1
|
Shin B, Chang SJ, MacNabb BW, Rothenberg EV. Transcriptional network dynamics in early T cell development. J Exp Med 2024; 221:e20230893. [PMID: 39167073 DOI: 10.1084/jem.20230893] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2024] [Revised: 06/07/2024] [Accepted: 07/10/2024] [Indexed: 08/23/2024] Open
Abstract
The rate at which cells enter the T cell pathway depends not only on the immigration of hematopoietic precursors into the strong Notch signaling environment of the thymus but also on the kinetics with which each individual precursor cell reaches T-lineage commitment once it arrives. Notch triggers a complex, multistep gene regulatory network in the cells in which the steps are stereotyped but the transition speeds between steps are variable. Progenitor-associated transcription factors delay T-lineage differentiation even while Notch-induced transcription factors within the same cells push differentiation forward. Progress depends on regulator cross-repression, on breaching chromatin barriers, and on shifting, competitive collaborations between stage-specific and stably expressed transcription factors, as reviewed here.
Collapse
Affiliation(s)
- Boyoung Shin
- Division of Biology and Biological Engineering California Institute of Technology , Pasadena, CA, USA
| | - Samantha J Chang
- Division of Biology and Biological Engineering California Institute of Technology , Pasadena, CA, USA
| | - Brendan W MacNabb
- Division of Biology and Biological Engineering California Institute of Technology , Pasadena, CA, USA
| | - Ellen V Rothenberg
- Division of Biology and Biological Engineering California Institute of Technology , Pasadena, CA, USA
| |
Collapse
|
2
|
Elias HK, Mitra S, da Silva MB, Rajagopalan A, Gipson B, Lee N, Kousa AI, Ali MAE, Grassman S, Zhang X, DeWolf S, Smith M, Andrlova H, Argyropoulos KV, Sharma R, Fei T, Sun JC, Dunbar CE, Park CY, Leslie CS, Bhandoola A, van den Brink MRM. An epigenetically distinct HSC subset supports thymic reconstitution. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.06.597775. [PMID: 38895335 PMCID: PMC11185715 DOI: 10.1101/2024.06.06.597775] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
Hematopoietic stem cells (HSCs) with multilineage potential are critical for effective T cell reconstitution and restoration of the adaptive immune system after allogeneic Hematopoietic Cell Transplantation (allo-HCT). The Kit lo subset of HSCs is enriched for multipotential precursors, 1, 2 but their T-cell lineage potential has not been well-characterized. We therefore studied the thymic reconstituting and T-cell potential of Kit lo HSCs. Using a preclinical allo-HCT model, we demonstrate that Kit lo HSCs support better thymic recovery, and T-cell reconstitution resulting in improved T cell responses to infection post-HCT. Furthermore, Kit lo HSCs with augmented BM lymphopoiesis mitigate age-associated thymic alterations, thus enhancing T-cell recovery in middle-aged hosts. We find the frequency of the Kit lo subset declines with age, providing one explanation for the reduced frequency of T-competent HSCs and reduced T-lymphopoietic potential in BM precursors of aged mice. 3, 4, 5 Chromatin profiling revealed that Kit lo HSCs exhibit higher activity of lymphoid-specifying transcription factors (TFs), including Zbtb1 . Deletion of Zbtb1 in Kit lo HSCs diminished their T-cell potential, while reinstating Zbtb1 in megakaryocytic-biased Kit hi HSCs rescued T-cell potential, in vitro and in vivo . Finally, we discover an analogous Kit lo HSC subset with enhanced lymphoid potential in human bone marrow. Our results demonstrate that Kit lo HSCs with enhanced lymphoid potential have a distinct underlying epigenetic program.
Collapse
|
3
|
Gamble N, Bradu A, Caldwell JA, McKeever J, Bolonduro O, Ermis E, Kaiser C, Kim Y, Parks B, Klemm S, Greenleaf WJ, Crabtree GR, Koh AS. PU.1 and BCL11B sequentially cooperate with RUNX1 to anchor mSWI/SNF to poise the T cell effector landscape. Nat Immunol 2024; 25:860-872. [PMID: 38632339 PMCID: PMC11089574 DOI: 10.1038/s41590-024-01807-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Accepted: 03/11/2024] [Indexed: 04/19/2024]
Abstract
Adaptive immunity relies on specialized effector functions elicited by lymphocytes, yet how antigen recognition activates appropriate effector responses through nonspecific signaling intermediates is unclear. Here we examined the role of chromatin priming in specifying the functional outputs of effector T cells and found that most of the cis-regulatory landscape active in effector T cells was poised early in development before the expression of the T cell antigen receptor. We identified two principal mechanisms underpinning this poised landscape: the recruitment of the nucleosome remodeler mammalian SWItch/Sucrose Non-Fermentable (mSWI/SNF) by the transcription factors RUNX1 and PU.1 to establish chromatin accessibility at T effector loci; and a 'relay' whereby the transcription factor BCL11B succeeded PU.1 to maintain occupancy of the chromatin remodeling complex mSWI/SNF together with RUNX1, after PU.1 silencing during lineage commitment. These mechanisms define modes by which T cells acquire the potential to elicit specialized effector functions early in their ontogeny and underscore the importance of integrating extrinsic cues to the developmentally specified intrinsic program.
Collapse
Affiliation(s)
- Noah Gamble
- Department of Pathology, University of Chicago, Chicago, IL, USA
- Graduate Program in Biophysical Sciences, University of Chicago, Chicago, IL, USA
| | - Alexandra Bradu
- Department of Pathology, University of Chicago, Chicago, IL, USA
| | - Jason A Caldwell
- Department of Pathology, University of Chicago, Chicago, IL, USA
| | - Joshua McKeever
- Department of Pathology, University of Chicago, Chicago, IL, USA
- Committee on Molecular Metabolism and Nutrition, University of Chicago, Chicago, IL, USA
| | - Olubusayo Bolonduro
- Department of Pathology, University of Chicago, Chicago, IL, USA
- Committee on Genetics, Genomics, Systems Biology, University of Chicago, Chicago, IL, USA
| | - Ebru Ermis
- Department of Pathology, University of Chicago, Chicago, IL, USA
| | - Caroline Kaiser
- Department of Pathology, University of Chicago, Chicago, IL, USA
- Department of Human Genetics, University of Chicago, Chicago, IL, USA
| | - YeEun Kim
- Immunology Program, Stanford University, Stanford, CA, USA
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Benjamin Parks
- Department of Genetics, Stanford University, Stanford, CA, USA
- Department of Computer Science, Stanford University, Stanford, CA, USA
| | - Sandy Klemm
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - William J Greenleaf
- Department of Computer Science, Stanford University, Stanford, CA, USA
- Department of Applied Physics, Stanford University, Stanford, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Gerald R Crabtree
- Department of Pathology, Stanford University, Stanford, CA, USA
- Department of Developmental Biology, Stanford University, Stanford, CA, USA
| | - Andrew S Koh
- Department of Pathology, University of Chicago, Chicago, IL, USA.
- Institute for Biophysical Dynamics, University of Chicago, Chicago, IL, USA.
| |
Collapse
|
4
|
Andersson E, Rothenberg EV, Peterson C, Olariu V. T-cell commitment inheritance-an agent-based multi-scale model. NPJ Syst Biol Appl 2024; 10:40. [PMID: 38632273 PMCID: PMC11024127 DOI: 10.1038/s41540-024-00368-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Accepted: 04/08/2024] [Indexed: 04/19/2024] Open
Abstract
T-cell development provides an excellent model system for studying lineage commitment from a multipotent progenitor. The intrathymic development process has been thoroughly studied. The molecular circuitry controlling it has been dissected and the necessary steps like programmed shut off of progenitor genes and T-cell genes upregulation have been revealed. However, the exact timing between decision-making and commitment stage remains unexplored. To this end, we implemented an agent-based multi-scale model to investigate inheritance in early T-cell development. Treating each cell as an agent provides a powerful tool as it tracks each individual cell of a simulated T-cell colony, enabling the construction of lineage trees. Based on the lineage trees, we introduce the concept of the last common ancestors (LCA) of committed cells and analyse their relations, both at single-cell level and population level. In addition to simulating wild-type development, we also conduct knockdown analysis. Our simulations predicted that the commitment is a three-step process that occurs on average over several cell generations once a cell is first prepared by a transcriptional switch. This is followed by the loss of the Bcl11b-opposing function approximately two to three generations later. This is when our LCA analysis indicates that the decision to commit is taken even though in general another one to two generations elapse before the cell actually becomes committed by transitioning to the DN2b state. Our results showed that there is decision inheritance in the commitment mechanism.
Collapse
Affiliation(s)
- Emil Andersson
- Computational Science for Health and Environment, Centre for Environmental and Climate Science, Lund University, Lund, Sweden
| | - Ellen V Rothenberg
- Division of Biology and Biological Engineering, 156-29, California Institute of Technology, Pasadena, CA, 91125, USA
| | - Carsten Peterson
- Computational Science for Health and Environment, Centre for Environmental and Climate Science, Lund University, Lund, Sweden
| | - Victor Olariu
- Computational Science for Health and Environment, Centre for Environmental and Climate Science, Lund University, Lund, Sweden.
| |
Collapse
|
5
|
Wu D, Bi X, Chow KHM. Identification of female-enriched and disease-associated microglia (FDAMic) contributes to sexual dimorphism in late-onset Alzheimer's disease. J Neuroinflammation 2024; 21:1. [PMID: 38178204 PMCID: PMC10765928 DOI: 10.1186/s12974-023-02987-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2023] [Accepted: 12/06/2023] [Indexed: 01/06/2024] Open
Abstract
BACKGROUND Late-onset Alzheimer's disease (LOAD) is the most common form of dementia; it disproportionally affects women in terms of both incidence rates and severity of progression. The cellular and molecular mechanisms underlying this clinical phenomenon remain elusive and ill-defined. METHODS In-depth analyses were performed with multiple human LOAD single-nucleus transcriptome datasets to thoroughly characterize cell populations in the cerebral cortex. ROSMAP bulk human brain tissue transcriptome and DNA methylome datasets were also included for validation. Detailed assessments of microglial cell subpopulations and their relevance to sex-biased changes at the tissue level were performed. Clinical trait associations, cell evolutionary trajectories, and transcription regulon analyses were conducted. RESULTS The relative numbers of functionally defective microglia were aberrantly increased uniquely among affected females. Substratification of the microglia into different subtypes according to their transcriptomic signatures identified a group of female-enriched and disease-associated microglia (FDAMic), the numbers of which were positively associated with disease severity. Phenotypically, these cells exhibit transcriptomic signatures that support active proliferation, MHC class II autoantigen presentation and amyloid-β binding, but they are also likely defective in phagocytosis. FDAMic are likely evolved from female activated response microglia (ARMic) with an APOE4 background and compromised estrogen receptor (ER) signaling that is deemed to be active among most subtypes of microglia. CONCLUSION This study offered important insights at both the cellular and molecular levels into how ER signaling affects microglial heterogeneity and function. FDAMic are associated with more advanced pathologies and severe trends of cognitive decline. Their emergence could, at least in part, explain the phenomenon of greater penetrance of the APOE4 genotype found in females. The biases of FDAMic emergence toward female sex and APOE4 status may also explain why hormone replacement therapy is more effective in APOE4 carriers. The pathologic nature of FDAMic suggests that selective modulations of these cells may help to regain brain neuroimmune homeostasis, serving as a new target for future drug development.
Collapse
Affiliation(s)
- Deng Wu
- School of Life Sciences, Faculty of Science, The Chinese University of Hong Kong, Hong Kong SAR, 999077, China
| | - Xiaoman Bi
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, College of Biomedical Information and Engineering, Hainan Medical University, Haikou, 571199, China
| | - Kim Hei-Man Chow
- School of Life Sciences, Faculty of Science, The Chinese University of Hong Kong, Hong Kong SAR, 999077, China.
- Gerald Choa Neuroscience Institute, The Chinese University of Hong Kong, Hong Kong SAR, 999077, China.
- Nexus of Rare Neurodegenerative Diseases, The Chinese University of Hong Kong, Hong Kong SAR, 999077, China.
| |
Collapse
|
6
|
Wang J, Zhang S, Wang Y, Zhu Y, Xu X, Guo J. RUNX3 pathway signature predicts clinical benefits of immune checkpoint inhibition plus tyrosine kinase inhibition in advanced renal cell carcinoma. BMC Urol 2024; 24:8. [PMID: 38172737 PMCID: PMC10765845 DOI: 10.1186/s12894-023-01356-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 11/01/2023] [Indexed: 01/05/2024] Open
Abstract
BACKGROUND Checkpoint inhibitor immunotherapy plus tyrosine kinase inhibitor (IO/TKI) have been recently recommended as standard first-line therapy for advanced renal cell carcinoma, while no clinical-available biomarker has been applied. This study aimed to investigate the associations between RUNX3 pathway signature and IO/TKI benefits in renal cell carcinoma (RCC). METHODS Two IO/TKI cohorts (ZS-MRCC, JAVELIN-101) and one high-risk localized RCC cohort (ZS-HRRCC) were included. All samples were evaluated by RNA-sequencing, and RUNX Family Transcription Factor 3 (RUNX3) pathway were determined by single sample gene set enrichment analysis. Flow cytometry were applied for immune cell infiltration and function. RESULTS RUNX3 signature was elevated in RCC samples, compared non-tumor tissues (P < 0.001). High-RUNX3 signature was associated with shorter progression-free survival (PFS) in both IO/TKI cohorts (ZS-MRCC cohort, P = 0.025; JAVELIN-101 cohort, P = 0.019). RUNX3 signature also predicted IO/TKI benefit in advanced RCC, compared with TKI monotherapy (interaction p = 0.027). RUNX3 signature was associated with decreased number of GZMB + CD8 + T cells (Spearman's ρ=-0.42, P = 0.006), and increased number of PD1 + CD8 + T cells (Spearman's ρ = 0.29, P = 0.072). Moreover, the integration of RUNX3 signature and GZMB expression showed predictive potential for TKI/IO (log-rank P < 0.001). In addition, the predictive value of RUNX3 signature for IO/TKI benefit was restricted in SETD2-wild type patients (log-rank P < 0.001). Finally, a risk score was established by random forest for IO/TKI benefit, showing remarkable predictive potency (Log-rank P < 0.001). CONCLUSIONS RUNX3 pathway signature could be a potential predictive biomarker for IO/TKI treatment in advanced RCC, for both prognosis and treatment selection between IO/TKI and TKI monotherapy.
Collapse
Affiliation(s)
- Jiajun Wang
- Department of Urology, Zhongshan Hospital, Fudan University, No.180 Fenglin Road, Shanghai, 200032, China
| | - Sihong Zhang
- Department of Urology, Zhongshan Hospital, Fudan University, No.180 Fenglin Road, Shanghai, 200032, China
| | - Ying Wang
- Department of Critical Care Medicine, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Yanjun Zhu
- Department of Urology, Zhongshan Hospital, Fudan University, No.180 Fenglin Road, Shanghai, 200032, China.
| | - Xianglai Xu
- Department of Urology, Zhongshan Hospital, Fudan University, No.180 Fenglin Road, Shanghai, 200032, China.
| | - Jianming Guo
- Department of Urology, Zhongshan Hospital, Fudan University, No.180 Fenglin Road, Shanghai, 200032, China.
| |
Collapse
|
7
|
Yu M, Thorner K, Parameswaran S, Wei W, Yu C, Lin X, Kopan R, Hass MR. The unique function of Runx1 in skeletal muscle differentiation and regeneration is mediated by an ETS interaction domain. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.21.568117. [PMID: 38045385 PMCID: PMC10690193 DOI: 10.1101/2023.11.21.568117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2023]
Abstract
The conserved Runt-related (RUNX) transcription factor family are well-known master regulators of developmental and regenerative processes. Runx1 and Runx2 are both expressed in satellite cells (SC) and skeletal myotubes. Conditional deletion of Runx1 in adult SC negatively impacted self-renewal and impaired skeletal muscle maintenance. Runx1- deficient SC retain Runx2 expression but cannot support muscle regeneration in response to injury. To determine the unique molecular functions of Runx1 that cannot be compensated by Runx2 we deleted Runx1 in C2C12 that retain Runx2 expression and established that myoblasts differentiation was blocked in vitro due in part to ectopic expression of Mef2c, a target repressed by Runx1 . Structure-function analysis demonstrated that the Ets-interacting MID/EID region of Runx1, absent from Runx2, is critical to regulating myoblasts proliferation, differentiation, and fusion. Analysis of in-house and published ChIP-seq datasets from Runx1 (T-cells, muscle) versus Runx2 (preosteoblasts) dependent tissue identified enrichment for a Ets:Runx composite site in Runx1 -dependent tissues. Comparing ATACseq datasets from WT and Runx1KO C2C12 cells showed that the Ets:Runx composite motif was enriched in peaks open exclusively in WT cells compared to peaks unique to Runx1KO cells. Thus, engagement of a set of targets by the RUNX1/ETS complex define the non-redundant functions of Runx1 .
Collapse
|
8
|
Spolski R, Li P, Chandra V, Shin B, Goel S, Sakamoto K, Liu C, Oh J, Ren M, Enomoto Y, West EE, Christensen SM, Wan ECK, Ge M, Lin JX, Yan B, Kazemian M, Yu ZX, Nagao K, Vijayanand P, Rothenberg EV, Leonard WJ. Distinct use of super-enhancer elements controls cell type-specific CD25 transcription and function. Sci Immunol 2023; 8:eadi8217. [PMID: 37922339 PMCID: PMC10832512 DOI: 10.1126/sciimmunol.adi8217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Accepted: 10/10/2023] [Indexed: 11/05/2023]
Abstract
The IL-2 receptor α chain (IL-2Rα/CD25) is constitutively expressed on double-negative (DN2/DN3 thymocytes and regulatory T cells (Tregs) but induced by IL-2 on T and natural killer (NK) cells, with Il2ra expression regulated by a STAT5-dependent super-enhancer. We investigated CD25 regulation and function using a series of mice with deletions spanning STAT5-binding elements. Deleting the upstream super-enhancer region mainly affected constitutive CD25 expression on DN2/DN3 thymocytes and Tregs, with these mice developing autoimmune alopecia, whereas deleting an intronic region decreased IL-2-induced CD25 on peripheral T and NK cells. Thus, distinct super-enhancer elements preferentially control constitutive versus inducible expression in a cell type-specific manner. The mediator-1 coactivator colocalized with specific STAT5-binding sites. Moreover, both upstream and intronic regions had extensive chromatin interactions, and deletion of either region altered the super-enhancer structure in mature T cells. These results demonstrate differential functions for distinct super-enhancer elements, thereby indicating previously unknown ways to manipulate CD25 expression in a cell type-specific fashion.
Collapse
Affiliation(s)
- Rosanne Spolski
- Laboratory of Molecular Immunology, Immunology Center, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Peng Li
- Laboratory of Molecular Immunology, Immunology Center, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Vivek Chandra
- La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Boyoung Shin
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Shubham Goel
- Cutaneous Leukocyte Biology Section, Dermatology Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Keiko Sakamoto
- Cutaneous Leukocyte Biology Section, Dermatology Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD, USA
- Hamamatsu University School of Medicine, Department of Dermatology, Hamamatsu, Japan
| | - Chengyu Liu
- Laboratory of Molecular Immunology, Immunology Center, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Jangsuk Oh
- Laboratory of Molecular Immunology, Immunology Center, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Min Ren
- Laboratory of Molecular Immunology, Immunology Center, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Yutaka Enomoto
- Laboratory of Molecular Immunology, Immunology Center, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Erin E West
- Laboratory of Molecular Immunology, Immunology Center, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Stephen M Christensen
- Laboratory of Molecular Immunology, Immunology Center, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Edwin C K Wan
- Laboratory of Molecular Immunology, Immunology Center, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Meili Ge
- Laboratory of Molecular Immunology, Immunology Center, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Jian-Xin Lin
- Laboratory of Molecular Immunology, Immunology Center, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Bingyu Yan
- Department of Biochemistry, Purdue University, West Lafayette, IN, USA
| | - Majid Kazemian
- Department of Biochemistry, Purdue University, West Lafayette, IN, USA
| | - Zu-Xi Yu
- Pathology Core, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Keisuke Nagao
- Cutaneous Leukocyte Biology Section, Dermatology Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD, USA
| | | | - Ellen V Rothenberg
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Warren J Leonard
- Laboratory of Molecular Immunology, Immunology Center, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| |
Collapse
|
9
|
Goldman N, Chandra A, Johnson I, Sullivan MA, Patil AR, Vanderbeck A, Jay A, Zhou Y, Ferrari EK, Mayne L, Aguilan J, Xue HH, Faryabi RB, John Wherry E, Sidoli S, Maillard I, Vahedi G. Intrinsically disordered domain of transcription factor TCF-1 is required for T cell developmental fidelity. Nat Immunol 2023; 24:1698-1710. [PMID: 37592014 PMCID: PMC10919931 DOI: 10.1038/s41590-023-01599-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 07/20/2023] [Indexed: 08/19/2023]
Abstract
In development, pioneer transcription factors access silent chromatin to reveal lineage-specific gene programs. The structured DNA-binding domains of pioneer factors have been well characterized, but whether and how intrinsically disordered regions affect chromatin and control cell fate is unclear. Here, we report that deletion of an intrinsically disordered region of the pioneer factor TCF-1 (termed L1) leads to an early developmental block in T cells. The few T cells that develop from progenitors expressing TCF-1 lacking L1 exhibit lineage infidelity distinct from the lineage diversion of TCF-1-deficient cells. Mechanistically, L1 is required for activation of T cell genes and repression of GATA2-driven genes, normally reserved to the mast cell and dendritic cell lineages. Underlying this lineage diversion, L1 mediates binding of TCF-1 to its earliest target genes, which are subject to repression as T cells develop. These data suggest that the intrinsically disordered N terminus of TCF-1 maintains T cell lineage fidelity.
Collapse
Affiliation(s)
- Naomi Goldman
- Department of Genetics, University of Pennsylvania, Philadelphia, Philadelphia, PA, USA
- Institute for Immunology and Immune Health, University of Pennsylvania, Philadelphia, Philadelphia, PA, USA
- Epigenetics Institute, University of Pennsylvania, Philadelphia, Philadelphia, PA, USA
| | - Aditi Chandra
- Department of Genetics, University of Pennsylvania, Philadelphia, Philadelphia, PA, USA
- Institute for Immunology and Immune Health, University of Pennsylvania, Philadelphia, Philadelphia, PA, USA
- Epigenetics Institute, University of Pennsylvania, Philadelphia, Philadelphia, PA, USA
| | - Isabelle Johnson
- Department of Genetics, University of Pennsylvania, Philadelphia, Philadelphia, PA, USA
- Institute for Immunology and Immune Health, University of Pennsylvania, Philadelphia, Philadelphia, PA, USA
- Epigenetics Institute, University of Pennsylvania, Philadelphia, Philadelphia, PA, USA
| | - Matthew A Sullivan
- Institute for Immunology and Immune Health, University of Pennsylvania, Philadelphia, Philadelphia, PA, USA
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, Philadelphia, PA, USA
- Graduate Group in Biochemistry and Molecular Biophysics, University of Pennsylvania, Philadelphia, Philadelphia, PA, USA
| | - Abhijeet R Patil
- Department of Genetics, University of Pennsylvania, Philadelphia, Philadelphia, PA, USA
- Institute for Immunology and Immune Health, University of Pennsylvania, Philadelphia, Philadelphia, PA, USA
- Epigenetics Institute, University of Pennsylvania, Philadelphia, Philadelphia, PA, USA
| | - Ashley Vanderbeck
- Institute for Immunology and Immune Health, University of Pennsylvania, Philadelphia, Philadelphia, PA, USA
- Division of Hematology-Oncology, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Philadelphia, PA, USA
| | - Atishay Jay
- Department of Genetics, University of Pennsylvania, Philadelphia, Philadelphia, PA, USA
- Institute for Immunology and Immune Health, University of Pennsylvania, Philadelphia, Philadelphia, PA, USA
- Epigenetics Institute, University of Pennsylvania, Philadelphia, Philadelphia, PA, USA
- Department of Bioengineering, School of Engineering and Applied Sciences, University of Pennsylvania, Philadelphia, Philadelphia, PA, USA
| | - Yeqiao Zhou
- Institute for Immunology and Immune Health, University of Pennsylvania, Philadelphia, Philadelphia, PA, USA
- Epigenetics Institute, University of Pennsylvania, Philadelphia, Philadelphia, PA, USA
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, Philadelphia, PA, USA
| | - Emily K Ferrari
- Department of Genetics, University of Pennsylvania, Philadelphia, Philadelphia, PA, USA
- Institute for Immunology and Immune Health, University of Pennsylvania, Philadelphia, Philadelphia, PA, USA
- Epigenetics Institute, University of Pennsylvania, Philadelphia, Philadelphia, PA, USA
| | - Leland Mayne
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Philadelphia, PA, USA
| | - Jennifer Aguilan
- Department of Biochemistry, Albert Einstein School of Medicine, New York City, NY, USA
| | - Hai-Hui Xue
- Center for Discovery and Innovation, Hackensack University Medical Center, Nutley, NJ, USA
- New Jersey Veterans Affairs Health Care System, East Orange, NJ, USA
| | - Robert B Faryabi
- Institute for Immunology and Immune Health, University of Pennsylvania, Philadelphia, Philadelphia, PA, USA
- Epigenetics Institute, University of Pennsylvania, Philadelphia, Philadelphia, PA, USA
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, Philadelphia, PA, USA
| | - E John Wherry
- Institute for Immunology and Immune Health, University of Pennsylvania, Philadelphia, Philadelphia, PA, USA
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, Philadelphia, PA, USA
- Institute for Diabetes, Obesity and Metabolism, University of Pennsylvania, Philadelphia, Philadelphia, PA, USA
- Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Philadelphia, PA, USA
| | - Simone Sidoli
- Department of Biochemistry, Albert Einstein School of Medicine, New York City, NY, USA
| | - Ivan Maillard
- Institute for Immunology and Immune Health, University of Pennsylvania, Philadelphia, Philadelphia, PA, USA
- Division of Hematology-Oncology, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Philadelphia, PA, USA
- Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Philadelphia, PA, USA
| | - Golnaz Vahedi
- Department of Genetics, University of Pennsylvania, Philadelphia, Philadelphia, PA, USA.
- Institute for Immunology and Immune Health, University of Pennsylvania, Philadelphia, Philadelphia, PA, USA.
- Epigenetics Institute, University of Pennsylvania, Philadelphia, Philadelphia, PA, USA.
- Institute for Diabetes, Obesity and Metabolism, University of Pennsylvania, Philadelphia, Philadelphia, PA, USA.
- Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Philadelphia, PA, USA.
| |
Collapse
|
10
|
Shin B, Zhou W, Wang J, Gao F, Rothenberg EV. Runx factors launch T cell and innate lymphoid programs via direct and gene network-based mechanisms. Nat Immunol 2023; 24:1458-1472. [PMID: 37563311 PMCID: PMC10673614 DOI: 10.1038/s41590-023-01585-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 07/12/2023] [Indexed: 08/12/2023]
Abstract
Runx factors are essential for lineage specification of various hematopoietic cells, including T lymphocytes. However, they regulate context-specific genes and occupy distinct genomic regions in different cell types. Here, we show that dynamic Runx binding shifts in mouse early T cell development are mostly not restricted by local chromatin state but regulated by Runx dosage and functional partners. Runx cofactors compete to recruit a limited pool of Runx factors in early T progenitor cells, and a modest increase in Runx protein availability at pre-commitment stages causes premature Runx occupancy at post-commitment binding sites. This increased Runx factor availability results in striking T cell lineage developmental acceleration by selectively activating T cell-identity and innate lymphoid cell programs. These programs are collectively regulated by Runx together with other, Runx-induced transcription factors that co-occupy Runx-target genes and propagate gene network changes.
Collapse
Affiliation(s)
- Boyoung Shin
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Wen Zhou
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
- Program in Biochemistry and Molecular Biophysics, California Institute of Technology, Pasadena, CA, USA
- BillionToOne, Menlo Park, CA, USA
| | - Jue Wang
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
- Program in Biochemistry and Molecular Biophysics, California Institute of Technology, Pasadena, CA, USA
| | - Fan Gao
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
- Bioinformatics Resource Center, Beckman Institute of California Institute of Technology, Pasadena, CA, USA
- Lyterian Therapeutics, South San Francisco, CA, USA
| | - Ellen V Rothenberg
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA.
| |
Collapse
|
11
|
Lowenstein ED, Ruffault PL, Misios A, Osman KL, Li H, Greenberg RS, Thompson R, Song K, Dietrich S, Li X, Vladimirov N, Woehler A, Brunet JF, Zampieri N, Kühn R, Liberles SD, Jia S, Lewin GR, Rajewsky N, Lever TE, Birchmeier C. Prox2 and Runx3 vagal sensory neurons regulate esophageal motility. Neuron 2023; 111:2184-2200.e7. [PMID: 37192624 DOI: 10.1016/j.neuron.2023.04.025] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 10/31/2022] [Accepted: 04/24/2023] [Indexed: 05/18/2023]
Abstract
Vagal sensory neurons monitor mechanical and chemical stimuli in the gastrointestinal tract. Major efforts are underway to assign physiological functions to the many distinct subtypes of vagal sensory neurons. Here, we use genetically guided anatomical tracing, optogenetics, and electrophysiology to identify and characterize vagal sensory neuron subtypes expressing Prox2 and Runx3 in mice. We show that three of these neuronal subtypes innervate the esophagus and stomach in regionalized patterns, where they form intraganglionic laminar endings. Electrophysiological analysis revealed that they are low-threshold mechanoreceptors but possess different adaptation properties. Lastly, genetic ablation of Prox2 and Runx3 neurons demonstrated their essential roles for esophageal peristalsis in freely behaving mice. Our work defines the identity and function of the vagal neurons that provide mechanosensory feedback from the esophagus to the brain and could lead to better understanding and treatment of esophageal motility disorders.
Collapse
Affiliation(s)
- Elijah D Lowenstein
- Developmental Biology/Signal Transduction, Max Delbrück Center for Molecular Medicine, Berlin, Germany; NeuroCure Cluster of Excellence, CharitéUniversitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Pierre-Louis Ruffault
- Developmental Biology/Signal Transduction, Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Aristotelis Misios
- Developmental Biology/Signal Transduction, Max Delbrück Center for Molecular Medicine, Berlin, Germany; NeuroCure Cluster of Excellence, CharitéUniversitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany; Systems Biology of Gene Regulatory Elements, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Kate L Osman
- Department of Otolaryngology - Head & Neck Surgery, University of Missouri School of Medicine, Columbia, MO, USA
| | - Huimin Li
- The First Affiliated Hospital, Jinan University, Guangzhou, China
| | - Rachel S Greenberg
- Howard Hughes Medical Institute, Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Rebecca Thompson
- Department of Otolaryngology - Head & Neck Surgery, University of Missouri School of Medicine, Columbia, MO, USA
| | - Kun Song
- Developmental Biology/Signal Transduction, Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Stephan Dietrich
- Development and Function of Neural Circuits, Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Xun Li
- Immune Regulation and Cancer, Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Nikita Vladimirov
- Systems Biology Imaging, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Andrew Woehler
- Systems Biology Imaging, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Jean-François Brunet
- Institut de Biologie de l'ENS (IBENS), Inserm, CNRS, École normale supérieure, PSL Research University, Paris, France
| | - Niccolò Zampieri
- Development and Function of Neural Circuits, Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Ralf Kühn
- Genome Engineering & Disease Models, Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Stephen D Liberles
- Howard Hughes Medical Institute, Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Shiqi Jia
- The First Affiliated Hospital, Jinan University, Guangzhou, China
| | - Gary R Lewin
- Molecular Physiology of Somatic Sensation, Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Nikolaus Rajewsky
- Systems Biology of Gene Regulatory Elements, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Teresa E Lever
- Department of Otolaryngology - Head & Neck Surgery, University of Missouri School of Medicine, Columbia, MO, USA
| | - Carmen Birchmeier
- Developmental Biology/Signal Transduction, Max Delbrück Center for Molecular Medicine, Berlin, Germany; NeuroCure Cluster of Excellence, CharitéUniversitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany.
| |
Collapse
|
12
|
Deichmann U. Self-Organization and Genomic Causality in Models of Morphogenesis. ENTROPY (BASEL, SWITZERLAND) 2023; 25:873. [PMID: 37372217 DOI: 10.3390/e25060873] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 05/25/2023] [Accepted: 05/26/2023] [Indexed: 06/29/2023]
Abstract
The debate about what causes the generation of form and structure in embryological development goes back to antiquity. Most recently, it has focused on the divergent views as to whether the generation of patterns and form in development is a largely self-organized process or is mainly determined by the genome, in particular, complex developmental gene regulatory processes. This paper presents and analyzes pertinent models of pattern formation and form generation in a developing organism in the past and the present, with a special emphasis on Alan Turing's 1952 reaction-diffusion model. I first draw attention to the fact that Turing's paper remained, at first, without a noticeable impact on the community of biologists because purely physical-chemical models were unable to explain embryological development and often also simple repetitive patterns. I then show that from the year 2000 and onwards, Turing's 1952 paper was increasingly cited also by biologists. The model was updated to include gene products and now seemed able to account for the generation of biological patterns, though discrepancies between models and biological reality remained. I then point out Eric Davidson's successful theory of early embryogenesis based on gene-regulatory network analysis and its mathematical modeling that not only was able to provide a mechanistic and causal explanation for gene regulatory events controlling developmental cell fate specification but, unlike reaction-diffusion models, also addressed the effects of evolution and organisms' longstanding developmental and species stability. The paper concludes with an outlook on further developments of the gene regulatory network model.
Collapse
Affiliation(s)
- Ute Deichmann
- The Jacques Loeb Centre for the History and Philosophy of the Life Sciences, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel
| |
Collapse
|
13
|
MacNabb BW, Rothenberg EV. Speed and navigation control of thymocyte development by the fetal T-cell gene regulatory network. Immunol Rev 2023; 315:171-196. [PMID: 36722494 PMCID: PMC10771342 DOI: 10.1111/imr.13190] [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] [Indexed: 02/02/2023]
Abstract
T-cell differentiation is a tightly regulated developmental program governed by interactions between transcription factors (TFs) and chromatin landscapes and affected by signals received from the thymic stroma. This process is marked by a series of checkpoints: T-lineage commitment, T-cell receptor (TCR)β selection, and positive and negative selection. Dynamically changing combinations of TFs drive differentiation along the T-lineage trajectory, through mechanisms that have been most extensively dissected in adult mouse T-lineage cells. However, fetal T-cell development differs from adult in ways that suggest that these TF mechanisms are not fully deterministic. The first wave of fetal T-cell differentiation occurs during a unique developmental window during thymic morphogenesis, shows more rapid kinetics of differentiation with fewer rounds of cell division, and gives rise to unique populations of innate lymphoid cells (ILCs) and invariant γδT cells that are not generated in the adult thymus. As the characteristic kinetics and progeny biases are cell-intrinsic properties of thymic progenitors, the differences could be based on distinct TF network circuitry within the progenitors themselves. Here, we review recent single-cell transcriptome data that illuminate the TF networks involved in T-cell differentiation in the fetal and adult mouse thymus.
Collapse
Affiliation(s)
- Brendan W MacNabb
- Division of Biology & Biological Engineering, California Institute of Technology, Pasadena, California, USA
| | - Ellen V Rothenberg
- Division of Biology & Biological Engineering, California Institute of Technology, Pasadena, California, USA
| |
Collapse
|
14
|
Shin B, Rothenberg EV. Multi-modular structure of the gene regulatory network for specification and commitment of murine T cells. Front Immunol 2023; 14:1108368. [PMID: 36817475 PMCID: PMC9928580 DOI: 10.3389/fimmu.2023.1108368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2022] [Accepted: 01/11/2023] [Indexed: 02/04/2023] Open
Abstract
T cells develop from multipotent progenitors by a gradual process dependent on intrathymic Notch signaling and coupled with extensive proliferation. The stages leading them to T-cell lineage commitment are well characterized by single-cell and bulk RNA analyses of sorted populations and by direct measurements of precursor-product relationships. This process depends not only on Notch signaling but also on multiple transcription factors, some associated with stemness and multipotency, some with alternative lineages, and others associated with T-cell fate. These factors interact in opposing or semi-independent T cell gene regulatory network (GRN) subcircuits that are increasingly well defined. A newly comprehensive picture of this network has emerged. Importantly, because key factors in the GRN can bind to markedly different genomic sites at one stage than they do at other stages, the genes they significantly regulate are also stage-specific. Global transcriptome analyses of perturbations have revealed an underlying modular structure to the T-cell commitment GRN, separating decisions to lose "stem-ness" from decisions to block alternative fates. Finally, the updated network sheds light on the intimate relationship between the T-cell program, which depends on the thymus, and the innate lymphoid cell (ILC) program, which does not.
Collapse
Affiliation(s)
- Boyoung Shin
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, United States
| | - Ellen V. Rothenberg
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, United States
| |
Collapse
|
15
|
Yu G, Chen Y, Hu Y, Zhou Y, Ding X, Zhou X. Roles of transducin-like enhancer of split (TLE) family proteins in tumorigenesis and immune regulation. Front Cell Dev Biol 2022; 10:1010639. [PMID: 36438567 PMCID: PMC9692235 DOI: 10.3389/fcell.2022.1010639] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 10/31/2022] [Indexed: 08/16/2023] Open
Abstract
Mammalian transducin-like enhancer of split family proteins (TLEs) are homologous to Drosophila Groucho (Gro) and are essential transcriptional repressors. Seven TLE family members, TLE1-7, have been identified to date. These proteins do not bind DNA directly; instead, they bind a set of transcription factors and thereby inhibit target gene expression. Loss of TLEs in mice usually leads to defective early development; however, TLE functions in developmentally mature cells are unclear. Recent studies have revealed that TLEs are dysregulated in certain human cancer types and may function as oncogenes or tumor suppressors in different contexts. TLE levels also affect the efficacy of cancer treatments and the development of drug resistance. In addition, TLEs play critical roles in the development and function of immune cells, including macrophages and lymphocytes. In this review, we provide updates on the expression, function, and mechanism of TLEs; discuss the roles played by TLEs in tumorigenesis and the inflammatory response; and elaborate on several TLE-associated signaling pathways, including the Notch, Wnt, and MAPK pathways. Finally, we discuss potential strategies for targeting TLEs in cancer therapy.
Collapse
Affiliation(s)
- Guiping Yu
- Department of Immunology, Nantong University, School of Medicine, Nantong, China
- Department of Cardiothoracic Surgery, The Affiliated Jiangyin Hospital of Nantong University, Jiangyin, China
| | - Yiqi Chen
- Department of Immunology, Nantong University, School of Medicine, Nantong, China
| | - Yuwen Hu
- Department of Immunology, Nantong University, School of Medicine, Nantong, China
| | - Yan Zhou
- Department of Periodontology, The Affiliated Nantong Stomatological Hospital of Nantong University, Nantong, China
| | - Xiaoling Ding
- Department of Gastroenterology, The Affiliated Hospital of Nantong University, Nantong, China
| | - Xiaorong Zhou
- Department of Immunology, Nantong University, School of Medicine, Nantong, China
| |
Collapse
|
16
|
Koizumi M, Kama Y, Hirano KI, Endo Y, Tanaka T, Hozumi K, Hosokawa H. Transcription factor Zbtb1 interacts with bridging factor Lmo2 and maintains the T-lineage differentiation capacity of lymphoid progenitor cells. J Biol Chem 2022; 298:102506. [PMID: 36126774 PMCID: PMC9582733 DOI: 10.1016/j.jbc.2022.102506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 09/13/2022] [Accepted: 09/15/2022] [Indexed: 11/19/2022] Open
Abstract
Hematopoietic stem and progenitor cells can differentiate into all types of blood cells. Regulatory mechanisms underlying pluripotency in progenitors, such as the ability of lymphoid progenitor cells to differentiate into T-lineage, remain unclear. We have previously reported that LIM domain only 2 (Lmo2), a bridging factor in large transcriptional complexes, is essential to retain the ability of lymphoid progenitors to differentiate into T-lineage. However, biochemical characterization of Lmo2 protein complexes in physiological hematopoietic progenitors remains obscure. Here, we identified approximately 600 Lmo2-interacting molecules in a lymphoid progenitor cell line by two-step affinity purification with LC-MS/MS analysis. Zinc finger and BTB domain containing 1 (Zbtb1) and CBFA2/RUNX1 partner transcriptional corepressor 3 (Cbfa2t3) were found to be the functionally important binding partners of Lmo2. We determined CRISPR/Cas9-mediated acute disruption of Zbtb1 or Cbfa2t3 in the lymphoid progenitor or bone marrow–derived primary hematopoietic progenitor cells causes significant defects in the initiation of T-cell development when Notch signaling is activated. Our transcriptome analysis of Zbtb1- or Cbfa2t3-deficient lymphoid progenitors revealed that Tcf7 was a common target for both factors. Additionally, ChIP-seq analysis showed that Lmo2, Zbtb1, and Cbfa2t3 cobind to the Tcf7 upstream enhancer region, which is occupied by the Notch intracellular domain/RBPJ transcriptional complex after Notch stimulation, in lymphoid progenitors. Moreover, transduction with Tcf7 restored the defect in the T-lineage potential of Zbtb1-deficient lymphoid progenitors. Thus, in lymphoid progenitors, the Lmo2/Zbtb1/Cbfa2t3 complex directly binds to the Tcf7 locus and maintains responsiveness to the Notch-mediated inductive signaling to facilitate T-lineage differentiation.
Collapse
Affiliation(s)
- Maria Koizumi
- Department of Immunology, Tokai University School of Medicine, Isehara, Kanagawa, Japan
| | - Yuichi Kama
- Department of Immunology, Tokai University School of Medicine, Isehara, Kanagawa, Japan
| | - Ken-Ichi Hirano
- Department of Immunology, Tokai University School of Medicine, Isehara, Kanagawa, Japan
| | - Yusuke Endo
- Laboratory of Medical Omics Research, Kazusa DNA Research Institute, Chiba, Japan; Department of Omics Medicine, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Tomoaki Tanaka
- Department of Molecular Diagnosis, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Katsuto Hozumi
- Department of Immunology, Tokai University School of Medicine, Isehara, Kanagawa, Japan
| | - Hiroyuki Hosokawa
- Department of Immunology, Tokai University School of Medicine, Isehara, Kanagawa, Japan; Institute of Medical Sciences, Tokai University, Isehara, Kanagawa, Japan.
| |
Collapse
|
17
|
Wang W, Meng Y, Chen Y, Yu Y, Wang H, Yang S, Sun W. A comprehensive analysis of LMO2 pathogenic regulatory profile during T-lineage development and leukemic transformation. Oncogene 2022; 41:4079-4090. [PMID: 35851847 DOI: 10.1038/s41388-022-02414-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 07/06/2022] [Accepted: 07/08/2022] [Indexed: 11/08/2022]
Abstract
LMO2 is a well-known leukemic proto-oncogene, its ectopic expression in T-lineage specifically initiates malignant transformation of immature T cells and ultimately causes the onset of acute T-lymphocytic leukemia (T-ALL) in both mouse models and human patients. In this study, we systematically explored the LMO2 performance on the profiles of transcriptome, DNA-binding and protein interactions during T-lineage development in the pre-leukemic stage. Our data indicated that large-scale transcriptional dysregulation caused by LMO2 primarily occurred in DN3 thymocytes, characterized by enriched upregulation of the target genes of typical LMO2 complex, RUNX, ETS and STATs, and ectopic LMO2 primarily targeted to RUNX motifs along with intensive interaction with RUNX1 and H3K4 methyltransferase component ASH2L in this stage. However, binding of LMO2 on specific motifs was largely reduced in the following DP and SP stages, along with gradually disappeared LMO2-RUNX1 and LMO2-ASH2L interactions and less alteration of certain transcriptional factor profiles. Moreover, LMO2 showed relatively less influence on cellular behavior of DN3 thymocyte whereas displayed more prominent effects in DP and SP stages, including promoting Notch signaling and cell cycles. These findings provide a high-resolution landscape of the pathogenic role of LMO2 during T-lineage development in molecular level, and may benefit further clinical investigations for LMO2-associated T-lineage malignancies.
Collapse
Affiliation(s)
- Wenhao Wang
- School of Medicine, Nankai University, Tianjin, China
| | - Yingying Meng
- School of Medicine, Nankai University, Tianjin, China
| | - Yaxin Chen
- School of Medicine, Nankai University, Tianjin, China
| | - Yanhong Yu
- School of Medicine, Nankai University, Tianjin, China
| | - Hang Wang
- School of Medicine, Nankai University, Tianjin, China
| | - Shuang Yang
- School of Medicine, Nankai University, Tianjin, China
| | - Wei Sun
- School of Medicine, Nankai University, Tianjin, China.
| |
Collapse
|
18
|
Fonseca R, Burn TN, Gandolfo LC, Devi S, Park SL, Obers A, Evrard M, Christo SN, Buquicchio FA, Lareau CA, McDonald KM, Sandford SK, Zamudio NM, Zanluqui NG, Zaid A, Speed TP, Satpathy AT, Mueller SN, Carbone FR, Mackay LK. Runx3 drives a CD8 + T cell tissue residency program that is absent in CD4 + T cells. Nat Immunol 2022; 23:1236-1245. [PMID: 35882933 DOI: 10.1038/s41590-022-01273-4] [Citation(s) in RCA: 47] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 06/17/2022] [Indexed: 11/09/2022]
Abstract
Tissue-resident memory T cells (TRM cells) provide rapid and superior control of localized infections. While the transcription factor Runx3 is a critical regulator of CD8+ T cell tissue residency, its expression is repressed in CD4+ T cells. Here, we show that, as a direct consequence of this Runx3-deficiency, CD4+ TRM cells lacked the transforming growth factor (TGF)-β-responsive transcriptional network that underpins the tissue residency of epithelial CD8+ TRM cells. While CD4+ TRM cell formation required Runx1, this, along with the modest expression of Runx3 in CD4+ TRM cells, was insufficient to engage the TGF-β-driven residency program. Ectopic expression of Runx3 in CD4+ T cells incited this TGF-β-transcriptional network to promote prolonged survival, decreased tissue egress, a microanatomical redistribution towards epithelial layers and enhanced effector functionality. Thus, our results reveal distinct programming of tissue residency in CD8+ and CD4+ TRM cell subsets that is attributable to divergent Runx3 activity.
Collapse
Affiliation(s)
- Raíssa Fonseca
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Thomas N Burn
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Luke C Gandolfo
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
- School of Mathematics and Statistics, The University of Melbourne, Melbourne, Victoria, Australia
- Walter and Eliza Hall Institute for Medical Research, Parkville, Victoria, Australia
| | - Sapna Devi
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Simone L Park
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Andreas Obers
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Maximilien Evrard
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Susan N Christo
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Frank A Buquicchio
- Department of Pathology, Stanford University, Stanford, CA, USA
- Program in Immunology, Stanford University, Stanford, CA, USA
| | - Caleb A Lareau
- Department of Pathology, Stanford University, Stanford, CA, USA
- Program in Immunology, Stanford University, Stanford, CA, USA
| | - Keely M McDonald
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Sarah K Sandford
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Natasha M Zamudio
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Nagela G Zanluqui
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
- Department of Immunology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Ali Zaid
- Menzies Health Institute Queensland, Griffith University, Gold Coast Campus, Southport, Queensland, Australia
| | - Terence P Speed
- School of Mathematics and Statistics, The University of Melbourne, Melbourne, Victoria, Australia
- Walter and Eliza Hall Institute for Medical Research, Parkville, Victoria, Australia
| | - Ansuman T Satpathy
- Department of Pathology, Stanford University, Stanford, CA, USA
- Program in Immunology, Stanford University, Stanford, CA, USA
- Parker Institute for Cancer Immunotherapy, Stanford University, Stanford, CA, USA
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
| | - Scott N Mueller
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Francis R Carbone
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Laura K Mackay
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia.
| |
Collapse
|
19
|
Hertweck A, Vila de Mucha M, Barber PR, Dagil R, Porter H, Ramos A, Lord GM, Jenner RG. The TH1 cell lineage-determining transcription factor T-bet suppresses TH2 gene expression by redistributing GATA3 away from TH2 genes. Nucleic Acids Res 2022; 50:4557-4573. [PMID: 35438764 PMCID: PMC9071441 DOI: 10.1093/nar/gkac258] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 03/28/2022] [Accepted: 04/13/2022] [Indexed: 11/12/2022] Open
Abstract
Lineage-determining transcription factors (LD-TFs) drive the differentiation of progenitor cells into a specific lineage. In CD4+ T cells, T-bet dictates differentiation of the TH1 lineage, whereas GATA3 drives differentiation of the alternative TH2 lineage. However, LD-TFs, including T-bet and GATA3, are frequently co-expressed but how this affects LD-TF function is not known. By expressing T-bet and GATA3 separately or together in mouse T cells, we show that T-bet sequesters GATA3 at its target sites, thereby removing GATA3 from TH2 genes. This redistribution of GATA3 is independent of GATA3 DNA binding activity and is instead mediated by the T-bet DNA binding domain, which interacts with the GATA3 DNA binding domain and changes GATA3's sequence binding preference. This mechanism allows T-bet to drive the TH1 gene expression program in the presence of GATA3. We propose that redistribution of one LD-TF by another may be a common mechanism that could explain how specific cell fate choices can be made even in the presence of other transcription factors driving alternative differentiation pathways.
Collapse
Affiliation(s)
- Arnulf Hertweck
- UCL Cancer Institute and Cancer Research UK UCL Centre, University College London (UCL), London, WC1E 6BT, UK
| | - Maria Vila de Mucha
- UCL Cancer Institute and Cancer Research UK UCL Centre, University College London (UCL), London, WC1E 6BT, UK
| | - Paul R Barber
- UCL Cancer Institute and Cancer Research UK UCL Centre, University College London (UCL), London, WC1E 6BT, UK.,Comprehensive Cancer Centre, School of Cancer & Pharmaceutical Sciences, King's College London, London, SE1 1UL, UK
| | - Robert Dagil
- Research Department of Structural and Molecular Biology, University College London, Darwin Building, Gower Street, London, WC1E 6XA, UK
| | - Hayley Porter
- UCL Cancer Institute and Cancer Research UK UCL Centre, University College London (UCL), London, WC1E 6BT, UK
| | - Andres Ramos
- Research Department of Structural and Molecular Biology, University College London, Darwin Building, Gower Street, London, WC1E 6XA, UK
| | - Graham M Lord
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester, M13 9NT, UK
| | - Richard G Jenner
- UCL Cancer Institute and Cancer Research UK UCL Centre, University College London (UCL), London, WC1E 6BT, UK
| |
Collapse
|
20
|
Miller RM, Jordan BT, Mehlferber MM, Jeffery ED, Chatzipantsiou C, Kaur S, Millikin RJ, Dai Y, Tiberi S, Castaldi PJ, Shortreed MR, Luckey CJ, Conesa A, Smith LM, Deslattes Mays A, Sheynkman GM. Enhanced protein isoform characterization through long-read proteogenomics. Genome Biol 2022; 23:69. [PMID: 35241129 PMCID: PMC8892804 DOI: 10.1186/s13059-022-02624-y] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 02/02/2022] [Indexed: 02/04/2023] Open
Abstract
BACKGROUND The detection of physiologically relevant protein isoforms encoded by the human genome is critical to biomedicine. Mass spectrometry (MS)-based proteomics is the preeminent method for protein detection, but isoform-resolved proteomic analysis relies on accurate reference databases that match the sample; neither a subset nor a superset database is ideal. Long-read RNA sequencing (e.g., PacBio or Oxford Nanopore) provides full-length transcripts which can be used to predict full-length protein isoforms. RESULTS We describe here a long-read proteogenomics approach for integrating sample-matched long-read RNA-seq and MS-based proteomics data to enhance isoform characterization. We introduce a classification scheme for protein isoforms, discover novel protein isoforms, and present the first protein inference algorithm for the direct incorporation of long-read transcriptome data to enable detection of protein isoforms previously intractable to MS-based detection. We have released an open-source Nextflow pipeline that integrates long-read sequencing in a proteomic workflow for isoform-resolved analysis. CONCLUSIONS Our work suggests that the incorporation of long-read sequencing and proteomic data can facilitate improved characterization of human protein isoform diversity. Our first-generation pipeline provides a strong foundation for future development of long-read proteogenomics and its adoption for both basic and translational research.
Collapse
Affiliation(s)
- Rachel M Miller
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Ben T Jordan
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA, USA
| | - Madison M Mehlferber
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA, USA
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, USA
| | - Erin D Jeffery
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA, USA
| | | | - Simi Kaur
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Robert J Millikin
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Yunxiang Dai
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Simone Tiberi
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
- Swiss Institute of Bioinformatics, University of Zurich, Zurich, Switzerland
| | - Peter J Castaldi
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Division of General Medicine and Primary Care, Brigham and Women's Hospital, Boston, MA, USA
| | | | - Chance John Luckey
- Department of Pathology, University of Virginia, Charlottesville, VA, USA
| | - Ana Conesa
- Institute for Integrative Systems Biology, Spanish National Research Council (CSIC), Paterna, Spain
- Microbiology and Cell Science Department, Institute for Food and Agricultural Sciences, University of Florida, Gainesville, FL, USA
| | - Lloyd M Smith
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Anne Deslattes Mays
- Office of Data Science and Sharing, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Rockville, MD, USA
| | - Gloria M Sheynkman
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA, USA.
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA.
- UVA Cancer Center, University of Virginia, Charlottesville, VA, USA.
| |
Collapse
|
21
|
Parsing the transcription factors governing T cell immunity. Nat Immunol 2021; 23:3-4. [PMID: 34937931 DOI: 10.1038/s41590-021-01075-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
|
22
|
Zhong Y, Walker SK, Pritykin Y, Leslie CS, Rudensky AY, van der Veeken J. Hierarchical regulation of the resting and activated T cell epigenome by major transcription factor families. Nat Immunol 2021; 23:122-134. [PMID: 34937932 PMCID: PMC8712421 DOI: 10.1038/s41590-021-01086-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Accepted: 11/02/2021] [Indexed: 12/24/2022]
Abstract
T cell activation, a key early event in the adaptive immune response, is subject to elaborate transcriptional control. Here, we examined how the activities of eight major transcription factor (TF) families are integrated to shape the epigenome of naïve and activated CD4 and CD8 T cells. By leveraging extensive polymorphisms in evolutionarily divergent mice, we identified the “heavy lifters” positively influencing chromatin accessibility. Members of Ets, Runx, and TCF/Lef TF families occupied the vast majority of accessible chromatin regions, acting as “housekeepers”, “universal amplifiers”, and “placeholders”, respectively, at sites that maintained or gained accessibility upon T cell activation. Additionally, a small subset of strongly induced immune response genes displayed a non-canonical TF recruitment pattern. Our study provides a key resource and foundation for the understanding of transcriptional and epigenetic regulation in T cells and offers a new perspective on the hierarchical interactions between critical TFs.
Collapse
|
23
|
Duah M, Li L, Shen J, Lan Q, Pan B, Xu K. Thymus Degeneration and Regeneration. Front Immunol 2021; 12:706244. [PMID: 34539637 PMCID: PMC8442952 DOI: 10.3389/fimmu.2021.706244] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 08/16/2021] [Indexed: 01/08/2023] Open
Abstract
The immune system’s ability to resist the invasion of foreign pathogens and the tolerance to self-antigens are primarily centered on the efficient functions of the various subsets of T lymphocytes. As the primary organ of thymopoiesis, the thymus performs a crucial role in generating a self-tolerant but diverse repertoire of T cell receptors and peripheral T cell pool, with the capacity to recognize a wide variety of antigens and for the surveillance of malignancies. However, cells in the thymus are fragile and sensitive to changes in the external environment and acute insults such as infections, chemo- and radiation-therapy, resulting in thymic injury and degeneration. Though the thymus has the capacity to self-regenerate, it is often insufficient to reconstitute an intact thymic function. Thymic dysfunction leads to an increased risk of opportunistic infections, tumor relapse, autoimmunity, and adverse clinical outcome. Thus, exploiting the mechanism of thymic regeneration would provide new therapeutic options for these settings. This review summarizes the thymus’s development, factors causing thymic injury, and the strategies for improving thymus regeneration.
Collapse
Affiliation(s)
- Maxwell Duah
- Department of Hematology, The Affiliated Hospital of Xuzhou Medical University, Xuzhou Medical University, Xuzhou, China.,Blood Diseases Institute, Xuzhou Medical University, Xuzhou, China
| | - Lingling Li
- Department of Hematology, The Affiliated Hospital of Xuzhou Medical University, Xuzhou Medical University, Xuzhou, China.,Blood Diseases Institute, Xuzhou Medical University, Xuzhou, China
| | - Jingyi Shen
- Department of Hematology, The Affiliated Hospital of Xuzhou Medical University, Xuzhou Medical University, Xuzhou, China.,Blood Diseases Institute, Xuzhou Medical University, Xuzhou, China
| | - Qiu Lan
- Department of Hematology, The Affiliated Hospital of Xuzhou Medical University, Xuzhou Medical University, Xuzhou, China.,Blood Diseases Institute, Xuzhou Medical University, Xuzhou, China
| | - Bin Pan
- Department of Hematology, The Affiliated Hospital of Xuzhou Medical University, Xuzhou Medical University, Xuzhou, China.,Blood Diseases Institute, Xuzhou Medical University, Xuzhou, China
| | - Kailin Xu
- Department of Hematology, The Affiliated Hospital of Xuzhou Medical University, Xuzhou Medical University, Xuzhou, China.,Blood Diseases Institute, Xuzhou Medical University, Xuzhou, China
| |
Collapse
|
24
|
Gao L, Zhou F. Comprehensive Analysis of RUNX and TGF-β Mediated Regulation of Immune Cell Infiltration in Breast Cancer. Front Cell Dev Biol 2021; 9:730380. [PMID: 34485309 PMCID: PMC8416425 DOI: 10.3389/fcell.2021.730380] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Accepted: 07/28/2021] [Indexed: 01/05/2023] Open
Abstract
Runt-related transcription factors (RUNXs) can serve as both transcription activators and repressors during biological development, including immune cell maturation. RUNX factors have both tumor-promoting and tumor-suppressive roles in carcinogenesis. Immune cell infiltration and the tumor immune microenvironment have been found to be key regulators in breast cancer progression, treatment response, and patient outcome. However, the relationship between the RUNX family and immune cell infiltration in breast cancer remains unclear. We performed a comprehensive analysis to reveal the role of RUNX factors in breast cancer. Analysis of patient data in the Oncomine database showed that the transcriptional levels of RUNX proteins in breast cancer were elevated. Kaplan–Meier plotter (KM plotter) analysis showed that breast cancer patients with higher expression of RUNX proteins had better survival outcomes. Through analysis of the UALCAN database, we found that the transcriptional levels of RUNX factors were significantly correlated with some breast cancer patient characteristics. cBio Cancer Genomics Portal (cBioPortal) analysis showed the proportions of different RUNX genomic alterations in various subclasses of breast cancer. We also performed gene ontology (GO) and pathway analyses for the significantly differentially expressed genes that were correlated with RUNX factors in breast cancer. TIMER database analysis showed that immune cell infiltration in breast cancer could be affected by the transcriptional level, mutation, and gene copy number of RUNX proteins. Using the Gene Set Cancer Analysis (GSCA) database, we analyzed the effects of RUNX gene methylation on the level of immune cell infiltration in breast cancer. We found that the methylation level changes of RUNX2 and RUNX3 had opposite effects on immune cell infiltration in breast cancer. We also analyzed the relationship between the methylation level of RUNX genes and the TGF-β signaling pathway using the TISIDB database. The results showed that the methylation levels of RUNX1 and RUNX3 were correlated with the expression of TGF-β1. In summary, our analysis found that the RUNX family members can influence the infiltration of various immune cells in breast cancer depending on their expression level, mutation, gene copy number, and methylation. The RUNX family is an important regulator of immune cell infiltration in breast cancer and may serve as a potential prognostic biomarker.
Collapse
Affiliation(s)
- Liang Gao
- Institutes of Biology and Medical Sciences, Soochow University, Suzhou, China
| | - Fangfang Zhou
- Institutes of Biology and Medical Sciences, Soochow University, Suzhou, China
| |
Collapse
|
25
|
Hirano KI, Hosokawa H, Koizumi M, Endo Y, Yahata T, Ando K, Hozumi K. LMO2 is essential to maintain the ability of progenitors to differentiate into T-cell lineage in mice. eLife 2021; 10:e68227. [PMID: 34382935 PMCID: PMC8360648 DOI: 10.7554/elife.68227] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Accepted: 07/31/2021] [Indexed: 12/20/2022] Open
Abstract
Notch signaling primarily determines T-cell fate. However, the molecular mechanisms underlying the maintenance of T-lineage potential in pre-thymic progenitors remain unclear. Here, we established two murine Ebf1-deficient pro-B cell lines, with and without T-lineage potential. The latter expressed lower levels of Lmo2; their potential was restored via ectopic expression of Lmo2. Conversely, the CRISPR/Cas9-mediated deletion of Lmo2 resulted in the loss of the T-lineage potential. Introduction of Bcl2 rescued massive cell death of Notch-stimulated pro-B cells without efficient LMO2-driven Bcl11a expression but was not sufficient to retain their T-lineage potential. Pro-B cells without T-lineage potential failed to activate Tcf7 due to DNA methylation; Tcf7 transduction restored this capacity. Moreover, direct binding of LMO2 to the Bcl11a and Tcf7 loci was observed. Altogether, our results highlight LMO2 as a crucial player in the survival and maintenance of T-lineage potential in T-cell progenitors via the regulation of the expression of Bcl11a and Tcf7.
Collapse
Affiliation(s)
- Ken-ichi Hirano
- Department of Immunology, Tokai University School of MedicineIseharaJapan
| | - Hiroyuki Hosokawa
- Department of Immunology, Tokai University School of MedicineIseharaJapan
- Institute of Medical Sciences, Tokai UniversityIseharaJapan
| | - Maria Koizumi
- Department of Immunology, Tokai University School of MedicineIseharaJapan
| | - Yusuke Endo
- Laboratory of Medical Omics Research, Kazusa DNA Research InstituteKisarazuJapan
- Department of Omics Medicine, Graduate School of Medicine, Chiba UniversityChibaJapan
| | - Takashi Yahata
- Institute of Medical Sciences, Tokai UniversityIseharaJapan
- Department of Innovative Medical Science, Tokai University School of MedicineIseharaJapan
| | - Kiyoshi Ando
- Institute of Medical Sciences, Tokai UniversityIseharaJapan
- Department of Hematology and Oncology, Tokai University School of MedicineIseharaJapan
| | - Katsuto Hozumi
- Department of Immunology, Tokai University School of MedicineIseharaJapan
| |
Collapse
|
26
|
Hosokawa H, Koizumi M, Masuhara K, Romero-Wolf M, Tanaka T, Nakayama T, Rothenberg EV. Stage-specific action of Runx1 and GATA3 controls silencing of PU.1 expression in mouse pro-T cells. J Exp Med 2021; 218:e20202648. [PMID: 34180951 PMCID: PMC8241539 DOI: 10.1084/jem.20202648] [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: 12/11/2020] [Revised: 05/01/2021] [Accepted: 06/10/2021] [Indexed: 12/16/2022] Open
Abstract
PU.1 (encoded by Spi1), an ETS-family transcription factor with many hematopoietic roles, is highly expressed in the earliest intrathymic T cell progenitors but must be down-regulated during T lineage commitment. The transcription factors Runx1 and GATA3 have been implicated in this Spi1 repression, but the basis of the timing was unknown. We show that increasing Runx1 and/or GATA3 down-regulates Spi1 expression in pro-T cells, while deletion of these factors after Spi1 down-regulation reactivates its expression. Leveraging the stage specificities of repression and transcription factor binding revealed an unconventional but functional site in Spi1 intron 2. Acute Cas9-mediated deletion or disruption of the Runx and GATA motifs in this element reactivates silenced Spi1 expression in a pro-T cell line, substantially more than disruption of other candidate elements, and counteracts the repression of Spi1 in primary pro-T cells during commitment. Thus, Runx1 and GATA3 work stage specifically through an intronic silencing element in mouse Spi1 to control strength and maintenance of Spi1 repression during T lineage commitment.
Collapse
Affiliation(s)
- Hiroyuki Hosokawa
- Department of Immunology, Tokai University School of Medicine, Isehara, Kanagawa, Japan
- Institute of Medical Sciences, Tokai University, Isehara, Kanagawa, Japan
- Division of Biology & Biological Engineering, California Institute of Technology, Pasadena, CA
| | - Maria Koizumi
- Department of Immunology, Tokai University School of Medicine, Isehara, Kanagawa, Japan
| | - Kaori Masuhara
- Department of Immunology, Tokai University School of Medicine, Isehara, Kanagawa, Japan
| | - Maile Romero-Wolf
- Division of Biology & Biological Engineering, California Institute of Technology, Pasadena, CA
| | - Tomoaki Tanaka
- Department of Molecular Diagnosis, Graduate School of Medicine, Chiba University, Chuo-ku, Chiba, Japan
| | - Toshinori Nakayama
- Department of Immunology, Graduate School of Medicine, Chiba University, Chuo-ku, Chiba, Japan
| | - Ellen V Rothenberg
- Division of Biology & Biological Engineering, California Institute of Technology, Pasadena, CA
| |
Collapse
|
27
|
ThymUS in times of stress. Nat Immunol 2021; 22:545-549. [PMID: 33692548 DOI: 10.1038/s41590-021-00897-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
|
28
|
Lefeivre T, Jones L, Trinquand A, Pinton A, Macintyre E, Laurenti E, Bond J. Immature acute leukaemias: lessons from the haematopoietic roadmap. FEBS J 2021; 289:4355-4370. [PMID: 34028982 DOI: 10.1111/febs.16030] [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: 02/02/2021] [Revised: 04/30/2021] [Accepted: 05/20/2021] [Indexed: 11/29/2022]
Abstract
It is essential to relate the biology of acute leukaemia to normal blood cell development. In this review, we discuss how modern models of haematopoiesis might inform approaches to diagnosis and management of immature leukaemias, with a specific focus on T-lymphoid and myeloid cases. In particular, we consider whether next-generation analytical tools could provide new perspectives that could improve our understanding of immature blood cancer biology.
Collapse
Affiliation(s)
- Thomas Lefeivre
- Systems Biology Ireland, School of Medicine, University College Dublin, Dublin, Ireland.,National Children's Research Centre, Dublin, Ireland
| | - Luke Jones
- Systems Biology Ireland, School of Medicine, University College Dublin, Dublin, Ireland.,National Children's Research Centre, Dublin, Ireland
| | - Amélie Trinquand
- National Children's Research Centre, Dublin, Ireland.,Children's Health Ireland at Crumlin, Dublin, Ireland
| | - Antoine Pinton
- Laboratory of Onco-Haematology, Assistance Publique-Hôpitaux de Paris (AP-HP), Hôpital Necker Enfants-Malades, Université de Paris, Paris, France.,Institut Necker-Enfants Malades (INEM), Institut national de la santé et de la recherche médicale (Inserm) U1151, Paris, France
| | - Elizabeth Macintyre
- Laboratory of Onco-Haematology, Assistance Publique-Hôpitaux de Paris (AP-HP), Hôpital Necker Enfants-Malades, Université de Paris, Paris, France.,Institut Necker-Enfants Malades (INEM), Institut national de la santé et de la recherche médicale (Inserm) U1151, Paris, France
| | - Elisa Laurenti
- Department of Haematology, University of Cambridge, Cambridge, UK.,Wellcome and MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Jonathan Bond
- Systems Biology Ireland, School of Medicine, University College Dublin, Dublin, Ireland.,National Children's Research Centre, Dublin, Ireland.,Children's Health Ireland at Crumlin, Dublin, Ireland
| |
Collapse
|
29
|
Chiara VD, Daxinger L, Staal FJT. The Route of Early T Cell Development: Crosstalk between Epigenetic and Transcription Factors. Cells 2021; 10:1074. [PMID: 33946533 PMCID: PMC8147249 DOI: 10.3390/cells10051074] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 04/25/2021] [Accepted: 04/26/2021] [Indexed: 12/21/2022] Open
Abstract
Hematopoietic multipotent progenitors seed the thymus and then follow consecutive developmental stages until the formation of mature T cells. During this process, phenotypic changes of T cells entail stage-specific transcriptional programs that underlie the dynamic progression towards mature lymphocytes. Lineage-specific transcription factors are key drivers of T cell specification and act in conjunction with epigenetic regulators that have also been elucidated as crucial players in the establishment of regulatory networks necessary for proper T cell development. In this review, we summarize the activity of transcription factors and epigenetic regulators that together orchestrate the intricacies of early T cell development with a focus on regulation of T cell lineage commitment.
Collapse
Affiliation(s)
- Veronica Della Chiara
- Department of Human Genetics, Leiden University Medical Centre (LUMC), 2300 RC Leiden, The Netherlands; (V.D.C.); (L.D.)
| | - Lucia Daxinger
- Department of Human Genetics, Leiden University Medical Centre (LUMC), 2300 RC Leiden, The Netherlands; (V.D.C.); (L.D.)
| | - Frank J. T. Staal
- Department of Immunology, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
| |
Collapse
|
30
|
Sidwell T, Rothenberg EV. Epigenetic Dynamics in the Function of T-Lineage Regulatory Factor Bcl11b. Front Immunol 2021; 12:669498. [PMID: 33936112 PMCID: PMC8079813 DOI: 10.3389/fimmu.2021.669498] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 03/23/2021] [Indexed: 11/18/2022] Open
Abstract
The transcription factor Bcl11b is critically required to support the development of diverse cell types, including T lymphocytes, type 2 innate lymphoid cells, neurons, craniofacial mesenchyme and keratinocytes. Although in T cell development its onset of expression is tightly linked to T-lymphoid lineage commitment, the Bcl11b protein in fact regulates substantially different sets of genes in different lymphocyte populations, playing strongly context-dependent roles. Somewhat unusually for lineage-defining transcription factors with site-specific DNA binding activity, much of the reported chromatin binding of Bcl11b appears to be indirect, or guided in large part by interactions with other transcription factors. We describe evidence suggesting that a further way in which Bcl11b exerts such distinct stage-dependent functions is by nucleating changes in regional suites of epigenetic modifications through recruitment of multiple families of chromatin-modifying enzyme complexes. Herein we explore what is - and what remains to be - understood of the roles of Bcl11b, its cofactors, and how it modifies the epigenetic state of the cell to enforce its diverse set of context-specific transcriptional and developmental programs.
Collapse
Affiliation(s)
- Tom Sidwell
- Division of Biology & Biological Engineering, California Institute of Technology, Pasadena, CA, United States
| | - Ellen V Rothenberg
- Division of Biology & Biological Engineering, California Institute of Technology, Pasadena, CA, United States
| |
Collapse
|
31
|
Rothenberg EV. Logic and lineage impacts on functional transcription factor deployment for T-cell fate commitment. Biophys J 2021; 120:4162-4181. [PMID: 33838137 PMCID: PMC8516641 DOI: 10.1016/j.bpj.2021.04.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Revised: 03/22/2021] [Accepted: 04/02/2021] [Indexed: 11/19/2022] Open
Abstract
Transcription factors are the major agents that read the regulatory sequence information in the genome to initiate changes in expression of specific genes, both in development and in physiological activation responses. Their actions depend on site-specific DNA binding and are largely guided by their individual DNA target sequence specificities. However, their action is far more conditional in a real developmental context than would be expected for simple reading of local genomic DNA sequence, which is common to all cells in the organism. They are constrained by slow-changing chromatin states and by interactions with other transcription factors, which affect their occupancy patterns of potential sites across the genome. These mechanisms lead to emergent discontinuities in function even for transcription factors with minimally changing expression. This is well revealed by diverse lineages of blood cells developing throughout life from hematopoietic stem cells, which use overlapping combinations of transcription factors to drive strongly divergent gene regulation programs. Here, using development of T lymphocytes from hematopoietic multipotent progenitor cells as a focus, recent evidence is reviewed on how binding specificity and dynamics, transcription factor cooperativity, and chromatin state changes impact the effective regulatory functions of key transcription factors including PU.1, Runx1, Notch-RBPJ, and Bcl11b.
Collapse
Affiliation(s)
- Ellen V Rothenberg
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California.
| |
Collapse
|
32
|
Hosokawa H, Masuhara K, Koizumi M. Transcription factors regulate early T cell development via redeployment of other factors: Functional dynamics of constitutively required factors in cell fate decisions. Bioessays 2021; 43:e2000345. [PMID: 33624856 DOI: 10.1002/bies.202000345] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 01/30/2021] [Accepted: 02/08/2021] [Indexed: 01/02/2023]
Abstract
Establishment of cell lineage identity from multipotent progenitors is controlled by cooperative actions of lineage-specific and stably expressed transcription factors, combined with input from environmental signals. Lineage-specific master transcription factors activate and repress gene expression by recruiting consistently expressed transcription factors and chromatin modifiers to their target loci. Recent technical advances in genome-wide and multi-omics analysis have shed light on unexpected mechanisms that underlie more complicated actions of transcription factors in cell fate decisions. In this review, we discuss functional dynamics of stably expressed and continuously required factors, Notch and Runx family members, throughout developmental stages of early T cell development in the thymus. Pre- and post-commitment stage-specific transcription factors induce dynamic redeployment of Notch and Runx binding genomic regions. Thus, together with stage-specific transcription factors, shared transcription factors across distinct developmental stages regulate acquisition of T lineage identity.
Collapse
Affiliation(s)
- Hiroyuki Hosokawa
- Department of Immunology, Tokai University School of Medicine, Isehara, Kanagawa, Japan.,Institute of Medical Sciences, Tokai University, Isehara, Kanagawa, Japan
| | - Kaori Masuhara
- Department of Immunology, Tokai University School of Medicine, Isehara, Kanagawa, Japan
| | - Maria Koizumi
- Department of Immunology, Tokai University School of Medicine, Isehara, Kanagawa, Japan
| |
Collapse
|