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Halasz H, Malekos E, Covarrubias S, Yitiz S, Montano C, Sudek L, Katzman S, Liu SJ, Horlbeck MA, Namvar L, Weissman JS, Carpenter S. CRISPRi screens identify the lncRNA, LOUP, as a multifunctional locus regulating macrophage differentiation and inflammatory signaling. Proc Natl Acad Sci U S A 2024; 121:e2322524121. [PMID: 38781216 PMCID: PMC11145268 DOI: 10.1073/pnas.2322524121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Accepted: 04/16/2024] [Indexed: 05/25/2024] Open
Abstract
Long noncoding RNAs (lncRNAs) account for the largest portion of RNA from the transcriptome, yet most of their functions remain unknown. Here, we performed two independent high-throughput CRISPRi screens to understand the role of lncRNAs in monocyte function and differentiation. The first was a reporter-based screen to identify lncRNAs that regulate TLR4-NFkB signaling in human monocytes and the second screen identified lncRNAs involved in monocyte to macrophage differentiation. We successfully identified numerous noncoding and protein-coding genes that can positively or negatively regulate inflammation and differentiation. To understand the functional roles of lncRNAs in both processes, we chose to further study the lncRNA LOUP [lncRNA originating from upstream regulatory element of SPI1 (also known as PU.1)], as it emerged as a top hit in both screens. Not only does LOUP regulate its neighboring gene, the myeloid fate-determining factor SPI1, thereby affecting monocyte to macrophage differentiation, but knockdown of LOUP leads to a broad upregulation of NFkB-targeted genes at baseline and upon TLR4-NFkB activation. LOUP also harbors three small open reading frames capable of being translated and are responsible for LOUP's ability to negatively regulate TLR4/NFkB signaling. This work emphasizes the value of high-throughput screening to rapidly identify functional lncRNAs in the innate immune system.
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Affiliation(s)
- Haley Halasz
- Department of Molecular, Cell and Developmental Biology, University of California Santa Cruz, CA95064
| | - Eric Malekos
- Department of Biomolecular Engineering, University of California Santa Cruz, CA95064
| | - Sergio Covarrubias
- Department of Molecular, Cell and Developmental Biology, University of California Santa Cruz, CA95064
| | - Samira Yitiz
- Department of Molecular, Cell and Developmental Biology, University of California Santa Cruz, CA95064
| | - Christy Montano
- Department of Molecular, Cell and Developmental Biology, University of California Santa Cruz, CA95064
| | - Lisa Sudek
- Department of Molecular, Cell and Developmental Biology, University of California Santa Cruz, CA95064
| | - Sol Katzman
- Department of Molecular, Cell and Developmental Biology, University of California Santa Cruz, CA95064
| | - S. John Liu
- Department of Radiation Oncology, University of California, San Francisco, CA94158
- Department of Neurological Surgery, University of California, San Francisco, CA94158
| | - Max A. Horlbeck
- Department of Radiation Oncology, University of California, San Francisco, CA94158
- Department of Neurological Surgery, University of California, San Francisco, CA94158
- Department of Pediatrics, Division of Genetics and Genomics, Boston Children’s Hospital, Boston, MA02115
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA02138
| | - Leila Namvar
- Department of Molecular, Cell and Developmental Biology, University of California Santa Cruz, CA95064
| | - Jonathan S. Weissman
- Whitehead Institute for Biomedical Research, Massachusetts Institute of Technology, Cambridge, MA02142
- HHMI, Chevy Chase, MD20815
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA02142
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA02142
| | - Susan Carpenter
- Department of Molecular, Cell and Developmental Biology, University of California Santa Cruz, CA95064
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2
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Yi W, Zhang J, Huang Y, Zhan Q, Zou M, Cheng X, Zhang X, Yin Z, Tao S, Cheng H, Wang F, Guo J, Ju Z, Chen Z. Ferritin-mediated mitochondrial iron homeostasis is essential for the survival of hematopoietic stem cells and leukemic stem cells. Leukemia 2024; 38:1003-1018. [PMID: 38402368 DOI: 10.1038/s41375-024-02169-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 01/26/2024] [Accepted: 02/02/2024] [Indexed: 02/26/2024]
Abstract
Iron metabolism plays a crucial role in cell viability, but its relationship with adult stem cells and cancer stem cells is not fully understood. The ferritin complex, responsible for intracellular iron storage, is important in this process. We report that conditional deletion of ferritin heavy chain 1 (Fth1) in the hematopoietic system reduced the number and repopulation capacity of hematopoietic stem cells (HSCs). These effects were associated with a decrease in cellular iron level, leading to impaired mitochondrial function and the initiation of apoptosis. Iron supplementation, antioxidant, and apoptosis inhibitors reversed the reduced cell viability of Fth1-deleted hematopoietic stem and progenitor cells (HSPCs). Importantly, leukemic stem cells (LSCs) derived from MLL-AF9-induced acute myeloid leukemia (AML) mice exhibited reduced Fth1 expression, rendering them more susceptible to apoptosis induced by the iron chelation compared to normal HSPCs. Modulating FTH1 expression using mono-methyl fumarate increased LSCs resistance to iron chelator-induced apoptosis. Additionally, iron supplementation, antioxidant, and apoptosis inhibitors protected LSCs from iron chelator-induced cell death. Fth1 deletion also extended the survival of AML mice. These findings unveil a novel mechanism by which ferritin-mediated iron homeostasis regulates the survival of both HSCs and LSCs, suggesting potential therapeutic strategies for blood cancer with iron dysregulation.
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Affiliation(s)
- Weiwei Yi
- Department of Cardiology, the First Affiliated Hospital of Jinan University, Guangzhou, 510630, Guangdong, China
- Key Laboratory of Regenerative Medicine of Ministry of Education, Institute of Aging and Regenerative Medicine, College of Life Science and Technology, Jinan University, Guangzhou, 510632, Guangdong, China
| | - Jinhua Zhang
- Department of Cardiology, the First Affiliated Hospital of Jinan University, Guangzhou, 510630, Guangdong, China
| | - Yingxin Huang
- Key Laboratory of Regenerative Medicine of Ministry of Education, Institute of Aging and Regenerative Medicine, College of Life Science and Technology, Jinan University, Guangzhou, 510632, Guangdong, China
| | - Qiang Zhan
- Key Laboratory of Regenerative Medicine of Ministry of Education, Institute of Aging and Regenerative Medicine, College of Life Science and Technology, Jinan University, Guangzhou, 510632, Guangdong, China
| | - Mi Zou
- Key Laboratory of Regenerative Medicine of Ministry of Education, Institute of Aging and Regenerative Medicine, College of Life Science and Technology, Jinan University, Guangzhou, 510632, Guangdong, China
| | - Xiang Cheng
- Department of Hematology, Children's Hospital, Capital Institute of Pediatrics, Beijing, 100020, China
| | - Xuguang Zhang
- Mengniu Institute of Nutrition Science, Global R&D Innovation Center, Shanghai, China
- Shanghai Institute of Nutrition and Health, The Chinese Academy of Sciences, Shanghai, China
| | - Zhinan Yin
- Guangdong Provincial Key Laboratory of Tumor Interventional Diagnosis and Treatment, Institute of Translational Medicine, Zhuhai People's Hospital Affiliated with Jinan University, Jinan University, Zhuhai, 519000, Guangdong, China
- The Biomedical Translational Research Institute, Health Science Center (School of Medicine), Jinan University, Guangzhou, 510632, Guangdong, China
| | - Si Tao
- Department of Oncology, The Second Affiliated Hospital of Nanchang University, Nanchang, 330006, Jiangxi, China
| | - Hui Cheng
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, 300020, China
| | - Fudi Wang
- The Second Affiliated Hospital, School of Public Health, State Key Laboratory of Experimental Hematology, Zhejiang University School of Medicine, Hangzhou, 310058, Zhejiang, China
- The First Affiliated Hospital, Basic Medical Sciences, School of Public Health, Hengyang Medical School, University of South China, Hengyang, 421001, Hunan, China
| | - Jun Guo
- Department of Cardiology, the First Affiliated Hospital of Jinan University, Guangzhou, 510630, Guangdong, China.
| | - Zhenyu Ju
- Key Laboratory of Regenerative Medicine of Ministry of Education, Institute of Aging and Regenerative Medicine, College of Life Science and Technology, Jinan University, Guangzhou, 510632, Guangdong, China.
| | - Zhiyang Chen
- Key Laboratory of Regenerative Medicine of Ministry of Education, Institute of Aging and Regenerative Medicine, College of Life Science and Technology, Jinan University, Guangzhou, 510632, Guangdong, China.
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3
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Long T, Bhattacharyya T, Repele A, Naylor M, Nooti S, Krueger S, Manu. The contributions of DNA accessibility and transcription factor occupancy to enhancer activity during cellular differentiation. G3 (BETHESDA, MD.) 2024; 14:jkad269. [PMID: 38124496 PMCID: PMC11090500 DOI: 10.1093/g3journal/jkad269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 11/01/2023] [Indexed: 12/23/2023]
Abstract
During gene regulation, DNA accessibility is thought to limit the availability of transcription factor (TF) binding sites, while TFs can increase DNA accessibility to recruit additional factors that upregulate gene expression. Given this interplay, the causative regulatory events in the modulation of gene expression remain unknown for the vast majority of genes. We utilized deeply sequenced ATAC-Seq data and site-specific knock-in reporter genes to investigate the relationship between the binding-site resolution dynamics of DNA accessibility and the expression dynamics of the enhancers of Cebpa during macrophage-neutrophil differentiation. While the enhancers upregulate reporter expression during the earliest stages of differentiation, there is little corresponding increase in their total accessibility. Conversely, total accessibility peaks during the last stages of differentiation without any increase in enhancer activity. The accessibility of positions neighboring C/EBP-family TF binding sites, which indicates TF occupancy, does increase significantly during early differentiation, showing that the early upregulation of enhancer activity is driven by TF binding. These results imply that a generalized increase in DNA accessibility is not sufficient, and binding by enhancer-specific TFs is necessary, for the upregulation of gene expression. Additionally, high-coverage ATAC-Seq combined with time-series expression data can infer the sequence of regulatory events at binding-site resolution.
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Affiliation(s)
- Trevor Long
- Department of Biology, University of North Dakota, Grand Forks, ND 58202-9019, USA
| | - Tapas Bhattacharyya
- Department of Biology, University of North Dakota, Grand Forks, ND 58202-9019, USA
| | - Andrea Repele
- Department of Biology, University of North Dakota, Grand Forks, ND 58202-9019, USA
| | - Madison Naylor
- Department of Biology, University of North Dakota, Grand Forks, ND 58202-9019, USA
| | - Sunil Nooti
- Department of Biology, University of North Dakota, Grand Forks, ND 58202-9019, USA
| | - Shawn Krueger
- Department of Biology, University of North Dakota, Grand Forks, ND 58202-9019, USA
| | - Manu
- Department of Biology, University of North Dakota, Grand Forks, ND 58202-9019, USA
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4
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Czimmerer Z, Nagy L. Epigenomic regulation of macrophage polarization: Where do the nuclear receptors belong? Immunol Rev 2023; 317:152-165. [PMID: 37074820 PMCID: PMC10524119 DOI: 10.1111/imr.13209] [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: 04/04/2023] [Accepted: 04/06/2023] [Indexed: 04/20/2023]
Abstract
Our laboratory has a long-standing research interest in understanding how lipid-activated transcription factors, nuclear hormone receptors, contribute to dendritic cell and macrophage gene expression regulation, subtype specification, and responses to a changing extra and intracellular milieu. This journey in the last more than two decades took us from identifying target genes for various RXR heterodimers to systematically mapping nuclear receptor-mediated pathways in dendritic cells to identifying hierarchies of transcription factors in alternative polarization in macrophages to broaden the role of nuclear receptors beyond strictly ligand-regulated gene expression. We detail here the milestones of the road traveled and draw conclusions regarding the unexpectedly broad role of nuclear hormone receptors as epigenomic components of dendritic cell and macrophage gene regulation as we are getting ready for the next challenges.
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Affiliation(s)
- Zsolt Czimmerer
- Institute of Genetics, Biological Research Centre, Eotvos Lorand Research Network, Szeged, Hungary
| | - Laszlo Nagy
- Departments Medicine and Biological Chemistry, Johns Hopkins University School of Medicine, and Institute for Fundamental Biomedical Research, Johns Hopkins All Children’s Hospital, St Petersburg, FL, United States
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5
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Naqvi S, Kim S, Hoskens H, Matthews HS, Spritz RA, Klein OD, Hallgrímsson B, Swigut T, Claes P, Pritchard JK, Wysocka J. Precise modulation of transcription factor levels identifies features underlying dosage sensitivity. Nat Genet 2023; 55:841-851. [PMID: 37024583 PMCID: PMC10181932 DOI: 10.1038/s41588-023-01366-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2022] [Accepted: 03/07/2023] [Indexed: 04/08/2023]
Abstract
Transcriptional regulation exhibits extensive robustness, but human genetics indicates sensitivity to transcription factor (TF) dosage. Reconciling such observations requires quantitative studies of TF dosage effects at trait-relevant ranges, largely lacking so far. TFs play central roles in both normal-range and disease-associated variation in craniofacial morphology; we therefore developed an approach to precisely modulate TF levels in human facial progenitor cells and applied it to SOX9, a TF associated with craniofacial variation and disease (Pierre Robin sequence (PRS)). Most SOX9-dependent regulatory elements (REs) are buffered against small decreases in SOX9 dosage, but REs directly and primarily regulated by SOX9 show heightened sensitivity to SOX9 dosage; these RE responses partially predict gene expression responses. Sensitive REs and genes preferentially affect functional chondrogenesis and PRS-like craniofacial shape variation. We propose that such REs and genes underlie the sensitivity of specific phenotypes to TF dosage, while buffering of other genes leads to robust, nonlinear dosage-to-phenotype relationships.
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Affiliation(s)
- Sahin Naqvi
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA, USA
- Departments of Genetics and Biology, Stanford University, Stanford, CA, USA
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Seungsoo Kim
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA, USA
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Hanne Hoskens
- Department of Human Genetics, KU Leuven, Leuven, Belgium
- Medical Imaging Research Center, University Hospitals Leuven, Leuven, Belgium
- Department of Cell Biology & Anatomy, Alberta Children's Hospital Research Institute and McCaig Bone and Joint Institute, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Harold S Matthews
- Department of Human Genetics, KU Leuven, Leuven, Belgium
- Medical Imaging Research Center, University Hospitals Leuven, Leuven, Belgium
| | - Richard A Spritz
- Human Medical Genetics and Genomics Program and Department of Pediatrics, University of Colorado School of Medicine, Aurora, CO, USA
| | - Ophir D Klein
- Departments of Orofacial Sciences and Pediatrics, Program in Craniofacial Biology, and Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA
- Department of Pediatrics, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Benedikt Hallgrímsson
- Department of Cell Biology & Anatomy, Alberta Children's Hospital Research Institute and McCaig Bone and Joint Institute, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Tomek Swigut
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Peter Claes
- Department of Human Genetics, KU Leuven, Leuven, Belgium
- Medical Imaging Research Center, University Hospitals Leuven, Leuven, Belgium
- Department of Electrical Engineering, ESAT/PSI, KU Leuven, Leuven, Belgium
- Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | | | - Joanna Wysocka
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA, USA.
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA, USA.
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA.
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6
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Long T, Bhattacharyya T, Repele A, Naylor M, Nooti S, Krueger S, Manu. The contributions of DNA accessibility and transcription factor occupancy to enhancer activity during cellular differentiation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.22.529579. [PMID: 37090616 PMCID: PMC10120690 DOI: 10.1101/2023.02.22.529579] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/25/2023]
Abstract
The upregulation of gene expression by enhancers depends upon the interplay between the binding of sequence-specific transcription factors (TFs) and DNA accessibility. DNA accessibility is thought to limit the ability of TFs to bind to their sites, while TFs can increase accessibility to recruit additional factors that upregulate gene expression. Given this interplay, the causative regulatory events underlying the modulation of gene expression during cellular differentiation remain unknown for the vast majority of genes. We investigated the binding-site resolution dynamics of DNA accessibility and the expression dynamics of the enhancers of an important neutrophil gene, Cebpa, during macrophage-neutrophil differentiation. Reporter genes were integrated in a site-specific manner in PUER cells, which are progenitors that can be differentiated into neutrophils or macrophages in vitro by activating the pan-leukocyte TF PU.1. Time series data show that two enhancers upregulate reporter expression during the first 48 hours of neutrophil differentiation. Surprisingly, there is little or no increase in the total accessibility, measured by ATAC-Seq, of the enhancers during the same time period. Conversely, total accessibility peaks 96 hrs after PU.1 activation-consistent with its role as a pioneer-but the enhancers do not upregulate gene expression. Combining deeply sequenced ATAC-Seq data with a new bias-correction method allowed the profiling of accessibility at single-nucleotide resolution and revealed protected regions in the enhancers that match all previously characterized TF binding sites and ChIP-Seq data. Although the accessibility of most positions does not change during early differentiation, that of positions neighboring TF binding sites, an indicator of TF occupancy, did increase significantly. The localized accessibility changes are limited to nucleotides neighboring C/EBP-family TF binding sites, showing that the upregulation of enhancer activity during early differentiation is driven by C/EBP-family TF binding. These results show that increasing the total accessibility of enhancers is not sufficient for upregulating their activity and other events such as TF binding are necessary for upregulation. Also, TF binding can cause upregulation without a perceptible increase in total accessibility. Finally, this study demonstrates the feasibility of comprehensively mapping individual TF binding sites as footprints using high coverage ATAC-Seq and inferring the sequence of events in gene regulation by combining with time-series gene expression data.
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Affiliation(s)
- Trevor Long
- Department of Biology, University of North Dakota, Grand Forks, 58202-9019 ND, USA
| | - Tapas Bhattacharyya
- Department of Biology, University of North Dakota, Grand Forks, 58202-9019 ND, USA
| | - Andrea Repele
- Department of Biology, University of North Dakota, Grand Forks, 58202-9019 ND, USA
| | - Madison Naylor
- Department of Biology, University of North Dakota, Grand Forks, 58202-9019 ND, USA
| | - Sunil Nooti
- Department of Biology, University of North Dakota, Grand Forks, 58202-9019 ND, USA
| | - Shawn Krueger
- Department of Biology, University of North Dakota, Grand Forks, 58202-9019 ND, USA
| | - Manu
- Department of Biology, University of North Dakota, Grand Forks, 58202-9019 ND, USA
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7
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CTCF controls three-dimensional enhancer network underlying the inflammatory response of bone marrow-derived dendritic cells. Nat Commun 2023; 14:1277. [PMID: 36882470 PMCID: PMC9992691 DOI: 10.1038/s41467-023-36948-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 02/24/2023] [Indexed: 03/09/2023] Open
Abstract
Dendritic cells are antigen-presenting cells orchestrating innate and adaptive immunity. The crucial role of transcription factors and histone modifications in the transcriptional regulation of dendritic cells has been extensively studied. However, it is not been well understood whether and how three-dimensional chromatin folding controls gene expression in dendritic cells. Here we demonstrate that activation of bone marrow-derived dendritic cells induces extensive reprogramming of chromatin looping as well as enhancer activity, both of which are implicated in the dynamic changes in gene expression. Interestingly, depletion of CTCF attenuates GM-CSF-mediated JAK2/STAT5 signaling, resulting in defective NF-κB activation. Moreover, CTCF is necessary for establishing NF-κB-dependent chromatin interactions and maximal expression of pro-inflammatory cytokines, which prime Th1 and Th17 cell differentiation. Collectively, our study provides mechanistic insights into how three-dimensional enhancer networks control gene expression during bone marrow-derived dendritic cells activation, and offers an integrative view of the complex activities of CTCF in the inflammatory response of bone marrow-derived dendritic cells.
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8
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Nabuco Leva Ferreira de Freitas JA, Bischof O. Dynamic modeling of the cellular senescence gene regulatory network. Heliyon 2023; 9:e14007. [PMID: 36938415 PMCID: PMC10015196 DOI: 10.1016/j.heliyon.2023.e14007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 02/13/2023] [Accepted: 02/17/2023] [Indexed: 02/27/2023] Open
Abstract
Cellular senescence is a cell fate that prominently impacts physiological and pathophysiological processes. Diverse cellular stresses induce it, and dramatic gene expression changes accompany it. However, determining the interactions comprising the gene regulatory network (GRN) governing senescence remains challenging. Recent advances in signal processing techniques provide opportunities to reconstruct GRNs. Here, we describe a GRN for senescence integrating time-series transcriptome and transcription factor depletion datasets. Specifically, we infer a set of differential equations using the "Sparse Identification of Nonlinear Dynamics" (SINDy) algorithm, discriminate genes with potential hidden regulators, validate the inferred GRN for time-points not included in the training data, and comprehensively benchmark our approach. Our work is a proof of concept for a data-driven GRN reconstruction method, consolidating an iterative, powerful mathematical platform for senescence modeling that can be used to test hypotheses in silico and has the potential for future discoveries of clinical impact.
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Affiliation(s)
- José Américo Nabuco Leva Ferreira de Freitas
- IMRB, Mondor Institute for Biomedical Research, INSERM U955 – Université Paris Est Créteil, UPEC, Faculté de Médecine de Créteil 8, rue du Général Sarrail, 94010 Créteil
- Sorbonne Université, UMR 8256, Biological Adaptation and Ageing B2A–IBPS, F-75005, Paris, France
- INSERM U1164, F-75005, Paris, France
| | - Oliver Bischof
- IMRB, Mondor Institute for Biomedical Research, INSERM U955 – Université Paris Est Créteil, UPEC, Faculté de Médecine de Créteil 8, rue du Général Sarrail, 94010 Créteil
- Corresponding author.
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9
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Geiger-Schuller K, Eraslan B, Kuksenko O, Dey KK, Jagadeesh KA, Thakore PI, Karayel O, Yung AR, Rajagopalan A, Meireles AM, Yang KD, Amir-Zilberstein L, Delorey T, Phillips D, Raychowdhury R, Moussion C, Price AL, Hacohen N, Doench JG, Uhler C, Rozenblatt-Rosen O, Regev A. Systematically characterizing the roles of E3-ligase family members in inflammatory responses with massively parallel Perturb-seq. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.23.525198. [PMID: 36747789 PMCID: PMC9900845 DOI: 10.1101/2023.01.23.525198] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
E3 ligases regulate key processes, but many of their roles remain unknown. Using Perturb-seq, we interrogated the function of 1,130 E3 ligases, partners and substrates in the inflammatory response in primary dendritic cells (DCs). Dozens impacted the balance of DC1, DC2, migratory DC and macrophage states and a gradient of DC maturation. Family members grouped into co-functional modules that were enriched for physical interactions and impacted specific programs through substrate transcription factors. E3s and their adaptors co-regulated the same processes, but partnered with different substrate recognition adaptors to impact distinct aspects of the DC life cycle. Genetic interactions were more prevalent within than between modules, and a deep learning model, comβVAE, predicts the outcome of new combinations by leveraging modularity. The E3 regulatory network was associated with heritable variation and aberrant gene expression in immune cells in human inflammatory diseases. Our study provides a general approach to dissect gene function.
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10
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Epigenomic landscape study reveals molecular subtypes and EBV-associated regulatory epigenome reprogramming in nasopharyngeal carcinoma. EBioMedicine 2022; 86:104357. [DOI: 10.1016/j.ebiom.2022.104357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 10/21/2022] [Accepted: 10/24/2022] [Indexed: 11/13/2022] Open
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11
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Identification of environmental factors that promote intestinal inflammation. Nature 2022; 611:801-809. [PMID: 36266581 PMCID: PMC9898826 DOI: 10.1038/s41586-022-05308-6] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Accepted: 09/01/2022] [Indexed: 02/06/2023]
Abstract
Genome-wide association studies have identified risk loci linked to inflammatory bowel disease (IBD)1-a complex chronic inflammatory disorder of the gastrointestinal tract. The increasing prevalence of IBD in industrialized countries and the augmented disease risk observed in migrants who move into areas of higher disease prevalence suggest that environmental factors are also important determinants of IBD susceptibility and severity2. However, the identification of environmental factors relevant to IBD and the mechanisms by which they influence disease has been hampered by the lack of platforms for their systematic investigation. Here we describe an integrated systems approach, combining publicly available databases, zebrafish chemical screens, machine learning and mouse preclinical models to identify environmental factors that control intestinal inflammation. This approach established that the herbicide propyzamide increases inflammation in the small and large intestine. Moreover, we show that an AHR-NF-κB-C/EBPβ signalling axis operates in T cells and dendritic cells to promote intestinal inflammation, and is targeted by propyzamide. In conclusion, we developed a pipeline for the identification of environmental factors and mechanisms of pathogenesis in IBD and, potentially, other inflammatory diseases.
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12
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An Expanded Interplay Network between NF-κB p65 (RelA) and E2F1 Transcription Factors: Roles in Physiology and Pathology. Cancers (Basel) 2022; 14:cancers14205047. [PMID: 36291831 PMCID: PMC9600032 DOI: 10.3390/cancers14205047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 09/30/2022] [Accepted: 10/10/2022] [Indexed: 11/17/2022] Open
Abstract
Transcription Factors (TFs) are the main regulators of gene expression, controlling among others cell homeostasis, identity, and fate. TFs may either act synergistically or antagonistically on nearby regulatory elements and their interplay may activate or repress gene expression. The family of NF-κB TFs is among the most important TFs in the regulation of inflammation, immunity, and stress-like responses, while they also control cell growth and survival, and are involved in inflammatory diseases and cancer. The family of E2F TFs are major regulators of cell cycle progression in most cell types. Several studies have suggested the interplay between these two TFs in the regulation of numerous genes controlling several biological processes. In the present study, we compared the genomic binding landscape of NF-κB RelA/p65 subunit and E2F1 TFs, based on high throughput ChIP-seq and RNA-seq data in different cell types. We confirmed that RelA/p65 has a binding profile with a high preference for distal enhancers bearing active chromatin marks which is distinct to that of E2F1, which mostly generates promoter-specific binding. Moreover, the RelA/p65 subunit and E2F1 cistromes have limited overlap and tend to bind chromatin that is in an active state even prior to immunogenic stimulation. Finally, we found that a fraction of the E2F1 cistrome is recruited by NF-κΒ near pro-inflammatory genes following LPS stimulation in immune cell types.
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13
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Jha A, Ahad A, Mishra GP, Sen K, Smita S, Minz AP, Biswas VK, Tripathy A, Senapati S, Gupta B, Acha-Orbea H, Raghav SK. SMRT and NCoR1 fine-tune inflammatory versus tolerogenic balance in dendritic cells by differentially regulating STAT3 signaling. Front Immunol 2022; 13:910705. [PMID: 36238311 PMCID: PMC9552960 DOI: 10.3389/fimmu.2022.910705] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 08/25/2022] [Indexed: 11/13/2022] Open
Abstract
Dendritic cell (DC) fine-tunes inflammatory versus tolerogenic responses to protect from immune-pathology. However, the role of co-regulators in maintaining this balance is unexplored. NCoR1-mediated repression of DC immune-tolerance has been recently reported. Here we found that depletion of NCoR1 paralog SMRT (NCoR2) enhanced cDC1 activation and expression of IL-6, IL-12 and IL-23 while concomitantly decreasing IL-10 expression/secretion. Consequently, co-cultured CD4+ and CD8+ T-cells depicted enhanced Th1/Th17 frequency and cytotoxicity, respectively. Comparative genomic and transcriptomic analysis demonstrated differential regulation of IL-10 by SMRT and NCoR1. SMRT depletion represses mTOR-STAT3-IL10 signaling in cDC1 by down-regulating NR4A1. Besides, Nfkbia and Socs3 were down-regulated in Ncor2 (Smrt) depleted cDC1, supporting increased production of inflammatory cytokines. Moreover, studies in mice showed, adoptive transfer of SMRT depleted cDC1 in OVA-DTH induced footpad inflammation led to increased Th1/Th17 and reduced tumor burden after B16 melanoma injection by enhancing oncolytic CD8+ T-cell frequency, respectively. We also depicted decreased Ncor2 expression in Rheumatoid Arthritis, a Th1/Th17 disease.
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Affiliation(s)
- Atimukta Jha
- Immuno-genomics & Systems Biology laboratory, Institute of Life Sciences (ILS), Bhubaneswar, OR, India
- Manipal Academy of Higher Education, Manipal, KA, India
| | - Abdul Ahad
- Immuno-genomics & Systems Biology laboratory, Institute of Life Sciences (ILS), Bhubaneswar, OR, India
- Manipal Academy of Higher Education, Manipal, KA, India
| | - Gyan Prakash Mishra
- Immuno-genomics & Systems Biology laboratory, Institute of Life Sciences (ILS), Bhubaneswar, OR, India
- Department of Biotechnology, Kalinga Institute of Industrial Technology (KIIT), Bhubaneswar, India
| | - Kaushik Sen
- Regional Centre for Biotechnology, NCR Biotech Science Cluster, Haryana, India
| | - Shuchi Smita
- Immuno-genomics & Systems Biology laboratory, Institute of Life Sciences (ILS), Bhubaneswar, OR, India
- Manipal Academy of Higher Education, Manipal, KA, India
| | - Aliva Prity Minz
- Immuno-genomics & Systems Biology laboratory, Institute of Life Sciences (ILS), Bhubaneswar, OR, India
| | - Viplov Kumar Biswas
- Immuno-genomics & Systems Biology laboratory, Institute of Life Sciences (ILS), Bhubaneswar, OR, India
- Department of Biotechnology, Kalinga Institute of Industrial Technology (KIIT), Bhubaneswar, India
| | - Archana Tripathy
- Department of Biotechnology, Kalinga Institute of Industrial Technology (KIIT), Bhubaneswar, India
| | - Shantibhushan Senapati
- Immuno-genomics & Systems Biology laboratory, Institute of Life Sciences (ILS), Bhubaneswar, OR, India
- Manipal Academy of Higher Education, Manipal, KA, India
| | - Bhawna Gupta
- Department of Biotechnology, Kalinga Institute of Industrial Technology (KIIT), Bhubaneswar, India
| | - Hans Acha-Orbea
- Department of Biochemistry Center of Immunity and Infection Lausanne (CIIL), University of Lausanne (UNIL), Epalinges, Switzerland
| | - Sunil Kumar Raghav
- Immuno-genomics & Systems Biology laboratory, Institute of Life Sciences (ILS), Bhubaneswar, OR, India
- Manipal Academy of Higher Education, Manipal, KA, India
- *Correspondence: Sunil Kumar Raghav, ;
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14
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Ito N, Sakata F, Hachisu M, Nagata K, Ito T, Nomura K, Nagaoka M, Inaba K, Hara M, Nakano N, Nakajima T, Yashiro T, Nishiyama C. The Ccl17 gene encoding TARC is synergistically transactivated by PU.1 and IRF4 driven by the mammalian common promoter in dendritic cells. Allergy 2022; 77:1054-1059. [PMID: 34807993 DOI: 10.1111/all.15184] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 10/30/2021] [Accepted: 11/16/2021] [Indexed: 12/15/2022]
Affiliation(s)
- Naoto Ito
- Department of Biological Science and Technology Faculty of Advanced Engineering Tokyo University of Science Tokyo Japan
| | - Fumiya Sakata
- Department of Biological Science and Technology Faculty of Advanced Engineering Tokyo University of Science Tokyo Japan
| | - Masakazu Hachisu
- Department of Biological Science and Technology Faculty of Advanced Engineering Tokyo University of Science Tokyo Japan
| | - Kazuki Nagata
- Department of Biological Science and Technology Faculty of Advanced Engineering Tokyo University of Science Tokyo Japan
| | - Tomoka Ito
- Department of Biological Science and Technology Faculty of Advanced Engineering Tokyo University of Science Tokyo Japan
| | - Kurumi Nomura
- Department of Biological Science and Technology Faculty of Advanced Engineering Tokyo University of Science Tokyo Japan
| | - Masanori Nagaoka
- Department of Biological Science and Technology Faculty of Advanced Engineering Tokyo University of Science Tokyo Japan
| | - Keito Inaba
- Department of Biological Science and Technology Faculty of Advanced Engineering Tokyo University of Science Tokyo Japan
| | - Mutsuko Hara
- Atopy (Allergy) Research Center Juntendo University Graduate School of Medicine Tokyo Japan
| | - Nobuhiro Nakano
- Atopy (Allergy) Research Center Juntendo University Graduate School of Medicine Tokyo Japan
| | - Tadaaki Nakajima
- Department of Biological Science and Technology Faculty of Advanced Engineering Tokyo University of Science Tokyo Japan
| | - Takuya Yashiro
- Department of Biological Science and Technology Faculty of Advanced Engineering Tokyo University of Science Tokyo Japan
| | - Chiharu Nishiyama
- Department of Biological Science and Technology Faculty of Advanced Engineering Tokyo University of Science Tokyo Japan
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15
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Reprogramming of H3K9bhb at regulatory elements is a key feature of fasting in the small intestine. Cell Rep 2021; 37:110044. [PMID: 34818540 PMCID: PMC8668154 DOI: 10.1016/j.celrep.2021.110044] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 08/31/2021] [Accepted: 11/01/2021] [Indexed: 12/25/2022] Open
Abstract
β-hydroxybutyrate (β-OHB) is an essential metabolic energy source during fasting and functions as a chromatin regulator by lysine β-hydroxybutyrylation (Kbhb) modification of the core histones H3 and H4. We report that Kbhb on histone H3 (H3K9bhb) is enriched at proximal promoters of critical gene subsets associated with lipolytic and ketogenic metabolic pathways in small intestine (SI) crypts during fasting. Similar Kbhb enrichment is observed in Lgr5+ stem cell-enriched epithelial spheroids treated with β-OHB in vitro. Combinatorial chromatin state analysis reveals that H3K9bhb is associated with active chromatin states and that fasting enriches for an H3K9bhb-H3K27ac signature at active metabolic gene promoters and distal enhancer elements. Intestinal knockout of Hmgcs2 results in marked loss of H3K9bhb-associated loci, suggesting that local production of β-OHB is responsible for chromatin reprogramming within the SI crypt. We conclude that modulation of H3K9bhb in SI crypts is a key gene regulatory event in response to fasting. Terranova et al. demonstrate that fasting induces production of HMGCS2 and β-hydroxybutyrate in small intestine (SI) crypt cells. This causes enrichment of H3K9bhb within regulatory regions of critical metabolic genes in crypt epithelial cells. Loss of intestinal Hmgcs2 impairs H3K9bhb enrichment and affects expression of H3K9bhb-associated metabolic gene programs.
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16
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Sethumadhavan DV, Jabeena CA, Govindaraju G, Soman A, Rajavelu A. The severity of SARS-CoV-2 infection is dictated by host factors? Epigenetic perspectives. CURRENT RESEARCH IN MICROBIAL SCIENCES 2021; 2:100079. [PMID: 34725650 PMCID: PMC8550886 DOI: 10.1016/j.crmicr.2021.100079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 10/02/2021] [Accepted: 10/24/2021] [Indexed: 12/15/2022] Open
Abstract
The emergence of COVID-19, caused by SARS-CoV-2 poses a significant threat to humans as it is highly contagious with increasing mortality. There exists a high degree of heterogeneity in the mortality rates of COVID-19 across the globe. There are multiple speculations on the varying degree of mortality. Still, all the clinical reports have indicated that preexisting chronic diseases like hypertension, diabetes, chronic obstructive pulmonary disease (COPD), kidney disorders, and cardiovascular diseases are associated with the increased risk for high mortality in SARS-CoV-2 infected patients. It is worth noting that host factors, mainly epigenetic factors could play a significant role in deciding the outcome of COVID-19 diseases. Over the recent years, it is evident that chronic diseases are developed due to altered epigenome that includes a selective loss/gain of DNA and histone methylation on the chromatin of the cells. Since, there is a high positive correlation between chronic diseases and elevated mortality due to SARS-CoV-2, in this review; we discuss the overall picture of the aberrant epigenome map in varying chronic ailments and its implications in COVID-19 disease severity and high mortality.
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Affiliation(s)
- Devadathan Valiyamangalath Sethumadhavan
- Pathogen Biology, Rajiv Gandhi Centre for Biotechnology (RGCB), Thycaud PO, Thiruvananthapuram 695014, Kerala, India.,Manipal Academy of Higher Education (MAHE), Tiger Circle Road, Madhav Nagar, Manipal, Karnataka 576104, India
| | - C A Jabeena
- Pathogen Biology, Rajiv Gandhi Centre for Biotechnology (RGCB), Thycaud PO, Thiruvananthapuram 695014, Kerala, India.,Manipal Academy of Higher Education (MAHE), Tiger Circle Road, Madhav Nagar, Manipal, Karnataka 576104, India
| | - Gayathri Govindaraju
- Pathogen Biology, Rajiv Gandhi Centre for Biotechnology (RGCB), Thycaud PO, Thiruvananthapuram 695014, Kerala, India.,Manipal Academy of Higher Education (MAHE), Tiger Circle Road, Madhav Nagar, Manipal, Karnataka 576104, India
| | - Aparna Soman
- Pathogen Biology, Rajiv Gandhi Centre for Biotechnology (RGCB), Thycaud PO, Thiruvananthapuram 695014, Kerala, India
| | - Arumugam Rajavelu
- Pathogen Biology, Rajiv Gandhi Centre for Biotechnology (RGCB), Thycaud PO, Thiruvananthapuram 695014, Kerala, India.,Department of Biotechnology, Bhupat & Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, Tamil Nadu 600 036, India
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17
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Meier-Soelch J, Mayr-Buro C, Juli J, Leib L, Linne U, Dreute J, Papantonis A, Schmitz ML, Kracht M. Monitoring the Levels of Cellular NF-κB Activation States. Cancers (Basel) 2021; 13:cancers13215351. [PMID: 34771516 PMCID: PMC8582385 DOI: 10.3390/cancers13215351] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Accepted: 10/18/2021] [Indexed: 12/12/2022] Open
Abstract
Simple Summary In stress and disease situations, cells must rapidly and in a coordinated manner change their gene expression patterns to respond adequately. The NF-κB system comprises five transcription factors that are released from the cytosol to enter the nucleus in response to a wide range of extracellular stimuli via a complex cytosolic signaling system. In the nucleus, activated NF-κB dimers bind to specific chromatin loci across the entire genome and induce the expression of a broad repertoire of genes that regulate immune and inflammatory responses. Consistent with its biological importance, the extent of NF-κB activity is regulated and controlled at multiple levels. The aim of this review is to comprehensively present and discuss the currently available conceptual and methodological approaches to monitor the molecular activation status of the NF-κB system, including multi-level single cell analysis. Abstract The NF-κB signaling system plays an important regulatory role in the control of many biological processes. The activities of NF-κB signaling networks and the expression of their target genes are frequently elevated in pathophysiological situations including inflammation, infection, and cancer. In these conditions, the outcome of NF-κB activity can vary according to (i) differential activation states, (ii) the pattern of genomic recruitment of the NF-κB subunits, and (iii) cellular heterogeneity. Additionally, the cytosolic NF-κB activation steps leading to the liberation of DNA-binding dimers need to be distinguished from the less understood nuclear pathways that are ultimately responsible for NF-κB target gene specificity. This raises the need to more precisely determine the NF-κB activation status not only for the purpose of basic research, but also in (future) clinical applications. Here we review a compendium of different methods that have been developed to assess the NF-κB activation status in vitro and in vivo. We also discuss recent advances that allow the assessment of several NF-κB features simultaneously at the single cell level.
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Affiliation(s)
- Johanna Meier-Soelch
- Rudolf Buchheim Institute of Pharmacology, Justus Liebig University, 35392 Giessen, Germany
| | - Christin Mayr-Buro
- Rudolf Buchheim Institute of Pharmacology, Justus Liebig University, 35392 Giessen, Germany
| | - Jana Juli
- Rudolf Buchheim Institute of Pharmacology, Justus Liebig University, 35392 Giessen, Germany
| | - Lisa Leib
- Rudolf Buchheim Institute of Pharmacology, Justus Liebig University, 35392 Giessen, Germany
| | - Uwe Linne
- Mass Spectrometry Facility of the Department of Chemistry, Philipps University, 35032 Marburg, Germany
| | - Jan Dreute
- Institute of Biochemistry, Justus Liebig University, 35392 Giessen, Germany
| | - Argyris Papantonis
- Institute of Pathology, University Medical Center Göttingen, 37075 Göttingen, Germany
| | - M Lienhard Schmitz
- Institute of Biochemistry, Justus Liebig University, 35392 Giessen, Germany
| | - Michael Kracht
- Rudolf Buchheim Institute of Pharmacology, Justus Liebig University, 35392 Giessen, Germany
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18
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Lecoeur H, Prina E, Gutiérrez-Sanchez M, Späth GF. Going ballistic: Leishmania nuclear subversion of host cell plasticity. Trends Parasitol 2021; 38:205-216. [PMID: 34666937 DOI: 10.1016/j.pt.2021.09.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 09/22/2021] [Accepted: 09/22/2021] [Indexed: 12/16/2022]
Abstract
Intracellular parasites have evolved intricate strategies to subvert host cell functions for their own survival. These strategies are particularly damaging to the host if the infection involves immune cells, as illustrated by protozoan parasites of the genus Leishmania that thrive inside mononuclear phagocytic cells, causing devastating immunopathologies. While the impact of Leishmania infection on host cell phenotype and functions has been well documented, the regulatory mechanisms underlying host cell subversion were only recently investigated. Here we summarize the current knowledge on how Leishmania infection affects host nuclear activities and propose thought-provoking new concepts on the reciprocal relationship between epigenetic and transcriptional regulation in host cell phenotypic plasticity, its potential subversion by the intracellular parasite, and its relevance for host-directed therapy.
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Affiliation(s)
- Hervé Lecoeur
- Institut Pasteur, Université de Paris, INSERM U1201, Unité de Parasitologie Moléculaire et Signalisation, Paris, France
| | - Eric Prina
- Institut Pasteur, Université de Paris, INSERM U1201, Unité de Parasitologie Moléculaire et Signalisation, Paris, France
| | - Maria Gutiérrez-Sanchez
- Institut Pasteur, Université de Paris, INSERM U1201, Unité de Parasitologie Moléculaire et Signalisation, Paris, France; UMR 8076 CNRS BioCIS, Université Paris-Sud, Université Paris-Saclay, Châtenay-Malabry, France
| | - Gerald F Späth
- Institut Pasteur, Université de Paris, INSERM U1201, Unité de Parasitologie Moléculaire et Signalisation, Paris, France.
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19
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Wang Y, Luo W, Huang L, Xiao J, Song X, Li F, Ma Y, Wang X, Jin F, Liu P, Zhu Y, Kitazato K, Wang Y, Ren Z. A novel lncRNA linc-AhRA negatively regulates innate antiviral response in murine microglia upon neurotropic herpesvirus infection. Am J Cancer Res 2021; 11:9623-9651. [PMID: 34646390 PMCID: PMC8490526 DOI: 10.7150/thno.64880] [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: 07/12/2021] [Accepted: 09/07/2021] [Indexed: 01/17/2023] Open
Abstract
Microglia are the primary cellular source of type I interferons (I-IFNs) in the brain upon neurotropic virus infection. Although the I-IFN-based antiviral innate immune response is crucial for eliminating viruses, overproduction led to immune disorders. Therefore, the relatively long-lasting I-IFNs must be precisely controlled, but the regulatory mechanism for the innate antiviral response in microglia remains largely unknown. Long non-coding RNAs (lncRNAs) are being recognized as crucial factors in numerous diseases, but their regulatory roles in the innate antiviral response in microglia are undefined. Methods: The high-throughput RNA sequencing was performed to obtain differentially expressed lncRNAs (DELs) in primary microglia infected with or without the neurotropic herpes simplex virus type 1 (HSV-1). We selected four DELs ranked in the top 15 in basic level and their fold change induced by HSV-1, i.e., FPKMHSV-1/FPKMCells.We subsequently found a key lncRNA affecting the innate antiviral response of microglia significantly. We next used dual-luciferase reporter assays, bioinformatical tools, and truncation mutants of both lncRNA and targeted proteins to elucidate the downstream and upstream mechanism of action of lncRNA. Further, we established microglia-specific knock-in (KI) mice to investigate the role of lncRNA in vivo. Results: We identified a long intergenic non-coding RNA, linc-AhRA, involved in regulating the innate antiviral response in murine microglia. linc-AhRA is activated by aryl hydrocarbon receptor (AhR) and restricts I-IFN production in microglia upon neurotropic herpesvirus infection and innate immune stimulation. Mechanistically, linc-AhRA binds to both tripartite motif-containing 27 (TRIM27) and TANK-binding kinase 1 (TBK1) through its conserved 117nt fragment as a molecular scaffold to enhance TRIM27-TBK1 interaction. This interaction facilitates the TRIM27-mediated ubiquitination of TBK1 and results in ubiquitin-proteasome-dependent degradation of TBK1. Consequently, linc-AhRA suppresses I-IFN production through facilitating TBK1 degradation and limits the microglial innate immune response against neurotropic herpesvirus infection. Microglia-specific KI of linc-AhRA mice shows a weakened antiviral immune response upon neurotropic herpesvirus challenge due to a reduction of TBK1 in microglia. Conclusion: Our findings indicate that linc-AhRA is a negative regulator of I-IFN production in microglia to avoid excessive autoimmune responses. These findings uncover a previously unappreciated role for lncRNA conserved fragments in the innate antiviral response, providing a strong foundation for developing nucleotide drugs based on conserved functional fragments within lncRNAs.
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20
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Akıncılar SC, Wu L, NG QF, Chua JYH, Unal B, Noda T, Chor WHJ, Ikawa M, Tergaonkar V. NAIL: an evolutionarily conserved lncRNA essential for licensing coordinated activation of p38 and NFκB in colitis. Gut 2021; 70:1857-1871. [PMID: 33239342 PMCID: PMC8458091 DOI: 10.1136/gutjnl-2020-322980] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 10/19/2020] [Accepted: 10/29/2020] [Indexed: 12/14/2022]
Abstract
OBJECTIVE NFκB is the key modulator in inflammatory disorders. However, the key regulators that activate, fine-tune or shut off NFκB activity in inflammatory conditions are poorly understood. In this study, we aim to investigate the roles that NFκB-specific long non-coding RNAs (lncRNAs) play in regulating inflammatory networks. DESIGN Using the first genetic-screen to identify NFκB-specific lncRNAs, we performed RNA-seq from the p65-/- and Ikkβ-/- mouse embryonic fibroblasts and report the identification of an evolutionary conserved lncRNA designated mNAIL (mice) or hNAIL (human). hNAIL is upregulated in human inflammatory disorders, including UC. We generated mNAILΔNFκB mice, wherein deletion of two NFκB sites in the proximal promoter of mNAIL abolishes its induction, to study its function in colitis. RESULTS NAIL regulates inflammation via sequestering and inactivating Wip1, a known negative regulator of proinflammatory p38 kinase and NFκB subunit p65. Wip1 inactivation leads to coordinated activation of p38 and covalent modifications of NFκB, essential for its genome-wide occupancy on specific targets. NAIL enables an orchestrated response for p38 and NFκB coactivation that leads to differentiation of precursor cells into immature myeloid cells in bone marrow, recruitment of macrophages to inflamed area and expression of inflammatory genes in colitis. CONCLUSION NAIL directly regulates initiation and progression of colitis and its expression is highly correlated with NFκB activity which makes it a perfect candidate to serve as a biomarker and a therapeutic target for IBD and other inflammation-associated diseases.
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Affiliation(s)
- Semih Can Akıncılar
- Laboratory of NFκB Signalling, Institute of Molecular and Cell Biology (IMCB), A*STAR (Agency for Science, Technology and Research), Institute of Molecular and Cell Biology, Singapore
| | - Lele Wu
- Laboratory of NFκB Signalling, Institute of Molecular and Cell Biology (IMCB), A*STAR (Agency for Science, Technology and Research), Institute of Molecular and Cell Biology, Singapore
| | - Qin Feng NG
- Laboratory of NFκB Signalling, Institute of Molecular and Cell Biology (IMCB), A*STAR (Agency for Science, Technology and Research), Institute of Molecular and Cell Biology, Singapore
| | - Joelle Yi Heng Chua
- Laboratory of NFκB Signalling, Institute of Molecular and Cell Biology (IMCB), A*STAR (Agency for Science, Technology and Research), Institute of Molecular and Cell Biology, Singapore
| | - Bilal Unal
- Laboratory of NFκB Signalling, Institute of Molecular and Cell Biology (IMCB), A*STAR (Agency for Science, Technology and Research), Institute of Molecular and Cell Biology, Singapore
| | - Taichi Noda
- Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Wei Hong Jeff Chor
- Laboratory of NFκB Signalling, Institute of Molecular and Cell Biology (IMCB), A*STAR (Agency for Science, Technology and Research), Institute of Molecular and Cell Biology, Singapore
| | - Masahito Ikawa
- Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Vinay Tergaonkar
- Laboratory of NFκB Signalling, Institute of Molecular and Cell Biology (IMCB), A*STAR (Agency for Science, Technology and Research), Institute of Molecular and Cell Biology, Singapore .,Department of Pathology, Yong Loo Lin School of Medicine, National University of Singapore (NUS), Singapore
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21
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Guenther C, Faisal I, Fusciello M, Sokolova M, Harjunpää H, Ilander M, Tallberg R, Vartiainen MK, Alon R, Gonzalez-Granado JM, Cerullo V, Fagerholm SC. β2-Integrin Adhesion Regulates Dendritic Cell Epigenetic and Transcriptional Landscapes to Restrict Dendritic Cell Maturation and Tumor Rejection. Cancer Immunol Res 2021; 9:1354-1369. [PMID: 34561280 DOI: 10.1158/2326-6066.cir-21-0094] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 05/29/2021] [Accepted: 09/15/2021] [Indexed: 11/16/2022]
Abstract
Dendritic cells (DC), the classic antigen-presenting cells of the immune system, switch from an adhesive, phagocytic phenotype in tissues, to a mature, nonadhesive phenotype that enables migration to lymph nodes to activate T cells and initiate antitumor responses. Monocyte-derived DCs are used in cancer immunotherapy, but their clinical efficacy is limited. Here, we show that cultured bone marrow-derived DCs (BM-DC) expressing dysfunctional β2-integrin adhesion receptors displayed enhanced tumor rejection capabilities in B16.OVA and B16-F10 melanoma models. This was associated with an increased CD8+ T-cell response. BM-DCs expressing dysfunctional β2-integrins or manipulated to disrupt integrin adhesion or integrin/actin/nuclear linkages displayed spontaneous maturation in ex vivo cultures (increased costimulatory marker expression, IL12 production, and 3D migration capabilities). This spontaneous maturation was associated with an altered DC epigenetic/transcriptional profile, including a global increase in chromatin accessibility and H3K4me3/H3K27me3 histone methylation. Genome-wide analyses showed that H3K4me3 methylation was increased on DC maturation genes, such as CD86, Il12, Ccr7, and Fscn1, and revealed a role for a transcription factor network involving Ikaros and RelA in the integrin-regulated phenotype of DCs. Manipulation of the integrin-regulated epigenetic landscape in wild-type ex vivo-cultured BM-DCs enhanced their functionality in tumor rejection in vivo. Thus, β2-integrin-mediated adhesion to the extracellular environment plays an important role in restricting DC maturation and antitumor responses through regulation of the cellular epigenetic and transcriptional landscape. Targeting β2-integrins could therefore be a new strategy to improve the performance of current DC-based cancer immunotherapies.
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Affiliation(s)
- Carla Guenther
- Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Imrul Faisal
- Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | | | - Maria Sokolova
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Heidi Harjunpää
- Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Mette Ilander
- Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Robert Tallberg
- Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | | | - Ronen Alon
- Weizmann Institute of Science, Rehovot, Israel
| | - Jose-Maria Gonzalez-Granado
- LamImSys Lab, Instituto de Investigación Hospital, Madrid, Spain
- Departamento de Fisiología, Facultad de Medicina, Universidad Autónoma de Madrid (UAM), Madrid, Spain
| | | | - Susanna Carola Fagerholm
- Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland.
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22
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Tamura I, Fujimura T, Doi-Tanaka Y, Takagi H, Shirafuta Y, Kajimura T, Mihara Y, Maekawa R, Taketani T, Sato S, Tamura H, Sugino N. The essential glucose transporter GLUT1 is epigenetically upregulated by C/EBPβ and WT1 during decidualization of the endometrium. J Biol Chem 2021; 297:101150. [PMID: 34478711 PMCID: PMC8458984 DOI: 10.1016/j.jbc.2021.101150] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 08/23/2021] [Accepted: 08/30/2021] [Indexed: 11/29/2022] Open
Abstract
Human endometrial stromal cells (ESCs) differentiate into decidual cells by the action of progesterone, which is essential for implantation and maintenance of pregnancy. We previously reported that glucose uptake by human ESCs increases during decidualization and that glucose is indispensable for decidualization. Although glucose transporter 1 (GLUT1) is upregulated during decidualization, it remains unclear whether it is involved in glucose uptake. Here, we attempted to determine the role of GLUT1 during decidualization as well as the factors underlying its upregulation. ESCs were incubated with cAMP to induce decidualization. Knockdown of GLUT1 suppressed cAMP-increased glucose uptake and the expressions of specific markers of decidualization, IGF-binding protein-1 (IGFBP-1), and prolactin (PRL). To investigate the regulation of GLUT1 expression, we focused on CCAAT enhancer-binding protein β (C/EBPβ) and Wilms' tumor 1 (WT1) as the upstream transcription factors regulating GLUT1 expression. Knockdown of either C/EBPβ or WT1 suppressed cAMP-increased GLUT1 expression and glucose uptake. cAMP treatment also increased the recruitment of C/EBPβ and WT1 to the GLUT1 promoter region. Interestingly, cAMP increased the H3K27 acetylation (H3K27ac) and p300 recruitment in the GLUT1 promoter region. Knockdown of C/EBPβ or WT1 inhibited these events, indicating that both C/EBPβ and WT1 contribute to the increase of H3K27ac by recruiting p300 to the GLUT1 promoter region during decidualization. These findings indicate that GLUT1 is involved in glucose uptake in ESCs during decidualization, thus facilitating the establishment of pregnancy.
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Affiliation(s)
- Isao Tamura
- Department of Obstetrics and Gynecology, Yamaguchi University Graduate School of Medicine, Ube, Japan.
| | - Taishi Fujimura
- Department of Obstetrics and Gynecology, Yamaguchi University Graduate School of Medicine, Ube, Japan
| | - Yumiko Doi-Tanaka
- Department of Obstetrics and Gynecology, Yamaguchi University Graduate School of Medicine, Ube, Japan
| | - Haruka Takagi
- Department of Obstetrics and Gynecology, Yamaguchi University Graduate School of Medicine, Ube, Japan
| | - Yuichiro Shirafuta
- Department of Obstetrics and Gynecology, Yamaguchi University Graduate School of Medicine, Ube, Japan
| | - Takuya Kajimura
- Department of Obstetrics and Gynecology, Yamaguchi University Graduate School of Medicine, Ube, Japan
| | - Yumiko Mihara
- Department of Obstetrics and Gynecology, Yamaguchi University Graduate School of Medicine, Ube, Japan
| | - Ryo Maekawa
- Department of Obstetrics and Gynecology, Yamaguchi University Graduate School of Medicine, Ube, Japan
| | - Toshiaki Taketani
- Department of Obstetrics and Gynecology, Yamaguchi University Graduate School of Medicine, Ube, Japan
| | - Shun Sato
- Department of Obstetrics and Gynecology, Yamaguchi University Graduate School of Medicine, Ube, Japan
| | - Hiroshi Tamura
- Department of Obstetrics and Gynecology, Yamaguchi University Graduate School of Medicine, Ube, Japan
| | - Norihiro Sugino
- Department of Obstetrics and Gynecology, Yamaguchi University Graduate School of Medicine, Ube, Japan
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23
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Cilenti F, Barbiera G, Caronni N, Iodice D, Montaldo E, Barresi S, Lusito E, Cuzzola V, Vittoria FM, Mezzanzanica L, Miotto P, Di Lucia P, Lazarevic D, Cirillo DM, Iannacone M, Genua M, Ostuni R. A PGE 2-MEF2A axis enables context-dependent control of inflammatory gene expression. Immunity 2021; 54:1665-1682.e14. [PMID: 34129840 PMCID: PMC8362890 DOI: 10.1016/j.immuni.2021.05.016] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 03/25/2021] [Accepted: 05/19/2021] [Indexed: 12/13/2022]
Abstract
Tight control of inflammatory gene expression by antagonistic environmental cues is key to ensure immune protection while preventing tissue damage. Prostaglandin E2 (PGE2) modulates macrophage activation during homeostasis and disease, but the underlying mechanisms remain incompletely characterized. Here we dissected the genomic properties of lipopolysaccharide (LPS)-induced genes whose expression is antagonized by PGE2. The latter molecule targeted a set of inflammatory gene enhancers that, already in unstimulated macrophages, displayed poorly permissive chromatin organization and were marked by the transcription factor myocyte enhancer factor 2A (MEF2A). Deletion of MEF2A phenocopied PGE2 treatment and abolished type I interferon (IFN I) induction upon exposure to innate immune stimuli. Mechanistically, PGE2 interfered with LPS-mediated activation of ERK5, a known transcriptional partner of MEF2. This study highlights principles of plasticity and adaptation in cells exposed to a complex environment and uncovers a transcriptional circuit for IFN I induction with relevance for infectious diseases or cancer.
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Affiliation(s)
- Francesco Cilenti
- Vita-Salute San Raffaele University, Milan, Italy; San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), Milan, Italy; Genomics of the Innate Immune System Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Giulia Barbiera
- San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), Milan, Italy; Genomics of the Innate Immune System Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Nicoletta Caronni
- San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), Milan, Italy; Genomics of the Innate Immune System Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Dario Iodice
- San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), Milan, Italy; Genomics of the Innate Immune System Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Elisa Montaldo
- San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), Milan, Italy; Genomics of the Innate Immune System Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Simona Barresi
- San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), Milan, Italy; Genomics of the Innate Immune System Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Eleonora Lusito
- San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), Milan, Italy; Genomics of the Innate Immune System Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Vincenzo Cuzzola
- San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), Milan, Italy; Genomics of the Innate Immune System Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Francesco Maria Vittoria
- Vita-Salute San Raffaele University, Milan, Italy; San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), Milan, Italy; Genomics of the Innate Immune System Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Luca Mezzanzanica
- Vita-Salute San Raffaele University, Milan, Italy; San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), Milan, Italy; Genomics of the Innate Immune System Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Paolo Miotto
- Emerging Bacterial Pathogens Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Pietro Di Lucia
- Dynamics of Immune Responses Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Dejan Lazarevic
- Center for Omics Sciences (COSR), IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Daniela Maria Cirillo
- Emerging Bacterial Pathogens Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Matteo Iannacone
- Vita-Salute San Raffaele University, Milan, Italy; Dynamics of Immune Responses Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy; Experimental Imaging Centre, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Marco Genua
- San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), Milan, Italy; Genomics of the Innate Immune System Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Renato Ostuni
- Vita-Salute San Raffaele University, Milan, Italy; San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), Milan, Italy; Genomics of the Innate Immune System Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy.
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24
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Maruyama K, Kidoya H, Takemura N, Sugisawa E, Takeuchi O, Kondo T, Eid MMA, Tanaka H, Martino MM, Takakura N, Takayama Y, Akira S, Vandenbon A, Kumagai Y. Zinc Finger Protein St18 Protects against Septic Death by Inhibiting VEGF-A from Macrophages. Cell Rep 2021; 32:107906. [PMID: 32668247 DOI: 10.1016/j.celrep.2020.107906] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Revised: 04/22/2020] [Accepted: 06/23/2020] [Indexed: 12/20/2022] Open
Abstract
Zinc finger protein St18 was initially reported as candidate tumor suppressor gene, and also suggested that fibroblast St18 positively regulates NF-κB activation. Despite the pleiotropic functions of St18, little is known about its roles in macrophages. Here, we report that myeloid St18 is a potent inhibitor of VEGF-A. Mice lacking St18 in myeloid lineages exhibit increased retinal vasculature with enhanced serum VEGF-A concentrations. Despite the normal activation of NF-κB target genes, these mice are highly susceptible to LPS-induced shock, polymicrobial sepsis, and experimental colitis, accompanied by enhanced vascular and intestinal leakage. Pharmacological inhibition of VEGF signaling rescued the high mortality rate of myeloid-specific St18-deficient mice in response to inflammation. Mechanistically, St18 directly binds to Sp1 and attenuates its activity, leading to the suppression of Sp1 target gene VEGF-A. Using mouse genetic and pharmacological models, we reveal myeloid St18 as a critical septic death protector.
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Affiliation(s)
- Kenta Maruyama
- WPI Immunology Frontier Research Center (IFReC), Osaka University, Osaka 565-0871, Japan; Division of Cell Signaling, Okazaki Institute for Integrative Bioscience (National Institute for Physiological Sciences), National Institutes of Natural Sciences, Aichi 444-8787, Japan.
| | - Hiroyasu Kidoya
- Department of Signal Transduction, Research Institute for Microbial Diseases, Osaka University, Osaka 565-0871, Japan
| | - Naoki Takemura
- Department of Mucosal Immunology, School of Medicine, Chiba University, Chiba 260-8670, Japan
| | - Erika Sugisawa
- WPI Immunology Frontier Research Center (IFReC), Osaka University, Osaka 565-0871, Japan
| | - Osamu Takeuchi
- Laboratory of Infection and Prevention, Department of Virus Research, Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto 606-8507, Japan
| | - Takeshi Kondo
- Department of Biochemistry, Faculty of Medicine and Graduate School of Medicine, Hokkaido University, Kita 15, Nishi 7, Kita-ku, Sapporo, Hokkaido 060-8636, Japan
| | | | - Hiroki Tanaka
- WPI Immunology Frontier Research Center (IFReC), Osaka University, Osaka 565-0871, Japan
| | - Mikaël M Martino
- European Molecular Biology Laboratory Australia, Australian Regenerative Medicine Institute, Monash University, Melbourne, VIC 3800, Australia
| | - Nobuyuki Takakura
- Department of Signal Transduction, Research Institute for Microbial Diseases, Osaka University, Osaka 565-0871, Japan
| | - Yasunori Takayama
- Division of Cell Signaling, Okazaki Institute for Integrative Bioscience (National Institute for Physiological Sciences), National Institutes of Natural Sciences, Aichi 444-8787, Japan; Department of Physiological Sciences, Graduate University for Advanced Studies, Aichi 444-8787, Japan
| | - Shizuo Akira
- WPI Immunology Frontier Research Center (IFReC), Osaka University, Osaka 565-0871, Japan
| | - Alexis Vandenbon
- Laboratory of Infection and Prevention, Department of Virus Research, Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto 606-8507, Japan
| | - Yutaro Kumagai
- Biotechnology Research Institute for Drug Discovery, Department of Life Science and Biotechnology, National Institute of Advanced Industrial Science and Technology, Tsukuba, Ibaraki 305-8565, Japan
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25
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Bar-Ziv R, Brodsky S, Chapal M, Barkai N. Transcription Factor Binding to Replicated DNA. Cell Rep 2021; 30:3989-3995.e4. [PMID: 32209462 DOI: 10.1016/j.celrep.2020.02.114] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Revised: 01/13/2020] [Accepted: 02/27/2020] [Indexed: 11/17/2022] Open
Abstract
Genome replication perturbs the DNA regulatory environment by displacing DNA-bound proteins, replacing nucleosomes, and introducing dosage imbalance between regions replicating at different S-phase stages. Recently, we showed that these effects are integrated to maintain transcription homeostasis: replicated genes increase in dosage, but their expression remains stable due to replication-dependent epigenetic changes that suppress transcription. Here, we examine whether reduced transcription from replicated DNA results from limited accessibility to regulatory factors by measuring the time-resolved binding of RNA polymerase II (Pol II) and specific transcription factors (TFs) to DNA during S phase in budding yeast. We show that the Pol II binding pattern is largely insensitive to DNA dosage, indicating limited binding to replicated DNA. In contrast, binding of three TFs (Reb1, Abf1, and Rap1) to DNA increases with the increasing DNA dosage. We conclude that the replication-specific chromatin environment remains accessible to regulatory factors but suppresses RNA polymerase recruitment.
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Affiliation(s)
- Raz Bar-Ziv
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel; The Howard Hughes Medical Institute, University of California Berkeley, Berkeley, CA 94720, USA
| | - Sagie Brodsky
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Michal Chapal
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Naama Barkai
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel.
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26
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Sun X, Zhang J, Nie Q. Inferring latent temporal progression and regulatory networks from cross-sectional transcriptomic data of cancer samples. PLoS Comput Biol 2021; 17:e1008379. [PMID: 33667222 PMCID: PMC7968745 DOI: 10.1371/journal.pcbi.1008379] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2020] [Revised: 03/17/2021] [Accepted: 02/15/2021] [Indexed: 12/19/2022] Open
Abstract
Unraveling molecular regulatory networks underlying disease progression is critically important for understanding disease mechanisms and identifying drug targets. The existing methods for inferring gene regulatory networks (GRNs) rely mainly on time-course gene expression data. However, most available omics data from cross-sectional studies of cancer patients often lack sufficient temporal information, leading to a key challenge for GRN inference. Through quantifying the latent progression using random walks-based manifold distance, we propose a latent-temporal progression-based Bayesian method, PROB, for inferring GRNs from the cross-sectional transcriptomic data of tumor samples. The robustness of PROB to the measurement variabilities in the data is mathematically proved and numerically verified. Performance evaluation on real data indicates that PROB outperforms other methods in both pseudotime inference and GRN inference. Applications to bladder cancer and breast cancer demonstrate that our method is effective to identify key regulators of cancer progression or drug targets. The identified ACSS1 is experimentally validated to promote epithelial-to-mesenchymal transition of bladder cancer cells, and the predicted FOXM1-targets interactions are verified and are predictive of relapse in breast cancer. Our study suggests new effective ways to clinical transcriptomic data modeling for characterizing cancer progression and facilitates the translation of regulatory network-based approaches into precision medicine.
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Affiliation(s)
- Xiaoqiang Sun
- Key Laboratory of Tropical Disease Control, Chinese Ministry of Education; Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
- School of Mathematics, Sun Yat-sen University, Guangzhou, China
| | - Ji Zhang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, China
| | - Qing Nie
- Department of Mathematics and Department of Developmental & Cell Biology, NSF-Simons Center for Multiscale Cell Fate Research, University of California Irvine, Irvine, California, United States of America
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27
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Vahedi G. Remodeling the chromatin landscape in T lymphocytes by a division of labor among transcription factors. Immunol Rev 2021; 300:167-180. [PMID: 33452686 DOI: 10.1111/imr.12942] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 12/18/2020] [Accepted: 12/23/2020] [Indexed: 12/16/2022]
Abstract
An extraordinary degree of condensation is required to fit the eukaryotic genome inside the nucleus. This compaction is attained by first coiling the DNA around structures called nucleosomes. Mammalian genomes are further folded into sophisticated three-dimensional (3D) configurations, enabling the genetic code to dictate a diverse range of cell fates. Recent advances in molecular and computational technologies have enabled the query of higher-order chromatin architecture at an unprecedented resolution and scale. In T lymphocytes, similar to other developmental programs, the hierarchical genome organization is shaped by a highly coordinated division of labor among different classes of sequence-specific transcription factors. In this review, we will summarize the general principles of 1D and 3D genome organization, introduce the common experimental and computational techniques to measure the multilayer chromatin organization, and discuss the pervasive role of transcription factors on chromatin organization in T lymphocytes.
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Affiliation(s)
- Golnaz Vahedi
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.,Institute for Immunology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.,Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.,Institute for Diabetes, Obesity and Metabolism, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
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28
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Tamura I, Maekawa R, Jozaki K, Ohkawa Y, Takagi H, Doi-Tanaka Y, Shirafuta Y, Mihara Y, Taketani T, Sato S, Tamura H, Sugino N. Transcription factor C/EBPβ induces genome-wide H3K27ac and upregulates gene expression during decidualization of human endometrial stromal cells. Mol Cell Endocrinol 2021; 520:111085. [PMID: 33232782 DOI: 10.1016/j.mce.2020.111085] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/04/2020] [Revised: 11/11/2020] [Accepted: 11/13/2020] [Indexed: 12/22/2022]
Abstract
We previously reported that H3K27 acetylation (H3K27ac) increases throughout the genome during decidualization of human endometrial stromal cells (ESCs). However, its mechanisms have not been clarified. We also reported that C/EBPβ acts as a pioneer factor initiating chromatin remodeling by increasing H3K27ac of IGFBP-1 and PRL promoters. Therefore, C/EBPβ may be involved in the genome-wide increase of H3K27ac during decidualization. In this study, we investigated whether C/EBPβ causes genome-wide H3K27ac modifications and regulates gene expressions during decidualization. cAMP was used to induce decidualization. Three types of cells (control cells, cAMP-treated cells, and cAMP-treated + C/EBPβ-knockdowned cells by siRNA) were generated. Of 4190 genes that were upregulated by cAMP, C/EBPβ knockdown inhibited these upregulation in 2239 genes (53.4%), indicating that they are under the regulation of C/EBPβ. cAMP increased H3K27ac in 1272 of the 2239 genes. C/EBPβ knockdown abolished the increase of H3K27ac in almost all genes (1263 genes, 99.3%), suggesting that C/EBPβ can upregulate gene expression by increasing H3K27ac. To investigate how C/EBPβ regulates H3K27ac throughout the genome, we tested the hypothesis that C/EBPβ binds to its binding regions and recruits cofactors with histone acetyltransferase activities. To do this, we collated our ChIP-sequence data with public ChIP-sequence database of transcription factors, and found that p300 is the most likely cofactor that binds to the H3K27ac-increased-regions with C/EBPβ. ChIP-qPCR of several genes confirmed that C/EBPβ binds to the target regions, recruits p300, and increases H3K27ac. Our genome-wide analysis revealed that C/EBPβ induces H3K27ac throughout the genome and upregulates gene expressions during decidualization by recruiting p300 to the promoters.
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Affiliation(s)
- Isao Tamura
- Department of Obstetrics and Gynecology, Yamaguchi University Graduate School of Medicine, Japan.
| | - Ryo Maekawa
- Department of Obstetrics and Gynecology, Yamaguchi University Graduate School of Medicine, Japan
| | - Kosuke Jozaki
- Department of Immunology, Yamaguchi University Graduate School of Medicine, Japan
| | - Yasuyuki Ohkawa
- Division of Transcriptomics, Medical Institute of Bioregulation, Kyushu University, Japan
| | - Haruka Takagi
- Department of Obstetrics and Gynecology, Yamaguchi University Graduate School of Medicine, Japan
| | - Yumiko Doi-Tanaka
- Department of Obstetrics and Gynecology, Yamaguchi University Graduate School of Medicine, Japan
| | - Yuichiro Shirafuta
- Department of Obstetrics and Gynecology, Yamaguchi University Graduate School of Medicine, Japan
| | - Yumiko Mihara
- Department of Obstetrics and Gynecology, Yamaguchi University Graduate School of Medicine, Japan
| | - Toshiaki Taketani
- Department of Obstetrics and Gynecology, Yamaguchi University Graduate School of Medicine, Japan
| | - Shun Sato
- Department of Obstetrics and Gynecology, Yamaguchi University Graduate School of Medicine, Japan
| | - Hiroshi Tamura
- Department of Obstetrics and Gynecology, Yamaguchi University Graduate School of Medicine, Japan
| | - Norihiro Sugino
- Department of Obstetrics and Gynecology, Yamaguchi University Graduate School of Medicine, Japan
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29
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Solus L, Wang Y, Uhler C. Consistency guarantees for greedy permutation-based causal inference algorithms. Biometrika 2021. [DOI: 10.1093/biomet/asaa104] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Summary
Directed acyclic graphical models are widely used to represent complex causal systems. Since the basic task of learning such a model from data is NP-hard, a standard approach is greedy search over the space of directed acyclic graphs or Markov equivalence classes of directed acyclic graphs. As the space of directed acyclic graphs on $p$ nodes and the associated space of Markov equivalence classes are both much larger than the space of permutations, it is desirable to consider permutation-based greedy searches. Here, we provide the first consistency guarantees, both uniform and high dimensional, of a greedy permutation-based search. This search corresponds to a simplex-like algorithm operating over the edge-graph of a subpolytope of the permutohedron, called a directed acyclic graph associahedron. Every vertex in this polytope is associated with a directed acyclic graph, and hence with a collection of permutations that are consistent with the directed acyclic graph ordering. A walk is performed on the edges of the polytope maximizing the sparsity of the associated directed acyclic graphs. We show via simulated and real data that this permutation search is competitive with current approaches.
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Affiliation(s)
- L Solus
- Institutionen för Matematik, KTH Royal Institute of Technology, 10044 Stockholm, Sweden
| | - Y Wang
- Institute for Interdisciplinary Information Sciences, Tsinghua University, Beijing 100084, China
| | - C Uhler
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, 77 Massachusetts Ave., Cambridge, Massachusetts 02139, U.S.A
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30
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Scheenstra MR, Martínez-Botía P, Acebes-Huerta A, Brouwer RWW, Caballero-Sánchez N, Gillemans N, De Bleser P, Nota B, De Cuyper IM, Salunkhe V, Woltman AM, van de Laar L, Rijkers E, Demmers JAA, van IJcken WFJ, Philipsen S, van den Berg TK, Kuijpers TW, Gutiérrez L. Comparison of the PU.1 transcriptional regulome and interactome in human and mouse inflammatory dendritic cells. J Leukoc Biol 2020; 110:735-751. [PMID: 33289106 DOI: 10.1002/jlb.6a1219-711rrr] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 11/18/2020] [Accepted: 11/18/2020] [Indexed: 12/17/2022] Open
Abstract
Dendritic cells (DCs) are key immune modulators and are able to mount immune responses or tolerance. DC differentiation and activation imply a plethora of molecular and cellular responses, including transcriptional changes. PU.1 is a highly expressed transcription factor in DCs and coordinates relevant aspects of DC biology. Due to their role as immune regulators, DCs pose as a promising immunotherapy tool. However, some of their functional features, such as survival, activation, or migration, are compromised due to the limitations to simulate in vitro the physiologic DC differentiation process. A better knowledge of transcriptional programs would allow the identification of potential targets for manipulation with the aim of obtaining "qualified" DCs for immunotherapy purposes. Most of the current knowledge regarding DC biology derives from studies using mouse models, which not always find a parallel in human. In the present study, we dissect the PU.1 transcriptional regulome and interactome in mouse and human DCs, in the steady state or LPS activated. The PU.1 transcriptional regulome was identified by performing PU.1 chromatin immunoprecipitation followed by high-throughput sequencing and pairing these data with RNAsequencing data. The PU.1 interactome was identified by performing PU.1 immunoprecipitation followed by mass spectrometry analysis. Our results portray PU.1 as a pivotal factor that plays an important role in the regulation of genes required for proper DC activation and function, and assures the repression of nonlineage genes. The interspecies differences between human and mouse DCs are surprisingly substantial, highlighting the need to study the biology of human DCs.
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Affiliation(s)
- Maaike R Scheenstra
- Department of Blood Cell Research, Sanquin Research and Landsteiner Laboratory, Academic Medical Center (AMC), University of Amsterdam, Amsterdam, The Netherlands
- Division of Infectious Diseases and Immunology, Department of Biomolecular Health Sciences, Utrecht University, Utrecht, The Netherlands
| | | | - Andrea Acebes-Huerta
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain
| | - Rutger W W Brouwer
- Center for Biomics, Erasmus MC, Rotterdam, The Netherlands
- Department of Cell Biology, Erasmus MC, Rotterdam, The Netherlands
| | | | - Nynke Gillemans
- Department of Cell Biology, Erasmus MC, Rotterdam, The Netherlands
| | - Pieter De Bleser
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
- VIB Center for Inflammation Research, Data Mining and Modeling for Biomedicine, Ghent, Belgium
| | - Benjamin Nota
- Department of Blood Cell Research, Sanquin Research and Landsteiner Laboratory, Academic Medical Center (AMC), University of Amsterdam, Amsterdam, The Netherlands
| | - Iris M De Cuyper
- Department of Blood Cell Research, Sanquin Research and Landsteiner Laboratory, Academic Medical Center (AMC), University of Amsterdam, Amsterdam, The Netherlands
| | - Vishal Salunkhe
- Department of Blood Cell Research, Sanquin Research and Landsteiner Laboratory, Academic Medical Center (AMC), University of Amsterdam, Amsterdam, The Netherlands
| | - Andrea M Woltman
- Department of Gastroenterology and Hepatology, Erasmus MC, Rotterdam, The Netherlands
- Current Address: Institute of Medical Education Research Rotterdam, Erasmus MC, Rotterdam, The Netherlands
| | - Lianne van de Laar
- Department of Gastroenterology and Hepatology, Erasmus MC, Rotterdam, The Netherlands
| | | | | | - Wilfred F J van IJcken
- Center for Biomics, Erasmus MC, Rotterdam, The Netherlands
- Department of Cell Biology, Erasmus MC, Rotterdam, The Netherlands
| | - Sjaak Philipsen
- Department of Cell Biology, Erasmus MC, Rotterdam, The Netherlands
| | - Timo K van den Berg
- Department of Blood Cell Research, Sanquin Research and Landsteiner Laboratory, Academic Medical Center (AMC), University of Amsterdam, Amsterdam, The Netherlands
| | - Taco W Kuijpers
- Department of Blood Cell Research, Sanquin Research and Landsteiner Laboratory, Academic Medical Center (AMC), University of Amsterdam, Amsterdam, The Netherlands
- Laboratory of Immunotherapy, Sanquin Research and Landsteiner Laboratory, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, The Netherlands
- Department of Molecular Cell Biology and Immunology, Amsterdam University Medical Center, Vrije University, Amsterdam, The Netherlands
| | - Laura Gutiérrez
- Department of Blood Cell Research, Sanquin Research and Landsteiner Laboratory, Academic Medical Center (AMC), University of Amsterdam, Amsterdam, The Netherlands
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain
- University of Oviedo, Oviedo, Spain
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31
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Zhang H, Madi A, Yosef N, Chihara N, Awasthi A, Pot C, Lambden C, Srivastava A, Burkett PR, Nyman J, Christian E, Etminan Y, Lee A, Stroh H, Xia J, Karwacz K, Thakore PI, Acharya N, Schnell A, Wang C, Apetoh L, Rozenblatt-Rosen O, Anderson AC, Regev A, Kuchroo VK. An IL-27-Driven Transcriptional Network Identifies Regulators of IL-10 Expression across T Helper Cell Subsets. Cell Rep 2020; 33:108433. [PMID: 33238123 PMCID: PMC7771052 DOI: 10.1016/j.celrep.2020.108433] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 07/14/2020] [Accepted: 11/04/2020] [Indexed: 12/16/2022] Open
Abstract
Interleukin-27 (IL-27) is an immunoregulatory cytokine that suppresses inflammation through multiple mechanisms, including induction of IL-10, but the transcriptional network mediating its diverse functions remains unclear. Combining temporal RNA profiling with computational algorithms, we predict 79 transcription factors induced by IL-27 in T cells. We validate 11 known and discover 5 positive (Cebpb, Fosl2, Tbx21, Hlx, and Atf3) and 2 negative (Irf9 and Irf8) Il10 regulators, generating an experimentally refined regulatory network for Il10. We report two central regulators, Prdm1 and Maf, that cooperatively drive the expression of signature genes induced by IL-27 in type 1 regulatory T cells, mediate IL-10 expression in all T helper cells, and determine the regulatory phenotype of colonic Foxp3+ regulatory T cells. Prdm1/Maf double-knockout mice develop spontaneous colitis, phenocopying ll10-deficient mice. Our work provides insights into IL-27-driven transcriptional networks and identifies two shared Il10 regulators that orchestrate immunoregulatory programs across T helper cell subsets. Zhang et al. construct a transcriptional network for IL-27-mediated Il10 production in CD4 T cells, characterize the function of 16 Il10 regulators, and uncover the role of two transcription factors, Prdm1 and Maf, in driving Il10 production in all T helper cells and in maintaining immune homeostasis in the colon.
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Affiliation(s)
- Huiyuan Zhang
- Evergrande Center for Immunologic Diseases and Ann Romney Center for Neurologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA, USA
| | - Asaf Madi
- Evergrande Center for Immunologic Diseases and Ann Romney Center for Neurologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA, USA; Department of Pathology, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel.
| | - Nir Yosef
- Evergrande Center for Immunologic Diseases and Ann Romney Center for Neurologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA, USA; Department of Electrical Engineering and Computer Science and Center for Computational Biology, University of California, Berkeley, CA, USA
| | - Norio Chihara
- Evergrande Center for Immunologic Diseases and Ann Romney Center for Neurologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA, USA; Division of Neurology, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Amit Awasthi
- Evergrande Center for Immunologic Diseases and Ann Romney Center for Neurologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA, USA; Center for Human Microbial Ecology, Translational Health Science and Technology Institute(an autonomous institute of the Department of Biotechnology, Government of India), NCR Biotech Science Cluster, Faridabad, India
| | - Caroline Pot
- Evergrande Center for Immunologic Diseases and Ann Romney Center for Neurologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA, USA; Laboratories of Neuroimmunology, Division of Neurology and Neuroscience Research Center, Department of Clinical Neurosciences, Lausanne University Hospital, Lausanne, Switzerland
| | - Conner Lambden
- Evergrande Center for Immunologic Diseases and Ann Romney Center for Neurologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA, USA; Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Patrick R Burkett
- Evergrande Center for Immunologic Diseases and Ann Romney Center for Neurologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA, USA; Biogen, 300 Binney St., Cambridge, MA, USA
| | - Jackson Nyman
- Evergrande Center for Immunologic Diseases and Ann Romney Center for Neurologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA, USA; Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Elena Christian
- Evergrande Center for Immunologic Diseases and Ann Romney Center for Neurologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA, USA; Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Yasaman Etminan
- Evergrande Center for Immunologic Diseases and Ann Romney Center for Neurologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA, USA
| | - Annika Lee
- Evergrande Center for Immunologic Diseases and Ann Romney Center for Neurologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA, USA
| | - Helene Stroh
- Evergrande Center for Immunologic Diseases and Ann Romney Center for Neurologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA, USA
| | - Junrong Xia
- Evergrande Center for Immunologic Diseases and Ann Romney Center for Neurologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA, USA
| | - Katarzyna Karwacz
- Evergrande Center for Immunologic Diseases and Ann Romney Center for Neurologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA, USA; Regeneron Pharmaceuticals, 777 Old Saw Mill River Road, Tarrytown, NY, USA
| | - Pratiksha I Thakore
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Nandini Acharya
- Evergrande Center for Immunologic Diseases and Ann Romney Center for Neurologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA, USA
| | - Alexandra Schnell
- Evergrande Center for Immunologic Diseases and Ann Romney Center for Neurologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA, USA
| | - Chao Wang
- Evergrande Center for Immunologic Diseases and Ann Romney Center for Neurologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA, USA
| | - Lionel Apetoh
- Evergrande Center for Immunologic Diseases and Ann Romney Center for Neurologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA, USA; INSERM, U1231, Dijon, France
| | | | - Ana C Anderson
- Evergrande Center for Immunologic Diseases and Ann Romney Center for Neurologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA, USA
| | - Aviv Regev
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Howard Hughes Medical Institute, Department of Biology, Koch Institute and Ludwig Center, Massachusetts Institute of Technology, Cambridge, MA, USA; Genentech, 1 DNA Way, South San Francisco, CA, USA.
| | - Vijay K Kuchroo
- Evergrande Center for Immunologic Diseases and Ann Romney Center for Neurologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA, USA; Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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32
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Chauvistré H, Seré K. Epigenetic aspects of DC development and differentiation. Mol Immunol 2020; 128:116-124. [PMID: 33126080 DOI: 10.1016/j.molimm.2020.10.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Revised: 09/09/2020] [Accepted: 10/14/2020] [Indexed: 02/06/2023]
Abstract
In this review we introduce the basic principles of epigenetic gene regulation and discuss them in the context of dendritic cell (DC) development and differentiation. Epigenetic mechanisms control the accessibility of chromatin for DNA binding proteins and thus they control gene expression. These mechanisms comprise chemical modifications of DNA and histones, chromatin remodeling and chromatin conformation. The variety of epigenetic mechanisms allow high-end fine tuning and flexibility of gene expression, a prerequisite in the process of DC lineage development.
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Affiliation(s)
- Heike Chauvistré
- Department of Dermatology, University Hospital Essen, West German Cancer Center, University Duisburg-Essen and the German Cancer Consortium (DKTK), Essen, Germany
| | - Kristin Seré
- Institute of Biomedical Engineering, Department of Cell Biology, RWTH Aachen University Medical School, Helmholtz Institute for Biomedical Engineering, RWTH Aachen University, Aachen, Germany.
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Regulation of the MIE Locus During HCMV Latency and Reactivation. Pathogens 2020; 9:pathogens9110869. [PMID: 33113934 PMCID: PMC7690695 DOI: 10.3390/pathogens9110869] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 10/19/2020] [Accepted: 10/20/2020] [Indexed: 12/20/2022] Open
Abstract
Human cytomegalovirus (HCMV) is a ubiquitous herpesviral pathogen that results in life-long infection. HCMV maintains a latent or quiescent infection in hematopoietic cells, which is broadly defined by transcriptional silencing and the absence of de novo virion production. However, upon cell differentiation coupled with immune dysfunction, the virus can reactivate, which leads to lytic replication in a variety of cell and tissue types. One of the mechanisms controlling the balance between latency and reactivation/lytic replication is the regulation of the major immediate-early (MIE) locus. This enhancer/promoter region is complex, and it is regulated by chromatinization and associated factors, as well as a variety of transcription factors. Herein, we discuss these factors and how they influence the MIE locus, which ultimately impacts the phase of HCMV infection.
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Tegally H, San JE, Giandhari J, de Oliveira T. Unlocking the efficiency of genomics laboratories with robotic liquid-handling. BMC Genomics 2020; 21:729. [PMID: 33081689 PMCID: PMC7576741 DOI: 10.1186/s12864-020-07137-1] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Accepted: 10/11/2020] [Indexed: 02/08/2023] Open
Abstract
In research and clinical genomics laboratories today, sample preparation is the bottleneck of experiments, particularly when it comes to high-throughput next generation sequencing (NGS). More genomics laboratories are now considering liquid-handling automation to make the sequencing workflow more efficient and cost effective. The question remains as to its suitability and return on investment. A number of points need to be carefully considered before introducing robots into biological laboratories. Here, we describe the state-of-the-art technology of both sophisticated and do-it-yourself (DIY) robotic liquid-handlers and provide a practical review of the motivation, implications and requirements of laboratory automation for genome sequencing experiments.
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Affiliation(s)
- Houriiyah Tegally
- Kwazulu-Natal Research and Innovation Sequencing Platform (KRISP), College of Health Sciences, K-RITH Tower Building, Nelson R Mandela School of Medicine, University of KwaZulu-Natal, 719 Umbilo Road, Durban, South Africa.
| | - James Emmanuel San
- Kwazulu-Natal Research and Innovation Sequencing Platform (KRISP), College of Health Sciences, K-RITH Tower Building, Nelson R Mandela School of Medicine, University of KwaZulu-Natal, 719 Umbilo Road, Durban, South Africa
| | - Jennifer Giandhari
- Kwazulu-Natal Research and Innovation Sequencing Platform (KRISP), College of Health Sciences, K-RITH Tower Building, Nelson R Mandela School of Medicine, University of KwaZulu-Natal, 719 Umbilo Road, Durban, South Africa
| | - Tulio de Oliveira
- Kwazulu-Natal Research and Innovation Sequencing Platform (KRISP), College of Health Sciences, K-RITH Tower Building, Nelson R Mandela School of Medicine, University of KwaZulu-Natal, 719 Umbilo Road, Durban, South Africa.
- Department of Global Health, University of Washington, 908 Jefferson Street, 13th Floor, Seattle, WA, 98104, USA.
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Vangala P, Murphy R, Quinodoz SA, Gellatly K, McDonel P, Guttman M, Garber M. High-Resolution Mapping of Multiway Enhancer-Promoter Interactions Regulating Pathogen Detection. Mol Cell 2020; 80:359-373.e8. [PMID: 32991830 PMCID: PMC7572724 DOI: 10.1016/j.molcel.2020.09.005] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2020] [Revised: 06/04/2020] [Accepted: 09/04/2020] [Indexed: 11/19/2022]
Abstract
Eukaryotic gene expression regulation involves thousands of distal regulatory elements. Understanding the quantitative contribution of individual enhancers to gene expression is critical for assessing the role of disease-associated genetic risk variants. Yet, we lack the ability to accurately link genes with their distal regulatory elements. To address this, we used 3D enhancer-promoter (E-P) associations identified using split-pool recognition of interactions by tag extension (SPRITE) to build a predictive model of gene expression. Our model dramatically outperforms models using genomic proximity and can be used to determine the quantitative impact of enhancer loss on gene expression in different genetic backgrounds. We show that genes that form stable E-P hubs have less cell-to-cell variability in gene expression. Finally, we identified transcription factors that regulate stimulation-dependent E-P interactions. Together, our results provide a framework for understanding quantitative contributions of E-P interactions and associated genetic variants to gene expression.
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Affiliation(s)
- Pranitha Vangala
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Rachel Murphy
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Sofia A Quinodoz
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Kyle Gellatly
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Patrick McDonel
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Mitchell Guttman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Manuel Garber
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA, USA; Department of Dermatology, Department of Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA; Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, USA.
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36
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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] [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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37
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Herrera-Uribe J, Liu H, Byrne KA, Bond ZF, Loving CL, Tuggle CK. Changes in H3K27ac at Gene Regulatory Regions in Porcine Alveolar Macrophages Following LPS or PolyIC Exposure. Front Genet 2020; 11:817. [PMID: 32973863 PMCID: PMC7468443 DOI: 10.3389/fgene.2020.00817] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2020] [Accepted: 07/08/2020] [Indexed: 12/17/2022] Open
Abstract
Changes in chromatin structure, especially in histone modifications (HMs), linked with chromatin accessibility for transcription machinery, are considered to play significant roles in transcriptional regulation. Alveolar macrophages (AM) are important immune cells for protection against pulmonary pathogens, and must readily respond to bacteria and viruses that enter the airways. Mechanism(s) controlling AM innate response to different pathogen-associated molecular patterns (PAMPs) are not well defined in pigs. By combining RNA sequencing (RNA-seq) with chromatin immunoprecipitation and sequencing (ChIP-seq) for four histone marks (H3K4me3, H3K4me1, H3K27ac and H3K27me3), we established a chromatin state map for AM stimulated with two different PAMPs, lipopolysaccharide (LPS) and Poly(I:C), and investigated the potential effect of identified histone modifications on transcription factor binding motif (TFBM) prediction and RNA abundance changes in these AM. The integrative analysis suggests that the differential gene expression between non-stimulated and stimulated AM is significantly associated with changes in the H3K27ac level at active regulatory regions. Although global changes in chromatin states were minor after stimulation, we detected chromatin state changes for differentially expressed genes involved in the TLR4, TLR3 and RIG-I signaling pathways. We found that regions marked by H3K27ac genome-wide were enriched for TFBMs of TF that are involved in the inflammatory response. We further documented that TF whose expression was induced by these stimuli had TFBMs enriched within H3K27ac-marked regions whose chromatin state changed by these same stimuli. Given that the dramatic transcriptomic changes and minor chromatin state changes occurred in response to both stimuli, we conclude that regulatory elements (i.e. active promoters) that contain transcription factor binding motifs were already active/poised in AM for immediate inflammatory response to PAMPs. In summary, our data provides the first chromatin state map of porcine AM in response to bacterial and viral PAMPs, contributing to the Functional Annotation of Animal Genomes (FAANG) project, and demonstrates the role of HMs, especially H3K27ac, in regulating transcription in AM in response to LPS and Poly(I:C).
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Affiliation(s)
- Juber Herrera-Uribe
- Department of Animal Science, Iowa State University, Ames, IA, United States
| | - Haibo Liu
- Department of Animal Science, Iowa State University, Ames, IA, United States
| | - Kristen A Byrne
- Food Safety and Enteric Pathogens Research Unit, National Animal Disease Center, USDA-Agriculture Research Service, Ames, IA, United States
| | - Zahra F Bond
- Food Safety and Enteric Pathogens Research Unit, National Animal Disease Center, USDA-Agriculture Research Service, Ames, IA, United States
| | - Crystal L Loving
- Food Safety and Enteric Pathogens Research Unit, National Animal Disease Center, USDA-Agriculture Research Service, Ames, IA, United States
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Brodsky S, Jana T, Mittelman K, Chapal M, Kumar DK, Carmi M, Barkai N. Intrinsically Disordered Regions Direct Transcription Factor In Vivo Binding Specificity. Mol Cell 2020; 79:459-471.e4. [DOI: 10.1016/j.molcel.2020.05.032] [Citation(s) in RCA: 99] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Revised: 03/10/2020] [Accepted: 05/21/2020] [Indexed: 11/25/2022]
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Ahad A, Smita S, Mishra GP, Biswas VK, Sen K, Gupta B, Garcin D, Acha‐Orbea H, Raghav SK. NCoR1 fine‐tunes type‐I IFN response in cDC1 dendritic cells by directly regulating Myd88‐IRF7 axis under TLR9. Eur J Immunol 2020; 50:1959-1975. [DOI: 10.1002/eji.202048566] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Revised: 05/06/2020] [Accepted: 06/26/2020] [Indexed: 12/26/2022]
Affiliation(s)
- Abdul Ahad
- Immuno‐genomics & Systems Biology Laboratory Institute of Life Sciences (ILS) Bhubaneswar India
- Manipal Academy of Higher Education Manipal India
| | - Shuchi Smita
- Immuno‐genomics & Systems Biology Laboratory Institute of Life Sciences (ILS) Bhubaneswar India
- Manipal Academy of Higher Education Manipal India
| | - Gyan Prakash Mishra
- Immuno‐genomics & Systems Biology Laboratory Institute of Life Sciences (ILS) Bhubaneswar India
- School of Biotechnology Kalinga Institute of Industrial Technology (KIIT) Bhubaneswar India
| | - Viplov Kumar Biswas
- Immuno‐genomics & Systems Biology Laboratory Institute of Life Sciences (ILS) Bhubaneswar India
- School of Biotechnology Kalinga Institute of Industrial Technology (KIIT) Bhubaneswar India
| | - Kaushik Sen
- Immuno‐genomics & Systems Biology Laboratory Institute of Life Sciences (ILS) Bhubaneswar India
- Regional Centre for Biotechnology NCR Biotech Science Cluster Faridabad India
| | - Bhawna Gupta
- School of Biotechnology Kalinga Institute of Industrial Technology (KIIT) Bhubaneswar India
| | - Dominique Garcin
- Department of Microbiology and Molecular Medicine University of Geneva (UNIGE) Geneva Switzerland
| | - Hans Acha‐Orbea
- Department of Biochemistry CIIL University of Lausanne (UNIL) Epalinges Switzerland
| | - Sunil K. Raghav
- Immuno‐genomics & Systems Biology Laboratory Institute of Life Sciences (ILS) Bhubaneswar India
- Manipal Academy of Higher Education Manipal India
- School of Biotechnology Kalinga Institute of Industrial Technology (KIIT) Bhubaneswar India
- Regional Centre for Biotechnology NCR Biotech Science Cluster Faridabad India
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40
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Martínez-Zamudio RI, Roux PF, de Freitas JANLF, Robinson L, Doré G, Sun B, Belenki D, Milanovic M, Herbig U, Schmitt CA, Gil J, Bischof O. AP-1 imprints a reversible transcriptional programme of senescent cells. Nat Cell Biol 2020; 22:842-855. [PMID: 32514071 PMCID: PMC7899185 DOI: 10.1038/s41556-020-0529-5] [Citation(s) in RCA: 98] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Accepted: 04/27/2020] [Indexed: 12/17/2022]
Abstract
Senescent cells affect many physiological and pathophysiological processes. While select genetic and epigenetic elements for senescence induction have been identified, the dynamics, epigenetic mechanisms and regulatory networks defining senescence competence, induction and maintenance remain poorly understood, precluding the deliberate therapeutic targeting of senescence for health benefits. Here, we examined the possibility that the epigenetic state of enhancers determines senescent cell fate. We explored this by generating time-resolved transcriptomes and epigenome profiles during oncogenic RAS-induced senescence and validating central findings in different cell biology and disease models of senescence. Through integrative analysis and functional validation, we reveal links between enhancer chromatin, transcription factor recruitment and senescence competence. We demonstrate that activator protein 1 (AP-1) 'pioneers' the senescence enhancer landscape and defines the organizational principles of the transcription factor network that drives the transcriptional programme of senescent cells. Together, our findings enabled us to manipulate the senescence phenotype with potential therapeutic implications.
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Affiliation(s)
- Ricardo Iván Martínez-Zamudio
- Institut Pasteur, Paris, France
- INSERM U993, Paris, France
- Center for Cell Signaling, Department of Microbiology, Biochemistry and Molecular Genetics, New Jersey Medical School of Rutgers Biomedical and Health Sciences, Rutgers University, Newark, NJ, USA
| | - Pierre-François Roux
- Institut Pasteur, Paris, France
- INSERM U993, Paris, France
- Johnson & Johnson, Upstream Skin Research, Issy-les-Moulineaux, France
| | | | - Lucas Robinson
- Institut Pasteur, Paris, France
- INSERM U993, Paris, France
- Université de Paris, Sorbonne Paris Cité, Paris, France
| | - Gregory Doré
- Institut Pasteur, Paris, France
- INSERM U993, Paris, France
| | - Bin Sun
- MRC London Institute of Medical Sciences (LMS), London, UK
- Institute of Clinical Sciences (ICS), Faculty of Medicine, Imperial College London, London, UK
| | - Dimitri Belenki
- Department of Hematology, Oncology and Tumor Immunology, Virchow Campus, and Molekulares Krebsforschungszentrum, Charité-University Medical Center, Berlin, Germany
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Maja Milanovic
- Department of Hematology, Oncology and Tumor Immunology, Virchow Campus, and Molekulares Krebsforschungszentrum, Charité-University Medical Center, Berlin, Germany
- Deutsches Konsortium für Translationale Krebsforschung (German Cancer Consortium), Berlin, Germany
| | - Utz Herbig
- Center for Cell Signaling, Department of Microbiology, Biochemistry and Molecular Genetics, New Jersey Medical School of Rutgers Biomedical and Health Sciences, Rutgers University, Newark, NJ, USA
| | - Clemens A Schmitt
- Department of Hematology, Oncology and Tumor Immunology, Virchow Campus, and Molekulares Krebsforschungszentrum, Charité-University Medical Center, Berlin, Germany
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
- Deutsches Konsortium für Translationale Krebsforschung (German Cancer Consortium), Berlin, Germany
- Department of Hematology and Oncology, Kepler University Hospital, Johannes Kepler University, Linz, Austria
| | - Jesús Gil
- MRC London Institute of Medical Sciences (LMS), London, UK
- Institute of Clinical Sciences (ICS), Faculty of Medicine, Imperial College London, London, UK
| | - Oliver Bischof
- Institut Pasteur, Paris, France.
- INSERM U993, Paris, France.
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41
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Hou P, Kapoor A, Zhang Q, Li J, Wu CJ, Li J, Lan Z, Tang M, Ma X, Ackroyd JJ, Kalluri R, Zhang J, Jiang S, Spring DJ, Wang YA, DePinho RA. Tumor Microenvironment Remodeling Enables Bypass of Oncogenic KRAS Dependency in Pancreatic Cancer. Cancer Discov 2020; 10:1058-1077. [PMID: 32341020 PMCID: PMC7334087 DOI: 10.1158/2159-8290.cd-19-0597] [Citation(s) in RCA: 83] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Revised: 03/19/2020] [Accepted: 04/22/2020] [Indexed: 11/16/2022]
Abstract
Oncogenic KRAS (KRAS*) is a key tumor maintenance gene in pancreatic ductal adenocarcinoma (PDAC), motivating pharmacologic targeting of KRAS* and its effectors. Here, we explored mechanisms involving the tumor microenvironment (TME) as a potential basis for resistance to targeting KRAS*. Using the inducible Kras G12D;Trp53 -/- PDAC mouse model, gain-of-function screens of epigenetic regulators identified HDAC5 as the top hit enabling KRAS* independent tumor growth. HDAC5-driven escaper tumors showed a prominent neutrophil-to-macrophage switch relative to KRAS*-driven tumors. Mechanistically, HDAC5 represses Socs3, a negative regulator of chemokine CCL2, resulting in increased CCL2, which recruits CCR2+ macrophages. Correspondingly, enforced Ccl2 promotes macrophage recruitment into the TME and enables tumor recurrence following KRAS* extinction. These tumor-associated macrophages in turn provide cancer cells with trophic support including TGFβ to enable KRAS* bypass in a SMAD4-dependent manner. Our work uncovers a KRAS* resistance mechanism involving immune cell remodeling of the PDAC TME. SIGNIFICANCE: Although KRAS* is required for PDAC tumor maintenance, tumors can recur following KRAS* extinction. The capacity of PDAC cancer cells to alter the TME myeloid cell composition to support KRAS*-independent tumor growth illuminates novel therapeutic targets that may enhance the effectiveness of therapies targeting KRAS* and its pathway components.See related commentary by Carr and Fernandez-Zapico, p. 910.This article is highlighted in the In This Issue feature, p. 890.
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Affiliation(s)
- Pingping Hou
- Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Avnish Kapoor
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Qiang Zhang
- Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jiexi Li
- Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Chang-Jiun Wu
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jun Li
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Zhengdao Lan
- Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Ming Tang
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Xingdi Ma
- Graduate School of Biomedical Sciences, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jeffrey J Ackroyd
- Graduate School of Biomedical Sciences, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Raghu Kalluri
- Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jianhua Zhang
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Shan Jiang
- Institute for Applied Cancer Science, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Denise J Spring
- Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Y Alan Wang
- Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas.
| | - Ronald A DePinho
- Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas.
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42
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de Laval B, Maurizio J, Kandalla PK, Brisou G, Simonnet L, Huber C, Gimenez G, Matcovitch-Natan O, Reinhardt S, David E, Mildner A, Leutz A, Nadel B, Bordi C, Amit I, Sarrazin S, Sieweke MH. C/EBPβ-Dependent Epigenetic Memory Induces Trained Immunity in Hematopoietic Stem Cells. Cell Stem Cell 2020; 26:657-674.e8. [PMID: 32169166 DOI: 10.1016/j.stem.2020.01.017] [Citation(s) in RCA: 144] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 08/23/2019] [Accepted: 01/23/2020] [Indexed: 02/08/2023]
Abstract
Hematopoietic stem cells (HSCs) maintain life-long production of immune cells and can directly respond to infection, but sustained effects on the immune response remain unclear. We show that acute immune stimulation with lipopolysaccharide (LPS) induced only transient changes in HSC abundance, composition, progeny, and gene expression, but persistent alterations in accessibility of specific myeloid lineage enhancers occurred, which increased responsiveness of associated immune genes to secondary stimulation. Functionally, this was associated with increased myelopoiesis of pre-exposed HSCs and improved innate immunity against the gram-negative bacterium P. aeruginosa. The accessible myeloid enhancers were enriched for C/EBPβ targets, and C/EBPβ deletion erased the long-term inscription of LPS-induced epigenetic marks and gene expression. Thus, short-term immune signaling can induce C/EBPβ-dependent chromatin accessibility, resulting in HSC-trained immunity, during secondary infection. This establishes a mechanism for how infection history can be epigenetically inscribed in HSCs as an integral memory function of innate immunity.
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Affiliation(s)
| | - Julien Maurizio
- Aix Marseille University, CNRS, INSERM, CIML, 13009 Marseille, France; Inovarion, 75005 Paris, France
| | - Prashanth K Kandalla
- Aix Marseille University, CNRS, INSERM, CIML, 13009 Marseille, France; Center for Regenerative Therapies Dresden (CRTD), Technische Universität Dresden, 01307 Dresden, Germany
| | - Gabriel Brisou
- Aix Marseille University, CNRS, INSERM, CIML, 13009 Marseille, France
| | - Louise Simonnet
- Aix Marseille University, CNRS, INSERM, CIML, 13009 Marseille, France
| | - Caroline Huber
- Aix Marseille University, CNRS, INSERM, CIML, 13009 Marseille, France
| | - Gregory Gimenez
- Aix Marseille University, CNRS, INSERM, CIML, 13009 Marseille, France; Max-Delbrück-Centrum für Molekulare Medizin in der Helmholtzgemeinschaft (MDC), 13125 Berlin, Germany
| | | | - Susanne Reinhardt
- Center for Regenerative Therapies Dresden (CRTD), Technische Universität Dresden, 01307 Dresden, Germany
| | - Eyal David
- Department of Immunology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Alexander Mildner
- Max-Delbrück-Centrum für Molekulare Medizin in der Helmholtzgemeinschaft (MDC), 13125 Berlin, Germany
| | - Achim Leutz
- Institute of Biology, Humboldt University of Berlin, 10115 Berlin, Germany; Max-Delbrück-Centrum für Molekulare Medizin in der Helmholtzgemeinschaft (MDC), 13125 Berlin, Germany
| | - Bertrand Nadel
- Aix Marseille University, CNRS, INSERM, CIML, 13009 Marseille, France
| | - Christophe Bordi
- Institut de Microbiologie de la Méditerranée, CNRS, 13009 Marseille, France
| | - Ido Amit
- Department of Immunology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Sandrine Sarrazin
- Aix Marseille University, CNRS, INSERM, CIML, 13009 Marseille, France.
| | - Michael H Sieweke
- Aix Marseille University, CNRS, INSERM, CIML, 13009 Marseille, France; Center for Regenerative Therapies Dresden (CRTD), Technische Universität Dresden, 01307 Dresden, Germany; Max-Delbrück-Centrum für Molekulare Medizin in der Helmholtzgemeinschaft (MDC), 13125 Berlin, Germany.
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43
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Cordeiro B, Jeon P, Boukhaled GM, Corrado M, Lapohos O, Roy DG, Williams K, Jones RG, Gruenheid S, Sagan SM, Krawczyk CM. MicroRNA-9 Fine-Tunes Dendritic Cell Function by Suppressing Negative Regulators in a Cell-Type-Specific Manner. Cell Rep 2020; 31:107585. [PMID: 32375032 DOI: 10.1016/j.celrep.2020.107585] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Revised: 08/08/2019] [Accepted: 04/07/2020] [Indexed: 12/12/2022] Open
Abstract
Dendritic cells, cells of the innate immune system, are found in a steady state poised to respond to activating stimuli. Once stimulated, they rapidly undergo dynamic changes in gene expression to adopt an activated phenotype capable of stimulating immune responses. We find that the microRNA miR-9 is upregulated in both bone marrow-derived DCs and conventional DC1s but not in conventional DC2s following stimulation. miR-9 expression in BMDCs and conventional DC1s promotes enhanced DC activation and function, including the ability to stimulate T cell activation and control tumor growth. We find that miR-9 regulated the expression of several negative regulators of transcription, including the transcriptional repressor Polycomb group factor 6 (Pcgf6). These findings demonstrate that miR-9 facilitates the transition of DCs from steady state to mature state by regulating the expression of several negative regulators of DC function in a cell-type-specific manner.
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Affiliation(s)
- Brendan Cordeiro
- Department of Microbiology and Immunology, McGill University, Montreal, QC H3G 1Y6, Canada
| | - Peter Jeon
- Goodman Cancer Research Center, Department of Physiology, McGill University, Montreal, QC H3G 1Y6, Canada
| | - Giselle M Boukhaled
- Goodman Cancer Research Center, Department of Physiology, McGill University, Montreal, QC H3G 1Y6, Canada
| | - Mario Corrado
- Goodman Cancer Research Center, Department of Physiology, McGill University, Montreal, QC H3G 1Y6, Canada
| | - Orsolya Lapohos
- Department of Microbiology and Immunology, McGill University, Montreal, QC H3G 1Y6, Canada
| | - Dominic G Roy
- Goodman Cancer Research Center, Department of Physiology, McGill University, Montreal, QC H3G 1Y6, Canada
| | - Kelsey Williams
- Metabolic and Nutritional Programming Group, Van Andel Institute, 333 Bostwick Avenue NE, Grand Rapids, MI 49503, USA
| | - Russell G Jones
- Goodman Cancer Research Center, Department of Physiology, McGill University, Montreal, QC H3G 1Y6, Canada; Metabolic and Nutritional Programming Group, Van Andel Institute, 333 Bostwick Avenue NE, Grand Rapids, MI 49503, USA
| | - Samantha Gruenheid
- Department of Microbiology and Immunology, McGill University, Montreal, QC H3G 1Y6, Canada
| | - Selena M Sagan
- Department of Microbiology and Immunology, McGill University, Montreal, QC H3G 1Y6, Canada
| | - Connie M Krawczyk
- Department of Microbiology and Immunology, McGill University, Montreal, QC H3G 1Y6, Canada; Goodman Cancer Research Center, Department of Physiology, McGill University, Montreal, QC H3G 1Y6, Canada; Metabolic and Nutritional Programming Group, Van Andel Institute, 333 Bostwick Avenue NE, Grand Rapids, MI 49503, USA.
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44
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Porta C, Consonni FM, Morlacchi S, Sangaletti S, Bleve A, Totaro MG, Larghi P, Rimoldi M, Tripodo C, Strauss L, Banfi S, Storto M, Pressiani T, Rimassa L, Tartari S, Ippolito A, Doni A, Soldà G, Duga S, Piccolo V, Ostuni R, Natoli G, Bronte V, Balzac F, Turco E, Hirsch E, Colombo MP, Sica A. Tumor-Derived Prostaglandin E2 Promotes p50 NF-κB-Dependent Differentiation of Monocytic MDSCs. Cancer Res 2020; 80:2874-2888. [PMID: 32265223 DOI: 10.1158/0008-5472.can-19-2843] [Citation(s) in RCA: 75] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Revised: 02/28/2020] [Accepted: 04/02/2020] [Indexed: 11/16/2022]
Abstract
Myeloid-derived suppressor cells (MDSC) include immature monocytic (M-MDSC) and granulocytic (PMN-MDSC) cells that share the ability to suppress adaptive immunity and to hinder the effectiveness of anticancer treatments. Of note, in response to IFNγ, M-MDSCs release the tumor-promoting and immunosuppressive molecule nitric oxide (NO), whereas macrophages largely express antitumor properties. Investigating these opposing activities, we found that tumor-derived prostaglandin E2 (PGE2) induces nuclear accumulation of p50 NF-κB in M-MDSCs, diverting their response to IFNγ toward NO-mediated immunosuppression and reducing TNFα expression. At the genome level, p50 NF-κB promoted binding of STAT1 to regulatory regions of selected IFNγ-dependent genes, including inducible nitric oxide synthase (Nos2). In agreement, ablation of p50 as well as pharmacologic inhibition of either the PGE2 receptor EP2 or NO production reprogrammed M-MDSCs toward a NOS2low/TNFαhigh phenotype, restoring the in vivo antitumor activity of IFNγ. Our results indicate that inhibition of the PGE2/p50/NO axis prevents MDSC-suppressive functions and restores the efficacy of anticancer immunotherapy. SIGNIFICANCE: Tumor-derived PGE2-mediated induction of nuclear p50 NF-κB epigenetically reprograms the response of monocytic cells to IFNγ toward an immunosuppressive phenotype, thus retrieving the anticancer properties of IFNγ. GRAPHICAL ABSTRACT: http://cancerres.aacrjournals.org/content/canres/80/13/2874/F1.large.jpg.
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Affiliation(s)
- Chiara Porta
- Department of Pharmaceutical Sciences, Università del Piemonte Orientale "Amedeo Avogadro", Novara, Italy.,Center for Translational Research on Autoimmune & Allergic Diseases (CAAD) Cso Trieste 15/A, Novara, Italy
| | | | - Sara Morlacchi
- Humanitas Clinical and Research Center - IRCCS, Rozzano, Milan, Italy
| | | | - Augusto Bleve
- Department of Pharmaceutical Sciences, Università del Piemonte Orientale "Amedeo Avogadro", Novara, Italy
| | | | - Paola Larghi
- Humanitas Clinical and Research Center - IRCCS, Rozzano, Milan, Italy
| | - Monica Rimoldi
- Humanitas Clinical and Research Center - IRCCS, Rozzano, Milan, Italy
| | - Claudio Tripodo
- Human Pathology Section, Department of Health Sciences, University of Palermo, Palermo, Italy
| | - Laura Strauss
- Department of Pharmaceutical Sciences, Università del Piemonte Orientale "Amedeo Avogadro", Novara, Italy
| | - Stefania Banfi
- Humanitas Clinical and Research Center - IRCCS, Rozzano, Milan, Italy
| | - Mariangela Storto
- Humanitas Clinical and Research Center - IRCCS, Rozzano, Milan, Italy
| | - Tiziana Pressiani
- Humanitas Clinical and Research Center - IRCCS, Rozzano, Milan, Italy
| | - Lorenza Rimassa
- Humanitas Clinical and Research Center - IRCCS, Rozzano, Milan, Italy
| | - Silvia Tartari
- Humanitas Clinical and Research Center - IRCCS, Rozzano, Milan, Italy
| | - Alessandro Ippolito
- Department of Pharmaceutical Sciences, Università del Piemonte Orientale "Amedeo Avogadro", Novara, Italy
| | - Andrea Doni
- Humanitas Clinical and Research Center - IRCCS, Rozzano, Milan, Italy
| | - Giulia Soldà
- Humanitas Clinical and Research Center - IRCCS, Rozzano, Milan, Italy.,Department of Biomedical Sciences, Humanitas University, Pieve Emanuele, Milan, Italy
| | - Stefano Duga
- Humanitas Clinical and Research Center - IRCCS, Rozzano, Milan, Italy.,Department of Biomedical Sciences, Humanitas University, Pieve Emanuele, Milan, Italy
| | - Viviana Piccolo
- Humanitas Clinical and Research Center - IRCCS, Rozzano, Milan, Italy
| | - Renato Ostuni
- San Raffaele Telethon Institute for Gene Therapy (SR-TIGET), IRCCS San Raffaele Scientific Institute, Milan, Italy.,Vita-Salute San Raffaele University, Milan, Italy
| | - Gioacchino Natoli
- Humanitas Clinical and Research Center - IRCCS, Rozzano, Milan, Italy.,Department of Biomedical Sciences, Humanitas University, Pieve Emanuele, Milan, Italy
| | - Vincenzo Bronte
- Department of Medicine, Verona University Hospital, Verona, Italy
| | - Fiorella Balzac
- Department of Molecular Biotechnology and Health Sciences, Molecular Biotechnology Center, University of Torino, Torino, Italy
| | - Emilia Turco
- Department of Molecular Biotechnology and Health Sciences, Molecular Biotechnology Center, University of Torino, Torino, Italy
| | - Emilio Hirsch
- Department of Molecular Biotechnology and Health Sciences, Molecular Biotechnology Center, University of Torino, Torino, Italy
| | - Mario P Colombo
- Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Antonio Sica
- Department of Pharmaceutical Sciences, Università del Piemonte Orientale "Amedeo Avogadro", Novara, Italy. .,Humanitas Clinical and Research Center - IRCCS, Rozzano, Milan, Italy
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45
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Boudra R, Ramsey MR. Understanding Transcriptional Networks Regulating Initiation of Cutaneous Wound Healing. THE YALE JOURNAL OF BIOLOGY AND MEDICINE 2020; 93:161-173. [PMID: 32226345 PMCID: PMC7087049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The epidermis has an essential function in creating a barrier against the external environment to retain proper fluid balance and block the entry of pathogens. When damage occurs to this barrier, the wound must quickly be sealed to avoid fluid loss, cleared of invading pathogens, and then keratinocytes must re-form an intact barrier. This requires complex integration of temporally and spatially distinct signals to execute orderly closure of the wound, and failure of this process can lead to chronic ulceration. Transcription factors serve as a key integration point for the myriad of information coming from the external environment, allowing for an orderly process of re-epithelialization. Importantly, transcription factors engage with and alter the chromatin structure around key target genes through association with different chromatin-modifying complexes. In this review, we will discuss the current understanding of how transcription is regulated during the initiation of re-epithelialization, and the exciting technological advances that will allow for a more refined mechanistic understanding of the re-epithelialization process.
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Affiliation(s)
- Rafik Boudra
- Brigham and Women’s Hospital Department of Dermatology, Boston, MA,Harvard Medical School, Boston, MA
| | - Matthew R. Ramsey
- Brigham and Women’s Hospital Department of Dermatology, Boston, MA,Harvard Medical School, Boston, MA,To whom all correspondence should be addressed: Matthew R. Ramsey, PhD, Brigham and Women’s Hospital, 77 Ave Louis Pasteur, HIM 668, Boston, MA 02115; Tel: (617) 525-5775, Fax: (617) 525-5571,
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46
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Qiu X, Rahimzamani A, Wang L, Ren B, Mao Q, Durham T, McFaline-Figueroa JL, Saunders L, Trapnell C, Kannan S. Inferring Causal Gene Regulatory Networks from Coupled Single-Cell Expression Dynamics Using Scribe. Cell Syst 2020; 10:265-274.e11. [PMID: 32135093 PMCID: PMC7223477 DOI: 10.1016/j.cels.2020.02.003] [Citation(s) in RCA: 63] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Revised: 06/08/2019] [Accepted: 02/05/2020] [Indexed: 01/13/2023]
Abstract
Here, we present Scribe (https://github.com/aristoteleo/Scribe-py), a toolkit for detecting and visualizing causal regulatory interactions between genes and explore the potential for single-cell experiments to power network reconstruction. Scribe employs restricted directed information to determine causality by estimating the strength of information transferred from a potential regulator to its downstream target. We apply Scribe and other leading approaches for causal network reconstruction to several types of single-cell measurements and show that there is a dramatic drop in performance for "pseudotime"-ordered single-cell data compared with true time-series data. We demonstrate that performing causal inference requires temporal coupling between measurements. We show that methods such as "RNA velocity" restore some degree of coupling through an analysis of chromaffin cell fate commitment. These analyses highlight a shortcoming in experimental and computational methods for analyzing gene regulation at single-cell resolution and suggest ways of overcoming it.
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Affiliation(s)
- Xiaojie Qiu
- Molecular & Cellular Biology Program, University of Washington, Seattle, WA, USA; Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Arman Rahimzamani
- Department of Electrical Engineering, University of Washington, Seattle, WA, USA
| | - Li Wang
- Department of Mathematics, University of Texas at Arlington, Arlington, TX, USA
| | - Bingcheng Ren
- College of Information Science and Engineering, Hunan Normal University, Changsha, China
| | - Qi Mao
- HERE company, Chicago, IL 60606, USA
| | - Timothy Durham
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | | | - Lauren Saunders
- Molecular & Cellular Biology Program, University of Washington, Seattle, WA, USA; Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Cole Trapnell
- Molecular & Cellular Biology Program, University of Washington, Seattle, WA, USA; Department of Genome Sciences, University of Washington, Seattle, WA, USA; Brotman-Baty Institute for Precision Medicine, Seattle, WA, USA.
| | - Sreeram Kannan
- Department of Electrical Engineering, University of Washington, Seattle, WA, USA.
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47
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Detavernier A, Azouz A, Shehade H, Splittgerber M, Van Maele L, Nguyen M, Thomas S, Achouri Y, Svec D, Calonne E, Fuks F, Oldenhove G, Goriely S. Monocytes undergo multi-step differentiation in mice during oral infection by Toxoplasma gondii. Commun Biol 2019; 2:472. [PMID: 31872076 PMCID: PMC6920430 DOI: 10.1038/s42003-019-0718-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Accepted: 11/27/2019] [Indexed: 01/01/2023] Open
Abstract
Monocytes play a major role in the defense against pathogens. They are rapidly mobilized to inflamed sites where they exert both proinflammatory and regulatory effector functions. It is still poorly understood how this dynamic and exceptionally plastic system is controlled at the molecular level. Herein, we evaluated the differentiation process that occurs in Ly6Chi monocytes during oral infection by Toxoplasma gondii. Flow cytometry and single-cell analysis revealed distinct activation status and gene expression profiles in the bone marrow, the spleen and the lamina propria of infected mice. We provide further evidence that acquisition of effector functions, such as the capacity to produce interleukin-27, is accompanied by distinct waves of epigenetic programming, highlighting a role for STAT1/IRF1 in the bone marrow and AP-1/NF-κB in the periphery. This work broadens our understanding of the molecular events that occur in vivo during monocyte differentiation in response to inflammatory cues.
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Affiliation(s)
- Aurélie Detavernier
- Université Libre de Bruxelles, Institute for Medical Immunology and ULB Center for Research in Immunology (U-CRI), Gosselies, Belgium
| | - Abdulkader Azouz
- Université Libre de Bruxelles, Institute for Medical Immunology and ULB Center for Research in Immunology (U-CRI), Gosselies, Belgium
| | - Hussein Shehade
- Université Libre de Bruxelles, Institute for Medical Immunology and ULB Center for Research in Immunology (U-CRI), Gosselies, Belgium
| | - Marion Splittgerber
- Université Libre de Bruxelles, Institute for Medical Immunology and ULB Center for Research in Immunology (U-CRI), Gosselies, Belgium
| | - Laurye Van Maele
- Université Libre de Bruxelles, Institute for Medical Immunology and ULB Center for Research in Immunology (U-CRI), Gosselies, Belgium
| | - Muriel Nguyen
- Université Libre de Bruxelles, Institute for Medical Immunology and ULB Center for Research in Immunology (U-CRI), Gosselies, Belgium
| | - Séverine Thomas
- Université Libre de Bruxelles, Institute for Medical Immunology and ULB Center for Research in Immunology (U-CRI), Gosselies, Belgium
| | - Younes Achouri
- Université Catholique de Louvain, Institut de Duve, Brussels, Belgium
| | - David Svec
- Institute of Biotechnology, Czech Academy of Science, 252 50 Vestec u prahy, Czech Republic
| | - Emilie Calonne
- Université Libre de Bruxelles, Laboratory of Cancer Epigenetics, Brussels, Belgium
| | - François Fuks
- Université Libre de Bruxelles, Laboratory of Cancer Epigenetics, Brussels, Belgium
| | - Guillaume Oldenhove
- Université Libre de Bruxelles, Laboratoire d’Immunobiologie, Gosselies, Belgium
| | - Stanislas Goriely
- Université Libre de Bruxelles, Institute for Medical Immunology and ULB Center for Research in Immunology (U-CRI), Gosselies, Belgium
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48
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Abstract
Structured models of ontogenic, phenotypic and functional diversity have been instrumental for a renewed understanding of the biology of immune cells, such as macrophages and lymphoid cells. However, there are no established models that can be used to define the diversity of neutrophils, the most abundant myeloid cells. This lack of an established model is largely due to the uniquely short lives of neutrophils, a consequence of their inability to divide once terminally differentiated, which has been perceived as a roadblock to functional diversity. This perception is rapidly evolving as multiple phenotypic and functional variants of neutrophils have been found, both in homeostatic and disease conditions. In this Opinion article, we present an overview of neutrophil heterogeneity and discuss possible mechanisms of diversification, including genomic regulation. We suggest that neutrophil heterogeneity is an important feature of immune pathophysiology, such that co-option of the mechanisms of diversification by cancer or other disorders contributes to disease progression.
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49
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Pires CF, Rosa FF, Kurochkin I, Pereira CF. Understanding and Modulating Immunity With Cell Reprogramming. Front Immunol 2019; 10:2809. [PMID: 31921109 PMCID: PMC6917620 DOI: 10.3389/fimmu.2019.02809] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Accepted: 11/15/2019] [Indexed: 12/30/2022] Open
Abstract
Cell reprogramming concepts have been classically developed in the fields of developmental and stem cell biology and are currently being explored for regenerative medicine, given its potential to generate desired cell types for replacement therapy. Cell fate can be experimentally reversed or modified by enforced expression of lineage specific transcription factors leading to pluripotency or attainment of another somatic cell type identity. The possibility to reprogram fibroblasts into induced dendritic cells (DC) competent for antigen presentation creates a paradigm shift for understanding and modulating the immune system with direct cell reprogramming. PU.1, IRF8, and BATF3 were identified as sufficient and necessary to impose DC fate in unrelated cell types, taking advantage of Clec9a, a C-type lectin receptor with restricted expression in conventional DC type 1. The identification of such minimal gene regulatory networks helps to elucidate the molecular mechanisms governing development and lineage heterogeneity along the hematopoietic hierarchy. Furthermore, the generation of patient-tailored reprogrammed immune cells provides new and exciting tools for the expanding field of cancer immunotherapy. Here, we summarize cell reprogramming concepts and experimental approaches, review current knowledge at the intersection of cell reprogramming with hematopoiesis, and propose how cell fate engineering can be merged to immunology, opening new opportunities to understand the immune system in health and disease.
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Affiliation(s)
- Cristiana F. Pires
- Cell Reprogramming in Hematopoiesis and Immunity Laboratory, Lund Stem Cell Center, Molecular Medicine and Gene Therapy, Lund University, Lund, Sweden
- Wallenberg Center for Molecular Medicine, Lund University, Lund, Sweden
- Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal
| | - Fábio F. Rosa
- Cell Reprogramming in Hematopoiesis and Immunity Laboratory, Lund Stem Cell Center, Molecular Medicine and Gene Therapy, Lund University, Lund, Sweden
- Wallenberg Center for Molecular Medicine, Lund University, Lund, Sweden
- Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal
| | - Ilia Kurochkin
- Center for Neurobiology and Brain Restoration, Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Carlos-Filipe Pereira
- Cell Reprogramming in Hematopoiesis and Immunity Laboratory, Lund Stem Cell Center, Molecular Medicine and Gene Therapy, Lund University, Lund, Sweden
- Wallenberg Center for Molecular Medicine, Lund University, Lund, Sweden
- Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal
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50
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Inoue F, Kreimer A, Ashuach T, Ahituv N, Yosef N. Identification and Massively Parallel Characterization of Regulatory Elements Driving Neural Induction. Cell Stem Cell 2019; 25:713-727.e10. [PMID: 31631012 PMCID: PMC6850896 DOI: 10.1016/j.stem.2019.09.010] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2018] [Revised: 07/15/2019] [Accepted: 09/26/2019] [Indexed: 12/16/2022]
Abstract
Epigenomic regulation and lineage-specific gene expression act in concert to drive cellular differentiation, but the temporal interplay between these processes is largely unknown. Using neural induction from human pluripotent stem cells (hPSCs) as a paradigm, we interrogated these dynamics by performing RNA sequencing (RNA-seq), chromatin immunoprecipitation sequencing (ChIP-seq), and assay for transposase accessible chromatin using sequencing (ATAC-seq) at seven time points during early neural differentiation. We found that changes in DNA accessibility precede H3K27ac, which is followed by gene expression changes. Using massively parallel reporter assays (MPRAs) to test the activity of 2,464 candidate regulatory sequences at all seven time points, we show that many of these sequences have temporal activity patterns that correlate with their respective cell-endogenous gene expression and chromatin changes. A prioritization method incorporating all genomic and MPRA data further identified key transcription factors involved in driving neural fate. These results provide a comprehensive resource of genes and regulatory elements that orchestrate neural induction and illuminate temporal frameworks during differentiation.
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Affiliation(s)
- Fumitaka Inoue
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA 94158, USA; Institute for Human Genetics, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Anat Kreimer
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA 94158, USA; Institute for Human Genetics, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Electrical Engineering and Computer Sciences and Center for Computational Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Tal Ashuach
- Department of Electrical Engineering and Computer Sciences and Center for Computational Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Nadav Ahituv
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA 94158, USA; Institute for Human Genetics, University of California, San Francisco, San Francisco, CA 94158, USA.
| | - Nir Yosef
- Department of Electrical Engineering and Computer Sciences and Center for Computational Biology, University of California, Berkeley, Berkeley, CA, USA; Chan-Zuckerberg Biohub, San Francisco, CA 94158, USA.
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