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Wang J, Watson JL, Lisanza SL. Protein Design Using Structure-Prediction Networks: AlphaFold and RoseTTAFold as Protein Structure Foundation Models. Cold Spring Harb Perspect Biol 2024; 16:a041472. [PMID: 38438190 PMCID: PMC11216169 DOI: 10.1101/cshperspect.a041472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/06/2024]
Abstract
Designing proteins with tailored structures and functions is a long-standing goal in bioengineering. Recently, deep learning advances have enabled protein structure prediction at near-experimental accuracy, which has catalyzed progress in protein design as well. We review recent studies that use structure-prediction neural networks to design proteins, via approaches such as activation maximization, inpainting, or denoising diffusion. These methods have led to major improvements over previous methods in wet-lab success rates for designing protein binders, metalloproteins, enzymes, and oligomeric assemblies. These results show that structure-prediction models are a powerful foundation for developing protein-design tools and suggest that continued improvement of their accuracy and generality will be key to unlocking the full potential of protein design.
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Affiliation(s)
- Jue Wang
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA
- Institute for Protein Design, University of Washington, Seattle, Washington 98195, USA
- Graduate Program in Biological Physics, Structure and Design, University of Washington, Seattle, Washington 98195, USA
- DeepMind, London EC4A 3BF, United Kingdom
| | - Joseph L Watson
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA
- Institute for Protein Design, University of Washington, Seattle, Washington 98195, USA
| | - Sidney L Lisanza
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA
- Institute for Protein Design, University of Washington, Seattle, Washington 98195, USA
- Graduate Program in Biological Physics, Structure and Design, University of Washington, Seattle, Washington 98195, USA
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2
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Verdura S, Encinar JA, Gratchev A, Llop-Hernández À, López J, Serrano-Hervás E, Teixidor E, López-Bonet E, Martin-Castillo B, Micol V, Bosch-Barrera J, Cuyàs E, Menendez JA. Silibinin is a suppressor of the metastasis-promoting transcription factor ID3. PHYTOMEDICINE : INTERNATIONAL JOURNAL OF PHYTOTHERAPY AND PHYTOPHARMACOLOGY 2024; 128:155493. [PMID: 38484626 DOI: 10.1016/j.phymed.2024.155493] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 01/31/2024] [Accepted: 02/26/2024] [Indexed: 05/01/2024]
Abstract
BACKGROUND ID3 (inhibitor of DNA binding/differentiation-3) is a transcription factor that enables metastasis by promoting stem cell-like properties in endothelial and tumor cells. The milk thistle flavonolignan silibinin is a phytochemical with anti-metastatic potential through largely unknown mechanisms. HYPOTHESIS/PURPOSE We have mechanistically investigated the ability of silibinin to inhibit the aberrant activation of ID3 in brain endothelium and non-small cell lung cancer (NSCLC) models. METHODS Bioinformatic analyses were performed to investigate the co-expression correlation between ID3 and bone morphogenic protein (BMP) ligands/BMP receptors (BMPRs) genes in NSCLC patient datasets. ID3 expression was assessed by immunoblotting and qRT-PCR. Luciferase reporter assays were used to evaluate the gene sequences targeted by silibinin to regulate ID3 transcription. In silico computational modeling and LanthaScreen TR-FRET kinase assays were used to characterize and validate the BMPR inhibitory activity of silibinin. Tumor tissues from NSCLC xenograft models treated with oral silibinin were used to evaluate the in vivo anti-ID3 effects of silibinin. RESULTS Analysis of lung cancer patient datasets revealed a top-ranked positive association of ID3 with the BMP9 endothelial receptor ACVRL1/ALK1 and the BMP ligand BMP6. Silibinin treatment blocked the BMP9-induced activation of the ALK1-phospho-SMAD1/5-ID3 axis in brain endothelial cells. Constitutive, acquired, and adaptive expression of ID3 in NSCLC cells were all significantly downregulated in response to silibinin. Silibinin blocked ID3 transcription via BMP-responsive elements in ID3 gene enhancers. Silibinin inhibited the kinase activities of BMPRs in the micromolar range, with the lower IC50 values occurring against ACVRL1/ALK1 and BMPR2. In an in vivo NSCLC xenograft model, tumoral overexpression of ID3 was completely suppressed by systematically achievable oral doses of silibinin. CONCLUSIONS ID3 is a largely undruggable metastasis-promoting transcription factor. Silibinin is a novel suppressor of ID3 that may be explored as a novel therapeutic approach to interfere with the metastatic dissemination capacity of NSCLC.
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Affiliation(s)
- Sara Verdura
- Program Against Cancer Therapeutic Resistance (ProCURE), Catalan Institute of Oncology, Girona, 17007, Spain; Metabolism and Cancer Group, Girona Biomedical Research Institute (IDIBGI), Girona 17190, Spain
| | - José Antonio Encinar
- Institute of Research, Development and Innovation in Health Biotechnology of Elche (IDiBE), Universitas Miguel Hernández (UMH), Elche 03202, Spain
| | - Alexei Gratchev
- Laboratory for Tumor Stromal Cell Biology, Institute of Carcinogenesis, Nikolaj Nikolajevich (N.N.) Blokhin National Medical Research Center of Oncology, Moscow 115478, Russia
| | - Àngela Llop-Hernández
- Program Against Cancer Therapeutic Resistance (ProCURE), Catalan Institute of Oncology, Girona, 17007, Spain; Metabolism and Cancer Group, Girona Biomedical Research Institute (IDIBGI), Girona 17190, Spain
| | - Júlia López
- Program Against Cancer Therapeutic Resistance (ProCURE), Catalan Institute of Oncology, Girona, 17007, Spain; Metabolism and Cancer Group, Girona Biomedical Research Institute (IDIBGI), Girona 17190, Spain
| | - Eila Serrano-Hervás
- Program Against Cancer Therapeutic Resistance (ProCURE), Catalan Institute of Oncology, Girona, 17007, Spain; Metabolism and Cancer Group, Girona Biomedical Research Institute (IDIBGI), Girona 17190, Spain
| | - Eduard Teixidor
- Precision Oncology Group (OncoGir-Pro), Girona Biomedical Research Institute (IDIBGI), Girona 17190, Spain; Medical Oncology, Catalan Institute of Oncology, Girona, 17007, Spain
| | - Eugeni López-Bonet
- Metabolism and Cancer Group, Girona Biomedical Research Institute (IDIBGI), Girona 17190, Spain; Department of Anatomical Pathology, Dr. Josep Trueta Hospital of Girona, Girona 17007, Spain
| | - Begoña Martin-Castillo
- Metabolism and Cancer Group, Girona Biomedical Research Institute (IDIBGI), Girona 17190, Spain; Unit of Clinical Research, Catalan Institute of Oncology, Girona, 17007, Spain
| | - Vicente Micol
- Institute of Research, Development and Innovation in Health Biotechnology of Elche (IDiBE), Universitas Miguel Hernández (UMH), Elche 03202, Spain; CIBER Fisiopatología de la Obesidad y la Nutrición (CIBEROBN), Instituto de Salud Carlos III (ISCIII), Madrid, 28029, Spain
| | - Joaquim Bosch-Barrera
- Precision Oncology Group (OncoGir-Pro), Girona Biomedical Research Institute (IDIBGI), Girona 17190, Spain; Medical Oncology, Catalan Institute of Oncology, Girona, 17007, Spain; Department of Medical Sciences, Medical School, University of Girona, Girona, Spain
| | - Elisabet Cuyàs
- Program Against Cancer Therapeutic Resistance (ProCURE), Catalan Institute of Oncology, Girona, 17007, Spain; Metabolism and Cancer Group, Girona Biomedical Research Institute (IDIBGI), Girona 17190, Spain
| | - Javier A Menendez
- Program Against Cancer Therapeutic Resistance (ProCURE), Catalan Institute of Oncology, Girona, 17007, Spain; Metabolism and Cancer Group, Girona Biomedical Research Institute (IDIBGI), Girona 17190, Spain.
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3
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Li Y, Deng D, Höfer CT, Kim J, Do Heo W, Xu Q, Liu X, Zi Z. Liebig's law of the minimum in the TGF-β/SMAD pathway. PLoS Comput Biol 2024; 20:e1012072. [PMID: 38753874 PMCID: PMC11135686 DOI: 10.1371/journal.pcbi.1012072] [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: 02/14/2024] [Revised: 05/29/2024] [Accepted: 04/11/2024] [Indexed: 05/18/2024] Open
Abstract
Cells use signaling pathways to sense and respond to their environments. The transforming growth factor-β (TGF-β) pathway produces context-specific responses. Here, we combined modeling and experimental analysis to study the dependence of the output of the TGF-β pathway on the abundance of signaling molecules in the pathway. We showed that the TGF-β pathway processes the variation of TGF-β receptor abundance using Liebig's law of the minimum, meaning that the output-modifying factor is the signaling protein that is most limited, to determine signaling responses across cell types and in single cells. We found that the abundance of either the type I (TGFBR1) or type II (TGFBR2) TGF-β receptor determined the responses of cancer cell lines, such that the receptor with relatively low abundance dictates the response. Furthermore, nuclear SMAD2 signaling correlated with the abundance of TGF-β receptor in single cells depending on the relative expression levels of TGFBR1 and TGFBR2. A similar control principle could govern the heterogeneity of signaling responses in other signaling pathways.
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Affiliation(s)
- Yuchao Li
- Max Planck Institute for Molecular Genetics, Otto Warburg Laboratory, Berlin, Germany
| | - Difan Deng
- German Federal Institute for Risk Assessment, Department of Experimental Toxicology and ZEBET, Berlin, Germany
| | - Chris Tina Höfer
- German Federal Institute for Risk Assessment, Department of Experimental Toxicology and ZEBET, Berlin, Germany
| | - Jihye Kim
- Department of Biological Sciences, KAIST Institute for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
| | - Won Do Heo
- Department of Biological Sciences, KAIST Institute for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
| | - Quanbin Xu
- Department of Biochemistry, University of Colorado Boulder, Boulder, Colorado, United States of America
| | - Xuedong Liu
- Department of Biochemistry, University of Colorado Boulder, Boulder, Colorado, United States of America
| | - Zhike Zi
- Max Planck Institute for Molecular Genetics, Otto Warburg Laboratory, Berlin, Germany
- German Federal Institute for Risk Assessment, Department of Experimental Toxicology and ZEBET, Berlin, Germany
- Key Laboratory of Quantitative Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
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4
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Mejias Rivera L, Shore EM, Mourkioti F. Cellular and Molecular Mechanisms of Heterotopic Ossification in Fibrodysplasia Ossificans Progressiva. Biomedicines 2024; 12:779. [PMID: 38672135 PMCID: PMC11048698 DOI: 10.3390/biomedicines12040779] [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: 03/12/2024] [Revised: 03/22/2024] [Accepted: 03/26/2024] [Indexed: 04/28/2024] Open
Abstract
Fibrodysplasia ossificans progressiva (FOP) is a debilitating genetic disorder characterized by recurrent episodes of heterotopic ossification (HO) formation in muscles, tendons, and ligaments. FOP is caused by a missense mutation in the ACVR1 gene (activin A receptor type I), an important signaling receptor involved in endochondral ossification. The ACVR1R206H mutation induces increased downstream canonical SMAD-signaling and drives tissue-resident progenitor cells with osteogenic potential to participate in endochondral HO formation. In this article, we review aberrant ACVR1R206H signaling and the cells that give rise to HO in FOP. FOP mouse models and lineage tracing analyses have been used to provide strong evidence for tissue-resident mesenchymal cells as cellular contributors to HO. We assess how the underlying mutation in FOP disrupts muscle-specific dynamics during homeostasis and repair, with a focus on muscle-resident mesenchymal cells known as fibro-adipogenic progenitors (FAPs). Accumulating research points to FAPs as a prominent HO progenitor population, with ACVR1R206H FAPs not only aberrantly differentiating into chondro-osteogenic lineages but creating a permissive environment for bone formation at the expense of muscle regeneration. We will further discuss the emerging role of ACVR1R206H FAPs in muscle regeneration and therapeutic targeting of these cells to reduce HO formation in FOP.
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Affiliation(s)
- Loreilys Mejias Rivera
- Cell and Molecular Biology, Genetics and Epigenetics Graduate Program, University of Pennsylvania, Philadelphia, PA 19104, USA;
- Department of Orthopaedic Surgery, Perelman School of Medicine, University of Pennsylvania, 3450 Hamilton Walk, Philadelphia, PA 19104, USA
- Center for Research in FOP and Related Disorders, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Eileen M. Shore
- Department of Orthopaedic Surgery, Perelman School of Medicine, University of Pennsylvania, 3450 Hamilton Walk, Philadelphia, PA 19104, USA
- Center for Research in FOP and Related Disorders, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Foteini Mourkioti
- Department of Orthopaedic Surgery, Perelman School of Medicine, University of Pennsylvania, 3450 Hamilton Walk, Philadelphia, PA 19104, USA
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Musculoskeletal Program, Penn Institute for Regenerative Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
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5
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Xu M, Wang H, Tian X, Li B, Wang S, Zhao X, He H. Opsin-Free Activation of Bmp Receptors by a Femtosecond Laser. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2308072. [PMID: 38239021 PMCID: PMC10933676 DOI: 10.1002/advs.202308072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 12/13/2023] [Indexed: 03/14/2024]
Abstract
Bone morphogenetic protein (BMP) signaling plays a vital role in differentiation, organogenesis, and various cell processes. As a member of TGF-β superfamily, the BMP initiation usually accompanies crosstalk with other signaling pathways and simultaneously activates some of them. It is quite challenging to solely initiate an individual pathway. In this study, an opsin-free optical method to specifically activate BMP receptors (BMPR) and subsequent pSmad1/5/8 cascades by a single-time scan of a tightly-focused femtosecond laser in the near infrared range is reported. Via transient two-photon excitation to intrinsic local flavins near the cell membrane, the photoactivation drives conformational changes of preformed BMPR complexes to enable their bonding and phosphorylation of the GS domain in BMPR-I by BMPR-II. The pSmad1/5/8 signaling is initiated by this method, while p38 and pSmad2 are rarely perturbed. Based on a microscopic system, primary adipose-derived stem cells in an area of 420 × 420 µm2 are photoactivated by a single-time laser scanning for 1.5 s and exhibit pSmad1/5/8 upregulation and osteoblastic differentiation after 21 days. Hence, an opsin-free, specific, and noninvasive optical method to initiate BMP signaling, easily accomplished by a two-photon microscope system is reported.
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Affiliation(s)
- Manjun Xu
- School of Biomedical EngineeringShanghai Jiao Tong UniversityShanghai200031China
| | - Haipeng Wang
- School of Biomedical EngineeringShanghai Jiao Tong UniversityShanghai200031China
| | - Xiaoying Tian
- School of Biomedical EngineeringShanghai Jiao Tong UniversityShanghai200031China
| | - Bingyi Li
- School of Biomedical EngineeringShanghai Jiao Tong UniversityShanghai200031China
| | - Shaoyang Wang
- School of Biomedical EngineeringHainan UniversityHaikou570228China
| | - Xiaohui Zhao
- School of Biomedical EngineeringShanghai Jiao Tong UniversityShanghai200031China
| | - Hao He
- School of Biomedical EngineeringShanghai Jiao Tong UniversityShanghai200031China
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6
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Markarian N, Van Auken KM, Ebert D, Sternberg PW. Enrichment on steps, not genes, improves inference of differentially expressed pathways. PLoS Comput Biol 2024; 20:e1011968. [PMID: 38527066 PMCID: PMC10994554 DOI: 10.1371/journal.pcbi.1011968] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 04/04/2024] [Accepted: 03/05/2024] [Indexed: 03/27/2024] Open
Abstract
Enrichment analysis is frequently used in combination with differential expression data to investigate potential commonalities amongst lists of genes and generate hypotheses for further experiments. However, current enrichment analysis approaches on pathways ignore the functional relationships between genes in a pathway, particularly OR logic that occurs when a set of proteins can each individually perform the same step in a pathway. As a result, these approaches miss pathways with large or multiple sets because of an inflation of pathway size (when measured as the total gene count) relative to the number of steps. We address this problem by enriching on step-enabling entities in pathways. We treat sets of protein-coding genes as single entities, and we also weight sets to account for the number of genes in them using the multivariate Fisher's noncentral hypergeometric distribution. We then show three examples of pathways that are recovered with this method and find that the results have significant proportions of pathways not found in gene list enrichment analysis.
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Affiliation(s)
- Nicholas Markarian
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, United States of America
- Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Kimberly M. Van Auken
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, United States of America
| | - Dustin Ebert
- Division of Bioinformatics, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Paul W. Sternberg
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, United States of America
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7
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Teague S, Primavera G, Chen B, Liu ZY, Yao L, Freeburne E, Khan H, Jo K, Johnson C, Heemskerk I. Time-integrated BMP signaling determines fate in a stem cell model for early human development. Nat Commun 2024; 15:1471. [PMID: 38368368 PMCID: PMC10874454 DOI: 10.1038/s41467-024-45719-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 02/02/2024] [Indexed: 02/19/2024] Open
Abstract
How paracrine signals are interpreted to yield multiple cell fate decisions in a dynamic context during human development in vivo and in vitro remains poorly understood. Here we report an automated tracking method to follow signaling histories linked to cell fate in large numbers of human pluripotent stem cells (hPSCs). Using an unbiased statistical approach, we discover that measured BMP signaling history correlates strongly with fate in individual cells. We find that BMP response in hPSCs varies more strongly in the duration of signaling than the level. However, both the level and duration of signaling activity control cell fate choices only by changing the time integral. Therefore, signaling duration and level are interchangeable in this context. In a stem cell model for patterning of the human embryo, we show that signaling histories predict the fate pattern and that the integral model correctly predicts changes in cell fate domains when signaling is perturbed. Our data suggest that mechanistically, BMP signaling is integrated by SOX2.
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Affiliation(s)
- Seth Teague
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, USA
| | - Gillian Primavera
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, USA
| | - Bohan Chen
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Zong-Yuan Liu
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - LiAng Yao
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Emily Freeburne
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Hina Khan
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Kyoung Jo
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Craig Johnson
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Idse Heemskerk
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, USA.
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI, USA.
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI, USA.
- Center for Cell Plasticity and Organ Design, University of Michigan Medical School, Ann Arbor, MI, USA.
- Department of Physics, University of Michigan, Ann Arbor, MI, USA.
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8
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Company C, Schmitt MJ, Dramaretska Y, Serresi M, Kertalli S, Jiang B, Yin JA, Aguzzi A, Barozzi I, Gargiulo G. Logical design of synthetic cis-regulatory DNA for genetic tracing of cell identities and state changes. Nat Commun 2024; 15:897. [PMID: 38316783 PMCID: PMC10844330 DOI: 10.1038/s41467-024-45069-6] [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: 10/13/2022] [Accepted: 01/12/2024] [Indexed: 02/07/2024] Open
Abstract
Descriptive data are rapidly expanding in biomedical research. Instead, functional validation methods with sufficient complexity remain underdeveloped. Transcriptional reporters allow experimental characterization and manipulation of developmental and disease cell states, but their design lacks flexibility. Here, we report logical design of synthetic cis-regulatory DNA (LSD), a computational framework leveraging phenotypic biomarkers and trans-regulatory networks as input to design reporters marking the activity of selected cellular states and pathways. LSD uses bulk or single-cell biomarkers and a reference genome or custom cis-regulatory DNA datasets with user-defined boundary regions. By benchmarking validated reporters, we integrate LSD with a computational ranking of phenotypic specificity of putative cis-regulatory DNA. Experimentally, LSD-designed reporters targeting a wide range of cell states are functional without minimal promoters. Applied to broadly expressed genes from human and mouse tissues, LSD generates functional housekeeper-like sLCRs compatible with size constraints of AAV vectors for gene therapy applications. A mesenchymal glioblastoma reporter designed by LSD outperforms previously validated ones and canonical cell surface markers. In genome-scale CRISPRa screens, LSD facilitates the discovery of known and novel bona fide cell-state drivers. Thus, LSD captures core principles of cis-regulation and is broadly applicable to studying complex cell states and mechanisms of transcriptional regulation.
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Affiliation(s)
- Carlos Company
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Robert-Rössle-Str. 10, 13092, Berlin, Germany
| | - Matthias Jürgen Schmitt
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Robert-Rössle-Str. 10, 13092, Berlin, Germany
| | - Yuliia Dramaretska
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Robert-Rössle-Str. 10, 13092, Berlin, Germany
| | - Michela Serresi
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Robert-Rössle-Str. 10, 13092, Berlin, Germany
| | - Sonia Kertalli
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Robert-Rössle-Str. 10, 13092, Berlin, Germany
| | - Ben Jiang
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Robert-Rössle-Str. 10, 13092, Berlin, Germany
| | - Jiang-An Yin
- Institute of Neuropathology, University Hospital Zurich, University of Zurich, 8091, Zurich, Switzerland
| | - Adriano Aguzzi
- Institute of Neuropathology, University Hospital Zurich, University of Zurich, 8091, Zurich, Switzerland
| | - Iros Barozzi
- Center for Cancer Research, Medical University of Vienna, Borschkegasse 8a, 1090, Vienna, Austria
- Department of Surgery and Cancer, Imperial College London, London, UK
| | - Gaetano Gargiulo
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Robert-Rössle-Str. 10, 13092, Berlin, Germany.
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9
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Wu M, Wu S, Chen W, Li YP. The roles and regulatory mechanisms of TGF-β and BMP signaling in bone and cartilage development, homeostasis and disease. Cell Res 2024; 34:101-123. [PMID: 38267638 PMCID: PMC10837209 DOI: 10.1038/s41422-023-00918-9] [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: 02/26/2023] [Accepted: 12/15/2023] [Indexed: 01/26/2024] Open
Abstract
Transforming growth factor-βs (TGF-βs) and bone morphometric proteins (BMPs) belong to the TGF-β superfamily and perform essential functions during osteoblast and chondrocyte lineage commitment and differentiation, skeletal development, and homeostasis. TGF-βs and BMPs transduce signals through SMAD-dependent and -independent pathways; specifically, they recruit different receptor heterotetramers and R-Smad complexes, resulting in unique biological readouts. BMPs promote osteogenesis, osteoclastogenesis, and chondrogenesis at all differentiation stages, while TGF-βs play different roles in a stage-dependent manner. BMPs and TGF-β have opposite functions in articular cartilage homeostasis. Moreover, TGF-β has a specific role in maintaining the osteocyte network. The precise activation of BMP and TGF-β signaling requires regulatory machinery at multiple levels, including latency control in the matrix, extracellular antagonists, ubiquitination and phosphorylation in the cytoplasm, nucleus-cytoplasm transportation, and transcriptional co-regulation in the nuclei. This review weaves the background information with the latest advances in the signaling facilitated by TGF-βs and BMPs, and the advanced understanding of their diverse physiological functions and regulations. This review also summarizes the human diseases and mouse models associated with disordered TGF-β and BMP signaling. A more precise understanding of the BMP and TGF-β signaling could facilitate the development of bona fide clinical applications in treating bone and cartilage disorders.
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Affiliation(s)
- Mengrui Wu
- Department of Cell and Developmental Biology, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China.
| | - Shali Wu
- Department of Cell and Developmental Biology, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Wei Chen
- Division in Cellular and Molecular Medicine, Department of Pathology and Laboratory Medicine, Tulane University School of Medicine, Tulane University, New Orleans, LA, USA
| | - Yi-Ping Li
- Division in Cellular and Molecular Medicine, Department of Pathology and Laboratory Medicine, Tulane University School of Medicine, Tulane University, New Orleans, LA, USA.
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10
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Granados AA, Kanrar N, Elowitz MB. Combinatorial expression motifs in signaling pathways. CELL GENOMICS 2024; 4:100463. [PMID: 38216284 PMCID: PMC10794782 DOI: 10.1016/j.xgen.2023.100463] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 08/02/2023] [Accepted: 11/15/2023] [Indexed: 01/14/2024]
Abstract
In animal cells, molecular pathways often comprise families of variant components, such as ligands or receptors. These pathway components are differentially expressed by different cell types, potentially tailoring pathway function to cell context. However, it has remained unclear how pathway expression profiles are distributed across cell types and whether similar profiles can occur in dissimilar cell types. Here, using single-cell gene expression datasets, we identified pathway expression motifs, defined as recurrent expression profiles that are broadly distributed across diverse cell types. Motifs appeared in core pathways, including TGF-β, Notch, Wnt, and the SRSF splice factors, and involved combinatorial co-expression of multiple components. Motif usage was weakly correlated between pathways in adult cell types and during dynamic developmental transitions. Together, these results suggest a mosaic view of cell type organization, in which different cell types operate many of the same pathways in distinct modes.
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Affiliation(s)
- Alejandro A Granados
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA; Howard Hughes Medical Institute and Department of Applied Physics, California Institute of Technology, Pasadena, CA 91125, USA
| | - Nivedita Kanrar
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA; Howard Hughes Medical Institute and Department of Applied Physics, California Institute of Technology, Pasadena, CA 91125, USA
| | - Michael B Elowitz
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA; Howard Hughes Medical Institute and Department of Applied Physics, California Institute of Technology, Pasadena, CA 91125, USA.
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11
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Grall E, Feregrino C, Fischer S, De Courten A, Sacher F, Hiscock TW, Tschopp P. Self-organized BMP signaling dynamics underlie the development and evolution of digit segmentation patterns in birds and mammals. Proc Natl Acad Sci U S A 2024; 121:e2304470121. [PMID: 38175868 PMCID: PMC10786279 DOI: 10.1073/pnas.2304470121] [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: 03/17/2023] [Accepted: 11/03/2023] [Indexed: 01/06/2024] Open
Abstract
Repeating patterns of synovial joints are a highly conserved feature of articulated digits, with variations in joint number and location resulting in diverse digit morphologies and limb functions across the tetrapod clade. During the development of the amniote limb, joints form iteratively within the growing digit ray, as a population of distal progenitors alternately specifies joint and phalanx cell fates to segment the digit into distinct elements. While numerous molecular pathways have been implicated in this fate choice, it remains unclear how they give rise to a repeating pattern. Here, using single-cell RNA sequencing and spatial gene expression profiling, we investigate the transcriptional dynamics of interphalangeal joint specification in vivo. Combined with mathematical modeling, we predict that interactions within the BMP signaling pathway-between the ligand GDF5, the inhibitor NOGGIN, and the intracellular effector pSMAD-result in a self-organizing Turing system that forms periodic joint patterns. Our model is able to recapitulate the spatiotemporal gene expression dynamics observed in vivo, as well as phenocopy digit malformations caused by BMP pathway perturbations. By contrasting in silico simulations with in vivo morphometrics of two morphologically distinct digits, we show how changes in signaling parameters and growth dynamics can result in variations in the size and number of phalanges. Together, our results reveal a self-organizing mechanism that underpins amniote digit segmentation and its evolvability and, more broadly, illustrate how Turing systems based on a single molecular pathway may generate complex repetitive patterns in a wide variety of organisms.
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Affiliation(s)
- Emmanuelle Grall
- Zoology, Department of Environmental Sciences, University of Basel, Basel4051, Switzerland
| | - Christian Feregrino
- Zoology, Department of Environmental Sciences, University of Basel, Basel4051, Switzerland
| | - Sabrina Fischer
- Zoology, Department of Environmental Sciences, University of Basel, Basel4051, Switzerland
| | - Aline De Courten
- Zoology, Department of Environmental Sciences, University of Basel, Basel4051, Switzerland
| | - Fabio Sacher
- Zoology, Department of Environmental Sciences, University of Basel, Basel4051, Switzerland
| | - Tom W. Hiscock
- Institute of Medical Sciences, University of Aberdeen, AberdeenAB25 2ZD, Scotland, United Kingdom
| | - Patrick Tschopp
- Zoology, Department of Environmental Sciences, University of Basel, Basel4051, Switzerland
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12
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Zhang M, Liu Q, Meng H, Duan H, Liu X, Wu J, Gao F, Wang S, Tan R, Yuan J. Ischemia-reperfusion injury: molecular mechanisms and therapeutic targets. Signal Transduct Target Ther 2024; 9:12. [PMID: 38185705 PMCID: PMC10772178 DOI: 10.1038/s41392-023-01688-x] [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: 01/29/2023] [Revised: 08/29/2023] [Accepted: 10/18/2023] [Indexed: 01/09/2024] Open
Abstract
Ischemia-reperfusion (I/R) injury paradoxically occurs during reperfusion following ischemia, exacerbating the initial tissue damage. The limited understanding of the intricate mechanisms underlying I/R injury hinders the development of effective therapeutic interventions. The Wnt signaling pathway exhibits extensive crosstalk with various other pathways, forming a network system of signaling pathways involved in I/R injury. This review article elucidates the underlying mechanisms involved in Wnt signaling, as well as the complex interplay between Wnt and other pathways, including Notch, phosphatidylinositol 3-kinase/protein kinase B, transforming growth factor-β, nuclear factor kappa, bone morphogenetic protein, N-methyl-D-aspartic acid receptor-Ca2+-Activin A, Hippo-Yes-associated protein, toll-like receptor 4/toll-interleukine-1 receptor domain-containing adapter-inducing interferon-β, and hepatocyte growth factor/mesenchymal-epithelial transition factor. In particular, we delve into their respective contributions to key pathological processes, including apoptosis, the inflammatory response, oxidative stress, extracellular matrix remodeling, angiogenesis, cell hypertrophy, fibrosis, ferroptosis, neurogenesis, and blood-brain barrier damage during I/R injury. Our comprehensive analysis of the mechanisms involved in Wnt signaling during I/R reveals that activation of the canonical Wnt pathway promotes organ recovery, while activation of the non-canonical Wnt pathways exacerbates injury. Moreover, we explore novel therapeutic approaches based on these mechanistic findings, incorporating evidence from animal experiments, current standards, and clinical trials. The objective of this review is to provide deeper insights into the roles of Wnt and its crosstalk signaling pathways in I/R-mediated processes and organ dysfunction, to facilitate the development of innovative therapeutic agents for I/R injury.
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Affiliation(s)
- Meng Zhang
- The Collaborative Innovation Center, Jining Medical University, Jining, Shandong, 272067, China
| | - Qian Liu
- Clinical Medical College, Jining Medical University, Jining, Shandong, 272067, China
| | - Hui Meng
- Clinical Medical College, Jining Medical University, Jining, Shandong, 272067, China
| | - Hongxia Duan
- Clinical Medical College, Jining Medical University, Jining, Shandong, 272067, China
| | - Xin Liu
- Second Clinical Medical College, Jining Medical University, Jining, Shandong, 272067, China
| | - Jian Wu
- Shanghai Institute of Cardiovascular Diseases, Zhongshan Hospital and Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Fei Gao
- The Collaborative Innovation Center, Jining Medical University, Jining, Shandong, 272067, China
- Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Shijun Wang
- Shanghai Institute of Cardiovascular Diseases, Zhongshan Hospital and Institutes of Biomedical Sciences, Fudan University, Shanghai, China.
| | - Rubin Tan
- Department of Physiology, Basic medical school, Xuzhou Medical University, Xuzhou, 221004, China.
| | - Jinxiang Yuan
- The Collaborative Innovation Center, Jining Medical University, Jining, Shandong, 272067, China.
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13
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Richardson L, Wilcockson SG, Guglielmi L, Hill CS. Context-dependent TGFβ family signalling in cell fate regulation. Nat Rev Mol Cell Biol 2023; 24:876-894. [PMID: 37596501 DOI: 10.1038/s41580-023-00638-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/30/2023] [Indexed: 08/20/2023]
Abstract
The transforming growth factor-β (TGFβ) family are a large group of evolutionarily conserved cytokines whose signalling modulates cell fate decision-making across varying cellular contexts at different stages of life. Here we discuss new findings in early embryos that reveal how, in contrast to our original understanding of morphogen interpretation, robust cell fate specification can originate from a noisy combination of signalling inputs and a broad range of signalling levels. We compare this evidence with novel findings on the roles of TGFβ family signalling in tissue maintenance and homeostasis during juvenile and adult life, spanning the skeletal, haemopoietic and immune systems. From these comparisons, it emerges that in contrast to robust developing systems, relatively small perturbations in TGFβ family signalling have detrimental effects at later stages in life, leading to aberrant cell fate specification and disease, for example in cancer or congenital disorders. Finally, we highlight novel strategies to target and amend dysfunction in signalling and discuss how gleaning knowledge from different fields of biology can help in the development of therapeutics for aberrant TGFβ family signalling in disease.
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Affiliation(s)
- Louise Richardson
- Developmental Signalling Laboratory, The Francis Crick Institute, London, UK
| | - Scott G Wilcockson
- Developmental Signalling Laboratory, The Francis Crick Institute, London, UK
| | - Luca Guglielmi
- Developmental Signalling Laboratory, The Francis Crick Institute, London, UK
- Division of Cell Biology, MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Caroline S Hill
- Developmental Signalling Laboratory, The Francis Crick Institute, London, UK.
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14
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Orcutt-Jahns B, Junior JRL, Rockne RC, Matache A, Branciamore S, Hung E, Rodin AS, Lee PP, Meyer AS. Systems profiling reveals recurrently dysregulated cytokine signaling responses in ER+ breast cancer patients' blood. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.31.564987. [PMID: 37961682 PMCID: PMC10635026 DOI: 10.1101/2023.10.31.564987] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Cytokines mediate cell-to-cell communication across the immune system and therefore are critical to immunosurveillance in cancer and other diseases. Several cytokines show dysregulated abundance or signaling responses in breast cancer, associated with the disease and differences in survival and progression. Cytokines operate in a coordinated manner to affect immune surveillance and regulate one another, necessitating a systems approach for a complete picture of this dysregulation. Here, we profiled cytokine signaling responses of peripheral immune cells from breast cancer patients as compared to healthy controls in a multidimensional manner across ligands, cell populations, and responsive pathways. We find alterations in cytokine responsiveness across pathways and cell types that are best defined by integrated signatures across dimensions. Alterations in the abundance of a cytokine's cognate receptor do not explain differences in responsiveness. Rather, alterations in baseline signaling and receptor abundance suggesting immune cell reprogramming are associated with altered responses. These integrated features suggest a global reprogramming of immune cell communication in breast cancer.
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Affiliation(s)
- Brian Orcutt-Jahns
- Department of Bioengineering, University of California, Los Angeles (UCLA), USA
| | | | - Russell C. Rockne
- Department of Computational and Quantitative Medicine, Beckman Research Institute of the City of Hope, Duarte, CA, USA
| | - Adina Matache
- Department of Computational and Quantitative Medicine, Beckman Research Institute of the City of Hope, Duarte, CA, USA
| | - Sergio Branciamore
- Department of Computational and Quantitative Medicine, Beckman Research Institute of the City of Hope, Duarte, CA, USA
| | - Ethan Hung
- Department of Bioengineering, University of California, Los Angeles (UCLA), USA
| | - Andrei S. Rodin
- Department of Computational and Quantitative Medicine, Beckman Research Institute of the City of Hope, Duarte, CA, USA
| | - Peter P. Lee
- Department of Immuno-Oncology, Beckman Research Institute of the City of Hope, Duarte, CA, USA
| | - Aaron S. Meyer
- Department of Bioengineering, University of California, Los Angeles (UCLA), USA
- Jonsson Comprehensive Cancer Center, UCLA, United States of America
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, UCLA, USA
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15
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Parres-Gold J, Levine M, Emert B, Stuart A, Elowitz MB. Principles of Computation by Competitive Protein Dimerization Networks. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.30.564854. [PMID: 37961250 PMCID: PMC10634983 DOI: 10.1101/2023.10.30.564854] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Many biological signaling pathways employ proteins that competitively dimerize in diverse combinations. These dimerization networks can perform biochemical computations, in which the concentrations of monomers (inputs) determine the concentrations of dimers (outputs). Despite their prevalence, little is known about the range of input-output computations that dimerization networks can perform (their "expressivity") and how it depends on network size and connectivity. Using a systematic computational approach, we demonstrate that even small dimerization networks (3-6 monomers) are expressive, performing diverse multi-input computations. Further, dimerization networks are versatile, performing different computations when their protein components are expressed at different levels, such as in different cell types. Remarkably, individual networks with random interaction affinities, when large enough (≥8 proteins), can perform nearly all (~90%) potential one-input network computations merely by tuning their monomer expression levels. Thus, even the simple process of competitive dimerization provides a powerful architecture for multi-input, cell-type-specific signal processing.
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Affiliation(s)
- Jacob Parres-Gold
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Matthew Levine
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Benjamin Emert
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Andrew Stuart
- Division of Engineering and Applied Sciences, California Institute of Technology, Pasadena, CA 91125, USA
| | - Michael B. Elowitz
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
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16
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Orcutt-Jahns B, Emmel PC, Snyder EM, Taylor SD, Meyer AS. Multivalent, asymmetric IL-2-Fc fusions show enhanced selectivity for regulatory T cells. Sci Signal 2023; 16:eadg0699. [PMID: 37847758 PMCID: PMC10658882 DOI: 10.1126/scisignal.adg0699] [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: 12/05/2022] [Accepted: 09/21/2023] [Indexed: 10/19/2023]
Abstract
The cytokine interleukin-2 (IL-2) has the potential to treat autoimmune disease but is limited by its modest specificity toward immunosuppressive regulatory T (Treg) cells. IL-2 receptors consist of combinations of α, β, and γ chains of variable affinity and cell specificity. Engineering IL-2 to treat autoimmunity has primarily focused on retaining binding to the relatively Treg-selective, high-affinity receptor while reducing binding to the less selective, low-affinity receptor. However, we found that refining the designs to focus on targeting the high-affinity receptor through avidity effects is key to optimizing Treg selectivity. We profiled the dynamics and dose dependency of signaling responses in primary human immune cells induced by engineered fusions composed of either wild-type IL-2 or mutant forms with altered affinity, valency, and fusion to the antibody Fc region for stability. Treg selectivity and signaling response variations were explained by a model of multivalent binding and dimer-enhanced avidity-a combined measure of the strength, number, and conformation of interaction sites-from which we designed tetravalent IL-2-Fc fusions that had greater Treg selectivity in culture than do current designs. Biasing avidity toward IL2Rα with an asymmetrical multivalent design consisting of one α/β chain-binding and one α chain-binding mutant further enhanced Treg selectivity. Comparative analysis revealed that IL2Rα was the optimal cell surface target for Treg selectivity, indicating that avidity for IL2Rα may be the optimal route to producing IL-2 variants that selectively target Tregs.
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Affiliation(s)
- Brian Orcutt-Jahns
- Department of Bioengineering, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Peter C. Emmel
- Department of Bioengineering, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Eli M. Snyder
- Department of Bioengineering, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Scott D. Taylor
- Department of Bioengineering, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Aaron S. Meyer
- Department of Bioengineering, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, Los Angeles, CA 90095, USA
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17
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Sheridan K, Berleant J, Bathe M, Condon A, Williams VV. Factorization and pseudofactorization of weighted graphs. DISCRETE APPLIED MATHEMATICS (AMSTERDAM, NETHERLANDS : 1988) 2023; 337:81-105. [PMID: 37213330 PMCID: PMC10194401 DOI: 10.1016/j.dam.2023.04.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
For unweighted graphs, finding isometric embeddings of a graph G is closely related to decompositions of G into Cartesian products of smaller graphs. When G is isomorphic to a Cartesian graph product, we call the factors of this product a factorization of G. When G is isomorphic to an isometric subgraph of a Cartesian graph product, we call those factors a pseudofactorization of G. Prior work has shown that an unweighted graph's pseudofactorization can be used to generate a canonical isometric embedding into a product of the smallest possible pseudofactors. However, for arbitrary weighted graphs, which represent a richer variety of metric spaces, methods for finding isometric embeddings or determining their existence remain elusive, and indeed pseudofactorization and factorization have not previously been extended to this context. In this work, we address the problem of finding the factorization and pseudofactorization of a weighted graph G, where G satisfies the property that every edge constitutes a shortest path between its endpoints. We term such graphs minimal graphs, noting that every graph can be made minimal by removing edges not affecting its path metric. We generalize pseudofactorization and factorization to minimal graphs and develop new proof techniques that extend the previously proposed algorithms due to Graham and Winkler [Graham and Winkler, '85] and Feder [Feder, '92] for pseudofactorization and factorization of unweighted graphs. We show that any n-vertex, m-edge graph with positive integer edge weights can be factored in O(m2) time, plus the time to find all pairs shortest paths (APSP) distances in a weighted graph, resulting in an overall running time of O(m2+n2 log log n) time. We also show that a pseudofactorization for such a graph can be computed in O(mn) time, plus the time to solve APSP, resulting in an O(mn+n2 log log n) running time.
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Affiliation(s)
- Kristin Sheridan
- Department of of Computer Science, University of Texas, Austin, TX
- To whom correspondence should be addressed:
| | - Joseph Berleant
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA
| | - Mark Bathe
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA
| | - Anne Condon
- Department of Computer Science, University of British Columbia, Vancouver, Canada
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18
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Massagué J, Sheppard D. TGF-β signaling in health and disease. Cell 2023; 186:4007-4037. [PMID: 37714133 PMCID: PMC10772989 DOI: 10.1016/j.cell.2023.07.036] [Citation(s) in RCA: 62] [Impact Index Per Article: 62.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 07/21/2023] [Accepted: 07/28/2023] [Indexed: 09/17/2023]
Abstract
The TGF-β regulatory system plays crucial roles in the preservation of organismal integrity. TGF-β signaling controls metazoan embryo development, tissue homeostasis, and injury repair through coordinated effects on cell proliferation, phenotypic plasticity, migration, metabolic adaptation, and immune surveillance of multiple cell types in shared ecosystems. Defects of TGF-β signaling, particularly in epithelial cells, tissue fibroblasts, and immune cells, disrupt immune tolerance, promote inflammation, underlie the pathogenesis of fibrosis and cancer, and contribute to the resistance of these diseases to treatment. Here, we review how TGF-β coordinates multicellular response programs in health and disease and how this knowledge can be leveraged to develop treatments for diseases of the TGF-β system.
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Affiliation(s)
- Joan Massagué
- Cancer Biology and Genetics Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.
| | - Dean Sheppard
- Department of Medicine and Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA 94158, USA
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19
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Berková L, Fazilaty H, Yang Q, Kubovčiak J, Stastna M, Hrckulak D, Vojtechova M, Dalessi T, Brügger MD, Hausmann G, Liberali P, Korinek V, Basler K, Valenta T. Terminal differentiation of villus tip enterocytes is governed by distinct Tgfβ superfamily members. EMBO Rep 2023; 24:e56454. [PMID: 37493498 PMCID: PMC10481656 DOI: 10.15252/embr.202256454] [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: 11/09/2022] [Revised: 06/23/2023] [Accepted: 06/30/2023] [Indexed: 07/27/2023] Open
Abstract
The protective and absorptive functions of the intestinal epithelium rely on differentiated enterocytes in the villi. The differentiation of enterocytes is orchestrated by sub-epithelial mesenchymal cells producing distinct ligands along the villus axis, in particular Bmps and Tgfβ. Here, we show that individual Bmp ligands and Tgfβ drive distinct enterocytic programs specific to villus zonation. Bmp4 is expressed from the centre to the upper part of the villus and activates preferentially genes connected to lipid uptake and metabolism. In contrast, Bmp2 is produced by villus tip mesenchymal cells and it influences the adhesive properties of villus tip epithelial cells and the expression of immunomodulators. Additionally, Tgfβ induces epithelial gene expression programs similar to those triggered by Bmp2. Bmp2-driven villus tip program is activated by a canonical Bmp receptor type I/Smad-dependent mechanism. Finally, we establish an organoid cultivation system that enriches villus tip enterocytes and thereby better mimics the cellular composition of the intestinal epithelium. Our data suggest that not only a Bmp gradient but also the activity of individual Bmp drives specific enterocytic programs.
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Affiliation(s)
- Linda Berková
- Laboratory of Cell and Developmental BiologyInstitute of Molecular Genetics of the Czech Academy of SciencesPragueCzech Republic
| | - Hassan Fazilaty
- Department of Molecular Life SciencesUniversity of ZurichZurichSwitzerland
| | - Qiutan Yang
- Friedrich Miescher Institute for Biomedical Research (FMI)BaselSwitzerland
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of ZoologyChinese Academy of SciencesBeijingChina
- Institute for Stem Cell and Regeneration, Chinese Academy of SciencesBeijingChina
- Beijing Institute for Stem Cell and Regenerative MedicineBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Jan Kubovčiak
- Laboratory of Genomics and BioinformaticsInstitute of Molecular Genetics of the Czech Academy of SciencesPragueCzech Republic
| | - Monika Stastna
- Laboratory of Cell and Developmental BiologyInstitute of Molecular Genetics of the Czech Academy of SciencesPragueCzech Republic
| | - Dusan Hrckulak
- Laboratory of Cell and Developmental BiologyInstitute of Molecular Genetics of the Czech Academy of SciencesPragueCzech Republic
| | - Martina Vojtechova
- Laboratory of Cell and Developmental BiologyInstitute of Molecular Genetics of the Czech Academy of SciencesPragueCzech Republic
| | - Tosca Dalessi
- Department of Molecular Life SciencesUniversity of ZurichZurichSwitzerland
| | | | - George Hausmann
- Department of Molecular Life SciencesUniversity of ZurichZurichSwitzerland
| | - Prisca Liberali
- Friedrich Miescher Institute for Biomedical Research (FMI)BaselSwitzerland
| | - Vladimir Korinek
- Laboratory of Cell and Developmental BiologyInstitute of Molecular Genetics of the Czech Academy of SciencesPragueCzech Republic
| | - Konrad Basler
- Department of Molecular Life SciencesUniversity of ZurichZurichSwitzerland
| | - Tomas Valenta
- Laboratory of Cell and Developmental BiologyInstitute of Molecular Genetics of the Czech Academy of SciencesPragueCzech Republic
- Department of Molecular Life SciencesUniversity of ZurichZurichSwitzerland
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20
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Allen RS, Jones WD, Hale M, Warder BN, Shore EM, Mullins MC. Reduced GS Domain Serine/Threonine Requirements of Fibrodysplasia Ossificans Progressiva Mutant Type I BMP Receptor ACVR1 in the Zebrafish. J Bone Miner Res 2023; 38:1364-1385. [PMID: 37329499 DOI: 10.1002/jbmr.4869] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 04/29/2023] [Accepted: 06/14/2023] [Indexed: 06/19/2023]
Abstract
Fibrodysplasia ossificans progressiva (FOP) is a rare human genetic condition characterized by altered skeletal development and extraskeletal bone formation. All cases of FOP are caused by mutations in the type I bone morphogenetic protein (BMP) receptor gene ACVR1 that result in overactivation of the BMP signaling pathway. Activation of the wild-type ACVR1 kinase requires assembly of a tetrameric type I and II BMP receptor complex followed by phosphorylation of the ACVR1 GS domain by type II BMP receptors. Previous studies showed that the FOP-mutant ACVR1-R206H required type II BMP receptors and presumptive glycine/serine-rich (GS) domain phosphorylation for overactive signaling. Structural modeling of the ACVR1-R206H mutant kinase domain supports the idea that FOP mutations alter the conformation of the GS domain, but it is unclear how this leads to overactive signaling. Here we show, using a developing zebrafish embryo BMP signaling assay, that the FOP-mutant receptors ACVR1-R206H and -G328R have reduced requirements for GS domain phosphorylatable sites to signal compared to wild-type ACVR1. Further, ligand-independent and ligand-dependent signaling through the FOP-mutant ACVR1 receptors have distinct GS domain phosphorylatable site requirements. ACVR1-G328R showed increased GS domain serine/threonine requirements for ligand-independent signaling compared to ACVR1-R206H, whereas it exhibited reduced serine/threonine requirements for ligand-dependent signaling. Remarkably, while ACVR1-R206H does not require the type I BMP receptor partner, Bmpr1, to signal, a ligand-dependent GS domain mutant of ACVR1-R206H could signal independently of Bmpr1 only when Bmp7 ligand was overexpressed. Of note, unlike human ACVR1-R206H, the zebrafish paralog Acvr1l-R203H does not show increased signaling activity. However, in domain-swapping studies, the human kinase domain, but not the human GS domain, was sufficient to confer overactive signaling to the Acvr1l-R203H receptor. Together these results reflect the importance of GS domain activation and kinase domain functions in regulating ACVR1 signaling and identify mechanisms of reduced regulatory constraints conferred by FOP mutations. © 2023 American Society for Bone and Mineral Research (ASBMR).
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Affiliation(s)
- Robyn S Allen
- Department of Cell and Developmental Biology, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
- Department of Orthopaedic Surgery, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
| | - William D Jones
- Department of Cell and Developmental Biology, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
| | - Maya Hale
- Department of Cell and Developmental Biology, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
| | - Bailey N Warder
- Department of Cell and Developmental Biology, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
| | - Eileen M Shore
- Department of Orthopaedic Surgery, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
- Department of Genetics, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
| | - Mary C Mullins
- Department of Cell and Developmental Biology, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
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21
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Lagasse E, Levin M. Future medicine: from molecular pathways to the collective intelligence of the body. Trends Mol Med 2023; 29:687-710. [PMID: 37481382 PMCID: PMC10527237 DOI: 10.1016/j.molmed.2023.06.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 06/20/2023] [Accepted: 06/22/2023] [Indexed: 07/24/2023]
Abstract
The remarkable anatomical homeostasis exhibited by complex living organisms suggests that they are inherently reprogrammable information-processing systems that offer numerous interfaces to their physiological and anatomical problem-solving capacities. We briefly review data suggesting that the multiscale competency of living forms affords a new path for biomedicine that exploits the innate collective intelligence of tissues and organs. The concept of tissue-level allostatic goal-directedness is already bearing fruit in clinical practice. We sketch a roadmap towards 'somatic psychiatry' by using advances in bioelectricity and behavioral neuroscience to design methods that induce self-repair of structure and function. Relaxing the assumption that cellular control mechanisms are static, exploiting powerful concepts from cybernetics, behavioral science, and developmental biology may spark definitive solutions to current biomedical challenges.
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Affiliation(s)
- Eric Lagasse
- McGowan Institute for Regenerative Medicine and Department of Pathology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Michael Levin
- Allen Discovery Center, Tufts University, Medford, MA, USA; Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA.
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22
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Zhu R, Santat LA, Markson JS, Nandagopal N, Gregrowicz J, Elowitz MB. Reconstitution of morphogen shuttling circuits. SCIENCE ADVANCES 2023; 9:eadf9336. [PMID: 37436981 DOI: 10.1126/sciadv.adf9336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 06/08/2023] [Indexed: 07/14/2023]
Abstract
Developing tissues form spatial patterns by establishing concentration gradients of diffusible signaling proteins called morphogens. The bone morphogenetic protein (BMP) morphogen pathway uses a family of extracellular modulators to reshape signaling gradients by actively "shuttling" ligands to different locations. It has remained unclear what circuits are sufficient to enable shuttling, what other patterns they can generate, and whether shuttling is evolutionarily conserved. Here, using a synthetic, bottom-up approach, we compared the spatiotemporal dynamics of different extracellular circuits. Three proteins-Chordin, Twsg, and the BMP-1 protease-successfully displaced gradients by shuttling ligands away from the site of production. A mathematical model explained the different spatial dynamics of this and other circuits. Last, combining mammalian and Drosophila components in the same system suggests that shuttling is a conserved capability. Together, these results reveal principles through which extracellular circuits control the spatiotemporal dynamics of morphogen signaling.
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Affiliation(s)
- Ronghui Zhu
- Howard Hughes Medical Institute and Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Leah A Santat
- Howard Hughes Medical Institute and Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Joseph S Markson
- Howard Hughes Medical Institute and Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | | | - Jan Gregrowicz
- Howard Hughes Medical Institute and Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Michael B Elowitz
- Howard Hughes Medical Institute and Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
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23
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Klumpe HE, Garcia-Ojalvo J, Elowitz MB, Antebi YE. The computational capabilities of many-to-many protein interaction networks. Cell Syst 2023; 14:430-446. [PMID: 37348461 PMCID: PMC10318606 DOI: 10.1016/j.cels.2023.05.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Revised: 04/14/2023] [Accepted: 05/11/2023] [Indexed: 06/24/2023]
Abstract
Many biological circuits comprise sets of protein variants that interact with one another in a many-to-many, or promiscuous, fashion. These architectures can provide powerful computational capabilities that are especially critical in multicellular organisms. Understanding the principles of biochemical computations in these circuits could allow more precise control of cellular behaviors. However, these systems are inherently difficult to analyze, due to their large number of interacting molecular components, partial redundancies, and cell context dependence. Here, we discuss recent experimental and theoretical advances that are beginning to reveal how promiscuous circuits compute, what roles those computations play in natural biological contexts, and how promiscuous architectures can be applied for the design of synthetic multicellular behaviors.
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Affiliation(s)
- Heidi E Klumpe
- Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA; Biological Design Center, Boston University, Boston, MA 02215, USA
| | - Jordi Garcia-Ojalvo
- Department of Medicine and Life Sciences, Pompeu Fabra University, 08003 Barcelona, Spain.
| | - Michael B Elowitz
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA.
| | - Yaron E Antebi
- Department of Molecular Genetics, Weizmann Institute of Science 76100, Rehovot, Israel.
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24
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Berleant J, Sheridan K, Condon A, Williams VV, Bathe M. Isometric Hamming embeddings of weighted graphs. DISCRETE APPLIED MATHEMATICS (AMSTERDAM, NETHERLANDS : 1988) 2023; 332:119-128. [PMID: 37982050 PMCID: PMC10653646 DOI: 10.1016/j.dam.2023.02.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2023]
Abstract
A mapping α : V ( G ) → V ( H ) from the vertex set of one graph G to another graph H is an isometric embedding if the shortest path distance between any two vertices in G equals the distance between their images in H . Here, we consider isometric embeddings of a weighted graph G into unweighted Hamming graphs, called Hamming embeddings, when G satisfies the property that every edge is a shortest path between its endpoints. Using a Cartesian product decomposition of G called its canonical isometric representation, we show that every Hamming embedding of G may be partitioned into a canonical partition, whose parts provide Hamming embeddings for each factor of the canonical isometric representation of G . This implies that G permits a Hamming embedding if and only if each factor of its canonical isometric representation is Hamming embeddable. This result extends prior work on unweighted graphs that showed that an unweighted graph permits a Hamming embedding if and only if each factor is a complete graph. When a graph G has nontrivial isometric representation, determining whether G has a Hamming embedding can be simplified to checking embeddability of two or more smaller graphs.
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Affiliation(s)
- Joseph Berleant
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, United States of America
| | - Kristin Sheridan
- Department of Computer Science, University of Texas at Austin, United States of America
| | - Anne Condon
- Department of Computer Science, University of British Columbia, Vancouver, Canada
| | - Virginia Vassilevska Williams
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA, United States of America
| | - Mark Bathe
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, United States of America
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25
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Xu AF, Molinuevo R, Fazzari E, Tom H, Zhang Z, Menendez J, Casey KM, Ruggero D, Hinck L, Pritchard JK, Barna M. Subfunctionalized expression drives evolutionary retention of ribosomal protein paralogs Rps27 and Rps27l in vertebrates. eLife 2023; 12:e78695. [PMID: 37306301 PMCID: PMC10313321 DOI: 10.7554/elife.78695] [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: 03/16/2022] [Accepted: 06/09/2023] [Indexed: 06/13/2023] Open
Abstract
The formation of paralogs through gene duplication is a core evolutionary process. For paralogs that encode components of protein complexes such as the ribosome, a central question is whether they encode functionally distinct proteins or whether they exist to maintain appropriate total expression of equivalent proteins. Here, we systematically tested evolutionary models of paralog function using the ribosomal protein paralogs Rps27 (eS27) and Rps27l (eS27L) as a case study. Evolutionary analysis suggests that Rps27 and Rps27l likely arose during whole-genome duplication(s) in a common vertebrate ancestor. We show that Rps27 and Rps27l have inversely correlated mRNA abundance across mouse cell types, with the highest Rps27 in lymphocytes and the highest Rps27l in mammary alveolar cells and hepatocytes. By endogenously tagging the Rps27 and Rps27l proteins, we demonstrate that Rps27- and Rps27l-ribosomes associate preferentially with different transcripts. Furthermore, murine Rps27 and Rps27l loss-of-function alleles are homozygous lethal at different developmental stages. However, strikingly, expressing Rps27 protein from the endogenous Rps27l locus or vice versa completely rescues loss-of-function lethality and yields mice with no detectable deficits. Together, these findings suggest that Rps27 and Rps27l are evolutionarily retained because their subfunctionalized expression patterns render both genes necessary to achieve the requisite total expression of two equivalent proteins across cell types. Our work represents the most in-depth characterization of a mammalian ribosomal protein paralog to date and highlights the importance of considering both protein function and expression when investigating paralogs.
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Affiliation(s)
- Adele Francis Xu
- Department of Genetics, Stanford UniversityStanfordUnited States
- Medical Scientist Training Program, Stanford School of MedicineStanfordUnited States
| | - Rut Molinuevo
- Department of Molecular, Cell, and Developmental Biology, University of California, Santa CruzSanta CruzUnited States
| | - Elisa Fazzari
- Helen Diller Family Comprehensive Cancer Center, University of California, Los AngelesLos AngelesUnited States
- Department of Cellular and Molecular Pharmacology, University of California, San FranciscoSan FranciscoUnited States
- Department of Urology, University of California, San FranciscoSan FranciscoUnited States
| | - Harrison Tom
- Helen Diller Family Comprehensive Cancer Center, University of California, Los AngelesLos AngelesUnited States
- Department of Cellular and Molecular Pharmacology, University of California, San FranciscoSan FranciscoUnited States
- Department of Urology, University of California, San FranciscoSan FranciscoUnited States
| | - Zijian Zhang
- Department of Chemical and Systems Biology, Stanford UniversityStanfordUnited States
| | - Julien Menendez
- Department of Molecular, Cell, and Developmental Biology, University of California, Santa CruzSanta CruzUnited States
| | - Kerriann M Casey
- Department of Biology, Stanford UniversityStanfordUnited States
- Department of Comparative Medicine, Stanford School of MedicineStanfordUnited States
| | - Davide Ruggero
- Department of Cellular and Molecular Pharmacology, University of California, San FranciscoSan FranciscoUnited States
- Department of Urology, University of California, San FranciscoSan FranciscoUnited States
| | - Lindsay Hinck
- Department of Molecular, Cell, and Developmental Biology, University of California, Santa CruzSanta CruzUnited States
| | | | - Maria Barna
- Department of Genetics, Stanford UniversityStanfordUnited States
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26
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Monsen VT, Attramadal H. Structural insights into regulation of CCN protein activities and functions. J Cell Commun Signal 2023:10.1007/s12079-023-00768-5. [PMID: 37245184 DOI: 10.1007/s12079-023-00768-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 05/07/2023] [Indexed: 05/29/2023] Open
Abstract
CCN proteins play important functions during development, in repair mechanisms following tissue injury, as well as in pathophysiologic mechanisms of metastasis of cancer. CCNs are secreted proteins that have a multimodular structure and are categorized as matricellular proteins. Although the prevailing view is that CCN proteins regulate biologic processes by interacting with a wide array of other proteins in the microenvironment of the extracellular matrix, the molecular mechanisms of action of CCN proteins are still poorly understood. Not dissuading the current view, however, the recent appreciation that these proteins are signaling proteins in their own right and may even be considered preproproteins controlled by endopeptidases to release a C-terminal bioactive peptide has opened new avenues of research. Also, the recent resolution of the crystal structure of two of the domains of CCN3 have provided new knowledge with implications for the entire CCN family. These resolved structures in combination with structural predictions based upon the AlphaFold artificial intelligence tool provide means to shed new light on CCN functions in context of the notable literature in the field. CCN proteins have emerged as important therapeutic targets in several disease conditions, and clinical trials are currently ongoing. Thus, a review that critically discusses structure - function relationship of CCN proteins, in particular as it relates to interactions with other proteins in the extracellular milieu and on the cell surface, as well as to cell signaling activities of these proteins, is very timely. Suggested mechanism for activation and inhibition of signaling by the CCN protein family (graphics generated with BioRender.com ).
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Affiliation(s)
- Vivi Talstad Monsen
- Institute for Surgical Research, Oslo University Hospital, Oslo, Norway
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Håvard Attramadal
- Institute for Surgical Research, Oslo University Hospital, Oslo, Norway.
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway.
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27
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Farahani PE, Yang X, Mesev EV, Fomby KA, Brumbaugh-Reed EH, Bashor CJ, Nelson CM, Toettcher JE. pYtags enable spatiotemporal measurements of receptor tyrosine kinase signaling in living cells. eLife 2023; 12:82863. [PMID: 37212240 DOI: 10.7554/elife.82863] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Accepted: 04/24/2023] [Indexed: 05/23/2023] Open
Abstract
Receptor tyrosine kinases (RTKs) are major signaling hubs in metazoans, playing crucial roles in cell proliferation, migration, and differentiation. However, few tools are available to measure the activity of a specific RTK in individual living cells. Here, we present pYtags, a modular approach for monitoring the activity of a user-defined RTK by live-cell microscopy. pYtags consist of an RTK modified with a tyrosine activation motif that, when phosphorylated, recruits a fluorescently labeled tandem SH2 domain with high specificity. We show that pYtags enable the monitoring of a specific RTK on seconds-to-minutes time scales and across subcellular and multicellular length scales. Using a pYtag biosensor for epidermal growth factor receptor (EGFR), we quantitatively characterize how signaling dynamics vary with the identity and dose of activating ligand. We show that orthogonal pYtags can be used to monitor the dynamics of EGFR and ErbB2 activity in the same cell, revealing distinct phases of activation for each RTK. The specificity and modularity of pYtags open the door to robust biosensors of multiple tyrosine kinases and may enable engineering of synthetic receptors with orthogonal response programs.
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Affiliation(s)
- Payam E Farahani
- Department of Chemical & Biological Engineering, Princeton University, Princeton, United States
| | - Xiaoyu Yang
- Department of Bioengineering, Rice University, Houston, United States
- Program in Systems, Synthetic, and Physical Biology, Rice University, Houston, United States
| | - Emily V Mesev
- Department of Molecular Biology, Princeton University, Princeton, United States
| | - Kaylan A Fomby
- Department of Molecular Biology, Princeton University, Princeton, United States
| | - Ellen H Brumbaugh-Reed
- Department of Molecular Biology, Princeton University, Princeton, United States
- IRCC International Research Collaboration Center, National Institutes of Natural Sciences, Tokyo, Japan
| | - Caleb J Bashor
- Department of Bioengineering, Rice University, Houston, United States
- Department of Biosciences, Rice University, Houston, United States
| | - Celeste M Nelson
- Department of Chemical & Biological Engineering, Princeton University, Princeton, United States
- Department of Molecular Biology, Princeton University, Princeton, United States
| | - Jared E Toettcher
- Department of Molecular Biology, Princeton University, Princeton, United States
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28
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Takei Y, Yang Y, White J, Yun J, Prasad M, Ombelets LJ, Schindler S, Cai L. High-resolution spatial multi-omics reveals cell-type specific nuclear compartments. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.07.539762. [PMID: 37214923 PMCID: PMC10197539 DOI: 10.1101/2023.05.07.539762] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
The mammalian nucleus is compartmentalized by diverse subnuclear structures. These subnuclear structures, marked by nuclear bodies and histone modifications, are often cell-type specific and affect gene regulation and 3D genome organization1-3. Understanding nuclear organization requires identifying the molecular constituents of subnuclear structures and mapping their associations with specific genomic loci in individual cells, within complex tissues. Here, we introduce two-layer DNA seqFISH+, which allows simultaneous mapping of 100,049 genomic loci, together with nascent transcriptome for 17,856 genes and a diverse set of immunofluorescently labeled subnuclear structures all in single cells in cell lines and adult mouse cerebellum. Using these multi-omics datasets, we showed that repressive chromatin compartments are more variable by cell type than active compartments. We also discovered a single exception to this rule: an RNA polymerase II (RNAPII)-enriched compartment was associated with long, cell-type specific genes (> 200kb), in a manner distinct from nuclear speckles. Further, our analysis revealed that cell-type specific facultative and constitutive heterochromatin compartments marked by H3K27me3 and H4K20me3 are enriched at specific genes and gene clusters, respectively, and shape radial chromosomal positioning and inter-chromosomal interactions in neurons and glial cells. Together, our results provide a single-cell high-resolution multi-omics view of subnuclear compartments, associated genomic loci, and their impacts on gene regulation, directly within complex tissues.
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Affiliation(s)
- Yodai Takei
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Yujing Yang
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Jonathan White
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Jina Yun
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Meera Prasad
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | | | | | - Long Cai
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
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29
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Rodrigues F, Coman T, Fouquet G, Côté F, Courtois G, Trovati Maciel T, Hermine O. A deep dive into future therapies for microcytic anemias and clinical considerations. Expert Rev Hematol 2023; 16:349-364. [PMID: 37092971 DOI: 10.1080/17474086.2023.2206556] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/25/2023]
Abstract
INTRODUCTION Microcytic anemias (MA) have frequent or rare etiologies. New discoveries in understanding and treatment of microcytic anemias need to be reviewed. AREAS COVERED Microcytic anemias with a focus on most frequent causes and on monogenic diseases that are relevant for understanding biocellular mechanisms of MA. All treatments excepting gene therapy, with a focus on recent advances. Pubmed search with references selected by expert opinion. EXPERT OPINION As the genetic and cellular background of dyserythropoiesis will continue to be clarified, collaboration with bioengineering of treatments acting specifically at the protein domain level will continue to provide new therapies in haematology as well as oncology and neurology.
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Affiliation(s)
- François Rodrigues
- Université de Paris, service d'hématologie adultes, Hôpital Necker - Enfants Malades, Asrsistance Publique- Hôpitaux de Paris, France
- Inserm U1163, CNRS ERL8254 Imagine Institute, Paris, France
| | - Tereza Coman
- Inserm U1163, CNRS ERL8254 Imagine Institute, Paris, France
- Département d'hématologie, Institut Gustave Roussy, Villejuif, France
| | - Guillemette Fouquet
- Université de Paris, service d'hématologie adultes, Hôpital Necker - Enfants Malades, Asrsistance Publique- Hôpitaux de Paris, France
- Hématologie clinique, Centre Hospitalier Sud Francilien, Corbeil Essonnes, France
| | - Francine Côté
- Inserm U1163, CNRS ERL8254 Imagine Institute, Paris, France
| | | | | | - Olivier Hermine
- Université de Paris, service d'hématologie adultes, Hôpital Necker - Enfants Malades, Asrsistance Publique- Hôpitaux de Paris, France
- Inserm U1163, CNRS ERL8254 Imagine Institute, Paris, France
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30
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Bauer M, Aguilar G, Wharton KA, Matsuda S, Affolter M. Heterodimerization-dependent secretion of bone morphogenetic proteins in Drosophila. Dev Cell 2023; 58:645-659.e4. [PMID: 37054707 PMCID: PMC10303954 DOI: 10.1016/j.devcel.2023.03.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 01/13/2023] [Accepted: 03/09/2023] [Indexed: 04/15/2023]
Abstract
Combinatorial signaling is key to instruct context-dependent cell behaviors. During embryonic development, adult homeostasis, and disease, bone morphogenetic proteins (BMPs) act as dimers to instruct specific cellular responses. BMP ligands can form both homodimers or heterodimers; however, obtaining direct evidence of the endogenous localization and function of each form has proven challenging. Here, we make use of precise genome editing and direct protein manipulation via protein binders to dissect the existence and functional relevance of BMP homodimers and heterodimers in the Drosophila wing imaginal disc. This approach identified in situ the existence of Dpp (BMP2/4)/Gbb (BMP5/6/7/8) heterodimers. We found that Gbb is secreted in a Dpp-dependent manner in the wing imaginal disc. Dpp and Gbb form a gradient of heterodimers, whereas neither Dpp nor Gbb homodimers are evident under endogenous physiological conditions. We find that the formation of heterodimers is critical for obtaining optimal signaling and long-range BMP distribution.
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Affiliation(s)
- Milena Bauer
- Biozentrum, University of Basel, Spitalstrasse 41, 4056 Basel, Switzerland
| | - Gustavo Aguilar
- Biozentrum, University of Basel, Spitalstrasse 41, 4056 Basel, Switzerland
| | | | - Shinya Matsuda
- Biozentrum, University of Basel, Spitalstrasse 41, 4056 Basel, Switzerland.
| | - Markus Affolter
- Biozentrum, University of Basel, Spitalstrasse 41, 4056 Basel, Switzerland.
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31
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Collu GM, Mlodzik M. The beauty of seeing the real thing: BMP heterodimer detection in vivo reveals dimer composition and activity. Dev Cell 2023; 58:633-634. [PMID: 37098324 DOI: 10.1016/j.devcel.2023.03.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 03/30/2023] [Accepted: 03/30/2023] [Indexed: 04/27/2023]
Abstract
BMP family ligands can direct cells to divide, differentiate, or die, depending on cell context and specific hetero- or homodimer combinations. In this issue of Developmental Cell, Bauer et al. detect endogenous Drosophila ligand dimers in situ and show that BMP dimer composition affects both signaling range and activity.
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Affiliation(s)
- Giovanna M Collu
- Department of Cell, Developmental, and Regenerative Biology, Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Marek Mlodzik
- Department of Cell, Developmental, and Regenerative Biology, Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
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32
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Teague S, Primavera G, Chen B, Freeburne E, Khan H, Jo K, Johnson C, Heemskerk I. The time integral of BMP signaling determines fate in a stem cell model for early human development. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.10.536068. [PMID: 37090515 PMCID: PMC10120633 DOI: 10.1101/2023.04.10.536068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/25/2023]
Abstract
How paracrine signals are interpreted to yield multiple cell fate decisions in a dynamic context during human development in vivo and in vitro remains poorly understood. Here we report an automated tracking method to follow signaling histories linked to cell fate in large numbers of human pluripotent stem cells (hPSCs). Using an unbiased statistical approach, we discovered that measured BMP signaling history correlates strongly with fate in individual cells. We found that BMP response in hPSCs varies more strongly in the duration of signaling than the level. However, we discovered that both the level and duration of signaling activity control cell fate choices only by changing the time integral of signaling and that duration and level are therefore interchangeable in this context. In a stem cell model for patterning of the human embryo, we showed that signaling histories predict the fate pattern and that the integral model correctly predicts changes in cell fate domains when signaling is perturbed. Using an RNA-seq screen we then found that mechanistically, BMP signaling is integrated by SOX2.
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Affiliation(s)
- Seth Teague
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, Michigan
| | - Gillian Primavera
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, Michigan
| | - Bohan Chen
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, Michigan
| | - Emily Freeburne
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, Michigan
| | - Hina Khan
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, Michigan
| | - Kyoung Jo
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, Michigan
| | - Craig Johnson
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, Michigan
| | - Idse Heemskerk
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, Michigan
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, Michigan
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, Michigan
- Center for Cell Plasticity and Organ Design, University of Michigan Medical School, Ann Arbor, Michigan
- Department of Physics, University of Michigan, Ann Arbor, Michigan
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33
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Bohn S, Hexemer L, Huang Z, Strohmaier L, Lenhardt S, Legewie S, Loewer A. State- and stimulus-specific dynamics of SMAD signaling determine fate decisions in individual cells. Proc Natl Acad Sci U S A 2023; 120:e2210891120. [PMID: 36857347 PMCID: PMC10013741 DOI: 10.1073/pnas.2210891120] [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: 06/27/2022] [Accepted: 01/07/2023] [Indexed: 03/02/2023] Open
Abstract
SMAD-mediated signaling regulates apoptosis, cell cycle arrest, and epithelial-to-mesenchymal transition to safeguard tissue homeostasis. However, it remains elusive how the relatively simple pathway can determine such a broad range of cell fate decisions and how it differentiates between varying ligands. Here, we systematically investigate how SMAD-mediated responses are modulated by various ligands of the transforming growth factor β (TGFβ) family and compare these ligand responses in quiescent and proliferating MCF10A cells. We find that the nature of the phenotypic response is mainly determined by the proliferation status, with migration and cell cycle arrest being dominant in proliferating cells for all tested TGFβ family ligands, whereas cell death is the major outcome in quiescent cells. In both quiescent and proliferating cells, the identity of the ligand modulates the strength of the phenotypic response proportional to the dynamics of induced SMAD nuclear-to-cytoplasmic translocation and, as a consequence, the corresponding gene expression changes. Interestingly, the proliferation state of a cell has little impact on the set of genes induced by SMAD signaling; instead, it modulates the relative cellular sensitivity to TGFβ superfamily members. Taken together, diversity of SMAD-mediated responses is mediated by differing cellular states, which determine ligand sensitivity and phenotypic effects, while the pathway itself merely serves as a quantitative relay from the cell membrane to the nucleus.
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Affiliation(s)
- Stefan Bohn
- Department of Biology, Technical University Darmstadt, 64287Darmstadt, Germany
| | - Lorenz Hexemer
- Department of Systems Biology, Institute for Biomedical Genetics, University of Stuttgart, 70569Stuttgart, Germany
| | - Zixin Huang
- Department of Biology, Technical University Darmstadt, 64287Darmstadt, Germany
| | - Laura Strohmaier
- Department of Systems Biology, Institute for Biomedical Genetics, University of Stuttgart, 70569Stuttgart, Germany
| | - Sonja Lenhardt
- Department of Biology, Technical University Darmstadt, 64287Darmstadt, Germany
| | - Stefan Legewie
- Department of Systems Biology, Institute for Biomedical Genetics, University of Stuttgart, 70569Stuttgart, Germany
- Stuttgart Research Center for Systems Biology, University of Stuttgart, 70569Stuttgart, Germany
| | - Alexander Loewer
- Department of Biology, Technical University Darmstadt, 64287Darmstadt, Germany
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34
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Kieffer C, Genot AJ, Rondelez Y, Gines G. Molecular Computation for Molecular Classification. Adv Biol (Weinh) 2023; 7:e2200203. [PMID: 36709492 DOI: 10.1002/adbi.202200203] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 09/28/2022] [Indexed: 01/30/2023]
Abstract
DNA as an informational polymer has, for the past 30 years, progressively become an essential molecule to rationally build chemical reaction networks endowed with powerful signal-processing capabilities. Whether influenced by the silicon world or inspired by natural computation, molecular programming has gained attention for diagnosis applications. Of particular interest for this review, molecular classifiers have shown promising results for disease pattern recognition and sample classification. Because both input integration and computation are performed in a single tube, at the molecular level, this low-cost approach may come as a complementary tool to molecular profiling strategies, where all biomarkers are quantified independently using high-tech instrumentation. After introducing the elementary components of molecular classifiers, some of their experimental implementations are discussed either using digital Boolean logic or analog neural network architectures.
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Affiliation(s)
- Coline Kieffer
- Laboratoire Gulliver, UMR 7083, CNRS, ESPCI Paris, PSL Research University, 10 rue Vauquelin, Paris, 75005, France
| | - Anthony J Genot
- LIMMS, CNRS-Institute of Industrial Science, IRL 2820, University of Tokyo, Tokyo, 153-8505, Japan
| | - Yannick Rondelez
- Laboratoire Gulliver, UMR 7083, CNRS, ESPCI Paris, PSL Research University, 10 rue Vauquelin, Paris, 75005, France
| | - Guillaume Gines
- Laboratoire Gulliver, UMR 7083, CNRS, ESPCI Paris, PSL Research University, 10 rue Vauquelin, Paris, 75005, France
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35
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Chen X, Liu Z, Lou C, Guan Y, Ouyang Q, Xiang Y. Improving cooperativity of transcription activators by oligomerization domains in mammalian cells. Synth Syst Biotechnol 2023; 8:114-120. [PMID: 36605704 PMCID: PMC9804245 DOI: 10.1016/j.synbio.2022.12.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 12/12/2022] [Accepted: 12/14/2022] [Indexed: 12/23/2022] Open
Abstract
Cooperative activation is critical for the applications of synthetic biology in mammalian cells. In this study, we have developed cooperative transcription factor by fusing oligomerization domain in mammalian cells. Firstly, we demonstrated that two oligomerized domains (CI434 and CI) successfully improved transcription factor cooperativity in bacterial cells but failed to increase cooperativity in mammalian cells, possibly because the additional mammalian activation domain disrupted their oligomerization capability. Therefore, we chose a different type of oligomerized domain (CarHC), whose ability to oligomerize is not dependent on its C-terminal domains, to fuse with a transcription factor (RpaR) and activation domain (VTR3), forming a potential cooperative transcription activator RpaR-CarH-VTR3 for mammalian regulatory systems. Compared with RpaR-VTR3, the cooperativity of RpaR-CarH-VTR3 was significantly improved with higher Hill coefficient and a narrower input range in the inducible switch system in mammalian cells. Moreover, a mathematical model based on statistical mechanics model was developed and the simulation results supported the hypothesis that the tetramer of the CarH domain in mammalian cells was the reason for the cooperative capacity of RpaR-CarH-VTR3.
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Affiliation(s)
- Xinmao Chen
- School of Physics, Peking University, Beijing, 100871, China
| | - Ziming Liu
- Center for Cell and Gene Circuit Design, CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics, Shenzhen Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Chunbo Lou
- Center for Cell and Gene Circuit Design, CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics, Shenzhen Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Ying Guan
- School of Physics, Peking University, Beijing, 100871, China
- Department of Chemical Engineering, Tsinghua University, Beijing, 100871, China
- Center for Cell and Gene Circuit Design, CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics, Shenzhen Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Qi Ouyang
- School of Physics, Peking University, Beijing, 100871, China
| | - Yanhui Xiang
- Center for Cell and Gene Circuit Design, CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics, Shenzhen Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
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36
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Ullo MF, Case LB. How cells sense and integrate information from different sources. WIREs Mech Dis 2023:e1604. [PMID: 36781396 DOI: 10.1002/wsbm.1604] [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: 06/24/2022] [Revised: 01/06/2023] [Accepted: 01/24/2023] [Indexed: 02/15/2023]
Abstract
Cell signaling is a fundamental cellular process that enables cells to sense and respond to information in their surroundings. At the molecular level, signaling is primarily carried out by transmembrane protein receptors that can initiate complex downstream signal transduction cascades to alter cellular behavior. In the human body, different cells can be exposed to a wide variety of environmental conditions, and cells express diverse classes of receptors capable of sensing and integrating different signals. Furthermore, different receptors and signaling pathways can crosstalk with each other to calibrate the cellular response. Crosstalk occurs through multiple mechanisms at different levels of signaling pathways. In this review, we discuss how cells sense and integrate different chemical, mechanical, and spatial signals as well as the mechanisms of crosstalk between pathways. To illustrate these concepts, we use a few well-studied signaling pathways, including receptor tyrosine kinases and integrin receptors. Finally, we discuss the implications of dysregulated cellular sensing on driving diseases such as cancer. This article is categorized under: Cancer > Molecular and Cellular Physiology Metabolic Diseases > Molecular and Cellular Physiology.
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Affiliation(s)
- Maria F Ullo
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Lindsay B Case
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
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37
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Quist-Løkken I, Andersson-Rusch C, Kastnes MH, Kolos JM, Jatzlau J, Hella H, Olsen OE, Sundan A, Knaus P, Hausch F, Holien T. FKBP12 is a major regulator of ALK2 activity in multiple myeloma cells. Cell Commun Signal 2023; 21:25. [PMID: 36717825 PMCID: PMC9885706 DOI: 10.1186/s12964-022-01033-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Accepted: 12/28/2022] [Indexed: 01/31/2023] Open
Abstract
BACKGROUND The immunophilin FKBP12 binds to TGF-β family type I receptors, including the BMP type I receptor ALK2. FKBP12 keeps the type I receptor in an inactive state and controls signaling activity. Removal of FKBP12 with drugs such as the FKBP-ligand FK506 enhances BMP activity in various cell types. In multiple myeloma cells, activation of SMAD1/5/8 leads to apoptosis. We hypothesized that removing FKBP12 from ALK2 in myeloma cells would potentiate BMP-induced ALK2-SMAD1/5/8 activity and in consequence cell death. METHODS Multiple myeloma cell lines were treated with FK506, or other FKBP-binding compounds, combined with different BMPs before analyzing SMAD1/5/8 activity and cell viability. SMAD1/5/8 activity was also investigated using a reporter cell line, INA-6 BRE-luc. To characterize the functional signaling receptor complex, we genetically manipulated receptor expression by siRNA, shRNA and CRISPR/Cas9 technology. RESULTS FK506 potentiated BMP-induced SMAD1/5/8 activation and apoptosis in multiple myeloma cell lines. By using FKBP-binding compounds with different affinity profiles, and siRNA targeting FKBP12, we show that the FK506 effect is mediated by binding to FKBP12. Ligands that typically signal via ALK3 in myeloma cells, BMP2, BMP4, and BMP10, did not induce apoptosis in cells lacking ALK3. Notably, BMP10 competed with BMP6 and BMP9 and antagonized their activity via ALK2. However, upon addition of FK506, we saw a surprising shift in specificity, as the ALK3 ligands gained the ability to signal via ALK2 and induce apoptosis. This indicates that the receptor complex can switch from an inactive non-signaling complex (NSC) to an active one by adding FK506. This gain of activity was also seen in other cell types, indicating that the observed effects have broader relevance. BMP2, BMP4 and BMP10 depended on BMPR2 as type II receptor to signal, which contrasts with BMP6 and BMP9, that activate ALK2 more potently when BMPR2 is knocked down. CONCLUSIONS In summary, our data suggest that FKBP12 is a major regulator of ALK2 activity in multiple myeloma cells, partly by switching an NSC into an active signaling complex. FKBP12 targeting compounds devoid of immunosuppressing activity could have potential in novel treatment strategies aiming at reducing multiple myeloma tumor load. Video Abstract.
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Affiliation(s)
- Ingrid Quist-Løkken
- grid.5947.f0000 0001 1516 2393Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology - NTNU, Trondheim, Norway
| | - Clara Andersson-Rusch
- grid.5947.f0000 0001 1516 2393Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology - NTNU, Trondheim, Norway
| | - Martin Haugrud Kastnes
- grid.5947.f0000 0001 1516 2393Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology - NTNU, Trondheim, Norway ,grid.5947.f0000 0001 1516 2393Centre of Molecular Inflammation Research, Norwegian University of Science and Technology - NTNU, Trondheim, Norway
| | - Jürgen Markus Kolos
- grid.6546.10000 0001 0940 1669Department of Chemistry, Technical University of Darmstadt, Darmstadt, Germany
| | - Jerome Jatzlau
- grid.14095.390000 0000 9116 4836Institute for Chemistry and Biochemistry, Freie Universität Berlin, Berlin, Germany
| | - Hanne Hella
- grid.5947.f0000 0001 1516 2393Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology - NTNU, Trondheim, Norway
| | - Oddrun Elise Olsen
- grid.5947.f0000 0001 1516 2393Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology - NTNU, Trondheim, Norway
| | - Anders Sundan
- grid.5947.f0000 0001 1516 2393Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology - NTNU, Trondheim, Norway ,grid.5947.f0000 0001 1516 2393Centre of Molecular Inflammation Research, Norwegian University of Science and Technology - NTNU, Trondheim, Norway ,grid.52522.320000 0004 0627 3560Department of Hematology, St. Olav’s University Hospital, Trondheim, Norway
| | - Petra Knaus
- grid.14095.390000 0000 9116 4836Institute for Chemistry and Biochemistry, Freie Universität Berlin, Berlin, Germany
| | - Felix Hausch
- grid.6546.10000 0001 0940 1669Department of Chemistry, Technical University of Darmstadt, Darmstadt, Germany
| | - Toril Holien
- grid.5947.f0000 0001 1516 2393Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology - NTNU, Trondheim, Norway ,grid.52522.320000 0004 0627 3560Department of Immunology and Transfusion Medicine, St. Olav’s University Hospital, Trondheim, Norway ,grid.52522.320000 0004 0627 3560Department of Hematology, St. Olav’s University Hospital, Trondheim, Norway ,grid.5947.f0000 0001 1516 2393Department of Biomedical Laboratory Science, Norwegian University of Science and Technology - NTNU, Trondheim, Norway
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Chen X, Wang T, Guan Y, Ouyang Q, Lou C, Qian L. The Topological Characteristics of Biological Ratio-Sensing Networks. Life (Basel) 2023; 13:life13020351. [PMID: 36836707 PMCID: PMC9965423 DOI: 10.3390/life13020351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 01/12/2023] [Accepted: 01/21/2023] [Indexed: 01/31/2023] Open
Abstract
Ratio sensing is a fundamental biological function observed in signal transduction and decision making. In the synthetic biology context, ratio sensing presents one of the elementary functions for cellular multi-signal computation. To investigate the mechanism of the ratio-sensing behavior, we explored the topological characteristics of biological ratio-sensing networks. With exhaustive enumeration of three-node enzymatic and transcriptional regulatory networks, we found that robust ratio sensing was highly dependent on network structure rather than network complexity. Specifically, a set of seven minimal core topological structures and four motifs were deduced to be capable of robust ratio sensing. Further investigations on the evolutionary space of robust ratio-sensing networks revealed highly clustered domains surrounding the core motifs which suggested their evolutionary plausibility. Our study revealed the network topological design principles of ratio-sensing behavior and provided a design scheme for constructing regulatory circuits with ratio-sensing behavior in synthetic biology.
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Affiliation(s)
- Xinmao Chen
- School of Physics, Peking University, Beijing 100871, China
| | - Tianze Wang
- Center for Quantitative Biology, Peking University, Beijing 100871, China
| | - Ying Guan
- Center for Cell and Gene Circuit Design, CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics, Shenzhen Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Qi Ouyang
- School of Physics, Peking University, Beijing 100871, China
- Center for Quantitative Biology, Peking University, Beijing 100871, China
- Correspondence: (Q.O.); (C.L.); (L.Q.)
| | - Chunbo Lou
- Center for Cell and Gene Circuit Design, CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics, Shenzhen Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
- Correspondence: (Q.O.); (C.L.); (L.Q.)
| | - Long Qian
- Center for Quantitative Biology, Peking University, Beijing 100871, China
- Correspondence: (Q.O.); (C.L.); (L.Q.)
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Furlan G, Huyghe A, Combémorel N, Lavial F. Molecular versatility during pluripotency progression. Nat Commun 2023; 14:68. [PMID: 36604434 PMCID: PMC9814743 DOI: 10.1038/s41467-022-35775-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 12/22/2022] [Indexed: 01/07/2023] Open
Abstract
A challenge during development is to ensure lineage segregation while preserving plasticity. Using pluripotency progression as a paradigm, we review how developmental transitions are coordinated by redeployments, rather than global resettings, of cellular components. We highlight how changes in response to extrinsic cues (FGF, WNT, Activin/Nodal, Netrin-1), context- and stoichiometry-dependent action of transcription factors (Oct4, Nanog) and reconfigurations of epigenetic regulators (enhancers, promoters, TrxG, PRC) may confer robustness to naïve to primed pluripotency transition. We propose the notion of Molecular Versatility to regroup mechanisms by which molecules are repurposed to exert different, sometimes opposite, functions in close stem cell configurations.
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Affiliation(s)
- Giacomo Furlan
- Cellular reprogramming, stem cells and oncogenesis laboratory - Equipe labellisée La Ligue Contre le Cancer - LabEx Dev2Can - Univ Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Centre Léon Bérard, Cancer Research Center of Lyon, Lyon, 69008, France.,Lunenfeld-Tanenbaum Research Institute, University of Toronto, Toronto, ON, Canada
| | - Aurélia Huyghe
- Cellular reprogramming, stem cells and oncogenesis laboratory - Equipe labellisée La Ligue Contre le Cancer - LabEx Dev2Can - Univ Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Centre Léon Bérard, Cancer Research Center of Lyon, Lyon, 69008, France
| | - Noémie Combémorel
- Cellular reprogramming, stem cells and oncogenesis laboratory - Equipe labellisée La Ligue Contre le Cancer - LabEx Dev2Can - Univ Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Centre Léon Bérard, Cancer Research Center of Lyon, Lyon, 69008, France
| | - Fabrice Lavial
- Cellular reprogramming, stem cells and oncogenesis laboratory - Equipe labellisée La Ligue Contre le Cancer - LabEx Dev2Can - Univ Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Centre Léon Bérard, Cancer Research Center of Lyon, Lyon, 69008, France.
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40
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Bone morphogenetic protein 4 inhibits rat stem/progenitor Leydig cell development and regeneration via SMAD-dependent and SMAD-independent signaling. Cell Death Dis 2022; 13:1039. [PMID: 36513649 PMCID: PMC9748027 DOI: 10.1038/s41419-022-05471-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 11/22/2022] [Accepted: 11/25/2022] [Indexed: 12/15/2022]
Abstract
Bone morphogenetic protein 4 (BMP4) is an important member of the transforming growth factor-β superfamily. BMP4 is expressed in the Leydig cell lineage. We hypothesized that BMP4 might regulate the development of stem/progenitor Leydig cells. The BMP4 receptors, BMPR1A, BMPR1B, and BMPR2 were found to be expressed in progenitor Leydig cells of prepubertal testis and isolated cells. BMP4 at 1 and 10 ng/mL significantly reduced androgen production and down-regulated steroidogenesis-related gene and protein expression possibly by activating the SMAD signaling pathway (increasing SMAD1/5 phosphorylation and SMAD4) at 24 h treatment. BMP4 at 0.1 ng/mL and higher concentrations markedly reduced the EdU labeling index of CD90+ stem Leydig cells after 24 h treatment and significantly reduced the number of EdU+ stem Leydig cells on the surface of seminiferous tubules after 7 days of culture. BMP4 at 0.01 ng/mL and higher concentrations significantly blocked the differentiation of stem Leydig cells into adult cells, as shown by the reduction of testosterone secretion and the downregulation of Lhcgr, Scarb1, Cyp11a1, Hsd11b1, and Insl3 and their function after 3D seminiferous tubule culture for 3 weeks, and this effect was reversed by co-treatment with the BMP4 antagonists noggin and doxomorphine. In addition, BMP4 also blocked stem Leydig cell differentiation through SMAD-independent signaling pathways (ERK1/2 and AMPK). Ethanedimethane sulfonate (EDS) single injection can result in reduction of testosterone, restoration can happen post treatment. In an in vivo model of Leydig cell regeneration following EDS treatment, intratesticular injection of BMP4 from day 14 to day 28 post-elimination significantly reduced serum testosterone levels and down-regulated the expression of Scarb1, Star, Hsd11b1, and Insl3 and its proteins, possibly through SMAD-dependent and SMAD-independent (ERK1/2 and AMPK) signaling pathways. In conclusion, BMP4 is expressed in cells of the Leydig cell lineage and blocks entry of stem/progenitor Leydig cells into adult Leydig cells through SMAD-dependent and SMAD-independent signaling pathways.
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41
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Hanson RL, Batchelor E. Coordination of MAPK and p53 dynamics in the cellular responses to DNA damage and oxidative stress. Mol Syst Biol 2022; 18:e11401. [PMID: 36472304 PMCID: PMC9724178 DOI: 10.15252/msb.202211401] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 11/01/2022] [Accepted: 11/07/2022] [Indexed: 12/12/2022] Open
Abstract
In response to different cellular stresses, the transcription factor p53 undergoes different dynamics. p53 dynamics, in turn, control cell fate. However, distinct stresses can generate the same p53 dynamics but different cell fate outcomes, suggesting integration of dynamic information from other pathways is important for cell fate regulation. To determine how MAPK activities affect p53-mediated responses to DNA breaks and oxidative stress, we simultaneously tracked p53 and either ERK, JNK, or p38 activities in single cells. While p53 dynamics were comparable between the stresses, cell fate outcomes were distinct. Combining MAPK dynamics with p53 dynamics was important for distinguishing between the stresses and for generating temporal ordering of cell fate pathways. Furthermore, cross-talk between MAPKs and p53 controlled the balance between proliferation and cell death. These findings provide insight into how cells integrate signaling pathways with distinct temporal patterns of activity to encode stress specificity and drive different cell fate decisions.
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Affiliation(s)
- Ryan L Hanson
- Department of Integrative Biology and PhysiologyUniversity of MinnesotaMinneapolisMNUSA
| | - Eric Batchelor
- Department of Integrative Biology and PhysiologyUniversity of MinnesotaMinneapolisMNUSA,Masonic Cancer CenterUniversity of MinnesotaMinneapolisMNUSA
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42
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Peng J, Zhao J, Tang Q, Wang J, Song W, Lu X, Huang X, Chen G, Zheng W, Zhang L, Han Y, Yan C, Wan Q, Chen L. Low intensity near-infrared light promotes bone regeneration via circadian clock protein cryptochrome 1. Int J Oral Sci 2022; 14:53. [PMID: 36376275 PMCID: PMC9663728 DOI: 10.1038/s41368-022-00207-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 09/04/2022] [Accepted: 10/12/2022] [Indexed: 11/16/2022] Open
Abstract
Bone regeneration remains a great clinical challenge. Low intensity near-infrared (NIR) light showed strong potential to promote tissue regeneration, offering a promising strategy for bone defect regeneration. However, the effect and underlying mechanism of NIR on bone regeneration remain unclear. We demonstrated that bone regeneration in the rat skull defect model was significantly accelerated with low-intensity NIR stimulation. In vitro studies showed that NIR stimulation could promote the osteoblast differentiation in bone mesenchymal stem cells (BMSCs) and MC3T3-E1 cells, which was associated with increased ubiquitination of the core circadian clock protein Cryptochrome 1 (CRY1) in the nucleus. We found that the reduction of CRY1 induced by NIR light activated the bone morphogenetic protein (BMP) signaling pathways, promoting SMAD1/5/9 phosphorylation and increasing the expression levels of Runx2 and Osterix. NIR light treatment may act through sodium voltage-gated channel Scn4a, which may be a potential responder of NIR light to accelerate bone regeneration. Together, these findings suggest that low-intensity NIR light may promote in situ bone regeneration in a CRY1-dependent manner, providing a novel, efficient and non-invasive strategy to promote bone regeneration for clinical bone defects.
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43
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VandenBroek MM, Skebo SI, Ormiston ML. Targeting BMPR-II in pulmonary arterial hypertension: a case of Hercules versus the Hydra? Expert Opin Ther Targets 2022; 26:1027-1030. [PMID: 36638064 DOI: 10.1080/14728222.2022.2168188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
| | - Sofia I Skebo
- Department of Biology, Queen's University, Kingston, K7L, Canada
| | - Mark L Ormiston
- Department of Medicine, Queen's University, Kingston, K7L, Canada.,Departments of Biomedical and Molecular Sciences and Surgery, Queen's University, Kingston, K7L, Canada
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44
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England JL. Self-organized computation in the far-from-equilibrium cell. BIOPHYSICS REVIEWS 2022; 3:041303. [PMID: 38505518 PMCID: PMC10903489 DOI: 10.1063/5.0103151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 12/12/2022] [Indexed: 03/21/2024]
Abstract
Recent progress in our understanding of the physics of self-organization in active matter has pointed to the possibility of spontaneous collective behaviors that effectively compute things about the patterns in the surrounding patterned environment. Here, we describe this progress and speculate about its implications for our understanding of the internal organization of the living cell.
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Affiliation(s)
- Jeremy L England
- School of Physics, Georgia Institute of Technology, 837 State St NW, Atlanta, Georgia 30332, USA and GSK.ai, GlaxoSmithKline, 46 Menachem Begin, Ninth Floor, Tel Aviv, Israel
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45
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BMP/Smad Pathway Is Involved in Lithium Carbonate-Induced Neural-Tube Defects in Mice and Neural Stem Cells. Int J Mol Sci 2022; 23:ijms232314831. [PMID: 36499158 PMCID: PMC9735442 DOI: 10.3390/ijms232314831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 11/03/2022] [Accepted: 11/25/2022] [Indexed: 12/05/2022] Open
Abstract
Neural-tube defects (NTDs) are one type of the most serious birth defects. Studies have shown that inositol deficiency is closely related to the occurrence of NTDs. Bone morphogenetic protein (BMP)-mediated Smad signaling pathways have been implicated in neurogenesis and neural-tube closure. However, the role of the BMP/Smad pathway in inositol-deficiency-induced NTDs remains unclear. Inositol-deficiency models in C57 mice and mouse neural stem cells (mNSCs) were induced with Li2CO3 treatment or inositol withdrawal. The role of the BMP/Smad pathway in the regulation of cell proliferation and the development of NTDs was determined utilizing qRT-PCR, HE staining, Western blot, immunostaining, MTT assay, EdU staining, and flow cytometry. The intraperitoneal injection of Li2CO3 at Embryonic Day 7.5 induced the occurrence of NTDs. The mRNA levels of Bmp2, Bmp4, Smad1, Smad5, Smad8 and Runx2, the phosphorylation of Smad1/5/8, and the nuclear translocation of Runx2 were significantly increased in NTD embryonic brain tissues and mNSCs exposed to Li2CO3 or an inositol-free medium, which were suppressed by BMP receptor selective inhibitor LDN-193189. The Li2CO3-induced phosphorylation of Smad1/5/8 was inhibited by inositol supplementation. Cell proliferation was significantly promoted by Li2CO3 exposure or the absence of inositol in mNSCs, which was reversed by LDN-193189. These results suggest that the activation of the BMP/Smad signaling pathway might play an important role in the development of NTDs induced by maternal Li2CO3 exposure via inositol deficiency.
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46
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Zhang CH, Gao Y, Hung HH, Zhuo Z, Grodzinsky AJ, Lassar AB. Creb5 coordinates synovial joint formation with the genesis of articular cartilage. Nat Commun 2022; 13:7295. [PMID: 36435829 PMCID: PMC9701237 DOI: 10.1038/s41467-022-35010-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Accepted: 11/15/2022] [Indexed: 11/28/2022] Open
Abstract
While prior work has established that articular cartilage arises from Prg4-expressing perichondrial cells, it is not clear how this process is specifically restricted to the perichondrium of synovial joints. We document that the transcription factor Creb5 is necessary to initiate the expression of signaling molecules that both direct the formation of synovial joints and guide perichondrial tissue to form articular cartilage instead of bone. Creb5 promotes the generation of articular chondrocytes from perichondrial precursors in part by inducing expression of signaling molecules that block a Wnt5a autoregulatory loop in the perichondrium. Postnatal deletion of Creb5 in the articular cartilage leads to loss of both flat superficial zone articular chondrocytes coupled with a loss of both Prg4 and Wif1 expression in the articular cartilage; and a non-cell autonomous up-regulation of Ctgf. Our findings indicate that Creb5 promotes joint formation and the subsequent development of articular chondrocytes by driving the expression of signaling molecules that both specify the joint interzone and simultaneously inhibit a Wnt5a positive-feedback loop in the perichondrium.
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Affiliation(s)
- Cheng-Hai Zhang
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute at Harvard Medical School, 240 Longwood Ave., Boston, MA, 02115, USA.
| | - Yao Gao
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute at Harvard Medical School, 240 Longwood Ave., Boston, MA, 02115, USA
| | - Han-Hwa Hung
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Zhu Zhuo
- Bioinformatics Core, Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA
| | - Alan J Grodzinsky
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Andrew B Lassar
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute at Harvard Medical School, 240 Longwood Ave., Boston, MA, 02115, USA.
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Mathieu M, Friedrich C, Ducrot N, Zannoni J, Sylvie T, Jerraya N, Rousseaux S, Chuffart F, Kosmider O, Karim Z, Park S. Luspatercept (RAP-536) modulates oxidative stress without affecting mutation burden in myelodysplastic syndromes. Ann Hematol 2022; 101:2633-2643. [PMID: 36195681 DOI: 10.1007/s00277-022-04993-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 09/23/2022] [Indexed: 11/27/2022]
Abstract
In low-risk myelodysplastic syndrome (LR-MDS), erythropoietin (EPO) is widely used for the treatment of chronic anemia. However, initial response to EPO has time-limited effects. Luspatercept reduces red blood cell transfusion dependence in LR-MDS patients. Here, we investigated the molecular action of luspatercept (RAP-536) in an in vitro model of erythroid differentiation of MDS, and also in a in vivo PDX murine model with primary samples of MDS patients carrying or not SF3B1 mutation. In our in vitro model, RAP-536 promotes erythroid proliferation by increasing the number of cycling cells without any impact on apoptosis rates. RAP-536 promoted late erythroid precursor maturation while decreasing intracellular reactive oxygen species level. RNA sequencing of erythroid progenitors obtained under RAP-536 treatment showed an enrichment of genes implicated in positive regulation of response to oxidative stress and erythroid differentiation. In our PDX model, RAP-536 induces a higher hemoglobin level. RAP-536 did not modify variant allele frequencies in vitro and did not have any effect against leukemic burden in our PDX model. These results suggest that RAP-536 promotes in vivo and in vitro erythroid cell differentiation by decreasing ROS level without any remarkable impact on iron homeostasis and on mutated allele burden.
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Affiliation(s)
- Meunier Mathieu
- Department of Hematology, CHU Grenoble Alpes, CS10217, 38043, Grenoble cedex 09, France.
- CNRS UMR 5309, INSERM, U1209, Université Grenoble Alpes, Institute for Advanced Bioscience, 38700, Grenoble, France.
| | - Chloé Friedrich
- Institut Cochin, Department Development, Reproduction and Cancer, 75014, Paris, France
| | - Nicolas Ducrot
- Université de Paris, INSERM, CNRS, Centre de Recherche Sur L'Inflammation (CRI), 75018, Paris, France
| | - Johanna Zannoni
- CNRS UMR 5309, INSERM, U1209, Université Grenoble Alpes, Institute for Advanced Bioscience, 38700, Grenoble, France
| | - Tondeur Sylvie
- Laboratoire de Génétique Des Hémopathies, CHU Grenoble Alpes, Grenoble, France
| | - Nelly Jerraya
- CNRS UMR 5309, INSERM, U1209, Université Grenoble Alpes, Institute for Advanced Bioscience, 38700, Grenoble, France
| | - Sophie Rousseaux
- CNRS UMR 5309, INSERM, U1209, Université Grenoble Alpes, Institute for Advanced Bioscience, 38700, Grenoble, France
| | - Florent Chuffart
- CNRS UMR 5309, INSERM, U1209, Université Grenoble Alpes, Institute for Advanced Bioscience, 38700, Grenoble, France
| | - Olivier Kosmider
- Institut Cochin, Department Development, Reproduction and Cancer, 75014, Paris, France
- Hematology Department, Hôpital Cochin, Assistance Publique-Hôpitaux de Paris, Université de Paris (APHP-CUP), 75014, Paris, France
| | - Zoubida Karim
- Université de Toulouse, INSERM, CNRS, Institut Toulousain Des Maladies Infectieuses Et Inflammatoires (Infinity), Université Paul Sabatier (UPS), Toulouse, France
| | - Sophie Park
- Department of Hematology, CHU Grenoble Alpes, CS10217, 38043, Grenoble cedex 09, France.
- CNRS UMR 5309, INSERM, U1209, Université Grenoble Alpes, Institute for Advanced Bioscience, 38700, Grenoble, France.
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48
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Intrinsically disordered BMP4 morphogen and the beak of the finch: Co-option of an ancient axial patterning system. Int J Biol Macromol 2022; 219:366-373. [PMID: 35931296 DOI: 10.1016/j.ijbiomac.2022.07.203] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 07/25/2022] [Indexed: 12/24/2022]
Abstract
Darwin's finches, with the primary diversity in the shape and size of their beaks, represent an excellent model system to study speciation and adaptive evolution. It is generally held that evolution depends on the natural selection of heritable phenotypic variations originating from the genetic mutations. However, it is now increasingly evident that epigenetic transgenerational inheritance of phenotypic variation can also guide evolutionary change. Several studies have shown that the bone morphogenetic protein BMP4 is a major driver of beak morphology. A recent study explored variability of the morphological, genetic, and epigenetic differences in the adjacent "urban" and "rural" populations of two species of ground Darwin's finches on the Galápagos Islands and revealed significant changes in methylation patterns in several genes including those involved in the BMP/TGFß pathway in the sperm DNA compared to erythrocyte DNA. These observations indicated that epigenetic changes caused by environmental fluctuations can be passed on to the offspring. Nonetheless, the mechanism by which dysregulated expression of BMP4 impacts beak morphology remains poorly understood. Here, we show that BMP4 is an intrinsically disordered protein and present a causal a link between epigenetic changes, BMP4 dysregulation and the evolution of the beak of the finch by natural selection.
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49
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Yang M, Jin C, Cheng X, Liu T, Ji Y, Meng F, Han X, Liang Q, Cao X, Huang L, Du X, Zeng X, Bu G. Corticosterone triggers anti-proliferative and apoptotic effects, and downregulates the ACVR1-SMAD1-ID3 cascade in chicken ovarian prehierarchical, but not preovulatory granulosa cells. Mol Cell Endocrinol 2022; 552:111675. [PMID: 35577112 DOI: 10.1016/j.mce.2022.111675] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 05/04/2022] [Accepted: 05/08/2022] [Indexed: 10/18/2022]
Abstract
The coordinated proliferation and apoptosis of granulosa cells plays a critical role in follicular development. To identify the exact mechanisms of how stress-driven glucocorticoid production suppresses reproduction, granulosa cells were isolated from chicken follicles at different developmental stages and then treated with corticosterone. Using CCK-8, EDU and TUNEL assays, we showed that corticosterone could trigger both anti-proliferative and pro-apoptotic effects in granulosa cells from 6 to 8 mm follicles only, while depicting no influence on granulosa cells from any preovulatory follicles. High-throughput transcriptomic analysis identified 1362 transcripts showing differential expression profiles in granulosa cells from 6 to 8 mm follicles after corticosterone treatment. Interestingly, Kyoto Encyclopedia of Genes and Genomes enrichment analysis revealed that 17 genes were enriched in the TGF-β signaling pathway, and 13 showed differential expression patterns consistent with corticosterone-induced effects. The differential expression profiles of these 13 genes were examined by quantitative real-time PCR in cultured chicken ovarian granulosa cells at diverse developmental stages following corticosterone challenge for a short (8 h) or long period (24 h). After 24 h of treatment, INHBB, FST, FMOD, NOG, ACVR1, SMAD1 and ID3 were the genes that responded consistently with corticosterone-induced proliferative and apoptotic events in all granulosa cells detected. However, only ACVR1, SMAD1 and ID3 could initiate coincident expression patterns after being treated for 8 h, suggesting their significance in corticosterone-mediated actions. Collectively, these findings indicate that corticosterone can inhibit proliferation and cause apoptosis in chicken ovarian prehierarchical, but not preovulatory granulosa cells, through impeding ACVR1-SMAD1-ID3 signaling presumptively.
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Affiliation(s)
- Ming Yang
- Isotope Research Laboratory, College of Life Science, Sichuan Agricultural University, Xinkang Road, Ya'an, 625014, PR China
| | - Chenchen Jin
- Department of Bio-engineering and Applied Biology, College of Life Science, Sichuan Agricultural University, Xinkang Road, Ya'an, 625014, PR China
| | - Xinyue Cheng
- Department of Bio-engineering and Applied Biology, College of Life Science, Sichuan Agricultural University, Xinkang Road, Ya'an, 625014, PR China
| | - Tuoyuan Liu
- Isotope Research Laboratory, College of Life Science, Sichuan Agricultural University, Xinkang Road, Ya'an, 625014, PR China
| | - Yu Ji
- Department of Bio-engineering and Applied Biology, College of Life Science, Sichuan Agricultural University, Xinkang Road, Ya'an, 625014, PR China
| | - Fengyan Meng
- Isotope Research Laboratory, College of Life Science, Sichuan Agricultural University, Xinkang Road, Ya'an, 625014, PR China; Department of Bio-engineering and Applied Biology, College of Life Science, Sichuan Agricultural University, Xinkang Road, Ya'an, 625014, PR China
| | - Xingfa Han
- Isotope Research Laboratory, College of Life Science, Sichuan Agricultural University, Xinkang Road, Ya'an, 625014, PR China; Department of Bio-engineering and Applied Biology, College of Life Science, Sichuan Agricultural University, Xinkang Road, Ya'an, 625014, PR China
| | - Qiuxia Liang
- Isotope Research Laboratory, College of Life Science, Sichuan Agricultural University, Xinkang Road, Ya'an, 625014, PR China; Department of Bio-engineering and Applied Biology, College of Life Science, Sichuan Agricultural University, Xinkang Road, Ya'an, 625014, PR China
| | - Xiaohan Cao
- Isotope Research Laboratory, College of Life Science, Sichuan Agricultural University, Xinkang Road, Ya'an, 625014, PR China; Department of Bio-engineering and Applied Biology, College of Life Science, Sichuan Agricultural University, Xinkang Road, Ya'an, 625014, PR China
| | - Linyan Huang
- Isotope Research Laboratory, College of Life Science, Sichuan Agricultural University, Xinkang Road, Ya'an, 625014, PR China; Department of Bio-engineering and Applied Biology, College of Life Science, Sichuan Agricultural University, Xinkang Road, Ya'an, 625014, PR China
| | - Xiaogang Du
- Isotope Research Laboratory, College of Life Science, Sichuan Agricultural University, Xinkang Road, Ya'an, 625014, PR China; Department of Bio-engineering and Applied Biology, College of Life Science, Sichuan Agricultural University, Xinkang Road, Ya'an, 625014, PR China
| | - Xianyin Zeng
- Isotope Research Laboratory, College of Life Science, Sichuan Agricultural University, Xinkang Road, Ya'an, 625014, PR China; Department of Bio-engineering and Applied Biology, College of Life Science, Sichuan Agricultural University, Xinkang Road, Ya'an, 625014, PR China.
| | - Guixian Bu
- Isotope Research Laboratory, College of Life Science, Sichuan Agricultural University, Xinkang Road, Ya'an, 625014, PR China; Department of Bio-engineering and Applied Biology, College of Life Science, Sichuan Agricultural University, Xinkang Road, Ya'an, 625014, PR China.
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50
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Emiliani FE, Hsu I, McKenna A. Multiplexed Assembly and Annotation of Synthetic Biology Constructs Using Long-Read Nanopore Sequencing. ACS Synth Biol 2022; 11:2238-2246. [PMID: 35695379 PMCID: PMC9295152 DOI: 10.1021/acssynbio.2c00126] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
Recombinant DNA is
a fundamental tool in biotechnology and medicine.
These DNA sequences are often built, replicated, and delivered in
the form of plasmids. Validation of these plasmid sequences is a critical
and time-consuming step, which has been dominated for the last 35
years by Sanger sequencing. As plasmid sequences grow more complex
with new DNA synthesis and cloning techniques, we need new approaches
that address the corresponding validation challenges at scale. Here
we prototype a high-throughput plasmid sequencing approach using DNA
transposition and Oxford Nanopore sequencing. Our method, Circuit-seq,
creates robust, full-length, and accurate plasmid assemblies without
prior knowledge of the underlying sequence. We demonstrate the power
of Circuit-seq across a wide range of plasmid sizes and complexities,
generating full-length, contiguous plasmid maps. We then leverage
our long-read data to characterize epigenetic marks and estimate plasmid
contamination levels. Circuit-seq scales to large numbers of samples
at a lower per-sample cost than commercial Sanger sequencing, accelerating
a key step in synthetic biology, while low equipment costs make it
practical for individual laboratories.
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Affiliation(s)
- Francesco E Emiliani
- Department of Molecular and Systems Biology, Geisel School of Medicine, Dartmouth College, Lebanon, New Hampshire 03756, United States
| | - Ian Hsu
- Department of Molecular and Systems Biology, Geisel School of Medicine, Dartmouth College, Lebanon, New Hampshire 03756, United States
| | - Aaron McKenna
- Department of Molecular and Systems Biology, Geisel School of Medicine, Dartmouth College, Lebanon, New Hampshire 03756, United States.,Norris Cotton Cancer Center, Dartmouth-Hitchcock Medical Center, Lebanon, New Hampshire 03756, United States
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