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Li Y, Gu Y, Yang P, Wang Y, Yu X, Li Y, Jin Z, Xu L. CD69 is a Promising Immunotherapy and Prognosis Prediction Target in Cancer. Immunotargets Ther 2024; 13:1-14. [PMID: 38223406 PMCID: PMC10787557 DOI: 10.2147/itt.s439969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Accepted: 12/22/2023] [Indexed: 01/16/2024] Open
Abstract
Immunotherapy utilizing T cells that attack tumors is a promising strategy for treatment, but immune suppressive T cell subsets, such as regulatory T cell (Treg), and immune checkpoint molecules, including programmed death-1 (PD-1), can suppress the intensity of a T cell immune reaction and thereby impair tumor clearance. Cluster of differentiation 69 (CD69), known as an early leukocyte activation marker, can be used as a measure or early marker of T cell activation. In recent years, the functions of CD69 in the regulation of Treg/Th17 (T helper cell 17) differentiation and in the tissue retention of T cells have attracted considerable interest. These functions are related to the role of CD69 in immune suppression in tumor environments (TME). In this review, we first summarized current perspectives in the biological function of CD69 and demonstrated that CD69 acts as a regulator of T cell activation, differentiation, retention, and exhaustion. Then, we discussed recent advances in understanding of CD69 deficiency and anti-CD69 antibody administration and shed light on the value of targeting on CD69 for cancer immunotherapy and prognosis prediction.
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Affiliation(s)
- Yuchen Li
- Institute of Hematology, School of Medicine, Key Laboratory for Regenerative Medicine of Ministry of Education, Department of Hematology, First Affiliated Hospital, Jinan University, Guangzhou, 510632, People’s Republic of China
| | - Yinfeng Gu
- Institute of Hematology, School of Medicine, Key Laboratory for Regenerative Medicine of Ministry of Education, Department of Hematology, First Affiliated Hospital, Jinan University, Guangzhou, 510632, People’s Republic of China
| | - Pengyue Yang
- Institute of Hematology, School of Medicine, Key Laboratory for Regenerative Medicine of Ministry of Education, Department of Hematology, First Affiliated Hospital, Jinan University, Guangzhou, 510632, People’s Republic of China
| | - Yan Wang
- Institute of Hematology, School of Medicine, Key Laboratory for Regenerative Medicine of Ministry of Education, Department of Hematology, First Affiliated Hospital, Jinan University, Guangzhou, 510632, People’s Republic of China
| | - Xibao Yu
- Institute of Hematology, School of Medicine, Key Laboratory for Regenerative Medicine of Ministry of Education, Department of Hematology, First Affiliated Hospital, Jinan University, Guangzhou, 510632, People’s Republic of China
| | - Yangqiu Li
- Institute of Hematology, School of Medicine, Key Laboratory for Regenerative Medicine of Ministry of Education, Department of Hematology, First Affiliated Hospital, Jinan University, Guangzhou, 510632, People’s Republic of China
| | - Zhenyi Jin
- Institute of Hematology, School of Medicine, Key Laboratory for Regenerative Medicine of Ministry of Education, Department of Hematology, First Affiliated Hospital, Jinan University, Guangzhou, 510632, People’s Republic of China
- Department of Pathology, School of Medicine, Jinan University, Guangzhou, 510632, People’s Republic of China
| | - Ling Xu
- Institute of Hematology, School of Medicine, Key Laboratory for Regenerative Medicine of Ministry of Education, Department of Hematology, First Affiliated Hospital, Jinan University, Guangzhou, 510632, People’s Republic of China
- Guangdong Provincial Key Laboratory of Virology, Institute of Medical Microbiology, Jinan University, Guangzhou, 510632, People’s Republic of China
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2
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Chen Z, Javed N, Moore M, Wu J, Sun G, Vinyard M, Collins A, Pinello L, Najm FJ, Bernstein BE. Integrative dissection of gene regulatory elements at base resolution. CELL GENOMICS 2023; 3:100318. [PMID: 37388913 PMCID: PMC10300548 DOI: 10.1016/j.xgen.2023.100318] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/25/2022] [Revised: 02/21/2023] [Accepted: 03/31/2023] [Indexed: 07/01/2023]
Abstract
Although vast numbers of putative gene regulatory elements have been cataloged, the sequence motifs and individual bases that underlie their functions remain largely unknown. Here, we combine epigenetic perturbations, base editing, and deep learning to dissect regulatory sequences within the exemplar immune locus encoding CD69. We converge on a ∼170 base interval within a differentially accessible and acetylated enhancer critical for CD69 induction in stimulated Jurkat T cells. Individual C-to-T base edits within the interval markedly reduce element accessibility and acetylation, with corresponding reduction of CD69 expression. The most potent base edits may be explained by their effect on regulatory interactions between the transcriptional activators GATA3 and TAL1 and the repressor BHLHE40. Systematic analysis suggests that the interplay between GATA3 and BHLHE40 plays a general role in rapid T cell transcriptional responses. Our study provides a framework for parsing regulatory elements in their endogenous chromatin contexts and identifying operative artificial variants.
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Affiliation(s)
- Zeyu Chen
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Gene Regulation Observatory, Broad Institute, Cambridge, MA, USA
- Department of Cell Biology and Pathology, Harvard Medical School, Boston, MA, USA
| | - Nauman Javed
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Gene Regulation Observatory, Broad Institute, Cambridge, MA, USA
- Department of Cell Biology and Pathology, Harvard Medical School, Boston, MA, USA
| | - Molly Moore
- Gene Regulation Observatory, Broad Institute, Cambridge, MA, USA
| | - Jingyi Wu
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Gene Regulation Observatory, Broad Institute, Cambridge, MA, USA
- Department of Cell Biology and Pathology, Harvard Medical School, Boston, MA, USA
| | - Gary Sun
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Cell Biology and Pathology, Harvard Medical School, Boston, MA, USA
| | - Michael Vinyard
- Gene Regulation Observatory, Broad Institute, Cambridge, MA, USA
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | | | - Luca Pinello
- Gene Regulation Observatory, Broad Institute, Cambridge, MA, USA
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Fadi J. Najm
- Gene Regulation Observatory, Broad Institute, Cambridge, MA, USA
| | - Bradley E. Bernstein
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Gene Regulation Observatory, Broad Institute, Cambridge, MA, USA
- Department of Cell Biology and Pathology, Harvard Medical School, Boston, MA, USA
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3
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Tak YE, Horng JE, Perry NT, Schultz HT, Iyer S, Yao Q, Zou LS, Aryee MJ, Pinello L, Joung JK. Augmenting and directing long-range CRISPR-mediated activation in human cells. Nat Methods 2021; 18:1075-1081. [PMID: 34354266 PMCID: PMC8446310 DOI: 10.1038/s41592-021-01224-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Accepted: 06/28/2021] [Indexed: 02/07/2023]
Abstract
Epigenetic editing is an emerging technology that uses artificial transcription factors (aTFs) to regulate expression of a target gene. Although human genes can be robustly upregulated by targeting aTFs to promoters, the activation induced by directing aTFs to distal transcriptional enhancers is substantially less robust and consistent. Here we show that long-range activation using CRISPR-based aTFs in human cells can be made more efficient and reliable by concurrently targeting an aTF to the target gene promoter. We used this strategy to direct target gene choice for enhancers capable of regulating more than one promoter and to achieve allele-selective activation of human genes by targeting aTFs to single-nucleotide polymorphisms embedded in distally located sequences. Our results broaden the potential applications of the epigenetic editing toolbox for research and therapeutics.
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Affiliation(s)
- Y. Esther Tak
- Molecular Pathology Unit, Massachusetts General Hospital, Charlestown, MA, USA,Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA, USA,Center for Computational and Integrative Biology, Massachusetts General Hospital, Charlestown, MA, USA,Department of Pathology, Harvard Medical School, Boston, MA, USA
| | - Joy E. Horng
- Molecular Pathology Unit, Massachusetts General Hospital, Charlestown, MA, USA,Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA, USA,Center for Computational and Integrative Biology, Massachusetts General Hospital, Charlestown, MA, USA,These authors contributed equally
| | - Nicholas T. Perry
- Molecular Pathology Unit, Massachusetts General Hospital, Charlestown, MA, USA,Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA, USA,Center for Computational and Integrative Biology, Massachusetts General Hospital, Charlestown, MA, USA,These authors contributed equally
| | - Hayley T. Schultz
- Molecular Pathology Unit, Massachusetts General Hospital, Charlestown, MA, USA,Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA, USA,Center for Computational and Integrative Biology, Massachusetts General Hospital, Charlestown, MA, USA
| | - Sowmya Iyer
- Molecular Pathology Unit, Massachusetts General Hospital, Charlestown, MA, USA
| | - Qiuming Yao
- Molecular Pathology Unit, Massachusetts General Hospital, Charlestown, MA, USA,Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA, USA,Department of Pathology, Harvard Medical School, Boston, MA, USA,Cell Circuits and Epigenomics Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Luli S. Zou
- Cell Circuits and Epigenomics Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA,Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Martin J. Aryee
- Molecular Pathology Unit, Massachusetts General Hospital, Charlestown, MA, USA,Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA, USA,Department of Pathology, Harvard Medical School, Boston, MA, USA,Cell Circuits and Epigenomics Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA,Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Luca Pinello
- Molecular Pathology Unit, Massachusetts General Hospital, Charlestown, MA, USA,Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA, USA,Department of Pathology, Harvard Medical School, Boston, MA, USA,Cell Circuits and Epigenomics Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - J. Keith Joung
- Molecular Pathology Unit, Massachusetts General Hospital, Charlestown, MA, USA,Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA, USA,Center for Computational and Integrative Biology, Massachusetts General Hospital, Charlestown, MA, USA,Department of Pathology, Harvard Medical School, Boston, MA, USA,Correspondence and requests for materials should be addressed to J. Keith Joung.
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Connolly A, Panes R, Tual M, Lafortune R, Bellemare-Pelletier A, Gagnon E. TMEM16F mediates bystander TCR-CD3 membrane dissociation at the immunological synapse and potentiates T cell activation. Sci Signal 2021; 14:eabb5146. [PMID: 33758060 DOI: 10.1126/scisignal.abb5146] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Electrostatic interactions regulate many aspects of T cell receptor (TCR) activity, including enabling the dynamic binding of the TCR-associated CD3ε and CD3ζ chains to anionic lipids in the plasma membrane to prevent spontaneous phosphorylation. Substantial changes in the electrostatic potential of the plasma membrane occur at the immunological synapse, the interface between a T cell and an antigen-presenting cell. Here, we investigated how the electrostatic interactions that promote dynamic membrane binding of the TCR-CD3 cytoplasmic domains are modulated during signaling and affect T cell activation. We found that Ca2+-dependent activation of the phosphatidylserine scramblase TMEM16F, which was previously implicated in T cell activation, reduced the electrostatic potential of the plasma membrane during immunological synapse formation by locally redistributing phosphatidylserine. This, in turn, increased the dissociation of bystander TCR-CD3 cytoplasmic domains from the plasma membrane and enhanced TCR-dependent signaling and consequently T cell activation. This study establishes the molecular basis for the role of TMEM16F in bystander TCR-induced signal amplification and identifies enhancement of TMEM16F function as a potential therapeutic strategy for promoting T cell activation.
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Affiliation(s)
- Audrey Connolly
- Institut de Recherche en Immunologie et Cancérologie, 2950 Chemin de la Polytechnique, Montréal, Québec H3T1J4, Canada
- Département de Microbiologie, Infectiologie et Immunologie, Faculté de Médecine, Université de Montréal, 2900 Édouard-Montpetit, Montréal, Québec H3T1J4, Canada
| | - Rébecca Panes
- Institut de Recherche en Immunologie et Cancérologie, 2950 Chemin de la Polytechnique, Montréal, Québec H3T1J4, Canada
- Département de Microbiologie, Infectiologie et Immunologie, Faculté de Médecine, Université de Montréal, 2900 Édouard-Montpetit, Montréal, Québec H3T1J4, Canada
| | - Margaux Tual
- Institut de Recherche en Immunologie et Cancérologie, 2950 Chemin de la Polytechnique, Montréal, Québec H3T1J4, Canada
- Département de Microbiologie, Infectiologie et Immunologie, Faculté de Médecine, Université de Montréal, 2900 Édouard-Montpetit, Montréal, Québec H3T1J4, Canada
| | - Raphaël Lafortune
- Département de Microbiologie, Infectiologie et Immunologie, Faculté de Médecine, Université de Montréal, 2900 Édouard-Montpetit, Montréal, Québec H3T1J4, Canada
| | - Angélique Bellemare-Pelletier
- Institut de Recherche en Immunologie et Cancérologie, 2950 Chemin de la Polytechnique, Montréal, Québec H3T1J4, Canada
| | - Etienne Gagnon
- Institut de Recherche en Immunologie et Cancérologie, 2950 Chemin de la Polytechnique, Montréal, Québec H3T1J4, Canada.
- Département de Microbiologie, Infectiologie et Immunologie, Faculté de Médecine, Université de Montréal, 2900 Édouard-Montpetit, Montréal, Québec H3T1J4, Canada
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5
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Hoffsten A, Markasz L, Lilja HE, Olsson KW, Sindelar R. Early Postnatal Comprehensive Biomarkers Cannot Identify Extremely Preterm Infants at Risk of Developing Necrotizing Enterocolitis. Front Pediatr 2021; 9:755437. [PMID: 34746064 PMCID: PMC8570110 DOI: 10.3389/fped.2021.755437] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/08/2021] [Accepted: 09/16/2021] [Indexed: 12/12/2022] Open
Abstract
Background: Necrotizing enterocolitis (NEC) is a fatal disease where current diagnostic tools are insufficient for preventing NEC. Early predictive biomarkers could be beneficial in identifying infants at high risk of developing NEC. Objective: To explore early biomarkers for predicting NEC in extremely preterm infants (EPIs). Methods: Blood samples were collected on day 2 (median 1.7; range 1.5-2.0) from 40 EPI (median 25 gestational weeks; range 22-27): 11 developed NEC and 29 did not (controls). In each infant, 189 inflammatory, oncological, and vascular proteomic biomarkers were quantified through Proximity Extension Assay. Biomarker expression and clinical data were compared between the NEC group and Controls. Based on biomarker differences, controls were sorted automatically into three subgroups (1, 2, and 3) by a two-dimensional hierarchical clustering analysis. Results: None of the biomarkers differed in expression between all controls and the NEC group. Two biomarkers were higher in Control 1, and 16 biomarkers were lower in Control group 2 compared with the NEC group. No biomarker distinguished Control 3 from the NEC group. Perinatal data were similar in the whole population. Conclusions: Early postnatal comprehensive biomarkers do not identify EPIs at risk of developing NEC in our study. Future studies of predictors of NEC should include sequential analysis of comprehensive proteomic markers in large cohorts.
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Affiliation(s)
- Alice Hoffsten
- Department of Women's and Children's Health, Uppsala University, Uppsala, Sweden
| | - Laszlo Markasz
- Department of Women's and Children's Health, Uppsala University, Uppsala, Sweden.,Neonatal Intensive Care Unit, University Children's Hospital, Uppsala, Sweden
| | - Helene Engstrand Lilja
- Department of Women's and Children's Health, Uppsala University, Uppsala, Sweden.,Section of Pediatric Surgery, University Children's Hospital, Uppsala, Sweden
| | - Karl Wilhelm Olsson
- Department of Women's and Children's Health, Uppsala University, Uppsala, Sweden.,Department of Surgical Sciences, Uppsala University, Uppsala, Sweden
| | - Richard Sindelar
- Department of Women's and Children's Health, Uppsala University, Uppsala, Sweden.,Neonatal Intensive Care Unit, University Children's Hospital, Uppsala, Sweden
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6
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Markasz L, Olsson KW, Holmström G, Sindelar R. Cluster Analysis of Early Postnatal Biochemical Markers May Predict Development of Retinopathy of Prematurity. Transl Vis Sci Technol 2020; 9:14. [PMID: 33344058 PMCID: PMC7726592 DOI: 10.1167/tvst.9.13.14] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 10/19/2020] [Indexed: 12/15/2022] Open
Abstract
Purpose Growth factors and inflammatory and angiogenetic proteins are involved in the development of retinopathy of prematurity (ROP). However, no early biochemical markers are in clinical use to predict ROP. By performing cluster analysis of multiple biomarkers, we aimed to determine patient groups with high and low risk for developing ROP. Methods In total, 202 protein markers in plasma were quantified by proximity extension assay from 35 extremely preterm infants on day 2 of life. Infants were sorted in groups by automated two-dimensional hierarchical clustering of all biomarkers. ROP was classified as stages I to III with or without surgical treatment. Predictive biomarkers were evaluated by analysis of variance and detected differences by two-sided paired t-test with Bonferroni corrections for multiple comparisons. Results Differences in 39 biochemical markers divided infants without ROP into two control groups (control 1, n = 7; control 2, n = 5; P < 0.05). Sixty-six biochemical markers defined differences between the control groups (n = 13) and all ROP infants (n = 23; P < 0.05). PARK7, VIM, MPO, CD69, and NEMO were markedly increased in control 1 compared to all ROP infants (P < 0.001). Lower TNFRSF4 and higher HER2 and GAL appeared in infants with ROP as compared to control 1 and/or 2 (P < 0.05, respectively). Conclusions Our data suggest that early elevated levels of PARK7, VIM, MPO, CD69, and NEMO may be associated with lower risk of developing ROP. Lower levels of TNFRSF4 with higher levels of HER2 and GAL may predict ROP development. Translational Relevance Cluster analysis of early postnatal biomarkers may help to identify infants with low or high risk of developing ROP.
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Affiliation(s)
- Laszlo Markasz
- Department of Women's and Children's Health, Uppsala University, Uppsala, Sweden
| | - Karl-Wilhelm Olsson
- Department of Women's and Children's Health, Uppsala University, Uppsala, Sweden.,Department of Surgical Sciences, Uppsala University, Uppsala, Sweden
| | - Gerd Holmström
- Department of Neuroscience/Ophthalmology, Uppsala University, Uppsala, Sweden
| | - Richard Sindelar
- Department of Women's and Children's Health, Uppsala University, Uppsala, Sweden
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7
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Redondo-Antón J, Fontela MG, Notario L, Torres-Ruiz R, Rodríguez-Perales S, Lorente E, Lauzurica P. Functional Characterization of a Dual Enhancer/Promoter Regulatory Element Leading Human CD69 Expression. Front Genet 2020; 11:552949. [PMID: 33193627 PMCID: PMC7652794 DOI: 10.3389/fgene.2020.552949] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 10/07/2020] [Indexed: 11/29/2022] Open
Abstract
The CD69 gene encodes a C-type lectin glycoprotein with immune regulatory properties which is expressed on the cell surfaces of all activated hematopoietic cells. CD69 activation kinetics differ by developmental stage, cell linage and activating conditions, and these differences have been attributed to the participation of complex gene regulatory networks. An evolutionarily conserved regulatory element, CNS2, located 4kb upstream of the CD69 gene transcriptional start site, has been proposed as the major candidate governing the gene transcriptional activation program. To investigate the function of human CNS2, we studied the effect of its endogenous elimination via CRISPR-Cas9 on CD69 protein and mRNA expression levels in various immune cell lines. Even when the entire promoter region was maintained, CNS2-/- cells did not express CD69, thus indicating that CNS2 has promoter-like characteristics. However, like enhancers, inverted CNS2 sustained transcription, although at a diminished levels, thereby suggesting that it has dual promoter and enhancer functions. Episomal luciferase assays further suggested that both functions are combined within the CNS2 regulatory element. In addition, CNS2 directs its own bidirectional transcription into two different enhancer-derived RNAs molecules (eRNAs) which are transcribed from two independent transcriptional start sites in opposite directions. This eRNA transcription is dependent on only the enhancer sequence itself, because in the absence of the CD69 promoter, sufficient RNA polymerase II levels are maintained at CNS2 to drive eRNA expression. Here, we describe a regulatory element with overlapping promoter and enhancer functions, which is essential for CD69 gene transcriptional regulation.
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Affiliation(s)
- Jennifer Redondo-Antón
- Immune Gene Regulation and Antigen Presentation Group, National Center for Microbiology, Institute of Health Carlos III (ISCIII), Madrid, Spain
| | - M G Fontela
- Immune Gene Regulation and Antigen Presentation Group, National Center for Microbiology, Institute of Health Carlos III (ISCIII), Madrid, Spain
| | - Laura Notario
- Immune Gene Regulation and Antigen Presentation Group, National Center for Microbiology, Institute of Health Carlos III (ISCIII), Madrid, Spain
| | - Raúl Torres-Ruiz
- Molecular Cytogenetics and Genome Editing Unit, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Sandra Rodríguez-Perales
- Molecular Cytogenetics and Genome Editing Unit, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Elena Lorente
- Immune Gene Regulation and Antigen Presentation Group, National Center for Microbiology, Institute of Health Carlos III (ISCIII), Madrid, Spain
| | - Pilar Lauzurica
- Immune Gene Regulation and Antigen Presentation Group, National Center for Microbiology, Institute of Health Carlos III (ISCIII), Madrid, Spain
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8
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Single-cell multiomic analysis identifies regulatory programs in mixed-phenotype acute leukemia. Nat Biotechnol 2019; 37:1458-1465. [PMID: 31792411 DOI: 10.1038/s41587-019-0332-7] [Citation(s) in RCA: 227] [Impact Index Per Article: 45.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 10/29/2019] [Indexed: 12/28/2022]
Abstract
Identifying the causes of human diseases requires deconvolution of abnormal molecular phenotypes spanning DNA accessibility, gene expression and protein abundance1-3. We present a single-cell framework that integrates highly multiplexed protein quantification, transcriptome profiling and analysis of chromatin accessibility. Using this approach, we establish a normal epigenetic baseline for healthy blood development, which we then use to deconvolve aberrant molecular features within blood from patients with mixed-phenotype acute leukemia4,5. Despite widespread epigenetic heterogeneity within the patient cohort, we observe common malignant signatures across patients as well as patient-specific regulatory features that are shared across phenotypic compartments of individual patients. Integrative analysis of transcriptomic and chromatin-accessibility maps identified 91,601 putative peak-to-gene linkages and transcription factors that regulate leukemia-specific genes, such as RUNX1-linked regulatory elements proximal to the marker gene CD69. These results demonstrate how integrative, multiomic analysis of single cells within the framework of normal development can reveal both distinct and shared molecular mechanisms of disease from patient samples.
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9
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Brait VH, Miró-Mur F, Pérez-de-Puig I, Notario L, Hurtado B, Pedragosa J, Gallizioli M, Jiménez-Altayó F, Arbaizar-Rovirosa M, Otxoa-de-Amezaga A, Monteagudo J, Ferrer-Ferrer M, de la Rosa X, Bonfill-Teixidor E, Salas-Perdomo A, Hernández-Vidal A, Garcia-de-Frutos P, Lauzurica P, Planas AM. CD69 Plays a Beneficial Role in Ischemic Stroke by Dampening Endothelial Activation. Circ Res 2019; 124:279-291. [PMID: 30582456 DOI: 10.1161/circresaha.118.313818] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
RATIONALE CD69 is an immunomodulatory molecule induced during lymphocyte activation. Following stroke, T-lymphocytes upregulate CD69 but its function is unknown. OBJECTIVE We investigated whether CD69 was involved in brain damage following an ischemic stroke. METHODS AND RESULTS We used adult male mice on the C57BL/6 or BALB/c backgrounds, including wild-type mice and CD69-/- mice, and CD69+/+ and CD69-/- lymphocyte-deficient Rag2-/- mice, and generated chimeric mice. We induced ischemia by transient or permanent middle cerebral artery occlusion. We measured infarct volume, assessed neurological function, and studied CD69 expression, as well as platelet function, fibrin(ogen) deposition, and VWF (von Willebrand factor) expression in brain vessels and VWF content and activity in plasma, and performed the tail-vein bleeding test and the carotid artery ferric chloride-induced thrombosis model. We also performed primary glial cell cultures and sorted brain CD45-CD11b-CD31+ endothelial cells for mRNA expression studies. We blocked VWF by intravenous administration of anti-VWF antibodies. CD69-/- mice showed larger infarct volumes and worse neurological deficits than the wild-type mice after ischemia. This worsening effect was not attributable to lymphocytes or other hematopoietic cells. CD69 deficiency lowered the time to thrombosis in the carotid artery despite platelet function not being affected. Ischemia upregulated Cd69 mRNA expression in brain endothelial cells. CD69-deficiency increased fibrin(ogen) accumulation in the ischemic tissue, and plasma VWF content and activity, and VWF expression in brain vessels. Blocking VWF reduced infarct volume and reverted the detrimental effect of CD69-/- deficiency. CONCLUSIONS CD69 deficiency promotes a prothrombotic phenotype characterized by increased VWF and worse brain damage after ischemic stroke. The results suggest that CD69 acts as a downregulator of endothelial activation.
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Affiliation(s)
- Vanessa H Brait
- From the Department of Brain Ischemia and Neurodegeneration (V.H.B., F.M.-M., I.P.-d.-P., J.P., M.G., M.A.-R., A.O.-d.-A., X.d.l.R., E.B.-T., A.M.P.), Institut d'Investigacions Biomèdiques de Barcelona (IIBB)-Consejo Superior de Investigaciones Científicas (CSIC), Spain.,Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain (V.H.B., F.M.-M., J.P., M.G., M.A.-R., A.O.-d.-A., M.F.-F., E.B.-T., A.S.-P., A.H.-V., A.M.P.)
| | - Francesc Miró-Mur
- From the Department of Brain Ischemia and Neurodegeneration (V.H.B., F.M.-M., I.P.-d.-P., J.P., M.G., M.A.-R., A.O.-d.-A., X.d.l.R., E.B.-T., A.M.P.), Institut d'Investigacions Biomèdiques de Barcelona (IIBB)-Consejo Superior de Investigaciones Científicas (CSIC), Spain.,Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain (V.H.B., F.M.-M., J.P., M.G., M.A.-R., A.O.-d.-A., M.F.-F., E.B.-T., A.S.-P., A.H.-V., A.M.P.)
| | - Isabel Pérez-de-Puig
- From the Department of Brain Ischemia and Neurodegeneration (V.H.B., F.M.-M., I.P.-d.-P., J.P., M.G., M.A.-R., A.O.-d.-A., X.d.l.R., E.B.-T., A.M.P.), Institut d'Investigacions Biomèdiques de Barcelona (IIBB)-Consejo Superior de Investigaciones Científicas (CSIC), Spain
| | - Laura Notario
- Grupo de Activación Inmunológica, Centro Nacional de Microbiología, Instituto de Salud Carlos III (ISCIII), Madrid, Spain (L.N., P.L.)
| | - Begoña Hurtado
- Department of Cell Death and Proliferation (B.H., P.G.-d.-F.), Institut d'Investigacions Biomèdiques de Barcelona (IIBB)-Consejo Superior de Investigaciones Científicas (CSIC), Spain
| | - Jordi Pedragosa
- From the Department of Brain Ischemia and Neurodegeneration (V.H.B., F.M.-M., I.P.-d.-P., J.P., M.G., M.A.-R., A.O.-d.-A., X.d.l.R., E.B.-T., A.M.P.), Institut d'Investigacions Biomèdiques de Barcelona (IIBB)-Consejo Superior de Investigaciones Científicas (CSIC), Spain.,Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain (V.H.B., F.M.-M., J.P., M.G., M.A.-R., A.O.-d.-A., M.F.-F., E.B.-T., A.S.-P., A.H.-V., A.M.P.)
| | - Mattia Gallizioli
- From the Department of Brain Ischemia and Neurodegeneration (V.H.B., F.M.-M., I.P.-d.-P., J.P., M.G., M.A.-R., A.O.-d.-A., X.d.l.R., E.B.-T., A.M.P.), Institut d'Investigacions Biomèdiques de Barcelona (IIBB)-Consejo Superior de Investigaciones Científicas (CSIC), Spain.,Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain (V.H.B., F.M.-M., J.P., M.G., M.A.-R., A.O.-d.-A., M.F.-F., E.B.-T., A.S.-P., A.H.-V., A.M.P.)
| | - Francesc Jiménez-Altayó
- Departament de Farmacologia, Terapèutica i Toxicologia, Institut de Neurociències, Facultat de Medicina, Universitat Autònoma de Barcelona, Bellaterra, Spain (F.J.A.)
| | - Maria Arbaizar-Rovirosa
- From the Department of Brain Ischemia and Neurodegeneration (V.H.B., F.M.-M., I.P.-d.-P., J.P., M.G., M.A.-R., A.O.-d.-A., X.d.l.R., E.B.-T., A.M.P.), Institut d'Investigacions Biomèdiques de Barcelona (IIBB)-Consejo Superior de Investigaciones Científicas (CSIC), Spain.,Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain (V.H.B., F.M.-M., J.P., M.G., M.A.-R., A.O.-d.-A., M.F.-F., E.B.-T., A.S.-P., A.H.-V., A.M.P.)
| | - Amaia Otxoa-de-Amezaga
- From the Department of Brain Ischemia and Neurodegeneration (V.H.B., F.M.-M., I.P.-d.-P., J.P., M.G., M.A.-R., A.O.-d.-A., X.d.l.R., E.B.-T., A.M.P.), Institut d'Investigacions Biomèdiques de Barcelona (IIBB)-Consejo Superior de Investigaciones Científicas (CSIC), Spain.,Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain (V.H.B., F.M.-M., J.P., M.G., M.A.-R., A.O.-d.-A., M.F.-F., E.B.-T., A.S.-P., A.H.-V., A.M.P.)
| | - Juan Monteagudo
- Hemotherapy and Haemostasis Service, Hospital Clinic, Barcelona, Spain (J.M.)
| | - Maura Ferrer-Ferrer
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain (V.H.B., F.M.-M., J.P., M.G., M.A.-R., A.O.-d.-A., M.F.-F., E.B.-T., A.S.-P., A.H.-V., A.M.P.)
| | - Xavier de la Rosa
- From the Department of Brain Ischemia and Neurodegeneration (V.H.B., F.M.-M., I.P.-d.-P., J.P., M.G., M.A.-R., A.O.-d.-A., X.d.l.R., E.B.-T., A.M.P.), Institut d'Investigacions Biomèdiques de Barcelona (IIBB)-Consejo Superior de Investigaciones Científicas (CSIC), Spain
| | - Ester Bonfill-Teixidor
- From the Department of Brain Ischemia and Neurodegeneration (V.H.B., F.M.-M., I.P.-d.-P., J.P., M.G., M.A.-R., A.O.-d.-A., X.d.l.R., E.B.-T., A.M.P.), Institut d'Investigacions Biomèdiques de Barcelona (IIBB)-Consejo Superior de Investigaciones Científicas (CSIC), Spain.,Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain (V.H.B., F.M.-M., J.P., M.G., M.A.-R., A.O.-d.-A., M.F.-F., E.B.-T., A.S.-P., A.H.-V., A.M.P.)
| | - Angélica Salas-Perdomo
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain (V.H.B., F.M.-M., J.P., M.G., M.A.-R., A.O.-d.-A., M.F.-F., E.B.-T., A.S.-P., A.H.-V., A.M.P.)
| | - Alba Hernández-Vidal
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain (V.H.B., F.M.-M., J.P., M.G., M.A.-R., A.O.-d.-A., M.F.-F., E.B.-T., A.S.-P., A.H.-V., A.M.P.)
| | - Pablo Garcia-de-Frutos
- Department of Cell Death and Proliferation (B.H., P.G.-d.-F.), Institut d'Investigacions Biomèdiques de Barcelona (IIBB)-Consejo Superior de Investigaciones Científicas (CSIC), Spain
| | - Pilar Lauzurica
- Grupo de Activación Inmunológica, Centro Nacional de Microbiología, Instituto de Salud Carlos III (ISCIII), Madrid, Spain (L.N., P.L.)
| | - Anna M Planas
- From the Department of Brain Ischemia and Neurodegeneration (V.H.B., F.M.-M., I.P.-d.-P., J.P., M.G., M.A.-R., A.O.-d.-A., X.d.l.R., E.B.-T., A.M.P.), Institut d'Investigacions Biomèdiques de Barcelona (IIBB)-Consejo Superior de Investigaciones Científicas (CSIC), Spain.,Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain (V.H.B., F.M.-M., J.P., M.G., M.A.-R., A.O.-d.-A., M.F.-F., E.B.-T., A.S.-P., A.H.-V., A.M.P.)
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10
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Fontela MG, Notario L, Alari-Pahissa E, Lorente E, Lauzurica P. The Conserved Non-Coding Sequence 2 (CNS2) Enhances CD69 Transcription through Cooperation between the Transcription Factors Oct1 and RUNX1. Genes (Basel) 2019; 10:genes10090651. [PMID: 31466317 PMCID: PMC6770821 DOI: 10.3390/genes10090651] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Revised: 07/29/2019] [Accepted: 08/23/2019] [Indexed: 02/02/2023] Open
Abstract
The immune regulatory receptor CD69 is expressed upon activation in all types of leukocytes and is strongly regulated at the transcriptional level. We previously described that, in addition to the CD69 promoter, there are four conserved noncoding regions (CNS1-4) upstream of the CD69 promoter. Furthermore, we proposed that CNS2 is the main enhancer of CD69 transcription. In the present study, we mapped the transcription factor (TF) binding sites (TFBS) from ChIP-seq databases within CNS2. Through luciferase reporter assays, we defined a ~60 bp sequence that acts as the minimum enhancer core of mouse CNS2, which includes the Oct1 TFBS. This enhancer core establishes cooperative interactions with the 3′ and 5′ flanking regions, which contain RUNX1 BS. In agreement with the luciferase reporter data, the inhibition of RUNX1 and Oct1 TF expression by siRNA suggests that they synergistically enhance endogenous CD69 gene transcription. In summary, we describe an enhancer core containing RUNX1 and Oct1 BS that is important for the activity of the most potent CD69 gene transcription enhancer.
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Affiliation(s)
- Miguel G. Fontela
- Microbiology National Center, Instituto de Salud Carlos III, Majadahonda, 28220 Madrid, Spain
| | - Laura Notario
- Microbiology National Center, Instituto de Salud Carlos III, Majadahonda, 28220 Madrid, Spain
| | - Elisenda Alari-Pahissa
- Department of Experimental and Health Science, University Pompeu Fabra, 08003 Barcelona, Spain
| | - Elena Lorente
- Microbiology National Center, Instituto de Salud Carlos III, Majadahonda, 28220 Madrid, Spain
| | - Pilar Lauzurica
- Microbiology National Center, Instituto de Salud Carlos III, Majadahonda, 28220 Madrid, Spain
- Correspondence: ; Tel.: +34-918222720
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11
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Kulemzin SV, Matvienko DA, Sabirov AH, Sokratyan AM, Chernikova DS, Belovezhets TN, Chikaev AN, Taranin AV, Gorchakov AA. Design and analysis of stably integrated reporters for inducible transgene expression in human T cells and CAR NK-cell lines. BMC Med Genomics 2019; 12:44. [PMID: 30871576 PMCID: PMC6417161 DOI: 10.1186/s12920-019-0489-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Background Cytotoxic activity of T- and NK-cells can be efficiently retargeted against cancer cells using chimeric antigen receptors (CARs) and rTCRs. In the context of solid cancers, use of armored CAR T- and NK cells secreting additional anti-cancer molecules such as cytokines, chemokines, antibodies, BiTEs, inverted cytokine receptors, and checkpoint inhibitors, appears particularly promising, as this may help overcome immunosuppressive tumor microenvironment, attract bystander immune cells, and boost CAR T/NK-cell persistence. Placing the expression of such molecules under the transcriptional control downstream of CAR-mediated T/NK-cell activation offers the advantage of targeted delivery, high local concentration, and reduced toxicity. Several canonic DNA sequences that are known to function as activation-inducible promoters in human T and B cells have been described to date and typically encompass the multimers of NFkB and NFAT binding sites. However, relatively little is known about the DNA sequences that may function as activation-driven switches in the context of NK cells. We set out to compare the functionality of several activation-inducible promoters in primary human T cells, as well as in NK cell lines NK-92 and YT. Methods Lentiviral constructs were engineered to express two fluorescent reporters: mCherry under 4xNFAT, 2xNFkB, 5xNFkB, 10xNFkB, 30xNFkB promoters, as well as two variants of the CD69 promoter, and copGFP under the strong constitutive promoter of the human EF1a gene. Pseudotyped lentiviral particles obtained using these constructs were transduced into primary human T cells and NK-92 and YT cell lines expressing a CAR specific for PSMA. The transgenic cells obtained were activated by CD3/CD28 beads (T cells) or via a CAR (CAR-NK cell lines). Promoter activity before and after activation was assayed using FACS analysis. Results In T cells, the CD69 promoter encompassing CNS1 and CNS2 regions displayed the highest signal/noise ratio. Intriguingly, in the context of CAR-YT cell line neither of the seven promoters tested displayed acceptable activation profile. In CAR-NK-92 cells, the largest fold activation (which was modest) was achieved with the 10xNFkB and 30xNFkB promoters, however its expression was clearly leaky in “resting” non-activated cells. Conclusions Unlike in T cells, the robust activation-driven inducible expression of genetic cassettes in NK cells requires unbiased genome-wide identification of promoter sequences. Electronic supplementary material The online version of this article (10.1186/s12920-019-0489-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Sergey V Kulemzin
- Institute of Molecular and Cellular Biology SB RAS, Novosibirsk, Russia
| | - Daria A Matvienko
- Institute of Molecular and Cellular Biology SB RAS, Novosibirsk, Russia.,Novosibirsk State University, Novosibirsk, Russia
| | - Artur H Sabirov
- Institute of Molecular and Cellular Biology SB RAS, Novosibirsk, Russia.,Novosibirsk State University, Novosibirsk, Russia
| | - Arpine M Sokratyan
- Institute of Molecular and Cellular Biology SB RAS, Novosibirsk, Russia.,Novosibirsk State University, Novosibirsk, Russia
| | - Daria S Chernikova
- Institute of Molecular and Cellular Biology SB RAS, Novosibirsk, Russia.,Novosibirsk State University, Novosibirsk, Russia
| | - Tatyana N Belovezhets
- Institute of Molecular and Cellular Biology SB RAS, Novosibirsk, Russia.,Novosibirsk State University, Novosibirsk, Russia
| | - Anton N Chikaev
- Institute of Molecular and Cellular Biology SB RAS, Novosibirsk, Russia
| | - Aleksandr V Taranin
- Institute of Molecular and Cellular Biology SB RAS, Novosibirsk, Russia.,Novosibirsk State University, Novosibirsk, Russia
| | - Andrey A Gorchakov
- Institute of Molecular and Cellular Biology SB RAS, Novosibirsk, Russia. .,Novosibirsk State University, Novosibirsk, Russia.
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12
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Simeonov DR, Gowen BG, Boontanrart M, Roth TL, Gagnon JD, Mumbach MR, Satpathy AT, Lee Y, Bray NL, Chan AY, Lituiev DS, Nguyen ML, Gate RE, Subramaniam M, Li Z, Woo JM, Mitros T, Ray GJ, Curie GL, Naddaf N, Chu JS, Ma H, Boyer E, Van Gool F, Huang H, Liu R, Tobin VR, Schumann K, Daly MJ, Farh KK, Ansel KM, Ye CJ, Greenleaf WJ, Anderson MS, Bluestone JA, Chang HY, Corn JE, Marson A. Discovery of stimulation-responsive immune enhancers with CRISPR activation. Nature 2017; 549:111-115. [PMID: 28854172 PMCID: PMC5675716 DOI: 10.1038/nature23875] [Citation(s) in RCA: 203] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Accepted: 07/25/2017] [Indexed: 12/19/2022]
Abstract
The majority of genetic variants associated with common human diseases map to enhancers, non-coding elements that shape cell-type-specific transcriptional programs and responses to extracellular cues. Systematic mapping of functional enhancers and their biological contexts is required to understand the mechanisms by which variation in non-coding genetic sequences contributes to disease. Functional enhancers can be mapped by genomic sequence disruption, but this approach is limited to the subset of enhancers that are necessary in the particular cellular context being studied. We hypothesized that recruitment of a strong transcriptional activator to an enhancer would be sufficient to drive target gene expression, even if that enhancer was not currently active in the assayed cells. Here we describe a discovery platform that can identify stimulus-responsive enhancers for a target gene independent of stimulus exposure. We used tiled CRISPR activation (CRISPRa) to synthetically recruit a transcriptional activator to sites across large genomic regions (more than 100 kilobases) surrounding two key autoimmunity risk loci, CD69 and IL2RA. We identified several CRISPRa-responsive elements with chromatin features of stimulus-responsive enhancers, including an IL2RA enhancer that harbours an autoimmunity risk variant. Using engineered mouse models, we found that sequence perturbation of the disease-associated Il2ra enhancer did not entirely block Il2ra expression, but rather delayed the timing of gene activation in response to specific extracellular signals. Enhancer deletion skewed polarization of naive T cells towards a pro-inflammatory T helper (TH17) cell state and away from a regulatory T cell state. This integrated approach identifies functional enhancers and reveals how non-coding variation associated with human immune dysfunction alters context-specific gene programs.
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MESH Headings
- Animals
- Antigens, CD/biosynthesis
- Antigens, CD/genetics
- Antigens, CD/immunology
- Antigens, Differentiation, T-Lymphocyte/biosynthesis
- Antigens, Differentiation, T-Lymphocyte/genetics
- Antigens, Differentiation, T-Lymphocyte/immunology
- Autoimmunity/genetics
- CRISPR-Cas Systems/genetics
- Cell Differentiation
- Cell Line
- Chromatin/genetics
- Clustered Regularly Interspaced Short Palindromic Repeats/genetics
- Enhancer Elements, Genetic/genetics
- Female
- Gene Expression Regulation/genetics
- Humans
- Interleukin-2 Receptor alpha Subunit/biosynthesis
- Interleukin-2 Receptor alpha Subunit/genetics
- Interleukin-2 Receptor alpha Subunit/immunology
- Lectins, C-Type/biosynthesis
- Lectins, C-Type/genetics
- Lectins, C-Type/immunology
- Mice
- Receptors, Antigen, T-Cell/genetics
- Receptors, Antigen, T-Cell/immunology
- Th17 Cells/cytology
- Th17 Cells/immunology
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Affiliation(s)
- Dimitre R Simeonov
- Biomedical Sciences Graduate Program, University of California, San Francisco, California 94143, USA
- Department of Microbiology and Immunology, University of California, San Francisco, California 94143, USA
- Diabetes Center, University of California, San Francisco, California 94143, USA
- Innovative Genomics Institute, University of California, Berkeley, California 94720, USA
| | - Benjamin G Gowen
- Innovative Genomics Institute, University of California, Berkeley, California 94720, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California 94720, USA
| | - Mandy Boontanrart
- Innovative Genomics Institute, University of California, Berkeley, California 94720, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California 94720, USA
| | - Theodore L Roth
- Biomedical Sciences Graduate Program, University of California, San Francisco, California 94143, USA
- Department of Microbiology and Immunology, University of California, San Francisco, California 94143, USA
- Diabetes Center, University of California, San Francisco, California 94143, USA
- Innovative Genomics Institute, University of California, Berkeley, California 94720, USA
| | - John D Gagnon
- Biomedical Sciences Graduate Program, University of California, San Francisco, California 94143, USA
- Department of Microbiology and Immunology, University of California, San Francisco, California 94143, USA
- Sandler Asthma Basic Research Center, University of California, San Francisco, California 94143, USA
| | - Maxwell R Mumbach
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, California 94305, USA
- Program in Epithelial Biology, Stanford University School of Medicine, Stanford, California 94305, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Ansuman T Satpathy
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, California 94305, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Youjin Lee
- Department of Microbiology and Immunology, University of California, San Francisco, California 94143, USA
- Diabetes Center, University of California, San Francisco, California 94143, USA
- Innovative Genomics Institute, University of California, Berkeley, California 94720, USA
| | - Nicolas L Bray
- Innovative Genomics Institute, University of California, Berkeley, California 94720, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California 94720, USA
| | - Alice Y Chan
- Diabetes Center, University of California, San Francisco, California 94143, USA
- Department of Pediatrics, University of California, San Francisco, California 94143, USA
| | - Dmytro S Lituiev
- Department of Epidemiology and Biostatistics, Department of Bioengineering and Therapeutic Sciences, Institute for Human Genetics (IHG), University of California, San Francisco, California 94143, USA
| | - Michelle L Nguyen
- Department of Microbiology and Immunology, University of California, San Francisco, California 94143, USA
- Diabetes Center, University of California, San Francisco, California 94143, USA
- Innovative Genomics Institute, University of California, Berkeley, California 94720, USA
| | - Rachel E Gate
- Department of Epidemiology and Biostatistics, Department of Bioengineering and Therapeutic Sciences, Institute for Human Genetics (IHG), University of California, San Francisco, California 94143, USA
- Biological and Medical Informatics Graduate Program, University of California, San Francisco, California 94158, USA
| | - Meena Subramaniam
- Department of Epidemiology and Biostatistics, Department of Bioengineering and Therapeutic Sciences, Institute for Human Genetics (IHG), University of California, San Francisco, California 94143, USA
- Biological and Medical Informatics Graduate Program, University of California, San Francisco, California 94158, USA
| | - Zhongmei Li
- Department of Microbiology and Immunology, University of California, San Francisco, California 94143, USA
- Diabetes Center, University of California, San Francisco, California 94143, USA
- Innovative Genomics Institute, University of California, Berkeley, California 94720, USA
| | - Jonathan M Woo
- Department of Microbiology and Immunology, University of California, San Francisco, California 94143, USA
- Diabetes Center, University of California, San Francisco, California 94143, USA
- Innovative Genomics Institute, University of California, Berkeley, California 94720, USA
| | - Therese Mitros
- Innovative Genomics Institute, University of California, Berkeley, California 94720, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California 94720, USA
| | - Graham J Ray
- Innovative Genomics Institute, University of California, Berkeley, California 94720, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California 94720, USA
| | - Gemma L Curie
- Innovative Genomics Institute, University of California, Berkeley, California 94720, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California 94720, USA
| | - Nicki Naddaf
- Innovative Genomics Institute, University of California, Berkeley, California 94720, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California 94720, USA
| | - Julia S Chu
- Innovative Genomics Institute, University of California, Berkeley, California 94720, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California 94720, USA
| | - Hong Ma
- Innovative Genomics Institute, University of California, Berkeley, California 94720, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California 94720, USA
| | - Eric Boyer
- Diabetes Center, University of California, San Francisco, California 94143, USA
- Innovative Genomics Institute, University of California, Berkeley, California 94720, USA
| | - Frederic Van Gool
- Diabetes Center, University of California, San Francisco, California 94143, USA
| | - Hailiang Huang
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114, USA
| | - Ruize Liu
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114, USA
| | - Victoria R Tobin
- Department of Microbiology and Immunology, University of California, San Francisco, California 94143, USA
- Diabetes Center, University of California, San Francisco, California 94143, USA
- Innovative Genomics Institute, University of California, Berkeley, California 94720, USA
| | - Kathrin Schumann
- Department of Microbiology and Immunology, University of California, San Francisco, California 94143, USA
- Diabetes Center, University of California, San Francisco, California 94143, USA
- Innovative Genomics Institute, University of California, Berkeley, California 94720, USA
| | - Mark J Daly
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114, USA
| | - Kyle K Farh
- Illumina Inc., 5200 Illumina Way, San Diego, California 92122, USA
| | - K Mark Ansel
- Department of Microbiology and Immunology, University of California, San Francisco, California 94143, USA
- Sandler Asthma Basic Research Center, University of California, San Francisco, California 94143, USA
| | - Chun J Ye
- Department of Epidemiology and Biostatistics, Department of Bioengineering and Therapeutic Sciences, Institute for Human Genetics (IHG), University of California, San Francisco, California 94143, USA
| | - William J Greenleaf
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, California 94305, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA
- Department of Applied Physics, Stanford University, Stanford, California 94025, USA
- Chan Zuckerberg Biohub, San Francisco, California 94158, USA
| | - Mark S Anderson
- Diabetes Center, University of California, San Francisco, California 94143, USA
- Department of Medicine, University of California, San Francisco, California 94143, USA
| | - Jeffrey A Bluestone
- Diabetes Center, University of California, San Francisco, California 94143, USA
| | - Howard Y Chang
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, California 94305, USA
- Program in Epithelial Biology, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Jacob E Corn
- Innovative Genomics Institute, University of California, Berkeley, California 94720, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California 94720, USA
| | - Alexander Marson
- Department of Microbiology and Immunology, University of California, San Francisco, California 94143, USA
- Diabetes Center, University of California, San Francisco, California 94143, USA
- Innovative Genomics Institute, University of California, Berkeley, California 94720, USA
- Chan Zuckerberg Biohub, San Francisco, California 94158, USA
- Department of Medicine, University of California, San Francisco, California 94143, USA
- UCSF Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, California 94158, USA
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