101
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Gene Expression at a Single Molecule Level: Implications for MDS and AML. Blood 2021; 138:625-636. [PMID: 34157070 DOI: 10.1182/blood.2019004261] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 12/03/2020] [Indexed: 12/11/2022] Open
Abstract
Non-genetic heterogeneity, or gene expression stochasticity, is an important source of variability in biological systems. With the advent and improvement of single molecule resolution technologies, it has been shown that transcription dynamics and resultant transcript number fluctuations generate significant cell-to-cell variability that has important biological effects and may contribute substantially to both tissue homeostasis and disease. In this respect, the pathophysiology of stem cell-derived malignancies such as AML and MDS, which has historically been studied at the ensemble level, may require re-evaluation. To that end, it is our aim in this review to highlight the results of recent single-molecule, biophysical, and systems studies of gene expression dynamics, with the explicit purpose of demonstrating how the insights from these basic science studies may help inform and progress the field of leukemia biology and, ultimately, research into novel therapies.
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102
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Covert MW, Gillies TE, Kudo T, Agmon E. A forecast for large-scale, predictive biology: Lessons from meteorology. Cell Syst 2021; 12:488-496. [PMID: 34139161 PMCID: PMC8217727 DOI: 10.1016/j.cels.2021.05.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 04/01/2021] [Accepted: 05/18/2021] [Indexed: 11/19/2022]
Abstract
Quantitative systems biology, in which predictive mathematical models are constructed to guide the design of experiments and predict experimental outcomes, is at an exciting transition point, where the foundational scientific principles are becoming established, but the impact is not yet global. The next steps necessary for mathematical modeling to transform biological research and applications, in the same way it has already transformed other fields, is not completely clear. The purpose of this perspective is to forecast possible answers to this question-what needs to happen next-by drawing on the experience gained in another field, specifically meteorology. We review here a number of lessons learned in weather prediction that are directly relevant to biological systems modeling, and that we believe can enable the same kinds of global impact in our field as atmospheric modeling makes today.
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Affiliation(s)
- Markus W Covert
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA.
| | - Taryn E Gillies
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Takamasa Kudo
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA 94305, USA
| | - Eran Agmon
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
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103
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Wu Y, Wu J, Deng M, Lin Y. Yeast cell fate control by temporal redundancy modulation of transcription factor paralogs. Nat Commun 2021; 12:3145. [PMID: 34035307 PMCID: PMC8149833 DOI: 10.1038/s41467-021-23425-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 04/28/2021] [Indexed: 11/19/2022] Open
Abstract
Recent single-cell studies have revealed that yeast stress response involves transcription factors that are activated in pulses. However, it remains unclear whether and how these dynamic transcription factors temporally interact to regulate stress survival. Here we show that budding yeast cells can exploit the temporal relationship between paralogous general stress regulators, Msn2 and Msn4, during stress response. We find that individual pulses of Msn2 and Msn4 are largely redundant, and cells can enhance the expression of their shared targets by increasing their temporal divergence. Thus, functional redundancy between these two paralogs is modulated in a dynamic manner to confer fitness advantages for yeast cells, which might feed back to promote the preservation of their redundancy. This evolutionary implication is supported by evidence from Msn2/Msn4 orthologs and analyses of other transcription factor paralogs. Together, we show a cell fate control mechanism through temporal redundancy modulation in yeast, which may represent an evolutionarily important strategy for maintaining functional redundancy between gene duplicates.
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Affiliation(s)
- Yan Wu
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
- The MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, Beijing, China
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
- School of Mathematical Sciences, Peking University, Beijing, China
| | - Jiaqi Wu
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
- The MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, Beijing, China
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Minghua Deng
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
- School of Mathematical Sciences, Peking University, Beijing, China
- Center for Statistical Science, Peking University, Beijing, China
| | - Yihan Lin
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China.
- The MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, Beijing, China.
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China.
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104
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Murugan A, Husain K, Rust MJ, Hepler C, Bass J, Pietsch JMJ, Swain PS, Jena SG, Toettcher JE, Chakraborty AK, Sprenger KG, Mora T, Walczak AM, Rivoire O, Wang S, Wood KB, Skanata A, Kussell E, Ranganathan R, Shih HY, Goldenfeld N. Roadmap on biology in time varying environments. Phys Biol 2021; 18:10.1088/1478-3975/abde8d. [PMID: 33477124 PMCID: PMC8652373 DOI: 10.1088/1478-3975/abde8d] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 01/21/2021] [Indexed: 02/02/2023]
Abstract
Biological organisms experience constantly changing environments, from sudden changes in physiology brought about by feeding, to the regular rising and setting of the Sun, to ecological changes over evolutionary timescales. Living organisms have evolved to thrive in this changing world but the general principles by which organisms shape and are shaped by time varying environments remain elusive. Our understanding is particularly poor in the intermediate regime with no separation of timescales, where the environment changes on the same timescale as the physiological or evolutionary response. Experiments to systematically characterize the response to dynamic environments are challenging since such environments are inherently high dimensional. This roadmap deals with the unique role played by time varying environments in biological phenomena across scales, from physiology to evolution, seeking to emphasize the commonalities and the challenges faced in this emerging area of research.
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Affiliation(s)
- Arvind Murugan
- James Franck Institute, Department of Physics, University of Chicago, Chicago, IL 60637, United States of America
| | - Kabir Husain
- James Franck Institute, Department of Physics, University of Chicago, Chicago, IL 60637, United States of America
| | - Michael J Rust
- Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, IL 60637, United States of America
- Department of Physics, University of Chicago, Chicago, IL 60637, United States of America
| | - Chelsea Hepler
- Department of Medicine, Feinberg School of Medicine, Division of Endocrinology, Metabolism and Molecular Medicine, Northwestern University, Chicago, IL 60611, United States of America
| | - Joseph Bass
- Department of Medicine, Feinberg School of Medicine, Division of Endocrinology, Metabolism and Molecular Medicine, Northwestern University, Chicago, IL 60611, United States of America
| | - Julian M J Pietsch
- SynthSys: Centre for Synthetic and Systems Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, United Kingdom
| | - Peter S Swain
- SynthSys: Centre for Synthetic and Systems Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, United Kingdom
| | - Siddhartha G Jena
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, United States of America
| | - Jared E Toettcher
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, United States of America
| | - Arup K Chakraborty
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States of America
- Department of Physics, Massachusetts Institute of Technology, Cambridge, MA 02139, United States of America
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, United States of America
- Institute for Medical Engineering & Science, Massachusetts Institute of Technology, Cambridge, MA 02139, United States of America
- Ragon Institute of the Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard, Cambridge, MA 02139, United States of America
| | - Kayla G Sprenger
- Institute for Medical Engineering & Science, Massachusetts Institute of Technology, Cambridge, MA 02139, United States of America
- Ragon Institute of the Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard, Cambridge, MA 02139, United States of America
| | - T Mora
- Laboratoire de physique, Ecole normale supérieure, CNRS, PSL Research University, Paris, France
| | - A M Walczak
- Laboratoire de physique, Ecole normale supérieure, CNRS, PSL Research University, Paris, France
| | - O Rivoire
- Center for Interdisciplinary Research in Biology (CIRB), Collège de France, CNRS, INSERM, PSL Research University, Paris, France
| | - Shenshen Wang
- Department of Physics and Astronomy, University of California, Los Angeles, Los Angeles, CA 90095, United States of America
| | - Kevin B Wood
- Departments of Biophysics and Physics, University of Michigan, Ann Arbor, MI 48109-1055, United States of America
| | - Antun Skanata
- Center for Genomics and Systems Biology, New York University, 12 Waverly Place, Rm. 206, New York, NY 10003, United States of America
| | - Edo Kussell
- Center for Genomics and Systems Biology, New York University, 12 Waverly Place, Rm. 206, New York, NY 10003, United States of America
| | - Rama Ranganathan
- Center for Physics of Evolving Systems, Biochemistry & Molecular Biology, and the Pritzker School for Molecular Engineering, University of Chicago, Chicago IL 60637, United States of America
| | - Hong-Yan Shih
- Department of Physics, University of Illinois at Urbana-Champaign, Champaign, Illinois 61801, United States of America
- Institute of Physics, Academia Sinica, Taipei 11529, Taiwan
| | - Nigel Goldenfeld
- Department of Physics, University of Illinois at Urbana-Champaign, Champaign, Illinois 61801, United States of America
- Carl R Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Champaign, Illinois 61801, United States of America
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105
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Cytokine combinations for human blood stem cell expansion induce cell type- and cytokine-specific signaling dynamics. Blood 2021; 138:847-857. [PMID: 33988686 DOI: 10.1182/blood.2020008386] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Accepted: 04/23/2021] [Indexed: 11/20/2022] Open
Abstract
How hematopoietic stem cells (HSCs) integrate signals from their environment to make fate decisions remains incompletely understood. Current knowledge is based on either averages of heterogeneous populations or snapshot analyses, both missing important information about the dynamics of intracellular signaling activity. By combining fluorescent biosensors with time-lapse imaging and microfluidics, we measured the activity of the extracellular signal-regulated kinase (ERK) pathway over time (i.e. dynamics) in live single human umbilical cord blood HSCs and multipotent progenitor cells (MPPs). In single cells, ERK signaling dynamics were highly heterogeneous and depended on the cytokines, their combinations, and cell types. ERK signaling was activated by SCF and FLT3L in HSCs, but by SCF, IL3 and GCSF in MPPs. Different cytokines and their combinations led to distinct ERK signaling dynamics frequencies, and ERK dynamics in HSCs were more transient than those in MPPs. A combination of 5 cytokines recently shown to maintain HSCs in long-term culture, had a more-than-additive effect in eliciting sustained ERK dynamics in HSCs. ERK signaling dynamics also predicted future cell fates. E.g. CD45RA expression increased more in HSC daughters with intermediate than with transient or sustained ERK signaling. We demonstrate heterogeneous, cytokine- and cell type- specific ERK signaling dynamics, illustrating their relevance in regulating HSPC fates.
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106
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Adelaja A, Taylor B, Sheu KM, Liu Y, Luecke S, Hoffmann A. Six distinct NFκB signaling codons convey discrete information to distinguish stimuli and enable appropriate macrophage responses. Immunity 2021; 54:916-930.e7. [PMID: 33979588 PMCID: PMC8184127 DOI: 10.1016/j.immuni.2021.04.011] [Citation(s) in RCA: 55] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Revised: 12/21/2020] [Accepted: 04/13/2021] [Indexed: 12/12/2022]
Abstract
Macrophages initiate inflammatory responses via the transcription factor NFκB. The temporal pattern of NFκB activity determines which genes are expressed and thus, the type of response that ensues. Here, we examined how information about the stimulus is encoded in the dynamics of NFκB activity. We generated an mVenus-RelA reporter mouse line to enable high-throughput live-cell analysis of primary macrophages responding to host- and pathogen-derived stimuli. An information-theoretic workflow identified six dynamical features-termed signaling codons-that convey stimulus information to the nucleus. In particular, oscillatory trajectories were a hallmark of responses to cytokine but not pathogen-derived stimuli. Single-cell imaging and RNA sequencing of macrophages from a mouse model of Sjögren's syndrome revealed inappropriate responses to stimuli, suggestive of confusion of two NFκB signaling codons. Thus, the dynamics of NFκB signaling classify immune threats through six signaling codons, and signal confusion based on defective codon deployment may underlie the etiology of some inflammatory diseases.
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Affiliation(s)
- Adewunmi Adelaja
- Institute for Quantitative and Computational Biosciences (QCBio), Molecular Biology Institute (MBI), and Department of Microbiology, Immunology, and Molecular Genetics (MIMG), University of California, Los Angeles (UCLA), 611 Charles E. Young Dr S, Los Angeles, CA 90093
| | - Brooks Taylor
- Institute for Quantitative and Computational Biosciences (QCBio), Molecular Biology Institute (MBI), and Department of Microbiology, Immunology, and Molecular Genetics (MIMG), University of California, Los Angeles (UCLA), 611 Charles E. Young Dr S, Los Angeles, CA 90093
| | - Katherine M Sheu
- Institute for Quantitative and Computational Biosciences (QCBio), Molecular Biology Institute (MBI), and Department of Microbiology, Immunology, and Molecular Genetics (MIMG), University of California, Los Angeles (UCLA), 611 Charles E. Young Dr S, Los Angeles, CA 90093
| | - Yi Liu
- Institute for Quantitative and Computational Biosciences (QCBio), Molecular Biology Institute (MBI), and Department of Microbiology, Immunology, and Molecular Genetics (MIMG), University of California, Los Angeles (UCLA), 611 Charles E. Young Dr S, Los Angeles, CA 90093
| | - Stefanie Luecke
- Institute for Quantitative and Computational Biosciences (QCBio), Molecular Biology Institute (MBI), and Department of Microbiology, Immunology, and Molecular Genetics (MIMG), University of California, Los Angeles (UCLA), 611 Charles E. Young Dr S, Los Angeles, CA 90093
| | - Alexander Hoffmann
- Institute for Quantitative and Computational Biosciences (QCBio), Molecular Biology Institute (MBI), and Department of Microbiology, Immunology, and Molecular Genetics (MIMG), University of California, Los Angeles (UCLA), 611 Charles E. Young Dr S, Los Angeles, CA 90093.
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107
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Zhu Z, Wang Y, Peng R, Chen P, Geng Y, He B, Ouyang S, Zheng K, Fan Y, Pan D, Jin N, Rudolf F, Hierlemann A. A microfluidic single-cell array for in situ laminar-flow-based comparative culturing of budding yeast cells. Talanta 2021; 231:122401. [PMID: 33965050 DOI: 10.1016/j.talanta.2021.122401] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2021] [Revised: 04/01/2021] [Accepted: 04/02/2021] [Indexed: 01/09/2023]
Abstract
To facilitate in situ comparative culturing of budding yeast cells in a precisely controlled microenvironment, we developed a microfluidic single-cell array (MiSCA) with 96 traps (16 rows × 6 columns) for single-cell immobilization. Through optimization of the distances between neighboring traps and the applied flow rates by using a hydraulic equivalent circuit of the fluidic network, yeast cells were delivered to each column of the array by laminar focused flows and reliably captured at the traps by hydrodynamic forces with about 90% efficiency of cell immobilization. Immobilized cells in different columns within the same device can then be cultured in parallel while being exposed to different media and compounds delivered by laminar flows. For biological validation of the comparative cell-culturing device, we used budding yeast that can express yellow fluorescent protein upon the addition of β-estradiol in cell-culturing medium. Experimental results show successful induction of fluorescence in cells immobilized in desired columns that have been dosed with β-estradiol. The MiSCA system allows for performing sets of experiments and control experiments in parallel in the same device, or for executing comparative experiments under well-defined laminar-perfusion conditions with different media, as well as in situ monitoring of dynamic cellular responses upon different analytical compounds or reagents for single-cell analysis.
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Affiliation(s)
- Zhen Zhu
- Southeast University, Key Laboratory of MEMS of Ministry of Education, Sipailou 2, Nanjing, 210096, China; ETH Zurich, Department of Biosystems Science and Engineering, Mattenstrasse 26, Basel, 4058, Switzerland.
| | - Yingying Wang
- Southeast University, Key Laboratory of MEMS of Ministry of Education, Sipailou 2, Nanjing, 210096, China
| | - Ruobo Peng
- ETH Zurich, Department of Biosystems Science and Engineering, Mattenstrasse 26, Basel, 4058, Switzerland
| | - Pan Chen
- Southeast University, Key Laboratory of MEMS of Ministry of Education, Sipailou 2, Nanjing, 210096, China
| | - Yangye Geng
- Southeast University, Key Laboratory of MEMS of Ministry of Education, Sipailou 2, Nanjing, 210096, China
| | - Bailiang He
- Southeast University, Key Laboratory of MEMS of Ministry of Education, Sipailou 2, Nanjing, 210096, China
| | - Shuiping Ouyang
- Nanjing Forestry University, College of Chemical Engineering, Longpan Road 159, Nanjing, 210037, China
| | - Ke Zheng
- Nanjing Forestry University, College of Chemical Engineering, Longpan Road 159, Nanjing, 210037, China
| | - Yimin Fan
- Nanjing Forestry University, College of Chemical Engineering, Longpan Road 159, Nanjing, 210037, China
| | - Dejing Pan
- Soochow University, CAM-SU Genomic Resource Center, Ren-ai Road 199, Suzhou, 215213, China
| | - Nan Jin
- Southeast University, ZhongDa Hospital, Dingjiaqiao 87, Nanjing, 210009, China
| | - Fabian Rudolf
- ETH Zurich, Department of Biosystems Science and Engineering, Mattenstrasse 26, Basel, 4058, Switzerland
| | - Andreas Hierlemann
- ETH Zurich, Department of Biosystems Science and Engineering, Mattenstrasse 26, Basel, 4058, Switzerland
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108
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Budikhina AS, Murugina NE, Maximchik PV, Dagil YA, Nikolaeva AM, Balyasova LS, Murugin VV, Selezneva EM, Pashchenkova YG, Chkadua GZ, Pinegin BV, Pashenkov MV. Interplay between NOD1 and TLR4 Receptors in Macrophages: Nonsynergistic Activation of Signaling Pathways Results in Synergistic Induction of Proinflammatory Gene Expression. THE JOURNAL OF IMMUNOLOGY 2021; 206:2206-2220. [PMID: 33846227 DOI: 10.4049/jimmunol.2000692] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Accepted: 02/21/2021] [Indexed: 11/19/2022]
Abstract
Interactions between pattern-recognition receptors shape innate immune responses to pathogens. NOD1 and TLR4 are synergistically interacting receptors playing a pivotal role in the recognition of Gram-negative bacteria. However, mechanisms of their cooperation are poorly understood. It is unclear whether synergy is produced at the level of signaling pathways downstream of NOD1 and TLR4 or at more distal levels such as gene transcription. We analyzed sequential stages of human macrophage activation by a combination of NOD1 and TLR4 agonists (N-acetyl-d-muramyl-l-alanyl-d-isoglutamyl-meso-diaminopimelic acid [M-triDAP] and LPS, respectively). We show that events preceding or not requiring activation of transcription, such as activation of signaling kinases, rapid boost of glycolysis, and most importantly, nuclear translocation of NF-κB, are regulated nonsynergistically. However, at the output of the nucleus, the combination of M-triDAP and LPS synergistically induces expression of a subset of M-triDAP- and LPS-inducible genes, particularly those encoding proinflammatory cytokines (TNF, IL1B, IL6, IL12B, and IL23A). This synergistic response develops between 1 and 4 h of agonist treatment and requires continuous signaling through NOD1. The synergistically regulated genes have a lower basal expression and higher inducibility at 4 h than those regulated nonsynergistically. Both gene subsets include NF-κB-inducible genes. Therefore, activation of the NF-κB pathway does not explain synergistic gene induction, implying involvement of other transcription factors. Inhibition of IKKβ or p38 MAPK lowers agonist-induced TNF mRNA expression but does not abolish synergy. Thus, nonsynergistic activation of NOD1- and TLR4-dependent signaling pathways results in the synergistic induction of a proinflammatory transcriptional program.
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Affiliation(s)
- Anna S Budikhina
- Laboratory of Clinical Immunology, National Research Center Institute of Immunology of the Federal Medical-Biological Agency of Russia, Moscow, Russia
| | - Nina E Murugina
- Laboratory of Clinical Immunology, National Research Center Institute of Immunology of the Federal Medical-Biological Agency of Russia, Moscow, Russia
| | - Polina V Maximchik
- Faculty of Fundamental Medicine, Lomonosov Moscow State University, Moscow, Russia
| | - Yulia A Dagil
- Laboratory of Clinical Immunology, National Research Center Institute of Immunology of the Federal Medical-Biological Agency of Russia, Moscow, Russia
| | - Anna M Nikolaeva
- Laboratory of Clinical Immunology, National Research Center Institute of Immunology of the Federal Medical-Biological Agency of Russia, Moscow, Russia.,Biological Faculty, Lomonosov Moscow State University, Moscow, Russia; and
| | - Lyudmila S Balyasova
- Laboratory of Clinical Immunology, National Research Center Institute of Immunology of the Federal Medical-Biological Agency of Russia, Moscow, Russia
| | - Vladimir V Murugin
- Laboratory of Clinical Immunology, National Research Center Institute of Immunology of the Federal Medical-Biological Agency of Russia, Moscow, Russia
| | | | - Yulia G Pashchenkova
- Laboratory of Clinical Immunology, National Research Center Institute of Immunology of the Federal Medical-Biological Agency of Russia, Moscow, Russia
| | - Georgy Z Chkadua
- Laboratory of Experimental Diagnostics and Biotherapy of Tumors, N.N. Blokhin National Medical Research Center of Oncology of the Ministry of Health of the Russian Federation, Moscow, Russia
| | - Boris V Pinegin
- Laboratory of Clinical Immunology, National Research Center Institute of Immunology of the Federal Medical-Biological Agency of Russia, Moscow, Russia
| | - Mikhail V Pashenkov
- Laboratory of Clinical Immunology, National Research Center Institute of Immunology of the Federal Medical-Biological Agency of Russia, Moscow, Russia;
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109
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Che B, Zhao W, Liu Y, Sun D, Jing G, Bai J, Feng X, Zhang C. Dynamic intracellular mechanical cues facilitate collective signaling responses. iScience 2021; 24:102396. [PMID: 33997681 PMCID: PMC8091894 DOI: 10.1016/j.isci.2021.102396] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 02/11/2021] [Accepted: 04/02/2021] [Indexed: 12/02/2022] Open
Abstract
Collective behavior emerges in diverse life machineries, e.g., the immune responses to dynamic stimulations. The essential questions that arise here are that whether and how cells in vivo collectively respond to stimulation frequencies higher than their intrinsic natural values, e.g., the acute inflammation conditions. In this work, we systematically studied morphological and signaling responses of population fibroblasts in an interconnected cell monolayer and uncovered that, besides the natural NF-κB oscillation frequency of 1/90 min−1, collective signaling response emerges in the cell monolayer at 1/20 min−1 TNF-α input periodicity as well. Using a customized microfluidic device, we independently induced dynamic chemical stimulation and cytoskeleton reorganization on the stand-alone cells to exclude the effect of cell-cell communication. Our results reveal that, at this particular frequency, chemical stimulation is translated into dynamic intracellular mechanical cues through RAC1-medicated induction of dynamic cell-cell connections and cytoskeleton reorganizations, which synergize with chemical input to facilitate collective signaling responses. Dynamic intracellular mechanical cues facilitate collective cellular responses The dynamic chemical stimulations are translated into intracellular mechanical cues The synergy between dynamic mechanical and chemical signal plays crucial roles
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Affiliation(s)
- Bingchen Che
- State Key Laboratory of Photon-Technology in Western China Energy, Institute of Photonics and Photon-Technology, Northwest University, Xi'an 710069, China
| | - Wei Zhao
- State Key Laboratory of Photon-Technology in Western China Energy, Institute of Photonics and Photon-Technology, Northwest University, Xi'an 710069, China
| | - Yanan Liu
- School of Physics, Northwest University, Xi'an 710069, China
| | - Dan Sun
- State Key Laboratory of Photon-Technology in Western China Energy, Institute of Photonics and Photon-Technology, Northwest University, Xi'an 710069, China
| | - Guangyin Jing
- School of Physics, Northwest University, Xi'an 710069, China
| | - Jintao Bai
- State Key Laboratory of Photon-Technology in Western China Energy, Institute of Photonics and Photon-Technology, Northwest University, Xi'an 710069, China
| | - Xiqiao Feng
- Institute of Biomechanics and Medical Engineering, Department of Engineering Mechanics, Tsinghua University, Beijing 100084, China
| | - Ce Zhang
- State Key Laboratory of Photon-Technology in Western China Energy, Institute of Photonics and Photon-Technology, Northwest University, Xi'an 710069, China
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110
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Jacques M, Dobrzyński M, Gagliardi PA, Sznitman R, Pertz O. CODEX, a neural network approach to explore signaling dynamics landscapes. Mol Syst Biol 2021; 17:e10026. [PMID: 33835701 PMCID: PMC8034356 DOI: 10.15252/msb.202010026] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 03/01/2021] [Accepted: 03/03/2021] [Indexed: 12/19/2022] Open
Abstract
Current studies of cell signaling dynamics that use live cell fluorescent biosensors routinely yield thousands of single-cell, heterogeneous, multi-dimensional trajectories. Typically, the extraction of relevant information from time series data relies on predefined, human-interpretable features. Without a priori knowledge of the system, the predefined features may fail to cover the entire spectrum of dynamics. Here we present CODEX, a data-driven approach based on convolutional neural networks (CNNs) that identifies patterns in time series. It does not require a priori information about the biological system and the insights into the data are built through explanations of the CNNs' predictions. CODEX provides several views of the data: visualization of all the single-cell trajectories in a low-dimensional space, identification of prototypic trajectories, and extraction of distinctive motifs. We demonstrate how CODEX can provide new insights into ERK and Akt signaling in response to various growth factors, and we recapitulate findings in p53 and TGFβ-SMAD2 signaling.
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Affiliation(s)
| | | | | | - Raphael Sznitman
- ARTORG Center for Biomedical Engineering ResearchUniversity of BernBernSwitzerland
| | - Olivier Pertz
- Institute of Cell BiologyUniversity of BernBernSwitzerland
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111
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Clark HR, McKenney C, Livingston NM, Gershman A, Sajjan S, Chan IS, Ewald AJ, Timp W, Wu B, Singh A, Regot S. Epigenetically regulated digital signaling defines epithelial innate immunity at the tissue level. Nat Commun 2021; 12:1836. [PMID: 33758175 PMCID: PMC7988009 DOI: 10.1038/s41467-021-22070-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Accepted: 02/26/2021] [Indexed: 02/08/2023] Open
Abstract
To prevent damage to the host or its commensal microbiota, epithelial tissues must match the intensity of the immune response to the severity of a biological threat. Toll-like receptors allow epithelial cells to identify microbe associated molecular patterns. However, the mechanisms that mitigate biological noise in single cells to ensure quantitatively appropriate responses remain unclear. Here we address this question using single cell and single molecule approaches in mammary epithelial cells and primary organoids. We find that epithelial tissues respond to bacterial microbe associated molecular patterns by activating a subset of cells in an all-or-nothing (i.e. digital) manner. The maximum fraction of responsive cells is regulated by a bimodal epigenetic switch that licenses the TLR2 promoter for transcription across multiple generations. This mechanism confers a flexible memory of inflammatory events as well as unique spatio-temporal control of epithelial tissue-level immune responses. We propose that epigenetic licensing in individual cells allows for long-term, quantitative fine-tuning of population-level responses.
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Affiliation(s)
- Helen R Clark
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Oncology Department, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- The Biochemistry, Cellular, and Molecular Biology Graduate Program, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Center for Cell Dynamics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Connor McKenney
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Oncology Department, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- The Biochemistry, Cellular, and Molecular Biology Graduate Program, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Center for Cell Dynamics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Nathan M Livingston
- The Biochemistry, Cellular, and Molecular Biology Graduate Program, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Center for Cell Dynamics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Ariel Gershman
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- The Biochemistry, Cellular, and Molecular Biology Graduate Program, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Seema Sajjan
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Oncology Department, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Center for Cell Dynamics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Isaac S Chan
- Oncology Department, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Center for Cell Dynamics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Andrew J Ewald
- Oncology Department, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Center for Cell Dynamics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Winston Timp
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Bin Wu
- Center for Cell Dynamics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Abhyudai Singh
- Electrical and Computer Engineering, University of Delaware, Newark, DE, USA
| | - Sergi Regot
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
- Oncology Department, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
- Center for Cell Dynamics, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
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112
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Single-Cell Proteomics. Trends Biochem Sci 2021; 46:661-672. [PMID: 33653632 DOI: 10.1016/j.tibs.2021.01.013] [Citation(s) in RCA: 86] [Impact Index Per Article: 28.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 01/08/2021] [Accepted: 01/27/2021] [Indexed: 02/06/2023]
Abstract
The inability to make broad, minimally biased measurements of a cell's proteome stands as a major bottleneck for understanding how gene expression translates into cellular phenotype. Unlike sequencing for nucleic acids, there is no dominant method for making single-cell proteomic measurements. Instead, methods typically focus on either absolute quantification of a small number of proteins or highly multiplexed protein measurements. Advances in microfluidics and output encoding have led to major improvements in both aspects. Here, we review the most recent progress that has enabled hundreds of protein measurements and ultrahigh-sensitivity quantification. We also highlight emerging technologies such as single-cell mass spectrometry that may enable unbiased measurement of cellular proteomes.
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113
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Friedel L, Loewer A. The guardian's choice: how p53 enables context-specific decision-making in individual cells. FEBS J 2021; 289:40-52. [PMID: 33590949 DOI: 10.1111/febs.15767] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Revised: 02/03/2021] [Accepted: 02/15/2021] [Indexed: 01/20/2023]
Abstract
p53 plays a central role in defending the genomic integrity of our cells. In response to genotoxic stress, this tumour suppressor orchestrates the expression of hundreds of target genes, which induce a variety of cellular outcomes ranging from damage repair to induction of apoptosis. In this review, we examine how the p53 response is regulated on several levels in individual cells to allow precise and context-specific fate decisions. We discuss that the p53 response is not only controlled by its canonical regulators but also controlled by interconnected signalling pathways that influence the dynamics of p53 accumulation upon damage and modulate its transcriptional activity at target gene promoters. Additionally, we consider how the p53 response is diversified through a variety of mechanisms at the promoter level and beyond to induce context-specific outcomes in individual cells. These layers of regulation allow p53 to react in a stimulus-specific manner and fine-tune its signalling according to the individual needs of a given cell, enabling it to take the right decision on survival or death.
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Affiliation(s)
- Laura Friedel
- Systems Biology of the Stress Response, Department of Biology, Technical University of Darmstadt, Germany
| | - Alexander Loewer
- Systems Biology of the Stress Response, Department of Biology, Technical University of Darmstadt, Germany
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114
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Han Y, Ouyang Z, Wawrose RA, Chen SR, Hallbaum M, Dong Q, Dando E, Tang Y, Wang B, Lee JY, Shaw JD, Kang JD, Sowa GA, Vo NN. ISSLS prize in basic science 2021: a novel inducible system to regulate transgene expression of TIMP1. EUROPEAN SPINE JOURNAL : OFFICIAL PUBLICATION OF THE EUROPEAN SPINE SOCIETY, THE EUROPEAN SPINAL DEFORMITY SOCIETY, AND THE EUROPEAN SECTION OF THE CERVICAL SPINE RESEARCH SOCIETY 2021; 30:1098-1107. [PMID: 33523281 PMCID: PMC8550652 DOI: 10.1007/s00586-021-06728-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 12/14/2020] [Accepted: 01/09/2021] [Indexed: 11/28/2022]
Abstract
Purpose Inflammatory and oxidative stress upregulates matrix metalloproteinase (MMP) activity, leading to intervertebral disc degeneration (IDD). Gene therapy using human tissue inhibitor of metalloproteinase 1 (hTIMP1) has effectively treated IDD in animal models. However, persistent unregulated transgene expression may have negative side effects. We developed a recombinant adeno-associated viral (AAV) gene vector, AAV-NFκB-hTIMP1, that only expresses the hTIMP1 transgene under conditions of stress. Methods Rabbit disc cells were transfected or transduced with AAV-CMV-hTIMP1, which constitutively expresses hTIMP1, or AAV-NFκB-hTIMP1. Disc cells were selectively treated with IL-1β. NFκB activation was verified by nuclear translocation. hTIMP1 mRNA and protein expression were measured by RT-PCR and ELISA, respectively. MMP activity was measured by following cleavage of a fluorogenic substrate. Results IL-1β stimulation activated NFκB demonstrating that IL-1β was a surrogate for inflammatory stress. Stimulating AAV-NFκB-hTIMP1 cells with IL-1β increased hTIMP1 expression compared to unstimulated cells. AAV-CMV-hTIMP1 cells demonstrated high levels of hTIMP1 expression regardless of IL-1β stimulation. hTIMP1 expression was comparable between IL-1β stimulated AAV-NFκB-hTIMP1 cells and AAV-CMV-hTIMP1 cells. MMP activity was decreased in AAV-NFκB-hTIMP1 cells compared to baseline levels or cells exposed to IL-1β. Conclusion AAV-NFκB-hTIMP1 is a novel inducible transgene delivery system. NFκB regulatory elements ensure that hTIMP1 expression occurs only with inflammation, which is central to IDD development. Unlike previous inducible systems, the AAV-NFκB-hTIMP1 construct is dependent on endogenous factors, which minimizes potential side effects caused by constitutive transgene overexpression. It also prevents the unnecessary production of transgene products in cells that do not require therapy.
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Affiliation(s)
- Yingchao Han
- Department of Spine Surgery, School of Medicine, Renji Hospital, Shanghai Jiao Tong University, Shanghai, China.,Department of Spine Surgery, School of Medicine, Shanghai East Hospital, Tongji University, Shanghai, China.,Ferguson Laboratory for Orthopaedic and Spine Research, Department of Orthopaedic Surgery, University of Pittsburgh, Pittsburgh, PA, USA
| | - Zhihua Ouyang
- Ferguson Laboratory for Orthopaedic and Spine Research, Department of Orthopaedic Surgery, University of Pittsburgh, Pittsburgh, PA, USA.,Department of Spine Surgery, The First Affiliated Hospital of Nanhua University, Hengyang, China
| | - Richard A Wawrose
- Ferguson Laboratory for Orthopaedic and Spine Research, Department of Orthopaedic Surgery, University of Pittsburgh, Pittsburgh, PA, USA
| | - Stephen R Chen
- Ferguson Laboratory for Orthopaedic and Spine Research, Department of Orthopaedic Surgery, University of Pittsburgh, Pittsburgh, PA, USA
| | - Maximiliane Hallbaum
- Ferguson Laboratory for Orthopaedic and Spine Research, Department of Orthopaedic Surgery, University of Pittsburgh, Pittsburgh, PA, USA
| | - Qing Dong
- Ferguson Laboratory for Orthopaedic and Spine Research, Department of Orthopaedic Surgery, University of Pittsburgh, Pittsburgh, PA, USA
| | - Emily Dando
- Ferguson Laboratory for Orthopaedic and Spine Research, Department of Orthopaedic Surgery, University of Pittsburgh, Pittsburgh, PA, USA
| | - Ying Tang
- Molecular Therapeutics Laboratory, Department of Orthopaedic Surgery, University of Pittsburgh, Pittsburgh, PA, USA
| | - Bing Wang
- Molecular Therapeutics Laboratory, Department of Orthopaedic Surgery, University of Pittsburgh, Pittsburgh, PA, USA
| | - Joon Y Lee
- Ferguson Laboratory for Orthopaedic and Spine Research, Department of Orthopaedic Surgery, University of Pittsburgh, Pittsburgh, PA, USA
| | - Jeremy D Shaw
- Ferguson Laboratory for Orthopaedic and Spine Research, Department of Orthopaedic Surgery, University of Pittsburgh, Pittsburgh, PA, USA
| | - James D Kang
- Department of Orthopaedics, School of Medicine, Brigham and Women's Hospital, Harvard University, Boston, MA, USA
| | - Gwendolyn A Sowa
- Ferguson Laboratory for Orthopaedic and Spine Research, Department of Orthopaedic Surgery, University of Pittsburgh, Pittsburgh, PA, USA. .,Department of Physical Medicine and Rehabilitation, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.
| | - Nam N Vo
- Ferguson Laboratory for Orthopaedic and Spine Research, Department of Orthopaedic Surgery, University of Pittsburgh, Pittsburgh, PA, USA.
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115
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Van Phan H, van Gent M, Drayman N, Basu A, Gack MU, Tay S. Fixed single-cell RNA sequencing for understanding virus infection and host response. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021. [PMID: 32995793 PMCID: PMC7523121 DOI: 10.1101/2020.09.17.302232] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Single-cell transcriptomic studies that require intracellular protein staining, rare cell sorting, or inactivation of infectious pathogens are severely limited because current high-throughput RNA sequencing methods are incompatible with paraformaldehyde treatment, a common tissue and cell fixation and preservation technique. Here we present FD-seq, a high-throughput method for droplet-based RNA sequencing of paraformaldehyde-fixed, stained and sorted single-cells. We show that FD-seq preserves the mRNA integrity and relative abundances during fixation and subsequent cell retrieval. Furthermore, FD-seq detects a higher number of genes and transcripts than methanol fixation. We applied FD-seq to investigate two important questions in Virology. First, by analyzing a rare population of cells supporting lytic reactivation of the human tumor virus KSHV, we identified TMEM119 as a host factor that mediates viral reactivation. Second, we found that upon infection with the betacoronavirus OC43, which causes the common cold and is a close relative of SARS-CoV-2, pro-inflammatory pathways are primarily upregulated in lowly-infected cells that are exposed to the virus but fail to express high levels of viral genes. FD-seq thus enables integrating phenotypic with transcriptomic information in rare cell populations, and preserving and inactivating pathogenic samples that cannot be handled under regular biosafety measures.
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Affiliation(s)
- Hoang Van Phan
- Pritzker School of Molecular Engineering, The University of Chicago, Chicago, IL, USA.,Institute for Genomics and Systems Biology, The University of Chicago, Chicago, IL, USA
| | - Michiel van Gent
- Department of Microbiology, The University of Chicago, Chicago, IL, USA.,Florida Research and Innovation Center, Cleveland Clinic, Port Saint Lucie, FL, USA
| | - Nir Drayman
- Pritzker School of Molecular Engineering, The University of Chicago, Chicago, IL, USA.,Institute for Genomics and Systems Biology, The University of Chicago, Chicago, IL, USA
| | - Anindita Basu
- Department of Medicine, The University of Chicago, Chicago, IL, USA
| | - Michaela U Gack
- Department of Microbiology, The University of Chicago, Chicago, IL, USA.,Florida Research and Innovation Center, Cleveland Clinic, Port Saint Lucie, FL, USA
| | - Savaş Tay
- Pritzker School of Molecular Engineering, The University of Chicago, Chicago, IL, USA.,Institute for Genomics and Systems Biology, The University of Chicago, Chicago, IL, USA
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116
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Son M, Wang AG, Tu HL, Metzig MO, Patel P, Husain K, Lin J, Murugan A, Hoffmann A, Tay S. NF-κB responds to absolute differences in cytokine concentrations. Sci Signal 2021; 14. [PMID: 34211635 DOI: 10.1126/scisignal.aaz4382] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Cells receive a wide range of dynamic signaling inputs during immune regulation, but how gene regulatory networks measure such dynamic inputs is not well understood. Here, we used microfluidic single-cell analysis and mathematical modeling to study how the NF-κB pathway responds to immune inputs that vary over time such as increasing, decreasing, or fluctuating cytokine signals. We found that NF-κB activity responded to the absolute difference in cytokine concentration and not to the concentration itself. Our analyses revealed that negative feedback by the regulatory proteins A20 and IκBα enabled differential responses to changes in cytokine dose by providing a short-term memory of previous cytokine concentrations and by continuously resetting kinase cycling and receptor abundance. Investigation of NF-κB target gene expression showed that cells exhibited distinct transcriptional responses under different dynamic cytokine profiles. Our results demonstrate how cells use simple network motifs and transcription factor dynamics to efficiently extract information from complex signaling environments.
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Affiliation(s)
- Minjun Son
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL 60637, USA.,Institute for Genomics and Systems Biology, University of Chicago, Chicago, IL 60637, USA
| | - Andrew G Wang
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL 60637, USA
| | - Hsiung-Lin Tu
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL 60637, USA.,Institute of Chemistry, Academia Sinica, Taipei 11529, Taiwan
| | - Marie Oliver Metzig
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, CA 90095, USA.,Institute for Quantitative and Computational Biosciences, University of California, Los Angeles, CA 90095, USA
| | - Parthiv Patel
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL 60637, USA
| | - Kabir Husain
- James Franck Institute and Department of Physics, University of Chicago, Chicago, IL 60637, USA
| | - Jing Lin
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL 60637, USA
| | - Arvind Murugan
- James Franck Institute and Department of Physics, University of Chicago, Chicago, IL 60637, USA
| | - Alexander Hoffmann
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, CA 90095, USA.,Institute for Quantitative and Computational Biosciences, University of California, Los Angeles, CA 90095, USA
| | - Savaş Tay
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL 60637, USA.,Institute for Genomics and Systems Biology, University of Chicago, Chicago, IL 60637, USA
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117
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Rodríguez Gama A, Miller T, Halfmann R. Mechanics of a molecular mousetrap-nucleation-limited innate immune signaling. Biophys J 2021; 120:1150-1160. [PMID: 33460595 PMCID: PMC8059202 DOI: 10.1016/j.bpj.2021.01.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 01/05/2021] [Accepted: 01/07/2021] [Indexed: 12/17/2022] Open
Abstract
Innate immune responses, such as cell death and inflammatory signaling, are typically switch-like in nature. They also involve "prion-like" self-templating polymerization of one or more signaling proteins into massive macromolecular assemblies known as signalosomes. Despite the wealth of atomic-resolution structural information on signalosomes, how the constituent polymers nucleate and whether the switch-like nature of that event at the molecular scale relates to the digital nature of innate immune signaling at the cellular scale remains unknown. In this perspective, we review current knowledge of innate immune signalosome assembly, with an emphasis on structural constraints that allow the proteins to accumulate in inactive soluble forms poised for abrupt polymerization. We propose that structurally encoded nucleation barriers to protein polymerization kinetically regulate the corresponding pathways, which allows for extremely sensitive, rapid, and decisive signaling upon pathogen detection. We discuss how nucleation barriers satisfy the rigorous on-demand functions of the innate immune system but also predispose the system to precocious activation that may contribute to progressive age-associated inflammation.
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Affiliation(s)
| | - Tayla Miller
- Stowers Institute for Medical Research, Kansas City, Missouri
| | - Randal Halfmann
- Stowers Institute for Medical Research, Kansas City, Missouri; Department of Molecular and Integrative Physiology, University of Kansas Medical Center, Kansas City, Kansas.
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118
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Johnson ME, Chen A, Faeder JR, Henning P, Moraru II, Meier-Schellersheim M, Murphy RF, Prüstel T, Theriot JA, Uhrmacher AM. Quantifying the roles of space and stochasticity in computer simulations for cell biology and cellular biochemistry. Mol Biol Cell 2021; 32:186-210. [PMID: 33237849 PMCID: PMC8120688 DOI: 10.1091/mbc.e20-08-0530] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Revised: 10/13/2020] [Accepted: 11/17/2020] [Indexed: 12/29/2022] Open
Abstract
Most of the fascinating phenomena studied in cell biology emerge from interactions among highly organized multimolecular structures embedded into complex and frequently dynamic cellular morphologies. For the exploration of such systems, computer simulation has proved to be an invaluable tool, and many researchers in this field have developed sophisticated computational models for application to specific cell biological questions. However, it is often difficult to reconcile conflicting computational results that use different approaches to describe the same phenomenon. To address this issue systematically, we have defined a series of computational test cases ranging from very simple to moderately complex, varying key features of dimensionality, reaction type, reaction speed, crowding, and cell size. We then quantified how explicit spatial and/or stochastic implementations alter outcomes, even when all methods use the same reaction network, rates, and concentrations. For simple cases, we generally find minor differences in solutions of the same problem. However, we observe increasing discordance as the effects of localization, dimensionality reduction, and irreversible enzymatic reactions are combined. We discuss the strengths and limitations of commonly used computational approaches for exploring cell biological questions and provide a framework for decision making by researchers developing new models. As computational power and speed continue to increase at a remarkable rate, the dream of a fully comprehensive computational model of a living cell may be drawing closer to reality, but our analysis demonstrates that it will be crucial to evaluate the accuracy of such models critically and systematically.
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Affiliation(s)
- M. E. Johnson
- Thomas C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, MD, 21218
| | - A. Chen
- Thomas C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, MD, 21218
| | - J. R. Faeder
- Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15260
| | - P. Henning
- Institute for Visual and Analytic Computing, University of Rostock, 18055 Rostock, Germany
| | - I. I. Moraru
- Department of Cell Biology, Center for Cell Analysis and Modeling, University of Connecticut Health Center, Farmington, CT 06030
| | - M. Meier-Schellersheim
- Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892
| | - R. F. Murphy
- Computational Biology Department, Department of Biological Sciences, Department of Biomedical Engineering, Machine Learning Department, Carnegie Mellon University, Pittsburgh, PA 15289
| | - T. Prüstel
- Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892
| | - J. A. Theriot
- Department of Biology and Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195
| | - A. M. Uhrmacher
- Institute for Visual and Analytic Computing, University of Rostock, 18055 Rostock, Germany
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119
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Bulgakov VP, Koren OG. Basic Protein Modules Combining Abscisic Acid and Light Signaling in Arabidopsis. FRONTIERS IN PLANT SCIENCE 2021; 12:808960. [PMID: 35046987 PMCID: PMC8762054 DOI: 10.3389/fpls.2021.808960] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Accepted: 11/23/2021] [Indexed: 05/02/2023]
Abstract
It is generally accepted that plants use the complex signaling system regulated by light and abscisic acid (ABA) signaling components to optimize growth and development in different situations. The role of ABA-light interactions is evident in the coupling of stress defense reactions with seed germination and root development, maintaining of stem cell identity and stem cell specification, stem elongation and leaf development, flowering and fruit formation, senescence, and shade avoidance. All these processes are regulated jointly by the ABA-light signaling system. Although a lot of work has been devoted to ABA-light signal interactions, there is still no systematic description of central signaling components and protein modules, which jointly regulate plant development. New data have emerged to promote understanding of how ABA and light signals are integrated at the molecular level, representing an extensively growing area of research. This work is intended to fill existing gaps by using literature data combined with bioinformatics analysis.
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120
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Zhang C, Yao S, Xu C, Chang Y, Zong Y, Zhang K, Zhang X, Zhang L, Chen C, Zhao Y, Jiang H, Gao X, Wang Y. 3D Imaging and Quantification of the Integrin at a Single-Cell Base on a Multisignal Nanoprobe and Synchrotron Radiation Soft X-ray Tomography Microscopy. Anal Chem 2020; 93:1237-1241. [DOI: 10.1021/acs.analchem.0c04662] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Chunyu Zhang
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety and CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology of China, Beijing 100090, China
- Department of Chemistry and Chemical Engineering, Beijing University of Technology, Beijing 100124, China
| | - Shengkun Yao
- School of Physical Science and Technology, Shanghai Tech University, Shanghai 201210, China
- Shandong Provincial Engineering and Technical Center of Light Manipulations & Shandong Provincial Key Laboratory of Optics and Photonic Device, School of Physics and Electronics, Shandong Normal University, Jinan 250358, China
| | - Chao Xu
- College of Chemistry and Material Science, Shandong Agricultural University, Tai’an 271018, China
| | - Yanan Chang
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing 100049, China
| | - Yunbing Zong
- School of Physical Science and Technology, Shanghai Tech University, Shanghai 201210, China
| | - Kai Zhang
- Beijing Synchrotron Radiation Facility, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing 100049, China
| | - Xiangzhi Zhang
- Shanghai Synchrotron Radiation Facility, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - Lijuan Zhang
- Shanghai Synchrotron Radiation Facility, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - Chunying Chen
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety and CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology of China, Beijing 100090, China
| | - Yuliang Zhao
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety and CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology of China, Beijing 100090, China
| | - Huaidong Jiang
- School of Physical Science and Technology, Shanghai Tech University, Shanghai 201210, China
| | - Xueyun Gao
- Department of Chemistry and Chemical Engineering, Beijing University of Technology, Beijing 100124, China
| | - Yaling Wang
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety and CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology of China, Beijing 100090, China
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121
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Salcedo-Jiménez R, Koenig JB, Lee OJ, Gibson TWG, Madan P, Koch TG. Extracorporeal Shock Wave Therapy Enhances the In Vitro Metabolic Activity and Differentiation of Equine Umbilical Cord Blood Mesenchymal Stromal Cells. Front Vet Sci 2020; 7:554306. [PMID: 33344521 PMCID: PMC7746774 DOI: 10.3389/fvets.2020.554306] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Accepted: 11/11/2020] [Indexed: 11/18/2022] Open
Abstract
Extracorporeal shock wave therapy (ESWT) has been shown to induce different biological effects on a variety of cells, including regulation and stimulation of their function and metabolism. ESWT can promote different biological responses such as proliferation, migration, and regenerations of cells. Recent studies have shown that mesenchymal stromal cells (MSCs) secrete factors that enhance the regeneration of tissues, stimulate proliferation and differentiation of cells, and decrease inflammatory and immune reactions. Clinically, the combination of these two therapies has been used as a treatment for tendon and ligament lesions in horses; however, there is no scientific evidence supporting this combination of therapies in vivo. Therefore, the objectives of the study were to evaluate the effects of ESWT on equine umbilical cord blood mesenchymal stromal cells (CB-MSCs) proliferative, metabolic, migrative, differentiation, and immunomodulatory properties in vitro. Three equine CB-MSC cultures from independent donors were treated using an electrohydraulic shock wave generator attached to a water bath. All experiments were performed as triplicates. Proliferation, viability, migration and immunomodulatory properties of the cells were evaluated. Equine CB-MSCs were induced to evaluate their trilineage differentiation potential. ESWT treated cells had increased metabolic activity, showed positive adipogenic, osteogenic, and chondrogenic differentiation, and showed higher potential for differentiation toward the adipogenic and osteogenic cell fates. ESWT treated cells showed similar immunomodulatory properties to none-ESWT treated cells. Equine CB-MSCs are responsive to ESWT treatment and showed increased metabolic, adipogenic and osteogenic activity, but unaltered immunosuppressive properties. In vivo studies are warranted to determine if synergistic effects occur in the treatment of musculoskeletal injuries if ESWT and equine CB-MSC therapies are combined.
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Affiliation(s)
| | - Judith B Koenig
- Department of Clinical Studies, University of Guelph, Guelph, ON, Canada
| | - Olivia J Lee
- Department of Biomedical Sciences, University of Guelph, Guelph, ON, Canada
| | - Thomas W G Gibson
- Department of Clinical Studies, University of Guelph, Guelph, ON, Canada
| | - Pavneesh Madan
- Department of Biomedical Sciences, University of Guelph, Guelph, ON, Canada
| | - Thomas G Koch
- Department of Biomedical Sciences, University of Guelph, Guelph, ON, Canada
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122
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Schuster B, Junkin M, Kashaf SS, Romero-Calvo I, Kirby K, Matthews J, Weber CR, Rzhetsky A, White KP, Tay S. Automated microfluidic platform for dynamic and combinatorial drug screening of tumor organoids. Nat Commun 2020; 11:5271. [PMID: 33077832 PMCID: PMC7573629 DOI: 10.1038/s41467-020-19058-4] [Citation(s) in RCA: 152] [Impact Index Per Article: 38.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Accepted: 09/25/2020] [Indexed: 12/13/2022] Open
Abstract
Three-dimensional (3D) cell culture technologies, such as organoids, are physiologically relevant models for basic and clinical applications. Automated microfluidics offers advantages in high-throughput and precision analysis of cells but is not yet compatible with organoids. Here, we present an automated, high-throughput, microfluidic 3D organoid culture and analysis system to facilitate preclinical research and personalized therapies. Our system provides combinatorial and dynamic drug treatments to hundreds of cultures and enables real-time analysis of organoids. We validate our system by performing individual, combinatorial, and sequential drug screens on human-derived pancreatic tumor organoids. We observe significant differences in the response of individual patient-based organoids to drug treatments and find that temporally-modified drug treatments can be more effective than constant-dose monotherapy or combination therapy in vitro. This integrated platform advances organoids models to screen and mirror real patient treatment courses with potential to facilitate treatment decisions for personalized therapy. The use of organoids in personalized medicine is promising but high throughput platforms are needed. Here the authors develop an automated, high-throughput, microfluidic 3D organoid culture system that allows combinatorial and dynamic drug treatments and real-time analysis of organoids.
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Affiliation(s)
- Brooke Schuster
- Pritzker School of Molecular Engineering, The University of Chicago, Chicago, IL, 60637, USA.,Institute for Genomics and Systems Biology, The University of Chicago, Chicago, IL, 60637, USA.,Department of Chemistry, The University of Chicago, Chicago, IL, 60637, USA
| | - Michael Junkin
- Pritzker School of Molecular Engineering, The University of Chicago, Chicago, IL, 60637, USA.,Institute for Genomics and Systems Biology, The University of Chicago, Chicago, IL, 60637, USA
| | - Sara Saheb Kashaf
- Pritzker School of Molecular Engineering, The University of Chicago, Chicago, IL, 60637, USA.,Institute for Genomics and Systems Biology, The University of Chicago, Chicago, IL, 60637, USA
| | - Isabel Romero-Calvo
- Institute for Genomics and Systems Biology, The University of Chicago, Chicago, IL, 60637, USA
| | - Kori Kirby
- Institute for Genomics and Systems Biology, The University of Chicago, Chicago, IL, 60637, USA
| | - Jonathan Matthews
- Pritzker School of Molecular Engineering, The University of Chicago, Chicago, IL, 60637, USA.,Institute for Genomics and Systems Biology, The University of Chicago, Chicago, IL, 60637, USA
| | - Christopher R Weber
- Department of Pathology, The University of Chicago Medicine, Chicago, IL, 60637, USA
| | - Andrey Rzhetsky
- Institute for Genomics and Systems Biology, The University of Chicago, Chicago, IL, 60637, USA.,Committee on Genetics, Genomics and Systems Biology, Departments of Medicine and Human Genetics, The University of Chicago, Chicago, IL, 60637, USA
| | - Kevin P White
- Institute for Genomics and Systems Biology, The University of Chicago, Chicago, IL, 60637, USA.,Tempus Labs, Chicago, IL, 60654, USA
| | - Savaş Tay
- Pritzker School of Molecular Engineering, The University of Chicago, Chicago, IL, 60637, USA. .,Institute for Genomics and Systems Biology, The University of Chicago, Chicago, IL, 60637, USA.
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123
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RNA timestamps identify the age of single molecules in RNA sequencing. Nat Biotechnol 2020; 39:320-325. [PMID: 33077959 DOI: 10.1038/s41587-020-0704-z] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 08/27/2020] [Accepted: 09/07/2020] [Indexed: 12/28/2022]
Abstract
Current approaches to single-cell RNA sequencing (RNA-seq) provide only limited information about the dynamics of gene expression. Here we present RNA timestamps, a method for inferring the age of individual RNAs in RNA-seq data by exploiting RNA editing. To introduce timestamps, we tag RNA with a reporter motif consisting of multiple MS2 binding sites that recruit the adenosine deaminase ADAR2 fused to an MS2 capsid protein. ADAR2 binding to tagged RNA causes A-to-I edits to accumulate over time, allowing the age of the RNA to be inferred with hour-scale accuracy. By combining observations of multiple timestamped RNAs driven by the same promoter, we can determine when the promoter was active. We demonstrate that the system can infer the presence and timing of multiple past transcriptional events. Finally, we apply the method to cluster single cells according to the timing of past transcriptional activity. RNA timestamps will allow the incorporation of temporal information into RNA-seq workflows.
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124
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Filtering input fluctuations in intensity and in time underlies stochastic transcriptional pulses without feedback. Proc Natl Acad Sci U S A 2020; 117:26608-26615. [PMID: 33046652 DOI: 10.1073/pnas.2010849117] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Stochastic pulsatile dynamics have been observed in an increasing number of biological circuits with known mechanism involving feedback control and bistability. Surprisingly, recent single-cell experiments in Escherichia coli flagellar synthesis showed that flagellar genes are activated in stochastic pulses without the means of feedback. However, the mechanism for pulse generation in these feedbackless circuits has remained unclear. Here, by developing a system-level stochastic model constrained by a large set of single-cell E. coli flagellar synthesis data from different strains and mutants, we identify the general underlying design principles for generating stochastic transcriptional pulses without feedback. Our study shows that an inhibitor (YdiV) of the transcription factor (FlhDC) creates a monotonic ultrasensitive switch that serves as a digital filter to eliminate small-amplitude FlhDC fluctuations. Furthermore, we find that the high-frequency (fast) fluctuations of FlhDC are filtered out by integration over a timescale longer than the timescale of the input fluctuations. Together, our results reveal a filter-and-integrate design for generating stochastic pulses without feedback. This filter-and-integrate mechanism enables a general strategy for cells to avoid premature activation of the expensive downstream gene expression by filtering input fluctuations in both intensity and time so that the system only responds to input signals that are both strong and persistent.
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125
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Hall MS, Decker JT, Shea LD. Towards systems tissue engineering: Elucidating the dynamics, spatial coordination, and individual cells driving emergent behaviors. Biomaterials 2020; 255:120189. [PMID: 32569865 PMCID: PMC7396312 DOI: 10.1016/j.biomaterials.2020.120189] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Revised: 04/20/2020] [Accepted: 06/09/2020] [Indexed: 12/11/2022]
Abstract
Biomaterial systems have enabled the in vitro production of complex, emergent tissue behaviors that were not possible with conventional two-dimensional culture systems, allowing for analysis of both normal development and disease processes. We propose that the path towards developing the design parameters for biomaterial systems lies with identifying the molecular drivers of emergent behavior through leveraging technological advances in systems biology, including single cell omics, genetic engineering, and high content imaging. This growing research opportunity at the intersection of the fields of tissue engineering and systems biology - systems tissue engineering - can uniquely interrogate the mechanisms by which complex tissue behaviors emerge with the potential to capture the contribution of i) dynamic regulation of tissue development and dysregulation, ii) single cell heterogeneity and the function of rare cell types, and iii) the spatial distribution and structure of individual cells and cell types within a tissue. By leveraging advances in both biological and materials data science, systems tissue engineering can facilitate the identification of biomaterial design parameters that will accelerate basic science discovery and translation.
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Affiliation(s)
- Matthew S Hall
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, USA
| | - Joseph T Decker
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, USA
| | - Lonnie D Shea
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, USA.
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126
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Xiong X, Sun J, Hu D, Xiao C, Wang J, Zhuo Q, Qin C, Dai L. Fabrication of polyvinyl alcohol hydrogels with excellent shape memory and ultraviolet-shielding behavior via the introduction of tea polyphenols. RSC Adv 2020; 10:35226-35234. [PMID: 35515656 PMCID: PMC9056856 DOI: 10.1039/d0ra06053d] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2020] [Accepted: 09/01/2020] [Indexed: 11/21/2022] Open
Abstract
Shape-memory hydrogels are expected to be used not only in an ordinary environment, but also in some special environments, such as under ultraviolet (UV) irradiation. Developing novel shape-memory polyvinyl alcohol (PVA)/tea polyphenol (TP) hydrogels with UV shielding performance is realistically important in application fields. Herein, we designed functional PVA/TP hydrogels with excellent UV-shielding ability and improved the shape memory on hot water stimuli. This study shows that the abundant hydrogen bonds between PVA and TP are the source of shape memory. The PVA hydrogels with 8 wt% TP loading could approximately recover their original shape after deformation when immersed in water at 50 °C for 30 s. Meanwhile, the hydrogels also had excellent UV shielding capacity. After ageing under UV for 16 days, the observed shape of the hydrogel with 8 wt% TP loading retained 74.7% of the original, and the hydrogel could effectively protect the skin of mice from damage under 10 mW cm-2 UV irradiation. With the understanding of the UV-shielding behavior of hydrogels, this study has been able to generate biomedical materials for human skin protection, specifically skin covering the joint areas, where shape memory of the applied materials is essential.
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Affiliation(s)
- Xike Xiong
- College of Chemistry, Chemical Engineering and Materials Science, Soochow University Suzhou Jiangsu 215123 People's Republic of China
| | - Jun Sun
- College of Chemistry, Chemical Engineering and Materials Science, Soochow University Suzhou Jiangsu 215123 People's Republic of China
| | - Di Hu
- College of Chemistry, Chemical Engineering and Materials Science, Soochow University Suzhou Jiangsu 215123 People's Republic of China
| | - Chao Xiao
- College of Chemistry, Chemical Engineering and Materials Science, Soochow University Suzhou Jiangsu 215123 People's Republic of China
| | - Jianjun Wang
- College of Chemistry, Chemical Engineering and Materials Science, Soochow University Suzhou Jiangsu 215123 People's Republic of China
| | - Qiqi Zhuo
- College of Material Science & Engineering, Jiangsu University of Science and Technology Zhenjiang Jiangsu 212003 People's Republic of China
| | - Chuanxiang Qin
- College of Chemistry, Chemical Engineering and Materials Science, Soochow University Suzhou Jiangsu 215123 People's Republic of China
| | - Lixing Dai
- College of Chemistry, Chemical Engineering and Materials Science, Soochow University Suzhou Jiangsu 215123 People's Republic of China
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127
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Mudla A, Jiang Y, Arimoto KI, Xu B, Rajesh A, Ryan AP, Wang W, Daugherty MD, Zhang DE, Hao N. Cell-cycle-gated feedback control mediates desensitization to interferon stimulation. eLife 2020; 9:58825. [PMID: 32945770 PMCID: PMC7500952 DOI: 10.7554/elife.58825] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 09/02/2020] [Indexed: 12/13/2022] Open
Abstract
Cells use molecular circuits to interpret and respond to extracellular cues, such as hormones and cytokines, which are often released in a temporally varying fashion. In this study, we combine microfluidics, time-lapse microscopy, and computational modeling to investigate how the type I interferon (IFN)-responsive regulatory network operates in single human cells to process repetitive IFN stimulation. We found that IFN-α pretreatments lead to opposite effects, priming versus desensitization, depending on input durations. These effects are governed by a regulatory network composed of a fast-acting positive feedback loop and a delayed negative feedback loop, mediated by upregulation of ubiquitin-specific peptidase 18 (USP18). We further revealed that USP18 upregulation can only be initiated at the G1/early S phases of cell cycle upon the treatment onset, resulting in heterogeneous and delayed induction kinetics in single cells. This cell cycle gating provides a temporal compartmentalization of feedback loops, enabling duration-dependent desensitization to repetitive stimulations.
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Affiliation(s)
- Anusorn Mudla
- Section of Molecular Biology, Division of Biological Sciences, University of California, San Diego, La Jolla, United States
| | - Yanfei Jiang
- Section of Molecular Biology, Division of Biological Sciences, University of California, San Diego, La Jolla, United States
| | - Kei-Ichiro Arimoto
- Section of Molecular Biology, Division of Biological Sciences, University of California, San Diego, La Jolla, United States
| | - Bingxian Xu
- Section of Molecular Biology, Division of Biological Sciences, University of California, San Diego, La Jolla, United States
| | - Adarsh Rajesh
- Department of Bioengineering, University of California, San Diego, La Jolla, United States
| | - Andy P Ryan
- Section of Molecular Biology, Division of Biological Sciences, University of California, San Diego, La Jolla, United States
| | - Wei Wang
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, United States
| | - Matthew D Daugherty
- Section of Molecular Biology, Division of Biological Sciences, University of California, San Diego, La Jolla, United States
| | - Dong-Er Zhang
- Section of Molecular Biology, Division of Biological Sciences, University of California, San Diego, La Jolla, United States.,Department of Pathology, Moores UCSD Cancer Center, University of California, San Diego, La Jolla, United States
| | - Nan Hao
- Section of Molecular Biology, Division of Biological Sciences, University of California, San Diego, La Jolla, United States
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128
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Jiao F, Zhu C. Regulation of Gene Activation by Competitive Cross Talking Pathways. Biophys J 2020; 119:1204-1214. [PMID: 32861266 PMCID: PMC7499120 DOI: 10.1016/j.bpj.2020.08.011] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Revised: 08/12/2020] [Accepted: 08/12/2020] [Indexed: 11/28/2022] Open
Abstract
The phenomenon of a gene expression burst has been attributed to random transitions between the active and inactive states of a gene. However, the mechanisms underlying regulation of the activation process in response to environmental changes remain unclear. Here, we model gene activation as a consequence of the competitive cross talk between a weak basal pathway and an inducible signaling pathway and reveal rich expression dynamics along with intricate dependence of noise and Fano factor on mean expression levels. These theoretical results are in good agreement with a large experimental data set in Escherichia coli, yeast, and mammalian cells. Furthermore, both theoretical analyses and supporting biological evidence converge to demonstrate the existence of a tradeoff that governs the sharp up- and downregulation of gene expression, suggesting an ordered scenario that activates a gene under varying conditions. These regulation modes, together with cross talk pathways, may provide new guidance for the analysis and interpretation of genetic data in various applications, ranging from genetic engineering to therapeutic targets of disease.
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Affiliation(s)
- Feng Jiao
- Center for Applied Mathematics, Guangzhou University, Guangzhou, P. R. China; College of Mathematics and Information Sciences, Guangzhou University, Guangzhou, P.R. China
| | - Chunjuan Zhu
- Modern Business and Management Department, Guangdong Construction Polytechnic, Guangzhou, P. R. China; College of Mathematics and Information Sciences, Guangzhou University, Guangzhou, P.R. China.
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129
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Chen SY, Osimiri LC, Chevalier M, Bugaj LJ, Nguyen TH, Greenstein RA, Ng AH, Stewart-Ornstein J, Neves LT, El-Samad H. Optogenetic Control Reveals Differential Promoter Interpretation of Transcription Factor Nuclear Translocation Dynamics. Cell Syst 2020; 11:336-353.e24. [PMID: 32898473 PMCID: PMC7648432 DOI: 10.1016/j.cels.2020.08.009] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Revised: 04/08/2020] [Accepted: 08/10/2020] [Indexed: 02/07/2023]
Abstract
Gene expression is thought to be affected not only by the concentration of transcription factors (TFs) but also the dynamics of their nuclear translocation. Testing this hypothesis requires direct control of TF dynamics. Here, we engineer CLASP, an optogenetic tool for rapid and tunable translocation of a TF of interest. Using CLASP fused to Crz1, we observe that, for the same integrated concentration of nuclear TF over time, changing input dynamics changes target gene expression: pulsatile inputs yield higher expression than continuous inputs, or vice versa, depending on the target gene. Computational modeling reveals that a dose-response saturating at low TF input can yield higher gene expression for pulsatile versus continuous input, and that multi-state promoter activation can yield the opposite behavior. Our integrated tool development and modeling approach characterize promoter responses to Crz1 nuclear translocation dynamics, extracting quantitative features that may help explain the differential expression of target genes. CLASP is a modular optogenetic strategy to control the nuclear localization of transcription factors (TFs) and elicit gene expression from their cognate promoters. CLASP control of Crz1 nuclear localization, coupled with computational modeling, revealed how promoters can differentially decode dynamic transcription factor signals. The integrated strategy of CLASP development and modeling presents a generalized approach to causally investigate the transcriptional consequences of dynamic TF nuclear shuttling.
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Affiliation(s)
- Susan Y Chen
- Department of Biochemistry and Biophysics, California Institute for Quantitative Biosciences, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Lindsey C Osimiri
- Department of Biochemistry and Biophysics, California Institute for Quantitative Biosciences, University of California, San Francisco, San Francisco, CA 94158, USA; The UC Berkeley-UCSF Graduate Program in Bioengineering, University of California, San Francisco, CA 94143, USA
| | - Michael Chevalier
- Department of Biochemistry and Biophysics, California Institute for Quantitative Biosciences, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Lukasz J Bugaj
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Taylor H Nguyen
- Department of Biochemistry and Biophysics, California Institute for Quantitative Biosciences, University of California, San Francisco, San Francisco, CA 94158, USA
| | - R A Greenstein
- Department of Microbiology and Immunology, George Williams Hooper Foundation, Tetrad Graduate Program, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Andrew H Ng
- Department of Biochemistry and Biophysics, California Institute for Quantitative Biosciences, University of California, San Francisco, San Francisco, CA 94158, USA; The UC Berkeley-UCSF Graduate Program in Bioengineering, University of California, San Francisco, CA 94143, USA; Cell Design Institute, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Jacob Stewart-Ornstein
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Lauren T Neves
- Department of Biochemistry and Biophysics, California Institute for Quantitative Biosciences, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Hana El-Samad
- Department of Biochemistry and Biophysics, California Institute for Quantitative Biosciences, University of California, San Francisco, San Francisco, CA 94158, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA; Cell Design Institute, University of California, San Francisco, San Francisco, CA 94158, USA.
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130
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Zambrano S, Loffreda A, Carelli E, Stefanelli G, Colombo F, Bertrand E, Tacchetti C, Agresti A, Bianchi ME, Molina N, Mazza D. First Responders Shape a Prompt and Sharp NF-κB-Mediated Transcriptional Response to TNF-α. iScience 2020; 23:101529. [PMID: 33083759 PMCID: PMC7509218 DOI: 10.1016/j.isci.2020.101529] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 08/05/2020] [Accepted: 09/01/2020] [Indexed: 12/01/2022] Open
Abstract
Nuclear factor (NF)-κB controls the transcriptional response to inflammatory signals by translocating into the nucleus, but we lack a single-cell characterization of the resulting transcription dynamics. Here we show that upon tumor necrosis factor (TNF)-α transcription of NF-κB target genes is heterogeneous in individual cells but results in an average nascent transcription profile that is prompt (i.e., occurs almost immediately) and sharp (i.e., increases and decreases rapidly) compared with NF-κB nuclear localization. Using an NF-κB-controlled MS2 reporter we show that the single-cell nascent transcription is more heterogeneous than NF-κB translocation dynamics, with a fraction of synchronized “first responders” that shape the average transcriptional profile and are more prone to respond to multiple TNF-α stimulations. A mathematical model combining NF-κB-mediated gene activation and a gene refractory state is able to reproduce these features. Our work shows how the expression of target genes induced by transcriptional activators can be heterogeneous across single cells and yet time resolved on average. Nascent transcription upon TNF-α is heterogeneous, with a subset of “first responders” The average nascent transcription is prompt and sharper than NF-κB response First responders do not depend on NF-κB dynamics and respond more to pulsed stimuli A model including NF-κB and a gene refractory state reproduces these observations
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Affiliation(s)
- Samuel Zambrano
- School of Medicine, Vita-Salute San Raffaele University, Milan 20132, Italy.,Division of Genetics and Cell Biology, IRCCS San Raffaele Scientific Institute, Milan 20132, Italy
| | - Alessia Loffreda
- Experimental Imaging Center, IRCCS San Raffaele Scientific Institute, Milan 20132, Italy
| | - Elena Carelli
- Division of Genetics and Cell Biology, IRCCS San Raffaele Scientific Institute, Milan 20132, Italy
| | - Giacomo Stefanelli
- Experimental Imaging Center, IRCCS San Raffaele Scientific Institute, Milan 20132, Italy
| | - Federica Colombo
- Division of Genetics and Cell Biology, IRCCS San Raffaele Scientific Institute, Milan 20132, Italy.,Department of Electronics, Information and Bioengineering, Politecnico di Milano, Milan 20133, Italy
| | - Edouard Bertrand
- Institut de Génétique Moléculaire de Montpellier, CNRS, Montpellier 34293, France
| | - Carlo Tacchetti
- School of Medicine, Vita-Salute San Raffaele University, Milan 20132, Italy.,Experimental Imaging Center, IRCCS San Raffaele Scientific Institute, Milan 20132, Italy
| | - Alessandra Agresti
- Division of Genetics and Cell Biology, IRCCS San Raffaele Scientific Institute, Milan 20132, Italy
| | - Marco E Bianchi
- School of Medicine, Vita-Salute San Raffaele University, Milan 20132, Italy.,Division of Genetics and Cell Biology, IRCCS San Raffaele Scientific Institute, Milan 20132, Italy
| | - Nacho Molina
- Institut de Génétique et Biologie Moléculaire Cellulaire, Illkirch-Graffenstaden 67404, France
| | - Davide Mazza
- Experimental Imaging Center, IRCCS San Raffaele Scientific Institute, Milan 20132, Italy
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131
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Multiplexing information flow through dynamic signalling systems. PLoS Comput Biol 2020; 16:e1008076. [PMID: 32745094 PMCID: PMC7425991 DOI: 10.1371/journal.pcbi.1008076] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 08/13/2020] [Accepted: 06/18/2020] [Indexed: 01/18/2023] Open
Abstract
We consider how a signalling system can act as an information hub by multiplexing information arising from multiple signals. We formally define multiplexing, mathematically characterise which systems can multiplex and how well they can do it. While the results of this paper are theoretical, to motivate the idea of multiplexing, we provide experimental evidence that tentatively suggests that the NF-κB transcription factor can multiplex information about changes in multiple signals. We believe that our theoretical results may resolve the apparent paradox of how a system like NF-κB that regulates cell fate and inflammatory signalling in response to diverse stimuli can appear to have the low information carrying capacity suggested by recent studies on scalar signals. In carrying out our study, we introduce new methods for the analysis of large, nonlinear stochastic dynamic models, and develop computational algorithms that facilitate the calculation of fundamental constructs of information theory such as Kullback–Leibler divergences and sensitivity matrices, and link these methods to a new theory about multiplexing information. We show that many current models such as those of the NF-κB system cannot multiplex effectively and provide models that overcome this limitation using post-transcriptional modifications. Cells use signalling systems to pass on information arising from their ever-changing environment to their processing units. These biochemical networks regulate the transmission of multiple signals within the noisy and complex cellular environment, controlling whether to turn on or off processes of cell defence, death, division, and others. The question of how they actually achieve that becomes particularly critical given that many diseases occur when signalling systems malfunction. In this paper, we develop methodology and computational tools for simulating, measuring and analysing the ability of signalling systems to transmit multi-dimensional signals. We specifically focus on the capacity of signalling systems to simultaneously transmit multiple signals, such as temperature changes, presence and concentration of cytokines, viral and bacterial pathogens or drugs, through a single noisy, dynamic signalling system. We argue that a signalling system can act as an information hub, sending information in a multiplexed fashion rather similar to the way in which telecommunications networks send multiple signals over a shared medium by combining them into one.
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132
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Mc Fie M, Koneva L, Collins I, Coveney CR, Clube AM, Chanalaris A, Vincent TL, Bezbradica JS, Sansom SN, Wann AKT. Ciliary proteins specify the cell inflammatory response by tuning NFκB signalling, independently of primary cilia. J Cell Sci 2020; 133:jcs.239871. [PMID: 32503942 PMCID: PMC7358134 DOI: 10.1242/jcs.239871] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Accepted: 05/21/2020] [Indexed: 12/17/2022] Open
Abstract
Complex inflammatory signalling cascades define the response to tissue injury but also control development and homeostasis, limiting the potential for these pathways to be targeted therapeutically. Primary cilia are subcellular regulators of cellular signalling, controlling how signalling is organized, encoded and, in some instances, driving or influencing pathogenesis. Our previous research revealed that disruption of ciliary intraflagellar transport (IFT), altered the cell response to IL-1β, supporting a putative link emerging between cilia and inflammation. Here, we show that IFT88 depletion affects specific cytokine-regulated behaviours, changing cytosolic NFκB translocation dynamics but leaving MAPK signalling unaffected. RNA-seq analysis indicates that IFT88 regulates one third of the genome-wide targets, including the pro-inflammatory genes Nos2, Il6 and Tnf. Through microscopy, we find altered NFκB dynamics are independent of assembly of a ciliary axoneme. Indeed, depletion of IFT88 inhibits inflammatory responses in the non-ciliated macrophage. We propose that ciliary proteins, including IFT88, KIF3A, TTBK2 and NPHP4, act outside of the ciliary axoneme to tune cytoplasmic NFκB signalling and specify the downstream cell response. This is thus a non-canonical function for ciliary proteins in shaping cellular inflammation. This article has an associated First Person interview with the first author of the paper. Summary: Ciliary proteins, acting independently of the ciliary axoneme, regulate the dynamics of cytosolic NFκB, but not other signalling pathways, defining an important subset of the inflammatory response.
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Affiliation(s)
- Megan Mc Fie
- Kennedy Institute of Rheumatology Research, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, Medical Sciences Division, University of Oxford, Oxford OX3 7FY, UK.,School of Engineering and Materials Science, Queen Mary University of London, Mile End Road, London E1 4NS, UK
| | - Lada Koneva
- Kennedy Institute of Rheumatology Research, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, Medical Sciences Division, University of Oxford, Oxford OX3 7FY, UK
| | - Isabella Collins
- Kennedy Institute of Rheumatology Research, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, Medical Sciences Division, University of Oxford, Oxford OX3 7FY, UK
| | - Clarissa R Coveney
- Kennedy Institute of Rheumatology Research, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, Medical Sciences Division, University of Oxford, Oxford OX3 7FY, UK
| | - Aisling M Clube
- Kennedy Institute of Rheumatology Research, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, Medical Sciences Division, University of Oxford, Oxford OX3 7FY, UK
| | - Anastasios Chanalaris
- Kennedy Institute of Rheumatology Research, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, Medical Sciences Division, University of Oxford, Oxford OX3 7FY, UK
| | - Tonia L Vincent
- Kennedy Institute of Rheumatology Research, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, Medical Sciences Division, University of Oxford, Oxford OX3 7FY, UK
| | - Jelena S Bezbradica
- Kennedy Institute of Rheumatology Research, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, Medical Sciences Division, University of Oxford, Oxford OX3 7FY, UK
| | - Stephen N Sansom
- Kennedy Institute of Rheumatology Research, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, Medical Sciences Division, University of Oxford, Oxford OX3 7FY, UK
| | - Angus K T Wann
- Kennedy Institute of Rheumatology Research, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, Medical Sciences Division, University of Oxford, Oxford OX3 7FY, UK
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133
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Hou R, Denisenko E, Forrest ARR. scMatch: a single-cell gene expression profile annotation tool using reference datasets. Bioinformatics 2020; 35:4688-4695. [PMID: 31028376 PMCID: PMC6853649 DOI: 10.1093/bioinformatics/btz292] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Revised: 03/28/2019] [Accepted: 04/21/2019] [Indexed: 12/17/2022] Open
Abstract
MOTIVATION Single-cell RNA sequencing (scRNA-seq) measures gene expression at the resolution of individual cells. Massively multiplexed single-cell profiling has enabled large-scale transcriptional analyses of thousands of cells in complex tissues. In most cases, the true identity of individual cells is unknown and needs to be inferred from the transcriptomic data. Existing methods typically cluster (group) cells based on similarities of their gene expression profiles and assign the same identity to all cells within each cluster using the averaged expression levels. However, scRNA-seq experiments typically produce low-coverage sequencing data for each cell, which hinders the clustering process. RESULTS We introduce scMatch, which directly annotates single cells by identifying their closest match in large reference datasets. We used this strategy to annotate various single-cell datasets and evaluated the impacts of sequencing depth, similarity metric and reference datasets. We found that scMatch can rapidly and robustly annotate single cells with comparable accuracy to another recent cell annotation tool (SingleR), but that it is quicker and can handle larger reference datasets. We demonstrate how scMatch can handle large customized reference gene expression profiles that combine data from multiple sources, thus empowering researchers to identify cell populations in any complex tissue with the desired precision. AVAILABILITY AND IMPLEMENTATION scMatch (Python code) and the FANTOM5 reference dataset are freely available to the research community here https://github.com/forrest-lab/scMatch. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Rui Hou
- Harry Perkins Institute of Medical Research, QEII Medical Centre and Centre for Medical Research, The University of Western Australia, Nedlands, Perth, WA 6009, Australia
| | - Elena Denisenko
- Harry Perkins Institute of Medical Research, QEII Medical Centre and Centre for Medical Research, The University of Western Australia, Nedlands, Perth, WA 6009, Australia
| | - Alistair R R Forrest
- Harry Perkins Institute of Medical Research, QEII Medical Centre and Centre for Medical Research, The University of Western Australia, Nedlands, Perth, WA 6009, Australia
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134
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Gillen J, Bridgwater C, Nita-Lazar A. Approaching complexity: systems biology and ms-based techniques to address immune signaling. Expert Rev Proteomics 2020; 17:341-354. [PMID: 32552048 DOI: 10.1080/14789450.2020.1780920] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
INTRODUCTION Studying immune signaling has been critical for our understanding of immunology, pathogenesis, cancer, and homeostasis. To enhance the breadth of the analysis, high throughput methods have been developed to survey multiple areas simultaneously, including transcriptomics, reporter assays, and ELISAs. While these techniques have been extremely informative, mass-spectrometry-based technologies have been gaining momentum and starting to be widely used in the studies of immune signaling and systems immunology. AREAS COVERED We present established proteomic methods that have been used to address immune signaling and discuss the new mass-spectrometry- based techniques of interest to the expanding field of systems immunology. Established and new proteomic methods and their applications discussed here include post-translational modification analysis, protein quantification, secretome analysis, and interactomics. In addition, we present developments in small molecule and metabolite analysis, mass spectrometry imaging, and single cell analysis. Finally, we discuss the role of multi-omic integration in aiding leading edge investigation. EXPERT OPINION In science, available techniques enhance the breadth and depth of the studies. By incorporating proteomic techniques and their innovative use, it will be possible to expand the current studies and to address novel questions at the forefront of scientific discovery.
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Affiliation(s)
- Joseph Gillen
- Functional Cellular Networks Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH) , Bethesda, MD, USA
| | - Caleb Bridgwater
- Functional Cellular Networks Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH) , Bethesda, MD, USA
| | - Aleksandra Nita-Lazar
- Functional Cellular Networks Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH) , Bethesda, MD, USA
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135
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Chen P, Li S, Guo Y, Zeng X, Liu BF. A review on microfluidics manipulation of the extracellular chemical microenvironment and its emerging application to cell analysis. Anal Chim Acta 2020; 1125:94-113. [PMID: 32674786 DOI: 10.1016/j.aca.2020.05.065] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 05/22/2020] [Accepted: 05/26/2020] [Indexed: 12/22/2022]
Abstract
Spatiotemporal manipulation of extracellular chemical environments with simultaneous monitoring of cellular responses plays an essential role in exploring fundamental biological processes and expands our understanding of underlying mechanisms. Despite the rapid progress and promising successes in manipulation strategies, many challenges remain due to the small size of cells and the rapid diffusion of chemical molecules. Fortunately, emerging microfluidic technology has become a powerful approach for precisely controlling the extracellular chemical microenvironment, which benefits from its integration capacity, automation, and high-throughput capability, as well as its high resolution down to submicron. Here, we summarize recent advances in microfluidics manipulation of the extracellular chemical microenvironment, including the following aspects: i) Spatial manipulation of chemical microenvironments realized by convection flow-, diffusion-, and droplet-based microfluidics, and surface chemical modification; ii) Temporal manipulation of chemical microenvironments enabled by flow switching/shifting, moving/flowing cells across laminar flows, integrated microvalves/pumps, and droplet manipulation; iii) Spatiotemporal manipulation of chemical microenvironments implemented by a coupling strategy and open-space microfluidics; and iv) High-throughput manipulation of chemical microenvironments. Finally, we briefly present typical applications of the above-mentioned technical advances in cell-based analyses including cell migration, cell signaling, cell differentiation, multicellular analysis, and drug screening. We further discuss the future improvement of microfluidics manipulation of extracellular chemical microenvironments to fulfill the needs of biological and biomedical research and applications.
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Affiliation(s)
- Peng Chen
- The Key Laboratory for Biomedical Photonics of MOE at Wuhan National Laboratory for Optoelectronics-Hubei Bioinformatics & Molecular Imaging Key Laboratory, Systems Biology Theme, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Shunji Li
- The Key Laboratory for Biomedical Photonics of MOE at Wuhan National Laboratory for Optoelectronics-Hubei Bioinformatics & Molecular Imaging Key Laboratory, Systems Biology Theme, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Yiran Guo
- The Key Laboratory for Biomedical Photonics of MOE at Wuhan National Laboratory for Optoelectronics-Hubei Bioinformatics & Molecular Imaging Key Laboratory, Systems Biology Theme, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Xuemei Zeng
- The Key Laboratory for Biomedical Photonics of MOE at Wuhan National Laboratory for Optoelectronics-Hubei Bioinformatics & Molecular Imaging Key Laboratory, Systems Biology Theme, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Bi-Feng Liu
- The Key Laboratory for Biomedical Photonics of MOE at Wuhan National Laboratory for Optoelectronics-Hubei Bioinformatics & Molecular Imaging Key Laboratory, Systems Biology Theme, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China.
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Ai X, Wu Y, Lu W, Zhang X, Zhao L, Tu P, Wang K, Jiang Y. A Precise Microfluidic Assay in Single-Cell Profile for Screening of Transient Receptor Potential Channel Modulators. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2020; 7:2000111. [PMID: 32537418 PMCID: PMC7284206 DOI: 10.1002/advs.202000111] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Revised: 03/03/2020] [Accepted: 03/08/2020] [Indexed: 05/14/2023]
Abstract
Transient receptor potential (TRP) channels are emerging drug targets, and TRP channel modulators possess therapeutic potential for many indications. However, there is a lack of intellectual and robust screening assays against TRP channels utilizing the least amount of compounds. Here, a precise microfluidic assay in single-cell profile is developed for the screening of TRP channel modulators. The geometrically optimized microchip is designed for both trapping single cells and utilizing passive pumping for sequential media replacement with low shear stress. The microfluidic chip exhibits superior performance in screening, repeatable compound administration, and improved reproducibility. Using this screening platform, the false-positive and negative rate of the commonly used Ca2+ imaging is reduced from 76.2% to 4.8% and four coumarin derivatives isolated from Murraya species that inhibit TRP channels are identified. One coumarin derivative B-304 reverses TRPA1-mediated inflammatory pain in vivo. Taken together, the data demonstrate that the established microfluidic assay in single-cell profile could be used for the screening of TRP channel modulators that may have therapeutic potential for the channelopathies.
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Affiliation(s)
- Xiaoni Ai
- State Key Laboratory of Natural and Biomimetic DrugsSchool of Pharmaceutical SciencesPeking UniversityBeijing100191China
| | - Yang Wu
- State Key Laboratory of Natural and Biomimetic DrugsSchool of Pharmaceutical SciencesPeking UniversityBeijing100191China
- Department of PharmacologyQingdao University School of Pharmacy38 Dengzhou RoadQingdao266021China
| | - Wenbo Lu
- State Key Laboratory of Natural and Biomimetic DrugsSchool of Pharmaceutical SciencesPeking UniversityBeijing100191China
| | - Xinran Zhang
- State Key Laboratory of Natural and Biomimetic DrugsSchool of Pharmaceutical SciencesPeking UniversityBeijing100191China
- Department of PharmacologyQingdao University School of Pharmacy38 Dengzhou RoadQingdao266021China
| | - Lin Zhao
- State Key Laboratory of Natural and Biomimetic DrugsSchool of Pharmaceutical SciencesPeking UniversityBeijing100191China
| | - Pengfei Tu
- State Key Laboratory of Natural and Biomimetic DrugsSchool of Pharmaceutical SciencesPeking UniversityBeijing100191China
| | - KeWei Wang
- Department of PharmacologyQingdao University School of Pharmacy38 Dengzhou RoadQingdao266021China
| | - Yong Jiang
- State Key Laboratory of Natural and Biomimetic DrugsSchool of Pharmaceutical SciencesPeking UniversityBeijing100191China
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Paszek A, Kardyńska M, Bagnall J, Śmieja J, Spiller DG, Widłak P, Kimmel M, Widlak W, Paszek P. Heat shock response regulates stimulus-specificity and sensitivity of the pro-inflammatory NF-κB signalling. Cell Commun Signal 2020; 18:77. [PMID: 32448393 PMCID: PMC7245923 DOI: 10.1186/s12964-020-00583-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Accepted: 04/16/2020] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Ability to adapt to temperature changes trough the Heat Shock Response (HSR) pathways is one of the most fundamental and clinically relevant cellular response systems. Heat Shock (HS) affects the signalling and gene expression responses of the Nuclear Factor κB (NF-κB) transcription factor, a critical regulator of proliferation and inflammation, however, our quantitative understanding of how cells sense and adapt to temperature changes is limited. METHODS We used live-cell time-lapse microscopy and mathematical modelling to understand the signalling of the NF-κB system in the human MCF7 breast adenocarcinoma cells in response to pro-inflammatory Interleukin 1β (IL1β) and Tumour Necrosis Factor α (TNFα) cytokines, following exposure to a 37-43 °C range of physiological and clinical temperatures. RESULTS We show that exposure to 43 °C 1 h HS inhibits the immediate NF-κB signalling response to TNFα and IL1β stimulation although uptake of cytokines is not impaired. Within 4 h after HS treatment IL1β-induced NF-κB responses return to normal levels, but the recovery of the TNFα-induced responses is still affected. Using siRNA knock-down of Heat Shock Factor 1 (HSF1) we show that this stimulus-specificity is conferred via the Inhibitory κB kinase (IKK) signalosome where HSF1-dependent feedback regulates TNFα, but not IL1β-mediated IKK recovery post HS. Furthermore, we demonstrate that through the temperature-dependent denaturation and recovery of IKK, TNFα and IL1β-mediated signalling exhibit different temperature sensitivity and adaptation to repeated HS when exposed to a 37-43 °C temperature range. Specifically, IL1β-mediated NF-κB responses are more robust to temperature changes in comparison to those induced by TNFα treatment. CONCLUSIONS We demonstrate that the kinetics of the NF-κB system following temperature stress is cytokine specific and exhibit differential adaptation to temperature changes. We propose that this differential temperature sensitivity is mediated via the IKK signalosome, which acts as a bona fide temperature sensor trough the HSR cross-talk. This novel quantitative understanding of NF-κB and HSR interactions is fundamentally important for the potential optimization of therapeutic hyperthermia protocols. Video Abstract.
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Affiliation(s)
- Anna Paszek
- Department of Systems Biology and Engineering, Silesian University of Technology, Gliwice, Poland
- System Microscopy Centre, School of Biology, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
- Maria Skłodowska-Curie National Research Institute of Oncology, Gliwice Branch, Gliwice, Poland
| | - Małgorzata Kardyńska
- Department of Systems Biology and Engineering, Silesian University of Technology, Gliwice, Poland
| | - James Bagnall
- System Microscopy Centre, School of Biology, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
| | - Jarosław Śmieja
- Department of Systems Biology and Engineering, Silesian University of Technology, Gliwice, Poland
| | - David G. Spiller
- System Microscopy Centre, School of Biology, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
| | - Piotr Widłak
- Maria Skłodowska-Curie National Research Institute of Oncology, Gliwice Branch, Gliwice, Poland
| | - Marek Kimmel
- Department of Systems Biology and Engineering, Silesian University of Technology, Gliwice, Poland
- Departments of Statistics and Bioengineering, Rice University, Houston, TX USA
| | - Wieslawa Widlak
- Maria Skłodowska-Curie National Research Institute of Oncology, Gliwice Branch, Gliwice, Poland
| | - Pawel Paszek
- System Microscopy Centre, School of Biology, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
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Capillary-assisted microfluidic biosensing platform captures single cell secretion dynamics in nanoliter compartments. Biosens Bioelectron 2020; 155:112113. [DOI: 10.1016/j.bios.2020.112113] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2019] [Revised: 02/06/2020] [Accepted: 02/18/2020] [Indexed: 02/07/2023]
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139
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Shi M, Zhang P, Vora SM, Wu H. Higher-order assemblies in innate immune and inflammatory signaling: A general principle in cell biology. Curr Opin Cell Biol 2020; 63:194-203. [PMID: 32272435 DOI: 10.1016/j.ceb.2020.03.002] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 03/08/2020] [Accepted: 03/09/2020] [Indexed: 12/12/2022]
Abstract
Higher-order supramolecular complexes-dubbed signalosomes carry out key signaling and effector functions in innate immunity and inflammation. In this review, we present several recently discovered signalosomes that are formed either by stable protein-protein interactions or by dynamic liquid-liquid phase separation. Structural features of these signalosomes are highlighted to elucidate their functions and biological insights.
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Affiliation(s)
- Ming Shi
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, and Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA; School of Life Science and Technology, Harbin Institute of Technology, Harbin, 150001, China.
| | - Pengfei Zhang
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, and Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA
| | - Setu M Vora
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, and Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA
| | - Hao Wu
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, and Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA.
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140
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Heemskerk I. Full of potential: Pluripotent stem cells for the systems biology of embryonic patterning. Dev Biol 2020; 460:86-98. [DOI: 10.1016/j.ydbio.2019.05.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Revised: 05/03/2019] [Accepted: 05/03/2019] [Indexed: 02/07/2023]
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141
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Le NH, Ye G, Peng C, Chen JIL. Metabolic mapping with plasmonic nanoparticle assemblies. Analyst 2020; 145:2586-2594. [PMID: 32182299 DOI: 10.1039/c9an02262g] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
A rapid and simple methodology for the biomolecular analysis of single cells and microenvironments via a stick-and-peel plasmonic sensing platform is reported. Substrate-bound assemblies of plasmonic gold nanoparticles linked by reconfigurable oligonucleotides undergo disassembly upon target binding. Changes in the light scattering intensity of thousands of discrete nanoparticle assemblies are extrapolated concomitantly to yield the mapping of local target concentrations. The methodology is completely free of labelling, purification and separation steps. We quantified the intracellular ATP levels for two ovarian cancer cell lines to elucidate the differences and cellular distribution, and demonstrated the potential of the stick-and-peel platform for mapping the microenvironment of a 2D heterogeneous surface. The portable and economical analytical platform may broaden the affordability and applicability of single-cell based analyses and enable new opportunities in clinical care such as on-site molecular pathology.
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Affiliation(s)
- Nguyen H Le
- Department of Chemistry, York University, 4700 Keele Street, Toronto, Ontario M3J 1P3, Canada.
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142
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Martin EW, Pacholewska A, Patel H, Dashora H, Sung MH. Integrative analysis suggests cell type-specific decoding of NF-κB dynamics. Sci Signal 2020; 13:13/620/eaax7195. [PMID: 32098801 DOI: 10.1126/scisignal.aax7195] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The complex signaling dynamics of transcription factors can encode both qualitative and quantitative information about the extracellular environment, which increases the information transfer capacity and potentially supports accurate cellular decision-making. An important question is how these signaling dynamics patterns are translated into functionally appropriate gene regulation programs. To address this question for transcription factors of the nuclear factor κB (NF-κB) family, we profiled the single-cell dynamics of two major NF-κB subunits, RelA and c-Rel, induced by a panel of pathogen-derived stimuli in immune and nonimmune cellular contexts. Diverse NF-κB-activating ligands produced different patterns of RelA and c-Rel signaling dynamic features, such as variations in duration or time-integrated activity. Analysis of nascent transcripts delineated putative direct targets of NF-κB as compared to genes controlled by other transcriptional and posttranscriptional mechanisms and showed that the transcription of more than half of the induced genes was tightly linked to specific dynamic features of NF-κB signaling. Fibroblast and macrophage cell lines shared a cluster of such "NF-κB dynamics-decoding" genes, as well as cell type-specific decoding genes. Dissecting the subunit specificity of dynamics-decoding genes suggested that target genes were most often linked to both RelA and c-Rel or to RelA alone. Thus, our analysis reveals the cell type-specific interpretation of pathogenic information through the signaling dynamics of NF-κB.
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Affiliation(s)
- Erik W Martin
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA
| | - Alicja Pacholewska
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA
| | - Heta Patel
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA
| | - Himanshu Dashora
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA
| | - Myong-Hee Sung
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA.
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143
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Muldoon JJ, Chuang Y, Bagheri N, Leonard JN. Macrophages employ quorum licensing to regulate collective activation. Nat Commun 2020; 11:878. [PMID: 32054845 PMCID: PMC7018708 DOI: 10.1038/s41467-020-14547-y] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2018] [Accepted: 12/19/2019] [Indexed: 01/23/2023] Open
Abstract
Macrophage-initiated inflammation is tightly regulated to eliminate threats such as infections while suppressing harmful immune activation. However, individual cells’ signaling responses to pro-inflammatory cues are heterogeneous, with subpopulations emerging with high or low activation states. Here, we use single-cell tracking and dynamical modeling to develop and validate a revised model for lipopolysaccharide (LPS)-induced macrophage activation that invokes a mechanism we term quorum licensing. The results show that bimodal phenotypic partitioning of macrophages is primed during the resting state, dependent on cumulative history of cell density, predicted by extrinsic noise in transcription factor expression, and independent of canonical LPS-induced intercellular feedback in the tumor necrosis factor (TNF) response. Our analysis shows how this density-dependent coupling produces a nonlinear effect on collective TNF production. We speculate that by linking macrophage density to activation, this mechanism could amplify local responses to threats and prevent false alarms. Macrophage activation is tightly regulated to maintain immune homeostasis, yet activation is also heterogeneous. Here, the authors show that macrophages coordinate activation by partitioning into two phenotypes that can nonlinearly amplify collective inflammatory cytokine production as a function of cell density.
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Affiliation(s)
- Joseph J Muldoon
- Interdisciplinary Biological Sciences Program, Northwestern University, Evanston, IL, 60208, USA.,Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, 60208, USA
| | - Yishan Chuang
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, 60208, USA
| | - Neda Bagheri
- Interdisciplinary Biological Sciences Program, Northwestern University, Evanston, IL, 60208, USA. .,Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, 60208, USA. .,Center for Synthetic Biology, Northwestern University, Evanston, IL, 60208, USA. .,Chemistry of Life Processes Institute, Northwestern University, Evanston, IL, 60208, USA. .,Member, Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Evanston, IL, 60208, USA. .,Biology and Chemical Engineering, University of Washington, Seattle, WA, 98195, USA.
| | - Joshua N Leonard
- Interdisciplinary Biological Sciences Program, Northwestern University, Evanston, IL, 60208, USA. .,Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, 60208, USA. .,Center for Synthetic Biology, Northwestern University, Evanston, IL, 60208, USA. .,Chemistry of Life Processes Institute, Northwestern University, Evanston, IL, 60208, USA. .,Member, Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Evanston, IL, 60208, USA.
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144
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Letort G, Montagud A, Stoll G, Heiland R, Barillot E, Macklin P, Zinovyev A, Calzone L. PhysiBoSS: a multi-scale agent-based modelling framework integrating physical dimension and cell signalling. Bioinformatics 2020; 35:1188-1196. [PMID: 30169736 PMCID: PMC6449758 DOI: 10.1093/bioinformatics/bty766] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Revised: 07/28/2018] [Accepted: 08/30/2018] [Indexed: 01/22/2023] Open
Abstract
MOTIVATION Due to the complexity and heterogeneity of multicellular biological systems, mathematical models that take into account cell signalling, cell population behaviour and the extracellular environment are particularly helpful. We present PhysiBoSS, an open source software which combines intracellular signalling using Boolean modelling (MaBoSS) and multicellular behaviour using agent-based modelling (PhysiCell). RESULTS PhysiBoSS provides a flexible and computationally efficient framework to explore the effect of environmental and genetic alterations of individual cells at the population level, bridging the critical gap from single-cell genotype to single-cell phenotype and emergent multicellular behaviour. PhysiBoSS thus becomes very useful when studying heterogeneous population response to treatment, mutation effects, different modes of invasion or isomorphic morphogenesis events. To concretely illustrate a potential use of PhysiBoSS, we studied heterogeneous cell fate decisions in response to TNF treatment. We explored the effect of different treatments and the behaviour of several resistant mutants. We highlighted the importance of spatial information on the population dynamics by considering the effect of competition for resources like oxygen. AVAILABILITY AND IMPLEMENTATION PhysiBoSS is freely available on GitHub (https://github.com/sysbio-curie/PhysiBoSS), with a Docker image (https://hub.docker.com/r/gletort/physiboss/). It is distributed as open source under the BSD 3-clause license. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Gaelle Letort
- Institut Curie, PSL Research University, Paris, France.,INSERM, U900, Paris, France.,CBIO-Centre for Computational Biology, MINES ParisTech, PSL Research University, Paris, France
| | - Arnau Montagud
- Institut Curie, PSL Research University, Paris, France.,INSERM, U900, Paris, France.,CBIO-Centre for Computational Biology, MINES ParisTech, PSL Research University, Paris, France
| | - Gautier Stoll
- Université Paris Descartes/Paris V, Sorbonne Paris Cité, Paris, France.,Gustave Roussy Cancer Campus, Villejuif, France.,INSERM, U1138, Paris, France.,Equipe 11 Labellisée par la Ligue Nationale Contre le Cancer, Centre de Recherche des Cordeliers, Paris, France
| | - Randy Heiland
- Intelligent Systems Engineering, Indiana University, Bloomington, IN, USA
| | - Emmanuel Barillot
- Institut Curie, PSL Research University, Paris, France.,INSERM, U900, Paris, France.,CBIO-Centre for Computational Biology, MINES ParisTech, PSL Research University, Paris, France
| | - Paul Macklin
- Intelligent Systems Engineering, Indiana University, Bloomington, IN, USA
| | - Andrei Zinovyev
- Institut Curie, PSL Research University, Paris, France.,INSERM, U900, Paris, France.,CBIO-Centre for Computational Biology, MINES ParisTech, PSL Research University, Paris, France
| | - Laurence Calzone
- Institut Curie, PSL Research University, Paris, France.,INSERM, U900, Paris, France.,CBIO-Centre for Computational Biology, MINES ParisTech, PSL Research University, Paris, France
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Huang HC, Cai BH, Suen CS, Lee HY, Hwang MJ, Liu FT, Kannagi R. BGN/TLR4/NF-B Mediates Epigenetic Silencing of Immunosuppressive Siglec Ligands in Colon Cancer Cells. Cells 2020; 9:cells9020397. [PMID: 32050430 PMCID: PMC7072454 DOI: 10.3390/cells9020397] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Revised: 02/06/2020] [Accepted: 02/06/2020] [Indexed: 12/28/2022] Open
Abstract
Human Toll-like receptor (TLR) signaling plays a vital role in intestinal inflammation by activating the NF-κB pathway. By querying GENT2 datasets, we identified the gene expression level of TLR2 and TLR4 as being substantially increased in colorectal cancer. Introduction of shRNAs for TLR4 but not TLR2 dramatically recovered disialyl Lewisa and sialyl 6-sulfo Lewisx glycans, which are preferentially expressed in non-malignant colonic epithelial cells and could serve as ligands for the immunosuppressive molecule Siglec-7. We screened several TLR4 ligands and found that among them BGN is highly expressed in cancers and is involved in the epigenetic silencing of Siglec-7 ligands. Suppression of BGN expression substantially downregulated NF-κB activity and the marker H3K27me3 in the promoter regions of the SLC26A2 and ST6GalNAc6 genes, which are involved in the synthesis of those glycans, and restored expression of normal glycans as well as Siglec-7 binding activities. We show that in the presence of TLR4, inflammatory stimuli initiate a positive loop involving NF-κB that activates BGN and further enhances TLR4 activity. Present findings indicate a putative mechanism for the promotion of carcinogenesis by loss of immunosuppressive ligands by the BGN/TLR4/ NF-κB pathway.
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Affiliation(s)
- Hsiang-Chi Huang
- Institute of Biomedical Sciences, Academia Sinica, Taipei 11529, Taiwan (B.-H.C.); (C.-S.S.); (H.-Y.L.); (M.-J.H.); (F.-T.L.)
| | - Bi-He Cai
- Institute of Biomedical Sciences, Academia Sinica, Taipei 11529, Taiwan (B.-H.C.); (C.-S.S.); (H.-Y.L.); (M.-J.H.); (F.-T.L.)
- Department of Medicine, College of Medicine, I-Shou University, Kaohsiung 82445, Taiwan
| | - Ching-Shu Suen
- Institute of Biomedical Sciences, Academia Sinica, Taipei 11529, Taiwan (B.-H.C.); (C.-S.S.); (H.-Y.L.); (M.-J.H.); (F.-T.L.)
| | - Hsueh-Yi Lee
- Institute of Biomedical Sciences, Academia Sinica, Taipei 11529, Taiwan (B.-H.C.); (C.-S.S.); (H.-Y.L.); (M.-J.H.); (F.-T.L.)
| | - Ming-Jing Hwang
- Institute of Biomedical Sciences, Academia Sinica, Taipei 11529, Taiwan (B.-H.C.); (C.-S.S.); (H.-Y.L.); (M.-J.H.); (F.-T.L.)
| | - Fu-Tong Liu
- Institute of Biomedical Sciences, Academia Sinica, Taipei 11529, Taiwan (B.-H.C.); (C.-S.S.); (H.-Y.L.); (M.-J.H.); (F.-T.L.)
| | - Reiji Kannagi
- Institute of Biomedical Sciences, Academia Sinica, Taipei 11529, Taiwan (B.-H.C.); (C.-S.S.); (H.-Y.L.); (M.-J.H.); (F.-T.L.)
- Correspondence: ; Tel.: +886-2-26523971
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Lee D, Jayaraman A, Kwon JS. Identification of cell‐to‐cell heterogeneity through systems engineering approaches. AIChE J 2020. [DOI: 10.1002/aic.16925] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Dongheon Lee
- Artie McFerrin Department of Chemical EngineeringTexas A&M University Texas
| | - Arul Jayaraman
- Artie McFerrin Department of Chemical EngineeringTexas A&M University Texas
| | - Joseph S.‐I. Kwon
- Artie McFerrin Department of Chemical EngineeringTexas A&M University Texas
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147
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Abstract
Specificity in signal transduction is determined by the ability of cells to "encode" and subsequently "decode" different environmental signals. Akin to computer software, this "signaling code" governs context-dependent execution of cellular programs through modulation of signaling dynamics and can be corrupted by disease-causing mutations. Class IA phosphoinositide 3-kinase (PI3K) signaling is critical for normal growth and development and is dysregulated in human disorders such as benign overgrowth syndromes, cancer, primary immune deficiency, and metabolic syndrome. Despite decades of PI3K research, understanding of context-dependent regulation of the PI3K pathway and of the underlying signaling code remains rudimentary. Here, we review current knowledge on context-specific PI3K signaling and how technological advances now make it possible to move from a qualitative to quantitative understanding of this pathway. Insight into how cellular PI3K signaling is encoded or decoded may open new avenues for rational pharmacological targeting of PI3K-associated diseases. The principles of PI3K context-dependent signal encoding and decoding described here are likely applicable to most, if not all, major cell signaling pathways.
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Affiliation(s)
- Ralitsa R Madsen
- UCL Cancer Institute, Paul O'Gorman Building, University College London, 72 Huntley Street, London WC1E 6DD, UK.
| | - Bart Vanhaesebroeck
- UCL Cancer Institute, Paul O'Gorman Building, University College London, 72 Huntley Street, London WC1E 6DD, UK.
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148
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Feng Y, Wang B, Tian Y, Chen H, Liu Y, Fan H, Wang K, Zhang C. Active fluidic chip produced using 3D-printing for combinatorial therapeutic screening on liver tumor spheroid. Biosens Bioelectron 2019; 151:111966. [PMID: 31999576 DOI: 10.1016/j.bios.2019.111966] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Revised: 11/19/2019] [Accepted: 12/13/2019] [Indexed: 12/12/2022]
Abstract
Known for their capabilities in automated fluid manipulation, microfluidic devices integrated with pneumatic valves are broadly used for researches in life science and clinical practice. The application is, however, hindered by the high cost and overly complex fabrication procedure. Here, we present an approach for fabricating molds of active fluidic devices using a benchtop 3D printer and a simple 2-step protocol (i.e. 3D printing and polishing). The entire workflow can be completed within 6 h, costing less than US$ 5 to produce all necessary templates for PDMS replica molding, which have smooth surface and round-shaped pneumatic valve structures. Moreover, 3D printing can create unique bespoke on-off objects of a wide range of dimensions. The millimeter- and centimeter-sized features allow examination of large-scale biological samples. Our results demonstrate that the 3D-printed active fluidic device has valve control capacities on par with those made by photolithography. Controlled nutrients and ligands delivery by on-off active valves allows generation of dynamic signals mimicking the ever-changing environmental stimuli, and combinatorial/sequential drug inputs for therapeutic screening on liver tumor spheroid. We believe that the proposed methodology can pave the way for integration of active fluidic systems in research labs, clinical settings and even household appliances for a broad range of application.
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Affiliation(s)
- Yibo Feng
- Institute of Photonics and Photon-Technology, State Key Laboratory of Cultivation Base for Photoelectric Technology and Functional Materials, Northwest University, 1 Xue Fu Avenue, Xi'an, 710127, Shaanxi, China
| | - Bingquan Wang
- Institute of Photonics and Photon-Technology, State Key Laboratory of Cultivation Base for Photoelectric Technology and Functional Materials, Northwest University, 1 Xue Fu Avenue, Xi'an, 710127, Shaanxi, China
| | - Yin Tian
- Laboratory of Stem Cell and Tissue Engineering, Chongqing Medical University, Chongqing, 400016, China
| | - Hao Chen
- College of Chemistry and Material Sciences, Northwest University, Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education, Northwest University, 1 Xue Fu Avenue, Xi'an, 710127, Shaanxi, China
| | - Yonggang Liu
- Laboratory of Stem Cell and Tissue Engineering, Chongqing Medical University, Chongqing, 400016, China
| | - Haiming Fan
- College of Chemistry and Material Sciences, Northwest University, Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education, Northwest University, 1 Xue Fu Avenue, Xi'an, 710127, Shaanxi, China
| | - Kaige Wang
- Institute of Photonics and Photon-Technology, State Key Laboratory of Cultivation Base for Photoelectric Technology and Functional Materials, Northwest University, 1 Xue Fu Avenue, Xi'an, 710127, Shaanxi, China
| | - Ce Zhang
- Institute of Photonics and Photon-Technology, State Key Laboratory of Cultivation Base for Photoelectric Technology and Functional Materials, Northwest University, 1 Xue Fu Avenue, Xi'an, 710127, Shaanxi, China.
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149
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Single-Cell Expression Variability Implies Cell Function. Cells 2019; 9:cells9010014. [PMID: 31861624 PMCID: PMC7017299 DOI: 10.3390/cells9010014] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Revised: 11/26/2019] [Accepted: 11/27/2019] [Indexed: 12/11/2022] Open
Abstract
As single-cell RNA sequencing (scRNA-seq) data becomes widely available, cell-to-cell variability in gene expression, or single-cell expression variability (scEV), has been increasingly appreciated. However, it remains unclear whether this variability is functionally important and, if so, what are its implications for multi-cellular organisms. Here, we analyzed multiple scRNA-seq data sets from lymphoblastoid cell lines (LCLs), lung airway epithelial cells (LAECs), and dermal fibroblasts (DFs) and, for each cell type, selected a group of homogenous cells with highly similar expression profiles. We estimated the scEV levels for genes after correcting the mean-variance dependency in that data and identified 465, 466, and 364 highly variable genes (HVGs) in LCLs, LAECs, and DFs, respectively. Functions of these HVGs were found to be enriched with those biological processes precisely relevant to the corresponding cell type’s function, from which the scRNA-seq data used to identify HVGs were generated—e.g., cytokine signaling pathways were enriched in HVGs identified in LCLs, collagen formation in LAECs, and keratinization in DFs. We repeated the same analysis with scRNA-seq data from induced pluripotent stem cells (iPSCs) and identified only 79 HVGs with no statistically significant enriched functions; the overall scEV in iPSCs was of negligible magnitude. Our results support the “variation is function” hypothesis, arguing that scEV is required for cell type-specific, higher-level system function. Thus, quantifying and characterizing scEV are of importance for our understating of normal and pathological cellular processes.
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150
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Rogers KW, Müller P. Optogenetic approaches to investigate spatiotemporal signaling during development. Curr Top Dev Biol 2019; 137:37-77. [PMID: 32143750 DOI: 10.1016/bs.ctdb.2019.11.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Embryogenesis is coordinated by signaling pathways that pattern the developing organism. Many aspects of this process are not fully understood, including how signaling molecules spread through embryonic tissues, how signaling amplitude and dynamics are decoded, and how multiple signaling pathways cooperate to pattern the body plan. Optogenetic approaches can be used to address these questions by providing precise experimental control over a variety of biological processes. Here, we review how these strategies have provided new insights into developmental signaling and discuss how they could contribute to future investigations.
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Affiliation(s)
- Katherine W Rogers
- Systems Biology of Development Group, Friedrich Miescher Laboratory of the Max Planck Society, Tübingen, Germany
| | - Patrick Müller
- Systems Biology of Development Group, Friedrich Miescher Laboratory of the Max Planck Society, Tübingen, Germany; Modeling Tumorigenesis Group, Translational Oncology Division, Eberhard Karls University Tübingen, Tübingen, Germany.
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