Cell Biology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Laura de Cubas
- Oxidative Stress and Cell Cycle Group, Universitat Pompeu Fabra, C/Dr. Aiguader, Barcelona, Spain
| | - Jürg Bähler
- Institute of Healthy Ageing and Department of Genetics, Evolution & Environment, University College London, London, United Kingdom
| | - José Ayté
- Oxidative Stress and Cell Cycle Group, Universitat Pompeu Fabra, C/Dr. Aiguader, Barcelona, Spain
| | - Elena Hidalgo
- Oxidative Stress and Cell Cycle Group, Universitat Pompeu Fabra, C/Dr. Aiguader, Barcelona, Spain
| | - Martin Převorovský
- Laboratory of Microbial Genomics, Department of Cell Biology, Faculty of Science, Charles University, Prague, Czech Republic
- * E-mail:
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9
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Dijkwel Y, Tremethick DJ. The Role of the Histone Variant H2A.Z in Metazoan Development. J Dev Biol 2022; 10:jdb10030028. [PMID: 35893123 PMCID: PMC9326617 DOI: 10.3390/jdb10030028] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 06/12/2022] [Accepted: 06/23/2022] [Indexed: 12/10/2022] Open
Abstract
During the emergence and radiation of complex multicellular eukaryotes from unicellular ancestors, transcriptional systems evolved by becoming more complex to provide the basis for this morphological diversity. The way eukaryotic genomes are packaged into a highly complex structure, known as chromatin, underpins this evolution of transcriptional regulation. Chromatin structure is controlled by a variety of different epigenetic mechanisms, including the major mechanism for altering the biochemical makeup of the nucleosome by replacing core histones with their variant forms. The histone H2A variant H2A.Z is particularly important in early metazoan development because, without it, embryos cease to develop and die. However, H2A.Z is also required for many differentiation steps beyond the stage that H2A.Z-knockout embryos die. H2A.Z can facilitate the activation and repression of genes that are important for pluripotency and differentiation, and acts through a variety of different molecular mechanisms that depend upon its modification status, its interaction with histone and nonhistone partners, and where it is deposited within the genome. In this review, we discuss the current knowledge about the different mechanisms by which H2A.Z regulates chromatin function at various developmental stages and the chromatin remodeling complexes that determine when and where H2A.Z is deposited.
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10
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Tabibzadeh S. Resolving Geroplasticity to the Balance of Rejuvenins and Geriatrins. Aging Dis 2022; 13:1664-1714. [DOI: 10.14336/ad.2022.0414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2022] [Accepted: 04/14/2022] [Indexed: 11/18/2022] Open
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11
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Sun C, An Q, Li R, Chen S, Gu X, An S, Wang Z. Calcitonin gene-related peptide induces the histone H3 lysine 9 acetylation in astrocytes associated with neuroinflammation in rats with neuropathic pain. CNS Neurosci Ther 2021; 27:1409-1424. [PMID: 34397151 PMCID: PMC8504526 DOI: 10.1111/cns.13720] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Revised: 08/04/2021] [Accepted: 08/06/2021] [Indexed: 02/06/2023] Open
Abstract
Aims Calcitonin gene‐related peptide (CGRP) as a regulator of astrocyte activation may facilitate spinal nociceptive processing. Histone H3 lysine 9 acetylation (H3K9ac) is considered an important regulator of cytokine and chemokine gene expression after peripheral nerve injury. In this study, we explored the relationship between CGRP and H3K9ac in the activation of astrocytes, and elucidated the underlying mechanisms in the pathogenesis of chronic neuropathic pain. Methods Astroglial cells (C6) were treated with CGRP and differentially enrichments of H3K9ac on gene promoters were examined using ChIP‐seq. A chronic constriction injury (CCI) rat model was used to evaluate the role of CGRP on astrocyte activation and H3K9ac signaling in CCI‐induced neuropathic pain. Specific inhibitors were employed to delineate the involved signaling. Results Intrathecal injection of CGRP and CCI increased the number of astrocytes displaying H3K9ac in the spinal dorsal horn of rats. Treatment of CGRP was able to up‐regulate H3K9ac and glial fibrillary acidic protein (GFAP) expression in astroglial cells. ChIP‐seq data indicated that CGRP significantly altered H3K9ac enrichments on gene promoters in astroglial cells following CGRP treatment, including 151 gaining H3K9ac and 111 losing this mark, which mostly enriched in proliferation, autophagy, and macrophage chemotaxis processes. qRT‐PCR verified expressions of representative candidate genes (ATG12, ATG4C, CX3CR1, MMP28, MTMR14, HMOX1, RET) and RTCA verified astrocyte proliferation. Additionally, CGRP treatment increased the expression of H3K9ac, CX3CR1, and IL‐1β in the spinal dorsal horn. CGRP antagonist and HAT inhibitor attenuated mechanical and thermal hyperalgesia in CCI rats. Such analgesic effects were concurrently associated with the reduced levels of H3K9ac, CX3CR1, and IL‐1β in the spinal dorsal horn of CCI rats. Conclusion Our findings highly indicate that CGRP is associated with the development of neuropathic pain through astrocytes‐mediated neuroinflammatory responses via H3K9ac in spinal dorsa horn following nerve injury. This study found that CGRP act on their astrocytic receptors and lead to H3K9 acetylation (H3K9ac), which are mainly associated with proliferation‐, autophagy‐, and inflammation‐related gene expression. The number of astrocytes with H3K9ac expression is increased after nerve injury. Inhibition of CGRP attenuates the development of neuropathic pain, which was accompanied by the suppression of H3K9ac, CX3CR1, and IL‐1β expression in CCI rats.
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Affiliation(s)
- Chenyan Sun
- Department of Human Anatomy, Shandong First Medical University & Shandong Academy of Medical Sciences, Taian, China
| | - Qi An
- Department of Human Anatomy, Shandong First Medical University & Shandong Academy of Medical Sciences, Taian, China
| | - Ruidi Li
- Department of Human Anatomy, Shandong First Medical University & Shandong Academy of Medical Sciences, Taian, China
| | - Shuhui Chen
- Department of Human Anatomy, Shandong First Medical University & Shandong Academy of Medical Sciences, Taian, China
| | - Xinpei Gu
- Department of Human Anatomy, Shandong First Medical University & Shandong Academy of Medical Sciences, Taian, China
| | - Shuhong An
- Department of Human Anatomy, Shandong First Medical University & Shandong Academy of Medical Sciences, Taian, China
| | - Zhaojin Wang
- Department of Human Anatomy, Shandong First Medical University & Shandong Academy of Medical Sciences, Taian, China
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12
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Fan X, Masamsetti VP, Sun JQ, Engholm-Keller K, Osteil P, Studdert J, Graham ME, Fossat N, Tam PP. TWIST1 and chromatin regulatory proteins interact to guide neural crest cell differentiation. eLife 2021; 10:62873. [PMID: 33554859 PMCID: PMC7968925 DOI: 10.7554/elife.62873] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Accepted: 02/05/2021] [Indexed: 12/11/2022] Open
Abstract
Protein interaction is critical molecular regulatory activity underlining cellular functions and precise cell fate choices. Using TWIST1 BioID-proximity-labeling and network propagation analyses, we discovered and characterized a TWIST-chromatin regulatory module (TWIST1-CRM) in the neural crest cells (NCC). Combinatorial perturbation of core members of TWIST1-CRM: TWIST1, CHD7, CHD8, and WHSC1 in cell models and mouse embryos revealed that loss of the function of the regulatory module resulted in abnormal differentiation of NCCs and compromised craniofacial tissue patterning. Following NCC delamination, low level of TWIST1-CRM activity is instrumental to stabilize the early NCC signatures and migratory potential by repressing the neural stem cell programs. High level of TWIST1 module activity at later phases commits the cells to the ectomesenchyme. Our study further revealed the functional interdependency of TWIST1 and potential neurocristopathy factors in NCC development. Shaping the head and face during development relies on a complex ballet of molecular signals that orchestrates the movement and specialization of various groups of cells. In animals with a backbone for example, neural crest cells (NCCs for short) can march long distances from the developing spine to become some of the tissues that form the skull and cartilage but also the pigment cells and nervous system. NCCs mature into specific cell types thanks to a complex array of factors which trigger a precise sequence of binary fate decisions at the right time and place. Amongst these factors, the protein TWIST1 can set up a cascade of genetic events that control how NCCs will ultimately form tissues in the head. To do so, the TWIST1 protein interacts with many other molecular actors, many of which are still unknown. To find some of these partners, Fan et al. studied TWIST1 in the NCCs of mice and cells grown in the lab. The experiments showed that TWIST1 interacted with CHD7, CHD8 and WHSC1, three proteins that help to switch genes on and off, and which contribute to NCCs moving across the head during development. Further work by Fan et al. then revealed that together, these molecular actors are critical for NCCs to form cells that will form facial bones and cartilage, as opposed to becoming neurons. This result helps to show that there is a trade-off between NCCs forming the face or being part of the nervous system. One in three babies born with a birth defect shows anomalies of the head and face: understanding the exact mechanisms by which NCCs contribute to these structures may help to better predict risks for parents, or to develop new approaches for treatment.
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Affiliation(s)
- Xiaochen Fan
- Embryology Unit, Children's Medical Research Institute, The University of Sydney, Sydney, Australia.,The University of Sydney, School of Medical Sciences, Faculty of Medicine and Health, Sydney, Australia
| | - V Pragathi Masamsetti
- Embryology Unit, Children's Medical Research Institute, The University of Sydney, Sydney, Australia
| | - Jane Qj Sun
- Embryology Unit, Children's Medical Research Institute, The University of Sydney, Sydney, Australia
| | - Kasper Engholm-Keller
- Synapse Proteomics Group, Children's Medical Research Institute, The University of Sydney, Sydney, Australia
| | - Pierre Osteil
- Embryology Unit, Children's Medical Research Institute, The University of Sydney, Sydney, Australia
| | - Joshua Studdert
- Embryology Unit, Children's Medical Research Institute, The University of Sydney, Sydney, Australia
| | - Mark E Graham
- Synapse Proteomics Group, Children's Medical Research Institute, The University of Sydney, Sydney, Australia
| | - Nicolas Fossat
- Embryology Unit, Children's Medical Research Institute, The University of Sydney, Sydney, Australia.,The University of Sydney, School of Medical Sciences, Faculty of Medicine and Health, Sydney, Australia
| | - Patrick Pl Tam
- Embryology Unit, Children's Medical Research Institute, The University of Sydney, Sydney, Australia.,The University of Sydney, School of Medical Sciences, Faculty of Medicine and Health, Sydney, Australia
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13
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Xu X, Du Y, Ma L, Zhang S, Shi L, Chen Z, Zhou Z, Hui Y, Liu Y, Fang Y, Fan B, Liu Z, Li N, Zhou S, Jiang C, Liu L, Zhang X. Mapping germ-layer specification preventing genes in hPSCs via genome-scale CRISPR screening. iScience 2021; 24:101926. [PMID: 33385119 PMCID: PMC7772566 DOI: 10.1016/j.isci.2020.101926] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 08/17/2020] [Accepted: 12/07/2020] [Indexed: 12/21/2022] Open
Abstract
Understanding the biological processes that determine the entry of three germ layers of human pluripotent stem cells (hPSCs) is a central question in developmental and stem cell biology. Here, we genetically engineered hPSCs with the germ layer reporter and inducible CRISPR/Cas9 knockout system, and a genome-scale screening was performed to define pathways restricting germ layer specification. Genes clustered in the key biological processes, including embryonic development, mRNA processing, metabolism, and epigenetic regulation, were centered in the governance of pluripotency and lineage development. Other than typical pluripotent transcription factors and signaling molecules, loss of function of mesendodermal specifiers resulted in advanced neuroectodermal differentiation, given their inter-germ layer antagonizing effect. Regarding the epigenetic superfamily, microRNAs enriched in hPSCs showed clear germ layer-targeting specificity. The cholesterol synthesis pathway maintained hPSCs via retardation of neuroectoderm specification. Thus, in this study, we identified a full landscape of genetic wiring and biological processes that control hPSC self-renewal and trilineage specification.
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Affiliation(s)
- Xiangjie Xu
- Translational Medical Center for Stem Cell Therapy, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China
- Key Laboratory of Neuroregeneration of Shanghai Universities, Tongji University School of Medicine, Shanghai 200092, China
- Shanghai Institute of Stem Cell Research and Clinical Translation, Shanghai 200120, China
| | - Yanhua Du
- Department of Immunology and Microbiology, Shanghai Institute of Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Lin Ma
- Translational Medical Center for Stem Cell Therapy, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China
- Key Laboratory of Neuroregeneration of Shanghai Universities, Tongji University School of Medicine, Shanghai 200092, China
- Shanghai Institute of Stem Cell Research and Clinical Translation, Shanghai 200120, China
- Department of Pathology and Pathophysiology, Tongji University School of Medicine, Shanghai 200092, China
| | - Shuwei Zhang
- Translational Medical Center for Stem Cell Therapy, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China
- Key Laboratory of Neuroregeneration of Shanghai Universities, Tongji University School of Medicine, Shanghai 200092, China
- Shanghai Institute of Stem Cell Research and Clinical Translation, Shanghai 200120, China
| | - Lei Shi
- Translational Medical Center for Stem Cell Therapy, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China
- Key Laboratory of Neuroregeneration of Shanghai Universities, Tongji University School of Medicine, Shanghai 200092, China
- Shanghai Institute of Stem Cell Research and Clinical Translation, Shanghai 200120, China
| | - Zhenyu Chen
- Translational Medical Center for Stem Cell Therapy, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China
- Key Laboratory of Neuroregeneration of Shanghai Universities, Tongji University School of Medicine, Shanghai 200092, China
- Shanghai Institute of Stem Cell Research and Clinical Translation, Shanghai 200120, China
| | - Zhongshu Zhou
- Translational Medical Center for Stem Cell Therapy, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China
- Key Laboratory of Neuroregeneration of Shanghai Universities, Tongji University School of Medicine, Shanghai 200092, China
- Shanghai Institute of Stem Cell Research and Clinical Translation, Shanghai 200120, China
| | - Yi Hui
- Translational Medical Center for Stem Cell Therapy, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China
- Key Laboratory of Neuroregeneration of Shanghai Universities, Tongji University School of Medicine, Shanghai 200092, China
- Shanghai Institute of Stem Cell Research and Clinical Translation, Shanghai 200120, China
| | - Yang Liu
- Translational Medical Center for Stem Cell Therapy, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China
- Key Laboratory of Neuroregeneration of Shanghai Universities, Tongji University School of Medicine, Shanghai 200092, China
- Shanghai Institute of Stem Cell Research and Clinical Translation, Shanghai 200120, China
| | - Yujiang Fang
- Translational Medical Center for Stem Cell Therapy, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China
- Key Laboratory of Neuroregeneration of Shanghai Universities, Tongji University School of Medicine, Shanghai 200092, China
- Shanghai Institute of Stem Cell Research and Clinical Translation, Shanghai 200120, China
- Department of Pathology and Pathophysiology, Tongji University School of Medicine, Shanghai 200092, China
| | - Beibei Fan
- Translational Medical Center for Stem Cell Therapy, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China
- Key Laboratory of Neuroregeneration of Shanghai Universities, Tongji University School of Medicine, Shanghai 200092, China
- Shanghai Institute of Stem Cell Research and Clinical Translation, Shanghai 200120, China
| | - Zhongliang Liu
- Translational Medical Center for Stem Cell Therapy, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China
- Key Laboratory of Neuroregeneration of Shanghai Universities, Tongji University School of Medicine, Shanghai 200092, China
- Shanghai Institute of Stem Cell Research and Clinical Translation, Shanghai 200120, China
| | - Nan Li
- Translational Medical Center for Stem Cell Therapy, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China
- Key Laboratory of Neuroregeneration of Shanghai Universities, Tongji University School of Medicine, Shanghai 200092, China
- Shanghai Institute of Stem Cell Research and Clinical Translation, Shanghai 200120, China
| | - Shanshan Zhou
- Translational Medical Center for Stem Cell Therapy, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China
- Key Laboratory of Neuroregeneration of Shanghai Universities, Tongji University School of Medicine, Shanghai 200092, China
- Shanghai Institute of Stem Cell Research and Clinical Translation, Shanghai 200120, China
| | - Cizhong Jiang
- The School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Ling Liu
- Translational Medical Center for Stem Cell Therapy, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China
- Key Laboratory of Neuroregeneration of Shanghai Universities, Tongji University School of Medicine, Shanghai 200092, China
- Shanghai Institute of Stem Cell Research and Clinical Translation, Shanghai 200120, China
- Brain and Spinal Cord Clinical Research Center, Tongji University School of Medicine, Shanghai 200092, China
- Department of Pathology and Pathophysiology, Tongji University School of Medicine, Shanghai 200092, China
| | - Xiaoqing Zhang
- Translational Medical Center for Stem Cell Therapy, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China
- Key Laboratory of Reconstruction and Regeneration of Spine and Spinal Cord Injury, Ministry of Education, Shanghai 200065, China
- Key Laboratory of Neuroregeneration of Shanghai Universities, Tongji University School of Medicine, Shanghai 200092, China
- Tsingtao Advanced Research Institute, Tongji University, Qingdao 266071, China
- Shanghai Institute of Stem Cell Research and Clinical Translation, Shanghai 200120, China
- Brain and Spinal Cord Clinical Research Center, Tongji University School of Medicine, Shanghai 200092, China
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14
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Chen H, Liang H. A High-Resolution Map of Human Enhancer RNA Loci Characterizes Super-enhancer Activities in Cancer. Cancer Cell 2020; 38:701-715.e5. [PMID: 33007258 PMCID: PMC7658066 DOI: 10.1016/j.ccell.2020.08.020] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Revised: 07/21/2020] [Accepted: 08/28/2020] [Indexed: 12/20/2022]
Abstract
Although enhancers play critical roles in cancer, quantifying enhancer activities in clinical samples remains challenging, especially for super-enhancers. Enhancer activities can be inferred from enhancer RNA (eRNA) signals, which requires enhancer transcription loci definition. Only a small proportion of human eRNA loci has been precisely identified, limiting investigations of enhancer-mediated oncogenic mechanisms. Here, we characterize super-enhancer regions using aggregated RNA sequencing (RNA-seq) data from large cohorts. Super-enhancers usually contain discrete loci featuring sharp eRNA expression peaks. We identify >300,000 eRNA loci in ∼377 Mb super-enhancer regions that are regulated by evolutionarily conserved, well-positioned nucleosomes and are frequently dysregulated in cancer. The eRNAs provide explanatory power for cancer phenotypes beyond that provided by mRNA expression through resolving intratumoral heterogeneity with enhancer cell-type specificity. Our study provides a high-resolution map of eRNA loci through which super-enhancer activities can be quantified by RNA-seq and a user-friendly data portal, enabling a broad range of biomedical investigations.
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Affiliation(s)
- Han Chen
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Han Liang
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
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15
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Hu X, Zheng W, Zhu Q, Gu L, Du Y, Han Z, Zhang X, Carter DR, Cheung BB, Qiu A, Jiang C. Increase in DNA Damage by MYCN Knockdown Through Regulating Nucleosome Organization and Chromatin State in Neuroblastoma. Front Genet 2019; 10:684. [PMID: 31396265 PMCID: PMC6667652 DOI: 10.3389/fgene.2019.00684] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 07/01/2019] [Indexed: 11/25/2022] Open
Abstract
As a transcription factor, MYCN regulates myriad target genes including the histone chaperone FACT. Moreover, FACT and MYCN expression form a forward feedback loop in neuroblastoma. It is unclear whether MYCN is involved in chromatin remodeling in neuroblastoma through regulation of its target genes. We showed here that MYCN knockdown resulted in loss of the nucleosome-free regions through nucleosome assembly in the promoters of genes functionally enriched for DNA repair. The active mark H3K9ac was removed or replaced by the repressive mark H3K27me3 in the promoters of double-strand break repair-related genes upon MYCN knockdown. Such chromatin state alterations occurred only in MYCN-bound promoters. Consistently, MYCN knockdown resulted in a marked increase in DNA damage in the treatment with hydroxyurea. In contrast, nucleosome reorganization and histone modification changes in the enhancers largely included target genes with tumorigenesis-related functions such as cell proliferation, cell migration, and cell–cell adhesion. The chromatin state significantly changed in both MYCN-bound and MYCN-unbound enhancers upon MYCN knockdown. Furthermore, MYCN knockdown independently regulated chromatin remodeling in the promoters and the enhancers. These findings reveal the novel epigenetic regulatory role of MYCN in chromatin remodeling and provide an alternative potential epigenetic strategy for MYCN-driven neuroblastoma treatment.
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Affiliation(s)
- Xinjie Hu
- Institute of Translational Research, Tongji Hospital, the School of Life Sciences and Technology, Shanghai Key Laboratory of Signaling and Disease Research, Tongji University, Shanghai, China
| | - Weisheng Zheng
- Institute of Translational Research, Tongji Hospital, the School of Life Sciences and Technology, Shanghai Key Laboratory of Signaling and Disease Research, Tongji University, Shanghai, China
| | - Qianshu Zhu
- Institute of Translational Research, Tongji Hospital, the School of Life Sciences and Technology, Shanghai Key Laboratory of Signaling and Disease Research, Tongji University, Shanghai, China
| | - Liang Gu
- Institute of Translational Research, Tongji Hospital, the School of Life Sciences and Technology, Shanghai Key Laboratory of Signaling and Disease Research, Tongji University, Shanghai, China
| | - Yanhua Du
- Institute of Translational Research, Tongji Hospital, the School of Life Sciences and Technology, Shanghai Key Laboratory of Signaling and Disease Research, Tongji University, Shanghai, China
| | - Zhe Han
- Institute of Translational Research, Tongji Hospital, the School of Life Sciences and Technology, Shanghai Key Laboratory of Signaling and Disease Research, Tongji University, Shanghai, China
| | - Xiaobai Zhang
- Institute of Translational Research, Tongji Hospital, the School of Life Sciences and Technology, Shanghai Key Laboratory of Signaling and Disease Research, Tongji University, Shanghai, China
| | - Daniel R Carter
- Children's Cancer Institute Australia, Lowy Cancer Research Centre, UNSW Sydney, Kensington, NSW, Australia.,School of Women's and Children's Health, UNSW Sydney, Randwick, NSW, Australia.,School of Biomedical Engineering, University of Technology, Sydney, NSW, Australia
| | - Belamy B Cheung
- Children's Cancer Institute Australia, Lowy Cancer Research Centre, UNSW Sydney, Kensington, NSW, Australia.,School of Women's and Children's Health, UNSW Sydney, Randwick, NSW, Australia
| | - Andong Qiu
- Institute of Translational Research, Tongji Hospital, the School of Life Sciences and Technology, Shanghai Key Laboratory of Signaling and Disease Research, Tongji University, Shanghai, China.,The Research Center of Stem Cells and Ageing, Tsingtao Advanced Research Institute, Tongji University, Tsingdao, China
| | - Cizhong Jiang
- Institute of Translational Research, Tongji Hospital, the School of Life Sciences and Technology, Shanghai Key Laboratory of Signaling and Disease Research, Tongji University, Shanghai, China.,The Research Center of Stem Cells and Ageing, Tsingtao Advanced Research Institute, Tongji University, Tsingdao, China
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16
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Chen X, Ye Y, Gu L, Sun J, Du Y, Liu WJ, Li W, Zhang X, Jiang C. H3K27me3 Signal in the Cis Regulatory Elements Reveals the Differentiation Potential of Progenitors During Drosophila Neuroglial Development. GENOMICS PROTEOMICS & BIOINFORMATICS 2019; 17:297-304. [PMID: 31195140 PMCID: PMC6818177 DOI: 10.1016/j.gpb.2018.12.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Revised: 10/14/2018] [Accepted: 12/14/2018] [Indexed: 01/24/2023]
Abstract
Drosophila neural development undergoes extensive chromatin remodeling and precise epigenetic regulation. However, the roles of chromatin remodeling in establishment and maintenance of cell identity during cell fate transition remain enigmatic. Here, we compared the changes in gene expression, as well as the dynamics of nucleosome positioning and key histone modifications between the four major neural cell types during Drosophila neural development. We find that the neural progenitors can be separated from the terminally differentiated cells based on their gene expression profiles, whereas nucleosome distribution in the flanking regions of transcription start sites fails to identify the relationships between the progenitors and the differentiated cells. H3K27me3 signal in promoters and enhancers can not only distinguish the progenitors from the differentiated cells but also identify the differentiation path of the neural stem cells (NSCs) to the intermediate progenitor cells to the glial cells. In contrast, H3K9ac signal fails to identify the differentiation path, although it activates distinct sets of genes with neuron-specific and glia-related functions during the differentiation of the NSCs into neurons and glia, respectively. Together, our study provides novel insights into the crucial roles of chromatin remodeling in determining cell type during Drosophila neural development.
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Affiliation(s)
- Xiaolong Chen
- Institute of Translational Research, Tongji Hospital, School of Life Sciences and Technology, Shanghai Key Laboratory of Signaling and Disease Research, Tongji University, Shanghai 200092, China
| | - Youqiong Ye
- Institute of Translational Research, Tongji Hospital, School of Life Sciences and Technology, Shanghai Key Laboratory of Signaling and Disease Research, Tongji University, Shanghai 200092, China
| | - Liang Gu
- Institute of Translational Research, Tongji Hospital, School of Life Sciences and Technology, Shanghai Key Laboratory of Signaling and Disease Research, Tongji University, Shanghai 200092, China
| | - Jin Sun
- Institute of Translational Research, Tongji Hospital, School of Life Sciences and Technology, Shanghai Key Laboratory of Signaling and Disease Research, Tongji University, Shanghai 200092, China
| | - Yanhua Du
- Institute of Translational Research, Tongji Hospital, School of Life Sciences and Technology, Shanghai Key Laboratory of Signaling and Disease Research, Tongji University, Shanghai 200092, China
| | - Wen-Ju Liu
- Institute of Translational Research, Tongji Hospital, School of Life Sciences and Technology, Shanghai Key Laboratory of Signaling and Disease Research, Tongji University, Shanghai 200092, China
| | - Wei Li
- Tongji University Library, Tongji University, Shanghai 200092, China
| | - Xiaobai Zhang
- Institute of Translational Research, Tongji Hospital, School of Life Sciences and Technology, Shanghai Key Laboratory of Signaling and Disease Research, Tongji University, Shanghai 200092, China
| | - Cizhong Jiang
- Institute of Translational Research, Tongji Hospital, School of Life Sciences and Technology, Shanghai Key Laboratory of Signaling and Disease Research, Tongji University, Shanghai 200092, China; Research Center of Stem Cells and Ageing, Tsingtao Advanced Research Institute, Tongji University, Tsingtao 266071, China.
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17
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Ma L, Wang Y, Hui Y, Du Y, Chen Z, Feng H, Zhang S, Li N, Song J, Fang Y, Xu X, Shi L, Zhang B, Cheng J, Zhou S, Liu L, Zhang X. WNT/NOTCH Pathway Is Essential for the Maintenance and Expansion of Human MGE Progenitors. Stem Cell Reports 2019; 12:934-949. [PMID: 31056478 PMCID: PMC6524734 DOI: 10.1016/j.stemcr.2019.04.007] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Revised: 04/04/2019] [Accepted: 04/08/2019] [Indexed: 12/18/2022] Open
Abstract
Medial ganglionic eminence (MGE)-like cells yielded from human pluripotent stem cells (hPSCs) hold great potentials for cell therapies of related neurological disorders. However, cues that orchestrate the maintenance versus differentiation of human MGE progenitors, and ways for large-scale expansion of these cells have not been investigated. Here, we report that WNT/CTNNB1 signaling plays an essential role in maintaining MGE-like cells derived from hPSCs. Ablation of CTNNB1 in MGE cells led to precocious cell-cycle exit and advanced neuronal differentiation. Activation of WNT signaling through genetic or chemical approach was sufficient to maintain MGE cells in an expandable manner with authentic neuronal differentiation potencies through activation of endogenous NOTCH signaling. Our findings reveal that WNT/NOTCH signaling cascade is a key player in governing the maintenance versus terminal differentiation of MGE progenitors in humans. Large-scale expansion of functional MGE progenitors for cell therapies can therefore be achieved by modifying WNT/NOTCH pathway. WNT/CTNNB1 signaling is robustly activated in specified human MGE progenitors Ablation of CTNNB1 in human MGE cells leads to advanced neuronal differentiation Activation of WNT signaling maintains MGE progenitors in a proliferative state WNT/CTNNB1 signaling maintains MGE progenitors via activation of NOTCH signaling
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Affiliation(s)
- Lin Ma
- Brain and Spinal Cord Innovative Research Center, Tongji Hospital, Tongji University School of Medicine, Shanghai 200065, China; Key Laboratory of Neuroregeneration of Shanghai Universities, Tongji University School of Medicine, 1239 Siping Road, Room 508, Shanghai 200092, China
| | - Yiran Wang
- Brain and Spinal Cord Innovative Research Center, Tongji Hospital, Tongji University School of Medicine, Shanghai 200065, China; Key Laboratory of Neuroregeneration of Shanghai Universities, Tongji University School of Medicine, 1239 Siping Road, Room 508, Shanghai 200092, China
| | - Yi Hui
- Brain and Spinal Cord Innovative Research Center, Tongji Hospital, Tongji University School of Medicine, Shanghai 200065, China; Key Laboratory of Neuroregeneration of Shanghai Universities, Tongji University School of Medicine, 1239 Siping Road, Room 508, Shanghai 200092, China
| | - Yanhua Du
- Brain and Spinal Cord Innovative Research Center, Tongji Hospital, Tongji University School of Medicine, Shanghai 200065, China; Key Laboratory of Neuroregeneration of Shanghai Universities, Tongji University School of Medicine, 1239 Siping Road, Room 508, Shanghai 200092, China
| | - Zhenyu Chen
- Brain and Spinal Cord Innovative Research Center, Tongji Hospital, Tongji University School of Medicine, Shanghai 200065, China; Key Laboratory of Neuroregeneration of Shanghai Universities, Tongji University School of Medicine, 1239 Siping Road, Room 508, Shanghai 200092, China
| | - Hexi Feng
- Brain and Spinal Cord Innovative Research Center, Tongji Hospital, Tongji University School of Medicine, Shanghai 200065, China; Key Laboratory of Neuroregeneration of Shanghai Universities, Tongji University School of Medicine, 1239 Siping Road, Room 508, Shanghai 200092, China
| | - Shuwei Zhang
- Brain and Spinal Cord Innovative Research Center, Tongji Hospital, Tongji University School of Medicine, Shanghai 200065, China; Key Laboratory of Neuroregeneration of Shanghai Universities, Tongji University School of Medicine, 1239 Siping Road, Room 508, Shanghai 200092, China
| | - Nan Li
- Brain and Spinal Cord Innovative Research Center, Tongji Hospital, Tongji University School of Medicine, Shanghai 200065, China; Key Laboratory of Neuroregeneration of Shanghai Universities, Tongji University School of Medicine, 1239 Siping Road, Room 508, Shanghai 200092, China
| | - Jianren Song
- Brain and Spinal Cord Innovative Research Center, Tongji Hospital, Tongji University School of Medicine, Shanghai 200065, China; Key Laboratory of Reconstruction and Regeneration of Spine and Spinal Cord Injury, Ministry of Education, Shanghai 200065, China
| | - Yujiang Fang
- Brain and Spinal Cord Innovative Research Center, Tongji Hospital, Tongji University School of Medicine, Shanghai 200065, China; Key Laboratory of Neuroregeneration of Shanghai Universities, Tongji University School of Medicine, 1239 Siping Road, Room 508, Shanghai 200092, China
| | - Xiangjie Xu
- Brain and Spinal Cord Innovative Research Center, Tongji Hospital, Tongji University School of Medicine, Shanghai 200065, China; Key Laboratory of Neuroregeneration of Shanghai Universities, Tongji University School of Medicine, 1239 Siping Road, Room 508, Shanghai 200092, China
| | - Lei Shi
- Brain and Spinal Cord Innovative Research Center, Tongji Hospital, Tongji University School of Medicine, Shanghai 200065, China; Key Laboratory of Neuroregeneration of Shanghai Universities, Tongji University School of Medicine, 1239 Siping Road, Room 508, Shanghai 200092, China
| | - Bowen Zhang
- Brain and Spinal Cord Innovative Research Center, Tongji Hospital, Tongji University School of Medicine, Shanghai 200065, China; Key Laboratory of Neuroregeneration of Shanghai Universities, Tongji University School of Medicine, 1239 Siping Road, Room 508, Shanghai 200092, China
| | - Jiayi Cheng
- Brain and Spinal Cord Innovative Research Center, Tongji Hospital, Tongji University School of Medicine, Shanghai 200065, China; Key Laboratory of Neuroregeneration of Shanghai Universities, Tongji University School of Medicine, 1239 Siping Road, Room 508, Shanghai 200092, China
| | - Shanshan Zhou
- Brain and Spinal Cord Innovative Research Center, Tongji Hospital, Tongji University School of Medicine, Shanghai 200065, China; Key Laboratory of Neuroregeneration of Shanghai Universities, Tongji University School of Medicine, 1239 Siping Road, Room 508, Shanghai 200092, China
| | - Ling Liu
- Brain and Spinal Cord Innovative Research Center, Tongji Hospital, Tongji University School of Medicine, Shanghai 200065, China; Key Laboratory of Reconstruction and Regeneration of Spine and Spinal Cord Injury, Ministry of Education, Shanghai 200065, China; Key Laboratory of Neuroregeneration of Shanghai Universities, Tongji University School of Medicine, 1239 Siping Road, Room 508, Shanghai 200092, China
| | - Xiaoqing Zhang
- Brain and Spinal Cord Innovative Research Center, Tongji Hospital, Tongji University School of Medicine, Shanghai 200065, China; Key Laboratory of Reconstruction and Regeneration of Spine and Spinal Cord Injury, Ministry of Education, Shanghai 200065, China; Key Laboratory of Neuroregeneration of Shanghai Universities, Tongji University School of Medicine, 1239 Siping Road, Room 508, Shanghai 200092, China; Tsingtao Advanced Research Institute, Tongji University, Shanghai 200092, China; Shanghai Institute of Stem Cell Research and Clinical Translation, Shanghai 200120, China; Translational Medical Center for Stem Cell Therapy, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China.
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Protection of ZIKV infection-induced neuropathy by abrogation of acute antiviral response in human neural progenitors. Cell Death Differ 2019; 26:2607-2621. [PMID: 30952992 PMCID: PMC7224299 DOI: 10.1038/s41418-019-0324-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Revised: 02/16/2019] [Accepted: 03/19/2019] [Indexed: 01/04/2023] Open
Abstract
It remains largely unknown how Zika virus (ZIKV) infection causes severe microcephaly in human newborns. We examined an Asian lineage ZIKV, SZ01, which similarly infected and demonstrated comparable growth arrest and apoptotic pathological changes in human neuroprogenitors (NPCs) from forebrain dorsal, forebrain ventral as well as hindbrain and spinal cord brain organoids derived from human pluripotent stem cells. Transcriptome profiling showed common overactivated antiviral response in all regional NPCs upon ZIKV infection. ZIKV infection directly activated a subset of IFN-stimulated genes (ISGs) in human NPCs, which depended on the presence of IRF3 and NF-κB rather than IFN production and secretion, highlighting a key role of IFN-independent acute antiviral pathway underlying ZIKV infection-caused neuropathy. Our findings therefore reveal that overactivated antiviral response is detrimental rather than protective in human NPCs, and the IFN-independent acute antiviral pathway may serve as a potential target to ameliorate ZIKV infection-triggered neuropathy.
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Perna S, Pinoli P, Ceri S, Wong L. TICA: Transcriptional Interaction and Coregulation Analyzer. GENOMICS, PROTEOMICS & BIOINFORMATICS 2018; 16:342-353. [PMID: 30578913 PMCID: PMC6364043 DOI: 10.1016/j.gpb.2018.05.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Revised: 05/11/2018] [Accepted: 05/18/2018] [Indexed: 11/16/2022]
Abstract
Transcriptional regulation is critical to cellular processes of all organisms. Regulatory mechanisms often involve more than one transcription factor (TF) from different families, binding together and attaching to the DNA as a single complex. However, only a fraction of the regulatory partners of each TF is currently known. In this paper, we present the Transcriptional Interaction and Coregulation Analyzer (TICA), a novel methodology for predicting heterotypic physical interaction of TFs. TICA employs a data-driven approach to infer interaction phenomena from chromatin immunoprecipitation and sequencing (ChIP-seq) data. Its prediction rules are based on the distribution of minimal distance couples of paired binding sites belonging to different TFs which are located closest to each other in promoter regions. Notably, TICA uses only binding site information from input ChIP-seq experiments, bypassing the need to do motif calling on sequencing data. We present our method and test it on ENCODE ChIP-seq datasets, using three cell lines as reference including HepG2, GM12878, and K562. TICA positive predictions on ENCODE ChIP-seq data are strongly enriched when compared to protein complex (CORUM) and functional interaction (BioGRID) databases. We also compare TICA against both motif/ChIP-seq based methods for physical TF-TF interaction prediction and published literature. Based on our results, TICA offers significant specificity (average 0.902) while maintaining a good recall (average 0.284) with respect to CORUM, providing a novel technique for fast analysis of regulatory effect in cell lines. Furthermore, predictions by TICA are complementary to other methods for TF-TF interaction prediction (in particular, TACO and CENTDIST). Thus, combined application of these prediction tools results in much improved sensitivity in detecting TF-TF interactions compared to TICA alone (sensitivity of 0.526 when combining TICA with TACO and 0.585 when combining with CENTDIST) with little compromise in specificity (specificity 0.760 when combining with TACO and 0.643 with CENTDIST). TICA is publicly available at http://geco.deib.polimi.it/tica/.
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Affiliation(s)
- Stefano Perna
- Dipartimento di Elettronica, Informazione e Bioingegneria, Politecnico di Milano, 20133 Milan, Italy.
| | - Pietro Pinoli
- Dipartimento di Elettronica, Informazione e Bioingegneria, Politecnico di Milano, 20133 Milan, Italy
| | - Stefano Ceri
- Dipartimento di Elettronica, Informazione e Bioingegneria, Politecnico di Milano, 20133 Milan, Italy
| | - Limsoon Wong
- School of Computing, National University of Singapore, Singapore 117417, Singapore
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