1
|
Milner PT, Zhang Z, Herde ZD, Vedire NR, Zhang F, Realff MJ, Wilson CJ. Performance Prediction of Fundamental Transcriptional Programs. ACS Synth Biol 2023; 12:1094-1108. [PMID: 36935615 PMCID: PMC10127286 DOI: 10.1021/acssynbio.2c00593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/21/2023]
Abstract
Transcriptional programming leverages systems of engineered transcription factors to impart decision-making (e.g., Boolean logic) in chassis cells. The number of components used to construct said decision-making systems is rapidly increasing, making an exhaustive experimental evaluation of iterations of biological circuits impractical. Accordingly, we posited that a predictive tool is needed to guide and accelerate the design of transcriptional programs. The work described here involves the development and experimental characterization of a large collection of network-capable single-INPUT logical operations─i.e., engineered BUFFER (repressor) and engineered NOT (antirepressor) logical operations. Using this single-INPUT data and developed metrology, we were able to model and predict the performances of all fundamental two-INPUT compressed logical operations (i.e., compressed AND gates and compressed NOR gates). In addition, we were able to model and predict the performance of compressed mixed phenotype logical operations (A NIMPLY B gates and complementary B NIMPLY A gates). These results demonstrate that single-INPUT data is sufficient to accurately predict both the qualitative and quantitative performance of a complex circuit. Accordingly, this work has set the stage for the predictive design of transcriptional programs of greater complexity.
Collapse
Affiliation(s)
- Prasaad T Milner
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332-2000, United States
| | - Ziqiao Zhang
- School of Electrical and Computer Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332-2000, United States
| | - Zachary D Herde
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332-2000, United States
| | - Namratha R Vedire
- School of Computer Science, Georgia Institute of Technology, Atlanta, Georgia 30332-2000, United States
| | - Fumin Zhang
- School of Electrical and Computer Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332-2000, United States
| | - Matthew J Realff
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332-2000, United States
| | - Corey J Wilson
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332-2000, United States
| |
Collapse
|
2
|
Davies J, Vallejo AF, Sirvent S, Porter G, Clayton K, Qumbelo Y, Stumpf P, West J, Gray CM, Chigorimbo-Murefu NTL, MacArthur B, Polak ME. An IRF1-IRF4 Toggle-Switch Controls Tolerogenic and Immunogenic Transcriptional Programming in Human Langerhans Cells. Front Immunol 2021; 12:665312. [PMID: 34211464 PMCID: PMC8239435 DOI: 10.3389/fimmu.2021.665312] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Accepted: 05/25/2021] [Indexed: 12/27/2022] Open
Abstract
Langerhans cells (LCs) reside in the epidermis as a dense network of immune system sentinels, coordinating both immunogenic and tolerogenic immune responses. To determine molecular switches directing induction of LC immune activation, we performed mathematical modelling of gene regulatory networks identified by single cell RNA sequencing of LCs exposed to TNF-alpha, a key pro-inflammatory signal produced by the skin. Our approach delineated three programmes of LC phenotypic activation (immunogenic, tolerogenic or ambivalent), and confirmed that TNF-alpha enhanced LC immunogenic programming. Through regulon analysis followed by mutual information modelling, we identified IRF1 as the key transcription factor for the regulation of immunogenicity in LCs. Application of a mathematical toggle switch model, coupling IRF1 with tolerance-inducing transcription factors, determined the key set of transcription factors regulating the switch between tolerance and immunogenicity, and correctly predicted LC behaviour in LCs derived from different body sites. Our findings provide a mechanistic explanation of how combinatorial interactions between different transcription factors can coordinate specific transcriptional programmes in human LCs, interpreting the microenvironmental context of the local tissue microenvironments.
Collapse
Affiliation(s)
- James Davies
- Clinical and Experimental Sciences, Sir Henry Wellcome Laboratories, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Andres F Vallejo
- Clinical and Experimental Sciences, Sir Henry Wellcome Laboratories, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Sofia Sirvent
- Clinical and Experimental Sciences, Sir Henry Wellcome Laboratories, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Gemma Porter
- Clinical and Experimental Sciences, Sir Henry Wellcome Laboratories, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Kalum Clayton
- Clinical and Experimental Sciences, Sir Henry Wellcome Laboratories, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Yamkela Qumbelo
- Division of Immunology, Institute of Infectious Disease and Molecular Medicine, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Patrick Stumpf
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, United Kingdom.,Institute for Life Sciences, University of Southampton, Southampton, United Kingdom
| | - Jonathan West
- Cancer Sciences, Faculty of Medicine, University of Southampton, Southampton, United Kingdom.,Institute for Life Sciences, University of Southampton, Southampton, United Kingdom
| | - Clive M Gray
- Division of Immunology, Institute of Infectious Disease and Molecular Medicine, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Nyaradzo T L Chigorimbo-Murefu
- Division of Immunology, Institute of Infectious Disease and Molecular Medicine, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Ben MacArthur
- Cancer Sciences, Faculty of Medicine, University of Southampton, Southampton, United Kingdom.,Institute for Life Sciences, University of Southampton, Southampton, United Kingdom
| | - Marta E Polak
- Clinical and Experimental Sciences, Sir Henry Wellcome Laboratories, Faculty of Medicine, University of Southampton, Southampton, United Kingdom.,Institute for Life Sciences, University of Southampton, Southampton, United Kingdom
| |
Collapse
|
3
|
Tolomeo AM, Laterza C, Grespan E, Michielin F, Canals I, Kokaia Z, Muraca M, Gagliano O, Elvassore N. NGN2 mmRNA-Based Transcriptional Programming in Microfluidic Guides hiPSCs Toward Neural Fate With Multiple Identities. Front Cell Neurosci 2021; 15:602888. [PMID: 33679325 PMCID: PMC7928329 DOI: 10.3389/fncel.2021.602888] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Accepted: 01/18/2021] [Indexed: 01/13/2023] Open
Abstract
Recent advancements in cell engineering have succeeded in manipulating cell identity with the targeted overexpression of specific cell fate determining transcription factors in a process named transcriptional programming. Neurogenin2 (NGN2) is sufficient to instruct pluripotent stem cells (PSCs) to acquire a neuronal identity when delivered with an integrating system, which arises some safety concerns for clinical applications. A non-integrating system based on modified messenger RNA (mmRNA) delivery method, represents a valuable alternative to lentiviral-based approaches. The ability of NGN2 mmRNA to instruct PSC fate change has not been thoroughly investigated yet. Here we aimed at understanding whether the use of an NGN2 mmRNA-based approach combined with a miniaturized system, which allows a higher transfection efficiency in a cost-effective system, is able to drive human induced PSCs (hiPSCs) toward the neuronal lineage. We show that NGN2 mRNA alone is able to induce cell fate conversion. Surprisingly, the outcome cell population accounts for multiple phenotypes along the neural development trajectory. We found that this mixed population is mainly constituted by neural stem cells (45% ± 18 PAX6 positive cells) and neurons (38% ± 8 βIIITUBULIN positive cells) only when NGN2 is delivered as mmRNA. On the other hand, when the delivery system is lentiviral-based, both providing a constant expression of NGN2 or only a transient pulse, the outcome differentiated population is formed by a clear majority of neurons (88% ± 1 βIIITUBULIN positive cells). Altogether, our data confirm the ability of NGN2 to induce neuralization in hiPSCs and opens a new point of view in respect to the delivery system method when it comes to transcriptional programming applications.
Collapse
Affiliation(s)
- Anna Maria Tolomeo
- Department of Industrial Engineering, University of Padua, Padua, Italy.,L.i.f.e.L.a.b. Program, Consorzio per la Ricerca Sanitaria (CORIS), Padua, Italy
| | - Cecilia Laterza
- Department of Industrial Engineering, University of Padua, Padua, Italy.,L.i.f.e.L.a.b. Program, Consorzio per la Ricerca Sanitaria (CORIS), Padua, Italy.,Veneto Institute of Molecular Medicine, Padua, Italy
| | - Eleonora Grespan
- Institute of Neuroscience, National Research Council, Padua, Italy
| | - Federica Michielin
- Department of Industrial Engineering, University of Padua, Padua, Italy.,Veneto Institute of Molecular Medicine, Padua, Italy
| | - Isaac Canals
- Stem Cells, Aging and Neurodegeneration Group, Lund Stem Cell Center, Lund University, Lund, Sweden
| | - Zaal Kokaia
- Laboratory of Stem Cells and Restorative Neurology, Lund Stem Cell Center, Lund University, Lund, Sweden
| | - Maurizio Muraca
- L.i.f.e.L.a.b. Program, Consorzio per la Ricerca Sanitaria (CORIS), Padua, Italy.,Department of Women's and Children's Health, Faculty of Medicine, University of Padua, Padua, Italy
| | - Onelia Gagliano
- Department of Industrial Engineering, University of Padua, Padua, Italy.,L.i.f.e.L.a.b. Program, Consorzio per la Ricerca Sanitaria (CORIS), Padua, Italy.,Veneto Institute of Molecular Medicine, Padua, Italy
| | - Nicola Elvassore
- Department of Industrial Engineering, University of Padua, Padua, Italy.,L.i.f.e.L.a.b. Program, Consorzio per la Ricerca Sanitaria (CORIS), Padua, Italy.,Veneto Institute of Molecular Medicine, Padua, Italy
| |
Collapse
|
4
|
Ridgley LA, Anderson AE, Maney NJ, Naamane N, Skelton AJ, Lawson CA, Emery P, Isaacs JD, Carmody RJ, Pratt AG. IL-6 Mediated Transcriptional Programming of Naïve CD4+ T Cells in Early Rheumatoid Arthritis Drives Dysregulated Effector Function. Front Immunol 2019; 10:1535. [PMID: 31333666 PMCID: PMC6618050 DOI: 10.3389/fimmu.2019.01535] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Accepted: 06/19/2019] [Indexed: 12/27/2022] Open
Abstract
Objective: We have previously shown that increased circulating interleukin-6 (IL-6) results in enhanced CD4+ T cell signaling via signal transduction and activator of transcription-3 (STAT3) in early rheumatoid arthritis (RA). We tested the hypothesis that transcriptional “imprinting” of T-cells by this mechanism skews downstream effector responses, reinforcing immune dysregulation at a critical, but targetable, disease phase. Methods: We modeled naïve CD4+ T cell exposure to pathophysiological concentrations of IL-6 in vitro, assessing the dynamic transcriptional and functional consequences for downstream effector cells utilizing microarray and flow cytometry. Fresh blood from treatment-naïve early arthritis patients was phenotyped in parallel for comparison. Results: T cell sensitivity to IL-6 was most marked in the naïve subset, and related to gp130 rather than IL-6R expression. Exposure of healthy naïve CD4+ T cells to IL-6 induced the same STAT3 target genes as previously seen to discriminate RA patients from disease controls. After TCR stimulation IL-6 pre-exposed cells exhibited enhanced proliferative capacity, activation, and a propensity toward Th1 differentiation, compared to non-exposed cells. An entirely analogous phenotype was observed in early RA compared to control CD4+ T cells. Conclusions: Sustained IL-6 exposure at a critical point in the natural history of RA “primes” the adaptive immune system to respond aberrantly to TCR stimulation, potentiating disease induction with implications for the optimal timing of targeted therapy.
Collapse
Affiliation(s)
- Laura A Ridgley
- Institute of Cellular Medicine (Musculoskeletal Research Group), Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Amy E Anderson
- Institute of Cellular Medicine (Musculoskeletal Research Group), Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Nicola J Maney
- Institute of Cellular Medicine (Musculoskeletal Research Group), Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Najib Naamane
- Institute of Cellular Medicine (Musculoskeletal Research Group), Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Andrew J Skelton
- Institute of Cellular Medicine (Musculoskeletal Research Group), Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Catherine A Lawson
- Leeds Institute of Rheumatic and Musculoskeletal Medicine, Chapel Allerton Hospital, University of Leeds, Leeds, United Kingdom.,Leeds NIHR Biomedical Research Centre, The Leeds Teaching Hospitals Trust, Leeds, United Kingdom
| | - Paul Emery
- Leeds Institute of Rheumatic and Musculoskeletal Medicine, Chapel Allerton Hospital, University of Leeds, Leeds, United Kingdom.,Leeds NIHR Biomedical Research Centre, The Leeds Teaching Hospitals Trust, Leeds, United Kingdom
| | - John D Isaacs
- Institute of Cellular Medicine (Musculoskeletal Research Group), Newcastle University, Newcastle upon Tyne, United Kingdom.,Directorate of Musculoskeletal Services, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, United Kingdom
| | - Ruaidhrí J Carmody
- Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, United Kingdom
| | - Arthur G Pratt
- Institute of Cellular Medicine (Musculoskeletal Research Group), Newcastle University, Newcastle upon Tyne, United Kingdom.,Directorate of Musculoskeletal Services, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, United Kingdom
| |
Collapse
|
5
|
Arends T, Dege C, Bortnick A, Danhorn T, Knapp JR, Jia H, Harmacek L, Fleenor CJ, Straign D, Walton K, Leach SM, Feeney AJ, Murre C, O'Connor BP, Hagman JR. CHD4 is essential for transcriptional repression and lineage progression in B lymphopoiesis. Proc Natl Acad Sci U S A 2019; 116:10927-10936. [PMID: 31085655 PMCID: PMC6561196 DOI: 10.1073/pnas.1821301116] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Cell lineage specification is a tightly regulated process that is dependent on appropriate expression of lineage and developmental stage-specific transcriptional programs. Here, we show that Chromodomain Helicase DNA-binding protein 4 (CHD4), a major ATPase/helicase subunit of Nucleosome Remodeling and Deacetylase Complexes (NuRD) in lymphocytes, is essential for specification of the early B cell lineage transcriptional program. In the absence of CHD4 in B cell progenitors in vivo, development of these cells is arrested at an early pro-B-like stage that is unresponsive to IL-7 receptor signaling and unable to efficiently complete V(D)J rearrangements at Igh loci. Our studies confirm that chromatin accessibility and transcription of thousands of gene loci are controlled dynamically by CHD4 during early B cell development. Strikingly, CHD4-deficient pro-B cells express transcripts of many non-B cell lineage genes, including genes that are characteristic of other hematopoietic lineages, neuronal cells, and the CNS, lung, pancreas, and other cell types. We conclude that CHD4 inhibits inappropriate transcription in pro-B cells. Together, our data demonstrate the importance of CHD4 in establishing and maintaining an appropriate transcriptome in early B lymphopoiesis via chromatin accessibility.
Collapse
Affiliation(s)
- Tessa Arends
- Program in Molecular Biology, University of Colorado Denver, Aurora, CO 80045
| | - Carissa Dege
- Department of Immunology and Microbiology, University of Colorado Denver, Aurora, CO 80045
| | - Alexandra Bortnick
- Section of Molecular Biology, University of California, San Diego, La Jolla, CA 92093
| | - Thomas Danhorn
- Center for Genes, Environment, and Health, National Jewish Health, Denver, CO 80206
| | - Jennifer R Knapp
- Center for Genes, Environment, and Health, National Jewish Health, Denver, CO 80206
| | - Haiqun Jia
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037
| | - Laura Harmacek
- Center for Genes, Environment, and Health, National Jewish Health, Denver, CO 80206
| | - Courtney J Fleenor
- Department of Biomedical Research, National Jewish Health, Denver, CO 80206
| | - Desiree Straign
- Department of Biomedical Research, National Jewish Health, Denver, CO 80206
| | - Kendra Walton
- Center for Genes, Environment, and Health, National Jewish Health, Denver, CO 80206
| | - Sonia M Leach
- Center for Genes, Environment, and Health, National Jewish Health, Denver, CO 80206
- Department of Biomedical Research, National Jewish Health, Denver, CO 80206
| | - Ann J Feeney
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037
| | - Cornelis Murre
- Section of Molecular Biology, University of California, San Diego, La Jolla, CA 92093
| | - Brian P O'Connor
- Department of Immunology and Microbiology, University of Colorado Denver, Aurora, CO 80045
- Center for Genes, Environment, and Health, National Jewish Health, Denver, CO 80206
- Department of Biomedical Research, National Jewish Health, Denver, CO 80206
| | - James R Hagman
- Program in Molecular Biology, University of Colorado Denver, Aurora, CO 80045;
- Department of Immunology and Microbiology, University of Colorado Denver, Aurora, CO 80045
- Department of Biomedical Research, National Jewish Health, Denver, CO 80206
| |
Collapse
|